Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens

Abstract

BackgroundNon-typhoidal Salmonella enterica serovars, associated with different foods including poultry products, are important causes of bacterial gastroenteritis worldwide. The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain. The aim of this study was to compare the genomes of 25 S. enterica serovars isolated from broiler chicken farms to assess their intra- and inter-genetic variability, with a focus on virulence and antibiotic resistance characteristics.Methodology/Principal FindingThe genomes of 25 S. enterica isolates covering five serovars (ten Typhimurium including three monophasic 4,[5],12:i:, four Enteritidis, three Hadar, four Heidelberg and four Kentucky) were sequenced. Most serovars were clustered in strongly supported phylogenetic clades, except for isolates of serovar Enteritidis that were scattered throughout the tree. Plasmids of varying sizes were detected in several isolates independently of serovars. Genes associated with the IncF plasmid and the IncI1 plasmid were identified in twelve and four isolates, respectively, while genes associated with the IncQ plasmid were found in one isolate. The presence of numerous genes associated with Salmonella pathogenicity islands (SPIs) was also confirmed. Components of the type III and IV secretion systems (T3SS and T4SS) varied in different isolates, which could explain in part, differences of their pathogenicity in humans and/or persistence in broilers. Conserved clusters of genes in the T3SS were detected that could be used in designing effective strategies (diagnostic, vaccination or treatments) to combat Salmonella. Antibiotic resistance genes (CMY, aadA, ampC, florR, sul1, sulI, tetAB, and srtA) and class I integrons were detected in resistant isolates while all isolates carried multidrug efflux pump systems regardless of their antibiotic susceptibility profile.Conclusions/SignificanceThis study showed that the predominant Salmonella serovars in broiler chickens harbor genes encoding adhesins, flagellar proteins, T3SS, iron acquisition systems, and antibiotic and metal resistance genes that may explain their pathogenicity, colonization ability and persistence in chicken. The existence of mobile genetic elements indicates that isolates from a given serovar could acquire and transfer genetic material. Conserved genes in the T3SS and T4SS that we have identified are promising candidates for identification of diagnostic, antimicrobial or vaccine targets for the control of Salmonella in broiler chickens.

Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: A review

“…Chicken‐isolated S . Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky possess genes encoding adhesins, flagellar proteins, type III secretion systems (T3SS), iron acquisition systems, and antibiotic and metal resistance genes that may account for their colonization capability and persistence in chickens (Dhanani et al, ). However, haemagglutination, motility and virulence‐associated plasmids have been tested and found non‐essential in Salmonella gut colonization in chickens (Barrow et al, ).…”

“…Salmonella colonization in chickens is complex and not much is known regarding the pathogen-related determinants of gut colonization. Chicken-isolated S. Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky possess genes encoding adhesins, flagellar proteins, type III secretion systems (T3SS), iron acquisition systems, and antibiotic and metal resistance genes that may account for their colonization capability and persistence in chickens (Dhanani et al, 2015).…”

First Detection of a Fosfomycin Resistance Gene, fosA7 , in Salmonella enterica Serovar Heidelberg Isolated from Broiler Chickens

“…We previously described Salmonella enterica serovar Heidelberg isolates harboring a glutathione S-transferase gene cluster having 76 to 80% amino acid sequence similarity with fosA (15). Since such similarities do not translate into a function for an antimicrobial resistance phenotype, and due to the clinical relevance of fosfomycin, the objective of this study was to investigate the ability of this new gene to confer a fosfomycin resistance phenotype in S. enterica serovars.…”

AtypicalSalmonella entericaserovars in murine and human infection models: Is it time to reassess our approach to the study of salmonellosis?

“…Whole genome sequencing was used to facilitate a comparative analysis of all 10 atypical serovars to elucidate the genetic variation among them with particular focus on virulence determinants and SPI loci gene content 35,36 . Sequencing was performed using the Illumina MiSeq and Pacific Biosciences RS II sequencing platforms.…”