Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources

Daniel F M Monte; Matthew A Nethery; Rodolphe Barrangou; Mariza Landgraf; Paula J Fedorka-Cray

doi:10.1016/j.fm.2020.103601

Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources

Food Microbiol. 2021 Feb:93:103601. doi: 10.1016/j.fm.2020.103601. Epub 2020 Aug 4.

Authors

Daniel F M Monte¹, Matthew A Nethery², Rodolphe Barrangou², Mariza Landgraf³, Paula J Fedorka-Cray⁴

Affiliations

¹ Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil; Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA. Electronic address: monte_dfm@usp.br.
² Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
³ Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil.
⁴ Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA. Electronic address: pjcray@ncsu.edu.

PMID: 32912589
DOI: 10.1016/j.fm.2020.103601

Abstract

For decades, Salmonella Typhimurium and Salmonella Enteritidis have prevailed in several countries as agents of salmonellosis outbreaks. In Brazil, the largest exporter of poultry meat, relatively little attention has been paid to infrequent serovars. Here, we report the emergence and characterization of rare serovars isolated from food and related sources collected between 2014 and 2016 in Brazil. Twenty-two Salmonella enterica isolates were analyzed through the use of whole-genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats (CRISPR) genotyping. These isolates were classified into 10 infrequent serovars, including S. Abony, S. Isangi, S. Rochdale, S. Saphra, S. Orion, S. Ouakam, S. Grumpensis, S. Carrau, S. Abaetetuba, and S. Idikan. The presence of six antimicrobial resistance (AMR) genes, qnrB19, bla_CMY-2, tetA, aac(6')-Iaa, sul2 and fosA7, which encode resistance to quinolones, third-generation cephalosporin, tetracycline, aminoglycoside, sulfonamide and fosfomycin, respectively, were confirmed by WGS. All S. Isangi harbored qnrB19 with conserved genomic context across strains, while S. Abony harbored bla_CMY-2. Twelve (54.5%) strains displayed chromosomal mutations in parC (Thr57→Ser). Most serovars were classified as independent lineages, except S. Abony and S. Abaetetuba, which phylogenetically nested with Salmonella strains from different countries. CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. These findings add valuable information to the epidemiology of S. enterica in Brazil, where the emergency of antibiotic-resistant Salmonella continues to evolve.

Keywords: Antibiotic resistance; CRISPR; Phylogeny; Salmonella serovars; Whole genome sequencing.

MeSH terms

Anti-Bacterial Agents / pharmacology*
Brazil
Clustered Regularly Interspaced Short Palindromic Repeats
Drug Resistance, Multiple, Bacterial / genetics*
Food Microbiology*
Genome, Bacterial
Genotype*
Genotyping Techniques
Microbial Sensitivity Tests
Salmonella / classification
Salmonella / genetics
Salmonella / isolation & purification
Salmonella Food Poisoning
Salmonella enterica / classification
Salmonella enterica / drug effects
Salmonella enterica / genetics*
Salmonella enterica / isolation & purification*
Serogroup*
Serotyping
Whole Genome Sequencing

Substances

Anti-Bacterial Agents