Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco
Identifieur interne : 000290 ( Main/Exploration ); précédent : 000289; suivant : 000291Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco
Auteurs : Nada Bouklata [Maroc] ; Philip Supply [France] ; Sanae Jaouhari [Maroc] ; Reda Charof [Maroc] ; Fouad Seghrouchni [Maroc] ; Khalid Sadki [Maroc] ; Youness El Achhab [Maroc] ; Chakib Nejjari [Maroc] ; Abdelkarim Filali-Maltouf [Maroc] ; Ouafae Lahlou [Maroc] ; Rajae El Aouad [Maroc]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- Adolescent (MeSH), Adulte (MeSH), Adulte d'âge moyen (MeSH), Analyse de regroupements (MeSH), Femelle (MeSH), Humains (MeSH), Jeune adulte (MeSH), Locus génétiques (génétique), Maroc (MeSH), Mycobacterium tuberculosis (effets des médicaments et des substances chimiques), Mycobacterium tuberculosis (génétique), Mycobacterium tuberculosis (isolement et purification), Mâle (MeSH), Répétitions minisatellites (génétique), Résistance bactérienne aux médicaments (génétique), Sujet âgé (MeSH), Sujet âgé de 80 ans ou plus (MeSH), Séquences répétées dispersées (génétique), Typage par séquençage multilocus (méthodes), Variation génétique (MeSH).
- MESH :
- effets des médicaments et des substances chimiques : Mycobacterium tuberculosis.
- génétique : Locus génétiques, Mycobacterium tuberculosis, Répétitions minisatellites, Résistance bactérienne aux médicaments, Séquences répétées dispersées.
- isolement et purification : Mycobacterium tuberculosis.
- méthodes : Typage par séquençage multilocus.
- Adolescent, Adulte, Adulte d'âge moyen, Analyse de regroupements, Femelle, Humains, Jeune adulte, Maroc, Mâle, Sujet âgé, Sujet âgé de 80 ans ou plus, Variation génétique.
- Wicri :
- geographic : Maroc.
English descriptors
- KwdEn :
- Adolescent (MeSH), Adult (MeSH), Aged (MeSH), Aged, 80 and over (MeSH), Cluster Analysis (MeSH), Drug Resistance, Bacterial (genetics), Female (MeSH), Genetic Loci (genetics), Genetic Variation (MeSH), Humans (MeSH), Interspersed Repetitive Sequences (genetics), Male (MeSH), Middle Aged (MeSH), Minisatellite Repeats (genetics), Morocco (MeSH), Multilocus Sequence Typing (methods), Mycobacterium tuberculosis (drug effects), Mycobacterium tuberculosis (genetics), Mycobacterium tuberculosis (isolation & purification), Young Adult (MeSH).
- MESH :
- geographic : Morocco.
- drug effects : Mycobacterium tuberculosis.
- genetics : Drug Resistance, Bacterial, Genetic Loci, Interspersed Repetitive Sequences, Minisatellite Repeats, Mycobacterium tuberculosis.
- isolation & purification : Mycobacterium tuberculosis.
- methods : Multilocus Sequence Typing.
- Adolescent, Adult, Aged, Aged, 80 and over, Cluster Analysis, Female, Genetic Variation, Humans, Male, Middle Aged, Young Adult.
Abstract
Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community.
During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTR
Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6).
24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context.
