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Keywords:

  • Africa;
  • clones;
  • community-acquired infections;
  • hospital infections;
  • methicillin-resistant Staphylococcus aureus;
  • Panton–Valentine leukocidin

Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

Clin Microbiol Infect 2011; 17: 160–165

Abstract

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Africa is poorly documented. From January 2007 to March 2008, we collected 86 MRSA isolates from five African towns, one each in Cameroon, Madagascar, Morocco, Niger and Senegal. Although one or two major clones, defined by the sequence type and staphylococcal cassette chromosome mec type, predominated at each site, genetic diversity (ten clones) was relatively limited in view of the large geographical area studied. Most of the isolates (n = 76, 88%) belonged to three major clones, namely ST239/241-III, a well-known pandemic clone (n = 34, 40%), ST88-IV (n = 24, 28%) and ST5-IV (n = 18, 21%). The latter two clones have only been sporadically described in other parts of the world. The spread of community-associated MRSA carrying the Panton–Valentine leukocidin genes is a cause for concern, especially in Dakar and possibly throughout Africa.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

Methicillin-resistant Staphylococcus aureus (MRSA) strains have spread throughout the world, first in the hospital setting and more recently in the community. Only five major ancestral hospital clones of MRSA are recognized, suggesting that acquisition of the staphylococcal cassette chromosome (SCC)mec, the genetic element harboring the mecA gene that confers methicillin resistance, has been a rare event. Most hospital-associated MRSA (HA-MRSA) clones are found worldwide, although their frequencies vary from country to country. For example, the major HA-MRSA clone (Lyon) found in France is neither dominant nor even frequent in neighboring countries [1].

Initially, community-associated MRSA (CA-MRSA) differed from HA-MRSA by their continental distribution but travel has rapidly blurred this distinction. For example, the CA-MRSA clone USA300, initially restricted to the USA, is now detected in many other countries [2], albeit at a low frequency. Likewise, all the most common CA-MRSA clones (USA 300, the European sequence type (ST) 80 clone and the Oceania ST30 clone) have been detected in Singapore, a major intercontinental travel hub [3]. Almost a quarter of a century elapsed between the emergence of MRSA in industrialized countries in the 1960s and its first description in Africa in 1988 [4]. However, data on the epidemiology of MRSA in Africa remain scarce [5–9].

We collected MRSA isolates from five major African towns in Morocco (North Africa), Senegal (West Africa), Niger (West Africa), Cameroon (Central Africa) and Madagascar (East Africa), and performed accessory gene regulator (agr) typing, multilocus sequence typing (MLST), staphylococcal protein A (spa) typing, and toxin profiling. Antimicrobial susceptibility was also evaluated.

Materials and methods

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

Study population

All patients with suspected staphylococcal infection were pre-included in seven major tertiary care centres located in five major African towns, namely Antananarivo (Madagascar), Casablanca (Morocco), Niamey (Niger), Dakar (Senegal) and Yaounde (Cameroon), between January 2007 and March 2008 (January 2007 to June 2007 in Casablanca). They were included in the study only if their S. aureus isolate was confirmed to be resistant to methicillin. A standardized specific medical record was filled out during the hospitalization. If more than one S. aureus isolate with the same toxin type was recovered from the same patient, only the first was included. Isolates were considered to be community-acquired if recovered by culture from a sample obtained within 48 h after admission in a patient with no risk factors for nosocomial acquisition in the previous year, namely hospitalization or surgery, use of an indwelling catheter or a percutaneous device, or frequent exposure to healthcare facilities for an underlying chronic disorder. All other isolates were considered hospital-acquired. The study protocol was approved by local ethics committees.

Microbiological analysis

S. aureus identification was based on Gram staining, morphology, catalase positivity (ID color Catalase; bioMérieux, Marcy l’Etoile, France), agglutination in the Pastorex Staph Plus® test (Bio-Rad, Marnes la Coquette, France) and free coagulase production (lyophilized rabbit plasma; bioMerieux).

DNA extraction, mecA detection, agr typing and SCCmec typing

Genomic DNA was extracted with a standard phenol–chloroform procedure [10]. Species identification was confirmed by multiplex PCR amplification of the agr locus [10], allowing concomitant determination of the agr allelic group. All isolates were screened for genes encoding methicillin resistance (mecA), staphylococcal enterotoxins (se) A, B, C, D, H, K, L, M, O, P, Q, and R (sea-d, seh, sek-m, seo-r), toxic shock syndrome toxin 1 (tst), exfoliative toxins A, B and D (eta, etb, etd), Panton–Valentine leukocidin (luk-PV), class F LukM leukocidin (lukM), β-haemolysin (hlb) and epidermal cell differentiation inhibitor (edinA/B/C), as previously described [10,11]. SCCmec types were determined by PCR with a simplified version of Kondo’s typing system, including M-PCR-1 and M-PCR-2, without considering the structure of the junkyard region [12].

