Genomic surveillance for antimicrobial resistance - a One Health perspective.
Journal
Nature reviews. Genetics
ISSN: 1471-0064
Titre abrégé: Nat Rev Genet
Pays: England
ID NLM: 100962779
Informations de publication
Date de publication:
25 Sep 2023
25 Sep 2023
Historique:
accepted:
02
08
2023
medline:
26
9
2023
pubmed:
26
9
2023
entrez:
25
9
2023
Statut:
aheadofprint
Résumé
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
Identifiants
pubmed: 37749210
doi: 10.1038/s41576-023-00649-y
pii: 10.1038/s41576-023-00649-y
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2023. Springer Nature Limited.
Références
Djordjevic, S. P., Stokes, H. W. & Chowdhury, P. R. Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota. Front. Microbiol. 4, 86 (2013). This study addresses the importance of understanding how resistance genes and the genetic scaffolds that mobilize them into clinically important bacteria are likely to have their origins in completely unrelated parts of the microbial biosphere.
pubmed: 23641238
pmcid: 3639385
doi: 10.3389/fmicb.2013.00086
Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, 00088 (2018). This study identifies the discerning features of MGEs that have the ability to move ARG cargo within or between DNA molecules and those that drive dissemination between bacterial cells.
doi: 10.1128/CMR.00088-17
Gillings, M. R. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann. N. Y. Acad. Sci. 1389, 20–36 (2017).
pubmed: 27706829
doi: 10.1111/nyas.13213
Christaki, E., Marcou, M. & Tofarides, A. Antimicrobial resistance in bacteria: mechanisms, evolution, and persistence. J. Mol. Evol. 88, 26–40 (2020).
pubmed: 31659373
doi: 10.1007/s00239-019-09914-3
Aronin, S. I., Dunne, M. W., Yu, K. C., Watts, J. A. & Gupta, V. Increased rates of extended-spectrum β-lactamase isolates in patients hospitalized with culture-positive urinary Enterobacterales in the United States: 2011–2020. Diagn. Microbiol. Infect. Dis. 103, 115717 (2022).
pubmed: 35635889
doi: 10.1016/j.diagmicrobio.2022.115717
Dejonckheere, Y., Desmet, S. & Knops, N. A study of the 20-year evolution of antimicrobial resistance patterns of pediatric urinary tract infections in a single center. Eur. J. Pediatr. https://doi.org/10.1007/s00431-022-04538-0 (2022). This study traces the evolution of drug resistance in paediatric patients with UTIs over a considerable time period.
doi: 10.1007/s00431-022-04538-0
pubmed: 35739294
Pires, J., Huisman, J. S., Bonhoeffer, S. & Van Boeckel, T. P. Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases. J. Antimicrob. Chemother. 77, 646–655 (2022).
pubmed: 34894245
doi: 10.1093/jac/dkab451
Schar, D. et al. Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia. Nat. Commun. 12, 5384 (2021). This large meta-analysis reports antibiotic-resistant bacteria from aquatic food animals in Asia from 2000 and highlights the need to study resistance to medically important antimicrobials in foodborne pathogens.
pubmed: 34508079
pmcid: 8433129
doi: 10.1038/s41467-021-25655-8
Turnidge, J. D., Meleady, K. T., Turnidge, J. D. & Meleady, K. T. Antimicrobial Use and Resistance in Australia (AURA) surveillance system: coordinating national data on antimicrobial use and resistance for Australia. Aust. Health Rev. 42, 272–276 (2017).
doi: 10.1071/AH16238
Wyrsch, E. R. et al. Urban wildlife crisis: Australian silver gull is a bystander host to widespread clinical antibiotic resistance. mSystems 7, e0015822 (2022). This comprehensive WGS study of E. coli from an urban-adapted bird species highlights carriage of emerging and novel multiple drug-resistant lineages carrying genes encoding resistance to clinically important antibiotics.
pubmed: 35469421
doi: 10.1128/msystems.00158-22
Medvecky, M. et al. Interspecies transmission of CMY-2-producing Escherichia coli sequence type 963 isolates between humans and gulls in Australia. mSphere 7, e00238-22 (2022).
pubmed: 35862807
pmcid: 9429958
doi: 10.1128/msphere.00238-22
Cummins, M. L., Reid, C. J. & Djordjevic, S. P. F Plasmid lineages in Escherichia coli ST95: implications for host range, antibiotic resistance, and zoonoses. mSystems 7, e01212–e01221 (2022). This study performs a phylogenomic analysis of ST95 and identifies lineages that carry different F virulence plasmids with implications for host colonization and zoonosis.
pubmed: 35076267
pmcid: 8788324
Inda-Díaz, J. S. et al. Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. Microbiome 11, 44 (2023). This work highlights knowledge gaps in defining the resistome and describes the creation of a reference database for existing and latent antimicrobial resistance genes.
pubmed: 36882798
pmcid: 9993715
doi: 10.1186/s40168-023-01479-0
Baker, S., Thomson, N., Weill, F.-X. & Holt, K. E. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science 360, 733–738 (2018).
pubmed: 29773743
pmcid: 6510332
doi: 10.1126/science.aar3777
Lane, C. R. et al. Search and contain: impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales. Clin. Infect. Dis. 73, e3912–e3920 (2021).
pubmed: 32663248
doi: 10.1093/cid/ciaa972
Sia, C. M. et al. Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia. Microb. Genom. 7, 000725 (2021).
pubmed: 34907895
pmcid: 8767345
Bharat, A. et al. Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr. Microorganisms 10, 292 (2022).
pubmed: 35208747
pmcid: 8875511
doi: 10.3390/microorganisms10020292
Rebelo, A. R. et al. One day in Denmark: comparison of phenotypic and genotypic antimicrobial susceptibility testing in bacterial isolates from clinical settings. Front. Microbiol. 13, 804627 (2022).
pubmed: 35756053
pmcid: 9226621
doi: 10.3389/fmicb.2022.804627
Sherry, N. L. et al. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nat. Commun. 14, 60 (2023). This paper is one of the first to demonstrate the certification of genomic interpretation of AMR to ISO standards, providing a framework for implementation into public health surveillance.
pubmed: 36599823
pmcid: 9813266
doi: 10.1038/s41467-022-35713-4
Hendriksen, R. S. et al. Using genomics to track global antimicrobial resistance. Front. Public Health 7, 00242 (2019).
