Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

Murray, C. J. L., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., et al. (2022) · The Lancet · doi:10.1016/s0140-6736(21)02724-0 · Cited by 16,316

ResFinder 4.0 for predictions of phenotypes from genotypes

Bortolaia, V., Kaas, R. S., Ruppe, E., Roberts, M. C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R. L., Rebelo, A. R., Florensa, A. F., et al. (2020) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkaa345 · Cited by 3,373

CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database

Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202

The shared antibiotic resistome of soil bacteria and human pathogens

Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O. A., & Dantas, G. (2012) · Science · doi:10.1126/science.1220761 · Cited by 1,650

Long-term ecological impacts of antibiotic administration on the human intestinal microbiota

Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

Arango-Argoty, G., Garner, E., Pruden, A. J., Heath, L. S., Vikesland, P. J., & Zhang, L. (2018) · Microbiome · doi:10.1186/s40168-018-0401-z · Cited by 1,010

Ecology drives a global network of gene exchange connecting the human microbiome

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011) · Nature · doi:10.1038/nature10571 · Cited by 992

An omics-based framework for assessing the health risk of antimicrobial resistance genes

Zhang, A., Gaston, J. M., Dai, C. L., Zhao, S., Poyet, M., Groussin, M., Yin, X., Li, L.-G., van Loosdrecht, M. C. M., Topp, E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25096-3 · Cited by 977

Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis

Paulsen, I. T., Banerjei, L., Myers, G. S. A., Nelson, W. C., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., et al. (2003) · Science · doi:10.1126/science.1080613 · Cited by 930

Genetic Analysis of a High-Level Vancomycin-Resistant Isolate of Staphylococcus aureus

Weigel, L. M., Clewell, D. B., Gill, S. R., Clark, N. C., McDougal, L. K., Flannagan, S. E., Kolonay, J. F., Shetty, J., Killgore, G., & Tenover, F. C. (2003) · Science · doi:10.1126/science.1090956 · Cited by 909

Functional characterization of the antibiotic resistance reservoir in the human microflora

Sommer, M. O. A., Dantas, G., & Church, G. M. (2009) · Science · doi:10.1126/science.1176950 · Cited by 878

Recovery of gut microbiota of healthy adults following antibiotic exposure

Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, T., Hansen, T. H., Liang, S., Feng, Q., Zhang, C., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0257-9 · Cited by 875

Human intestinal bacteria as reservoirs for antibiotic resistance genes

Salyers, A. A., GUPTA, A., & WANG, Y. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.07.004 · Cited by 847

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

Hu, Y., Yang, X., Qin, J., Lü, N., Cheng, G., Wu, N., Pan, Y., Li, J., Zhu, L., Wang, X., et al. (2013) · Nature Communications · doi:10.1038/ncomms3151 · Cited by 796

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

Yin, X., Jiang, X., Chai, B., Li, L., Yang, Y. J., Cole, J. R., Tiedje, J. M., & Zhang, T. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty053 · Cited by 713

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

Pärnänen, K. M. M., Karkman, A., Hultman, J., Lyra, C., Bengtsson‐Palme, J., Larsson, D. G. J., Rautava, S., Isolauri, E., Salminen, S., Kumar, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06393-w · Cited by 690

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

Gibson, M. K., Forsberg, K. J., & Dantas, G. A. (2014) · The ISME Journal · doi:10.1038/ismej.2014.106 · Cited by 670

Dramatic uneven urbanization of large cities throughout the world in recent decades

Sun, L., Chen, J., Li, Q., & Huang, D. (2020) · Nature Communications · doi:10.1038/s41467-020-19158-1 · Cited by 653

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

Pärnänen, K. M. M., Narciso‐da‐Rocha, C., Kneis, D., Berendonk, T. U., Cacace, D., Thùy, T., Elpers, C., Fatta‐Kassinos, D., Henriques, I. S., Jaeger, T., et al. (2019) · Science Advances · doi:10.1126/sciadv.aau9124 · Cited by 623

