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Keywords:

  • Lateral Gene Transfer;
  • antibiotic resistance;
  • mobile genetic elements;
  • nosocomial infection;
  • transposon;
  • integron

Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Bacteria have methods of gene exchange that are distinct from those in eukaryotes, but they still conform to the laws of evolution by natural selection. When considering the antibiotic resistance problem, this fundamental point should not be forgotten (Antonovics et al., 2007). Our real challenge is to understand the repertoire of processes and genetic elements that prokaryotes have available to them, and upon which natural selection can act. Lateral Gene Transfer, or more recently, Lateral Genetic Transfer (LGT) (Ragan & Beiko, 2009) is an important process in moving and rearranging DNA in prokaryotes. The extent of LGT is substantial, with estimates that up to 25% of some bacterial genomes can be derived from LGT over evolutionary periods of time (Ochman et al., 2000). Even over much shorter time frames, the evolution of genomes by inheritance of large blocks of DNA from elsewhere can generate phenomenal amounts of diversity, particularly where selection is very strong. For instance, Escherichia coli can follow many different evolutionary paths based on DNA that is present in only some strains. This diversity is impressive, with the ‘pan genome’ of E. coli encompassing nearly 18 000 genes despite the fact that the coding content of a single cell of this species is slightly over 2000 genes (Touchon et al., 2009).

The most overt example of evolution driven by selection is the selection for antibiotic resistance in pathogens. The dissemination of resistance genes is a direct consequence of LGT and this has enormous ramifications for human health. Indeed, it has been argued that the antibiotic/antibiotic resistance arms race is one that humans are losing (Falagas & Bliziotis, 2007). If so, one of the main reasons is that LGT potentially makes all genes in the microbial biosphere a single, common and shared resource. In the same way that wars can be won by nations with the greatest industrial capacity, so it is that bacteria can draw on a global resource that, with the means of LGT, can mobilize and transfer useful genes across physical and phylogenetic distances very rapidly. Unlike eukaryotes, therefore, bacteria are not dependent on random variation in genes within cell lines as templates on which natural selection can act. In existing and newly emerging pathogens, the survival and amplification of strains with enhanced pathogenicity may result from the acquisition of genes that evolved in an environment remote from humans and in a bacterium that is yet to be cultured. Managing infectious disease in the long term can only be achieved by understanding the basic concepts of evolutionary biology and how they apply to prokaryotes (Summers, 2002; Nesse & Stearns, 2008).

What is LGT?

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

The literature on LGT, also known as Horizontal Gene Transfer (HGT) (Frost et al., 2005), is extensive. However, most of this literature focuses on the implications of LGT for the evolution of microbial genomes (Boto, 2010) or on issues relating to microbial phylogeny and the relevance of the species concept as it applies to prokaryotes (Bapteste et al., 2009; Gribaldo & Brochier, 2009). Ironically, despite a focus on LGT and the arguments for its key role in microbial evolution, the concept itself is often poorly defined. It is beyond the scope of this review to fully describe the process, but some general issues need to be clearly understood. We define LGT as the process whereby DNA from one cell is physically transferred from one cell to another without an absolute requirement for cell division and the incorporation of that DNA into the recipient's genome such that it can be stably inherited. Without reflecting on a specific formal definition, this would be most people's understanding of the process. Thus, LGT requires at least two independent processes to occur: (1) physical movement of DNA and (2) incorporation into the receiving genome such as to allow stable inheritance (Table 1).

Table 1.   The collective forces that drive Lateral Gene Transfer
Mechanisms of transferMechanisms of incorporationMobile elements*
  • A successful LGT event requires the action of at least one transfer mechanism and one integration mechanism. All of the mobile elements named have the potential to move by any of the transfer mechanisms shown, although plasmids and integrative and conjugative elements most commonly transfer by conjugation.

  • *

    Numbers in brackets identify the major mechanism of incorporation. That is, the major process by which DNA achieves the ability to maintain itself in the receiving genome after physical transfer or uptake has taken place as described in the text.

  • Plasmids and integrative and conjugative elements are also agents of gene transfer because they can move genes between cells by conjugation as well as integrate them.

  • Integrons lack the ability to integrate autonomously. However, the so-called mobile integrons have become associated with transposons and plasmids (or both). In these contexts, they piggyback on the functions of the associated element. With the acceleration of the evolution of mobile DNA and the appearance of multiple copies of similar, or identical elements in the same cell, homologous recombination can be considered an integrating mechanism for any of the elements listed.

Conjugation1 – Autonomous replicationPlasmids (1)
Transformation2 – TranspositionTransposons (2)
Transduction3 – Site-specific recombinationInsertion sequence common regions (2)
4 – Homologous recombinationIntegrative and conjugative elements (3) Gene cassettes (3) Integrons

Each of these two steps can occur via a relatively small number of mechanisms. Physical movement occurs by one of the processes of conjugation, transduction or transformation and incorporation of DNA either by homologous or illegitimate recombination, transposition, site-specific recombination or by virtue of the transferred DNA being an independent replicon (Thomas & Nielsen, 2005). A successful transfer outcome requires the agency of at least one of the processes of movement and at least one of incorporation. The advent of very strong and near-global selection for antibiotic resistance has seen a huge increase in the number of cells carrying the corresponding resistance genes. This increase in the abundance of specific genes and their mobilizing elements allows more opportunity for the mechanisms of LGT to act cooperatively. Thus, mobile antibiotic resistance genes that make up parts of increasingly complex mosaic structures of identical or related sequences allow the capture of DNA by combinatorial exchange involving all of the factors listed in Table 1. Other features of LGT include the fact that it is both infectious – transfer can be associated with DNA replication resulting in a net increase of DNA per cell – and promiscuous – DNA transfer can occur across species. In environments uncorrupted by humans, these phenomena are probably more limited, in the case of promiscuity because barriers to trans-species DNA movement are known (Thomas & Nielsen, 2005). However, the strong selection being applied by the use of antibiotics is likewise seeing a breakdown of some of these natural limiting mechanisms.

Where do antibiotic resistance genes come from?

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Antibiotics are not a human invention. Equally, antibiotic resistance genes did not evolve in bacterial pathogens as a defence against humans inventions. Rather, both antibiotics and the proteins that protect against them have a broad environmental origin (Martinez, 2008) that dates back millions and possibly billions of years (Baltz, 2008). The presence of antibiotics and of genes that confer resistance to them is an outcome of Darwinian selection in the microbial world. It has long been regarded that a major role of antibiotic production in natural environments is to allow niche exploitation on the part of those bacteria that produce them and that resistance is a selective response to such production on the part of the producers themselves as well as their potential targets (Waksman & Woodruff, 1940). There is good evidence to support this hypothesis (Wiener, 1996), although it is also clear that antibiotic production (Davies et al., 2006) and resistance may have other roles to play in natural environments, both at the community and at the cellular level (Groh et al., 2007; Martinez, 2008). With the many roles that antibiotics play in the microbial biosphere, it has long been expected that antibiotic resistance genes and bacteria would be very common. In contemporary times, there is substantial evidence that this is true. Firstly, antibiotic resistance genes have been enriched and extensively mobilized through the widespread use of antibiotics by humans (this will be explored in detail later). Secondly, tools of the genomics era have provided a window into the diversity that has always existed in the microbial biosphere. Early studies predominantly found resistance genes reflective of those already found in clinical contexts (Benveniste & Davies, 1973) because they were most easy to select for and recover. In contrast, contemporary studies (D'Costa et al., 2006), especially those using metagenomics approaches that encompass yet to be cultured bacteria, recover much more diverse resistance genes, including some that would not be readily be identifiable as such by bioinformatics analysis alone (Riesenfeld et al., 2004; Allen et al., 2009a). This has obvious ramifications for the management of antibiotic resistance because it implies that the pool of resistance genes that cause the current clinical problem may be the tip of a large iceberg. Compounding this problem is the fact that novel resistance determinants may already be undergoing mobilization by processes of LGT (Rowe-Magnus et al., 2001; Nield et al., 2004). The global nature of the resistance evolution problem is summarized in Fig. 1, whereby many low copy number resistance genes and mobilizing elements are distributed throughout the microbial biosphere. Over time (which is very short in the context of bacterial evolution), the recruitment of some resistance genes into some mobile elements has seen the subsequent introduction of both into pathogens. Once this began, further selection acted to accelerate this process, ultimately allowing the global spread and amplification of a small number of genes and mobile element types.

image

Figure 1.  Recruitment of resistance genes and mobilizing elements into pathogens. (a) Diagrammatic representation of the global distribution of mobile genes, mobilizable genes and mobilizing genetic elements as found in the preantibiotic era. (b) Pre- and postantibiotic era random rearrangements bring together mobilizing agents and genes encoding adaptive genes in niche environments. (c) Mobilizing genes move through microbial communities including human pathogens (in pink). (d) With strong selection as occurred in pathogens in the antibiotic era, selected organisms underwent clonal and global expansion.

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Resistance determinants in vectors, bacterial species and animal hosts

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

The accumulation of antimicrobial resistance genes in pathogens has generated a world-wide crisis in the management of infectious disease (Davies, 2007). To control the spread of existing and novel resistance genes, we need an understanding of the genetic elements involved, of the dynamics of LTG and of microbial ecology (Salyers & Shoemaker, 2006). In turn, this requires the assembly of many different kinds of data, much of which we do not yet have.

What kinds of information might be required to understand the ecology of resistance and what is the most efficient way to approach the problem? The dynamics of resistance genes must be examined at a variety of different scales (Baquero, 2009), including the diversity of the genes themselves, the families of mosaic DNA elements that carry them, the bacterial strains and species in which they occur and the animals that host these bacteria (see Fig. 2). We also need to assess the probability that potential resistance mechanisms exist and the likelihood that genes encoding these mechanisms can successfully disseminate under conditions where selection will fix the recipients in populations (Martinez et al., 2007). Above all, we need to move towards a broader evolutionary and ecological perspective on the problem (Aminov & Mackie, 2007).

image

Figure 2.  Movement and mobilization of antibiotic resistance genes. The lateral transfer of resistance determinants can be examined from different perspectives: (a) Movement of individual resistance determinants can be mapped to particular chromosomal locations, plasmids, transposons or integrons. (b) Mobile vectors that carry these determinants can be tracked through different bacterial species. (c) Bacterial strains containing these vectors can be identified in different host animals. Lateral events can occur at any of these levels. For instance, a resistance gene may transpose from a chromosome to a plasmid, which then conjugates from an environmentally acquired bacterium into a commensal species residing in a new host. In each case, the lateral transfer can be recognized by genetic identity, but the direction of the transfer cannot be reliably ascribed without extensive temporal data.

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Characterizing the units of transfer (Fig. 2a), particularly the resistance genes themselves, is an important first step, and one in which significant progress has been made. For instance, there have been two recent, comprehensive reviews on genes for β-lactamases, dealing with their diversity, mobility and epidemiology (Smet et al., 2009; Poirel et al., 2010). Similarly, the resistance genes encoded by integron gene cassettes have been systematically tabulated (Partridge et al., 2009).

Compilations of resistance determinants generally deal with known genes characterized from known organisms. However, it is now widely accepted that culturable bacteria represent only a small fraction of bacterial genetic diversity, and consequently, the extent and diversity of resistance genes in the bacterial metagenome also need to be considered. Diverse, unusual β-lactamase genes and additional, novel genes encoding resistance to aminoglycosides and tetracycline have been readily recovered in metagenomic libraries generated from soil bacteria (Riesenfeld et al., 2004; Allen et al., 2009b). Other metagenomic studies of soil and marine sediments have demonstrated that the pool of novel gene cassettes available to integrons is vast and diverse (Michael et al., 2004; Koenig et al., 2008). While the phenotypes encoded by these environmental gene cassettes are for the most part unknown (Holmes et al., 2003; Boucher et al., 2007; Moura et al., 2010), all are likely to be adaptive under some circumstances. Databases of integron gene cassettes and their associated recombination machinery are now available (Joss et al., 2009; Moura et al., 2009) and will continue to grow. There is also considerable interest in characterizing the antibiotic resistome more generally from environmental samples (D'Costa et al., 2006; Wright, 2007), with a view to predicting novel resistance mechanisms and informing the rational development of new antibiotics. In the near future, the application of next-generation sequencing technologies will rapidly increase our catalogue of resistance genes.

The movement of resistance genes between physical locations is facilitated by a variety of genetic elements such as integrons, transposons, integrative conjugative elements (ICEs), plasmids and genomic islands, which are themselves also units of lateral transfer (Fig. 2b). Some of these elements are extraordinarily abundant. For example, transposases are ubiquitous and the most abundant genes in nature (Aziz et al., 2010). For this reason, understanding the origins of such mobile elements is complex and is further complicated by the fact that mobile elements often form mosaics, built up from different genes and subelements, each with different evolutionary histories (Toussaint & Merlin, 2002; Norman et al., 2009). The mosaic complexity of such molecules allows diverse interactions with other genetic elements, promoting exchanges that, in turn, generate more diversity (Garriss et al., 2009; Wozniak & Waldor, 2010). A further complication arises in analyses of mobile genetic elements because they do not ‘belong’ to a particular cell or lineage and have independent evolutionary trajectories when compared to phylogenetic trees. One consequence of this independence is that genome sequencing of individual strains or species of Bacteria is not an efficient way to collect data on mobile elements (Frost et al., 2005), although more efficient and cost-effective genome sequencing will progressively help this problem. Nonetheless, means of directly accessing the mobile gene pool need to be developed, and frameworks for consistent classification and nomenclature of mobile elements need to be used (Roberts et al., 2008a; Leplae et al., 2010).

Reservoirs of resistance?

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

What about the species of bacteria in which mobile vectors and resistance genes reside (Fig. 2c)? Most attention in the literature appears to be focused on characterizing pathogens by first identifying the species and the strain/clone involved and then examining the resistance genes contained therein. While this is a laudable exercise for particular clinical circumstances, if the phenotypes of interest (virulence, resistance, etc.) are encoded on mobile DNA, then the DNA element is probably the factor of most importance, not necessarily the cellular background. Because of the selection pressure imposed by antibiotics, even transitory colonization by allochthonous bacteria offers ample opportunity for the fixation of rare lateral transfer events between species, and the movement of resistance genes and their vectors between animal hosts is not surprising. Therefore, if individual environments are considered in isolation, without taking into account the power of natural selection and LGT, any environment can appear to be a ‘source’ of resistance genes.

Naturally occurring antibiotic resistance genes have been a feature of microbial communities for a long time. Putting aside the question of what elements may be contributing to the LGT of resistance genes, one key question is: what do we know about the link between different environments in the microbial biosphere? Specifically, what environments can act as a source for the recruitment of antibiotic resistance genes into bacterial pathogens, especially those that cause nosocomial infections? This is a subject of interest for obvious reasons, and in recent years, many studies have identified a variety of environments and organisms that are potential ‘reservoirs’ of antibiotic resistance genes.

The references cited in Tables 2 and 3 were published in the interval of 2008–2010 and deal with the detection of one specific family of mobile elements – integrons – in animals and natural environments. Almost one-third of these publications (36 of 114) mention animals or environments as a ‘reservoir’ of antibiotic resistance. Slightly less than a third (33 of 114) use the more accurate term ‘dissemination’ to describe the movement of genes between genetic, biological and physical locations. The fact that the descriptor reservoir has come to be applied so ubiquitously is in itself an argument that the definition is inappropriate and that the concept is unhelpful. Rather, what the collective literature in this area reinforces is that, notwithstanding the qualitative and quantitative differences between environments, antibiotic resistance genes are a near-universal feature of the microbial biosphere. Although ‘reservoir’ may not be a good descriptor, we believe that E. coli (Bailey et al., 2010) may be a particularly important contributor to the spread of antibiotic resistance genes globally. There are three reasons for this: (1) E. coli is an important animal commensal, (2) it can persist in the environment well away from an animal host and (3) strain variants of this species can commonly be pathogenic. To varying degrees, the same argument can be extended to other genera and species that meet these criteria (Salyers et al., 2004).

Table 2.   Reports of class 1 and class 2 integrons in domesticated animals and food animals, 2008–2010*
CountryAnimal hostBacterial hostintI1Cassette array(s)intI2Cassette array(s)Reference/s
  • *

    Table is based on English-language papers published between 2008 and 2010 recovered from PubMed using the search terms integron × animal.

  • Gene and cassette nomenclature is based on that used in the original papers. In some cases, gene names are at variance with standard gene naming nomenclature. A standardized nomenclature has recently been published by Partridge et al. (2009). Individual cassette arrays are given on separate lines.

  • ND, Not determined.

