The evolutionary history of Shigella flexneri serotype 6 in Asia | Microbiology Society

The evolutionary history of Shigella flexneri serotype 6 in Asia | Microbiology Society
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1887
Microbial Genomics
Volume 7, Issue 12
Research Article
Open Access
The evolutionary history of
Shigella flexneri
serotype 6 in Asia
Si-Nguyen T. Mai
1​,2​
Ladaporn Bodhidatta
3​
Paul Turner
4​,5​
Sonam Wangchuk
6​
Tuyen Ha Thanh
1​
Phat Voong Vinh
1​
Duy Thanh Pham
1​,5​
Maia A. Rabaa
1​,5​
Guy E. Thwaites
1​,5​
Nicholas R. Thomson
7​,8​
Stephen Baker
9​
and
Hao Chung The
1​
View Affiliations
Hide Affiliations
1​
Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
2​
Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
3​
Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
4​
Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
5​
Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
6​
Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
7​
The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
8​
London School of Hygiene and Tropical Medicine, Bloomsbury, London WC1E 7HT, UK
9​
Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
*Correspondence:
Hao Chung The,
[email protected]
Published:
14 December 2021
Abstract
Shigella flexneri
serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as
S. flexneri
Shigella flexneri
serotype 6 is phylogenetically distinct from other
S. flexneri
serotypes and more closely related to
S. boydii
. This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of
Shigella flexneri
serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian
Shigella flexneri
serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian
S. flexneri
serotype 6 could be traced back to an inferred common ancestor arising in the 18
th
century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian
S. flexneri
serotypes. Similar to other
S. flexneri
serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied
Shigella flexneri
serotype 6, providing a new piece in the puzzle of
Shigella
epidemiology and evolution.
Received:
11/08/2021
Accepted:
30/10/2021
Published Online:
14/12/2021
Keyword(s):
antimicrobial resistance
reductive evolution
Shigella evolution
Shigella flexneri serotype 6
Shigella genomic
and
Shigella phylogeny
Funding
This study was supported by the:
Wellcome Trust
(Award 215515/Z/19/Z)
Principal Award Recipient:
StephenBaker
Wellcome Trust
(Award 218726/Z/19/Z)
Principal Award Recipient:
HaoChung The
This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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The evolutionary history of Shigella flexneri serotype 6 in Asia
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First article published in
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Microbiology Society:
10.1099/mgen.0.000736
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