Url:
DOI: 10.1371/journal.pone.0135695
PubMed: 26285026
PubMed Central: 4540494
Affiliations:
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Morocco</title><author><name sortKey="Bouklata, Nada" sort="Bouklata, Nada" uniqKey="Bouklata N" first="Nada" last="Bouklata">Nada Bouklata</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>INSERMU1018, Lille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INSERMU1018, Lille</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>CNRS UMR8204, Lille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CNRS UMR8204, Lille</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Université de Lille, Lille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université de Lille, Lille</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff009"><addr-line>Genoscreen, Lille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Genoscreen, Lille</wicri:regionArea></affiliation></author><author><name sortKey="Jaouhari, Sanae" sort="Jaouhari, Sanae" uniqKey="Jaouhari S" first="Sanae" last="Jaouhari">Sanae Jaouhari</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Charof, Reda" sort="Charof, Reda" uniqKey="Charof R" first="Reda" last="Charof">Reda Charof</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Seghrouchni, Fouad" sort="Seghrouchni, Fouad" uniqKey="Seghrouchni F" first="Fouad" last="Seghrouchni">Fouad Seghrouchni</name><affiliation wicri:level="1"><nlm:aff id="aff010"><addr-line>Laboratory of Cell Immunology, Department of Immunology, National Institute of Hygiene, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Cell Immunology, Department of Immunology, National Institute of Hygiene, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Sadki, Khalid" sort="Sadki, Khalid" uniqKey="Sadki K" first="Khalid" last="Sadki">Khalid Sadki</name><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Achhab, Youness" sort="El Achhab, Youness" uniqKey="El Achhab Y" first="Youness" last="El Achhab">Youness El Achhab</name><affiliation wicri:level="1"><nlm:aff id="aff007"><addr-line>Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes</wicri:regionArea></affiliation></author><author><name sortKey="Nejjari, Chakib" sort="Nejjari, Chakib" uniqKey="Nejjari C" first="Chakib" last="Nejjari">Chakib Nejjari</name><affiliation wicri:level="1"><nlm:aff id="aff007"><addr-line>Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes</wicri:regionArea></affiliation></author><author><name sortKey="Filali Maltouf, Abdelkarim" sort="Filali Maltouf, Abdelkarim" uniqKey="Filali Maltouf A" first="Abdelkarim" last="Filali-Maltouf">Abdelkarim Filali-Maltouf</name><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Lahlou, Ouafae" sort="Lahlou, Ouafae" uniqKey="Lahlou O" first="Ouafae" last="Lahlou">Ouafae Lahlou</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Aouad, Rajae" sort="El Aouad, Rajae" uniqKey="El Aouad R" first="Rajae" last="El Aouad">Rajae El Aouad</name><affiliation wicri:level="1"><nlm:aff id="aff008"><addr-line>School of Public Health and Management System Health, University Mohamed VI of Sciences and Health, Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>School of Public Health and Management System Health, University Mohamed VI of Sciences and Health, Casablanca</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adolescent (MeSH)</term><term>Adult (MeSH)</term><term>Aged (MeSH)</term><term>Aged, 80 and over (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Drug Resistance, Bacterial (genetics)</term><term>Female (MeSH)</term><term>Genetic Loci (genetics)</term><term>Genetic Variation (MeSH)</term><term>Humans (MeSH)</term><term>Interspersed Repetitive Sequences (genetics)</term><term>Male (MeSH)</term><term>Middle Aged (MeSH)</term><term>Minisatellite Repeats (genetics)</term><term>Morocco (MeSH)</term><term>Multilocus Sequence Typing (methods)</term><term>Mycobacterium tuberculosis (drug effects)</term><term>Mycobacterium tuberculosis (genetics)</term><term>Mycobacterium tuberculosis (isolation & purification)</term><term>Young Adult (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adolescent (MeSH)</term><term>Adulte (MeSH)</term><term>Adulte d'âge moyen (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Femelle (MeSH)</term><term>Humains (MeSH)</term><term>Jeune adulte (MeSH)</term><term>Locus génétiques (génétique)</term><term>Maroc (MeSH)</term><term>Mycobacterium tuberculosis (effets des médicaments et des substances chimiques)</term><term>Mycobacterium tuberculosis (génétique)</term><term>Mycobacterium tuberculosis (isolement et purification)</term><term>Mâle (MeSH)</term><term>Répétitions minisatellites (génétique)</term><term>Résistance bactérienne aux médicaments (génétique)</term><term>Sujet âgé (MeSH)</term><term>Sujet âgé de 80 ans ou plus (MeSH)</term><term>Séquences répétées dispersées (génétique)</term><term>Typage par séquençage multilocus (méthodes)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Morocco</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Mycobacterium