AustraliaCattleEnterobacteriaceae+aadA1, aadA2, catB8-aadA1, cmlA5-blaOXA−10-aadA1, dfrA1-aadA1, dfrA17-aadA5, dfrA12-orf-aadA2 dfrA7, dfr2d-catB3-aadA1, dfrV, sat-orf+dfrA1-sat2-aadA1, estX-sat2-aadA1, sat2-aadA1Barlow et al. (2008, 2009)
PigS. enterica serovars+dfrA12-orfF-aadA2, δorfF-aadA2Evershed et al. (2009)
BrazilPigS. enterica Bredeney+dfrA12-blaOXA−129-aadA1+dfrA1-sat1-aadA1Michael et al. (2008)
CanadaChickenE. coli+aadA1, dhfrI Bonnet et al. (2009)
ChilePigSalmonella spp.+aadA1+dfrA1-sat1-aadA1San Martin et al. (2008)
ChickenE. coli+aadA1, dfr-A1-aadA1+dfrA1-sat1-aadA1, estX-sat2-aadA1Lapierre et al. (2008)
Pig +aadA1, dfrA1-aadA1+dfrA1-aadA1, dfrA1-sat1-aadA1, estX-sat2-aadA1 
Czech RepublicCattleE. coli+aadA1, dhfr1-aadA1, dhfr17-aadA5ND Dolejska et al. (2008)
PigE. coli+aadA1, aadA2, blaOXA-aadA1, dhfr1-aadA1, dhfr12-aadA2, estX-aadA1, estX-aadA2+estX-sat-aadA1, sat-aadA1Literak et al. (2009)
DenmarkChickenE. coli+NDND Trobos et al. (2008)
EgyptCattleE. coli+aac(3)-Id-aadA7 aadA1, aadA23, dfrA1-aadA1, dfrA12-orf-aadA2, dfrA15, dfrA17-aadA5+dfrA1-sat2, dfrA1-sat2-aadA1Ahmed et al. (2009d)
CattleS. enterica serovars+aadA1, dfrA1-aadA1, aadA2, dfrA15, dfrA17-aadA5+dfrA1-sat2-aadA1Ahmed et al. (2009c)
FranceCattleS. enterica Typhimurium+blaPSE−1, aadA2ND Targant et al. (2010)
GermanyCatE. coli+aadA1, dfrA1-aadA1, dfrA12-orfF-aadA2+dfrA1-sat2-aadA1Kadlec & Schwarz (2008)
Dog +aadA1, dfrA1-aadA1, dfrA1-catB3-aadA4, dfrA12-orfF-aadA2, dfrA17-aadA5+dfrA1-sat2-aadA1, estX-sat2-aadA1 
Horse +aadA1, dfrA1-aadA1, dfrA12-orfF-aadA2, dfrA17-aadA5+dfrA1-sat2-aadA1 
Pig +aadA1, aadB-aadA1, dfrA1-aadA1, dfrA12-orfF-aadA2, dfrA14-aadA6, dfrA17-aadA5+dfrA1-sat2-aadA1, estX-sat2-aadA1 
CatSalmonella serovars+aadB, blaPSE−1 Rodriguez et al. (2009)
Chicken +aadA1, dfrA1-aadA1+dfrA1-sat2-aadA1 
Horse +aadB, blaPSE−1  
Pig +dfrA1-aadA1  
GreeceChickenE. coli+aacA4-catB3-dfrA1 aadA1, aadA1-dfrA1 aadA2-orfF-dfrA12, aadA5-dfrA17, satND Vasilakopoulou et al. (2009)
Hong KongCattleE. coli+dfrA17-aadA5 Ho et al. (2009)
Chicken +dfrA1-aadA1  
Pig +aadA23, arr3, dfrA1-aadA1, dfrA17-aadA5  
HungaryChickenS. infantis+NDND Nogrady et al. (2008)
IrelandCattleE. coli+aadA1, dfr1-aadA1ND Ekkapobyotin et al. (2008)
ChickenS. enterica Kentucky+aadB, satND Boyle et al. (2010)
ItalyCattleE. coli+NDND Alessiani et al. (2009)
Chicken +NDND  
JapanCattleS. enterica Typhimurium+aadA1, aadA2, aadA2-blaPSE−1, blaPSE−1 Ahmed et al. (2009c)
ChickenE. coli+aadA1, dfrA1-aadA1, dfrA1-orf, dfrA7+dfrA1-sat2-aadA1Ahmed et al. (2009b)
ChickenSalmonella serovars+aadA1, aadB-catB3+estX-sat2-aadA1Ahmed et al. (2009a)
ChickenSalmonella infantis+aadA1, aadA2, dfrA5ND Shahada et al. (2010)
PigS. enterica Typhimurium+aadA1, aadA2, dhfrXII-orfF-aadA2 Ahmed et al. (2009a), Futagawa-Saito et al. (2010)
HorseS. enterica Typhimurium+NDND Niwa et al. (2009)
KoreaPigS. enterica Typhimurium+aadA1, dhfrXII-orfF-aadA2 Rayamajhi et al. (2008)
LithuaniaCattleE. coli+aadA1, dfrA1, dfrA1-aadA1, dfrA14, dfrA14-aadA6, dfrA17, dfrA17-aadA5, estX-aadA1+dfrA1, dfrA1-sat-aadA1Povilonis et al. (2010), Seputiene et al. (2010)
Chicken +aacA4-catB3-dfrA1-orfX, aadA1, dfrA1-aadA1, dfrA5, dfrA12-orfF-aadA2, dfrA14+dfrA1, dfrA1-sat, dfrA1-sat-aadA1 
Pig +aadA1, dfrA1, dfrA1-aadA1, dfrA12, estX-aadA1+dfrA1, dfrA1-sat-aadA1, estX-sat2-aadA1 
ChickenS. enterica+aadA2, dfrA1-aadA1 Povilonis et al. (2010)
Pig +aadA1, aadA7-aadA7, estX-aadA1, dfrA12-orfF-aadA2  
MexicoCattleS. enterica Typhimurium+aadA1, dfrA17-aadA5, dfrA12-orfF-aadA2ND Wiesner et al. (2009)
Chicken +dfrA17-aadA5, dfrA12-orfF-aadA2ND  
Pig +aadA1, dfrA17-aadA5, dfrA12-orfF-aadA2ND  
PortugalChickenEnterobacteriaceae+aadA1, aadA1a, aadA2, blaP1, dfrA1-aadA1, dfrA12-orfF-aadA2, dfrA17-aadA5, estX-aadA1+dfrA1-sat2-aadA1-orfX, estX-sat2-aadA1-orfXMachado et al. (2008)
Pig +aadA1, aadA13-estX, dfrA1-aadA1, dfrA14-aadA1-catB2, dfrA17-aadA5, estX-aadA1+aadA1, dfrA1-sat2-aadA1-orfX, estX-sat2-aadA1-orfX 
ChinaChickenE. coli+aadA1, aadA22, aadB-orf1-cmlA, arr3, arr3-dfr16, dfrA1-aadA1, dfrA1-orfC, dfrA12-aadA2, dfr17-aadA5, dhfrXII-orfF-aadA2, dfr1-aadA1, yheSΔ-yheR-kefBÄ+dfrA1-sat1-aadA1, dfrA1-sat1-aadA1-orfXZhang et al. (2009c), Li et al. (2010b), Lu et al. (2010)
CattleArcanobacterium pyogenes+aadA1-aadB-cmlA6, aadA5, aadA24-orf1 Liu et al. (2009b)
CattleE. coli+yheSΔ-yheR-kefBÄ+ Song et al. (2010)
PigE. coli+aadA1, aadA2, aadA23B, blaP1a-aadA2-ereA, dfrA1-aacA4-catB3, dfrA1-aadA1, dfrA1-orfC, dfrA12-aadA2, dfr17-aadA5, dhfrXII-orfF-aadA2, yheSΔ-yheR-kefBÄ+dfrA1-sat1-aadA1Zhang et al. (2009c), Lu et al. (2010)
Saudi ArabiaChickenE. coli+NDND Altalhi et al. (2009)
South KoreaCattleE. coli+ND Unno et al. (2010)
Chicken +ND  
Duck +ND  
Pig +ND  
TaiwanPigS. enterica Choleraesuis+aadA1, aadA-qacH, aadA22, dfrA1-UN, dfr12-orfF-aadA2, sat-psp-aadA2-cmlA1- Lee et al. (2009)
ThailandCattleSalmonella serovars+aadA2ND Chuanchuen et al. (2010)
Chicken, PigS. enterica serovars+aadA2, aadA4a, blaPSE−1, codB-dfrA12-aadA2, dfrA1-orfC, dfrA12-aadA2, sat-dfrA12-aadA2, silB Chuanchuen & Padungtod (2009)
TunisiaCattleE. coli+dfrA17-aadA5 Slama et al. (2010)
Chicken +aadA1, dfrA1, dfrA5, dfrA5-ereA, dfrA12-orf-aadA2, dfrA14, dfrA17-aadA5, dfrA25 sat-psp-aadA2-cmlA1+dfrA1-satA1-aadA1-orfXSoufi et al. (2009), Slama et al. (2010)
Pig +dfrA1-aadA, dfrA17-aadA5 Slama et al. (2010)
TurkeyChickenS. enterica Enteritidis+aadAND Kalender et al. (2009)
UKPigE. coli+  Liu et al. (2009a)
USACatE. coli+aadA1, aadA1-UN+dfrA1-sat1-aadA1Shaheen et al. (2010)
Dog +aadA1, aadA1-UN, dfrA1-aadA1, dfrA17-aadA5, dfrA12-aadA2, dfrA12-orfF-aadA2, aadB-aadA1d, aacA4-catB3-dfrA1, aadB-aadA1-cmlA6+dfrA1-sat1-aadA1Shaheen et al. (2010), Yang et al. (2010)
PigS. enterica Heidelberg+aadA1, aadA2 Patchanee et al. (2008), Lynne et al. (2009)
Cattle +aadA1, aadA2, aadA5, aadA9, dhfr Lynne et al. (2009)
Turkey +aadA1  
CattleSalmonella serovars+NDND Alam et al. (2009)
TurkeySalmonella serovars+aadA1, aadA2ND Nde & Logue (2008), Zou et al. (2009)
TurkeyS. enterica serovars+aadA, aadB, and dfr variantsND Zhao et al. (2009)
VietnamCattleSalmonella serovars+aadA2ND Vo et al. (2010)
Chicken +blaPSE−1, dfrA1-orfCND  
Pig +aadA2, blaPSE−1ND  
Table 3.   Reports of class 1 and class 2 integrons in wild animals and environmental samples, 2008–2010*
CountryAnimal host/environmentBacterial host/sourceintI1Cassette array(s)intI2Reference
  • *

    Table is based on English-language papers published between 2008 and 2010 recovered from PubMed using the search terms integron × environment.

  • Gene and cassette nomenclature is based on that used in the original papers. In some cases, gene names are at variance with standard gene naming nomenclature. A standardized nomenclature has recently been published by Partridge et al. (2009). Individual cassette arrays are given on separate lines, although in some cases, full cassette arrays were not characterized, and entries list gene cassettes detected.

  • Cassette arrays for class 2 integrons were dfrA1-sat2-aadA1 or setX-sat-aadA1.

  • ND, not determined.

ArgentinaRiver waterPseudomonas sp.ND +Ramirez et al. (2010)
AustraliaFreshwater sedimentDiverse heterotrophs+aadA11, orf3-qacF, novel ORFs, no cassetteNDRosewarne et al. (2010)
Freshwater sedimentMetagenomic+NDNDHardwick et al. (2008)
Freshwater biofilmMetagenomic+Diverse, novel ORFs linked to members of the qac gene familyGillings et al. (2009a)
Soil, water, biofilm +Diverse, novel ORFs Gillings et al. (2008)
PrawnAcinetobacter sp.+msrB/msrA/ctr-aadA2Gillings et al. (2009b)
CanadaAtlantic salmonAeromonas salmonicida+aadA7McIntosh et al. (2008)
Polluted estuaryMetagenomic+Diverse, novel ORFsKoenig et al. (2009)
ColumbiaParacheridon exelrodiAeromonas hydrophila+Cassettes include dfr12, aac61b, aadA1NDVerner-Jeffreys et al. (2009)
Corydora melanistusAeromonas hydrophila+Cassettes include dfr12, aadA2ND 
Carriage waterMetagenomic+Cassettes include aadA1, dfrA21, dfrA22, dfrA23, qacE2ND 
Czech RepublicPigeonE. coli+No cassette+Radimersky et al. (2010)
Black-headed gullE. coli+aadA1, aadA2, blaOXA−1-aadA1, dhfr1, dhfr1-aadA1, dhfr1-catB3-aadA4, dhfr17-aadA5+Dolejska et al. (2009)
Pond waterE. coli+aadA5, dhfr1-aadA1, dhfr12-aadA2 
Koi carpAeromonas spp.+aadA1, aadA2, dhfr12-aadA2Cizek et al. (2010)
FranceEstuarine waterE. coli+aadA1, dfrA1-aadA1, dfrA5-ereA2, dfrA17-aadA5+Laroche et al. (2009)
GermanyManured soilMetagenomic+aadA1, aadA2, aadA9, aadA11, aadA13NDBinh et al. (2009)
GuyanaThree lined pencil fishAeromonas hydrophila+Cassettes include dfr12, orfFNDVerner-Jeffreys et al. (2009)
Silver hatchetAeromonas hydrophila+Cassettes include aadA2, dfr12ND 
Carriage waterMetagenomic+Cassettes include aadA1, aadA2, dfrA5, dfrA17, dfrA27, qacE2ND 
IndiaRiver waterAcinetobacter johnsonii+dfrA28-aadA1Kumar et al. (2010)
ItalyHerring gullE. coli+aadB, aadA1a, dfrA17-aadA5, estX-aadA1aNDGionechetti et al. (2008)
Herring gullProteus mirabilis+aadB-aadA2, aacCA5-aadA7, dfrA1-aadA1a, dfrA15, estX, estX-smr-2-aadA1a, orf1-cat-orf2-aadA1aND 
Urban wastewaterPseudomonas spp.+blaIMP−22-orfXX, blaIMP−22-orfXX-aacA4Pellegrini et al. (2009)
MexicoDustE. coli+NDNDDiaz-Mejia et al. (2008)
Activated sludge tankE. coli+NDND 
MozambiqueWaste waterVibrio spp.+aadA2Taviani et al. (2008)
Posttreatment waterVibrio cholerae+blaP1, dfrA15 
PortugalBuzzardE. coli+NDRadhouani et al. (2010)
Yellow-legged gullE. coli+aadA, dfrA1-aadA1, dfrA12-orfF-aadA2, sat-psp-aadA2+Radhouani et al. (2009)
Seagull speciesE. coli+blaOXA−1-aadA1, dfrA1-aadA1, sat-psp-aadA, sat-aadA1+Poeta et al. (2008)
Wild boarE. coli+ND+Poeta et al. (2009)
ChinaWastewaterDiverse species+aacA4, aadA1, aadA5, aadB-qacH, aadA4a, aadA11bNDLi et al. (2009a)
Lake, river, sedimentMetagenomic+NDNDZhang et al. (2009a)
Sewage treatmentMetagenomic+NDND 
WastewaterGammaproteobacteria+Cassettes include aadA1, aadA2, aadA2a, dfrA1, dfrA12, qacGNDLi et al. (2010a)
WastewaterAeromonas punctata+aacA4-qnrVC4-aacA4-catB3Xia et al. (2010)
SingaporeGuppyAeromonas hydrophila+dfr12NDVerner-Jeffreys et al. (2009)
Harlequin rasboraAeromonas hydrophila+dfrA1ND 
Redwag platyAeromonas punctata+Cassettes include dfr12, aac61b, aadA1, catB8ND 
Carriage waterMetagenomic+Cassettes include aadA1, aadA2, dfrA1ND 
SwitzerlandLake waterAeromonas allosaccharophila+aac61b-blaOXA−1-catB3-arr3NDPicao et al. (2008)
TanzaniaFlamingoE. coli+dfrA7+Sato et al. (2009)
FlamingoSalmonella arizonae+dfrA7 
TurkeyRiver waterE. coli+Cassettes include aadA1, aadA5, blaOXA30, dfrA1, dfr2d, dfrA7, dfrA16, dfrA17, sat1+Ozgumus et al. (2009)
UKKoi carpAeromonas hydrophila+Cassettes include aadA1, dfrA1NDVerner-Jeffreys et al. (2009)
Agricultural soilDiverse species+ND+Byrne-Bailey et al. (2009)
USACatfishAeromonas veronii+NDNawaz et al. (2010)
CatfishE. coli+dfrA17-aadA5, dfrA12-orfF-aadA2NDNawaz et al. (2009)
Forest soilDiverse species+No cassettesNDSrinivasan et al. (2008)
Dairy soilCitrobacter spp. others+aadA2, dfrA12-aadA2ND 
Soil, water, compost, manureDiverse species+aadA1, aadA7, aadA9, dfr16NDYang et al. (2010)
Estuarine habitatMetagenomic+Diverse, novel ORFsNDWright et al. (2008)
Riverine habitatMetagenomic+Diverse, novel ORFsND 
Sewage treatmentMetagenomic+NDNDGhosh et al. (2009)
CompostE. coli+aadA1, aadA1-dfrA1, aadA1-dfrA15, aadA2-dfrA12NDHeringa et al. (2010)

Conduits of LGT

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Most genes that are now mobile in clinical isolates probably originated as genes with a fixed chromosomal origin. Where this origin can be identified, it may be possible to ascribe putative origins to resistance genes or gene families as has been suggested for qnr genes (Poirel et al., 2005). However, we argue that reference to reservoirs is unhelpful in understanding resistance gene flow, even in cases like E. coli, and is an impediment to ultimately managing the problem of clinical resistance. When we observe identical genetic elements residing in two different vectors or species, we can only say that there has been a lateral transfer event. However, we cannot reliably ascribe the direction of that transfer, nor establish that the transfer occurred directly between the two locations currently occupied by that particular genetic element. Despite this fundamental problem, an implicit assumption of direction is contained in the ‘reservoir’ hypothesis of antibiotic resistance (Salyers & Shoemaker, 2006). The term ‘reservoir’ suggests a pool of genes that flows downwards, usually into human beings and their pathogens, and this is probably too simplistic.