doi: 10.3389/fpubh.2019.00242
Papp, M. & Solymosi, N. Review and comparison of antimicrobial resistance gene databases. Antibiotics 11, 339 (2022).
pubmed: 35326803
pmcid: 8944830
doi: 10.3390/antibiotics11030339
Kim, J. I. et al. Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective. Clin. Microbiol. Rev. 35, e00179-21 (2022).
pubmed: 35612324
pmcid: 9491192
doi: 10.1128/cmr.00179-21
Meyer, F. et al. Critical assessment of metagenome interpretation: the second round of challenges. Nat. Methods 19, 429–440 (2022).
pubmed: 35396482
pmcid: 9007738
doi: 10.1038/s41592-022-01431-4
DeMaere, M. Z. & Darling, A. E. bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes. Genome Biol. 20, 46 (2019).
pubmed: 30808380
pmcid: 6391755
doi: 10.1186/s13059-019-1643-1
Zankari, E. et al. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J. Antimicrob. Chemother. 72, 2764–2768 (2017).
pubmed: 29091202
pmcid: 5890747
doi: 10.1093/jac/dkx217
Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).
pubmed: 22782487
pmcid: 3468078
doi: 10.1093/jac/dks261
McArthur, A. G. et al. The Comprehensive Antibiotic Resistance Database. Antimicrob. Agents Chemother. 57, 3348–3357 (2013).
pubmed: 23650175
pmcid: 3697360
doi: 10.1128/AAC.00419-13
Feldgarden, M. et al. Curation of the AMRFinderPlus databases: applications, functionality and impact. Microb. Genom. 8, mgen000832 (2022).
pubmed: 35675101
pmcid: 9455714
Arango-Argoty, G. A. et al. ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. Bioinformatics 36, 2966–2973 (2020).
pubmed: 32058567
doi: 10.1093/bioinformatics/btaa095
Gibson, M. K., Forsberg, K. J. & Dantas, G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 9, 207–216 (2015).
pubmed: 25003965
doi: 10.1038/ismej.2014.106
Hunt, M. et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Micro. Genom. 3, e000131 (2017).
Clausen, P. T. L. C., Aarestrup, F. M. & Lund, O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinforma. 19, 307 (2018).
doi: 10.1186/s12859-018-2336-6
Steinig, E. et al. Phylodynamic signatures in the emergence of community-associated MRSA. Proc. Natl Acad. Sci. USA 119, e2204993119 (2022).
pubmed: 36322765
pmcid: 9659408
doi: 10.1073/pnas.2204993119
Steinig, E. et al. Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing. Mol. Biol. Evol. 39, msac040 (2022).
pubmed: 35171290
pmcid: 8963328
doi: 10.1093/molbev/msac040
Rife, B. D. et al. Phylodynamic applications in 21st century global infectious disease research. Glob. Health Res. Policy 2, 13 (2017).
pubmed: 29202081
pmcid: 5683535
doi: 10.1186/s41256-017-0034-y
Dawson, D., Rasmussen, D., Peng, X. & Lanzas, C. Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen. J. R. Soc. Interface 18, 20210041 (2021).
pubmed: 34102084
pmcid: 8187012
doi: 10.1098/rsif.2021.0041
Ingle, D. J., Howden, B. P. & Duchene, S. Development of phylodynamic methods for bacterial pathogens. Trends Microbiol. 29, 788–797 (2021). This important review highlights the potential utility of phylodynamic analyses to enhance understanding of bacterial evolution and transmission.
pubmed: 33736902
doi: 10.1016/j.tim.2021.02.008
Miłobedzka, A. et al. Monitoring antibiotic resistance genes in wastewater environments: the challenges of filling a gap in the One-Health cycle. J. Hazard. Mater. 424, 127407 (2022).
pubmed: 34629195
doi: 10.1016/j.jhazmat.2021.127407
Munk, P. et al. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat. Commun. 13, 7251 (2022).
pubmed: 36456547
pmcid: 9715550
doi: 10.1038/s41467-022-34312-7
Liguori, K. et al. Antimicrobial resistance monitoring of water environments: a framework for standardized methods and quality control. Environ. Sci. Technol. 56, 9149–9160 (2022). This work presents a framework developed in consultation with experts in academia, government and water utility management, and through analyses of the literature, describes standardized methods for monitoring AMR in water.
pubmed: 35732277
pmcid: 9261269
doi: 10.1021/acs.est.1c08918
Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019). This work presents metagenomic sequencing of sewage as an economically and ethically acceptable approach to global AMR surveillance, providing important insights into AMR carriage in the healthy human gut in a region-specific manner.
pubmed: 30850636
pmcid: 6408512
doi: 10.1038/s41467-019-08853-3
Banerjee, S. & van der Heijden, M. G. A. Soil microbiomes and one health. Nat. Rev. Microbiol. 21, 6–20 (2023).
pubmed: 35999468
doi: 10.1038/s41579-022-00779-w
Larsson, D. G. J. & Flach, C.-F. Antibiotic resistance in the environment. Nat. Rev. Microbiol. 20, 257–269 (2022). This review examines risk scenarios, surveillance methods and potential factors driving antibiotic resistance, and identifies actionable measures to mitigate the risks associated with antibiotic resistance in the environment.
pubmed: 34737424
doi: 10.1038/s41579-021-00649-x
Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).
doi: 10.1016/S0140-6736(21)02724-0
Kim, D.-W. & Cha, C.-J. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp. Mol. Med. 53, 301–309 (2021).
pubmed: 33642573
pmcid: 8080597
doi: 10.1038/s12276-021-00569-z
Lamberte, L. E. & van Schaik, W. Antibiotic resistance in the commensal human gut microbiota. Curr. Opin. Microbiol. 68, 102150 (2022).
pubmed: 35490629
doi: 10.1016/j.mib.2022.102150
Crits-Christoph, A., Hallowell, H. A., Koutouvalis, K. & Suez, J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 14, 2055944 (2022).
pubmed: 35332832
pmcid: 8959533
doi: 10.1080/19490976.2022.2055944
Arumugam, K. et al. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. npj Biofilms Microbiomes 7, 1–13 (2021).
doi: 10.1038/s41522-021-00196-6
Bertrand, D. et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat. Biotechnol. 37, 937–944 (2019).
pubmed: 31359005
doi: 10.1038/s41587-019-0191-2
Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020).
