Prospects & Overviews
Metagenomic insights into the human gut resistome and the forces that shape it
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Abstract
We show how metagenomic analysis of the human gut antibiotic resistome, compared across large populations and against environmental or agricultural resistomes, suggests a strong anthropogenic cause behind increasing antibiotic resistance in bacteria. This area has been the subject of intense and polarized debate driven by economic and political concerns; therefore such recently available insights address an important need. We derive and compare antibiotic resistomes of human gut microbes from 832 individuals from ten different countries. We observe and describe significant differences between samples from these countries in the gut resistance potential, in line with expectations from antibiotic usage and exposure in medical and food production contexts. Our results imply roles for both of these sources in increased resistance among pathogens in recent history. In contrast, other available metadata such as age, body mass index, sex, or health status have little effect on the antibiotic resistance potential of human gut microbes.
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Citing Literature
Number of times cited according to CrossRef: 28
- Shiv K. Sarin, Apurva Pande and Bernd Schnabl, Microbiome as a therapeutic target in alcohol-related liver disease, Journal of Hepatology, 10.1016/j.jhep.2018.10.019, 70, 2, (260-272), (2019).
- P.C. Barko, M.A. McMichael, K.S. Swanson and D.A. Williams, The Gastrointestinal Microbiome: A Review, Journal of Veterinary Internal Medicine, 32, 1, (9-25), (2017).
- Jie Feng, Bing Li, Xiaotao Jiang, Ying Yang, George F. Wells, Tong Zhang and Xiaoyan Li, Antibiotic resistome in a large‐scale healthy human gut microbiota deciphered by metagenomic and network analyses, Environmental Microbiology, 20, 1, (355-368), (2017).
- Alvaro San Millan, Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context, Trends in Microbiology, 10.1016/j.tim.2018.06.007, 26, 12, (978-985), (2018).
- Renxin Zhao, Jie Feng, Xiaole Yin, Jie Liu, Wenjie Fu, Thomas U. Berendonk, Tong Zhang, Xiaoyan Li and Bing Li, Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis, Water Research, 10.1016/j.watres.2018.01.063, 134, (126-139), (2018).
- Jian‐Qiang Su, Li Cui, Qing‐Lin Chen, Xin‐Li An and Yong‐Guan Zhu, Application of genomic technologies to measure and monitor antibiotic resistance in animals, Annals of the New York Academy of Sciences, 1388, 1, (121-135), (2016).
- Ana B. Flórez, Lucía Vázquez and Baltasar Mayo, A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria, Frontiers in Microbiology, 8, (2017).
- Graham Rose, Alexander G. Shaw, Kathleen Sim, David J. Wooldridge, Ming-Shi Li, Saheer Gharbia, Raju Misra and John Simon Kroll, Antibiotic resistance potential of the healthy preterm infant gut microbiome, PeerJ, 5, (e2928), (2017).
- Abby D. Mutic, Sheila Jordan, Sara M. Edwards, Erin P. Ferranti, Taylor A. Thul and Irene Yang, The Postpartum Maternal and Newborn Microbiomes, MCN, The American Journal of Maternal/Child Nursing, 42, 6, (326), (2017).
- Eric van der Helm, Lejla Imamovic, Mostafa M. Hashim Ellabaan, Willem van Schaik, Anna Koza and Morten O.A. Sommer, Rapid resistome mapping using nanopore sequencing, Nucleic Acids Research, (gkw1328), (2017).
- Patricia Munsch-Alatossava, Susanna Jääskeläinen, Tapani Alatossava and Jean-Pierrre Gauchi, N2 Gas Flushing Limits the Rise of Antibiotic-Resistant Bacteria in Bovine Raw Milk during Cold Storage, Frontiers in Microbiology, 8, (2017).
- Daniel Ryan, Sangeeta Jaiswal and Mrutyunjay Suar, Role of External and Environmental Factors in Drug Resistance Emergence: Gut Microbiota, Drug Resistance in Bacteria, Fungi, Malaria, and Cancer, 10.1007/978-3-319-48683-3_12, (287-305), (2017).
- Matthias Willmann and Silke Peter, Translational metagenomics and the human resistome: confronting the menace of the new millennium, Journal of Molecular Medicine, 95, 1, (41), (2017).