In contrast, we believe that most and possibly all environments/organisms act as conduits for resistance gene flow. Some organisms like E. coli play a particularly important role, but all bacteria may have a role to play. Global gene flow acts in multiple directions, allowing the introduction of new resistance genes into human pathogens and shuttling known, clinically important resistance genes back into the broader bacterial population for subsequent cycling into other clinical contexts (Fig. 3). The ability of organisms like E. coli to facilitate resistance gene flow has other possible ramifications for understanding the epidemiology of gene transfer that are not adequately conveyed by concepts of reservoirs. An alternative useful view is offered by source–sink modelling. Under this model, sinks – in this case clinical pathogens – acquire DNA from sources – the broader environment. The model is constructive because it does not preclude two-way flow, and experimental data suggest that immigration into the sink can result in faster rates of adaptation, which, in a clinical context, translates into faster adaptation to antibiotic resistance (Pulliam, 1988; Sokurenko et al., 2006; Perron et al., 2007). The concept is consistent with conduits because source–sink modelling provides insights into the primary direction of flow and how the process started, whereas conduits imply a mechanism of transfer. Generally, these types of models reinforce observations that resistance genes (Knapp et al., 2010) and the elements that mobilize them tend to increase in abundance over time even in the absence of selection for all of their components.

image

Figure 3.  Conduits of gene transfer between different bacterial species, animal hosts and the environment. Genes can potentially move directly between various host environments including humans, food animals, domestic animals, wild animals and the general environment. In the case of gene cassettes containing antibiotic resistance determinants, this lateral transfer may be mediated via transformation with free gene cassettes, integrons, transposons or plasmids. Alternately, genes can spread by conjugation between various commensals and pathogens transferred between host environments.

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The scale and evolutionary history of LGT makes it inevitable that practically any gene can find its way into any bacterial cell. The key to understanding this ongoing process is to quantify both the opportunity for lateral transfer and the strength of selection for particular transferred genes and the phenotypes they confer (Martinez et al., 2007). The specific lateral transfer events that have led to the current crisis in antibiotic resistance management have probably occurred many thousands of times in the evolutionary past, but under circumstances where they conferred no selective advantage. Under strong selection, however, antibiotic resistance genes can come to dominate a population or, with LGT, an entire community. While it is the case that the acquisition of an antibiotic resistance gene can come at a fitness cost, at least initially, compensatory mutations can arise to counteract this (Andersson, 2003). Thus, a reduction in antibiotic usage does not necessarily lead to a significant reduction in resistance gene frequency in a population.

Understanding the dissemination of resistance determinants requires the investigation of all the locations where antibiotic-resistant Bacteria might reside. There are five sources/sinks that are of particular interest: human beings, domestic animals, companion animals, wild animals and the general environment (Fig. 3). The high level of interest in the dissemination of resistance genes between these locations can be gauged by the contents of Tables 2 and 3, which deal with recent reports of integrons in animals and in the general environment. As schematically illustrated in Fig. 3, transfers of mobile elements and linked resistance genes (integrons or otherwise) can potentially occur directly between any of these sources/sinks, and it is likely that that new vectors or combinations of resistance genes arising in one host can rapidly circulate through all locations.

Of all the mobile elements in Gram-negative bacteria, class 1 integrons have been most extensively surveyed in clinical contexts. As we will discuss below, the ease with which integrons can be surveyed is itself an impediment, because it introduces a bias in focus, and is not helpful in understanding the resistance problem from the perspective of the microbial biosphere. Bearing this caveat in mind, it is still the case that there is a wealth of published evidence for the LGT of integrons, mobilized by other elements or processes, between most of the sources and sinks depicted in Fig. 3. We will give some examples of transfers of particular interest, but unfortunately cannot cover the complete literature in this review.

Transfer between humans and their domestic animals

Class 1 and class 2 integrons are widely disseminated in E. coli and Salmonella isolated from a range of companion and food animals (Table 2). These integrons are in many cases identical to those found in human commensals and pathogens, establishing that a conduit of lateral transfer exists between humans and these animals (Goldstein et al., 2001; Schwarz & Chaslus-Dancla, 2001; Schwarz et al., 2001; Antunes et al., 2006; Hsu et al., 2006; van Essen-Zandbergen et al., 2007). The presence of identical integrons and cassette arrays in various Salmonella serovars and E. coli strains demonstrates that lateral transfer occurs within and between these species, even when residing in different hosts (Box et al., 2005; Singh et al., 2005; Hammerum et al., 2006; Ajiboye et al., 2009). Integrons have also spread from the terrestrial environment into E. coli and Aeromonas strains associated with aquaculture (Cabello, 2006; McIntosh et al., 2008; Nawaz et al., 2009, 2010). Because the prevalence of integrons in all animals increases with vicinity to humans, it has been suggested that the presence of integrons in animals is due to transmission from humans rather than the reverse (Skurnik et al., 2006).

Transfer between humans/domestic animals and wild animals

There are difficulties in establishing the directionality of transfer of bacteria or genes. Nevertheless, a good case can be made in some instances (Table 3). A number of studies have suggested that wild birds such as gulls and pigeons can acquire integrons and antibiotic resistance genes by feeding on waste or from contaminated waters (Gionechetti et al., 2008; Poeta et al., 2008; Bonnedahl et al., 2009; Dolejska et al., 2009; Radimersky et al., 2010). Anthropogenic transfer of integrons and resistance genes to wild boars and buzzards has also been suggested (Poeta et al., 2009; Literak et al., 2010; Radhouani et al., 2010). It seems very likely that integrons in wild animals, zoo animals and ornamental fish (Ahmed et al., 2007; Sato et al., 2009; Verner-Jeffreys et al., 2009) (Table 3) have their origins in humans or their domesticated animals. There also appears to be transfer of enterobacteria and resistance determinants between humans and chimpanzees in Uganda (Goldberg et al., 2007).

Transfer between humans/domestic animals and the more general environment

Integrons from animal husbandry operations make their way into the general environment via the spread of manure (Agerso & Sandvang, 2005; Binh et al., 2009; Byrne-Bailey et al., 2009) and in compost (Heringa et al., 2010; Yang et al., 2010) (Table 3). Human waste streams disseminate integrons and resistance genes, initially to wastewater treatment plants (Schluter et al., 2007; Ghosh et al., 2009; Zhang et al., 2009b), but also more generally into rivers and estuaries (Laroche et al., 2009). Escherichia coli strains containing plasmids and multidrug resistance have even made their way into remote areas, including isolated communities in the Peruvian Amazonas and birds in the Arctic (Sjolund et al., 2008; Bartoloni et al., 2009).

Potential for transfer back into human populations

When antibiotic resistance genes and vectors are spread from human-dominated ecosystems, they can penetrate new bacterial hosts. Transfer of integron-mediated antibiotic resistance between E. coli strains has been demonstrated in bovine faeces and in storm water (Nagachinta & Chen, 2008). Similarly, a class 1 integron carrying a novel blaIMP has moved from Pseudomonas aeruginosa in a nosocomial environment into P. fluorescens in wastewater (Pellegrini et al., 2009). Such activity has the potential to generate novel opportunistic pathogens. Antibiotic resistance integrons may also interact with diverse mobile elements in the environment and acquire new resistance and pathogenicity determinants. Novel integron gene cassettes conferring trimethoprim and quinolone resistance have recently been recovered from environmental Acinetobacter and Aeromonas isolates, respectively (Kumar et al., 2010; Xia et al., 2010). Clinical class 1 integrons have made their way into the commensal bacteria of wild animals, where they continue to acquire novel cassettes. A class 1 integron has been described in E. coli from a wild reindeer that carried an ant(3″)-Ia resistance cassette, and had also acquired a gene cassette with homology to a cassette of unknown function described from Xanthomonas (Sunde, 2005).

Does human use of antimicrobial agents change the tempo of lateral transfer?

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

It has been argued that humans are the ‘World's greatest evolutionary force’ (Palumbi, 2001), a recognition of our ability to engineer the biosphere. One particularly apt example of this concept is our impact on the accelerated evolution of antibiotic resistance. The use of antibiotics may have changed the dynamics of bacterial evolution by increasing the basal rate of mutation, enhancing LGT and promoting the generation of novel DNA elements. We know that antimicrobial compounds induce stress in bacterial cells, leading to changes in transcriptomic profiles (Davies et al., 2006) and other mechanisms that increase evolvability (Baquero, 2009). For instance, the evolution of resistance in E. coli is accelerated by exposure to multiple antibiotics (Hegreness et al., 2008).

It is likely that the ecology of human dominated ecosystems helps to stimulate the generation of novel genetic elements. Exposure of cells to various antibiotics induces an SOS response that has widespread effects on the bacterial genome (Miller et al., 2004; Aertsen & Michiels, 2006). These responses include promoting lateral transfer of antibiotic resistance genes (Beaber et al., 2004) and increasing integron recombination events (Guerin et al., 2009). Consequently, the release of antibiotics in human waste streams is likely to have an impact on LGT and on the activity and complexity of large gene cassette arrays carried by the diverse chromosomal integrons found in environmental samples.

Waste streams from human-dominated ecosystems simultaneously release resistance determinants, their DNA vectors and the antimicrobial agents that select for them (Baquero et al., 2008; Martinez, 2009). Wastewater brings together diverse cells, plasmids, integrons and resistance genes, creating a hotspot for interaction between these elements in an environment that contains subinhibitory concentrations of the selective agents to which they exhibit resistance (Schluter et al., 2007, 2008; Moura et al., 2010). Such environments allow complex mosaics of subelements to be built up (Toussaint & Merlin, 2002; Norman et al., 2009), and because these complex DNA elements share homologous regions, recombination is enhanced, thus promoting still further diversity (Garriss et al., 2009).

It is clear that the fixation of antimicrobial resistance genes in pathogens and commensals is driven by the selection imposed by antibiotics. The transfer of such genes has been occurring for millennia, but not necessarily under conditions where such transfers conferred any advantage to the recipient cell. The propensity for such LGTs should be balanced by two opposing selective forces: the potential advantage accrued through the acquisition of foreign genes, balanced against the deleterious effects of invasion by transposons, bacteriophage and other detrimental DNA elements (Fig. 4).

image

Figure 4.  Barriers to lateral gene transfer. For any species, the barriers to lateral gene transfer are set by two opposing and balanced selective forces: the ability to resist infection by bacteriophage and/or barriers to transposons (upward arrows) and the advantage conferred by the ability to acquire new phenotypes (downward arrows). The widespread dissemination of antibiotics may have altered this equilibrium, selecting for increased lateral transfer capability.

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It therefore seems reasonable to suggest that porosity to lateral transfer is under balancing selection, and that different species, and even cells within species, fall along a gradient of porosity. The widespread human use of antibiotics and their distribution via human waste streams (Baquero et al., 2008; Martinez, 2009) may have altered the strength of this balancing selection, such that cells and species with a greater porosity to lateral transfer have an inherent advantage because some members of their lineage will acquire and express resistance genes. Hence, it is highly probable that the general tempo of lateral transfer has actually increased due to selection on cells with inherently higher rates of lateral transfer (Fig. 4).

The recent discovery of the CRISPR system provides a potential mechanism for restricting the uptake of foreign DNA. Changes to this system may have the result of modulating the rate of uptake of DNA mobilized by LGT. The clustered regularly interspaced short palindromic repeat (CRISPR) system is a bacterial form of acquired immunity (van der Oost et al., 2009). The CRISPR system is complex and remarkably sophisticated, but the key component providing the acquired immunity is the presence of small RNA guides that target specific DNA sequences that act to prevent the incorporation of incoming DNA that possess complementary sequences. The system is analogous, but unrelated to interfering RNA found in eukaryotes. The extent to which a bacterial cell can limit LGT is determined by the number and type of RNA guides, which in turn varies between individual cells (Marraffini & Sontheimer, 2008). Genomic analysis would suggest that CRISPR systems are common among the prokaryotes (van der Oost et al., 2009) and that they may influence the evolution of pathogenesis (Marraffini, 2010). The CRISPR system is likely to be important in influencing cell fitness because it has been argued that it may help in providing a balance between the potential positive vs. the negative impacts of acquiring DNA by LGT (van der Oost et al., 2009). Coevolution of the system with its host should occur such that in environments where acquiring DNA may be detrimental, an increase in the CRISPR content would occur and a decrease would occur where ‘foreign’ DNA may be advantageous (Vale & Little, 2010). This has direct relevance for the spread of antibiotic resistance because the global use of antibiotics could see a substantial decrease in the CRISPR content in bacterial populations, leading to a general increase in the rate of mobilization of DNA by LGT as measured by successful transfer events. In support of this, an inverse correlation between CRISPR content and the extent of multidrug resistance has been reported recently (Palmer & Gilmore, 2010).

The agents of gene capture and spread

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

All of the mobilizing elements associated with the movement of resistance genes in pathogens long predate the antibiotic era. Analysis of at least one extensive strain collection dating from the early 20th century demonstrated that plasmids were a common feature of strains of the Enterobacteriaceae (Hughes & Datta, 1983; Jones & Stanley, 1992). Similarly, transposons were a common feature of soil dwelling bacteria in the preindustrial era (Kholodii et al., 2003; Mindlin et al., 2005). Integrons, based on their phylogenetic history, have been features of bacterial chromosomes for at least several hundred million years (Mazel, 2006; Boucher et al., 2007). Where they can be directly examined, mobile elements from before the antibiotic era are clearly related to contemporary elements that carry resistance genes. Thus, preantibiotic era plasmids belong to the same incompatibility groups as those seen today (Hughes & Datta, 1983) and bacteria from ancient permafrost possess mercury resistance transposons related to those found in pathogens (Mindlin et al., 2001, 2005). While the evidence is more circumstantial, it is also likely that the class 1 integron, responsible for spreading resistance genes, was quite broadly distributed in the Proteobacteria before the antibiotic era (Stokes et al., 2006; Gillings et al., 2008). What does distinguish these mobile DNA elements in early isolates from those in contemporary pathogens is that the former are rarely found in association with antibiotic resistance genes, whereas the latter are substantial carriers of these genes. Secondly, in contemporary bacteria, a high degree of clustering is observed such that multidrug resistance regions are commonly mosaics made up of many of the mobile genetic elements described. This cooperation between disparate mechanisms of LGT has considerably facilitated the global spread of resistance genes (Walsh, 2006) and is contributing to the evolution of multidrug-resistant pathogens with enhanced virulence, via the accumulation of disparate virulence factors in pathogenicity islands (Juhas et al., 2009) and virulence plasmids (Villa & Carattoli, 2005).

With time and ongoing selection, the trend is towards increasing complexity of multidrug resistance elements. This increase in complexity is driven by combinatorial exchanges between existing elements, recruitment of new elements (Walsh, 2006; Garriss et al., 2009) and by coselection for genes that confer resistance to environmental compounds and pollutants (Baker-Austin et al., 2006).

Plasmids

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

The central role of plasmids in contributing to LGT is not disputed. It was the discovery of these genetic agents that led to a paradigm shift where bacterial evolution was viewed as more than spontaneous mutation and binary fission of haploid cells (Lederberg & Tatum, 1946). It was then described by Salvador Luria as ‘… among the most fundamental advances in the whole history of bacteriological science’ (Luria, 1947). Given subsequent developments, including the key role of plasmids in making the gene cloning revolution possible, the statement is still true. The central role of plasmids is inferred in Table 1, where it can be seen that at least some plasmids are autonomous, both with respect to their physical movement (via conjugation) and through their autonomous replication. Notwithstanding these basics, plasmids are extraordinarily versatile in that their size and (commonly) circular form means that they are readily mobilizable by transformation, a factor that may be important in soil-dwelling organisms (Sikorski et al., 2002) and represents an obvious mechanism for the spread of nonconjugative plasmids.

