The genomic approach of antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Lima, Peru

Raquel Hurtado; Debmalya Barh; Luís Cláudio Lima de Jesus; Marcus Vinicius Canário Viana; Sandeep Tiwari; Flávia Figueira Aburjaile; Dennis E Carhuaricra Huaman; Bertram Brenig; Lenin Maturrano Hernández; Vasco Azevedo

doi:10.1016/j.resmic.2023.104086

The genomic approach of antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Lima, Peru

Res Microbiol. 2023 Sep-Oct;174(7):104086. doi: 10.1016/j.resmic.2023.104086. Epub 2023 Jun 10.

Affiliations

¹ Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil. Electronic address: raquelgen1@gmail.com.
² Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil; Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, 721172, India. Electronic address: dr.barh@gmail.com.
³ Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil. Electronic address: luiislimma@gmail.com.
⁴ Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil. Electronic address: canarioviana@gmail.com.
⁵ Pós-graduação em Microbiologia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahía, Brazil; Programa de Pós-graduação em Imunologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahía, Brazil. Electronic address: sandip_sbtbi@yahoo.com.
⁶ Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: faburjaile@gmail.com.
⁷ SANIGEN, Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, San Borja, Lima, 15021, Peru. Electronic address: heraud04@gmail.com.
⁸ Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany. Electronic address: bbrenig@gwdg.de.
⁹ SANIGEN, Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, San Borja, Lima, 15021, Peru. Electronic address: amaturranoh@unmsm.edu.pe.
¹⁰ Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil. Electronic address: vascoariston@gmail.com.

PMID: 37307910
DOI: 10.1016/j.resmic.2023.104086

Abstract

Salmonella Typhimurium is an important agent of foodborne diseases. In Peru, the emergence of multidrug-resistant isolates of S. Typhimurium from the food chain could be linked to guinea pig farming as a potential reservoir and their uncontrolled antibiotic treatment against salmonellosis. In this study, we performed the sequencing, genomic diversity, and characterization of resistance elements transmitted by isolates from farm and meat guinea pigs. The genomic diversity and antimicrobial resistance of S. Typhimurium isolates were performed using nucleotide similarity, cgMLST, serotyping, phylogenomic analyses, and characterization of resistance plasmids. We found at least four populations of isolates from farm guinea pigs and four populations from meat guinea pigs without finding isolated transmission between both resources. Genotypic resistance to antibiotics was observed in at least 50% of the isolates. Among the farm guinea pig isolates, ten were found to be resistant to nalidixic acid, and two isolates exhibited multidrug resistance to aminoglycosides, tetracycline-fluoroquinolone (carrying strA-strB-tetA-tetB genes and gyrA S83F mutation), or trimethoprim-sulfonamide (carrying AaadA1-drfA15-sul1 genes). Additionally, two isolates from the meat source were resistant to fluoroquinolones (one of which had enrofloxacin resistance). The transmissible resistance plasmids with insertion sequences (IS) such as IncI-gamma-K1-ISE3-IS6, IncI1-I (alpha)-IS21-Tn10, and Col (pHAD28) were commonly found in isolates belonging to the HC100-9757 cluster from both guinea pigs and human hosts. Altogether, our work provides resistance determinants profiles and Salmonella sp. circulating lineages using WGS data that can promote better sanitary control and adequate antimicrobial prescription.

Keywords: Antimicrobial resistance; Foodborne disease; Genetic mobile elements; SNPs; Salmonellosis; Whole-genome sequencing.