Spa typing and MLST

Spa sequence typing was performed with the Ridom Staph Type standard protocol (http://www.3.ridom.de.doc/Ridom_spa_sequencing.pdf) and the Ridom SpaServer, which automatically analyzes spa repeats and assigns spa types (http://spa.ridom.de/index.shtml). MLST was performed as described previously [13]. MLST and spa typing were performed on 23 representative isolates of all toxin types within each agr type.

Antimicrobial susceptibility

Susceptibility to penicillin, oxacillin, cefoxitin, gentamicin, kanamycin, tobramycin, tetracycline, erythromycin, lincomycin, pristinamycin, fosfomycin, fusidic acid, rifampicin, pefloxacin, co-trimoxazole and vancomycin was determined by each participating laboratory, in accordance with the guidelines of the French Society for Microbiology [14]. S. aureus strain ATCC 25923 was used for quality control. External quality control was ensured by the French National Antibiotic Reference Center (Pasteur Institute, Paris, France).

Results and Discussion

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

In total, 542 patients were included during the study period. Six hundred and nine biological samples were taken and 555 S. aureus strains were collected, of which 86 were resistant to methicillin. The low prevalence of MRSA (15%), combined with the lack of systematic samples for bacteriological culture and frequent initiation of antibiotic therapy before biological sampling, explains the small number of MRSA isolates. Nevertheless, this represents the largest collection of clinical MRSA isolates ever studied on the African continent, excluding Nigeria and South Africa. Isolates were recovered mainly from male patients (64%). The patients’ median age was 29.0 years (mean 32.4 years; range 2 months to 84 years). Nine isolates (10%) were recovered in Yaounde (Cameroon), 11 (13%) in Niamey (Niger), 16 (19%) in Antananarivo (Madagascar), 21 (24%) in Casablanca (Morocco) and 29 (34%) in Dakar (Senegal) (Fig. 1). Forty-four isolates (51%) were associated with skin and soft-tissue infections, 27 (31%) with surgical wound infections, nine (10%) with bacteraemia/septicaemia, four (5%) with urinary/genital tract infections and two (2%) with osteomyelitis/myositis. The small number of isolates associated with bacteraemia/septicaemia reflects the lack of routine blood culture in the participating centres.

image

Figure 1.  The distribution of methicillin-resistant Staphylococcus aureus (MRSA) clones, each defined by their sequence type (ST) followed by their staphylococcal cassette chromosome mec type, in five African towns (Antananarivo, Casablanca, Dakar, Niamey and Yaounde). The proportions of clones at each sampling location are displayed as pie charts, with size indicating the number of isolates (red numbers).

Download figure to PowerPoint

The 86 isolates belonged to seven STs and five clonal complexs (CCs). The isolates were assigned to ten different clones according to their sequence type and SCCmec type. Most of the isolates (n = 76, 88%) belonged to only three major clones, namely ST239/241-III (n = 34, 40%), ST88-IV (= 24, 28%) and ST5-IV (n = 18, 21%) (Table 1).

Table 1.   Molecular characteristics of CA-MRSA and HA-MRSA isolates recovered in five African towns (Antananarivo, Casablanca, Dakar, Niamey and Yaounde)
Clonal complexST-agr SCCmec typespa type (no.)Toxin genes (no.)HA-MRSA (n = 77)CA-MRSA (n = 9)
Location (n)TotalLocation (n)Total
  1. CA-MRSA, community-associated methicillin-resistant Staphylococcus aureus; HA-MRSA, hospital-associated methicillin-resistant Staphylococcus aureus; ST, sequence type; agr, accessory gene regulator; SCCmec, staphylococcal cassette chromosome mec; spa, staphylococcal protein A; edin, epidermal cell differentiation inhibitor; eta, exfoliatin A; etb, exfoliatin B; etd, exfoliatin D; hlb, β-haemolysin; luk, staphylococcal leukocidin; se, staphylococcal enterotoxin; tst, toxic shock syndrome toxin; A, Antananarivo; C, Casablanca; D, Dakar; N, Niamey; Y, Yaounde.

