Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. (February 2021)

• Record Type: Journal Article
• Authors: Monte, Daniel F.M.; Nethery, Matthew A.; Barrangou, Rodolphe; Landgraf, Mariza; Fedorka-Cray, Paula J.
• Is Part Of: Food microbiology. Volume 93(2021)
• Publication Date: 2021-02
• Subjects: Antibiotic resistance -- CRISPR -- Phylogeny -- Salmonella serovars -- Whole genome sequencing; Food Microbiology -- Periodicals; Aliments -- Microbiologie -- Périodiques; Food -- Microbiology; Periodicals; Food -- Microbiology -- Periodicals; Food contamination -- Periodicals; 664.001579
• DOI: 10.1016/j.fm.2020.103601
• Languages: English
• ISSNs: 0740-0020

Abstract

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. Highlights: WGS-CRISPR analysis reveal ten rare Salmonella serovars in food and related sources. Six clinically-relevant AMR genes were found in uncommon Salmonella serotypes. CRISPR arrays were highly conserved within Salmonella serovars. WGS-CRISPR genomic inspection provides high-resolution genotyping of Salmonella.