Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates
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{"title"=>"Relationship between distinct African Cholera epidemics revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates", "type"=>"journal", "authors"=>[{"first_name"=>"Sandra", "last_name"=>"Moore", "scopus_author_id"=>"55966058100"}, {"first_name"=>"Berthe", "last_name"=>"Miwanda", "scopus_author_id"=>"55221795800"}, {"first_name"=>"Adodo Yao", "last_name"=>"Sadji", "scopus_author_id"=>"56707378500"}, {"first_name"=>"Hélène", "last_name"=>"Thefenne", "scopus_author_id"=>"55941527400"}, {"first_name"=>"Fakhri", "last_name"=>"Jeddi", "scopus_author_id"=>"26655700100"}, {"first_name"=>"Stanislas", "last_name"=>"Rebaudet", "scopus_author_id"=>"21741331400"}, {"first_name"=>"Hilde", "last_name"=>"de Boeck", "scopus_author_id"=>"55221874000"}, {"first_name"=>"Bawimodom", "last_name"=>"Bidjada", "scopus_author_id"=>"55584548000"}, {"first_name"=>"Jean Jacques", "last_name"=>"Depina", "scopus_author_id"=>"7801472796"}, {"first_name"=>"Didier", "last_name"=>"Bompangue", "scopus_author_id"=>"24376471500"}, {"first_name"=>"Aaron Aruna", "last_name"=>"Abedi", "scopus_author_id"=>"55891712000"}, {"first_name"=>"Lamine", "last_name"=>"Koivogui", "scopus_author_id"=>"18233653300"}, {"first_name"=>"Sakoba", "last_name"=>"Keita", "scopus_author_id"=>"56237053700"}, {"first_name"=>"Eric", "last_name"=>"Garnotel", "scopus_author_id"=>"6602778922"}, {"first_name"=>"Pierre Denis", "last_name"=>"Plisnier", "scopus_author_id"=>"6602740627"}, {"first_name"=>"Raymond", "last_name"=>"Ruimy", "scopus_author_id"=>"7003423362"}, {"first_name"=>"Nicholas", "last_name"=>"Thomson", "scopus_author_id"=>"7201917002"}, {"first_name"=>"Jean Jacques", "last_name"=>"Muyembe", "scopus_author_id"=>"16234181300"}, {"first_name"=>"Renaud", "last_name"=>"Piarroux", "scopus_author_id"=>"7003681059"}], "year"=>2015, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"issn"=>"19352735", "pui"=>"605059926", "sgr"=>"84934774695", "scopus"=>"2-s2.0-84934774695", "pmid"=>"26110870", "doi"=>"10.1371/journal.pntd.0003817", "isbn"=>"1935-2727"}, "id"=>"6cc17c38-23e2-36f1-b0ea-97ecf4794942", "abstract"=>"BACKGROUND Since cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa. METHODOLOGY/PRINCIPAL FINDINGS In this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 Vibrio cholerae isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these Vibrio cholerae populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates. CONCLUSIONS/SIGNIFICANCE To effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing Vibrio cholerae isolates.", "link"=>"http://www.mendeley.com/research/relationship-between-distinct-african-cholera-epidemics-revealed-via-mlva-haplotyping-337-vibrio-cho", "reader_count"=>37, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>11, "Student > Bachelor"=>2, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>11, "Student > Bachelor"=>2, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Environmental Science"=>1, "Nursing and Health Professions"=>5, "Mathematics"=>1, "Medicine and Dentistry"=>13, "Agricultural and Biological Sciences"=>7, "Business, Management and Accounting"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>13}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>5}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2149149"], "description"=>"<p>Each MLVA type is represented by a node, and the size of the nodes reflects the number of isolates with the indicated MLVA type. The relationships between isolate MLVA types are indicated by the type of connecting segments and the length of the segment between nodes. The solid lines indicate the most likely SLV, and the dashed lines represent DLV. The distance between the nodes represents the number of varying VNTRs. The colors reflect the distinct country and period of isolate origin (grouped by epidemic populations). Pie charts were used to indicate the distribution of strains isolated from different time periods or countries displaying identical an MLVA type.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463885, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.g002", "stats"=>{"downloads"=>5, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Minimum_Spanning_Tree_based_on_the_MLVA_types_of_337_V_cholerae_isolates_derived_from_several_recent_African_epidemics_/1463885", "title"=>"Minimum Spanning Tree based on the MLVA types of 337 <i>V</i>. <i>cholerae</i> isolates derived from several recent African epidemics.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149148"], "description"=>"<p>Upper panel: the four countries from which <i>V</i>. <i>cholerae</i> isolates were collected are indicated in different colors on the map of Africa (i.e., Guinea, green; Togo, red; Democratic Republic of the Congo (DRC), violet and Zambia: blue). Ghana and Nigeria are also labeled. Lower panel: detailed maps of Guinea and the DRC are shown. Lower right: DRC; the cities (red squares) and provinces mentioned are indicated on the map. The Congo River and Lake Tanganyika are also shown (in blue). Lower left: Guinea; the capital, Conakry, and Kaback Island are indicated along the Atlantic coast.