pubmed: 33020656
doi: 10.1038/s41592-020-00971-x
Pellow, D. et al. SCAPP: an algorithm for improved plasmid assembly in metagenomes. Microbiome 9, 144 (2021).
pubmed: 34172093
pmcid: 8228940
doi: 10.1186/s40168-021-01068-z
Somerville, V. et al. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. BMC Microbiol. 19, 143 (2019).
pubmed: 31238873
pmcid: 6593500
doi: 10.1186/s12866-019-1500-0
Fitzpatrick, F., Doherty, A. & Lacey, G. Using artificial intelligence in infection prevention. Curr. Treat. Options Infect. Dis. 12, 135–144 (2020).
pubmed: 32218708
pmcid: 7095094
doi: 10.1007/s40506-020-00216-7
Wheeler, N. E., Gardner, P. P. & Barquist, L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genet. 14, e1007333 (2018).
pubmed: 29738521
pmcid: 5940178
doi: 10.1371/journal.pgen.1007333
Lupolova, N., Dallman, T. J., Holden, N. J. & Gally, D. L. Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli. Microb. Genom. 3, e000135 (2017).
pubmed: 29177093
pmcid: 5695212
Munck, N., Njage, P. M. K., Leekitcharoenphon, P., Litrup, E. & Hald, T. Application of whole-genome sequences and machine learning in source attribution of Salmonella typhimurium. Risk Anal. 40, 1693–1705 (2020).
pubmed: 32515055
pmcid: 7540586
doi: 10.1111/risa.13510
Tanui, C. K., Benefo, E. O., Karanth, S. & Pradhan, A. K. A machine learning model for food source attribution of Listeria monocytogenes. Pathogens 11, 691 (2022).
pubmed: 35745545
pmcid: 9230378
doi: 10.3390/pathogens11060691
Li, L.-G., Yin, X. & Zhang, T. Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. Microbiome 6, 93 (2018).
pubmed: 29793542
pmcid: 5966912
doi: 10.1186/s40168-018-0480-x
Vassallo, A., Kett, S., Purchase, D. & Marvasi, M. Antibiotic-resistant genes and bacteria as evolving contaminants of emerging concerns (e-CEC): is it time to include evolution in risk assessment? Antibiotics 10, 1066 (2021).
pubmed: 34572648
pmcid: 8469798
doi: 10.3390/antibiotics10091066
Ikhimiukor, O. O., Odih, E. E., Donado-Godoy, P. & Okeke, I. N. A bottom-up view of antimicrobial resistance transmission in developing countries. Nat. Microbiol. 7, 757–765 (2022).
pubmed: 35637328
doi: 10.1038/s41564-022-01124-w
O’Neill, J. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. Wellcome Collection https://wellcomecollection.org/works/rdpck35v/items (2014).
Flowers, P. Antimicrobial resistance: a biopsychosocial problem requiring innovative interdisciplinary and imaginative interventions. J. Infect. Prev. 19, 195–199 (2018).
pubmed: 30013625
pmcid: 6039911
doi: 10.1177/1757177418755308
Raboisson, D., Ferchiou, A., Sans, P., Lhermie, G. & Dervillé, M. The economics of antimicrobial resistance in veterinary medicine: optimizing societal benefits through mesoeconomic approaches from public and private perspectives. One Health 10, 100145 (2020).
pubmed: 33117866
pmcid: 7582218
doi: 10.1016/j.onehlt.2020.100145
George, A. Antimicrobial resistance (AMR) in the food chain: trade, One Health and Codex. Trop. Med. Infect. Dis. 4, 54 (2019).
pubmed: 30917589
pmcid: 6473514
doi: 10.3390/tropicalmed4010054
Queenan, K., Häsler, B. & Rushton, J. A One Health approach to antimicrobial resistance surveillance: is there a business case for it? Int. J. Antimicrob. Agents 48, 422–427 (2016).
pubmed: 27496533
doi: 10.1016/j.ijantimicag.2016.06.014
Collignon, P. J. & McEwen, S. A. One Health—its importance in helping to better control antimicrobial resistance. Trop. Med. Infect. Dis. 4, 22 (2019).
pubmed: 30700019
pmcid: 6473376
doi: 10.3390/tropicalmed4010022
McEwen, S. A. & Collignon, P. J. Antimicrobial resistance: a One Health perspective. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.arba-0009-2017 (2018).
doi: 10.1128/microbiolspec.arba-0009-2017
pubmed: 30003871
World Health Organization. The fight against antimicrobial resistance is closely linked to the sustainable development goals. https://apps.who.int/iris/handle/10665/337519 . (WHO, 2020).
Sartelli, M. et al. Antibiotic use in low and middle-income countries and the challenges of antimicrobial resistance in surgery. Antibiotics 9, 497 (2020).
pubmed: 32784880
pmcid: 7459633
doi: 10.3390/antibiotics9080497
Collignon, P., Athukorala, P., Senanayake, S. & Khan, F. Antimicrobial resistance: the major contribution of poor governance and corruption to this growing problem. PLoS ONE 10, e0116746 (2015).
pubmed: 25786027
pmcid: 4364737
doi: 10.1371/journal.pone.0116746
Harant, A. Assessing transparency and accountability of national action plans on antimicrobial resistance in 15 African countries. Antimicrob. Resist. Infect. Control 11, 15 (2022).
pubmed: 35073967
pmcid: 8785006
doi: 10.1186/s13756-021-01040-4
Musoke, D. et al. The role of environmental health in preventing antimicrobial resistance in low- and middle-income countries. Environ. Health Prev. Med. 26, 100 (2021).
pubmed: 34610785
pmcid: 8493696
doi: 10.1186/s12199-021-01023-2
Muloi, D. M. et al. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat. Microbiol. 7, 581–589 (2022). This WGS analysis of E. coli from humans, livestock and wildlife across households in Nairobi, Kenya shows evidence of interhost and interhousehold transmission, with implications for the emergence of zoonoses and the spread of AMR.
pubmed: 35288654
pmcid: 8975746
doi: 10.1038/s41564-022-01079-y
Horrigan, L., Lawrence, R. S. & Walker, P. How sustainable agriculture can address the environmental and human health harms of industrial agriculture. Environ. Health Perspect. 110, 445–456 (2002).