Interconnected microbiomes and resistomes in low-income human habitats

Pehrsson, E. C., Tsukayama, P., Patel, S., Mejía-Bautista, M., Sosa-Soto, G., Navarrete, K. M., Calderon, M., Cabrera, L., Hoyos-Arango, W., Bertoli, M. T., et al. (2016) · Nature · doi:10.1038/nature17672 · Cited by 607

Global Spread of Vancomycin-resistant Enterococcus faecium from Distinct Nosocomial Genetic Complex

Willems, R. J. L., Top, J., van Santen, M., Robinson, D. A., Coque, T. M., Baquero, F., Grundmann, H., & Bonten, M. J. M. (2005) · Emerging infectious diseases · doi:10.3201/eid1106.041204 · Cited by 577

Evidence for Extensive Resistance Gene Transfer among Bacteroides spp. and among Bacteroides and Other Genera in the Human Colon

Shoemaker, N. B., Vlamakis, H. C., Hayes, K., & Salyers, A. A. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.2.561-568.2001 · Cited by 529

Vancomycin-resistant enterococcal infections: epidemiology, clinical manifestations, and optimal management

Crank, C. W., & O’Driscoll, T. (2015) · Infection and Drug Resistance · doi:10.2147/idr.s54125 · Cited by 518

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Maldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

Stecher, B., Denzler, R., Maier, L., Bernet, F., Sanders, M. J., Pickard, D. J., Barthel, M., Westendorf, A. M., Krogfelt, K. A., Walker, A. W., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113246109 · Cited by 492

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

Lebreton, F., van Schaik, W., Manson, A. L., Godfrey, P. A., Griggs, A. D., Mazumdar, V., Corander, J., Cheng, L., Saif, S., Young, S., et al. (2013) · mBio · doi:10.1128/mbio.00534-13 · Cited by 476

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

Gibson, M. K., Wang, B., Ahmadi, S., Burnham, C.-A. D., Tarr, P. I., Warner, B. B., & Dantas, G. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.24 · Cited by 457

Country-specific antibiotic use practices impact the human gut resistomePreprint

Forslund, S. K., Sunagawa, S., Kultima, J. R., Mende, D. R., Arumugam, M., Typas, A., & Bork, P. (2013) · Genome Research · doi:10.1101/gr.155465.113 · Cited by 450

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

Enault, F., Briet, A., Bouteille, L., Roux, S., Sullivan, M. B., & Petit, M. (2016) · The ISME Journal · doi:10.1038/ismej.2016.90 · Cited by 432

Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches

Zhao, R., Yu, K., Zhang, J., Zhang, G., Huang, J., Ma, L., Deng, C., Li, X., & Li, B. J. (2020) · Water Research · doi:10.1016/j.watres.2020.116318 · Cited by 381

“Blooming” in the gut: how dysbiosis might contribute to pathogen evolution.

Stecher, B., Maier, L., & Hardt, W.-D. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2989 · Cited by 378

Forecasting the dissemination of antibiotic resistance genes across bacterial genomes

Ellabaan, M. M. H., Munck, C., Porse, A., Imamovic, L., & Sommer, M. O. A. (2021) · Nature Communications · doi:10.1038/s41467-021-22757-1 · Cited by 364

Elevated rates of horizontal gene transfer in the industrialized human microbiome

Groussin, M., Poyet, M., Sistiaga, A., Kearney, S. M., Moniz, K., Noel, M., Hooker, J., Gibbons, S. M., Ségurel, L., Froment, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.052 · Cited by 342

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

Kaminski, J., Gibson, M. K., Franzosa, E. A., Segata, N., Dantas, G. A., & Huttenhower, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004557 · Cited by 332

Spatial organization of bacterial flora in normal and inflamed intestine: A fluorescence in situ hybridization study in mice

