Genomic analysis of the emergence of 20th century epidemic dysentery

BMC Genomics

Samuel I Miller⁵  Kyle R Hager³  Susana Matamouros³  Elizabeth H Sims-Day³  John M Kemner³  Anthony J Hager³  Kaisar Ali Talukder⁴  Yves Germani²  Matthew Radey³  Eli J Weiss³  Didier Hocquet¹  Hillary S Hayden³  Christine Fong³  Mitchell J Brittnacher³  Michael A Jacobs³  Laurence Rohmer³ 

[1] UMR6249 Chrono-Environnement, Université de Franche-Comté, Besançon, France;Institut Pasteur, Paris, France;Department of Microbiology, University of Washington, Seattle, WA, USA;International Centre for Diarrheal Disease Research, Dhaka, Bangladesh;Department of Medicine, University of Washington, Seattle, WA, USA

关键词: Pandemic;    Human carrier;    Genomic adaptation;    Antibiotic resistance;    Phylogeny;    Genome evolution;    Dysentery;    Shigella dysenteriae;   

Others  :  1217243
DOI  :  10.1186/1471-2164-15-355

 received in 2013-10-04, accepted in 2014-04-15,  发布年份 2014

【 摘 要 】

Background

Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid emergence of antibiotic resistant Sd1 strains. Sd1 is only detected in the context of human infections, and the circumstances under which epidemics emerge and regress remain unknown.

Results

Phylogenomic analyses of 56 isolates collected worldwide over the past 60 years indicate that the Sd1 clone responsible for the recent pandemics emerged at the turn of the 20^th century, and that the two world wars likely played a pivotal role for its dissemination. Several lineages remain ubiquitous and their phylogeny indicates several recent intercontinental transfers. Our comparative genomics analysis reveals that isolates responsible for separate outbreaks, though closely related to one another, have independently accumulated antibiotic resistance genes, suggesting that there is little or no selection to retain these genes in-between outbreaks. The genomes appear to be subjected to genetic drift that affects a number of functions currently used by diagnostic tools to identify Sd1, which could lead to the potential failure of such tools.

Conclusions

Taken together, the Sd1 population structure and pattern of evolution suggest a recent emergence and a possible human carrier state that could play an important role in the epidemic pattern of infections of this human-specific pathogen. This analysis highlights the important role of whole-genome sequencing in studying pathogens for which epidemiological or laboratory investigations are particularly challenging.

【 授权许可】

   
2014 Rohmer et al.; licensee BioMed Central Ltd.

【 图 表 】

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