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Mounsey O, Marchetti L, Parada J, Alarcón LV, Aliverti F, Avison MB, Ayala CS, Ballesteros C, Best CM, Bettridge J, Buchamer A, Buldain D, Carranza A, Corti Isgro M, Demeritt D, Escobar MP, Gortari Castillo L, Jaureguiberry M, Lucas MF, Madoz LV, Marconi MJ, Moiso N, Nievas HD, Ramirez Montes De Oca MA, Reding C, Reyher KK, Vass L, Williams S, Giraudo J, De La Sota RL, Mestorino N, Moredo FA, Pellegrino M. Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms. Appl Environ Microbiol 2024; 90:e0179123. [PMID: 38334306 PMCID: PMC10952494 DOI: 10.1128/aem.01791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the β-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region. IMPORTANCE Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.
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Affiliation(s)
- Oliver Mounsey
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Laura Marchetti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Julián Parada
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura V. Alarcón
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Florencia Aliverti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matthew B. Avison
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Carlos S. Ayala
- University of Bristol Veterinary School, Langford, United Kingdom
| | | | - Caroline M. Best
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Judy Bettridge
- University of Bristol Veterinary School, Langford, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham, United Kingdom
| | - Andrea Buchamer
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Daniel Buldain
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alicia Carranza
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Maite Corti Isgro
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - David Demeritt
- Department of Geography, King’s College London, London, United Kingdom
| | | | - Lihuel Gortari Castillo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Jaureguiberry
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mariana F. Lucas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Universidad del Salvador, Facultad de Ciencias Agrarias y Veterinarias, Pilar, Argentina
| | - L. Vanina Madoz
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María José Marconi
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolás Moiso
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Hernán D. Nievas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | | | - Carlos Reding
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | | | - Lucy Vass
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Sara Williams
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - José Giraudo
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - R. Luzbel De La Sota
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nora Mestorino
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Fabiana A. Moredo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matías Pellegrino
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Cuarto, Facultad de Ciencias Exactas, Físico Químicas y Naturales, Río Cuarto, Argentina
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