1
|
Machado E, Vasconcellos SEG, Cerdeira C, Gomes LL, Junqueira R, Carvalho LDD, Ramos JP, Redner P, Campos CED, Caldas PCDS, Gomes APCS, Goldenberg T, Montes FF, Mello FCDQ, Mussi VDO, Lasunskaia E, Soolingen DV, Miranda ABD, Rigouts L, Jong BCD, Meehan CJ, Catanho M, Suffys PN. Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity. Mem Inst Oswaldo Cruz 2018; 113:e180085. [PMID: 29947722 PMCID: PMC6012682 DOI: 10.1590/0074-02760180085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/05/2018] [Indexed: 11/02/2022] Open
Abstract
Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.
Collapse
Affiliation(s)
- Edson Machado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil
| | - Sidra Ezidio Gonçalves Vasconcellos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Camillo Cerdeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil.,Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Computacional e Sistemas, Rio de Janeiro, RJ, Brasil
| | - Lia Lima Gomes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Ricardo Junqueira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Computacional e Sistemas, Rio de Janeiro, RJ, Brasil
| | - Luciana Distasio de Carvalho
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Jesus Pais Ramos
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Paulo Redner
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Carlos Eduardo Dias Campos
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Paulo Cesar de Souza Caldas
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Ana Paula Chaves Sobral Gomes
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Telma Goldenberg
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Fatima Fandinho Montes
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública, Centro de Referência Professor Hélio Fraga, Laboratório de Referência Nacional para Tuberculose, Rio de Janeiro, RJ, Brasil
| | | | - Vinicius de Oliveira Mussi
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Laboratório de Biologia do Reconhecer, Campos dos Goytacazes, RJ, Brasil
| | - Elena Lasunskaia
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Laboratório de Biologia do Reconhecer, Campos dos Goytacazes, RJ, Brasil
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Antonio Basílio de Miranda
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Computacional e Sistemas, Rio de Janeiro, RJ, Brasil
| | - Leen Rigouts
- Institute of Tropical Medicine, Unit of Mycobacteriology, Antwerp, Belgium
| | - Bouke C de Jong
- Institute of Tropical Medicine, Unit of Mycobacteriology, Antwerp, Belgium
| | - Conor J Meehan
- Institute of Tropical Medicine, Unit of Mycobacteriology, Antwerp, Belgium
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil
| | - Philip N Suffys
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil.,Institute of Tropical Medicine, Unit of Mycobacteriology, Antwerp, Belgium
| |
Collapse
|
2
|
Bakuła Z, Brzostek A, Borówka P, Żaczek A, Szulc-Kiełbik I, Podpora A, Parniewski P, Strapagiel D, Dziadek J, Proboszcz M, Bielecki J, van Ingen J, Jagielski T. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis. Sci Rep 2018; 8:4462. [PMID: 29535391 PMCID: PMC5849605 DOI: 10.1038/s41598-018-21562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
Collapse
Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Paulina Borówka
- Department of Anthropology, University of Łódź, Łódź, Poland
| | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Agata Podpora
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| |
Collapse
|