Swidsinski, A. (2005) · World Journal of Gastroenterology · doi:10.3748/wjg.v11.i8.1131 · Cited by 314

Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections

Stracy, M., Snitser, O., Yelin, I., Amer, Y., Parizade, M., Katz, R., Rimler, G., Wolf, T., Herzel, E., Koren, G., et al. (2022) · Science · doi:10.1126/science.abg9868 · Cited by 311

Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium

Caballero, S., Kim, S., Carter, R. A., Leiner, I. M., Sušac, B., Miller, L., Kim, G. J., Ling, L., & Pamer, E. G. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.002 · Cited by 308

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms

Sun, J. G., Liao, X., D’Souza, A. W., Boolchandani, M., Li, S., Cheng, K., Martínez, J. L., Li, L., Feng, Y.-J., Fang, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15222-y · Cited by 287

Antibiotic resistance spread in food

Perreten, V., Schwarz, F., Cresta, L., Boeglin, M., Dasen, G., & Teuber, M. (1997) · Nature · doi:10.1038/39767 · Cited by 267

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut

Bakkeren, E., Huisman, J. S., Fattinger, S. A., Hausmann, A., Furter, M., Egli, A., Slack, E. M. C., Sellin, M. E., Bonhoeffer, S., Regoes, R. R., et al. (2019) · Nature · doi:10.1038/s41586-019-1521-8 · Cited by 264

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner

Montassier, E., Valdés-Mas, R., Batard, E., Zmora, N., Dori-Bachash, M., Suez, J., & Elinav, E. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00920-0 · Cited by 256

Antibiotic resistance genes in the environment: prioritizing risks

Bengtsson-Palme, J., & Larsson, D. G. J. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3399-c1 · Cited by 244

Both Oral Metronidazole and Oral Vancomycin Promote Persistent Overgrowth of Vancomycin-Resistant Enterococci during Treatment of Clostridium difficile -Associated Disease

Al‐Nassir, W. N., Sethi, A. K., Li, Y., Pultz, M. J., Riggs, M. M., & Donskey, C. J. (2008) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00090-08 · Cited by 241

In Vivo Transfer of the vanA Resistance Gene from an Enterococcus faecium Isolate of Animal Origin to an E. faecium Isolate of Human Origin in the Intestines of Human Volunteers

Lester, C. H., Frimodt‐Møller, N., Sørensen, T. L., Monnet, D. L., & Hammerum, A. M. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.50.2.596-599.2006 · Cited by 238

Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With Recurrent Clostridium difficile Infection

Millan, B., Park, H., Hotte, N., Mathieu, O., Burguière, P., Tompkins, T. A., Kao, D. H., & Madsen, K. L. (2016) · Clinical Infectious Diseases · doi:10.1093/cid/ciw185 · Cited by 220

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J., & Brito, I. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18164-7 · Cited by 216

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

Burton, J. N., Liachko, I., Dunham, M. J., & Shendure, J. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.011825 · Cited by 203

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J., & Polz, M. F. (2019) · Cell · doi:10.1016/j.cell.2019.06.033 · Cited by 201

Antibiotic resistome in a large‐scale healthy human gut microbiota deciphered by metagenomic and network analyses

Feng, J., Li, B. J., Jiang, X., Yang, Y. J., Wells, G., Zhang, T., & Li, X. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.14009 · Cited by 188

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

Moore, A. M., Patel, S., Forsberg, K. J., Wang, B., Bentley, G. J., Razia, Y., Qin, X. G., Tarr, P. I., & Dantas, G. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078822 · Cited by 183

Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation

Yu, Z., Wang, Y., Henderson, I. R., & Guo, J. (2021) · The ISME Journal · doi:10.1038/s41396-021-01095-6 · Cited by 182

In vitro conjugal transfer of tetracycline resistance fromLactobacillusisolates to other Gram-positive bacteria

