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Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico

  • Microbial Genetics, Genomics and Molecular Biology
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Abstract

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is increasingly common worldwide. While food animals are thought to contribute to the growing antimicrobial resistance (AMR) problem, limited data is documenting this relationship, especially in low and middle-income countries (LMIC). Herein, we aimed to assess the role of non-clinical NTS of bovine origin as reservoirs of AMR genes of human clinical significance. We evaluated the phenotypic and genotypic AMR profiles in a set of 44 bovine-associated NTS. For comparative purposes, we also included genotypic AMR data of additional isolates from Mexico (n = 1,067) that are publicly available. The most frequent AMR phenotypes in our isolates involved tetracycline (40/44), trimethoprim-sulfamethoxazole (26/44), chloramphenicol (19/44), ampicillin (18/44), streptomycin (16/44), and carbenicillin (13/44), while nearly 70% of the strains were MDR. These phenotypes were correlated with a widespread distribution of AMR genes (i.e. tetA, aadA, dfrA12, dfrA17, sul1, sul2, bla-TEM-1, blaCARB-2) against multiple antibiotic classes, with some of them contributed by plasmids and/or class-1 integrons. We observed different AMR genotypes for betalactams and tetracycline resistance, providing evidence of convergent evolution and adaptive AMR. The probability of MDR genotype occurrence was higher in meat-associated isolates than in those from other sources (odds ratio 11.2, 95% confidence interval 4.5–27.9, P < 0.0001). The study shows that beef cattle are a significant source of MDR NTS in Mexico, highlighting the role of animal production on the emergence and spread of MDR Salmonella in LMIC.

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Authors and Affiliations

  1. Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico

    Enrique Jesús Delgado-Suárez & María Salud Rubio-Lozano

  2. Tecnológico de Monterrey, School of Medicine and Health Sciences, Monterrey, Mexico

    Rocío Ortíz-López

  3. College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA

    Wondwossen A. Gebreyes

  4. Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA

    Marc W. Allard

  5. Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico

    Francisco Barona-Gómez

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  1. Enrique Jesús Delgado-Suárez
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  3. Wondwossen A. Gebreyes
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  6. María Salud Rubio-Lozano
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Correspondence to Enrique Jesús Delgado-Suárez.

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12275_2019_8421_MOESM3_ESM.xlsx

Supplementary data Table S2. Database of isolates from Mexico with AMR genotypes that were publicly available at NCBI as of July 24 2018

Supplementary data Table S3. Summary of genome assembly and annotation results

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Delgado-Suárez, E.J., Ortíz-López, R., Gebreyes, W.A. et al. Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico. J Microbiol. 57, 271–280 (2019). https://doi.org/10.1007/s12275-019-8421-3

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