Once direct evidence for the existence of extrachromosomal DNA in bacteria was established, the early years of plasmid biology were dominated by the characterization of their basic properties including size, the fundamentals of incompatibility, entry exclusion and the replication and transfer genes they carried (Novick, 1969). The link between plasmids and resistance genes was noted very early and resulted in P. aeruginosa emerging as a major focus of genetic study in the Gram negatives (Holloway, 1969). The reasons for this included the fact that it is a significant opportunistic pathogen and a common cause of nosocomial infections. In a plasmid context, P. aeruginosa is a source of a number of resistance (or RP) factors and many of these were unusual at the time in that they were able to easily cross species boundaries (Sykes & Richmond, 1970; Grinsted et al., 1972). With the characterization of these resistance factors, it was realized that the emergence of multidrug resistance was a result of the comobilization of several genes and that this was now a major clinical problem, not just a rare inconvenience involving the transfer of resistance to a specific single drug (Anonymous, 1974). This same period also saw the onset of the first resistance epidemiology studies and the establishment of the link between the clinical use of antibiotics and an increase in resistance carriage (James et al., 1975; Krcmery et al., 1975). Ironically, it was just at this time that the potential of plasmids to play a role in adaptation to the clinical application of antibiotics was becoming obvious. Also, at this time, more early data hinted at the presence of other mechanisms of resistance gene mobilization. Specifically, it was found that R plasmids could be targets for translocating pieces of DNA that carried resistance genes and that the process by which this occurred was independent of homologous recombination pathways (Bennett & Richmond, 1976). Thus, the fundamental advances first articulated by Salvador Luria 30 years previously were clearly all still to be unravelled. The systems biology approaches available in contemporary times to analyse mobile DNA, although more sophisticated, make it clear that the role played by plasmids in particular to bacterial adaptation is a long way from being fully understood (Johnson & Nolan, 2009; Halary et al., 2010; Smillie et al., 2010).

Transposons

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Why are some mobile elements more commonly associated with antibiotic resistance genes in pathogens than others? There may be a number of reasons for this outcome, including an element of chance. Chance may play a role, since the first capture event(s) of resistance gene(s) in a particular element remove the selective advantage conferred by infiltration of other elements carrying the same or similar genes. Alternatively, some groups of mobile elements may have been ‘primed’ for infiltration into pathogens. This is notably the case for mercury-resistant transposons existing before the antibiotic era (Fig. 5). The redox potential of mercury can vary, but only the oxidized state is toxic (Foster, 1987). The bacterial inactivation of mercury is via a reduction reaction. The proteins that detoxify mercury therefore probably first arose when the biosphere became oxygenated (Barkay et al., 2010) and mercury resistance transposons have been a feature of soil-dwelling bacteria for a very long time (Mindlin et al., 2001, 2005). Many of these are very closely related to multidrug resistance transposons in contemporary pathogenic isolates (Kholodii et al., 2003). Having begun to capture resistance genes, particular types of these transposons demonstrated very rapid rates of evolution, driven by selection pressure in the antibiotic era. The best examples of this phenomenon are derivatives of the Tn21 family (Liebert et al., 1999). Before human impacts, mercury was present in some environments at low levels and it likely that bacteria play a role in the global cycling of this element (Baldi, 1997). Even in pristine and/or preindustrial era soils, resident bacteria can possess highly evolved and regulated operons for the chemical transformation of mercury (Barkay et al., 2003; Barkay & Wagner-Dobler, 2005). In environments where anthropogenic disturbance has seen the introduction of elevated levels of mercury, corresponding enrichment for resistant bacteria has occurred (Barkay & Pritchard, 1988; Sprocati et al., 2006). This enrichment was probably occurring before the antibiotic era both in the general environment and through the use of topical disinfectants that included mercury. The mining industry has also contributed to the increased resistance in the general environment throughout the industrial era (Ball et al., 2007).

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Figure 5.  Coselection and recruitment of transposons and class 1 integrons into pathogens. The schematic represents a model describing the order of events leading to complex and highly mobile multiresistance regions in contemporary Gram-negative pathogens. The use of disinfectants led to the linking of qac genes to class 1 integrons before the antibiotic era. This structure then linked to a Tn402-like transposition module and became mobile. At about the same time, with the onset of extreme selection pressure via the use of antibiotics, antibiotic resistance genes began to be recruited into this structure and its descendants. In parallel, the presence of mercury in the environment – both natural and human induced – led to the enrichment for mercury-resistant transposons. These also began to independently recruit resistance genes from the onset of the antibiotic era. At the same time and subsequently, the res targeting mechanism associated with Tn402-like class 1 integrons made the linking of a broad range of transposition modules to site-specific recombination functions inevitable.

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Another source of relatively high concentrations of mercury is amalgam dental fillings. From an ecological perspective, this is potentially an important one because it is an environment at the interface of commensal and human pathogenic bacteria. Some early data suggested that mercury released from such fillings can promote an increase in both mercury and antibiotic resistance (Summers et al., 1993). The idea was considered controversial, at least by the dental community (Shearer, 1993), and more recently, some studies adopt a more equivocal stand on the notion that a strong link exists (Roberts et al., 2008b). However, similar to trying to identify specific reservoirs of resistance, these studies probably serve to underscore the difficulty of identifying single specific causes for a problem that is multifactorial in nature. Thus, dental amalgams are possibly one further step in the enrichment for antibiotic resistance, but not the single cause of that selection. Whatever the main driving forces, it is clear that antibiotic resistance genes began to appear on mercury resistant transposons and plasmids soon after the clinical introduction of antibiotics (Smith, 1967) and that co-selection is driving the increasing linkage of resistance genes to mercury resistance transposons.

Whatever the cause, it is clear that there is a strong link between antibiotic resistance and mercury resistance. While there are many genetic contexts in which antibiotic resistance and mercury resistance genes are found together, probably the most prevalent linkage is that between class 1 integrons and specific families of mercury resistance transposons. Of the latter, the most prevalent includes the Tn21 transposon family (Liebert et al., 1999). The success of the class 1 integron/Tn21 combination can be partly explained by the res hunting ability of the Tn402 transposition system and the fact that Tn21 and its relatives were already widespread in environmental bacteria before the onset of the antibiotic era (Mindlin et al., 2001, 2005; Kholodii et al., 2003). In contemporary times, this linkage between antibiotic resistance and mercury resistance may see coselection work ‘both ways’ to reinforce the link. That is, selection for antibiotic resistance may facilitate an increase in mercury resistance genes in bacteria and selection for mercury resistance via the environmental presence of mercury (whether natural or human induced) may be facilitating the retention of antibiotic resistance genes (Summers et al., 1993; Skurnik et al., 2010).

Integrons

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

The class 1 integrons provide an unrelated, but parallel example of selection priming. Integrons have been present in the Proteobacteria for a very long time (Mazel, 2006; Boucher et al., 2007). The defining feature of these elements is the presence of a site-specific recombination system capable of capturing individual genes when part of mobile gene cassettes (Martinez & de la Cruz, 1988; Stokes & Hall, 1989; Demarre et al., 2007). Over 100 classes of this element have been identified based on differences in the amino acid sequence of the site-specific recombinase protein, IntI. Although there may be site selection differences and modulation of the recombination reaction based on environmental parameters, it is nonetheless the case that members of different integron classes appear to operate by essentially the same biochemical process (Biskri et al., 2005; Guerin et al., 2009; Shearer & Summers, 2009). Why then are the class 1 integrons almost exclusively responsible for disseminating resistance genes by site-specific recombination in Gram-negative pathogens, and why are they so abundant in these same organisms (Partridge et al., 2009)? Integrons are generally located in bacterial chromosomes and most are not readily mobile, although they do show evidence having moved by LGT over evolutionary time periods (Boucher et al., 2007). The class 1 integrons from multi-drug-resistant pathogens, however, are highly mobile and are embedded in a plethora of mobile elements, including plasmids and transposons or, more frequently, both. In particular, the ‘clinical’ type of class 1 integron is found in association with the remnants of a transposon, the functional exemplar of which is Tn402, also known as Tn5090 (Shapiro & Sporn, 1977; Radstrom et al., 1994). When first named, the definition of integrons was based on both the function (the components of the site-specific recombination system) and the structural features of the clinical type of class 1 integrons that included all of the sequence common to this type when different examples were compared. This structural definition therefore additionally encompassed sequences between the Tn402-like inverted repeats designated IRi and IRt (Stokes & Hall, 1989; Partridge et al., 2001), reflecting the apparent universal association of class 1 integrons with Tn402-like transposition functions. In these same class 1 integrons, part of the transposition module had been lost and replaced with a 3′-conserved segment (3′-CS) (Stokes & Hall, 1989). Despite the fact that these integrons were defective transposons, transposition could still occur if deleted functions were provided in trans (Brown et al., 1996). This association with a transposon is regarded as a key step in promoting the LGT of this integron class in pathogens (Liebert et al., 1999).

Tn402 and relatives are examples of transposons that are res hunters, meaning that the transposition event targets the resolution regions important in the replication and/or the mobility of many plasmids and transposons (Kholodii et al., 1995; Petrovski & Stanisich, 2010). This ability to target other mobile elements was another key factor in the spread of class-1-associated antibiotic resistance genes from the earliest days of the antibiotic era. Thus, numerous examples are known of plasmids originally isolated in the 1950s and 1960s that carry resistance genes as a consequence of either the direct insertion of a class 1 integron into a plasmid res site (Brown & Willetts, 1981; Ward & Grinsted, 1982; Swedberg & Skold, 1983; Hall & Vockler, 1987) or via the acquisition of a transposon such as Tn21 (Swedberg & Skold, 1983; Hall & Vockler, 1987) that itself had captured a class 1 integron.

The res hunter family of transposons is commonly associated with mercury resistance, although in the Tn402-like integron version the integron module has replaced the mer module (Kholodii et al., 1995). In most clinical class 1 integrons, the tni module has undergone one or more deletions after the acquisition of the 3′-CS, which includes a sulphonamide resistance determinant. Class 1 integrons/transposons with a complete transposition module and no 3′-CS are known, although they are uncommon, and so the acquisition of the 3′-CS is generally presumed to have occurred soon after the clinical application of antibiotics (Brown et al., 1996). Very recently, however, this has been called into question with the discovery from permafrost dating back at least 15 000 years of a Pseudomonas sp. that possesses a class 1 integron with all the features seen in clinical isolates including a known resistance gene cassette and a 3′-CS (Petrova et al., 2011). This observation, if correct, does not necessarily change the order of steps involved in the evolution of the clinical type of class 1 integron, but would obviously impact on the timing. In our view, this observation is so radical as to require interpretation with caution. In particular, it needs to be established that contamination with contemporary isolates has not occurred and additional independent isolates need to be found.

While the defective integron/transposon version is undoubtedly the most common type of class 1 integrons in clinical isolates, the functional ancestor may also be more frequent than realized because the most common form of PCR screening for class 1 integrons is based on a primer that targets the 3′-CS (Levesque et al., 1995). Consequently, testing for other variants, most notably those with a complete transposition module (Post et al., 2007), would be highly desirable. Putting aside differences in the inserted cassette arrays, more than one functional transposon version has been identified (Labbate et al., 2008; Marchiaro et al., 2010). One of these, Tn6007, is from a human commensal bacterium and the associated integron has a complete tni module that is a hybrid when compared with Tn402 (Labbate et al., 2008). This is a significant observation because it implies either that independent capture events involving the res hunter transposons and class 1 integrons can occur or that rearrangements between Tn402 like integron/transposons and other members of the res hunter family are similarly occurring. In either event, it is likely that other analogous variants can be found because the bacterium containing Tn6007 was recovered in the absence of any selection beyond the ability to grow on complete medium (Labbate et al., 2008). One very common feature of class 1 integrons associated with a complete or a partial Tn402 module is evidence of the presence of a gene conferring resistance to quaternary ammonium compounds. In those class 1 integrons with a 3′-CS, this qacE gene has undergone a deletion, a consequence of the creation of this segment (Stokes & Hall, 1989). In the fully functional class 1 integron/transposons Tn402 and Tn6007, complete qacE gene are present as part of mobile gene cassettes (Radstrom et al., 1994; Labbate et al., 2008). Where present, the qac genes in such functional class 1 integrons/transposons are in functional cassettes (as distinct from the nonfunctional qacE cassette in the 3′-CS); hence, loss of such a cassette is as likely as for a typical antibiotic resistance cassette. Thus, if the progenitor class 1 integron that was captured by the transposition module brought in a qac gene, its absence could be explained by cassette deletion. In our view, it is likely that a qac gene was present when capture occurred because surveys of class 1 integrons that are embedded in Tn402-like transposons very commonly have qac cassettes linked to them (Gillings et al., 2009c) as discussed below.

The linking of the class 1 integron to a res hunter-type transposon was clearly an important step (Fig. 5) in the introduction of these elements into pathogens, and recent analysis of environmental bacteria has shed some light on how this occurred. When various Proteobacteria from nonclinical environments were tested for the presence of class 1 integrons, it was found that these elements were readily recoverable at a frequency of about 2% of bacteria screened. The study was noteworthy in that bacteria were recovered without selection for antibiotic resistance, the bacteria came from environments that were not under any overt selection for such resistance and the recovery of class 1 integrons was carried out in such a way as to not bias towards association with res hunter transposons (Stokes et al., 2006). While some of the integrons recovered were the clinical (i.e. possessed a 3′-CS) Tn402-like variants, most were not. This second group was distributed among different Proteobacteria, thereby implying LGT events that were independent of Tn402-like transposition systems. Subsequent studies reinforced this point (Gillings et al., 2008), making it clear that class 1 integrons are being mobilized independent of res hunter transposons, notwithstanding the prevalence of this type in clinical isolates, and this mobilization probably began well before the beginning of the antibiotic era. The pre-Tn402-like integrons commonly possess cassette arrays, although none of the cassette genes are obvious antibiotic resistances genes. Instead, they are more typical of cassettes from chromosomal arrays in the sense of being novel with no close (if any) homologues in the databases. The one exception to this, however, is the common presence of qac containing cassettes. In studies based on the ‘random’ recovery of class 1 integrons from environmental DNA and pure cultures, it was found that over half of the recovered pre-Tn402 integrons included qac cassettes in its array (Gillings et al., 2009c) and that in some communities these cassettes were being actively exchanged (Gillings et al., 2009a). This observation suggests a parallel with mercury-resistant tranpsosons as described above. Specifically, disinfectants predate the clinical use of antibiotics by at least 50 years (Gilbert & Moore, 2005) and quaternary ammonium compounds were a major fraction of these. Given the association of qac genes to mobilized, but non-Tn402-like class 1 integrons, and the presence of qac cassettes in Tn402-like integrons that predate the 3′-CS, we argue that selection for qac resistance led to at least the partial mobilization of class 1 and amplified their numbers in the Proteobacteria even before the application of the first antibiotics (Gillings et al., 2009c) (Fig. 5). With this scenario, when antibiotics came into broad clinical use, it would be almost inevitable that class 1 integrons would come to play a major role in the dissemination of antibiotic resistance in the same way as mercury-resistant transposons play a similar role.

It is also noteworthy that the debate over the role disinfectant use has in selecting for multi-drug-resistant bacteria is still very much ongoing. As is the case for coselection for antibiotic resistance with mercury, studies also claim that links are lacking between qac and antibiotic coselection (Weber & Rutala, 2006). However, we believe that reductionist studies that look at defined environments over limited time frames are missing real-world events. Given the power of LGT, the antibiotic resistance problem can only be understood and potentially controlled by considering gene flow through the biosphere over time. This point is reinforced by the fact that metagenomic studies, which are culture independent and therefore represent a more inclusive sample of the microbial biosphere, reveal that mobilizing elements like integrons are extraordinarily abundant and that selection in stressed environments with respect to such compounds as heavy metals are enriched with antibiotic resistance genes (Wright et al., 2008; Rosewarne et al., 2010).

The success of the Tn402-like class 1 integrons in disseminating antibiotic resistance genes is striking. Other integron classes have been recruited into mobile elements, but their impact has been more limited. The two best examples are class 2 and class 3 integrons. Class 2 integrons were first described around the time of the class 1, when site-specific recombination functions were identified in Tn7 (Sundstrom et al., 1988). However, this original version, along with most other examples found since, has a nonfunctional DNA integrase via the presence of a premature stop codon in the corresponding gene (Hansson et al., 2002). Not surprisingly, the diversity of the cassette arrays is low compared with class 1 integrons, although some differences can be found (Hansson et al., 2002; Biskri & Mazel, 2003; Plante et al., 2003). This outcome is presumed to be achieved by providing an integrase function in trans.