Gevers, D., Huys, G. R. B., & Swings, J. (2003) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(03)00505-6 · Cited by 176

Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

Willmann, M., Vehreschild, M. J. G. T., Biehl, L. M., Vogel, W., Dörfel, D., Hamprecht, A. G., Seifert, H., Autenrieth, I. B., & Peter, S. (2019) · BMC Biology · doi:10.1186/s12915-019-0692-y · Cited by 166

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

Coyne, M. J., Zitomersky, N. L., Manson, A. L., Earl, A. M., & Comstock, L. E. (2014) · mBio · doi:10.1128/mbio.01305-14 · Cited by 164

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

Yaffe, E., & Relman, D. A. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0625-0 · Cited by 160

Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats

Jacobsen, L., Wilcks, A., Hammer, K., Huys, G. R. B., Gevers, D., & Andersen, S. R. (2006) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2006.00212.x · Cited by 158

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands

Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

Evans, D. R., Griffith, M. P., Sundermann, A. J., Shutt, K. A., Saul, M. I., Mustapha, M. M., Marsh, J. W., Cooper, V. S., Harrison, L. H., & Tyne, D. V. (2020) · eLife · doi:10.7554/elife.53886 · Cited by 151

A framework for identifying the recent origins of mobile antibiotic resistance genes

Ebmeyer, S., Kristiansson, E., & Larsson, D. G. J. (2021) · Communications Biology · doi:10.1038/s42003-020-01545-5 · Cited by 150

Transfer of Carbapenem-Resistant Plasmid fromKlebsiella pneumoniaeST258 toEscherichia coliin Patient

Goren, M. G., Carmeli, Y., Schwaber, M. J., Chmelnitsky, I., Schechner, V., & Navon‐Venezia, S. (2010) · Emerging infectious diseases · doi:10.3201/eid1606.091671 · Cited by 138

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

Li, X., Stokholm, J., Brejnrod, A., Vestergaard, G., Russel, J., Trivedi, U., Thorsen, J., Gupta, S., Hjelmsø, M. H., Shah, S. A., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.017 · Cited by 133

Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics

Karami, N., Martner, A., Enne, V. I., Swerkersson, S., Adlerberth, I., & Wold, A. E. (2007) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkm327 · Cited by 129

Enterococcal vanB resistance locus in anaerobic bacteria in human faeces

Stinear, T. P., Olden, D., Johnson, P. D. R., Davies, J. K., & Grayson, M. L. (2001) · The Lancet · doi:10.1016/s0140-6736(00)04206-9 · Cited by 127

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

Arango-Argoty, G., Dai, D., Pruden, A. J., Vikesland, P. J., Heath, L. S., & Zhang, L. (2019) · Microbiome · doi:10.1186/s40168-019-0703-9 · Cited by 122

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study

Doyle, R., O’Sullivan, D. M., Aller, S., Bruchmann, S., Clark, T. G., Pelegrin, A. C., Cormican, M., Benavente, E. D., Ellington, M. J., McGrath, E., et al. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000335 · Cited by 120

Transfer of Vancomycin Resistance Transposon Tn 1549 from Clostridium symbiosum to Enterococcus spp. in the Gut of Gnotobiotic Mice

Launay, A., Ballard, S. A., Johnson, P. D. R., Grayson, M. L., & Lambert, T. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.50.3.1054-1062.2006 · Cited by 113

Characterization of the human skin resistome and identification of two microbiota cutotypes

Li, Z., Xia, J., Jiang, L., Tan, Y., An, Y., Zhu, X., Ruan, J., Chen, Z., Zhen, H., Ma, Y., et al. (2021) · Microbiome · doi:10.1186/s40168-020-00995-7 · Cited by 113

Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study

Salvetti, E., Orrù, L., Capozzi, V., Martina, A., Lamontanara, A., Keller, D., Cash, H. A., Felis, G. E., Cattivelli, L., Torriani, S., et al. (2016) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-016-7416-9 · Cited by 112