- Vesna Milanović, Andrea Osimani, Lucia Aquilanti, Stefano Tavoletti, Cristiana Garofalo, Serena Polverigiani, Alice Litta‐Mulondo, Luca Cocolin, Ilario Ferrocino, Raffaella Di Cagno, Silvia Turroni, Camilla Lazzi, Nicoletta Pellegrini and Francesca Clementi, Occurrence of antibiotic resistance genes in the fecal DNA of healthy omnivores, ovo‐lacto vegetarians and vegans, Molecular Nutrition & Food Research, 61, 9, (2017).
- Karin Jepsen and Søren Jepsen, Antibiotics/antimicrobials: systemic and local administration in the therapy of mild to moderately advanced periodontitis, Periodontology 2000, 71, 1, (82-112), (2016).
- Frédéric Raymond, Amin A Ouameur, Maxime Déraspe, Naeem Iqbal, Hélène Gingras, Bédis Dridi, Philippe Leprohon, Pier-Luc Plante, Richard Giroux, Ève Bérubé, Johanne Frenette, Dominique K Boudreau, Jean-Luc Simard, Isabelle Chabot, Marc-Christian Domingo, Sylvie Trottier, Maurice Boissinot, Ann Huletsky, Paul H Roy, Marc Ouellette, Michel G Bergeron and Jacques Corbeil, The initial state of the human gut microbiome determines its reshaping by antibiotics, The ISME Journal, 10, 3, (707), (2016).
- Hannah Landecker, Antibiotic Resistance and the Biology of History, Body & Society, 22, 4, (19), (2016).
- Heidi Mulcahy-O’Grady and Matthew L. Workentine, The Challenge and Potential of Metagenomics in the Clinic, Frontiers in Immunology, 7, (2016).
- Guojun Wu, Chenhong Zhang, Jing Wang, Feng Zhang, Ruirui Wang, Jian Shen, Linghua Wang, Xiaoyan Pang, Xiaojun Zhang, Liping Zhao and Menghui Zhang, Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children, Scientific Reports, 6, 1, (2016).
- Fernando Baquero, Val F. Lanza, Rafael Cantón and Teresa M. Coque, Public health evolutionary biology of antimicrobial resistance: priorities for intervention, Evolutionary Applications, 8, 3, (223-239), (2014).
- W. van Schaik, The human gut resistome, Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 1670, (20140087), (2015).
- Wei-Ying Ouyang, Fu-Yi Huang, Yi Zhao, Hu Li and Jian-Qiang Su, Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China, Applied Microbiology and Biotechnology, 99, 13, (5697), (2015).
- Simone Rampelli, Stephanie L. Schnorr, Clarissa Consolandi, Silvia Turroni, Marco Severgnini, Clelia Peano, Patrizia Brigidi, Alyssa N. Crittenden, Amanda G. Henry and Marco Candela, Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota, Current Biology, 25, 13, (1682), (2015).
- Aimee M. Moore, Sara Ahmadi, Sanket Patel, Molly K. Gibson, Bin Wang, I. Malick Ndao, Elena Deych, William Shannon, Phillip I. Tarr, Barbara B. Warner and Gautam Dantas, Gut resistome development in healthy twin pairs in the first year of life, Microbiome, 3, 1, (2015).
- Anita Y Voigt, Paul I Costea, Jens Roat Kultima, Simone S Li, Georg Zeller, Shinichi Sunagawa and Peer Bork, Temporal and technical variability of human gut metagenomes, Genome Biology, 16, 1, (2015).
- Julie Guthman, Garrett Broad, Kendra Klein and Hannah Landecker, Beyond the Sovereign Body, Gastronomica: The Journal of Food and Culture, 14, 3, (46), (2014).
- Julie A. Perry and Gerard D. Wright, Forces shaping the antibiotic resistome, BioEssays, 36, 12, (1179-1184), (2014).
- Sabine Leroy, Souad Christieans and Régine Talon, Tetracycline Gene Transfer in Staphylococcus xylosus in situ During Sausage Fermentation, Frontiers in Microbiology, 10.3389/fmicb.2019.00392, 10, (2019).
