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Global MLST of Salmonella Typhi revisited in post-genomic era: genetic conservation, population structure, and comparative genomics of rare sequence types

Yap, Kien-Pong, Ho, Wing S., Gan, Han Ming, Chai, Lay C. and Thong, Kwai L. 2016, Global MLST of Salmonella Typhi revisited in post-genomic era: genetic conservation, population structure, and comparative genomics of rare sequence types, Frontiers in microbiology, vol. 7, pp. 1-12, doi: 10.3389/fmicb.2016.00270.

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Title Global MLST of Salmonella Typhi revisited in post-genomic era: genetic conservation, population structure, and comparative genomics of rare sequence types
Author(s) Yap, Kien-Pong
Ho, Wing S.
Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Chai, Lay C.
Thong, Kwai L.
Journal name Frontiers in microbiology
Volume number 7
Article ID 270
Start page 1
End page 12
Total pages 12
Publisher Frontiers Research Foundation
Place of publication Lausanne, Switzerland
Publication date 2016-03-02
ISSN 1664-302X
Keyword(s) MLST
phylogenomic
Salmonella Typhi
sequence types
typhoid
whole genome sequencing
Summary Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.
Language eng
DOI 10.3389/fmicb.2016.00270
Field of Research 060408 Genomics
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2016, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30101936

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.