Abundance and diversity of resistomes differ between healthy human oral cavities and gut

Carr, V. R., Witherden, E. A., Lee, S., Shoaie, S., Mullany, P. P., Proctor, G., Gómez-Cabrero, D., & Moyes, D. L. (2020) · Nature Communications · doi:10.1038/s41467-020-14422-w · Cited by 112

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults

MacPherson, C. W., Mathieu, O., Tremblay, J., Champagne, J., Nantel, A., Girard, S., & Tompkins, T. A. (2018) · Scientific Reports · doi:10.1038/s41598-018-29229-5 · Cited by 110

Gut resistome development in healthy twin pairs in the first year of life

Moore, A. M., Ahmadi, S., Patel, S., Gibson, M. K., Wang, B., Ndao, I. M., Deych, E., Shannon, W., Tarr, P. I., Warner, B. B., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0090-9 · Cited by 109

Functions predict horizontal gene transfer and the emergence of antibiotic resistance

Zhou, H., Beltrán, J. F., & Brito, I. (2021) · Science Advances · doi:10.1126/sciadv.abj5056 · Cited by 107

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

Rahman, S. F., Olm, M. R., Morowitz, M. J., & Banfield, J. F. (2018) · mSystems · doi:10.1128/msystems.00123-17 · Cited by 105

Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants

Esaiassen, E., Hjerde, E., Cavanagh, J. P., Pedersen, T., Andresen, J. H., Rettedal, S. I., Støen, R., Nakstad, B., Willassen, N. P., & Klingenberg, C. (2018) · Frontiers in Pediatrics · doi:10.3389/fped.2018.00347 · Cited by 102

In Vivo Horizontal Gene Transfer of the Carbapenemase OXA-48 During a Nosocomial Outbreak

Göttig, S., Gruber, T. M., Stecher, B., Wichelhaus, T. A., & Kempf, V. A. J. (2015) · Clinical Infectious Diseases · doi:10.1093/cid/civ191 · Cited by 98

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

Sakoparnig, T., Field, C. M., & van Nimwegen, E. (2021) · eLife · doi:10.7554/elife.65366 · Cited by 93

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

Langdon, A. E., Schwartz, D. J., Bulow, C., Sun, X., Hink, T., Reske, K. A., Jones, C. R., Burnham, C. D., Dubberke, E. R., & Dantas, G. A. (2021) · Genome Medicine · doi:10.1186/s13073-021-00843-9 · Cited by 90

Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine

Trobos, M., Lester, C. H., Olsen, J. E., Møller, J. K., & Hammerum, A. M. (2008) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkn437 · Cited by 83

Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials

Bajaj, J. S., Shamsaddini, A., Fagan, A., Sterling, R. K., Gavis, E. A., Khoruts, A., Fuchs, M. A., Lee, H., Sikaroodi, M., & Gillevet, P. M. (2020) · Hepatology Communications · doi:10.1002/hep4.1639 · Cited by 83

Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters

Diallinas, G. (2014) · Frontiers in Pharmacology · doi:10.3389/fphar.2014.00207 · Cited by 79

Probiotic Properties of Escherichia coli Nissle in Human Intestinal Organoids

Pradhan, S. K., & Weiss, A. A. (2020) · mBio · doi:10.1128/mbio.01470-20 · Cited by 79

R-plasmic transfer from Serratia liquefaciens to Escherichia coli in vitro and in vivo in the digestive tract of gnotobiotic mice associated with human fecal flora

Duval‐Iflah, Y., Raibaud, P., Tancrède, C., & Rousseau, M. (1980) · Infection and Immunity · doi:10.1128/iai.28.3.981-990.1980 · Cited by 76

Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion

Cheng, G., Hu, Y., Yin, Y., Yang, X., Xiang, C., Wang, B., Chen, Y., Yang, F., Lei, F., Wu, N., et al. (2012) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2012.02647.x · Cited by 74

Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection

Leung, V. C. M., Vincent, C., Edens, T. J., Miller, M., & Manges, A. R. (2017) · Clinical Infectious Diseases · doi:10.1093/cid/cix821 · Cited by 71

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library

Fouhy, F., Ogilvie, L. A., Jones, B. V., Ross, R. P., Ryan, C. A., Dempsey, E. M., Fitzgerald, G. F., Stanton, C., & Cotter, P. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108016 · Cited by 67

Promiscuity in multidrug recognition and transport: the bacterial MFS Mdr transporters

Lewinson, O., Adler, J., Sigal, N., & Bibi, E. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05254.x · Cited by 66

Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage

Zhang, J., Zhao, J., Jin, H., Lv, R., Shi, H., De, G., Yang, B. K., Sun, Z., & Zhang, H. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1722054 · Cited by 64

Revealing antibiotic resistance in therapeutic and dietary probiotic supplements

Selvin, J., Maity, D., Sajayan, A., & Kiran, G. S. (2020) · Journal of Global Antimicrobial Resistance · doi:10.1016/j.jgar.2020.02.007 · Cited by 63

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals

Arredondo-Alonso, S., Top, J., Corander, J., Willems, R. J. L., & Schürch, A. C. (2021) · Genome Medicine · doi:10.1186/s13073-020-00825-3 · Cited by 63

Glycopeptide ResistancevanAOperons inPaenibacillusStrains Isolated from Soil

Guardabassi, L., Périchon, B., van HEIJENOORT, J., Blanot, D., & Courvalin, P. M. (2005) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.49.10.4227-4233.2005 · Cited by 60

Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1

Alayande, K. A., Aiyegoro, O. A., Nengwekhulu, T. M., Katata‐Seru, L., & Ateba, C. N. (2020) · PLoS ONE · doi:10.1371/journal.pone.0235873 · Cited by 57

The structural basis of promiscuity in small multidrug resistance transporters

Kermani, A. A., Macdonald, C. B., Burata, O. E., Koff, B. B., Koide, A., Denbaum, E., Koide, S., & Stockbridge, R. B. (2020) · Nature Communications · doi:10.1038/s41467-020-19820-8 · Cited by 57

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children

Wu, G. G., Zhang, C., Wang, J., Zhang, F., Wang, R., Shen, J., Wang, L., Pang, X., Zhang, X., Zhao, L., et al. (2016) · Scientific Reports · doi:10.1038/srep24030 · Cited by 56

Poultry as a vector for emerging multidrug resistant Enterococcus spp.: First report of vancomycin (van) and the chloramphenicol–florfenicol (cat-fex-cfr) resistance genes from pigeon and duck faeces

Osman, K. M., Badr, J., Orabi, A., Elbehiry, A., Saad, A. S. A., Ibrahim, M. D. S., & Hanafy, M. H. (2019) · Microbial Pathogenesis · doi:10.1016/j.micpath.2019.01.006 · Cited by 54

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

D’Souza, A. W., Boolchandani, M., Patel, S., Galazzo, G., van Hattem, J. M., Arcilla, M. S., Melles∗, D. C., de Jong, M. D., Schultsz, C., Bootsma, M., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00893-z · Cited by 54

Probiotic potential and safety assessment of bacteriocinogenic Enterococcus faecium strains with antibacterial activity against Listeria and vancomycin-resistant enterococci

Fugaban, J. I. I., Holzapfel, W. H., & Todorov, S. D. (2021) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2021.100070 · Cited by 54

Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora

Crémet, L., Bourigault, C., Lepelletier, D., Guillouzouic, A., Juvin, M. E., Reynaud, A., Corvec, S., & Caroff, N. (2012) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkr547 · Cited by 52

Functional Metagenomics to Study Antibiotic Resistance

Boolchandani, M., Patel, S., & Dantas, G. A. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6634-9_19 · Cited by 49

