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

Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS - PLoS ONE (2015)

Bottom Line: The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain.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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.

ABSTRACT

Background: Non-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 finding: The 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/significance: This 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.

No MeSH data available.


Related in: MedlinePlus

Heatmap showing the distribution of 18 flagellar proteins.Another 40 ubiquitous proteins are not shown. Labels, colors and clustering are consistent with Fig 2 (no flagellar proteins were predicted to be plasmid associated).
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pone.0128773.g005: Heatmap showing the distribution of 18 flagellar proteins.Another 40 ubiquitous proteins are not shown. Labels, colors and clustering are consistent with Fig 2 (no flagellar proteins were predicted to be plasmid associated).

Mentions: Flagella confer mobility to bacterial. In general, all 25 isolates had a cluster profile similar to the selected reference Salmonella. In total, 58 flagella-associated proteins were found in the newly sequenced Salmonella genomes; forty of these, comprising most structural components of the flagellum, were found in all serovars (Fig 5). FlgE, a flagellar hook protein, was clustered in two separate groups, one found only in isolates of serovar Kentucky with a 22 amino-acid deletion, while the second group was present in all other isolates. However, a Heidelberg isolate harboured a gene encoding a truncated version of the protein with deletions at the N-terminus and the conserved C-terminus. Additionally, the same two isolates of serovar Enteritidis were carrying an identical in length but dissimilar in sequence (split into two clusters) copy of fliD and Phase-1 flagellin compared to all other 23 studied isolates (Fig 5). The structural flagellin gene fliC was present in all isolates of serovars Typhimurium and Kentucky (full length) and in all isolates of serovars Heidelberg, Hadar and Enteritidis (partial length).


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

Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS - PLoS ONE (2015)

Heatmap showing the distribution of 18 flagellar proteins.Another 40 ubiquitous proteins are not shown. Labels, colors and clustering are consistent with Fig 2 (no flagellar proteins were predicted to be plasmid associated).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4470630&req=5

pone.0128773.g005: Heatmap showing the distribution of 18 flagellar proteins.Another 40 ubiquitous proteins are not shown. Labels, colors and clustering are consistent with Fig 2 (no flagellar proteins were predicted to be plasmid associated).
Mentions: Flagella confer mobility to bacterial. In general, all 25 isolates had a cluster profile similar to the selected reference Salmonella. In total, 58 flagella-associated proteins were found in the newly sequenced Salmonella genomes; forty of these, comprising most structural components of the flagellum, were found in all serovars (Fig 5). FlgE, a flagellar hook protein, was clustered in two separate groups, one found only in isolates of serovar Kentucky with a 22 amino-acid deletion, while the second group was present in all other isolates. However, a Heidelberg isolate harboured a gene encoding a truncated version of the protein with deletions at the N-terminus and the conserved C-terminus. Additionally, the same two isolates of serovar Enteritidis were carrying an identical in length but dissimilar in sequence (split into two clusters) copy of fliD and Phase-1 flagellin compared to all other 23 studied isolates (Fig 5). The structural flagellin gene fliC was present in all isolates of serovars Typhimurium and Kentucky (full length) and in all isolates of serovars Heidelberg, Hadar and Enteritidis (partial length).

Bottom Line: The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain.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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.

ABSTRACT

Background: Non-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 finding: The 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/significance: This 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.

No MeSH data available.


Related in: MedlinePlus