Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing

Abstract

Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.

Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

“…Nowadays, the plasmid-mediated quinolone resistance (PMQR) is an effective threat to the therapeutic use of quinolone (Rodríguez-Martínez et al, 2016). The plasmid quinolone resistance qnr genes include a set of genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrE, in which the latest has been circulating in South America since 2000 (Strahilevitz et al, 2009;Almeida et al, 2018;Panzenhagen et al, 2018a;Monte et al, 2019b;Soares et al, 2019).…”

“…This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. Several national studies have focused on analyzing the phenotypic antimicrobial resistance in Salmonella ( Dias de Oliveira et al, 2005 ; Campioni et al, 2012 ; Mattiello et al, 2015 ; Zishiri et al, 2016 ; Rodrigues et al, 2020 ), but few recent studies have focused on whole-genome sequence (WGS) analyses of resistant genes ( Almeida et al, 2018 ; Monte et al, 2019a ). Moreover, the current global trend is to use whole-genome sequencing in outbreak detection and surveillance routine of pathogenic bacteria ( Didelot et al, 2012 ; Wilson, 2012 ; Leekitcharoenphon et al, 2014 ).…”

Genomic comparison of diverse Salmonella serovars isolated from swine

“…Chloramphenicol was used to treat MDR infections in human and animals [55][56][57]. The sulfisoxazole resistance genes sul1 (located within 3'-conserved segment [3'-CS] of class 1 integrons) and sul2 (associated with small multicopy plasmids or large transmissible multiresistance plasmids) are the most frequently found genes for sulfonamide resistance among sulfonamide-resistant isolates from food animals and humans, whereas sul3 is detected in various large Salmonella plasmids [58,59].…”

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

“…The sequence alignment of variant sites was used to generate a maximum likelihood phylogenetic tree with RAxML using the GTRCAT model implemented with an extended majority-rule consensus tree criterion [102]. The genome sequence of S. Heidelberg (NC_011083.1) was used as an outgroup in the analysis to identify the root and common ancestor of all S. Typhimurium strains as a previous study has indicated both Heidelberg and Saintpaul serovars to be appropriate [103]. HierBaps (hierarchical Bayesian analysis of Population Structure) [16] was used to estimate population structure using three nested levels of molecular variation and 10 independent runs of the optimization algorithm as reported previously [104].…”