Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper

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 facil...

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Bibliographic Details
Published in:	PLoS neglected tropical diseases Vol. 13; no. 5; p. e0007330
Main Authors:	Bénard, Angèle H M, Guenou, Etienne, Fookes, Maria, Ateudjieu, Jerome, Kasambara, Watipaso, Siever, Matthew, Rebaudet, Stanislas, Boncy, Jacques, Adrien, Paul, Piarroux, Renaud, Sack, David A, Thomson, Nicholas, Debes, Amanda K
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 01-05-2019 Public Library of Science (PLoS)
Subjects:	Biology and Life Sciences Cholera Cholera - microbiology Cholera toxin Computer and Information Sciences Culture Death Deoxyribonucleic acid Diarrhea DNA DNA sequencing Engineering and Technology Enrichment Epidemiology Evolution Filter paper Gene mapping Gene sequencing Genes Genetic aspects Genome, Bacterial Genomes Genomics Genotypes Global health Health aspects Health care facilities Humans Identification Identification and classification Infections Innovations Internet Intestinal flora Intestinal microflora Laboratories Mapping Medicine and Health Sciences Microbiomes Molecular diagnostic techniques Nucleotide sequence Outbreaks Pandemics Pathogenic microorganisms Pathogens Peptones Phylogeny Public health Public health administration Public policy Research and analysis methods Sequencing Strains Tolls Toxins Tropical diseases Vibrio cholerae Vibrio cholerae - classification Vibrio cholerae - genetics Vibrio cholerae - isolation & purification Water purification Waterborne diseases Whole Genome Sequencing - instrumentation Whole Genome Sequencing - methods World health United Kingdom Haiti Cameroon United Kingdom > UK United States > US Africa France Maryland Baltimore Maryland
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Summary:	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. 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 7th pandemic El Tor. 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.
Bibliography:	new_version ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 The authors have declared that no competing interests exist.
ISSN:	1935-2735 1935-2727 1935-2735
DOI:	10.1371/journal.pntd.0007330