Two functional variants of intI2 have been found. One is from Provdentia stuartii isolates from cattle in Australia (Barlow & Gobius, 2006) and the second is from an E. coli isolate in Uruguay (Marquez et al., 2008a). Both sets of isolates were additionally noteworthy in that they included gene cassettes that did not possess obvious antibiotic resistance genes. Both these sets of integrons are, or are likely to be, on plasmids and so this may suggest that functional mobile integrons are beginning to recruit other types of genes. The Uruguayan isolate (Fig. 6) highlights the ramifications of this phenomenon for the management of pathogens, because the organism is an actual pathogen and the cassette array carries a known antibiotic resistance gene along with a cassette that includes a gene that encodes a likely lipopolysaccharide signal peptidase (Marquez et al., 2008a). The precise function of this protein is unknown, but bioinformatic analysis strongly suggests a link to a protein family that can impact host pathogenicity. If it is subsequently found that this gene product does have a direct link to virulence, it may be an early portent that integrons in multiresistant strains are beginning to recruit other types of cassettes that enhance pathogenicity. The rules of LGT do not prevent this, because if resistance genes can be recruited, appropriate selection will, by the same rules, see other types of genes appear. Intuitively, if every member of a population is multidrug resistant, the next logical step would be the recruitment of other genes that assist in niche adaptation over competitors. There is at least one other example of an analogous array structure. In a class 1 integron recovered from an Acinetobacter from a prawn gut, a two-cassette array was identified (Gillings et al., 2009b). One cassette carried a previously identified resistance gene. The second cassette included an msr operon. The msr family of genes encodes methionine sulphoxide reductases, multiple copies of which assist in adapting to high-stress environments especially in relation to oxidative stress tolerance in the intestinal tract. This particular integron is from a commensal of an invertebrate that is a popular human food. We consider this link to be a potentially major conduit and we predict that this msr cassette will be identified in an integron array in a human pathogen in the near future.

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Figure 6.  Structure of functional class 2 integron and associated cassette array from an Escherichia coli pathogen. intI2, functional class 2 DNA integrase; attI2, class 2 integron attachment site; dfrA14, trimethoprim resistance gene cassette; lsp, putative lipoprotein signal peptidase gene cassette; and lip, putative lipoprotein gene. This lip gene is not cassette associated. Asterisk indicates the relative position of internal stop codon. Letters indicate a putative signal peptidase cleavage recognition site. The resident strain and other features are as described previously (Marquez et al., 2008a, b).

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Class 3 integrons were first identified in Japan in 1995 (Arakawa et al., 1995). A later integron survey in Japan suggested that this integron class may be relatively common in that country, although not to the extent of the class 1 (Shibata et al., 2003). The class 3 integron has the potential to spread as it is on a plasmid and has been found in different species within and outside Japan (Correia et al., 2003), but is not common. In systematic screens for mobile integrons, class 3 integrons are rarely detected, suggesting that they have not infiltrated the clinical environments where class 1 (and to a lesser extent class 2 integrons) were common (van Essen-Zandbergen et al., 2007; Laroche et al., 2009). Why is this class relatively rare? One explanation may be the one given above – the class 1 integrons managed to infiltrate clinical isolates in greater numbers first. Another contributing factor, however, may be the fact that the associated class 3 integrase is not as efficient in capturing mobile cassettes as the class 1 in comparative experiments (Collis et al., 2002), thereby potentially conferring another selective advantage on the latter.

Elements within elements

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

The development of multidrug resistance regions in Gram-negative bacteria in the antibiotic era has been driven by tapping into the vast resource of mobile elements that have evolved in the microbial biosphere over very long periods of time. Some of these preexisting elements have been particularly important in concentrating resistance genes in pathogens. The recruitment of these elements may have been a result of chance or some degree of preselection as described above. In either event, it is clear that only a subset of the available pool of mobile elements has been recruited into pathogens. While small in number, selection has made them extraordinarily abundant. Partly as a consequence of this, drug resistance-carrying mobile elements are cooperating in a way that probably did not occur in the preantibiotic era. Thus, we tend to talk today of multidrug resistance regions and not individual genes. In many cases, the development of multidrug resistance regions has taken place in the chromosome. Several important Gram-negative pathogens are known to have quite variable genomes when different strains are compared and these variable regions, genomic islands, can include concentrations of resistance genes (Dobrindt et al., 2004; Hall, 2010). The expansion of these islands, with ongoing selection, is a major clinical problem in Acinetobacter baumannii, where they can extend over several tens of kilobases and comprise dozens of resistance genes (Fournier et al., 2006; Adams et al., 2008). Pathogenicity islands are a form of genomic island that carry known and/or inferred virulence factors. In several organisms, they contribute substantially to strain-specific pathogenicity and can excise and integrate as a large single unit (Dobrindt et al., 2004). Both genomic islands and pathogenicity islands commonly contain the same types of mobilizing elements seen in extrachromosomal DNA. Genomic islands often include integrated plasmids (Smillie et al., 2010) and the mobilization of pathogenicity islands is mediated by processes similar to that seen for ICEs with respect to incision/excision mechanisms. Indeed, this may be at least partly driven by the integration of whole plasmids or ICEs into the chromosome (Burrus & Waldor, 2004). Movement of genomic islands can occur by conjugation even when conjugation genes are not linked. For example, the conjugal spread of the Salmonella genomic island SG1 can be mediated by IncA/C plasmids, specifically those that carry multidrug resistance regions (Douard et al., 2010), providing another remarkable example of mobile genetic regions that ‘cooperate’ with each other. Other types of large chromosomal regions with properties shared with genomic and pathogenicity islands are also beginning to appear. One possible emerging example of this distinctive genomic resistance module has recently been reported at a defined location in E. coli clonal group A (Lescat et al., 2009), which includes determinants conferring resistance to antibiotics, antiseptics and heavy metals.

The extraordinary power of mobile elements to cooperate is commonly seen in the accumulation and concentration of resistance genes into promiscuous plasmids. This cooperation is recent because, while the individual elements that comprise them have existed since before the antibiotic era, they were not seen together. In pathogens, cooperation is the norm and the abundance and myriad of combinations is accelerating the rate of resistance evolution (Walsh, 2006; Marquez et al., 2008b; Garriss et al., 2009). This level of cooperation is remarkable, given that theory would suggest that such cooperation is not a stable evolutionary strategy (Wagner, 2006). However, this is not something that provides a degree of hope in solving the resistance crisis, because strong selection is the driver of this cooperation. Also, game theory makes the point that cooperation is not stable over evolutionary periods of time. Thus, even if selection were to suddenly stop, multiresistance regions would persist well beyond time frames relevant to humans. In the meantime, it is inevitable that ever more larger and complex DNA elements will evolve. At least to some extent, this is likely to be driven by the recruitment of new mobilizing elements linking resistance to mobilizable regions in plasmids. There are now several examples of new families of elements, one of which are the ISCR elements. These are a group of insertion sequences with similarities, structural and functional, to the IS91 family. One of their defining features is a process of one-ended transposition that allows the co-option of adjacent sequences (Toleman et al., 2006). This has ramifications for the dissemination of antibiotic resistance because ISCR elements are commonly linked to antibiotic resistance genes in pathogens. Although their name did not come until later, they were first observed nearly 20 years ago in clinical isolates (Stokes et al., 1993). However, they appear to have become especially prevalent in recent years and there are now some 19 distinct groups based on sequence differences and there is evidence that, like other types of mobile elements, recombination is beginning to generate novel hybrids (Li et al., 2009b). They are also linked to, or embedded in, other types of mobile elements, with perhaps the best example being the common linkage of ISCR1 to class 1 integrons (Sohn et al., 2009), where they act cooperatively to mobilize an increasingly diverse range of antibiotic resistance genes.

Another example of resistance recruitment elements are the ISEcp1 family of mobile elements. These are mobile and mobilizing elements that contribute to the growing antibiotic resistance problem. These elements are transposon-like in their mode of movement, but are also commonly found adjacent to various resistance genes in a manner structurally similar to the ISCR family of elements. Where this linkage is found, the ISEcp1 element has the potential to both mobilize and express the linked resistance gene (Karim et al., 2001). ISEcp1 elements were first described in the context of the spread of CTX-M family of β-lactamase genes (Karim et al., 2001; Poirel et al., 2003) and numerous examples of linkage of such genes to an ISEcp1 element are now known (Canton & Coque, 2006). However, linkage of an ISEcp1 to other resistance gene families are also known including to qnr (Cattoir et al., 2008), blaCMY (Verdet et al., 2009) and rmt (Wachino et al., 2006). ISEcp1 regions are commonly linked to other mobile elements such as other transposons, class 1 integrons and ISCR1 elements so as to generate quite large and complex regions that potentially move as single discrete units (Canton & Coque, 2006; Rice et al., 2008).

Some families of insertion sequences are frequently found in association with antibiotic resistance regions. One of these is IS26. Superficially, this is an example of the very common family of insertion sequences, which, like all members of this family, comprises a transposase gene flanked with characteristic inverted repeats. However, in recent years, it has become clear that this insertion sequence is very commonly associated with resistance regions both in plasmids and in chromosomal genomic islands where, when present, it can be often found in multiple copies (Hall, 2007; Doublet et al., 2009; Dawes et al., 2010). The presence of multiple copies of IS26 probably enhances the mobilization of resistance in a manner directly analogous to that seen for composite transposons. As well, multiple copies can also result in the deletion of resistance and other regions. Thus, IS26 is driving the evolution of clonal lines at a regional and global level (Post et al., 2010). Mobilization of resistance regions by IS26 may not be confined to conventional transposition since it has recently been reported that single IS26 copies may be able to mobilize adjacent regions, including resistance genes via a circular intermediate (Cain et al., 2010). If so, this would probably be a form of mobilization analogous to the ISCR elements. Another family of insertion sequences – the IS1111 family – is associated with resistance regions and its association with these regions is likely to grow in prominence with time. Members of this family are atypical of transposons in some respects, most notably in that movement does not generate a target site duplication (Partridge & Hall, 2003). Also, these elements target the inverted repeats of other mobile elements including the Tn21 family of transposons (Partridge & Hall, 2003) and the attC sites found in integron-associated mobile gene cassettes (Tetu & Holmes, 2008; Post & Hall, 2009).

Finally, a mobilizing element recently identified in pathogenic bacteria in association with class 1 integrons is the miniature inverted transposable element (MITE). This is a diverse element family with respect to both sequence and properties, with no single set of universal defining characteristics (Delihas, 2008). They do, however, have the potential to move themselves and mobilize other DNA by a nonhomologous recombination mechanism. There are two recent examples where these elements are linked to class 1 integrons and resistance genes. One is from a clinical Enterobacter cloacae isolate, where it was shown that when transposition functions were supplied in trans, the so-called integron mobilization unit was translocated, with this region including the flanking MITE sequences, the integron and its associated resistance array (Poirel et al., 2009). The second example is from the msr cassette containing the strain described above (Gillings et al., 2009b). As noted, this came from an Acinetobacter strain that was not a clinical isolate. Also, the two sets of MITE sequences are not identical in sequence, suggesting two independent capture events, although their arrangement with respect to class 1 integrons is similar. We would again suggest that this family of elements will begin to appear in clinical isolates in growing numbers.

Overall, there is a clear ongoing trend towards increasing size and complexity for resistance regions that involves all of the elements described above. These multifactorial interactions are increasing the opportunities for the recruitment of new resistance and other genes into pathogens. Numerous examples of this have been provided, but a further one is offered. In 2009, the recovery of a new metallo-β-lactamase – NDM-1 – was reported from a Klebsiella pneumoniae clinical isolate (Yong et al., 2009). Since its first identification, the gene has spread and it has rapidly become a global problem. Even worse is the fact that the gene product inactivates almost all known β-lactam antibiotics and is found in association with other complex multi-drug-resistant regions (Moellering, 2010) such that it is being labelled as contributing to the creation of a new type of superbug (Anonymous, 2010). Examination of the genetic architecture of the resistance regions found in the original isolate (Yong et al., 2009) revealed that the new NDM-1 gene was flanked by a pathogenicity island at one end and a defective IS26/Tn3 region at the other. Other resistance genes/regions were located in association with a class 1 integron (which also included a second novel resistance gene in a cassette), an ISCR1 element and an ISEcP1. All these regions are located on a conjugative plasmid spreading by LGT. This complexity and cooperativity is, thus, now at a point where our ability to identify and characterize these newly emerging mobile regions is testing the limits of sophisticated contemporary clinical and molecular diagnostic tools.

Concluding remarks

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

What does the future hold for the management of antibiotic resistance? Based on past experience, the future is not promising. Despite the enormous resources devoted to combating and managing the antibiotic resistance problem, positive outcomes are hard to identify, because the problem continues to grow unabated as determined by any measurable metric. There are global increases in the number of multi-drug-resistant nosocomial infections, the number of resistance genes per pathogen, the range of resistant pathogens and the number of infections refractory to antibiotic treatment. Ironically, this arms race is ‘funded’ by humans through the use and misuse of antibiotics. This is leading to infections that are nearly impossible to treat, and equally concerning, may begin to kill more quickly through the recruitment of other types of virulence factors. Also, the unrestrained growth of the problem has come about despite the fact that the problem has not been ignored. Rather, the literature contains in excess of 200 000 publications devoted to the problem of antibiotic resistance since the 1950s (Davies & Davies, 2010).

To address the problem, we believe that it has to be tackled at a global level. This global approach has to be considered from a number of perspectives. The first of these is that antibiotic resistance is fundamentally an evolutionary problem, and one in which LGT, combined with human-induced selection pressures, virtually makes the entire microbial biosphere into a single evolving community. Both management strategies and basic scientific analysis could benefit by better trans-border coordination. In the case of the former, there has been some progress and to a lesser extent the latter in recent years; however, there is still probably a long way to go. The increasing power of high-throughput technologies also has the potential to analyse mobile DNA at a scale needed to understand the problem globally and provide the data needed to devise better management strategies. This requires a shift away from a focus on reductionist strategies that analyse the problem from the perspective of specific sets of resistance gene types, specific organisms or specific locations. The need to understand the problem as a global one and, in part, recognize that it is another consequence of globalization, and therefore requires global solutions is recognized by economists (Rudholm, 2002). It is clearly incumbent on microbiologists at the ‘coal face’ to recognize the same.

Acknowledgements

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References

Aspects of the work of the authors are supported by the Australian Research Council, the National Health and Medical Research Council of Australia, the University of Technology, Sydney and Macquarie University. We thank the reviewers for their thoughtful and constructive critical comments on the manuscript.