239ST239/241-agr1
 SCCmec IIIt037 (29) t138 (5)sek (34), selq (34) sea (13), selp (7)C (20), D (8), N (6)34  
 SCCmec Vt037 (1)sea (1), sek (1), selq (1)N (1)1  
88ST88-agr3
 SCCmec IVt168 (1) t186 (15) t729 (8)eta (9), hlb (2)A (10), D (1), N (5), Y (4)20A (3), D (1)4
 SCCmec Vt729 (1) A (1)1  
ST1289-agr3
 SCCmec IVt1339 (1)eta (1), sem (1), seo(1), luk-PV (1)Y (1)1  
5ST5-agr2
 SCCmec IIt311 (2)sem (2), seo (2), luk-PV (2), edin A/B/C (2)D (2)2  
 SCCmec IVt311 (18)seb (1), selq (1), sem (18), seo (18), luk-PV (17), edin A/B/C (13)D (13), C (1)14D (4)4
 SCCmec Vt311 (1)seb (1), selq (1), sem (1), seo (1), luk-PV (1), edin A/B/C (1), hlb (1)Y (1)1  
8ST8-agr1
 SCCmec IVt121 (1) t451 (1) t024 (1)sea (2), seb (1), sek (1), luk-PV (1)A (1), Y (2)3Y (1)1
30ST30-agr3
 SCCmec Vt4686 (1)seb (1), sem (1), seo (1), selp (1)A (1)1  

The first major clone (34 isolates, 40%) was related to the Brazilian/Hungarian one, a well-known HA-MRSA clone of CC239 with the following characteristics: ST239 or ST241, agr 1, SCCmec type III and spa-type t037 or related [15]. This clone was detected in three of the five towns, namely Casablanca (n = 20, 59%), Dakar (n = 8, 24%) and Niamey (n = 6, 18%). It was the dominant clone in Casablanca (95% of all MRSA isolates from this site) and Niamey (55%) (Table 1).

The sek and selq genes were detected in all the isolates belonging to this clone, whereas the sea and selp genes were present in only 38% and 21% of such isolates, respectively. Isolates belonging to this clone were all resistant to kanamycin, tobramycin, gentamicin, tetracycline and pefloxacin (Table 2). This clone has already been extensively described as a major clone in many countries in Asia, Europe and South America [15]. The results obtained in the present study, together with data from Algeria [9] and Nigeria [6], suggest that this pandemic multidrug-resistant clone is also spreading in Africa.

Table 2.   Susceptibility pattern of the three major methicillin-resistant Staphylococcus aureus clones identified
ST-SCCmecNon-β-lactam drug susceptibility
Always resistant (n)Variably resistant (n)
  1. ST, sequence type; SCCmec, staphylococcal cassette chromosome mec; KAN, kanamycin; TOB, tobramy cin; GEN, gentamicin; ERY, erythromycin; LIN, lincomycin; PEF, pefloxacin; TET, tetracycline; RIF, rifampicin; FOS, fosfomycin; FU, fusidic acid; SXT, co-trimoxazole.

ST88-SCCmec IV (n = 24) KAN (1), TOB (1), ERY (10), LIN (1), TET (18), RIF (9), SXT (15)
ST5-SCCmec IV (n = 18) KAN (4), TOB (4), GEN (4), PEF (1), TET (15), SXT (16)
ST239/241-SCCmec III (n = 34)KAN, TOB, GEN, PEF, TETERY (25), LIN (14), RIF (20), FOS (1), FU (12), SXT (24)

The second major clone accounted for 24 (28%) of the 86 isolates. Unexpectedly, it was ST88-IV, agr 3 and spa-type t186 or related (except for one isolate that was spa-type t168). The only toxin genes present in these isolates were hlb (n = 2) and eta (n = 8). Antimicrobial susceptibility was highly variable (ten different antibiotypes), but was mainly characterized by resistance to methicillin and susceptibility to aminoglycosides (92%) and fluoroquinolones (96%). ST88-IV has not previously been described as an epidemic MRSA clone; it has been reported only sporadically and in very few countries, including one isolate each in Belgium [16] and Portugal [17], as well as ten isolates in Sweden [18]. By contrast, this clone was detected in all the participating centres in the present study, apart from Casablanca, and was the predominant clone in Antananarivo (= 13, 81%), Niamey (n = 5, 45%) and Yaounde (n = 4, 44%). The high prevalence of this clone in Africa is confirmed by reports of its recent detection in Nigeria [5], as well as in children from Western Africa who had surgery in Switzerland and had been hospitalized in their home countries [19]. Furthermore, this clone appeared to be present in both the community and hospital settings in Antananarivo and Dakar. All these findings cause concern because they highlight: (i) the ability of this clone to spread over a large geographic area, including Central, East and West Africa, and (ii) the potential role of the African continent as a reservoir for this clone. Moreover, two isolates, one of ST88-V and spa-type t729 lacking toxin genes, and one of ST1289-IV (a single-locus variant of ST88) and spa-type 1339 associated with eta plus the luk-PV genes, clustered in the same clonal complex, CC88, and corresponded to none of the previously described clones. The emergence of a clone harboring both eta (involved in staphylococcal scalded-skin syndrome and bullous impetigo) [20] and luk-PV (able to induce necrotizing syndromes) [21] genes is a major concern.