pubmed: 12003747
pmcid: 1240832
doi: 10.1289/ehp.02110445
Sanz-García, F. et al. Translating eco-evolutionary biology into therapy to tackle antibiotic resistance. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-023-00902-5 (2023).
doi: 10.1038/s41579-023-00902-5
pubmed: 37208461
David, S. et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat. Microbiol. 4, 1919–1929 (2019).
pubmed: 31358985
pmcid: 7244338
doi: 10.1038/s41564-019-0492-8
Denamur, E. et al. High frequency of mutator strains among human uropathogenic Escherichia coli isolates. J. Bacteriol. 184, 605–609 (2002).
pubmed: 11751844
pmcid: 139564
doi: 10.1128/JB.184.2.605-609.2002
Denamur, E. & Matic, I. Evolution of mutation rates in bacteria. Mol. Microbiol. 60, 820–827 (2006).
pubmed: 16677295
doi: 10.1111/j.1365-2958.2006.05150.x
Reeves, P. R. et al. Rates of mutation and host transmission for an Escherichia coli clone over 3 years. PLoS ONE 6, e26907 (2011).
pubmed: 22046404
pmcid: 3203180
doi: 10.1371/journal.pone.0026907
Duval, A., Opatowski, L. & Brisse, S. Defining genomic epidemiology thresholds for common-source bacterial outbreaks: a modelling study. Lancet Microbe 4, e349–e357 (2023).
pubmed: 37003286
pmcid: 10156608
doi: 10.1016/S2666-5247(22)00380-9
Thorpe, H. A. et al. A large-scale genomic snapshot of Klebsiella spp. isolates in northern Italy reveals limited transmission between clinical and non-clinical settings. Nat. Microbiol. 7, 2054–2067 (2022).
pubmed: 36411354
pmcid: 9712112
doi: 10.1038/s41564-022-01263-0
Rice, L. B. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J. Infect. Dis. 197, 1079–1081 (2008).
pubmed: 18419525
doi: 10.1086/533452
Rice, L. B. Progress and challenges in implementing the research on ESKAPE pathogens. Infect. Control. Hosp. Epidemiol. 31 (Suppl. 1), S7–S10 (2010).
pubmed: 20929376
doi: 10.1086/655995
Boucher, H. W. et al. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48, 1–12 (2009).
pubmed: 19035777
doi: 10.1086/595011
Pendleton, J. N., Gorman, S. P. & Gilmore, B. F. Clinical relevance of the ESKAPE pathogens. Expert. Rev. Anti Infect. Ther. 11, 297–308 (2013).
pubmed: 23458769
doi: 10.1586/eri.13.12
Diekema, D. J. et al. The microbiology of bloodstream infection: 20-year trends from the SENTRY antimicrobial surveillance program. Antimicrob. Agents Chemother. 63, e00355-19 (2019).
pubmed: 31010862
pmcid: 6591610
doi: 10.1128/AAC.00355-19
Kajihara, T., Yahara, K., Hirabayashi, A., Shibayama, K. & Sugai, M. Japan Nosocomial Infections Surveillance (JANIS): current status, international collaboration, and future directions for a comprehensive antimicrobial resistance surveillance system. Jpn. J. Infect. Dis. 74, 87–96 (2021).
pubmed: 32863357
doi: 10.7883/yoken.JJID.2020.499
Wyres, K. L. & Holt, K. E. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr. Opin. Microbiol. 45, 131–139 (2018). This paper presents data to support the contention that Klebsiella spp. as a genus may play a seminal role in capturing and spreading AMR genes from environmental microbial populations into the ESKAPE and other clinically important pathogens.
pubmed: 29723841
doi: 10.1016/j.mib.2018.04.004
von Wintersdorff, C. J. H. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).
O’Neal, L., Alvarez, D., Mendizábal-Cabrera, R., Ramay, B. M. & Graham, J. Community-acquired antimicrobial resistant Enterobacteriaceae in Central America: a One Health systematic review. Int. J. Environ. Res. Public Health 17, 7622 (2020).
pubmed: 33086731
pmcid: 7589814
doi: 10.3390/ijerph17207622
Campos-Madueno, E. I. et al. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones. J. Glob. Antimicrob. Resist. 28, 206–215 (2022).
pubmed: 35085791
doi: 10.1016/j.jgar.2022.01.016
D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).
pubmed: 21881561
doi: 10.1038/nature10388
Poirel, L. et al. Identification of FosA8, a plasmid-encoded fosfomycin resistance determinant from Escherichia coli, and its origin in Leclercia adecarboxylata. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.01403-19 (2019).
doi: 10.1128/aac.01403-19
pubmed: 31640981
pmcid: 6879240
Poirel, L., Rodriguez-Martinez, J.-M., Mammeri, H., Liard, A. & Nordmann, P. Origin of plasmid-mediated quinolone resistance determinant QnrA. Antimicrob. Agents Chemother. 49, 3523–3525 (2005).
pubmed: 16048974
pmcid: 1196254
doi: 10.1128/AAC.49.8.3523-3525.2005
Tacão, M., Araújo, S., Vendas, M., Alves, A. & Henriques, I. Shewanella species as the origin of bla
pubmed: 28666748
doi: 10.1016/j.ijantimicag.2017.05.014
Canton, R., Gonzalez-Alba, J. M. & Galán, J. C. CTX-M enzymes: origin and diffusion. Front. Microbiol. 3, 110 (2012).
pubmed: 22485109
pmcid: 3316993
doi: 10.3389/fmicb.2012.00110
Rodríguez, M. M. et al. Chromosome-encoded CTX-M-3 from Kluyvera ascorbata: a possible origin of plasmid-borne CTX-M-1-derived cefotaximases. Antimicrob. Agents Chemother. 48, 4895–4897 (2004).
pubmed: 15561876
pmcid: 529199
doi: 10.1128/AAC.48.12.4895-4897.2004
Sekizuka, T. et al. Complete sequencing of the blaNDM-1-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens. PLoS ONE 6, e25334 (2011).
pubmed: 21966500
pmcid: 3179503
doi: 10.1371/journal.pone.0025334
Wang, R. et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun. 9, 1179 (2018).
pubmed: 29563494
pmcid: 5862964
doi: 10.1038/s41467-018-03205-z
Castillo-Ramírez, S. Zoonotic Acinetobacter baumannii: the need for genomic epidemiology in a One Health context. Lancet Microbe 3, e895–e896 (2022).
