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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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Alarcón LV, Cipriotti PA, Monterubbianessi M, Perfumo C, Mateu E, Allepuz A. Network analysis of pig movements in Argentina: Identification of key farms in the spread of infectious diseases and their biosecurity levels. Transbound Emerg Dis 2019; 67:1152-1163. [PMID: 31785089 DOI: 10.1111/tbed.13441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022]
Abstract
This study uses network analysis to evaluate how swine movements in Argentina could contribute to disease spread. Movement data for the 2014-2017 period were obtained from Argentina's online livestock traceability registry and categorized as follows: animals of high genetic value sent to other farms, animals to or from markets, animals sent to finisher operations and slaughterhouse. A network analysis was carried out considering the first three movement types. First, descriptive, centrality and cohesion measures were calculated for each movement type and year. Next, to determine whether networks had a small-world topology, these were compared with the results from random Erdös-Rényi network simulations. Then, the basic reproductive number (R0 ) of the genetic network, the group of farms with higher potential for disease spread standing at the top of the production chain, was calculated to identify farms acting as super-spreaders. Finally, their external biosecurity scores were evaluated. The genetic network in Argentina presented a scale-free and small-world topology. Thus, we estimate that disease spread would be fast, preferably to highly connected nodes and with little chances of being contained. Throughout the study, 31 farms were identified as super-spreaders in the genetic network for all years, while other 55 were super-spreaders at least once, from an average of 1,613 farms per year. Interestingly, removal of less than 5% of higher degree and betweenness farms resulted in a >90% reduction of R0 indicating that few farms have a key role in disease spread. When biosecurity scores of the most relevant super-spreaders were examined, it was evident that many were at risk of introducing and disseminating new pathogens across the whole of Argentina's pig production network. These results highlight the usefulness of establishing targeted surveillance and intervention programmes, emphasizing the need for better biosecurity scores in Argentinean swine production units, especially in super-spreader farms.
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Affiliation(s)
- Laura V Alarcón
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain.,Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Pablo A Cipriotti
- Facultad de Agronomía - IFEVA, Universidad de Buenos Aires/CONICET, Buenos Aires, Argentina
| | - Mariela Monterubbianessi
- National Service for Health and AgriFood Quality (SENASA), Ministerio de Producción y Trabajo, Buenos Aires, Argentina
| | - Carlos Perfumo
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Enric Mateu
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
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Alarcón LV, Monterubbianesi M, Perelman S, Sanguinetti HR, Perfumo CJ, Mateu E, Allepuz A. Biosecurity assessment of Argentinian pig farms. Prev Vet Med 2019; 170:104637. [PMID: 31421498 DOI: 10.1016/j.prevetmed.2019.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 11/26/2022]
Abstract
The pig industry is growing very fast in Argentina with an increasing need for replacement animals, feedstuff and transportation of animals. One of the main competitive advantages of the Argentinian pig industry is its being free of most major pig diseases. Within this context, applying measures aimed to reduce the risk of introduction and spread of pathogens is critical. The aim of the present study was to assess the biosecurity of Argentinian pig farms. Two types of farms were assessed: firstly, all official suppliers of high-genetic-value (n = 110) and secondly, a sample from commercial farms (n = 192). Data on the external and internal biosecurity practices applied on the farms was collected with a questionnaire. Data was analysed using a correspondence analysis and a hierarchical clustering analysis, which allowed identification of types of farms with regard to the biosecurity measures applied. Key variables characterizing the clusters were identified through an indicator value analysis. In addition, the external biosecurity of the farms was evaluated by using risk assessment tools with respect to the potential introduction of porcine epidemic diarrhoea virus. Results made evident three clusters: the first one which, amongst other measures, applied several barriers to prevent the entry of people, trucks and other vehicles, and could be considered as a group of high biosecurity, and the two other groups which applied a lower number of external and internal biosecurity measures. The results of the risk assessment showed that the routes with the highest risk of disease introduction were: replacement animals, vehicles transporting feed or animals, and visitors. The assessment of the external biosecurity showed that most Argentinian farms were not prepared for the contingency of a pathogen such as porcine epidemic diarrhoea virus. Special efforts should be made in official suppliers of high-genetic-value farms with poor biosecurity scores since they are at the top of the pig production chain and can be key for the spread of diseases.
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Affiliation(s)
- L V Alarcón
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193, Bellaterra, Barcelona, Spain; Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118, La Plata, Buenos Aires, Laboratorio de Patología Especial Veterinaria, Argentina.
| | - M Monterubbianesi
- National Service for Health and AgriFood Quality, Av. Paseo Colón n°367, ACD1063, Buenos Aires, Argentina
| | - S Perelman
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martin, 4453 C1417DSE, Buenos Aires, Argentina
| | - H R Sanguinetti
- National Service for Health and AgriFood Quality, Av. Paseo Colón n°367, ACD1063, Buenos Aires, Argentina
| | - C J Perfumo
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118, La Plata, Buenos Aires, Laboratorio de Patología Especial Veterinaria, Argentina
| | - E Mateu
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193, Bellaterra, Barcelona, Spain; Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - A Allepuz
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193, Bellaterra, Barcelona, Spain; Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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