Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants

Branchu, Priscilla; Bawn, Matt; Kingsley, Robert A.

doi:10.1128/iai.00079-18

Cited by 107 publications

(120 citation statements)

References 106 publications

(185 reference statements)

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“…The invasiveness index metric is the fraction of decision trees in a random forest algorithm that vote for an invasive phenotype. The invasiveness index was significantly greater (p<0.05, Wilcoxon test) in clade-β than clade-α, consistent with the epidemiology and pathogenicity of the isolates located in these clades 3,4 .…”

Section: Resultssupporting

confidence: 71%

“…The topology of this phylogroup was similar to that of serotypes of S. enterica subspecies I 34, 35 , with internal branches radiating from a common ancestor, defined by the accumulation of hundreds of SNPs in S. Typhimurium compared with tens of thousands of SNPs defining lineages of representative strains of S. enterica subspecies I serotypes 4 .…”

Section: Discussionmentioning

confidence: 87%

“…The main Typhimurium phylogroup exhibited a star shape phylogeny with multiple deeply rooted branches emerging from a common ancestor, with diversification at the terminal branches in some cases, associated with clonal expansion of epidemic clonal groups. The topology of the this phylogroup was similar to that of serotypes of S. enterica subspecies I 34, 35 , with internal branches radiating from a common ancestor, defined by the accumulation of hundreds of SNPs in S. Typhimurium compared with tens of thousands of SNPs defining lineages of representative strains of S. enterica subspecies I serotypes 4 .…”

Section: Discussionmentioning

confidence: 91%

“…Therefore, the presence of HACS in virulence associated genes was almost exclusively associated with subclades containing strains with strong epidemiological evidence of host adaptation 4 . Despite the S. Typhimurium DT104 complex strain NCTC13348 (clade α15) exhibiting a high level of genome degradation that was uncharacteristic for α subclades and the broad host range epidemiology of the clonal group 45 , no virulence or multicellular behaviour genes were HACS 45 .…”

Section: Discussionmentioning

confidence: 99%

“…Although S. Typhimurium is considered to be a broad host range serotype, the epidemiological record of S. Typhimurium phage types identifies several S. Typhimurium pathovariants with distinct host range, pathogenicity and risk to food safety 3,4 . The pathovariant commonly associated with this serotype, has a broad host range and is associated with gastroenteritis in the human population.…”

mentioning

confidence: 99%

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

Bawn

Thilliez

Kirkwood

et al. 2019

Preprint

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Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide, and a model organism for host pathogen interactions. Genotypic variation of S. Typhimurium results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of α and β strains was reflected in distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage, awhile acquisition of large genetic islands (SGI-1 and 4) was restricted to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade α.Together, our data are consistent with the view that a broad host range common ancestor of S.Typhimurium diversified with clade α lineages remained largely associated with multiple domesticated animal species, while clade β spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.

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Section: Resultssupporting

confidence: 71%

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

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

Bawn

Thilliez

Kirkwood

et al. 2019

Preprint

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show abstract

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2020

Structure and Function of the Bacterial Genome

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Plant‐Made Vaccines Targeting Enteric Pathogens—Safe Alternatives for Vaccination in Developing Countries

Trujillo,

Angulo

2024

Biotech & Bioengineering

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Enteric diseases by pathogenic organisms are one of the leading causes of death worldwide, particularly in low‐income countries. Despite antibiotics, access to clean water and vaccination are the most economically affordable options to prevent those infections and their health consequences. Vaccines, such as those approved for rotavirus and cholera, have played a key role in preventing several enteric diseases. However, vaccines for other pathogens are still in clinical trials. Distribution and cost remain significant barriers to vaccine access in developing regions due to poor healthcare infrastructure, cold‐chain requirements, and high production costs. Plant‐made vaccines offer a promising alternative to address these challenges. Plants can be easily grown, lowering production costs, and can be administered in oral forms, potentially eliminating cold‐chain dependency. Although there are some promising prototypes of vaccines produced in plants, challenges remain, including yields and achieving sufficient immunogenicity. This review aims to describe common enteric pathogens and available vaccines, followed by a strategic summary of plant‐made vaccine development and a discussion of plant‐made enteric vaccine prototypes. Trends to overcome the key challenges for plant‐made vaccines are identified and placed in perspective for the development of affordable and effective vaccines for populations at the highest risk of enteric diseases.

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Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants

Abstract: Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S.

Cited by 107 publications

References 106 publications

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

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

References

Plant‐Made Vaccines Targeting Enteric Pathogens—Safe Alternatives for Vaccination in Developing Countries

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