1
|
Sisco MC, Brum Fontes AN, Lessmann LC, Rada E, Prado Palacios YY, Vasconcellos SEG, de Waard JH, Suffys PN. Antimicrobial resistance and genotyping of Mycobacterium leprae in Venezuela. Front Trop Dis 2023. [DOI: 10.3389/fitd.2023.1067439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Leprosy is a neglected tropical disease that leads to physical disability and social discrimination. The active surveillance of new cases and vigilance for drug resistance can decrease the incidence, and improve the clinical outcomes of people affected by it. We analyzed, with molecular biology techniques, a set of skin biopsy samples from 25 Venezuelan patients. The patients had been diagnosed with leprosy in 2014 and early 2015, and 15 were relapse cases. The samples were tested for molecular drug resistance to dapsone, rifampicin, and fluoroquinolones. In addition, we performed molecular epidemiology analysis through multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) typing. We did not find evidence of drug resistance and 76% of the samples (n = 16) had isolates belonging to SNP type 3. Genotype profiles allowed us to rule out the possibility of re-infection in a patient with persistent symptoms after treatment, as well as that of household transmission in two more patients. Although our sampling is relatively small, very similar or even identical Mycobacterium leprae genotypes were observed in Miranda State. The presence of this cluster is highly suggestive of high rates of local transmission and, in turn, the need to better control this disease. Finally, the copy number distribution of minisatellite 18–8 in a considerable number of SNP type 3 strains strongly suggests the presence of a sublineage of this disease that is particular to Venezuela.
Collapse
|
2
|
Mussi VO, Simão TLBV, Almeida FM, Machado E, de Carvalho LD, Calixto SD, Sales GAM, Carvalho ECQ, Vasconcellos SEG, Catanho M, Suffys PN, Lasunskaia EB. A Murine Model of Mycobacterium kansasii Infection Reproducing Necrotic Lung Pathology Reveals Considerable Heterogeneity in Virulence of Clinical Isolates. Front Microbiol 2021; 12:718477. [PMID: 34504483 PMCID: PMC8422904 DOI: 10.3389/fmicb.2021.718477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/28/2021] [Indexed: 12/04/2022] Open
Abstract
Among non-tuberculous mycobacteria, Mycobacterium kansasii is one of the most pathogenic, able to cause pulmonary disease indistinguishable from tuberculosis in immunocompetent susceptible adults. The lack of animal models that reproduce human-like lung disease, associated with the necrotic lung pathology, impairs studies of M. kansasii virulence and pathogenicity. In this study, we examined the ability of the C57BL/6 mice, intratracheally infected with highly virulent M. kansasii strains, to produce a chronic infection and necrotic lung pathology. As a first approach, we evaluated ten M. kansasii strains isolated from Brazilian patients with pulmonary disease and the reference strain M. kansasii ATCC 12478 for virulence-associated features in macrophages infected in vitro; five of these strains differing in virulence were selected for in vivo analysis. Highly virulent isolates induced progressive lung disease in mice, forming large encapsulated caseous granulomas in later stages (120–150 days post-infection), while the low-virulent strain was cleared from the lungs by day 40. Two strains demonstrated increased virulence, causing premature death in the infected animals. These data demonstrate that C57BL/6 mice are an excellent candidate to investigate the virulence of M. kansasii isolates. We observed considerable heterogeneity in the virulence profile of these strains, in which the presence of highly virulent strains allowed us to establish a clinically relevant animal model. Comparing public genomic data between Brazilian isolates and isolates from other geographic regions worldwide demonstrated that at least some of the highly pathogenic strains isolated in Brazil display remarkable genomic similarities with the ATCC strain 12478 isolated in the United States 70 years ago (less than 100 SNPs of difference), as well as with some recent European clinical isolates. These data suggest that few pathogenic clones have been widely spread within M. kansasii population around the world.
Collapse
Affiliation(s)
- Vinicius O Mussi
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| | - Thatiana L B V Simão
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| | - Fabrício M Almeida
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| | - Edson Machado
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Luciana D de Carvalho
- National Reference Laboratory for Tuberculosis, Reference Center Professor Helio Fraga, National School of Public Health, Fiocruz, Rio de Janeiro, Brazil
| | - Sanderson D Calixto
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| | - Guilherme A M Sales
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| | - Eulógio C Q Carvalho
- Laboratory of Animal Morphology and Pathology, State University of North Fluminense, Campos, Brazil
| | - Sidra E G Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Elena B Lasunskaia
- Laboratory of Biology of Recognition, State University of North Fluminense, Campos, Brazil
| |
Collapse
|
3
|
Rosa PS, D'Espindula HRS, Melo ACL, Fontes ANB, Finardi AJ, Belone AFF, Sartori BGC, Pires CAA, Soares CT, Marques FB, Branco FJD, Baptista IMFD, Trino LM, Fachin LRV, Xavier MB, Floriano MC, Ura S, Diório SM, Delanina WFB, Moraes MO, Virmond MCL, Suffys PN, Mira MT. Emergence and Transmission of Drug-/Multidrug-resistant Mycobacterium leprae in a Former Leprosy Colony in the Brazilian Amazon. Clin Infect Dis 2021; 70:2054-2061. [PMID: 31260522 PMCID: PMC7201420 DOI: 10.1093/cid/ciz570] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Leprosy has been treated with multidrug therapy, which has been distributed for free across the globe and regarded as highly efficient. However, the impossibility of growing Mycobacterium leprae in axenic media has historically impaired assessments of M. leprae resistance, a parameter only recently detectable through molecular methods. METHODS A systematic, population-based search for M. leprae resistance in suspected leprosy relapse cases and contacts was performed in Prata Village, an isolated, hyperendemic, former leprosy colony located in the Brazilian Amazon. Results led to an extended active search involving the entire Prata population. Confirmed leprosy cases were investigated for bacterial resistance using a combination of in vivo testing and direct sequencing of resistance genes folP1, rpoB, and gyrA. A molecular epidemiology analysis was performed using data from 17 variable number tandem repeats (VNTR). RESULTS Mycobacterium leprae was obtained from biopsies of 37 leprosy cases (18 relapses and 19 new cases): 16 (43.24%) displayed drug-resistance variants. Multidrug resistance to rifampicin and dapsone was observed in 8 relapses and 4 new cases. Single resistance to rifampicin was detected in 1 new case. Resistance to dapsone was present in 2 relapses and 1 new case. Combined molecular resistance and VNTR data revealed evidence of intra-familial primary transmission of resistant M. leprae. CONCLUSIONS A comprehensive, population-based systematic approach to investigate M. leprae resistance in a unique population revealed an alarming scenario of the emergence and transmission of resistant strains. These findings may be used for the development of new strategies for surveillance of drug resistance in other populations.
Collapse
Affiliation(s)
- Patrícia S Rosa
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Helena R S D'Espindula
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Ana C L Melo
- Centro de Referência Nacional em Dermatologia Sanitária Dona Libânia, Fortaleza, Ceará, Brazil
| | - Amanda N B Fontes
- Laboratory of Molecular Biology Applied in Mycobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda J Finardi
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Andréa F F Belone
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Beatriz G C Sartori
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Carla A A Pires
- Core of Tropical Diseases, Universidade Federal do Pará, Belém, Brazil
| | - Cleverson T Soares
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Flávio B Marques
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Francisco J D Branco
- Centro de Referência Nacional em Dermatologia Sanitária Dona Libânia, Fortaleza, Ceará, Brazil
| | - Ida M F D Baptista
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Lázara M Trino
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Luciana R V Fachin
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Marília B Xavier
- Core of Tropical Diseases, Universidade Federal do Pará, Belém, Brazil.,Center for Biological and Health Sciences, Universidade do Estado do Pará, Belém, Brazil
| | - Marcos C Floriano
- Department of Dermatology, Universidade Federal de São Paulo, Brazil
| | - Somei Ura
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Suzana M Diório
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Wladimir F B Delanina
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Milton O Moraes
- Laboratory of Molecular Biology Applied in Mycobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcos C L Virmond
- Division of Research and Education, Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied in Mycobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcelo T Mira
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| |
Collapse
|
4
|
Kluyber D, Desbiez ALJ, Attias N, Massocato GF, Gennari SM, Soares HS, Bagagli E, Bosco SMG, Garcés HG, Ferreira JDS, Fontes ANB, Suffys PN, Meireles LR, Jansen AM, Luna EJA, Roque ALR. Zoonotic parasites infecting free-living armadillos from Brazil. Transbound Emerg Dis 2020; 68:1639-1651. [PMID: 32964690 DOI: 10.1111/tbed.13839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/21/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022]
Abstract
Armadillos are specialist diggers and their burrows are used to find food, seek shelter and protect their pups. These burrows can also be shared with dozens of vertebrate and invertebrate species and; consequently, their parasites including the zoonotics. The aim of this study was to diagnose the presence of zoonotic parasites in four wild-caught armadillo species from two different Brazilian ecosystems, the Cerrado (Brazilian savanna) and the Pantanal (wetland). The investigated parasites and their correspondent diseases were: Toxoplasma gondii (toxoplasmosis), Trypanosoma cruzi (Chagas disease), Leishmania spp., (leishmaniasis), Paracoccidioides brasiliensis (Paracoccidioidomicosis) and Mycobacterium leprae (Hansen's disease). Forty-three free-living armadillos from Pantanal and seven road-killed armadillos from the Cerrado were sampled. Trypanosoma cruzi DTU TcIII were isolated from 2 out of 43 (4.65%) armadillos, including one of them also infected with Trypanosoma rangeli. Antibodies anti-T. gondii were detected in 13 out of 43 (30.2%) armadillos. All seven armadillos from Cerrado tested positive for P. brasiliensis DNA, in the lungs, spleen, liver fragments. Also, by molecular analysis, all 43 individuals were negative for M. leprae and Leishmania spp. Armadillos were infected by T. cruzi, T. rangeli, P. brasiliensis and presented seric antibodies to T. gondii, highlighting the importance of those armadillos could have in the epidemiology of zoonotic parasites.
Collapse
Affiliation(s)
- Danilo Kluyber
- Associate Researcher, Naples Zoo at Caribbeans Gardens, Naples, FL, USA.,Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil
| | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Associate Researcher, The Royal Zoological Society of Scotland (RZSS), Edinburgh, Scotland
| | - Nina Attias
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Mato Grosso do Sul, Campo Grande, Brazil
| | - Gabriel F Massocato
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Associate Researcher, Houston Zoo, Houston, TX, USA
| | - Solange M Gennari
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, USP, São Paulo, Brazil.,Programa de Pós Graduação em Saúde Única e Bem-Estar Animal, Universidade Santo Amaro, UNISA, São Paulo, Brazil
| | - Herbert S Soares
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, USP, São Paulo, Brazil.,Programa de Pós Graduação em Saúde Única e Bem-Estar Animal, Universidade Santo Amaro, UNISA, São Paulo, Brazil
| | - Eduardo Bagagli
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Sandra M G Bosco
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Hans G Garcés
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Jessica da S Ferreira
- Laboratório Multi-user do, Departamento de Parasitologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Rio de Janeiro, Seropédica, Brazil.,Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda N B Fontes
- Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Philip N Suffys
- Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Luciana R Meireles
- Laboratório de Protozoologia, Instituto de Medicina Tropical de São Paulo da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana M Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Expedito J A Luna
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - André L R Roque
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Avanzi C, Singh P, Truman RW, Suffys PN. Molecular epidemiology of leprosy: An update. Infect Genet Evol 2020; 86:104581. [PMID: 33022427 DOI: 10.1016/j.meegid.2020.104581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022]
Abstract
Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology of leprosy bacilli through genomic approaches, the exact mechanisms of transmission is still unclear and the factors underlying pathological variation of the disease in different patients remain as major gaps in our knowledge about leprosy. Despite these difficulties, the last two decades have seen the development of genotyping procedures based on PCR-sequencing of target loci as well as by the genome-wide analysis of an increasing number of geographically diverse isolates of leprosy bacilli. This has provided a foundation for molecular epidemiology studies that are bringing a better understanding of strain evolution associated with ancient human migrations, and phylogeographical insights about the spread of disease globally. This review discusses the advantages and drawbacks of the main tools available for molecular epidemiological investigations of leprosy and summarizes various methods ranging from PCR-based genotyping to genome-typing techniques. We also describe their main applications in analyzing the short-range and long-range transmission of the disease. Finally, we summarise the current gaps and challenges that remain in the field of molecular epidemiology of leprosy.
Collapse
Affiliation(s)
- Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Pushpendra Singh
- Indian Council of Medical Research - National Institute of Research in Tribal Health, Jabalpur, India
| | - