PandemieGrippaleV1, Main, Exploration, bibRecord, 000239

Genomic insights into the 2016–2017 cholera epidemic in Yemen

Identifieur interne : 000239 ( Main/Exploration ); précédent : 000238; suivant : 000240

Genomic insights into the 2016–2017 cholera epidemic in Yemen

Auteurs : François-Xavier Weill [France] ; Daryl Domman [Royaume-Uni] ; Elisabeth Njamkepo [France] ; Abdullrahman Almesbahi [Yémen] ; Mona Naji [Yémen] ; Samar Saeed Nasher [Yémen] ; Ankur Rakesh [France] ; Abdullah Assiri [Arabie saoudite] ; Naresh Chand Sharma ; Samuel Kariuki [Kenya] ; Mohammad Reza Pourshafie [Iran] ; Jean Rauzier [France] ; Abdinasir Abubakar [Égypte] ; Jane Carter [Kenya] ; Joseph Wamala [Suisse] ; Caroline Seguin [Émirats arabes unis] ; Christiane Bouchier [France] ; Thérèse Malliavin [France] ; Bita Bakhshi [Iran] ; Hayder Abulmaali [Iraq] ; Dhirendra Kumar [Inde] ; Samuel Njoroge [Kenya] ; Mamunur Rahman Malik [Égypte] ; John Kiiru [Kenya] ; Francisco Luquero [France] ; Andrew Azman [États-Unis] ; Thandavarayan Ramamurthy [Inde] ; Nicholas Thomson [Royaume-Uni] ; Marie-Laure Quilici [France]

Source :

Nature [ 0028-0836 ] ; 2019-01.

RBID : Hal:pasteur-02019696

Abstract

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

Url:

https://hal-pasteur.archives-ouvertes.fr/pasteur-02019696

DOI: 10.1038/s41586-018-0818-3

Affiliations:

Arabie saoudite, France, Inde, Iran, Iraq, Kenya, Royaume-Uni, Suisse, Yémen, Égypte, Émirats arabes unis, États-Unis