Safety Assessment of Lactiplantibacillus (formerly Lactobacillus) plantarum Q180

Kwon, Y. J., Chun, B. H., Jung, H. S., Chu, J., Joung, H., Park, S. Y., Kim, B. K., & Jeon, C. O. (2021) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2106.06066 · Cited by 48

Reduction of Antibiotic Resistance Genes in Intestinal Microbiota of Patients With Recurrent Clostridium difficile Infection After Fecal Microbiota Transplantation

Jouhten, H., Mattila, E. J., Arkkila, P., & Satokari, R. M. (2016) · Clinical Infectious Diseases · doi:10.1093/cid/ciw390 · Cited by 47

Metagenomic Analysis Reveals the Distribution of Antibiotic Resistance Genes in a Large-Scale Population of Healthy Individuals and Patients With Varied Diseases

Qiu, Q., Wang, J., Yan, Y., Roy, B., Chen, Y., Shang, X., Dou, T., & Han, L. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.590018 · Cited by 46

Functional and structural characterization of a two-MAb cocktail for delayed treatment of enterovirus D68 infections

Zhang, C., Xu, C., Dai, W., Wang, Y., Liu, Z., Zhang, X., Wang, X., Wang, H., Gong, S., Cong, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23199-5 · Cited by 36

Potential Elimination of Human Gut Resistome by Exploiting the Benefits of Functional Foods

Tsigalou, C., Konstantinidis, T. G., Stavropoulou, E., Bezirtzoglou, E., & Tsakris, A. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00050 · Cited by 35

Probiotic treatment induced change of inflammation related metabolites in IBS-D patients/double-blind, randomized, placebo-controlled trial

Kim, J., Cho, K., Kim, J. S., Jung, H. C., Kim, B., Park, M. S., Ji, G. E., Cho, J., & Hong, K. S. (2019) · Food Science and Biotechnology · doi:10.1007/s10068-019-00717-2 · Cited by 29

Genomic-, phenotypic-, and toxicity-based safety assessment and probiotic potency of Bacillus coagulans IDCC 1201 isolated from green malt

Bang, W. Y., Ban, O., Lee, B. S., Oh, S., Park, C., Park, M., Jung, S. K., Yang, J., & Jung, Y. H. (2021) · Journal of Industrial Microbiology & Biotechnology · doi:10.1093/jimb/kuab026 · Cited by 29

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic IslandsPreprint

Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.31.997171 · Cited by 26

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Suwono, B., Eckmanns, T., Kaspar, H., Merle, R., Zacher, B., Kollas, C., Weiser, A. A., Noll, I., Feig, M., & Tenhagen, B. (2021) · PLoS ONE · doi:10.1371/journal.pone.0244413 · Cited by 22

Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation

Silveira, M. C., da Silva, R. A., da Mota, F. F., Catanho, M., Jardim, R., Guimarães, A. C. R., & de Miranda, A. B. (2018) · Evolutionary Bioinformatics · doi:10.1177/1176934318797351 · Cited by 16

Fecal microbiota transplantation for antibiotic resistant bacteria decolonization

Amrane, S., & Lagier, J. (2020) · Human Microbiome Journal · doi:10.1016/j.humic.2020.100071 · Cited by 15

Genomic and Proteomic Characterization of the Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain

Jaén‐Luchoro, D., Busquets, A., Karlsson, R., Salvà‐Serra, F., Åhrén, C., Karami, N., & Moore, E. R. B. (2020) · Microorganisms · doi:10.3390/microorganisms8060893 · Cited by 15

Safety assessment of the candidate oral probiotic Lactobacillus crispatus YIT 12319: Analysis of antibiotic resistance and virulence-associated genes

Terai, T., Kato, K., Ishikawa, E., Nakao, M., Ito, M., Miyazaki, K., Kushiro, A., Imai, S., Nomura, Y., Hanada, N., et al. (2020) · Food and Chemical Toxicology · doi:10.1016/j.fct.2020.111278 · Cited by 14

