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.
Highlights
Vibrio cholerae causes cholera, a severe diarrheal disease, with hundreds of thousands of cases recorded annually in Africa and Asia (Ali et al 2015)
Vibrio cholerae isolates clustered in genetically related groups by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (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
Summary
A severe diarrheal disease, with hundreds of thousands of cases recorded annually in Africa and Asia (Ali et al 2015). Extensive genetic variation among cholera strains has been observed by multilocus variable-number tandem-repeat analysis (MLVA) (Kendall et al 2010). These repeats are short DNA sequence motifs that are repeated multiple times (2–25, with the number of repeats determining the allele number) at a specific locus. For V. cholerae, at least five tandem-repeat loci are highly polymorphic (Danin-Poleg et al 2007). MLVA of these loci has revealed a clustering of clinical isolates of V. cholerae from different geographic regions and different times of collection (Ghosh et al 2008; Stine et al 2008). Isolates comprising a single MLVA-CC are hypothesized to have arisen from a common ancestor, with isolates of two separate MLVA-CCs assumed to represent independent genetic lineages
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