The third major clone, ST5-IV (n = 18, 21%), was recovered once in Casablanca (Morocco), whereas the remaining isolates were all from Dakar, Senegal, where this clone predominated (17 of 29 isolates, 59%). These isolates possessed an agr2 allele and were all assigned to spa type t311. They were susceptible to most antibiotics, with the noteworthy exceptions of tetracycline (83% resistant) and cotrimoxazole (89% resistant). Their toxin genes included sem and seo, usually associated with luk-PV (n = 17, 94%) and edin A/B/C (n = 13, 72%).

These characteristics match the molecular and phenotypic features of CA-MRSA. The Panton–Valentine leukocidin (PVL)-positive ST5-IV isolates were from 17 patients (male:female ratio 0.59, median age 35.0 years, mean age 32.7 years, range 2 months to 58 years) with skin and soft-tissue infections in nine cases, surgical wound infections in six cases and bacteraemia/septicaemia and osteomyelitis in one case each. Thirteen (76%) of the 17 infections were hospital-acquired. The presence of luk-PV in MRSA with the ST5 genetic background is uncommon and of particular concern because: (i) several pandemic clones (New York/Japan and Pediatric clones) associated with the ST5 genetic background have shown strong epidemic potential in hospital settings; (ii) the SCCmec IV cassette, a small genetic element, does not have a biological fitness cost and allows stable populations of MRSA to emerge [22]; and (iii) the luk-PV genes encoding PVL, a major virulence factor, are associated with skin and soft-tissue infections and also with severe necrotizing pneumonia [21,23]. Recently, such community-acquired ST5-IV MRSA isolates harboring PVL genes have been reported sporadically in Algeria, France, Switzerland, Ireland and Slovenia, and have started to emerge in healthcare settings in Argentina [24–27]. Further studies are needed to evaluate their spread through Africa and its genetic and epidemiological links with previously described ST5-IV isolates.

We identified two other infrequent clones (ST5-II, n = 2 and ST5-V, n = 1), which, interestingly, harbored the luk-PV gene and also clustered within CC5. PVL genes are carried on a prophage, implying that these genes could have been incorporated into S. aureus lineages through horizontal transfer, either before or after the acquisition of mecA gene. Alternatively, these clones could illustrate genetic recombination involving the SCCmec cassette.

Finally, we identified some sporadic clones, such as ST8-IV (three isolates in Yaounde and one in Antananarivo) belonging to CC8, and ST30-V (one isolate in Antananarivo) belonging to CC30.

In the last decade, CA-MRSA, which are epidemiologically and genetically different from HA-MRSA [28], have presented a growing challenge in terms of its pathogenicity and antimicrobial resistance. Many data have been published on the temporal and geographic dynamics of CA-MRSA in industrialized countries. Our findings suggest that Africa is not exempt from these trends and is also seeing the emergence and spread of PVL-positive MRSA clones (n = 20, 23% of all isolates) carrying SCCmec cassette type IV or V and susceptible to most antibiotics other than β-lactams [28]. As most of these isolates (n = 16, 80%) were detected in Dakar (Senegal), further investigations are needed to assess the spread of such clones in other African countries.