Host genetic and environmental factors shape the human gut resistomePreprint

Roy, C. I. L., Bowyer, R. C. E., Carr, V. R., Costeira, R., Fernandez, J. C., Martin, T. C., Spector, T. D., Steves, C. J., Moyes, D. L., Forslund, S. K., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.18.092973 · Cited by 6

Prospects of probiotic strains of bifidobacteria and enterococcus in treatment and prevention of diseases in gastroenterology

Ших, Е. В., Махова, А. А., Astapovskiy, A. A., & Владимирович, П. А. (2021) · Voprosy Pitaniya · doi:10.33029/0042-8833-2021-90-2-15-25 · Cited by 4

Author response: Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

Evans, D. R., Griffith, M. P., Sundermann, A. J., Shutt, K. A., Saul, M. I., Mustapha, M. M., Marsh, J. W., Cooper, V. S., Harrison, L. H., & Tyne, D. V. (2020) · eLife · doi:10.7554/elife.53886.sa2 · Cited by 3

Emerging issues in probiotic safety: 2023 perspectives

Merenstein, D., Pot, B., Leyer, G., Ouwehand, A. C., Preidis, G. A., Elkins, C. A., Hill, C., Lewis, Z. T., Shane, A. L., Zmora, N., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2185034 · Cited by 481

Genomic surveillance for antimicrobial resistance — a One Health perspective

Djordjevic, S. P., Jarocki, V. M., Seemann, T., Cummins, M. L., Watt, A. E., Drigo, B., Wyrsch, E. R., Reid, C. J., Donner, E., & Howden, B. P. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00649-y · Cited by 388

The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches

Nazir, A., Nazir, A., Zuhair, V., Aman, S., Sadiq, S. U. R., Hasan, A. H., Tariq, M., Rehman, L. U., Mustapha, M. J., & Bulimbe, D. B. (2025) · Health Science Reports · doi:10.1002/hsr2.71077 · Cited by 192

Antibiotic resistance in potential probiotic lactic acid bacteria of fermented foods and human origin from Nigeria

Duche, R. T., Singh, A., Wandhare, A. G., Sangwan, V., Sihag, M. K., Nwagu, T. N., Panwar, H., & Ezeogu, L. I. (2023) · BMC Microbiology · doi:10.1186/s12866-023-02883-0 · Cited by 151

Genome-resolved metagenomics: a game changer for microbiome medicine

Kim, N., Ma, J., Kim, W., Kim, J., Belenky, P. A., & Lee, I. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01262-7 · Cited by 134

The human gut resistome

van Schaik, W. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0087 · Cited by 372

Horizontal transfer of antibiotic resistance genes in the human gut microbiome

McInnes, R. S., McCallum, G. E., Lamberte, L. E., & van Schaik, W. (2020) · Current Opinion in Microbiology · doi:10.1016/j.mib.2020.02.002 · Cited by 401

The Role of Gut Microbiota in Antimicrobial Resistance: A Mini-Review

Firoozeh, F., & Zibaei, M. (2019) · Anti-Infective Agents · doi:10.2174/2211352517666190716154013 · Cited by 4

THE HUMAN GUT MICROBIOTA AS A RESISTOME CARRYING ANTIBIOTIC RESISTANCE GENES: A HIDDEN EPIDEMIOLOGICAL THREAT TO PUBLIC HEALTH

Akmalovich, M. B., & Makhmudovich, R. S. (2026) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.21965248

Antibiotics and Antimicrobial Resistance Genes in a Gut Microbiota as a Reservoir—A Review

Dabuo, B., Abubakari, A., Sankah, F. E., & Aryee, H. A. (2025) · Advanced Gut & Microbiome Research · doi:10.1155/agm3/6574751 · Cited by 11