References

  1. Top of page
  2. Abstract
  3. Introduction
  4. What is LGT?
  5. Where do antibiotic resistance genes come from?
  6. Resistance determinants in vectors, bacterial species and animal hosts
  7. Reservoirs of resistance?
  8. Conduits of LGT
  9. Does human use of antimicrobial agents change the tempo of lateral transfer?
  10. The agents of gene capture and spread
  11. Plasmids
  12. Transposons
  13. Integrons
  14. Elements within elements
  15. Concluding remarks
  16. Acknowledgements
  17. References
  • Adams MD, Goglin K, Molyneaux N et al. (2008) Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. J Bacteriol 190: 80538064.
  • Aertsen A & Michiels CW (2006) Upstream of the SOS response: figure out the trigger. Trends Microbiol 14: 421423.
  • Agerso Y & Sandvang D (2005) Class 1 integrons and tetracycline resistance genes in alcaligenes, arthrobacter, and Pseudomonas spp. isolated from pigsties and manured soil. Appl Environ Microb 71: 79417947.
  • Ahmed AM, Motoi Y, Sato M, Maruyama A, Watanabe H, Fukumoto Y & Shimamoto T (2007) Zoo animals as reservoirs of gram-negative bacteria harboring integrons and antimicrobial resistance genes. Appl Environ Microb 73: 66866690.
  • Ahmed AM, Ishida Y & Shimamoto T (2009a) Molecular characterization of antimicrobial resistance in Salmonella isolated from animals in Japan. J Appl Microbiol 106: 402409.
  • Ahmed AM, Shimabukuro H & Shimamoto T (2009b) Isolation and molecular characterization of multidrug-resistant strains of Escherichia coli and Salmonella from retail chicken meat in Japan. J Food Sci 74: M405M410.
  • Ahmed AM, Younis EE, Ishida Y & Shimamoto T (2009c) Genetic basis of multidrug resistance in Salmonella enterica serovars Enteritidis and Typhimurium isolated from diarrheic calves in Egypt. Acta Trop 111: 144149.
  • Ahmed AM, Younis EE, Osman SA, Ishida Y, El-Khodery SA & Shimamoto T (2009d) Genetic analysis of antimicrobial resistance in Escherichia coli isolated from diarrheic neonatal calves. Vet Microbiol 136: 397402.
  • Ajiboye RM, Solberg OD, Lee BM, Raphael E, Debroy C & Riley LW (2009) Global spread of mobile antimicrobial drug resistance determinants in human and animal Escherichia coli and Salmonella strains causing community-acquired infections. Clin Infect Dis 49: 365371.
  • Alam MJ, Renter DG, Ives SE, Thomson DU, Sanderson MW, Hollis LC & Nagaraja TG (2009) Potential associations between fecal shedding of Salmonella in feedlot cattle treated for apparent respiratory disease and subsequent adverse health outcomes. Vet Res 40: 02.
  • Alessiani A, Di Giannatale E, Perilli M, Forcella C, Amicosante G & Zilli K (2009) Preliminary investigations into fluoroquinolone resistance in Escherichia coli strains resistant to nalidixic acid isolated from animal faeces. Vet Ital 45: 521527.
  • Allen HK, Cloud-Hansen KA, Wolinski JM et al. (2009a) Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA Cell Biol 28: 109117.
  • Allen HK, Moe LA, Rodbumrer J, Gaarder A & Handelsman J (2009b) Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil. ISME J 3: 243251.
  • Altalhi AD, Gherbawy YA & Hassan SA (2009) Antibiotic Resistance in Escherichia coli Isolated from Retail Raw Chicken Meat in Taif, Saudi Arabia. Foodborne Pathog Dis 7: 281285.
  • Aminov RI & Mackie RI (2007) Evolution and ecology of antibiotic resistance genes. FEMS Microbiol Lett 271: 147161.
  • Andersson DI (2003) Persistence of antibiotic resistant bacteria. Curr Opin Microbiol 6: 452456.
  • Anonymous (1974) Plasmids. Lancet 310: 249250.
  • Anonymous (2010) Antimicrobial resistance: revisiting the “tragedy of the commons”. B World Health Organ 88: 805806.
  • Antonovics J, Abbate JL, Baker CH et al. (2007) Evolution by any other name: antibiotic resistance and avoidance of the E-word. PLoS Biol 5: e30.
  • Antunes P, Machado J & Peixe L (2006) Characterization of antimicrobial resistance and class 1 and 2 integrons in Salmonella enterica isolates from different sources in Portugal. J Antimicrob Chemoth 58: 297304.
  • Arakawa Y, Murakami M, Suzuki K et al. (1995) A novel integron-like element carrying the metallo-β-lactamase gene blaIMP. Antimicrob Agents Ch 39: 16121615.
  • Aziz RK, Breitbart M & Edwards RA (2010) Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res 38: 42074217.
  • Bailey JK, Pinyon JL, Anantham S & Hall R (2010) Commensal Escherichia coli of healthy humans - a reservoir for antibiotic resistance determinants. J Med Microbiol 59: 13311339.
  • Baker-Austin C, Wright MS, Stepanauskas R & McArthur JV (2006) Co-selection of antibiotic and metal resistance. Trends Microbiol 14: 176182.
  • Baldi F (1997) Microbial transformation of mercury species and their importance in the biogeochemical cycle of mercury. Met Ions Biol Syst 34: 213257.
  • Ball MM, Carrero P, Castro D & Yarzabal LA (2007) Mercury resistance in bacterial strains isolated from tailing ponds in a gold mining area near El Callao (Bolivar State, Venezuela). Curr Microbiol 54: 149154.
  • Baltz RH (2008) Renaissance in antibacterial discovery from actinomycetes. Curr Opin Pharmacol 8: 557563.
  • Bapteste E, O'Malley MA, Beiko RG et al. (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4: 34.
  • Baquero F (2009) Environmental stress and evolvability in microbial systems. Clin Microbiol Infec 15 (suppl 1): 510.
  • Baquero F, Martinez JL & Canton R (2008) Antibiotics and antibiotic resistance in water environments. Curr Opin Biotech 19: 260265.
  • Barkay T & Pritchard H (1988) Adaptation of aquatic microbial communities to pollutant stress. Microbiol Sci 5: 165169.
  • Barkay T & Wagner-Dobler I (2005) Microbial transformations of mercury: potentials, challenges, and achievements in controlling mercury toxicity in the environment. Adv Appl Microbiol 57: 152.
  • Barkay T, Miller SM & Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27: 355384.
  • Barkay T, Kritee K, Boyd E & Geesey G (2010) A thermophilic bacteria origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. Environ Microbiol 12: 29042917.
  • Barlow RS & Gobius KS (2006) Diverse class 2 integrons in bacteria from beef cattle sources. J Antimicrob Chemoth 58: 11331138.
  • Barlow RS, Fegan N & Gobius KS (2008) A comparison of antibiotic resistance integrons in cattle from separate beef meat production systems at slaughter. J Appl Microbiol 104: 651658.
  • Barlow RS, Fegan N & Gobius KS (2009) Integron-containing bacteria in faeces of cattle from different production systems at slaughter. J Appl Microbiol 107: 540545.
  • Bartoloni A, Pallecchi L, Rodriguez H et al. (2009) Antibiotic resistance in a very remote Amazonas community. Int J Antimicrob Ag 33: 125129.
  • Beaber JW, Hochhut B & Waldor MK (2004) SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427: 7274.
  • Bennett PM & Richmond MH (1976) Translocation of a discrete piece of deoxyribonucleic acid carrying an amp gene between replicons in Eschericha coli. J Bacteriol 126: 16.
  • Benveniste R & Davies J (1973) Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. P Natl Acad Sci USA 70: 22762280.
  • Binh CT, Heuer H, Kaupenjohann M & Smalla K (2009) Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure. Res Microbiol 160: 427433.
  • Biskri L & Mazel D (2003) Erythromycin esterase gene ere(A) is located in a functional gene cassette in an unusual class 2 integron. Antimicrob Agents Ch 47: 33263331.
  • Biskri L, Bouvier M, Guerout AM, Boisnard S & Mazel D (2005) Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities. J Bacteriol 187: 17401750.
  • Bonnedahl J, Drobni M, Gauthier-Clerc M et al. (2009) Dissemination of Escherichia coli with CTX-M type ESBL between humans and yellow-legged gulls in the south of France. PLoS One 4: e5958.
  • Bonnet C, Diarrassouba F, Brousseau R, Masson L, Topp E & Diarra MS (2009) Pathotype and antibiotic resistance gene distributions of Escherichia coli isolates from broiler chickens raised on antimicrobial-supplemented diets. Appl Environ Microb 75: 69556962.
  • Boto L (2010) Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci 277: 819827.
  • Boucher Y, Labbate M, Koenig JE & Stokes HW (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 15: 301309.
  • Box AT, Mevius DJ, Schellen P, Verhoef J & Fluit AC (2005) Integrons in Escherichia coli from food-producing animals in The Netherlands. Microb Drug Resist 11: 5357.
  • Boyle F, Morris D, O'Connor J, Delappe N, Ward J & Cormican M (2010) First report of extended-spectrum-β-lactamase-producing Salmonella enterica serovar Kentucky isolated from poultry in Ireland. Antimicrob Agents Ch 54: 551553.
  • Brown AM & Willetts NS (1981) A physical and genetic map of the IncN plasmid R46. Plasmid 5: 188201.
  • Brown HJ, Stokes HW & Hall RM (1996) The integrons In0, In2, and In5 are defective transposon derivatives. J Bacteriol 178: 44294437.
  • Burrus V & Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155: 376386.
  • Byrne-Bailey KG, Gaze WH, Kay P, Boxall AB, Hawkey PM & Wellington EM (2009) Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrob Agents Ch 53: 696702.
  • Cabello FC (2006) Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. Environ Microbiol 8: 11371144.
  • Cain AK, Liu X, Djordjevic SP & Hall RM (2010) Transposons related to Tn1696 in IncHI2 plasmids in multiply antibiotic resistant Salmonella enterica serovar Typhimurium from Australian animals. Microb Drug Resist 16: 197202.
  • Canton R & Coque TM (2006) The CTX-M β-lactamase pandemic. Curr Opin Microbiol 9: 466475.
  • Cattoir V, Nordmann P, Silva-Sanchez J, Espinal P & Poirel L (2008) ISEcp1-mediated transposition of qnrB-like gene in Escherichia coli. Antimicrob Agents Ch 52: 29292932.
  • Chuanchuen R & Padungtod P (2009) Antimicrobial resistance genes in Salmonella enterica isolates from poultry and swine in Thailand. J Vet Med Sci 71: 13491355.
  • Chuanchuen R, Ajariyakhajorn K, Koowatananukul C, Wannaprasat W, Khemtong S & Samngamnim S (2010) Antimicrobial resistance and virulence genes in Salmonella enterica isolates from dairy cows. Foodborne Pathog Dis 7: 6369.
  • Cizek A, Dolejska M, Sochorova R, Strachotova K, Piackova V & Vesely T (2010) Antimicrobial resistance and its genetic determinants in aeromonads isolated in ornamental (koi) carp (Cyprinus carpio koi) and common carp (Cyprinus carpio). Vet Microbiol 142: 435439.
  • Collis CM, Kim MJ, Partridge SR, Stokes HW & Hall RM (2002) Characterization of the class 3 integron and the site-specific recombination system it determines. J Bacteriol 184: 30173026.
  • Correia M, Boavida F, Grosso F et al. (2003) Molecular characterization of a new class 3 integron in Klebsiella pneumoniae. Antimicrob Agents Ch 47: 28382843.
  • Davies J (2007) Microbes have the last word. A drastic re-evaluation of antimicrobial treatment is needed to overcome the threat of antibiotic-resistant bacteria. EMBO Rep 8: 616621.
  • Davies J & Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol R 74: 417433.
  • Davies J, Spiegelman GB & Yim G (2006) The world of subinhibitory antibiotic concentrations. Curr Opin Microbiol 9: 445453.
  • Dawes FE, Kuzevski A, Bettelheim KA, Hornitzky MA, Djordjevic SP & Walker MJ (2010) Distribution of class 1 integrons with IS26-mediated deletions in their 3′-conserved segments in Escherichia coli of human and animal origin. PLoS One 5: e12754.
  • D'Costa VM, McGrann KM, Hughes DW & Wright GD (2006) Sampling the antibiotic resistome. Science 311: 374377.
  • Delihas N (2008) Small mobile sequences in bacteria display diverse structure/function motifs. Mol Microbiol 67: 475481.
  • Demarre G, Frumerie C, Gopaul DN & Mazel D (2007) Identification of key structural determinants of the IntI1 integron integrase that influence attC×attI1 recombination efficiency. Nucleic Acids Res 35: 64756489.
  • Diaz-Mejia JJ, Amabile-Cuevas CF, Rosas I & Souza V (2008) An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins. Microbiology 154: 94102.
  • Dobrindt U, Hochhut B, Hentschel U & Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2: 414424.
  • Dolejska M, Senk D, Cizek A, Rybarikova J, Sychra O & Literak I (2008) Antimicrobial resistant Escherichia coli isolates in cattle and house sparrows on two Czech dairy farms. Res Vet Sci 85: 491494.
  • Dolejska M, Bierosova B, Kohoutova L, Literak I & Cizek A (2009) Antibiotic-resistant Salmonella and Escherichia coli isolates with integrons and extended-spectrum β-lactamases in surface water and sympatric black-headed gulls. J Appl Microbiol 106: 19411950.
  • Douard G, Praud K, Cloeckaert A & Doublet B (2010) The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family. PLoS One 5: e15302.
  • Doublet B, Praud K, Weill FX & Cloeckaert A (2009) Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1. J Antimicrob Chemoth 63: 282289.
  • Ekkapobyotin C, Padungtod P & Chuanchuen R (2008) Antimicrobial resistance of Campylobacter coli isolates from swine. Int J Food Microbiol 128: 325328.
  • Evershed NJ, Levings RS, Wilson NL, Djordjevic SP & Hall RM (2009) Unusual class 1 integron-associated gene cassette configuration found in IncA/C plasmids from Salmonella enterica. Antimicrob Agents Ch 53: 26402642.
  • Falagas ME & Bliziotis IA (2007) Pandrug-resistant Gram-negative bacteria: the dawn of the post-antibiotic era? Int J Antimicrob Ag 29: 630636.
  • Foster TJ (1987) The genetics and biochemistry of mercury resistance. Crit Rev Microbiol 15: 117140.
  • Fournier PE, Vallenet D, Barbe V et al. (2006) Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet 2: e7.
  • Frost LS, Leplae R, Summers AO & Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722732.
  • Futagawa-Saito K, Okatani AT, Sakurai-Komada N, Ba-Thein W & Fukuyasu T (2010) Epidemiological characteristics of Salmonella enterica serovar typhimurium from healthy pigs in Japan. J Vet Med Sci 72: 6166.
  • Garriss G, Waldor MK & Burrus V (2009) Mobile antibiotic resistance encoding elements promote their own diversity. PLoS Genet 5: e1000775.
  • Ghosh S, Ramsden SJ & LaPara TM (2009) The role of anaerobic digestion in controlling the release of tetracycline resistance genes and class 1 integrons from municipal wastewater treatment plants. Appl Microbiol Biot 84: 791796.
  • Gilbert P & Moore LE (2005) Cationic antiseptics: diversity of action under a common epithet. J Appl Microbiol 99: 703715.
  • Gillings M, Boucher Y, Labbate M, Holmes A, Krishnan S, Holley M & Stokes HW (2008) The evolution of class 1 integrons and the rise of antibiotic resistance. J Bacteriol 190: 50955100.
  • Gillings MR, Holley MP & Stokes HW (2009a) Evidence for dynamic exchange of qac gene cassettes between class 1 integrons and other integrons in freshwater biofilms. FEMS Microbiol Lett 296: 282288.
  • Gillings MR, Labbate M, Sajjad A, Giguere NJ, Holley MP & Stokes HW (2009b) Mobilization of a Tn402-like class 1 integron with a novel cassette array via flanking miniature inverted-repeat transposable element-like structures. Appl Environ Microb 75: 60026004.
  • Gillings MR, Xuejun D, Hardwick SA, Holley MP & Stokes HW (2009c) Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons? ISME J 3: 209215.
  • Gionechetti F, Zucca P, Gombac F et al. (2008) Characterization of antimicrobial resistance and class 1 integrons in Enterobacteriaceae isolated from Mediterranean herring gulls (Larus cachinnans). Microb Drug Resist 14: 9399.
  • Goldberg TL, Gillespie TR, Rwego IB, Wheeler E, Estoff EL & Chapman CA (2007) Patterns of gastrointestinal bacterial exchange between chimpanzees and humans involved in research and tourism in western Uganda. Biol Conserv 135: 511517.
  • Goldstein C, Lee MD, Sanchez S et al. (2001) Incidence of class 1 and 2 integrases in clinical and commensal bacteria from livestock, companion animals, and exotics. Antimicrob Agents Ch 45: 723726.
  • Gribaldo S & Brochier C (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 160: 513521.
  • Grinsted J, Saunders JR, Ingram LC, Sykes RB & Richmond MH (1972) Properties of a R factor which originated in Pseudomonas aeruginosa 1822. J Bacteriol 110: 529537.
  • Groh JL, Luo Q, Ballard JD & Krumholz LR (2007) Genes that enhance the ecological fitness of Shewanella oneidensis MR-1 in sediments reveal the value of antibiotic resistance. Appl Environ Microb 73: 492498.
  • Guerin E, Cambray G, Sanchez-Alberola N et al. (2009) The SOS response controls integron recombination. Science 324: 1034.
  • Halary S, Leigh JW, Cheaib B, Lopez P & Bapteste E (2010) Network analyses structure genetic diversity in independent genetic worlds. P Natl Acad Sci USA 107: 127132.
  • Hall RM (2007) Antibiotic resistance gene cluster of pAPEC-O1-R. Antimicrob Agents Ch 51: 34613462.
  • Hall RM (2010) Salmonella genomic islands and antibiotic resistance in Salmonella enterica. Future Microbiol 5: 15251538.
