title: The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.
abstract: BACKGROUND
  Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century.
  
  
  RESULTS
  Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters.
  
  
  CONCLUSIONS
  The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates.
authors: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
authors: Moataz
authors: M
authors: Abd El Ghany
authors: Department of Microbiology, Government Medical College Hospital (GMCH), Chandigarh, India.
authors: Jagadish
authors: J
authors: Chander
authors: The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors: Ankur
authors: A
authors: Mutreja
authors: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
authors: Mamoon
authors: M
authors: Rashid
authors: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia; Marie Bashir Institute for Infectious Diseases and Biosecurity and School of Public Health, University of Sydney, Sydney, Australia.
authors: Grant A
authors: GA
authors: Hill-Cawthorne
authors: Bioscience Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
authors: Shahjahan
authors: S
authors: Ali
authors: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
authors: Raeece
authors: R
authors: Naeem
authors: The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors: Nicholas R
authors: NR
authors: Thomson
authors: The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors: Gordon
authors: G
authors: Dougan
authors: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
authors: Arnab
authors: A
authors: Pain
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D002771:Cholera / Q000453:epidemiology / Q000382:microbiology; D005260:Female; D006801:Humans; D007194:India / Q000453:epidemiology; D007223:Infant; D008297:Male; D058889:Molecular Typing; D014734:Vibrio cholerae / Q000145:classification / Q000235:genetics; D055815:Young Adult