Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1

Mahamud ur Rashid, Mathieu Almeida, Andrew S. Azman, Brianna R. Lindsay, David A. Sack, Rita R. Colwell, Anwar Huq, J. Glenn Morris, Munirul Alam, O. Colin Stine

Research output: Contribution to journalLetterpeer-review

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.

Original languageEnglish (US)
Article numberfnw116
Pages (from-to)1-6
Number of pages6
JournalFEMS microbiology letters
Volume363
Issue number12
DOIs
StatePublished - Jun 1 2016

Keywords

  • Cholera
  • Multilocus variable tandem-repeat analysis (MLVA)
  • Recombination
  • Vibrio cholerae
  • Whole genome sequencing (WGS)

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Genetics

Fingerprint Dive into the research topics of 'Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1'. Together they form a unique fingerprint.

Cite this