  • Hall RM & Vockler C (1987) The region of the IncN plasmid R46 coding for resistance to β-lactam antibiotics, streptomycin/spectinomycin and sulphonamides is closely related to antibiotic resistance segments found in IncW plasmids and in Tn21-like transposons. Nucleic Acids Res 15: 74917501.
  • Hammerum AM, Sandvang D, Andersen SR, Seyfarth AM, Porsbo LJ, Frimodt-Moller N & Heuer OE (2006) Detection of sul1, sul2 and sul3 in sulphonamide resistant Escherichia coli isolates obtained from healthy humans, pork and pigs in Denmark. Int J Food Microbiol 106: 235237.
  • Hansson K, Sundstrom L, Pelletier A & Roy PH (2002) IntI2 integron integrase in Tn7. J Bacteriol 184: 17121721.
  • Hardwick SA, Stokes HW, Findlay S, Taylor M & Gillings MR (2008) Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR. FEMS Microbiol Lett 278: 207212.
  • Hegreness M, Shoresh N, Damian D, Hartl D & Kishony R (2008) Accelerated evolution of resistance in multidrug environments. P Natl Acad Sci USA 105: 1397713981.
  • Heringa S, Kim J, Shepherd MW, Singh R & Jiang X (2010) The presence of antibiotic resistance and integrons in Escherichia coli isolated from compost. Foodborne Pathog Dis 7: 12971304.
  • Ho PL, Wong RC, Chow KH & Que TL (2009) Distribution of integron-associated trimethoprim-sulfamethoxazole resistance determinants among Escherichia coli from humans and food-producing animals. Lett Appl Microbiol 49: 627634.
  • Holloway BW (1969) Genetics of Pseudomonas. Bacteriol Rev 33: 419443.
  • Holmes AJ, Gillings MR, Nield BS, Mabbutt BC, Nevalainen KM & Stokes HW (2003) The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ Microbiol 5: 383394.
  • Hsu SC, Chiu TH, Pang JC, Hsuan-Yuan CH, Chang GN & Tsen HY (2006) Characterisation of antimicrobial resistance patterns and class 1 integrons among Escherichia coli and Salmonella enterica serovar Choleraesuis strains isolated from humans and swine in Taiwan. Int J Antimicrob Ag 27: 383391.
  • Hughes VM & Datta N (1983) Conjugative plasmids in bacteria of the ‘pre-antibiotic’ era. Nature 302: 725726.
  • James BO, Wells DM & Grant LS (1975) Resistance-factors in the hospital and non-hospital environment. Trop Geogr Med 27: 3946.
  • Johnson TJ & Nolan LK (2009) Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol R 73: 750774.
  • Jones C & Stanley J (1992) Salmonella plasmids of the pre-antibiotic era. J Gen Microbiol 138: 189197.
  • Joss MJ, Koenig JE, Labbate M et al. (2009) ACID: annotation of cassette and integron data. BMC Bioinformatics 10: 118.
  • Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW & Crook DW (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33: 376393.
  • Kadlec K & Schwarz S (2008) Analysis and distribution of class 1 and class 2 integrons and associated gene cassettes among Escherichia coli isolates from swine, horses, cats and dogs collected in the BfT-GermVet monitoring study. J Antimicrob Chemoth 62: 469473.
  • Kalender H, Sen S, Hasman H, Hendriksen RS & Aarestrup FM (2009) Antimicrobial susceptibilities, phage types, and molecular characterization of Salmonella enterica serovar Enteritidis from chickens and chicken meat in turkey. Foodborne Pathog Dis 6: 265271.
  • Karim A, Poirel L, Nagarajan S & Nordmann P (2001) Plasmid-mediated extended-spectrum β-lactamase (CTX-M-3 like) from India and gene association with insertion sequence ISEcp1. FEMS Microbiol Lett 201: 237241.
  • Kholodii G, Mindlin S, Petrova M & Minakhina S (2003) Tn5060 from the Siberian permafrost is most closely related to the ancestor of Tn21 prior to integron acquisition. FEMS Microbiol Lett 226: 251255.
  • Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV & Nikiforov VG (1995) Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol Microbiol 17: 11891200.
  • Knapp CW, Dolfing J, Ehlert PA & Graham DW (2010) Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ Sci Technol 44: 580587.
  • Koenig JE, Boucher Y, Charlebois RL et al. (2008) Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ Microbiol 10: 10241038.
  • Koenig JE, Sharp C, Dlutek M, Curtis B, Joss M, Boucher Y & Doolittle WF (2009) Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds. PLoS One 4: e5276.
  • Krcmery V, Grunt J, Rosival L & Vymola F (1975) Nation-wide survey of antibiotic resistance by means of a computer. Analysis of 200.000 strains of problem bacteria isolated in 1973. Zentralbl Bakteriol Orig A 231: 250258.
  • Kumar A, Mukherjee S & Chakraborty R (2010) Characterization of a novel trimethoprim resistance gene, dfrA28, in class 1 integron of an oligotrophic Acinetobacter johnsonii strain, MB52, isolated from River Mahananda, India. Microb Drug Resist 16: 2937.
  • Labbate M, Chowdhury PR & Stokes HW (2008) A class 1 integron present in a human commensal has a hybrid transposition module compared to Tn402: evidence of interaction with mobile DNA from natural environments. J Bacteriol 190: 53185327.
  • Lapierre L, Cornejo J, Borie C, Toro C & San Martin B (2008) Genetic characterization of antibiotic resistance genes linked to class 1 and class 2 integrons in commensal strains of Escherichia coli isolated from poultry and swine. Microb Drug Resist 14: 265272.
  • Laroche E, Pawlak B, Berthe T, Skurnik D & Petit F (2009) Occurrence of antibiotic resistance and class 1, 2 and 3 integrons in Escherichia coli isolated from a densely populated estuary (Seine, France). FEMS Microbiol Ecol 68: 118130.
  • Lederberg J & Tatum EL (1946) Gene recombination in Escherichia coli. Nature 158: 558.
  • Lee MF, Chen YH & Peng CF (2009) Molecular characterisation of class 1 integrons in Salmonella enterica serovar Choleraesuis isolates from southern Taiwan. Int J Antimicrob Ag 33: 216222.
  • Leplae R, Lima-Mendez G & Toussaint A (2010) ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 38: D5761.
  • Lescat M, Calteau A, Hoede C et al. (2009) A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A. Antimicrob Agents Ch 53: 22832288.
  • Levesque C, Piche L, Larose C & Roy PH (1995) PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Ch 39: 185191.
  • Li D, Yang M, Hu J et al. (2009a) Antibiotic-resistance profile in environmental bacteria isolated from penicillin production wastewater treatment plant and the receiving river. Environ Microbiol 11: 15061517.
  • Li D, Yu T, Zhang Y, Yang M, Li Z, Liu M & Qi R (2010a) Antibiotic resistance characteristics of environmental bacteria from an oxytetracycline production wastewater treatment plant and the receiving river. Appl Environ Microb 76: 34443451.
  • Li H, Walsh TR & Toleman MA (2009b) Molecular analysis of the sequences surrounding blaOXA−45 reveals acquisition of this gene by Pseudomonas aeruginosa via a novel ISCR element, ISCR5. Antimicrob Agents Ch 53: 12481251.
  • Li J, Ma Y, Hu C et al. (2010b) Dissemination of cefotaxime-M-producing Escherichia coli isolates in poultry farms, but not swine farms, in China. Foodborne Pathog Dis 7: 13871392.
  • Liebert CA, Hall RM & Summers AO (1999) Transposon Tn21, flagship of the floating genome. Microbiol Mol Biol R 63: 507522.
  • Literak I, Dolejska M, Rybarikova J et al. (2009) Highly variable patterns of antimicrobial resistance in commensal Escherichia coli isolates from pigs, sympatric rodents, and flies. Microb Drug Resist 15: 229237.
  • Literak I, Dolejska M, Radimersky T et al. (2010) Antimicrobial-resistant faecal Escherichia coli in wild mammals in central Europe: multiresistant Escherichia coli producing extended-spectrum β-lactamases in wild boars. J Appl Microbiol 108: 17021711.
  • Liu J, Keelan P, Bennett PM & Enne VI (2009a) Characterization of a novel macrolide efflux gene, mef(B), found linked to sul3 in porcine Escherichia coli. J Antimicrob Chemoth 63: 423426.
  • Liu MC, Wu CM, Liu YC, Zhao JC, Yang YL & Shen JZ (2009b) Identification, susceptibility, and detection of integron-gene cassettes of Arcanobacterium pyogenes in bovine endometritis. J Dairy Sci 92: 36593666.
  • Lu L, Dai L, Wang Y et al. (2010) Characterization of antimicrobial resistance and integrons among Escherichia coli isolated from animal farms in Eastern China. Acta Trop 113: 2025.
  • Luria SE (1947) Recent Advances in Bacterial Genetics. Bacteriol Rev 11: 140.
  • Lynne AM, Kaldhone P, David D, White DG & Foley SL (2009) Characterization of antimicrobial resistance in Salmonella enterica serotype Heidelberg isolated from food animals. Foodborne Pathog Dis 6: 207215.
  • Machado E, Coque TM, Canton R, Sousa JC & Peixe L (2008) Antibiotic resistance integrons and extended-spectrum β-lactamases among Enterobacteriaceae isolates recovered from chickens and swine in Portugal. J Antimicrob Chemoth 62: 296302.
  • Marchiaro P, Viale AM, Ballerini V, Rossignol G, Vila AJ & Limansky A (2010) First report of a Tn402-like class 1 integron carrying blaVIM−2 in Pseudomonas putida from Argentina. J Infect Dev Ctries 4: 412416.
  • Marquez C, Labbate M, Ingold AJ et al. (2008a) Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection. Antimicrob Agents Ch 52: 41534154.
  • Marquez C, Labbate M, Raymondo C et al. (2008b) Urinary tract infections in a South American population: dynamic spread of class 1 integrons and multidrug resistance by homologous and site-specific recombination. J Clin Microbiol 46: 34173425.
  • Marraffini LA (2010) Impact of CRIPSR immunity on the emergence of bacterial pathogens. Future Microbiol 5: 693695.
  • Marraffini LA & Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 18431845.
  • Martinez E & de la Cruz F (1988) Transposon Tn21 encodes a RecA-independent site-specific integration system. Mol Gen Genet 211: 320325.
  • Martinez JL (2008) Antibiotics and antibiotic resistance genes in natural environments. Science 321: 365367.
  • Martinez JL (2009) Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ Pollut 157: 28932902.
  • Martinez JL, Baquero F & Andersson DI (2007) Predicting antibiotic resistance. Nat Rev Microbiol 5: 958965.
  • Mazel D (2006) Integrons: agents of bacterial evolution. Nat Rev Microbiol 4: 608620.
  • McIntosh D, Cunningham M, Ji B et al. (2008) Transferable, multiple antibiotic and mercury resistance in Atlantic Canadian isolates of Aeromonas salmonicida subsp. salmonicida is associated with carriage of an IncA/C plasmid similar to the Salmonella enterica plasmid pSN254. J Antimicrob Chemoth 61: 12211228.
  • Michael CA, Gillings MR, Holmes AJ, Hughes L, Andrew NR, Holley MP & Stokes HW (2004) Mobile gene cassettes: a fundamental resource for bacterial evolution. Am Nat 164: 112.
  • Michael GB, Cardoso M & Schwarz S (2008) Molecular analysis of multiresistant porcine Salmonella enterica subsp. enterica serovar Bredeney isolates from Southern Brazil: identification of resistance genes, integrons and a group II intron. Int J Antimicrob Ag 32: 120129.
  • Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H & Cohen SN (2004) SOS response induction by β-lactams and bacterial defense against antibiotic lethality. Science 305: 16291631.
  • Mindlin S, Kholodii G, Gorlenko Z et al. (2001) Mercury resistance transposons of gram-negative environmental bacteria and their classification. Res Microbiol 152: 811822.
  • Mindlin S, Minakhin L, Petrova M, Kholodii G, Minakhina S, Gorlenko Z & Nikiforov V (2005) Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene. Res Microbiol 156: 9941004.
  • Moellering RC Jr (2010) NDM-1–a cause for worldwide concern. New Engl J Med 363: 23772379.
  • Moura A, Soares M, Pereira C, Leitao N, Henriques I & Correia A (2009) INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 25: 10961098.
  • Moura A, Henriques I, Smalla K & Correia A (2010) Wastewater bacterial communities bring together broad-host range plasmids, integrons and a wide diversity of uncharacterized gene cassettes. Res Microbiol 161: 5866.
  • Nagachinta S & Chen J (2008) Transfer of class 1 integron-mediated antibiotic resistance genes from shiga toxin-producing Escherichia coli to a susceptible E. coli K-12 strain in storm water and bovine feces. Appl Environ Microb 74: 50635067.
  • Nawaz M, Khan AA, Khan S, Sung K, Kerdahi K & Steele R (2009) Molecular characterization of tetracycline-resistant genes and integrons from avirulent strains of Escherichia coli isolated from catfish. Foodborne Pathog Dis 6: 553559.
  • Nawaz M, Khan SA, Khan AA, Sung K, Tran Q, Kerdahi K & Steele R (2010) Detection and characterization of virulence genes and integrons in Aeromonas veronii isolated from catfish. Food Microbiol 27: 327331.
  • Nde CW & Logue CM (2008) Characterization of antimicrobial susceptibility and virulence genes of Salmonella serovars collected at a commercial turkey processing plant. J Appl Microbiol 104: 215223.
  • Nesse RM & Stearns SC (2008) The great opportunity: evolutionary applications to medicine and public health. Evol Appl 1: 2848.
  • Nield BS, Willows RD, Torda AE et al. (2004) New enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an RNA-methyltransferase. Protein Sci 13: 16511659.
  • Niwa H, Anzai T, Izumiya H et al. (2009) Antimicrobial resistance and genetic characteristics of Salmonella Typhimurium isolated from horses in Hokkaido, Japan. J Vet Med Sci 71: 11151119.
  • Nogrady N, Kardos G, Bistyak A et al. (2008) Prevalence and characterization of Salmonella infantis isolates originating from different points of the broiler chicken-human food chain in Hungary. Int J Food Microbiol 127: 162167.
  • Norman A, Hansen LH & Sorensen SJ (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci 364: 22752289.
  • Novick RP (1969) Extrachromosomal inheritance in bacteria. Bacteriol Rev 33: 210263.
  • Ochman H, Lawrence JG & Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299304.
  • Ozgumus OB, Sandalli C, Sevim A, Celik-Sevim E & Sivri N (2009) Class 1 and class 2 integrons and plasmid-mediated antibiotic resistance in coliforms isolated from ten rivers in northern Turkey. J Microbiol 47: 1927.
  • Palmer KL & Gilmore MS (2010) Multidrug-resistant Enterococci lack CRISPR-cas. mBio 1: e0022710.
  • Palumbi SR (2001) Humans as the world's greatest evolutionary force. Science 293: 17861790.
  • Partridge SR & Hall RM (2003) The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons. J Bacteriol 185: 63716384.
  • Partridge SR, Recchia GD, Stokes HW & Hall RM (2001) Family of class 1 integrons related to In4 from Tn1696. Antimicrob Agents Ch 45: 30143020.
  • Partridge SR, Tsafnat G, Coiera E & Iredell JR (2009) Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 33: 757784.
  • Patchanee P, Zewde BM, Tadesse DA, Hoet A & Gebreyes WA (2008) Characterization of multidrug-resistant Salmonella enterica serovar Heidelberg isolated from humans and animals. Foodborne Pathog Dis 5: 839851.
  • Pellegrini C, Mercuri PS, Celenza G et al. (2009) Identification of blaIMP−22 in Pseudomonas spp. in urban wastewater and nosocomial environments: biochemical characterization of a new IMP metallo-enzyme variant and its genetic location. J Antimicrob Chemoth 63: 901908.
  • Perron GG, Gonzalez A & Buckling A (2007) Source-sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost. Proc Biol Sci 274: 23512356.
  • Petrova M, Gorlenko Z & Mindlin S (2011) Tn5045, a novel integron-containing antibiotic and chromate resistance transposon isolated from a permafrost bacterium. Res Microbiol 162: 337345.
  • Petrovski S & Stanisich VA (2010) Tn502 and Tn512 are res site hunters that provide evidence of resolvase-independent transposition to random sites. J Bacteriol 192: 18651874.
  • Picao RC, Poirel L, Demarta A, Silva CS, Corvaglia AR, Petrini O & Nordmann P (2008) Plasmid-mediated quinolone resistance in Aeromonas allosaccharophila recovered from a Swiss lake. J Antimicrob Chemoth 62: 948950.
  • Plante I, Centron D & Roy PH (2003) An integron cassette encoding erythromycin esterase, ere(A), from Providencia stuartii. J Antimicrob Chemoth 51: 787790.
  • Poeta P, Radhouani H, Igrejas G et al. (2008) Seagulls of the Berlengas natural reserve of Portugal as carriers of fecal Escherichia coli harboring CTX-M and TEM extended-spectrum β-lactamases. Appl Environ Microb 74: 74397441.
  • Poeta P, Radhouani H, Pinto L et al. (2009) Wild boars as reservoirs of extended-spectrum β-lactamase (ESBL) producing Escherichia coli of different phylogenetic groups. J Basic Microb 49: 584588.
  • Poirel L, Decousser JW & Nordmann P (2003) Insertion sequence ISEcp1B is involved in expression and mobilization of a bla(CTX-M) β-lactamase gene. Antimicrob Agents Ch 47: 29382945.
  • Poirel L, Liard A, Rodriguez-Martinez JM & Nordmann P (2005) Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants. J Antimicrob Chemoth 56: 11181121.
  • Poirel L, Carrer A, Pitout JD & Nordmann P (2009) Integron mobilization unit as a source of mobility of antibiotic resistance genes. Antimicrob Agents Ch 53: 24922498.
  • Poirel L, Naas T & Nordmann P (2010) Diversity, epidemiology, and genetics of class D β-lactamases. Antimicrob Agents Ch 54: 2438.