pubmed: 36150399
pmcid: 9489090
doi: 10.1016/S2666-5247(22)00255-5
Prity, F. T. et al. The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate. Microb. Genom. 9, mgen001010 (2023).
pubmed: 37171842
pmcid: 10272872
Liu, C. M. et al. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health https://doi.org/10.1016/j.onehlt.2023.100518 (2023). This large, geographically matched, comparative genomic analysis of contemporaneous clinical and meat-source E. coli isolates identifies source-associated MGEs and estimates that approximately 8% of human extraintestinal E. coli infections are potentially attributable to foodborne zoonotic E. coli.
doi: 10.1016/j.onehlt.2023.100518
pubmed: 37638210
pmcid: 10288062
Matlock, W. et al. Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK. eLife 12, e85302 (2023). This pan-genome analysis of plasmid clusters in a geographically and temporally selected subset of isolates shows evidence of widespread plasmid sharing across species and niches and accessory cargo exchange.
pubmed: 36961866
doi: 10.7554/eLife.85302
Swarthout, J. M., Chan, E. M. G., Garcia, D., Nadimpalli, M. L. & Pickering, A. J. Human colonization with antibiotic-resistant bacteria from nonoccupational exposure to domesticated animals in low- and middle-income countries: a critical review. Environ. Sci. Technol. 56, 14875–14890 (2022).
pubmed: 35947446
doi: 10.1021/acs.est.2c01494
Price, L. B., Hungate, B. A., Koch, B. J., Davis, G. S. & Liu, C. M. Colonizing opportunistic pathogens (COPs): the beasts in all of us. PLoS Pathog. 13, e1006369 (2017). E. coli (ExPEC), K. pneumoniae and Streptococcus pneumoniae are important examples of colonizing opportunistic pathogens with a benign existence in the human body, but when conditions favour their transition to a pathogenic state, often in a different body site, they exact a horrendous toll on human health.
pubmed: 28796836
pmcid: 5552013
doi: 10.1371/journal.ppat.1006369
Castillo-Ramírez, S., Ghaly, T. & Gillings, M. Non-clinical settings—the understudied facet of antimicrobial drug resistance. Environ. Microbiol. 23, 7271–7274 (2021).
pubmed: 34773441
doi: 10.1111/1462-2920.15841
Montalbano Di Filippo, M. et al. Exploring the nature of interaction between shiga toxin producing Escherichia coli (STEC) and free-living amoeba—Acanthamoeba sp. Front. Cell. Infect. Microbiol. 12, 926127 (2022).
pubmed: 36159652
pmcid: 9504058
doi: 10.3389/fcimb.2022.926127
Loest, D. et al. Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework. Epidemiol. Infect. 150, e148 (2022).
pubmed: 35968840
pmcid: 9386791
doi: 10.1017/S0950268822001030
Zhang, Q. et al. Rapid increase in carbapenemase-producing Enterobacteriaceae in retail meat driven by the spread of the bla
pubmed: 31182541
pmcid: 6658802
doi: 10.1128/AAC.00573-19
Jamin, C. et al. Genetic analysis of plasmid-encoded mcr-1 resistance in Enterobacteriaceae derived from poultry meat in the Netherlands. JAC Antimicrob. Resist. 3, dlab156 (2021).
pubmed: 34806003
pmcid: 8597959
doi: 10.1093/jacamr/dlab156
Feng, J. et al. Characterization of carbapenem-resistant enterobacteriaceae cultured from retail meat products, patients, and porcine excrement in China. Front. Microbiol. 12, 743468 (2021).
pubmed: 35002997
pmcid: 8734966
doi: 10.3389/fmicb.2021.743468
Reid, C. J., Blau, K., Jechalke, S., Smalla, K. & Djordjevic, S. P. Whole genome sequencing of Escherichia coli from store-bought produce. Front. Microbiol. 10, 3050 (2020).
pubmed: 32063888
pmcid: 7000624
doi: 10.3389/fmicb.2019.03050
Igbinosa, E. O., Beshiru, A., Igbinosa, I. H., Cho, G.-S. & Franz, C. M. A. P. Multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Escherichia coli from farm produce and agricultural environments in Edo State, Nigeria. PLoS ONE 18, e0282835 (2023).
pubmed: 36897838
pmcid: 10004523
doi: 10.1371/journal.pone.0282835
Chelaghma, W. et al. Occurrence of extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables, an increasing human health concern in Algeria. Antibiotics 11, 988 (2022).
pubmed: 35892378
pmcid: 9332692
doi: 10.3390/antibiotics11080988
Manageiro, V., Jones-Dias, D., Ferreira, E. & Caniça, M. Plasmid-mediated colistin resistance (mcr-1) in Escherichia coli from non-imported fresh vegetables for human consumption in Portugal. Microorganisms 8, 429 (2020).
pubmed: 32197505
pmcid: 7143947
doi: 10.3390/microorganisms8030429
Teng, L. et al. A cross-sectional study of companion animal-derived multidrug-resistant Escherichia coli in Hangzhou, China. Microbiol. Spectr. 11, e02113–e02122 (2023).
pubmed: 36840575
pmcid: 10100847
doi: 10.1128/spectrum.02113-22
Marques, C. et al. Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J. Antimicrob. Chemother. 73, 377–384 (2018).
pubmed: 29136156
doi: 10.1093/jac/dkx401
Garcês, A. et al. Bacterial isolates from urinary tract infection in dogs and cats in Portugal, and their antibiotic susceptibility pattern: a retrospective study of 5 years (2017–2021). Antibiotics 11, 1520 (2022).
pubmed: 36358175
pmcid: 9686987
doi: 10.3390/antibiotics11111520
Sano, E. et al. One Health clones of multidrug-resistant Escherichia coli carried by synanthropic animals in Brazil. One Health 16, 100476 (2023).
pubmed: 36691392
doi: 10.1016/j.onehlt.2022.100476
Devnath, P., Karah, N., Graham, J. P., Rose, E. S. & Asaduzzaman, M. Evidence of antimicrobial resistance in bats and its planetary health impact for surveillance of zoonotic spillover events: a scoping review. Int. J. Environ. Res. Public Health 20, 243 (2023).
doi: 10.3390/ijerph20010243
Martín-Maldonado, B. et al. Urban birds as antimicrobial resistance sentinels: white storks showed higher multidrug-resistant Escherichia coli levels than seagulls in Central Spain. Animals 12, 2714 (2022).
pubmed: 36230455
pmcid: 9558531
doi: 10.3390/ani12192714
Torres, R. T. et al. A walk on the wild side: wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M β-lactamases. Environ. Pollut. 306, 119367 (2022).
pubmed: 35489528
doi: 10.1016/j.envpol.2022.119367
Martinson, J. N. V. et al. Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults. ISME J. 13, 2306–2318 (2019).
pubmed: 31089259
pmcid: 6776003
doi: 10.1038/s41396-019-0435-7
Martinson, J. N. V. & Walk, S. T. Escherichia coli residency in the gut of healthy human adults. EcoSal 9, ESP0003 (2020).
