Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018.

MSphere
Lang YangHongbin Song

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. flexn...Continue Reading

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Datasets Mentioned

BETA
AE005674
PRJNA590276

Methods Mentioned

BETA
PCR

Software Mentioned

nucmer
SAMtools
MLST )
SPAdes
BEAST
TreeAnnotator
Tracer
Burrows Aligner ( BWA )
RAxML
LogCombiner

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