Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella

Gao, Ruimin; Huang, Hongsheng; Hamel, Jérémie; Levesque, Roger C.; Goodridge, Lawrence; Ogunremi, Dele

doi:10.3390/microorganisms10020369

Cited by 5 publications

(5 citation statements)

References 33 publications

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“…The roles of rfb genes, which were primarily classified in the survival/host persistence virulence category, are not as well investigated as the lpf operon but appear to be involved in the biosynthesis of the O-antigen and lipopolysaccharide structuring. A recent report suggests that the full complement of rfb genes leads to higher virulence in experimentally infected chickens [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

Fenske,

Pouzou,

Pouillot

et al. 2023

PLoS ONE

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The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward’s method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2–5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results show that S. enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.

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Section: Discussionmentioning

confidence: 99%

The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

Fenske,

Pouzou,

Pouillot

et al. 2023

PLoS ONE

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show abstract

“…The roles of rfb genes are not as well investigated as the lpf operon but appear to be involved in the biosynthesis of the O-antigen and lipopolysaccharide structuring. A recent report suggests that the full complement of rfb genes leads to higher virulence in experimentally infected chickens [54].…”

Section: Discussionmentioning

confidence: 99%

The genomic and epidemiological virulence patterns ofSalmonella entericaserovars in the United States

Fenske

Pouzou

Pouillot

et al. 2022

Preprint

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The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. Grouping Salmonella isolates and serovars by their public health risk can provide better Salmonella control targets along the food chain. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the virulence clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined. Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results demonstrate that S. enterica strains with the highest incidence of human infections share a common virulence repertoire. This work could be used in combination with foodborne surveillance information to best target serovars of public health concern.

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“…Indole can affect the expression of the AcrB efflux pump and mediate AR through the induction of oxidative stress pathways and phage shock response. Additionally, DSF-and indole-mediated QS have also been reported in S. enterica serovar Typhimurium and are known to play a fundamental role in virulence regulation and AR [10,14,[38][39][40][41][42].…”

Section: Salmonella Enterica Serovar Typhimurium Quorum Sensing Inter...mentioning

confidence: 99%

Polyphenols and CRISPR as Quorum Quenching Agents in Antibiotic-Resistant Foodborne Human Pathogens (Salmonella Typhimurium, Campylobacter jejuni and Escherichia coli 0157:H7)

Higuera-Ciapara,

Benitez-Vindiola,

Figueroa-Yañez

et al. 2024

Foods

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Antibiotic resistance in foodborne pathogens is an increasing threat to global human health. Among the most prevalent antibiotic-resistant bacteria are Salmonella enterica serovar Typhimurium, Campylobacter jejuni and E. coli 0157:H7. Control of these and other pathogens requires innovative approaches, i.e., discovering new molecules that will inactivate them, or render them less virulent without inducing resistance. Recently, several polyphenol molecules have been shown to possess such characteristics. Also, the use of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) approaches has recently been proposed for such purpose. This review summarizes the main findings regarding the application of both approaches to control the above-mentioned foodborne pathogens by relying on Quorum Sensing interference (Quorum Quenching) mechanisms and highlights the avenues needed for further research.

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Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella

Cited by 5 publications

References 33 publications

The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

The genomic and epidemiological virulence patterns ofSalmonella entericaserovars in the United States

Polyphenols and CRISPR as Quorum Quenching Agents in Antibiotic-Resistant Foodborne Human Pathogens (Salmonella Typhimurium, Campylobacter jejuni and Escherichia coli 0157:H7)

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