Yu, D., Ryu, K., Zhi, S., Otto, S. J. G. & Neumann, N. F. Naturalized Escherichia coli in wastewater and the co-evolution of bacterial resistance to water treatment and antibiotics. Front. Microbiol. 13, 810312 (2022).
pubmed: 35707173
pmcid: 9189398
doi: 10.3389/fmicb.2022.810312
Guragain, M., Brichta-Harhay, D. M., Bono, J. L. & Bosilevac, J. M. Locus of heat resistance (LHR) in meat-borne Escherichia coli: screening and genetic characterization. Appl. Environ. Microbiol. 87, e02343-20 (2021).
pubmed: 33483306
pmcid: 8091618
doi: 10.1128/AEM.02343-20
Marin, J. et al. The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France. Appl. Environ. Microbiol. 88, e00664-22 (2022).
pubmed: 35862685
pmcid: 9361829
doi: 10.1128/aem.00664-22
Massot, M. et al. Phylogenetic, virulence and antibiotic resistance characteristics of commensal strain populations of Escherichia coli from community subjects in the Paris area in 2010 and evolution over 30 years. Microbiology 162, 642–650 (2016).
pubmed: 26822436
doi: 10.1099/mic.0.000242
Flannery, D. D. et al. Antibiotic susceptibility of Escherichia coli among infants admitted to neonatal intensive care units across the US from 2009 to 2017. JAMA Pediatr. 175, 168–175 (2021).
pubmed: 33165599
doi: 10.1001/jamapediatrics.2020.4719
Cassini, A. et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect. Dis. 19, 56–66 (2019).
pubmed: 30409683
pmcid: 6300481
doi: 10.1016/S1473-3099(18)30605-4
Poolman, J. T. & Wacker, M. Extraintestinal pathogenic Escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field. J. Infect. Dis. 213, 6–13 (2016).
pubmed: 26333944
doi: 10.1093/infdis/jiv429
Weiner-Lastinger, L. M. et al. Antimicrobial-resistant pathogens associated with adult healthcare-associated infections: summary of data reported to the National Healthcare Safety Network, 2015–2017. Infect. Control. Hospital Epidemiol. 41, 1–18 (2020).
doi: 10.1017/ice.2019.296
Foxman, B. Urinary tract infection syndromes: occurrence, recurrence, bacteriology, risk factors, and disease burden. Infect. Dis. Clin. North Am. 28, 1–13 (2014).
pubmed: 24484571
doi: 10.1016/j.idc.2013.09.003
Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318–327 (2018).
pubmed: 29276051
doi: 10.1016/S1473-3099(17)30753-3
United Nations Environment Programme. Bracing for superbugs: strengthening environmental action in the One Health response to antimicrobial resistance https://www.unep.org/resources/superbugs/environmental-action (2023).
World Health Organization. WHO integrated global surveillance on ESBL-producing E. coli using a “One Health” approach: implementation and opportunities. (WHO, 2021).
Livermore, D. M. Defining an extended-spectrum β-lactamase. Clin. Microbiol. Infect. 14, 3–10 (2008).
pubmed: 18154524
doi: 10.1111/j.1469-0691.2007.01857.x
Livermore, D. M. & Hawkey, P. M. CTX-M: changing the face of ESBLs in the UK. J. Antimicrob. Chemother. 56, 451–454 (2005).
pubmed: 16006451
doi: 10.1093/jac/dki239
Ludden, C. et al. Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. Lancet Microbe 2, e472–e480 (2021).
pubmed: 34485958
pmcid: 8410606
doi: 10.1016/S2666-5247(21)00117-8
Manges, A. R. Escherichia coli causing bloodstream and other extraintestinal infections: tracking the next pandemic. Lancet Infect. Dis. 19, 1269–1270 (2019).
pubmed: 31653525
doi: 10.1016/S1473-3099(19)30538-9
Mills, E. G. et al. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network. Genome Med. 14, 147 (2022).
pubmed: 36585742
pmcid: 9801656
doi: 10.1186/s13073-022-01150-7
Stephens, C. M., Adams-Sapper, S., Sekhon, M., Johnson, J. R. & Riley, L. W. Genomic analysis of factors associated with low prevalence of antibiotic resistance in extraintestinal pathogenic Escherichia coli sequence type 95 strains. mSphere 2, e00390 (2017).
pubmed: 28405633
pmcid: 5381267
doi: 10.1128/mSphere.00390-16
Carrilero, L., Dunn, S. J., Moran, R. A., McNally, A. & Brockhurst, M. A. Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse Escherichia coli lineages. mSystems 8, e0071322 (2023).
pubmed: 36722946
doi: 10.1128/msystems.00713-22
Reid, C. J. et al. A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58. Nat. Commun. 13, 1–15 (2022). This report explores important concepts that underpin the emergence of a pathogenic lineage of E. coli with emphasis on the role played by the stable co-acquisition of key virulence-associated genes.
doi: 10.1038/s41467-022-28342-4
Li, L. et al. Genomic characterization of mcr-1-carrying foodborne Salmonella enterica serovar Typhimurium and identification of a transferable plasmid carrying mcr-1, bla
pubmed: 35847096
pmcid: 9277226
doi: 10.3389/fmicb.2022.903268
Macori, G. et al. Characterisation of early positive mcr-1 resistance gene and plasmidome in Escherichia coli pathogenic strains associated with variable phylogroups under colistin selection. Antibiotics 10, 1041 (2021).
pubmed: 34572623
pmcid: 8466100
doi: 10.3390/antibiotics10091041
Zhang, X. et al. Spread and molecular characteristics of enterobacteriaceae carrying fosA-like genes from farms in China. Microbiol. Spectr. 10, e005422 (2022).
