Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil

Handle URI:
http://hdl.handle.net/10754/583107
Title:
Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil
Authors:
Dalla Costa, Elis R.; Vasconcelos, Sidra E. G.; Esteves, Leonardo S.; Gomes, Harrison M.; Gomes, Lia L. ( 0000-0002-1478-0509 ) ; Almeida da Silva, Pedro; Perdigão, João; Portugal, Isabel; Viveiros, Miguel; McNerney, Ruth; Pain, Arnab ( 0000-0002-1755-2819 ) ; Clark, Taane G.; Rastogi, Nalin; Unis, Gisela; Rossetti, Maria Lucia R.; Suffys, Philip Noel
Abstract:
We recently detected the spoligotype patterns of strains of Mycobacterium pinnipedii, a species of the Mycobacterium tuberculosis complex, in sputum samples from nine cases with pulmonary tuberculosis residing in Porto Alegre, South Brazil. Because this species is rarely encountered in humans, we further characterized these nine isolates by additional genotyping techniques, including 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing, verification of the loci TbD1, RD9, pks15/1, RDRio, and fbpC, the insertion of IS6110 at a site specific to the M. tuberculosis Latin American Mediterranean (LAM) lineage, and whole-genome sequencing. The combined analysis of these markers revealed that the isolates are in fact M. tuberculosis and more specifically belong to the LAM genotype. Most of these isolates (n = 8) were shown to be multidrug resistant (MDR), which prompted us to perform partial sequencing of the rpoA, rpoB, rpoC, katG, and inhA genes. Seven isolates (77.8%) carried the S315T mutation in katG, and one of these (11%) also presented the C(−17)T single-nucleotide polymorphism (SNP) in inhA. Interestingly, six of the MDR isolates also presented an undescribed insertion of 12 nucleotides (CCA GAA CAA CCC) in codon 516 of rpoB. No putative compensatory mutation was found in either rpoA or rpoC. This is the first report of an M. tuberculosis LAM family strain with a convergent M. pinnipedii spoligotype. These spoligotypes are observed in genotype databases at a modest frequency, highlighting that care must be taken when identifying isolates in the M. tuberculosis complex on the basis of single genetic markers.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil 2015:JCM.02012-15 Journal of Clinical Microbiology
Publisher:
American Society for Microbiology
Journal:
Journal of Clinical Microbiology
Issue Date:
23-Sep-2015
DOI:
10.1128/JCM.02012-15
Type:
Article
ISSN:
0095-1137; 1098-660X
Additional Links:
http://jcm.asm.org/lookup/doi/10.1128/JCM.02012-15
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorDalla Costa, Elis R.en
dc.contributor.authorVasconcelos, Sidra E. G.en
dc.contributor.authorEsteves, Leonardo S.en
dc.contributor.authorGomes, Harrison M.en
dc.contributor.authorGomes, Lia L.en
dc.contributor.authorAlmeida da Silva, Pedroen
dc.contributor.authorPerdigão, Joãoen
dc.contributor.authorPortugal, Isabelen
dc.contributor.authorViveiros, Miguelen
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorPain, Arnaben
dc.contributor.authorClark, Taane G.en
dc.contributor.authorRastogi, Nalinen
dc.contributor.authorUnis, Giselaen
dc.contributor.authorRossetti, Maria Lucia R.en
dc.contributor.authorSuffys, Philip Noelen
dc.date.accessioned2015-12-02T12:28:54Zen
dc.date.available2015-12-02T12:28:54Zen
dc.date.issued2015-09-23en
dc.identifier.citationMultidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil 2015:JCM.02012-15 Journal of Clinical Microbiologyen
dc.identifier.issn0095-1137en
dc.identifier.issn1098-660Xen
dc.identifier.doi10.1128/JCM.02012-15en
dc.identifier.urihttp://hdl.handle.net/10754/583107en
dc.description.abstractWe recently detected the spoligotype patterns of strains of Mycobacterium pinnipedii, a species of the Mycobacterium tuberculosis complex, in sputum samples from nine cases with pulmonary tuberculosis residing in Porto Alegre, South Brazil. Because this species is rarely encountered in humans, we further characterized these nine isolates by additional genotyping techniques, including 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing, verification of the loci TbD1, RD9, pks15/1, RDRio, and fbpC, the insertion of IS6110 at a site specific to the M. tuberculosis Latin American Mediterranean (LAM) lineage, and whole-genome sequencing. The combined analysis of these markers revealed that the isolates are in fact M. tuberculosis and more specifically belong to the LAM genotype. Most of these isolates (n = 8) were shown to be multidrug resistant (MDR), which prompted us to perform partial sequencing of the rpoA, rpoB, rpoC, katG, and inhA genes. Seven isolates (77.8%) carried the S315T mutation in katG, and one of these (11%) also presented the C(−17)T single-nucleotide polymorphism (SNP) in inhA. Interestingly, six of the MDR isolates also presented an undescribed insertion of 12 nucleotides (CCA GAA CAA CCC) in codon 516 of rpoB. No putative compensatory mutation was found in either rpoA or rpoC. This is the first report of an M. tuberculosis LAM family strain with a convergent M. pinnipedii spoligotype. These spoligotypes are observed in genotype databases at a modest frequency, highlighting that care must be taken when identifying isolates in the M. tuberculosis complex on the basis of single genetic markers.en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.urlhttp://jcm.asm.org/lookup/doi/10.1128/JCM.02012-15en
dc.rightsArchived with thanks to Journal of Clinical Microbiologyen
dc.titleMultidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazilen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalJournal of Clinical Microbiologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionFundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, Brazilen
dc.contributor.institutionLaboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazilen
dc.contributor.institutionUniversidade Luterana do Brasil (ULBRA/RS), Porto Alegre, Brazilen
dc.contributor.institutionNúcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazilen
dc.contributor.institutionInstituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugalen
dc.contributor.institutionGrupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHMT), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugalen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdomen
dc.contributor.institutionFaculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdomen
dc.contributor.institutionUnité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, Franceen
dc.contributor.institutionHospital Sanatório Partenon (HSP), Porto Alegre, Brazilen
dc.contributor.institutionUnit of Mycobacteriology at the Institute of Tropical Medicine, Antwerp, Belgiumen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben
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