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Ceres K, Zehr JD, Murrell C, Millet JK, Sun Q, McQueary HC, Horton A, Cazer C, Sams K, Reboul G, Andreopoulos WB, Mitchell PK, Anderson R, Franklin-Guild R, Cronk BD, Stanhope BJ, Burbick CR, Wolking R, Peak L, Zhang Y, McDowall R, Krishnamurthy A, Slavic D, Sekhon PK, Tyson GH, Ceric O, Stanhope MJ, Goodman LB. Evolutionary genomic analyses of canine E. coli infections identify a relic capsular locus associated with resistance to multiple classes of antimicrobials. Appl Environ Microbiol 2024; 90:e0035424. [PMID: 39012166 DOI: 10.1128/aem.00354-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/08/2024] [Indexed: 07/17/2024] Open
Abstract
Infections caused by antimicrobial-resistant Escherichia coli are the leading cause of death attributed to antimicrobial resistance (AMR) worldwide, and the known AMR mechanisms involve a range of functional proteins. Here, we employed a pan-genome wide association study (GWAS) approach on over 1,000 E. coli isolates from sick dogs collected across the US and Canada and identified a strong statistical association (empirical P < 0.01) of AMR, involving a range of antibiotics to a group 1 capsular (CPS) gene cluster. This cluster included genes under relaxed selection pressure, had several loci missing, and had pseudogenes for other key loci. Furthermore, this cluster is widespread in E. coli and Klebsiella clinical isolates across multiple host species. Earlier studies demonstrated that the octameric CPS polysaccharide export protein Wza can transmit macrolide antibiotics into the E. coli periplasm. We suggest that the CPS in question, and its highly divergent Wza, functions as an antibiotic trap, preventing antimicrobial penetration. We also highlight the high diversity of lineages circulating in dogs across all regions studied, the overlap with human lineages, and regional prevalence of resistance to multiple antimicrobial classes. IMPORTANCE Much of the human genomic epidemiology data available for E. coli mechanism discovery studies has been heavily biased toward shiga-toxin producing strains from humans and livestock. E. coli occupies many niches and produces a wide variety of other significant pathotypes, including some implicated in chronic disease. We hypothesized that since dogs tend to share similar strains with their owners and are treated with similar antibiotics, their pathogenic isolates will harbor unexplored AMR mechanisms of importance to humans as well as animals. By comparing over 1,000 genomes with in vitro antimicrobial susceptibility data from sick dogs across the US and Canada, we identified a strong multidrug resistance association with an operon that appears to have once conferred a type 1 capsule production system.
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Affiliation(s)
| | | | | | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Qi Sun
- Cornell University, Ithaca, New York, USA
| | | | | | | | - Kelly Sams
- Cornell University, Ithaca, New York, USA
| | | | | | | | | | | | | | | | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Rebecca Wolking
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Laura Peak
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Yan Zhang
- Ohio Department of Agriculture Animal Disease Diagnostic Laboratory, Reynoldsburg, Ohio, USA
| | - Rebeccah McDowall
- University of Guelph, Animal Health Laboratory, Guelph, Ontario, Canada
| | | | - Durda Slavic
- University of Guelph, Animal Health Laboratory, Guelph, Ontario, Canada
| | | | - Gregory H Tyson
- US Food and Drug Administration, Veterinary Laboratory Investigation and Response Network, Laurel, Maryland, USA
| | - Olgica Ceric
- US Food and Drug Administration, Veterinary Laboratory Investigation and Response Network, Laurel, Maryland, USA
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Jewell M, Fuhrmeister ER, Roberts MC, Weissman SJ, Rabinowitz PM, Hawes SE. Associations between Isolation Source, Clonal Composition, and Antibiotic Resistance Genes in Escherichia coli Collected in Washington State, USA. Antibiotics (Basel) 2024; 13:103. [PMID: 38275332 PMCID: PMC10812632 DOI: 10.3390/antibiotics13010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem stemming from the use of antibiotics in humans, animals, and the environment. This study used whole-genome sequencing (WGS) of E. coli to explore patterns of AMR across sectors in Washington State, USA (WA). The WGS data from 1449 E. coli isolates were evaluated for isolation source (humans, animals, food, or the environment) and the presence of antibiotic resistance genes (ARGs). We performed sequence typing using PubMLST and used ResFinder to identify ARGs. We categorized isolates as being pan-susceptible, resistant, or multidrug-resistant (MDR), defined as carrying resistance genes for at least three or more antimicrobial drug classes. In total, 60% of isolates were pan-susceptible, while 18% were resistant, and 22% exhibited MDR. The proportion of resistant isolates varied significantly according to the source of the isolates (p < 0.001). The greatest resistance was detected in isolates from humans and then animals, while environmental isolates showed the least resistance. This study demonstrates the feasibility of comparing AMR across various sectors in Washington using WGS and a One Health approach. Such analysis can complement other efforts for AMR surveillance and potentially lead to targeted interventions and monitoring activities to reduce the overall burden of AMR.
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Affiliation(s)
- Mary Jewell
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA; (M.J.); (S.E.H.)
| | - Erica R. Fuhrmeister
- Department of Environmental and Occupational Health, School of Public Health, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA; (E.R.F.); (P.M.R.)
- Department of Civil and Environmental Engineering, University of Washington, 3760 E. Stevens Way NE, Seattle, WA 98195, USA
| | - Marilyn C. Roberts
- Department of Environmental and Occupational Health, School of Public Health, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA; (E.R.F.); (P.M.R.)
| | - Scott J. Weissman
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, WA 98105, USA;
| | - Peter M. Rabinowitz
- Department of Environmental and Occupational Health, School of Public Health, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA; (E.R.F.); (P.M.R.)
- Center for One Health Research, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA
| | - Stephen E. Hawes
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA; (M.J.); (S.E.H.)
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