tuberculosis</term></keywords><keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Mycobacterium tuberculosis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drug Resistance, Bacterial</term><term>Genetic Loci</term><term>Interspersed Repetitive Sequences</term><term>Minisatellite Repeats</term><term>Mycobacterium tuberculosis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Locus génétiques</term><term>Mycobacterium tuberculosis</term><term>Répétitions minisatellites</term><term>Résistance bactérienne aux médicaments</term><term>Séquences répétées dispersées</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Mycobacterium tuberculosis</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Mycobacterium tuberculosis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Multilocus Sequence Typing</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Typage par séquençage multilocus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adolescent</term><term>Adult</term><term>Aged</term><term>Aged, 80 and over</term><term>Cluster Analysis</term><term>Female</term><term>Genetic Variation</term><term>Humans</term><term>Male</term><term>Middle Aged</term><term>Young Adult</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adolescent</term><term>Adulte</term><term>Adulte d'âge moyen</term><term>Analyse de regroupements</term><term>Femelle</term><term>Humains</term><term>Jeune adulte</term><term>Maroc</term><term>Mâle</term><term>Sujet âgé</term><term>Sujet âgé de 80 ans ou plus</term><term>Variation génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Maroc</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="sec001"><title>Background</title><p>Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community.</p></sec><sec id="sec002"><title>Methodology</title><p>During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTR<italic>plus</italic> database.</p></sec><sec id="sec003"><title>Principal Findings</title><p>Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6).</p></sec><sec id="sec004"><title>Conclusions</title><p>24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Region, Wp" uniqKey="Region W">WP Region</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Supply, P" uniqKey="Supply P">P Supply</name></author><author><name sortKey="Allix, C" uniqKey="Allix C">C Allix</name></author><author><name sortKey="Lesjean, S" uniqKey="Lesjean S">S Lesjean</name></author><author><name sortKey="Cardoso Oelemann, M" 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Blom</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Walker, Tm" uniqKey="Walker T">TM Walker</name></author><author><name sortKey="Ip, Cl" uniqKey="Ip C">CL Ip</name></author><author><name sortKey="Harre, Rh" uniqKey="Harre R">RH Harre</name></author><author><name sortKey="Evans, Jt" uniqKey="Evans J">JT Evans</name></author><author><name sortKey="Kapatai, G" uniqKey="Kapatai G">G Kapatai</name></author><author><name sortKey="Dedicoat, Mj" uniqKey="Dedicoat M">MJ Dedicoat</name></author><author><name sortKey="Eyre, Dw" uniqKey="Eyre D">DW Eyre</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Maroc</li></country></list><tree><country name="Maroc"><noRegion><name sortKey="Bouklata, Nada" sort="Bouklata, Nada" uniqKey="Bouklata N" first="Nada" last="Bouklata">Nada Bouklata</name></noRegion><name sortKey="Bouklata, Nada" sort="Bouklata, Nada" uniqKey="Bouklata N" first="Nada" last="Bouklata">Nada Bouklata</name><name sortKey="Charof, Reda" sort="Charof, Reda" uniqKey="Charof R" first="Reda" last="Charof">Reda Charof</name><name sortKey="El Achhab, Youness" sort="El Achhab, Youness" uniqKey="El Achhab Y" first="Youness" last="El Achhab">Youness El Achhab</name><name sortKey="El Aouad, Rajae" sort="El Aouad, Rajae" uniqKey="El Aouad R" first="Rajae" last="El Aouad">Rajae El Aouad</name><name sortKey="Filali Maltouf, Abdelkarim" sort="Filali Maltouf, Abdelkarim" uniqKey="Filali Maltouf A" first="Abdelkarim" last="Filali-Maltouf">Abdelkarim Filali-Maltouf</name><name sortKey="Jaouhari, Sanae" sort="Jaouhari, Sanae" uniqKey="Jaouhari S" first="Sanae" last="Jaouhari">Sanae Jaouhari</name><name sortKey="Lahlou, Ouafae" sort="Lahlou, Ouafae" uniqKey="Lahlou O" first="Ouafae" last="Lahlou">Ouafae Lahlou</name><name sortKey="Nejjari, Chakib" sort="Nejjari, Chakib" uniqKey="Nejjari C" first="Chakib" last="Nejjari">Chakib Nejjari</name><name sortKey="Sadki, Khalid" sort="Sadki, Khalid" uniqKey="Sadki K" first="Khalid" last="Sadki">Khalid Sadki</name><name sortKey="Seghrouchni, Fouad" sort="Seghrouchni, Fouad" uniqKey="Seghrouchni F" first="Fouad" last="Seghrouchni">Fouad Seghrouchni</name></country><country name="France"><noRegion><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name></noRegion><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name><name sortKey="Supply, Philip" sort="Supply, Philip" uniqKey="Supply P" first="Philip" last="Supply">Philip Supply</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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