1. Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper
- Author
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Paul Adrien, Maria Fookes, Nicholas R. Thomson, Jerome Ateudjieu, Jacques Boncy, Etienne Guenou, Matthew Siever, Stanislas Rebaudet, David A. Sack, Amanda K. Debes, Watipaso Kasambara, Angèle Bénard, Renaud Piarroux, The Wellcome Trust Sanger Institute [Cambridge], University of Buéa, Université de Dschang, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Assistance Publique - Hôpitaux de Marseille (APHM), Hôpital Européen [Fondation Ambroise Paré - Marseille], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne Université (SU), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Gestionnaire, Hal Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
- Subjects
Bacterial Diseases ,0301 basic medicine ,Molecular biology ,[SDV]Life Sciences [q-bio] ,RC955-962 ,Pathology and Laboratory Medicine ,medicine.disease_cause ,El Tor ,Genome ,0302 clinical medicine ,Filter Paper ,Cholera ,Arctic medicine. Tropical medicine ,Medicine and Health Sciences ,DNA extraction ,Vibrio cholerae ,Phylogeny ,Data Management ,Genetics ,biology ,Database and informatics methods ,Cholera toxin ,Sequence analysis ,1. No poverty ,Phylogenetic Analysis ,Genomics ,Bacterial Pathogens ,3. Good health ,Laboratory Equipment ,Phylogenetics ,[SDV] Life Sciences [q-bio] ,Infectious Diseases ,Medical Microbiology ,Engineering and Technology ,Pathogens ,Public aspects of medicine ,RA1-1270 ,Research Article ,Neglected Tropical Diseases ,Paper ,Computer and Information Sciences ,Bioinformatics ,030231 tropical medicine ,Equipment ,Biomolecular isolation ,Microbiology ,03 medical and health sciences ,Extraction techniques ,medicine ,Humans ,Evolutionary Systematics ,Microbial Pathogens ,DNA sequence analysis ,Vibrio ,Taxonomy ,Whole genome sequencing ,Evolutionary Biology ,Sequence Assembly Tools ,Bacteria ,Whole Genome Sequencing ,Organisms ,Public Health, Environmental and Occupational Health ,Biology and Life Sciences ,Computational Biology ,Outbreak ,Tropical Diseases ,Genome Analysis ,medicine.disease ,biology.organism_classification ,DNA isolation ,Research and analysis methods ,Molecular biology techniques ,030104 developmental biology ,13. Climate action ,Genome, Bacterial - Abstract
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 7th 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., Author summary Cholera affects more than 4 million people globally every year; people predominantly living in poverty or in resource-constrained conditions including political crises or natural disasters. Cholera’s typical presentation is characterized by rapid onset of acute watery diarrhea and vomiting which can progress from watery stool to shock in as little as four hours. Laboratory conditions needed for culture confirmation and strain preservation are rarely to never present in these affected areas. In fact, many cholera endemic areas in Sub-Saharan African are so remote that even treatment response alone is often challenging. Here we present the genomic analysis of DNA extracted from dried filter paper, which is a low-cost, low-tech and sustainable method. Previously this method has facilitated cholera confirmation by PCR, but we demonstrate that this method is also suitable for whole genome sequencing and subsequent strain characterization by presenting the analysis of samples from an outbreak in a remote area of Cameroon. This method will facilitate the understanding of the molecular epidemiology in cholera-prone areas, which were previously too challenging to attempt. It also introduces a method that can be used on a broader scale for diarrheal disease surveillance, including providing a window into co-infection and microbiome analyses.
- Published
- 2019