Open AccessWhole genome sequence of Vibrio cholerae directly from dried spotted filter paper
Author(s) -
Angèle Bénard,
Etienne Guenou,
María Fookes,
Jérôme Ateudjieu,
Watipaso Kasambara,
Matthew Siever,
Stanislas Rebaudet,
Jacques Boncy,
Paul Adrien,
Renaud Piarroux,
David A. Sack,
Nicholas R. Thomson,
Amanda K. Debes
Publication year - 2019
Publication title -
plos neglected tropical diseases
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.99
H-Index - 135
eISSN - 1935-2735
pISSN - 1935-2727
DOI - 10.1371/journal.pntd.0007330
Subject(s) - vibrio cholerae , cholera , cholera toxin , whole genome sequencing , biology , el tor , genome , outbreak , cholera vaccine , microbiology and biotechnology , phylogenetic tree , multilocus sequence typing , genetics , virology , gene , bacteria , genotype
Background Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately contribute new information to shape public policy response on cholera control and elimination. Methodology/Principal findings Whole genome sequencing (WGS) recovered close to a complete sequence of the V . cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V . cholerae culture isolates, both spotted on filter paper. The minimum concentration of V . cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7 th pandemic El Tor. Conclusions WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers. This provided valuable molecular epidemiological sequence information on V . cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V . cholerae strains causing outbreaks in cholera-endemic areas.