We identified four different lineages corresponding to CA-MRSA types, namely ST5-IV (n = 17), ST5-V (n = 1), ST8-IV (= 1) and ST1289-IV (n = 1) (a fifth PVL-positive clone, ST5-II, was detected but did not share features of CA-MRSA). These four lineages were found in Dakar (Senegal), Yaounde (Cameroon) and Casablanca (Morocco). The successful PVL-positive CA-MRSA clone, ST80-SCCmec IV described in Algeria [9], was not detected in the present study. A large proportion of the isolates investigated in the present study (n = 16, 80%) were recovered from patients considered to have hospital-acquired infections, although this must be interpreted with caution. First, definitions based on time after hospital admission and care-associated risk factors may underestimate the importance of the CA-MRSA reservoir, particularly in African hospitals where patients are not systematically sampled for bacteriological culture within the first 48 h after admission as a result of organizational problems. However, molecular typing methods are often useful for defining CA-MRSA strains [29]. Second, when their prevalence in the community is high, CA-MRSA clones are able to spread into hospitals [29]. Unfortunately, we did not study the MRSA community reservoir in these African towns and we cannot exclude the possibility that the PVL-positive ST5-IV clone, mainly found in Dakar, could have emerged locally in the hospital setting rather than in the community. To test this hypothesis, further studies are needed to determine the prevalence and molecular characteristics of MRSA clones in the community in Senegal. Third, few African hospitals (except in North Africa and South Africa) are able to implement all the measures required to prevent nosocomial infections (i.e. measures that also act as a barrier between the community and hospital settings), such as isolation of infected patients, stringent hand hygiene, cleaning and disinfection of environmental surfaces, sterilization of medical materials, and standard precautions during care procedures (hand washing, gloves, mask, gown, linen and environmental control). Fourth, the permanent presence of friends and relatives in African hospitals, who share some healthcare responsibilities for these patients, increases the risk of MRSA circulation between the community and hospital settings [30].

We studied 86 isolates from only one or two centres in each country, which may not be representative of the global situation. However, the present study provides an overview of MRSA clones currently circulating in seven hospitals in five major African towns, and is the first of its type and scale. The small number of isolates may also reflect the relatively low incidence of MRSA infection in Africa. The healthcare institutions studied were among the major tertiary hospitals in each country. Although we found one or two predominant MRSA clones in each country, as classically reported in Europe, the clonal diversity was somewhat limited for such a large geographical area. However, given the small number of MRSA isolates recovered at each site, the absence of certain clones in this collection does not rule out their presence. Although the major clone identified here is a well-known pandemic clone (ST239/241-III), the distribution of the other major clonal lineages (ST88-IV, ST5-IV) is very different from that seen elsewhere in the world.

Acknowledgements

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

We thank F. Boulez, F. Bintou Badji and F. Bintou Dieye (Institut Pasteur, Dakar, Senegal) for their technical help, and all the clinicians involved in the conduct of this study. We also thank M. Bes (National Reference Centre for Staphylococci, Lyon, France) for helpful discussions, and I. Eronini and D. Young for editorial assistance.

Transparency Declaration

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

This study was supported by grants from the Institut Pasteur (Grant PTR 197) and Institut de Veille Sanitaire (InVS, Saint-Maurice, France) and was performed within institutes belonging to the Institut Pasteur International Network. All the authors declare that they have no conflicts of interest.

References

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  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix
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Appendix

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and methods
  5. Results and Discussion
  6. Acknowledgements
  7. Transparency Declaration
  8. References
  9. Appendix

The Working Group on Staphylococcus aureus infections included: F. Diene-Sarr, Institut Pasteur, Dakar, Senegal A. Maudry, Institut Pasteur, Dakar, Senegal; A. Seck, Institut Pasteur, Dakar, Senegal; M. Cisse, Le Dantec University Hospital, Dakar, Senegal; A. Gaye-Diallo, Le Dantec University Hospital, Dakar, P. I. Ndiaye, Le Dantec University Hospital, Dakar, Senegal; S. Guyomard, Principal Hospital, Dakar, Senegal; S. Ka, Principal Hospital, Dakar, Senegal; A. Sow, Principal Hospital, Dakar, Senegal; K. A. Wade, Principal Hospital, Dakar, Senegal; M. Sembene, Cheikh Anta Diop University, Dakar, Senegal; M. Bekkali, Hassan II University, Casablanca, Morocco; N. El Mdaghri, Ibn Rochd University Hospital, Casablanca, Morocco; M. Timinouni, Institut Pasteur, Casablanca, Morocco; K. Zerouali, Ibn Rochd University Hospital, Casablanca, Morocco; J. F. Carod, Institut Pasteur, Antananarivo, Madagascar; J. B. Chretien, Institut Pasteur, Antananarivo, Madagascar; E. Ratsima, Institut Pasteur, Antananarivo, Madagascar; V. Richard, Institut Pasteur, Antananarivo, Madagascar; L. Vaillant, Institut Pasteur, Antananarivo, Madagascar; A. Ngandjio, Centre Pasteur, Yaounde, Cameroon; M. Tejiokem, Centre Pasteur, Yaounde, Cameroon; and A. Zakou, CERMES, Niamey, Niger.