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic insights into the 2016–2017 cholera epidemic in Yemen</title>
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<author><name sortKey="Njamkepo, Elisabeth" sort="Njamkepo, Elisabeth" uniqKey="Njamkepo E" first="Elisabeth" last="Njamkepo">Elisabeth Njamkepo</name>
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</author>
<author><name sortKey="Almesbahi, Abdullrahman" sort="Almesbahi, Abdullrahman" uniqKey="Almesbahi A" first="Abdullrahman" last="Almesbahi">Abdullrahman Almesbahi</name>
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<country>Yémen</country>
</affiliation>
</author>
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<author><name sortKey="Nasher, Samar Saeed" sort="Nasher, Samar Saeed" uniqKey="Nasher S" first="Samar Saeed" last="Nasher">Samar Saeed Nasher</name>
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<author><name sortKey="Assiri, Abdullah" sort="Assiri, Abdullah" uniqKey="Assiri A" first="Abdullah" last="Assiri">Abdullah Assiri</name>
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<country>Arabie saoudite</country>
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</author>
<author><name sortKey="Sharma, Naresh Chand" sort="Sharma, Naresh Chand" uniqKey="Sharma N" first="Naresh Chand" last="Sharma">Naresh Chand Sharma</name>
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<author><name sortKey="Pourshafie, Mohammad Reza" sort="Pourshafie, Mohammad Reza" uniqKey="Pourshafie M" first="Mohammad Reza" last="Pourshafie">Mohammad Reza Pourshafie</name>
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<author><name sortKey="Abubakar, Abdinasir" sort="Abubakar, Abdinasir" uniqKey="Abubakar A" first="Abdinasir" last="Abubakar">Abdinasir Abubakar</name>
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<author><name sortKey="Bakhshi, Bita" sort="Bakhshi, Bita" uniqKey="Bakhshi B" first="Bita" last="Bakhshi">Bita Bakhshi</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-197295" status="VALID">          <orgName>Tarbiat Modares University [Tehran]</orgName>
          <desc>            <address>              <addrLine>Jalal Ale Ahmad Highway, P.O.Box: 14115-111, Tehran</addrLine>
              <country key="IR"></country>
            </address>
          </desc>
        </hal:affiliation>
<country>Iran</country>
</affiliation>
</author>
<author><name sortKey="Abulmaali, Hayder" sort="Abulmaali, Hayder" uniqKey="Abulmaali H" first="Hayder" last="Abulmaali">Hayder Abulmaali</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-553836" status="INCOMING">          <orgName>Ministry of Health [Iraq]</orgName>
          <desc>            <address>              <country key="IQ"></country>
            </address>
          </desc>
        </hal:affiliation>
<country>Iraq</country>
</affiliation>
</author>
<author><name sortKey="Kumar, Dhirendra" sort="Kumar, Dhirendra" uniqKey="Kumar D" first="Dhirendra" last="Kumar">Dhirendra Kumar</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-553827" status="VALID">          <orgName>Maharishi Valmiki Hospital</orgName>
          <desc>            <address>              <addrLine>Dehli</addrLine>
              <country key="IN"></country>
            </address>
          </desc>
        </hal:affiliation>
<country>Inde</country>
</affiliation>
</author>
<author><name sortKey="Njoroge, Samuel" sort="Njoroge, Samuel" uniqKey="Njoroge S" first="Samuel" last="Njoroge">Samuel Njoroge</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-330350" status="VALID">          <orgName>Kenya Medical Research Institute</orgName>
          <orgName type="acronym">KEMRI</orgName>
          <date type="start">1971</date>
          <desc>            <address>              <addrLine>Nairobi</addrLine>
              <country key="KE"></country>
            </address>
          </desc>
        </hal:affiliation>
<country>Kenya</country>
</affiliation>
</author>
<author><name sortKey="Malik, Mamunur Rahman" sort="Malik, Mamunur Rahman" uniqKey="Malik M" first="Mamunur Rahman" last="Malik">Mamunur Rahman Malik</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-553228" status="VALID">          <orgName>Regional Office for the Eastern Mediterranean [Cairo]</orgName>
          <orgName type="acronym">EMRO</orgName>
          <desc>            <address>              <addrLine>Monazamet El Seha El Alamia Str, Extension of Abdel Razak El Sanhouri Street, Nasr City, Cairo 11371, Egypt</addrLine>
              <country key="EG"></country>
            </address>
            <ref type="url">https://www.who.int/about/regions/emro/en/</ref>
          </desc>
          <listRelation>            <relation active="#struct-548010" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-548010" type="direct"><org type="institution" xml:id="struct-548010" status="VALID">          <orgName>Organisation Mondiale de la Santé / World Health Organization Office</orgName>
          <orgName type="acronym">OMS / WHO</orgName>
