title: Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1.
abstract: Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10(-6)) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.
authors.affiliation: School of Medicine, University of Maryland, Baltimore, MD 21201, USA Department of Microbiology, International Centre for Diarrheal Disease Research, Mohakhali, 1212 Dhaka, Bangladesh.
authors.forename: Mahamud-Ur
authors.initials: MU
authors.lastname: Rashid
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, Paint Branch Road, College Park, MD 20742, USA.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Almeida
authors.affiliation: Department of International Health, Johns Hopkins Bloomberg School of Public Health, North Wolfe Street, Baltimore, MD 21205, USA.
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Azman
authors.affiliation: School of Medicine, University of Maryland, Baltimore, MD 21201, USA Merck & Co., Philadelphia, PA 19454, USA.
authors.forename: Brianna R
authors.initials: BR
authors.lastname: Lindsay
authors.affiliation: Department of International Health, Johns Hopkins Bloomberg School of Public Health, North Wolfe Street, Baltimore, MD 21205, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Sack
authors.affiliation: Maryland Pathogen Research Institute, College of Chemical and Life Sciences, University of Maryland, College Park, MD 20742, USA.
authors.forename: Rita R
authors.initials: RR
authors.lastname: Colwell
authors.affiliation: Maryland Pathogen Research Institute, College of Chemical and Life Sciences, University of Maryland, College Park, MD 20742, USA.
authors.forename: Anwar
authors.initials: A
authors.lastname: Huq
authors.affiliation: Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32610, USA.
authors.forename: J Glenn
authors.initials: JG
authors.lastname: Morris
authors.affiliation: Department of Microbiology, International Centre for Diarrheal Disease Research, Mohakhali, 1212 Dhaka, Bangladesh.
authors.forename: Munirul
authors.initials: M
authors.lastname: Alam
authors.affiliation: School of Medicine, University of Maryland, Baltimore, MD 21201, USA ostin001@umaryland.edu.
authors.forename: O Colin
authors.initials: OC
authors.lastname: Stine
mesh_terms: D002771:Cholera / Q000382:microbiology / Q000635:transmission; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018598:Minisatellite Repeats; D058889:Molecular Typing / Q000379:methods*; D011995:Recombination, Genetic; D014734:Vibrio cholerae / Q000145:classification / Q000235:genetics*; D041241:Vibrio cholerae O1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification
keywords: Vibrio cholerae; cholera; multilocus variable tandem-repeat analysis (MLVA); recombination; whole genome sequencing (WGS)