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463884, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.g001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_African_countries_implicated_in_study_/1463884", "title"=>"Map of African countries implicated in study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149153"], "description"=>"<p>The Fst values for all pairs of populations were calculated with GenoDive 2.0b25, considering 328 clinical <i>V</i>. <i>cholerae</i> isolates and six loci. The Fst values are listed on the top triangle, while the corresponding p-values are listed in the lower triangle.</p><p>Pairwise differentiation.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463889, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.t004", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_differentiation_/1463889", "title"=>"Pairwise differentiation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149151"], "description"=>"<p>Genetic diversity (Nei, 1987) of 328 <i>V</i>. <i>cholerae</i> isolates, considering six loci, was calculated in GenoDive 2.0b25. Num = number of alleles; Eff num = effective number of alleles; Pop div = gene diversity within populations; IOD = Index of Diversity; Corr IOD = corrected Index of Diversity.</p><p>Indices of genetic diversity per locus and observed PCR product size range.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463887, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indices_of_genetic_diversity_per_locus_and_observed_PCR_product_size_range_/1463887", "title"=>"Indices of genetic diversity per locus and observed PCR product size range.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149152"], "description"=>"<p>Genetic diversity (Nei, 1987) per population of the 328 <i>V</i>. <i>cholerae</i> isolates was calculated in GenoDive 2.0b25.</p><p>Indices of genetic diversity per population.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463888, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.t003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indices_of_genetic_diversity_per_population_/1463888", "title"=>"Indices of genetic diversity per population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149150"], "description"=>"<p><sup><b>1</b></sup> Chr.: chromosome.</p><p><sup>2</sup> Based on the reference strain El Tor N16961 (GenBank accession numbers: AE003852.1 and AE003853.1).</p><p>Characteristics and primer sequences of the six tested <i>V</i>. <i>cholerae</i> VNTRs.</p>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463886, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003817.t001", "stats"=>{"downloads"=>6, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_and_primer_sequences_of_the_six_tested_V_cholerae_VNTRs_/1463886", "title"=>"Characteristics and primer sequences of the six tested <i>V</i>. <i>cholerae</i> VNTRs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-25 03:16:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2149154", "https://ndownloader.figshare.com/files/2149155"], "description"=>"<div><p>Background</p><p>Since cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa.</p><p>Methodology/Principal Findings</p><p>In this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 <i>Vibrio cholerae</i> isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these <i>Vibrio cholerae</i> populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates.</p><p>Conclusions/Significance</p><p>To effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing <i>Vibrio cholerae</i> isolates.</p></div>", "links"=>[], "tags"=>["Vibrio cholerae populations", "drc", "cholera outbreaks", "guinea", "337 Vibrio cholerae", "337 Vibrio cholerae Isolates BackgroundSince cholera", "west", "mlva", "African Great Lakes Region", "epidemic", "relationship", "Cholera Epidemics Revealed", "zambia"], "article_id"=>1463890, "categories"=>["Uncategorised"], "users"=>["Sandra Moore", "Berthe Miwanda", "Adodo Yao Sadji", "Hélène Thefenne", "Fakhri Jeddi", "Stanislas Rebaudet", "Hilde de Boeck", "Bawimodom Bidjada", "Jean-Jacques Depina", "Didier Bompangue", "Aaron Aruna Abedi", "Lamine Koivogui", "Sakoba Keita", "Eric Garnotel", "Pierre-Denis Plisnier", "Raymond Ruimy", "Nicholas Thomson", "Jean-Jacques Muyembe", "Renaud Piarroux"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0003817.s001", "https://dx.doi.org/10.1371/journal.pntd.0003817.s002"], "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Relationship_between_Distinct_African_Cholera_Epidemics_Revealed_via_MLVA_Haplotyping_of_337_Vibrio_cholerae_Isolates/1463890", "title"=>"Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 <i>Vibrio cholerae</i> Isolates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-25 03:16:28"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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