Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent

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dc.contributor.authorHanekom, Madeleineen_ZA
dc.contributor.authorStreicher, Elizabeth Men_ZA
dc.contributor.authorVan de Berg, Doreenen_ZA
dc.contributor.authorCox, Helenen_ZA
dc.contributor.authorMcDermid, Cherylen_ZA
dc.contributor.authorBosman, Marleinen_ZA
dc.contributor.authorvan Pittius, Nicolaas C Geyen_ZA
dc.contributor.authorVictor, Tommie Cen_ZA
dc.contributor.authorKidd, Martinen_ZA
dc.contributor.authorvan Soolingen, Dicken_ZA
dc.date.accessioned2015-12-28T06:47:28Z
dc.date.available2015-12-28T06:47:28Z
dc.date.issued2013en_ZA
dc.description.abstractBACKGROUND: Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. Aim This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis strain genotypes in primary Mycobacterial Growth Indicator Tubes (MGIT) and Löwenstein-Jensen (LJ) cultures to identify mixed infections and to establish whether the growth media influenced the recovery of certain strain genotypes. Method A convenience sample of 206 paired MGIT and LJ M. tuberculosis cultures from pulmonary tuberculosis patients resident in Khayelitsha, South Africa were genotyped using an in-house PCR-based method to detect defined M. tuberculosis strain genotypes. RESULTS: The sensitivity and specificity of the PCR-based method for detecting Beijing, Haarlem, S-family, and LAM genotypes was 100%, and 75% and 50% for detecting the Low Copy Clade, respectively. Thirty-one (15%) of the 206 cases showed the presence of more than one M. tuberculosis strain genotype. Strains of the Beijing and Haarlem genotypes were significantly more associated with a mixed infection (on both media) when compared to infections with a single strain (Beijing MGIT p = 0.02; LJ, p<0.01) and (Haarlem: MGIT p<0.01; LJ, p = 0.01). Strains with the Beijing genotype were less likely to be with "other genotype" strains (p<0.01) while LAM, Haarlem, S-family and LCC occurred independently with the Beijing genotype. CONCLUSION: The PCR-based method was able to identify mixed infection in at least 15% of the cases. LJ media was more sensitive in detecting mixed infections than MGIT media, implying that the growth characteristics of M. tuberculosis on different media may influence our ability to detect mixed infections. The Beijing and Haarlem genotypes were more likely to occur in a mixed infection than any of the other genotypes tested suggesting pathogen-pathogen compatibility.en_ZA
dc.identifier.apacitationHanekom, M., Streicher, E. M., Van de Berg, D., Cox, H., McDermid, C., Bosman, M., ... van Soolingen, D. (2013). Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent. <i>PLoS One</i>, http://hdl.handle.net/11427/16028en_ZA
dc.identifier.chicagocitationHanekom, Madeleine, Elizabeth M Streicher, Doreen Van de Berg, Helen Cox, Cheryl McDermid, Marlein Bosman, Nicolaas C Gey van Pittius, Tommie C Victor, Martin Kidd, and Dick van Soolingen "Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent." <i>PLoS One</i> (2013) http://hdl.handle.net/11427/16028en_ZA
dc.identifier.citationHanekom, M., Streicher, E. M., Berg, D. V., Cox, H., McDermid, C., Bosman, M., ... & Warren, R. M. (2013). Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent. PLoS One, 8(7). doi:10.1371/journal.pone.0070178en_ZA
dc.identifier.ris TY - Journal Article AU - Hanekom, Madeleine AU - Streicher, Elizabeth M AU - Van de Berg, Doreen AU - Cox, Helen AU - McDermid, Cheryl AU - Bosman, Marlein AU - van Pittius, Nicolaas C Gey AU - Victor, Tommie C AU - Kidd, Martin AU - van Soolingen, Dick AB - BACKGROUND: Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. Aim This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis strain genotypes in primary Mycobacterial Growth Indicator Tubes (MGIT) and Löwenstein-Jensen (LJ) cultures to identify mixed infections and to establish whether the growth media influenced the recovery of certain strain genotypes. Method A convenience sample of 206 paired MGIT and LJ M. tuberculosis cultures from pulmonary tuberculosis patients resident in Khayelitsha, South Africa were genotyped using an in-house PCR-based method to detect defined M. tuberculosis strain genotypes. RESULTS: The sensitivity and specificity of the PCR-based method for detecting Beijing, Haarlem, S-family, and LAM genotypes was 100%, and 75% and 50% for detecting the Low Copy Clade, respectively. Thirty-one (15%) of the 206 cases showed the presence of more than one M. tuberculosis strain genotype. Strains of the Beijing and Haarlem genotypes were significantly more associated with a mixed infection (on both media) when compared to infections with a single strain (Beijing MGIT p = 0.02; LJ, p<0.01) and (Haarlem: MGIT p<0.01; LJ, p = 0.01). Strains with the Beijing genotype were less likely to be with "other genotype" strains (p<0.01) while LAM, Haarlem, S-family and LCC occurred independently with the Beijing genotype. CONCLUSION: The PCR-based method was able to identify mixed infection in at least 15% of the cases. LJ media was more sensitive in detecting mixed infections than MGIT media, implying that the growth characteristics of M. tuberculosis on different media may influence our ability to detect mixed infections. The Beijing and Haarlem genotypes were more likely to occur in a mixed infection than any of the other genotypes tested suggesting pathogen-pathogen compatibility. DA - 2013 DB - OpenUCT DO - 10.1371/journal.pone.0070178 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2013 T1 - Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent TI - Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent UR - http://hdl.handle.net/11427/16028 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16028
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0070178
dc.identifier.vancouvercitationHanekom M, Streicher EM, Van de Berg D, Cox H, McDermid C, Bosman M, et al. Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent. PLoS One. 2013; http://hdl.handle.net/11427/16028.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2013 Hanekom et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherMycobacterium tuberculosisen_ZA
dc.subject.otherTuberculosisen_ZA
dc.subject.otherPolymerase chain reactionen_ZA
dc.subject.otherRoot structureen_ZA
dc.subject.otherSputumen_ZA
dc.subject.otherGenotypingen_ZA
dc.subject.otherCulture mediaen_ZA
dc.subject.otherSouth Africaen_ZA
dc.titlePopulation Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependenten_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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