Zhao, W.-H. & Hu, Z.-Q. Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria. Crit. Rev. Microbiol. 39, 79–101 (2013).
pubmed: 22697133
doi: 10.3109/1040841X.2012.691460
Du, P. et al. Novel IS26-mediated hybrid plasmid harbouring tet
pubmed: 32247809
doi: 10.1016/j.jgar.2020.03.018
He, D. et al. Emergence of a hybrid plasmid derived from IncN1-F33:A−:B− and mcr-1-bearing plasmids mediated by IS26. J. Antimicrob. Chemother. 74, 3184–3189 (2019).
pubmed: 31360994
doi: 10.1093/jac/dkz327
Vinué, L. et al. Plasmids and genes contributing to high-level quinolone resistance in Escherichia coli. Int. J. Antimicrob. Agents 56, 105987 (2020).
pubmed: 32330582
doi: 10.1016/j.ijantimicag.2020.105987
Porse, A., Schønning, K., Munck, C. & Sommer, M. O. A. Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts. Mol. Biol. Evol. 33, 2860–2873 (2016).
pubmed: 27501945
pmcid: 5062321
doi: 10.1093/molbev/msw163
Venturini, C., Beatson, S. A., Djordjevic, S. P. & Walker, M. J. Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid. FASEB J. 24, 1160–1166 (2010).
pubmed: 19917674
doi: 10.1096/fj.09-144972
Harmer, C. J. & Hall, R. M. IS26 cannot move alone. J. Antimicrob. Chemother. 76, 1428–1432 (2021).
pubmed: 33686401
doi: 10.1093/jac/dkab055
Dawes, F. E. et al. 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 (2010).
pubmed: 20856797
pmcid: 2939871
doi: 10.1371/journal.pone.0012754
Harmer, C. J. & Hall, R. M. An analysis of the IS6/IS26 family of insertion sequences: is it a single family? Microb. Genom. 5, e000291 (2019).
pubmed: 31486766
pmcid: 6807381
Tedijanto, C., Olesen, S. W., Grad, Y. H. & Lipsitch, M. Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. Proc. Natl Acad. Sci. USA 115, E11988–E11995 (2018).
pubmed: 30559213
pmcid: 6304942
doi: 10.1073/pnas.1810840115
Cummins, M. L. et al. Whole-genome sequence analysis of an extensively drug-resistant Salmonella enterica serovar Agona isolate from an Australian silver gull (Chroicocephalus novaehollandiae) reveals the acquisition of multidrug resistance plasmids. mSphere 5, e00743-20 (2020).
pubmed: 33239365
pmcid: 7690955
doi: 10.1128/mSphere.00743-20
Nyirabahizi, E. et al. Evaluation of Escherichia coli as an indicator for antimicrobial resistance in Salmonella recovered from the same food or animal ceca samples. Food Control. 115, 107280 (2020).
doi: 10.1016/j.foodcont.2020.107280
United Nations Environment Programme. Environmental dimensions of antimicrobial resistance: summary for policymakers. https://wedocs.unep.org/bitstream/handle/20.500.11822/38373/antimicrobial_R.pdf (2022).
Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A. & Collins, J. J. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130, 797–810 (2007).
pubmed: 17803904
doi: 10.1016/j.cell.2007.06.049
Miller, C. et al. SOS response induction by β-lactams and bacterial defense against antibiotic lethality. Science 305, 1629–1631 (2004).
pubmed: 15308764
doi: 10.1126/science.1101630
Shapiro, R. S. Antimicrobial-induced DNA damage and genomic instability in microbial pathogens. PLoS Pathog. 11, e1004678 (2015).
pubmed: 25811381
pmcid: 4374783
doi: 10.1371/journal.ppat.1004678
Cheng, Y.-Y. et al. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol. Syst. Biol. 19, e11406 (2023).
pubmed: 36714980
pmcid: 9996237
doi: 10.15252/msb.202211406
Fornelos, N., Browning, D. F. & Butala, M. The use and abuse of LexA by mobile genetic elements. Trends Microbiol. 24, 391–401 (2016).
pubmed: 26970840
doi: 10.1016/j.tim.2016.02.009
Baharoglu, Z., Bikard, D. & Mazel, D. Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genet. 6, e1001165 (2010).
pubmed: 20975940
pmcid: 2958807
doi: 10.1371/journal.pgen.1001165
Ginn, O. et al. Open waste canals as potential sources of antimicrobial resistance genes in aerosols in urban Kanpur, India. Am. J. Trop. Med. Hyg. 104, 1761–1767 (2021).
pubmed: 33684068
pmcid: 8103454
doi: 10.4269/ajtmh.20-1222
Karkman, A., Pärnänen, K. & Larsson, D. G. J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat. Commun. 10, 80 (2019).
pubmed: 30622259
pmcid: 6325112
doi: 10.1038/s41467-018-07992-3
Dolejska, M. & Papagiannitsis, C. C. Plasmid-mediated resistance is going wild. Plasmid 99, 99–111 (2018).
pubmed: 30243983
doi: 10.1016/j.plasmid.2018.09.010
Snaith, A. E. et al. The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microb. Genom. 9, 001000 (2023).
Rodríguez-Molina, D. et al. International travel as a risk factor for carriage of extended-spectrum β-lactamase-producing Escherichia coli in a large sample of European individuals—The AWARE Study. Int. J. Environ. Res. Public Health 19, 4758 (2022).
pubmed: 35457624
pmcid: 9029788
doi: 10.3390/ijerph19084758
Ginn, O. et al. Detection and quantification of enteric pathogens in aerosols near open wastewater canals in cities with poor sanitation. Environ. Sci. Technol. 55, 14758–14771 (2021). This study emphasizes that aerosols generated in densely populated regions with comparatively poor sanitation practices are under-recognized as a mechanism of transmission of ARGs and enteric pathogens.
pubmed: 34669386
doi: 10.1021/acs.est.1c05060
Xin, H. et al. Animal farms are hot spots for airborne antimicrobial resistance. Sci. Total Environ. 851, 158050 (2022).
pubmed: 35985594
doi: 10.1016/j.scitotenv.2022.158050
Lv, B. et al. Abundances and profiles of antibiotic resistance genes as well as co-occurrences with human bacterial pathogens in ship ballast tank sediments from a shipyard in Jiangsu Province, China. Ecotoxicol. Environ. Saf. 157, 169–175 (2018).
pubmed: 29621708
doi: 10.1016/j.ecoenv.2018.03.053
Lv, B. et al. Vessel transport of antibiotic resistance genes across oceans and its implications for ballast water management. Chemosphere 253, 126697 (2020).
pubmed: 32298915
doi: 10.1016/j.chemosphere.2020.126697
Elankumaran, P., Browning, G. F., Marenda, M. S., Reid, C. J. & Djordjevic, S. P. Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127. Curr. Res. Microb. Sci. 3, 100106 (2022).
pubmed: 35128493
pmcid: 8803956
Abdullahi, I. N. et al. Clonal relatedness of coagulase-positive staphylococci among healthy dogs and dog-owners in Spain. Detection of multidrug-resistant-MSSA-CC398 and novel linezolid-resistant-MRSA-CC5. Front. Microbiol. 14, 1121564 (2023).
pubmed: 36937268
pmcid: 10017961
doi: 10.3389/fmicb.2023.1121564
Yang, Q. E. et al. Environmental dissemination of mcr-1 positive Enterobacteriaceae by Chrysomya spp. (common blowfly): an increasing public health risk. Environ. Int. 122, 281–290 (2019). This study sheds light on the role of blow flies in disseminating clinically important ARGs, particularly in resource-poor environments.
pubmed: 30455105
doi: 10.1016/j.envint.2018.11.021
Tyrrell, C. et al. Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland. Sci. Total Environ. 886, 163926 (2023).
pubmed: 37156383
doi: 10.1016/j.scitotenv.2023.163926
Marutescu, L. G. et al. Insights into the impact of manure on the environmental antibiotic residues and resistance pool. Front. Microbiol. 13, 965132 (2022).
pubmed: 36187968
pmcid: 9522911
doi: 10.3389/fmicb.2022.965132
Klein, E. Y. et al. Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc. Natl Acad. Sci. USA 115, E3463–E3470 (2018).
pubmed: 29581252
pmcid: 5899442
doi: 10.1073/pnas.1717295115
Kuppusamy, S. et al. Veterinary antibiotics (VAs) contamination as a global agro-ecological issue: a critical view. Agric. Ecosyst. Environ. 257, 47–59 (2018).
doi: 10.1016/j.agee.2018.01.026
Ma, F., Xu, S., Tang, Z., Li, Z. & Zhang, L. Use of antimicrobials in food animals and impact of transmission of antimicrobial resistance on humans. Biosaf. Health 3, 32–38 (2021).
doi: 10.1016/j.bsheal.2020.09.004
Tiseo, K., Huber, L., Gilbert, M., Robinson, T. P. & Van Boeckel, T. P. Global trends in antimicrobial use in food animals from 2017 to 2030. Antibiotics 9, E918 (2020).
doi: 10.3390/antibiotics9120918
Van Boeckel, T. P. et al. Global trends in antimicrobial use in food animals. Proc. Natl Acad. Sci. USA 112, 5649–5654 (2015).
pubmed: 25792457
pmcid: 4426470
doi: 10.1073/pnas.1503141112
Kemper, N. Veterinary antibiotics in the aquatic and terrestrial environment. Ecol. Indic. 8, 1–13 (2008).
doi: 10.1016/j.ecolind.2007.06.002
Zhang, N. et al. Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils. Geoderma 382, 114760 (2021).
doi: 10.1016/j.geoderma.2020.114760
Berendes, D. M., Yang, P. J., Lai, A., Hu, D. & Brown, J. Estimation of global recoverable human and animal faecal biomass. Nat. Sustain. 1, 679–685 (2018). This study estimates the global production of human and animal faeces, emphasizing the increasing animal to human ratio with time (6:1 by 2050), and highlights the importance of managing the persistent threats to global public health particularly in LMICs as well as the opportunities for recovery of resources via circular economies, with implications for zoonosis, One Health and AMR.
doi: 10.1038/s41893-018-0167-0
Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).
pubmed: 31213707
pmcid: 7136171
doi: 10.1038/s41579-019-0222-5
MacFadden, D. R., McGough, S. F., Fisman, D., Santillana, M. & Brownstein, J. S. Antibiotic resistance increases with local temperature. Nat. Clim. Change 8, 510–514 (2018).
doi: 10.1038/s41558-018-0161-6
McGough, S. F., MacFadden, D. R., Hattab, M. W., Mølbak, K. & Santillana, M. Rates of increase of antibiotic resistance and ambient temperature in Europe: a cross-national analysis of 28 countries between 2000 and 2016. Eurosurveillance 25, 1900414 (2020).
pubmed: 33183408
pmcid: 7667635
doi: 10.2807/1560-7917.ES.2020.25.45.1900414
Walsh, T. R., Weeks, J., Livermore, D. M. & Toleman, M. A. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect. Dis. 11, 355–362 (2011).
pubmed: 21478057
doi: 10.1016/S1473-3099(11)70059-7
Reckien, D. & Aalst, M. K. van. in Climate Change 2022: Impacts, Adaptation and Vulnerability: Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Pörtner, H.O, Roberts, D.C, Tignor, M., Poloczanska, E.S., Mintenbeck, K., Alegría, A., Craig, M., Langsdorf, S., Löschke, S., Möller, V., Okem, A., Rama, B. (eds.), 3–33 (Cambridge Univ. Press, 2022).
Fouladkhah, A. C., Thompson, B. & Camp, J. S. The threat of antibiotic resistance in changing climate. Microorganisms 8, E748 (2020).
doi: 10.3390/microorganisms8050748
Delgado-Baquerizo, M. et al. The proportion of soil-borne pathogens increases with warming at the global scale. Nat. Clim. Chang. 10, 550–554 (2020).
doi: 10.1038/s41558-020-0759-3
Escobar, L. E. et al. A global map of suitability for coastal Vibrio cholerae under current and future climate conditions. Acta Trop. 149, 202–211 (2015).
pubmed: 26048558
doi: 10.1016/j.actatropica.2015.05.028
Mora, C. et al. Over half of known human pathogenic diseases can be aggravated by climate change. Nat. Clim. Chang. 12, 869–875 (2022).
pubmed: 35968032
pmcid: 9362357
doi: 10.1038/s41558-022-01426-1