Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogene...

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Autores principales:	Lang Yang, Bing Lü, Quanyi Wang, Kaiying Wang, Yanfeng Lin, Chaojie Yang, Shaofu Qiu, Peng Li, Hongbin Song
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	S. flexneri whole-genome sequencing MDR determinants population dynamics clonal evolution Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/fbcb008b83694577b2a04a4d9ed288f0
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spelling	oai:doaj.org-article:fbcb008b83694577b2a04a4d9ed288f02021-11-15T15:30:50ZPhylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 201810.1128/mSphere.00161-202379-5042https://doaj.org/article/fbcb008b83694577b2a04a4d9ed288f02020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00161-20https://doaj.org/toc/2379-5042ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.Lang YangBing LüQuanyi WangKaiying WangYanfeng LinChaojie YangShaofu QiuPeng LiHongbin SongAmerican Society for MicrobiologyarticleS. flexneriwhole-genome sequencingMDR determinantspopulation dynamicsclonal evolutionMicrobiologyQR1-502ENmSphere, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	S. flexneri whole-genome sequencing MDR determinants population dynamics clonal evolution Microbiology QR1-502
spellingShingle	S. flexneri whole-genome sequencing MDR determinants population dynamics clonal evolution Microbiology QR1-502 Lang Yang Bing Lü Quanyi Wang Kaiying Wang Yanfeng Lin Chaojie Yang Shaofu Qiu Peng Li Hongbin Song Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
description	ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.
format	article
author	Lang Yang Bing Lü Quanyi Wang Kaiying Wang Yanfeng Lin Chaojie Yang Shaofu Qiu Peng Li Hongbin Song
author_facet	Lang Yang Bing Lü Quanyi Wang Kaiying Wang Yanfeng Lin Chaojie Yang Shaofu Qiu Peng Li Hongbin Song
author_sort	Lang Yang
title	Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
title_short	Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
title_full	Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
title_fullStr	Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
title_full_unstemmed	Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018
title_sort	phylogenetic characterization reveals prevalent <named-content content-type="genus-species">shigella flexneri</named-content> st100 clone in beijing, china, 2005 to 2018
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/fbcb008b83694577b2a04a4d9ed288f0
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Phylogenetic Characterization Reveals Prevalent <named-content content-type="genus-species">Shigella flexneri</named-content> ST100 Clone in Beijing, China, 2005 to 2018

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