The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India
Publication Date
July 24, 2014
Journal
PLOS Neglected Tropical Diseases
Authors
Moataz Abd El Ghany, Jagadish Chander, Ankur Mutreja, Mamoon Rashid, et al
Volume
8
Issue
7
Pages
e2981
DOI
https://dx.plos.org/10.1371/journal.pntd.0002981
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0002981
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25058483
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109905
Europe PMC
http://europepmc.org/abstract/MED/25058483
Web of Science
000340551500030
Scopus
84905443301
Mendeley
http://www.mendeley.com/research/population-structure-vibrio-cholerae-chandigarh-region-northern-india
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Mendeley | Further Information

{"title"=>"The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India", "type"=>"journal", "authors"=>[{"first_name"=>"Moataz", "last_name"=>"Abd El Ghany", "scopus_author_id"=>"56310375900"}, {"first_name"=>"Jagadish", "last_name"=>"Chander", "scopus_author_id"=>"56310156200"}, {"first_name"=>"Ankur", "last_name"=>"Mutreja", "scopus_author_id"=>"35798676400"}, {"first_name"=>"Mamoon", "last_name"=>"Rashid", "scopus_author_id"=>"36724234000"}, {"first_name"=>"Grant A.", "last_name"=>"Hill-Cawthorne", "scopus_author_id"=>"55963500700"}, {"first_name"=>"Shahjahan", "last_name"=>"Ali", "scopus_author_id"=>"55316682800"}, {"first_name"=>"Raeece", "last_name"=>"Naeem", "scopus_author_id"=>"55578549000"}, {"first_name"=>"Nicholas R.", "last_name"=>"Thomson", "scopus_author_id"=>"7201917002"}, {"first_name"=>"Gordon", "last_name"=>"Dougan", "scopus_author_id"=>"7102366949"}, {"first_name"=>"Arnab", "last_name"=>"Pain", "scopus_author_id"=>"7004341451"}], "year"=>2014, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"sgr"=>"84905443301", "doi"=>"10.1371/journal.pntd.0002981", "pui"=>"373701298", "issn"=>"19352735", "pmid"=>"25058483", "scopus"=>"2-s2.0-84905443301"}, "id"=>"79275c5e-2f83-3e44-b846-dfb899475981", "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. METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.", "link"=>"http://www.mendeley.com/research/population-structure-vibrio-cholerae-chandigarh-region-northern-india", "reader_count"=>17, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Nursing and Health Professions"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>6, "Arts and Humanities"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1608728"], "description"=>"<p>The structures of the SXT of <i>V. cholerae</i> isolates from Chandigarh were compared to published isolates from Nepal and Haiti. Reads were mapped to ICE<i>Vch</i>Hai1 (accession number JN648379). Plot showing presence (blue) or absence (white) of the genes of ICEVchHai1. The antibiotic resistance genes within the SXT cluster are highlighted in red.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "genetics", "genomics", "variations", "sxt"], "article_id"=>1117352, "categories"=>["Biological Sciences"], "users"=>["Moataz Abd El Ghany", "Jagadish Chander", "Ankur Mutreja", "Mamoon Rashid", "Grant A. Hill-Cawthorne", "Shahjahan Ali", "Raeece Naeem", "Nicholas R. Thomson", "Gordon Dougan", "Arnab Pain"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002981.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_variations_in_SXT_among_V_cholerae_isolates_/1117352", "title"=>"Structural variations in SXT among <i>V. cholerae</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-24 04:00:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1608726"], "description"=>"<p>The <i>V. cholerae</i> El Tor reference N16961 was used as the root of the tree. The colour key corresponds to location, clade, MLST type, VSP-II variants, <i>ctxB</i> alleles, SXT variants and the MLVA type. The scale of the tree is given as substitutions per variable site.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "genetics", "genomics", "snp", "phylogeny", "chandigarh"], "article_id"=>1117350, "categories"=>["Biological Sciences"], "users"=>["Moataz Abd El Ghany", "Jagadish Chander", "Ankur Mutreja", "Mamoon Rashid", "Grant A. Hill-Cawthorne", "Shahjahan Ali", "Raeece Naeem", "Nicholas R. Thomson", "Gordon Dougan", "Arnab Pain"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002981.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_SNP_based_maximum_likelihood_phylogeny_of_the_Chandigarh_V_cholera_/1117350", "title"=>"A SNP based maximum likelihood phylogeny of the Chandigarh <i>V. cholera</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-24 04:00:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1608723"], "description"=>"<p>The locations of the clinics where the <i>V. cholerae</i> isolates were obtained are illustrated. Each district has been assigned a different colour (Chandigarh; orange, Yamuna Nagar; violet, Ambala; red, Patiala; blue and Morinda; green). Source of the map is ESRI ArcGIS geomapping software.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "genetics", "genomics", "chandigarh"], "article_id"=>1117347, "categories"=>["Biological Sciences"], "users"=>["Moataz Abd El Ghany", "Jagadish Chander", "Ankur Mutreja", "Mamoon Rashid", "Grant A. Hill-Cawthorne", "Shahjahan Ali", "Raeece Naeem", "Nicholas R. Thomson", "Gordon Dougan", "Arnab Pain"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002981.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Map_of_the_Chandigarh_region_of_India_/1117347", "title"=>"A Map of the Chandigarh region of India.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-24 04:00:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1608724"], "description"=>"<p>The phylogenetic tree shows the relation between the 2009 isolates from Chandigarh and the global collection of <i>V. cholera</i> genomes published by Mutreja et al <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002981#pntd.0002981-Mutreja1\" target=\"_blank\">[1]</a>. The positions of the isolates from Chandigarh are indicated with colour bars on the right representing the district they were isolated from (see <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002981#pntd-0002981-g001\" target=\"_blank\">Figure 1</a>). Other sub-clades that map close by on the tree to the Chandigarh isolates have been marked to highlight their global phylo-geographical context. The pre-seventh pandemic isolate M66 (2) was used as an out-group to root the tree. The scale given represents substitutions per variable site.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "genetics", "genomics", "snp", "phylogeny", "pandemic"], "article_id"=>1117348, "categories"=>["Biological Sciences"], "users"=>["Moataz Abd El Ghany", "Jagadish Chander", "Ankur Mutreja", "Mamoon Rashid", "Grant A. Hill-Cawthorne", "Shahjahan Ali", "Raeece Naeem", "Nicholas R. Thomson", "Gordon Dougan", "Arnab Pain"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002981.g002", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_SNP_based_maximum_likelihood_phylogeny_of_the_seventh_pandemic_V_cholerae_lineage_/1117348", "title"=>"A SNP based maximum likelihood phylogeny of the seventh pandemic <i>V. cholerae</i> lineage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-24 04:00:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1608729"], "description"=>"<p>A: resistance to Streptomycin, Sulfisoxazole/Sulfamethoxazole and Trimethoprim and susceptible to Tetracycline, Chloramphenicol, and Ciprofloxacin. B: Susceptible to all antibiotics used in the study except Trimethoprim. NK = not known, ND = not done.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "genetics", "genomics", "isolates"], "article_id"=>1117353, "categories"=>["Biological Sciences"], "users"=>["Moataz Abd El Ghany", "Jagadish Chander", "Ankur Mutreja", "Mamoon Rashid", "Grant A. Hill-Cawthorne", "Shahjahan Ali", "Raeece Naeem", "Nicholas R. Thomson", "Gordon Dougan", "Arnab Pain"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002981.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_V_cholerae_isolates_from_Chandigarh_/1117353", "title"=>"Characterization of <i>V. cholerae</i> isolates from Chandigarh.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-24 04:00:36"}

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