Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar

ABSTRACT Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed...

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Autores principales:	Robert A. Kingsley, Sally Kay, Thomas Connor, Lars Barquist, Leanne Sait, Kathryn E. Holt, Karthi Sivaraman, Thomas Wileman, David Goulding, Simon Clare, Christine Hale, Aswin Seshasayee, Simon Harris, Nicholas R. Thomson, Paul Gardner, Wolfgang Rabsch, Paul Wigley, Tom Humphrey, Julian Parkhill, Gordon Dougan
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/4b06e14fee8e4516874cd9a84c370df9
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spelling	oai:doaj.org-article:4b06e14fee8e4516874cd9a84c370df92021-11-15T15:42:47ZGenome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar10.1128/mBio.00565-132150-7511https://doaj.org/article/4b06e14fee8e4516874cd9a84c370df92013-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00565-13https://doaj.org/toc/2150-7511ABSTRACT Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster within S. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 and S. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely related S. Typhimurium strains. We report a novel in silico approach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartate in vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility. IMPORTANCE Whereas Salmonella enterica serovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within a Salmonella serovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2) S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.Robert A. KingsleySally KayThomas ConnorLars BarquistLeanne SaitKathryn E. HoltKarthi SivaramanThomas WilemanDavid GouldingSimon ClareChristine HaleAswin SeshasayeeSimon HarrisNicholas R. ThomsonPaul GardnerWolfgang RabschPaul WigleyTom HumphreyJulian ParkhillGordon DouganAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 5 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Robert A. Kingsley Sally Kay Thomas Connor Lars Barquist Leanne Sait Kathryn E. Holt Karthi Sivaraman Thomas Wileman David Goulding Simon Clare Christine Hale Aswin Seshasayee Simon Harris Nicholas R. Thomson Paul Gardner Wolfgang Rabsch Paul Wigley Tom Humphrey Julian Parkhill Gordon Dougan Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
description	ABSTRACT Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster within S. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 and S. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely related S. Typhimurium strains. We report a novel in silico approach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartate in vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility. IMPORTANCE Whereas Salmonella enterica serovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within a Salmonella serovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2) S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.
format	article
author	Robert A. Kingsley Sally Kay Thomas Connor Lars Barquist Leanne Sait Kathryn E. Holt Karthi Sivaraman Thomas Wileman David Goulding Simon Clare Christine Hale Aswin Seshasayee Simon Harris Nicholas R. Thomson Paul Gardner Wolfgang Rabsch Paul Wigley Tom Humphrey Julian Parkhill Gordon Dougan
author_facet	Robert A. Kingsley Sally Kay Thomas Connor Lars Barquist Leanne Sait Kathryn E. Holt Karthi Sivaraman Thomas Wileman David Goulding Simon Clare Christine Hale Aswin Seshasayee Simon Harris Nicholas R. Thomson Paul Gardner Wolfgang Rabsch Paul Wigley Tom Humphrey Julian Parkhill Gordon Dougan
author_sort	Robert A. Kingsley
title	Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
title_short	Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
title_full	Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
title_fullStr	Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
title_full_unstemmed	Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar
title_sort	genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted <named-content content-type="genus-species">salmonella enterica</named-content> serovar typhimurium pathovar
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/4b06e14fee8e4516874cd9a84c370df9
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Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Typhimurium Pathovar

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