  • Post V & Hall RM (2009) Insertion sequences in the IS1111 family that target the attC recombination sites of integron-associated gene cassettes. FEMS Microbiol Lett 290: 182187.
  • Post V, Recchia GD & Hall RM (2007) Detection of gene cassettes in Tn402-like class 1 integrons. Antimicrob Agents Ch 51: 34673468.
  • Post V, White PA & Hall RM (2010) Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii. J Antimicrob Chemoth 65: 11621170.
  • Povilonis J, Seputiene V, Ruzauskas M, Siugzdiniene R, Virgailis M, Pavilonis A & Suziedeliene E (2010) Transferable Class 1 and 2 integrons in Escherichia coli and Salmonella enterica isolates of human and animal origin in Lithuania. Foodborne Pathog Dis 7: 11851192.
  • Pulliam HR (1988) Sources, Sinks, and Population Regulation. Am Nat 132: 652661.
  • Radhouani H, Poeta P, Igrejas G, Goncalves A, Vinue L & Torres C (2009) Antimicrobial resistance and phylogenetic groups in isolates of Escherichia coli from seagulls at the Berlengas nature reserve. Vet Rec 165: 138142.
  • Radhouani H, Pinto L, Coelho C et al. (2010) Detection of Escherichia coli harbouring extended-spectrum β-lactamases of the CTX-M classes in faecal samples of common buzzards (Buteo buteo). J Antimicrob Chemoth 65: 171173.
  • Radimersky T, Frolkova P, Janoszowska D et al. (2010) Antibiotic resistance in faecal bacteria (Escherichia coli, Enterococcus spp.) in feral pigeons. J Appl Microbiol 109: 16871695.
  • Radstrom P, Skold O, Swedberg G, Flensburg J, Roy PH & Sundstrom L (1994) Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements. J Bacteriol 176: 32573268.
  • Ragan MA & Beiko RG (2009) Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci 364: 22412251.
  • Ramirez MS, Pineiro S & Centron D (2010) Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Ch 54: 699706.
  • Rayamajhi N, Kang SG, Kang ML, Lee HS, Park KY & Yoo HS (2008) Assessment of antibiotic resistance phenotype and integrons in Salmonella enterica serovar Typhimurium isolated from swine. J Vet Med Sci 70: 11331137.
  • Rice LB, Carias LL, Hutton RA, Rudin SD, Endimiani A & Bonomo RA (2008) The KQ element, a complex genetic region conferring transferable resistance to carbapenems, aminoglycosides, and fluoroquinolones in Klebsiella pneumoniae. Antimicrob Agents Ch 52: 34273429.
  • Riesenfeld CS, Goodman RM & Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6: 981989.
  • Roberts AP, Chandler M, Courvalin P et al. (2008a) Revised nomenclature for transposable genetic elements. Plasmid 60: 167173.
  • Roberts MC, Leroux BG, Sampson J, Luis HS, Bernardo M & Leitao J (2008b) Dental amalgam and antibiotic- and/or mercury-resistant bacteria. J Dent Res 87: 475479.
  • Rodriguez I, Barownick W, Helmuth R, Mendoza MC, Rodicio MR, Schroeter A & Guerra B (2009) Extended-spectrum β-lactamases and AmpC β-lactamases in ceftiofur-resistant Salmonella enterica isolates from food and livestock obtained in Germany during 2003-07. J Antimicrob Chemoth 64: 301309.
  • Rosewarne CP, Pettigrove V, Stokes HW & Parsons YM (2010) Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance. FEMS Microbiol Ecol 72: 3546.
  • Rowe-Magnus DA, Guerout AM, Ploncard P, Dychinco B, Davies J & Mazel D (2001) The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. P Natl Acad Sci USA 98: 652657.
  • Rudholm N (2002) Economic implications of antibiotic resistance in a global economy. Health Econ 21: 10711083.
  • Salyers A & Shoemaker NB (2006) Reservoirs of antibiotic resistance genes. Anim Biotechnol 17: 137146.
  • Salyers AA, Gupta A & Wang Y (2004) Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol 12: 412416.
  • San Martin B, Lapierre L, Cornejo J & Bucarey S (2008) Characterization of antibiotic resistance genes linked to class 1 and 2 integrons in strains of Salmonella spp. isolated from swine. Can J Microbiol 54: 569576.
  • Sato M, Ahmed AM, Noda A, Watanabe H, Fukumoto Y & Shimamoto T (2009) Isolation and molecular characterization of multidrug-resistant Gram-negative bacteria from imported flamingos in Japan. Acta Vet Scand 51: 46.
  • Schluter A, Szczepanowski R, Puhler A & Top EM (2007) Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 31: 449477.
  • Schluter A, Krause L, Szczepanowski R, Goesmann A & Puhler A (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. J Biotechnol 136: 6576.
  • Schwarz S & Chaslus-Dancla E (2001) Use of antimicrobials in veterinary medicine and mechanisms of resistance. Vet Res 32: 201225.
  • Schwarz S, Kehrenberg C & Walsh TR (2001) Use of antimicrobial agents in veterinary medicine and food animal production. Int J Antimicrob Ag 17: 431437.
  • Seputiene V, Povilonis J, Ruzauskas M, Pavilonis A & Suziedeliene E (2010) Prevalence of trimethoprim resistance genes in Escherichia coli isolates of human and animal origin in Lithuania. J Med Microbiol 59: 315322.
  • Shahada F, Chuma T, Dahshan H, Akiba M, Sueyoshi M & Okamoto K (2010) Detection and characterization of extended-spectrum β-lactamase (TEM-52)-producing Salmonella serotype Infantis from broilers in Japan. Foodborne Pathog Dis 7: 515521.
  • Shaheen BW, Oyarzabal OA & Boothe DM (2010) The role of class 1 and 2 integrons in mediating antimicrobial resistance among canine and feline clinical E. coli isolates from the US. Vet Microbiol 144: 363370.
  • Shapiro JA & Sporn P (1977) Tn402: a new transposable element determining trimethoprim resistance that inserts in bacteriophage lambda. J Bacteriol 129: 16321635.
  • Shearer BG (1993) Dental amalgam and multiple antibiotic resistance: an untested hypothesis. Antimicrob Agents Ch 37: 17301731.
  • Shearer JE & Summers AO (2009) Intracellular steady-state concentration of integron recombination products varies with integrase level and growth phase. J Mol Biol 386: 316331.
  • Shibata N, Doi Y, Yamane K et al. (2003) PCR typing of genetic determinants for metallo-β-lactamases and integrases carried by gram-negative bacteria isolated in Japan, with focus on the class 3 integron. J Clin Microbiol 41: 54075413.
  • Sikorski J, Teschner N & Wackernagel W (2002) Highly different levels of natural transformation are associated with genomic subgroups within a local population of Pseudomonas stutzeri from soil. Appl Environ Microb 68: 865873.
  • Singh R, Schroeder CM, Meng J et al. (2005) Identification of antimicrobial resistance and class 1 integrons in Shiga toxin-producing Escherichia coli recovered from humans and food animals. J Antimicrob Chemoth 56: 216219.
  • Sjolund M, Bonnedahl J, Hernandez J et al. (2008) Dissemination of multidrug-resistant bacteria into the Arctic. Emerg Infect Dis 14: 7072.
  • Skurnik D, Ruimy R, Andremont A, Amorin C, Rouquet P, Picard B & Denamur E (2006) Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli. J Antimicrob Chemoth 57: 12151219.
  • Skurnik D, Ruimy R, Ready D et al. (2010) Is exposure to mercury a driving force for the carriage of antibiotic resistance genes? J Med Microbiol 59: 804807.
  • Slama KB, Jouini A, Sallem RB et al. (2010) Prevalence of broad-spectrum cephalosporin-resistant Escherichia coli isolates in food samples in Tunisia, and characterization of integrons and antimicrobial resistance mechanisms implicated. Int J Food Microbiol 137: 281286.
  • Smet A, Martel A, Persoons D et al. (2009) Broad-spectrum β-lactamases among Enterobacteriaceae of animal origin: molecular aspects, mobility and impact on public health. FEMS Microbiol Rev 34: 295316.
  • Smillie C, Garcillan-Barcia MP, Francia MV, Rocha EP & de la Cruz F (2010) Mobility of plasmids. Microbiol Mol Biol R 74: 434452.
  • Smith DH (1967) R factors mediate resistance to mercury, nickel, and cobalt. Science 156: 11141116.
  • Sohn SG, Lee JJ, Song JS et al. (2009) Nomenclature of ISCRl elements capable of mobilizing antibiotic resistance genes present in complex class 1 integrons. J Microbiol 47: 514516.
  • Sokurenko EV, Gomulkiewicz R & Dykhuizen DE (2006) Source-sink dynamics of virulence evolution. Nat Rev Microbiol 4: 548555.
  • Song L, Ning Y, Shen J, Fan X, Zhang C, Yang C & Han J (2010) Investigation of integrons/cassettes in antimicrobial-resistant Escherichia coli isolated from food animals in China. Sci China Life Sci 53: 613619.
  • Soufi L, Abbassi MS, Saenz Y et al. (2009) Prevalence and diversity of integrons and associated resistance genes in Escherichia coli isolates from poultry meat in Tunisia. Foodborne Pathog Dis 6: 10671073.
  • Sprocati AR, Alisi C, Segre L, Tasso F, Galletti M & Cremisini C (2006) Investigating heavy metal resistance, bioaccumulation and metabolic profile of a metallophile microbial consortium native to an abandoned mine. Sci Total Environ 366: 649658.
  • Srinivasan V, Nam HM, Sawant AA, Headrick SI, Nguyen LT & Oliver SP (2008) Distribution of tetracycline and streptomycin resistance genes and class 1 integrons in Enterobacteriaceae isolated from dairy and nondairy farm soils. Microb Ecol 55: 184193.
  • Stokes HW & Hall RM (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3: 16691683.
  • Stokes HW, Tomaras C, Parsons Y & Hall RM (1993) The partial 3′-conserved segment duplications in the integrons In6 from pSa and In7 from pDGO100 have a common origin. Plasmid 30: 3950.
  • Stokes HW, Nesbo CL, Holley M, Bahl MI, Gillings MR & Boucher Y (2006) Class 1 integrons potentially predating the association with Tn402-like transposition genes are present in a sediment microbial community. J Bacteriol 188: 57225730.
  • Summers AO (2002) Generally overlooked fundamentals of bacterial genetics and ecology. Clin Infect Dis 34 (suppl 3): S85S92.
  • Summers AO, Wireman J, Vimy MJ et al. (1993) Mercury released from dental “silver” fillings provokes an increase in mercury- and antibiotic-resistant bacteria in oral and intestinal floras of primates. Antimicrob Agents Ch 37: 825834.
  • Sunde M (2005) Class I integron with a group II intron detected in an Escherichia coli strain from a free-range reindeer. Antimicrob Agents Ch 49: 25122514.
  • Sundstrom L, Radstrom P, Swedberg G & Skold O (1988) Site-specific recombination promotes linkage between trimethoprim- and sulfonamide resistance genes. Sequence characterization of dhfrV and sulI and a recombination active locus of Tn21. Mol Gen Genet 213: 191201.
  • Swedberg G & Skold O (1983) Plasmid-borne sulfonamide resistance determinants studied by restriction enzyme analysis. J Bacteriol 153: 12281237.
  • Sykes RB & Richmond MH (1970) Intergeneric transfer of a β-lactamase gene between Ps. aeruginosa and E. coli. Nature 226: 952954.
  • Targant H, Ponsin C, Brunet C, Doublet B, Cloeckaert A, Madec JY & Meunier D (2010) Characterization of resistance genes in multidrug-resistant Salmonella enterica serotype Typhimurium isolated from diseased cattle in France (2002 to 2007). Foodborne Pathog Dis 7: 419425.
  • Taviani E, Ceccarelli D, Lazaro N, Bani S, Cappuccinelli P, Colwell RR & Colombo MM (2008) Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons. FEMS Microbiol Ecol 64: 4554.
  • Tetu SG & Holmes AJ (2008) A family of insertion sequences that impacts integrons by specific targeting of gene cassette recombination sites, the IS1111-attC Group. J Bacteriol 190: 49594970.
  • Thomas CM & Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711721.
  • Toleman MA, Bennett PM & Walsh TR (2006) ISCR elements: novel gene-capturing systems of the 21st century? Microbiol Mol Biol Rv 70: 296316.
  • Touchon M, Hoede C, Tenaillon O et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5: e1000344.
  • Toussaint A & Merlin C (2002) Mobile elements as a combination of functional modules. Plasmid 47: 2635.
  • Trobos M, Jakobsen L, Olsen KE et al. (2008) Prevalence of sulphonamide resistance and class 1 integron genes in Escherichia coli isolates obtained from broilers, broiler meat, healthy humans and urinary infections in Denmark. Int J Antimicrob Ag 32: 367369.
  • Unno T, Han D, Jang J et al. (2010) High diversity and abundance of antibiotic-resistant Escherichia coli isolated from humans and farm animal hosts in Jeonnam Province, South Korea. Sci Total Environ 408: 34993506.
  • Vale PF & Little TJ (2010) CRISPR-mediated phage resistance and the ghost of coevolution past. Proc Biol Sci 277: 20972103.
  • van der Oost J, Jore MM, Westra ER, Lundgren M & Brouns SJ (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34: 401407.
  • van Essen-Zandbergen A, Smith H, Veldman K & Mevius D (2007) Occurrence and characteristics of class 1, 2 and 3 integrons in Escherichia coli, Salmonella and Campylobacter spp. in the Netherlands. J Antimicrob Chemoth 59: 746750.
  • Vasilakopoulou A, Psichogiou M, Tzouvelekis L et al. (2009) Prevalence and characterization of class 1 integrons in Escherichia coli of poultry and human origin. Foodborne Pathog Dis 6: 12111218.
  • Verdet C, Gautier V, Chachaty E, Ronco E, Hidri N, Decre D & Arlet G (2009) Genetic context of plasmid-carried blaCMY-2-like genes in Enterobacteriaceae. Antimicrob Agents Ch 53: 40024006.
  • Verner-Jeffreys DW, Welch TJ, Schwarz T et al. (2009) High prevalence of multidrug-tolerant bacteria and associated antimicrobial resistance genes isolated from ornamental fish and their carriage water. PLoS One 4: e8388.
  • Villa L & Carattoli A (2005) Integrons and transposons on the Salmonella enterica serovar typhimurium virulence plasmid. Antimicrob Agents Ch 49: 11941197.
  • Vo AT, van Duijkeren E, Gaastra W & Fluit AC (2010) Antimicrobial resistance, class 1 integrons, and genomic island 1 in Salmonella isolates from Vietnam. PLoS One 5: e9440.
  • Wachino J, Yamane K, Kimura K, Shibata N, Suzuki S, Ike Y & Arakawa Y (2006) Mode of transposition and expression of 16S rRNA methyltransferase gene rmtC accompanied by ISEcp1. Antimicrob Agents Ch 50: 32123215.
  • Wagner A (2006) Cooperation is fleeting in the world of transposable elements. PLoS Comput Biol 2: e162.
  • Waksman SA & Woodruff HB (1940) The soil as a source of microorganisms antagonistic to disease-producing bacteria. J Bacteriol 40: 581600.
  • Walsh TR (2006) Combinatorial genetic evolution of multiresistance. Curr Opin Microbiol 9: 476482.
  • Ward JM & Grinsted J (1982) Physical and genetic analysis of the Inc-W group plasmids R388, Sa, and R7K. Plasmid 7: 239250.
  • Weber DJ & Rutala WA (2006) Use of germicides in the home and the healthcare setting: is there a relationship between germicide use and antibiotic resistance? Infect Control Hosp Epidemiol 27: 11071119.
  • Wiener P (1996) Experimental studies on the ecological role of antibiotic production in bacteria. Evol Ecol 10: 405421.
  • Wiesner M, Zaidi MB, Calva E, Fernandez-Mora M, Calva JJ & Silva C (2009) Association of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains. BMC Microbiol 9: 131.
  • Wozniak RA & Waldor MK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8: 552563.
  • Wright GD (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5: 175186.
  • Wright MS, Baker-Austin C, Lindell AH, Stepanauskas R, Stokes HW & McArthur JV (2008) Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities. ISME J 2: 417428.
  • Xia R, Guo X, Zhang Y & Xu H (2010) qnrVC-like gene located in a novel complex class 1 integron harboring the ISCR1 element in an Aeromonas punctata strain from an aquatic environment in Shandong Province, China. Antimicrob Agents Ch 54: 34713474.
  • Yang H, Byelashov OA, Geornaras I et al. (2010) Characterization and transferability of class 1 integrons in commensal bacteria isolated from farm and nonfarm environments. Foodborne Pathog Dis 7: 14411451.
  • Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K & Walsh TR (2009) Characterization of a new metallo-β-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Ch 53: 50465054.
  • Zhang X, Wu B, Zhang Y et al. (2009a) Class 1 integronase gene and tetracycline resistance genes tetA and tetC in different water environments of Jiangsu Province, China. Ecotoxicology 18: 652660.
  • Zhang XX, Zhang T, Zhang M, Fang HH & Cheng SP (2009b) Characterization and quantification of class 1 integrons and associated gene cassettes in sewage treatment plants. Appl Microbiol Biot 82: 11691177.
  • Zhang XY, Ding LJ & Yue J (2009c) Occurrence and characteristics of class 1 and class 2 integrons in resistant Escherichia coli isolates from animals and farm workers in northeastern China. Microb Drug Resist 15: 323328.
  • Zhao S, Blickenstaff K, Glenn A, Ayers SL, Friedman SL, Abbott JW & McDermott PF (2009) β-Lactam resistance in salmonella strains isolated from retail meats in the United States by the National Antimicrobial Resistance Monitoring System between 2002 and 2006. Appl Environ Microb 75: 76247630.
  • Zou W, Frye JG, Chang CW, Liu J, Cerniglia CE & Nayak R (2009) Microarray analysis of antimicrobial resistance genes in Salmonella enterica from preharvest poultry environment. J Appl Microbiol 107: 906914.