          <desc>            <address>              <addrLine>Genève</addrLine>
              <country key="CH"></country>
            </address>
            <ref type="url">https://www.who.int/</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>Égypte</country>
</affiliation>
</author>
<author><name sortKey="Kiiru, John" sort="Kiiru, John" uniqKey="Kiiru J" first="John" last="Kiiru">John Kiiru</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-330350" status="VALID">          <orgName>Kenya Medical Research Institute</orgName>
          <orgName type="acronym">KEMRI</orgName>
          <date type="start">1971</date>
          <desc>            <address>              <addrLine>Nairobi</addrLine>
              <country key="KE"></country>
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          </desc>
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<country>Kenya</country>
</affiliation>
</author>
<author><name sortKey="Luquero, Francisco" sort="Luquero, Francisco" uniqKey="Luquero F" first="Francisco" last="Luquero">Francisco Luquero</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-335654" status="VALID">          <orgName>Epicentre [Paris] [Médecins Sans Frontières]</orgName>
          <desc>            <address>              <addrLine>55 Rue Crozatier, 75012 Paris</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">http://www.epicentre.msf.org/</ref>
          </desc>
        </hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Azman, Andrew" sort="Azman, Andrew" uniqKey="Azman A" first="Andrew" last="Azman">Andrew Azman</name>
<affiliation wicri:level="1"><hal:affiliation type="regrouplaboratory" xml:id="struct-466567" status="VALID">          <orgName>Johns Hopkins Bloomberg School of Public Health [Baltimore]</orgName>
          <desc>            <address>              <addrLine>615 N Wolfe St, Baltimore, MD 21205</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">https://www.jhsph.edu/</ref>
          </desc>
          <listRelation>            <relation active="#struct-7668" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-7668" type="direct"><org type="institution" xml:id="struct-7668" status="VALID">          <orgName>Johns Hopkins University</orgName>
          <orgName type="acronym">JHU</orgName>
          <desc>            <address>              <addrLine>Baltimore, Maryland 410-516-8000</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.jhu.edu/</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Ramamurthy, Thandavarayan" sort="Ramamurthy, Thandavarayan" uniqKey="Ramamurthy T" first="Thandavarayan" last="Ramamurthy">Thandavarayan Ramamurthy</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-450296" status="VALID">          <orgName>Translational Health Science and Technology Institute [Faridabad]</orgName>
          <orgName type="acronym">THSTI</orgName>
          <desc>            <address>              <addrLine>NCR Biotech Science Cluster, 3rd Milestone, Faridabad – Gurgaon Expressway, Faridabad, Haryana 121001, Inde</addrLine>
              <country key="IN"></country>
            </address>
            <ref type="url">http://www.thsti.res.in/</ref>
          </desc>
        </hal:affiliation>
<country>Inde</country>
</affiliation>
</author>
<author><name sortKey="Thomson, Nicholas" sort="Thomson, Nicholas" uniqKey="Thomson N" first="Nicholas" last="Thomson">Nicholas Thomson</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-232748" status="VALID">          <orgName>The Wellcome Trust Sanger Institute [Cambridge]</orgName>
          <desc>            <address>              <addrLine>Hinxton, Cambridge CB10 1SA, UK</addrLine>
              <country key="GB"></country>
            </address>
            <ref type="url">http://www.sanger.ac.uk/</ref>
          </desc>
        </hal:affiliation>
<country>Royaume-Uni</country>
</affiliation>
</author>
<author><name sortKey="Quilici, Marie Laure" sort="Quilici, Marie Laure" uniqKey="Quilici M" first="Marie-Laure" last="Quilici">Marie-Laure Quilici</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-51769" status="VALID">          <orgName>Bactéries pathogènes entériques</orgName>
          <orgName type="acronym">BPE</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 28, rue du Docteur Roux 75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/fr/team/enteric-bacterial-pathogens/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
</analytic>
<idno type="DOI">10.1038/s41586-018-0818-3</idno>
<series><title level="j">Nature</title>
<idno type="ISSN">0028-0836</idno>
<imprint><date type="datePub">2019-01</date>
</imprint>
</series>
</biblStruct>
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<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">              <p>Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.</p>
            </div>
</front>
</TEI>
<affiliations><list><country><li>Arabie saoudite</li>
<li>France</li>
<li>Inde</li>
<li>Iran</li>
<li>Iraq</li>
<li>Kenya</li>
<li>Royaume-Uni</li>
<li>Suisse</li>
<li>Yémen</li>
<li>Égypte</li>
<li>Émirats arabes unis</li>
<li>États-Unis</li>
</country>
</list>
<tree><noCountry><name sortKey="Sharma, Naresh Chand" sort="Sharma, Naresh Chand" uniqKey="Sharma N" first="Naresh Chand" last="Sharma">Naresh Chand Sharma</name>
</noCountry>
<country name="France"><noRegion><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="François-Xavier" last="Weill">François-Xavier Weill</name>
</noRegion>
<name sortKey="Bouchier, Christiane" sort="Bouchier, Christiane" uniqKey="Bouchier C" first="Christiane" last="Bouchier">Christiane Bouchier</name>
<name sortKey="Luquero, Francisco" sort="Luquero, Francisco" uniqKey="Luquero F" first="Francisco" last="Luquero">Francisco Luquero</name>
<name sortKey="Malliavin, Therese" sort="Malliavin, Therese" uniqKey="Malliavin T" first="Thérèse" last="Malliavin">Thérèse Malliavin</name>
<name sortKey="Njamkepo, Elisabeth" sort="Njamkepo, Elisabeth" uniqKey="Njamkepo E" first="Elisabeth" last="Njamkepo">Elisabeth Njamkepo</name>
<name sortKey="Quilici, Marie Laure" sort="Quilici, Marie Laure" uniqKey="Quilici M" first="Marie-Laure" last="Quilici">Marie-Laure Quilici</name>
<name sortKey="Rakesh, Ankur" sort="Rakesh, Ankur" uniqKey="Rakesh A" first="Ankur" last="Rakesh">Ankur Rakesh</name>
<name sortKey="Rauzier, Jean" sort="Rauzier, Jean" uniqKey="Rauzier J" first="Jean" last="Rauzier">Jean Rauzier</name>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Domman, Daryl" sort="Domman, Daryl" uniqKey="Domman D" first="Daryl" last="Domman">Daryl Domman</name>
</noRegion>
<name sortKey="Thomson, Nicholas" sort="Thomson, Nicholas" uniqKey="Thomson N" first="Nicholas" last="Thomson">Nicholas Thomson</name>
</country>
<country name="Yémen"><noRegion><name sortKey="Almesbahi, Abdullrahman" sort="Almesbahi, Abdullrahman" uniqKey="Almesbahi A" first="Abdullrahman" last="Almesbahi">Abdullrahman Almesbahi</name>
</noRegion>
<name sortKey="Naji, Mona" sort="Naji, Mona" uniqKey="Naji M" first="Mona" last="Naji">Mona Naji</name>
<name sortKey="Nasher, Samar Saeed" sort="Nasher, Samar Saeed" uniqKey="Nasher S" first="Samar Saeed" last="Nasher">Samar Saeed Nasher</name>
</country>
<country name="Arabie saoudite"><noRegion><name sortKey="Assiri, Abdullah" sort="Assiri, Abdullah" uniqKey="Assiri A" first="Abdullah" last="Assiri">Abdullah Assiri</name>
</noRegion>
</country>
<country name="Kenya"><noRegion><name sortKey="Kariuki, Samuel" sort="Kariuki, Samuel" uniqKey="Kariuki S" first="Samuel" last="Kariuki">Samuel Kariuki</name>
</noRegion>
<name sortKey="Carter, Jane" sort="Carter, Jane" uniqKey="Carter J" first="Jane" last="Carter">Jane Carter</name>
<name sortKey="Kiiru, John" sort="Kiiru, John" uniqKey="Kiiru J" first="John" last="Kiiru">John Kiiru</name>
<name sortKey="Njoroge, Samuel" sort="Njoroge, Samuel" uniqKey="Njoroge S" first="Samuel" last="Njoroge">Samuel Njoroge</name>
</country>
<country name="Iran"><noRegion><name sortKey="Pourshafie, Mohammad Reza" sort="Pourshafie, Mohammad Reza" uniqKey="Pourshafie M" first="Mohammad Reza" last="Pourshafie">Mohammad Reza Pourshafie</name>
</noRegion>
<name sortKey="Bakhshi, Bita" sort="Bakhshi, Bita" uniqKey="Bakhshi B" first="Bita" last="Bakhshi">Bita Bakhshi</name>
</country>
<country name="Égypte"><noRegion><name sortKey="Abubakar, Abdinasir" sort="Abubakar, Abdinasir" uniqKey="Abubakar A" first="Abdinasir" last="Abubakar">Abdinasir Abubakar</name>
</noRegion>
<name sortKey="Malik, Mamunur Rahman" sort="Malik, Mamunur Rahman" uniqKey="Malik M" first="Mamunur Rahman" last="Malik">Mamunur Rahman Malik</name>
</country>
<country name="Suisse"><noRegion><name sortKey="Wamala, Joseph" sort="Wamala, Joseph" uniqKey="Wamala J" first="Joseph" last="Wamala">Joseph Wamala</name>
</noRegion>
</country>
<country name="Émirats arabes unis"><noRegion><name sortKey="Seguin, Caroline" sort="Seguin, Caroline" uniqKey="Seguin C" first="Caroline" last="Seguin">Caroline Seguin</name>
</noRegion>
</country>
<country name="Iraq"><noRegion><name sortKey="Abulmaali, Hayder" sort="Abulmaali, Hayder" uniqKey="Abulmaali H" first="Hayder" last="Abulmaali">Hayder Abulmaali</name>
</noRegion>
</country>
<country name="Inde"><noRegion><name sortKey="Kumar, Dhirendra" sort="Kumar, Dhirendra" uniqKey="Kumar D" first="Dhirendra" last="Kumar">Dhirendra Kumar</name>
</noRegion>
<name sortKey="Ramamurthy, Thandavarayan" sort="Ramamurthy, Thandavarayan" uniqKey="Ramamurthy T" first="Thandavarayan" last="Ramamurthy">Thandavarayan Ramamurthy</name>
</country>
<country name="États-Unis"><noRegion><name sortKey="Azman, Andrew" sort="Azman, Andrew" uniqKey="Azman A" first="Andrew" last="Azman">Andrew Azman</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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Genomic insights into the 2016–2017 cholera epidemic in Yemen

Genomic insights into the 2016–2017 cholera epidemic in Yemen

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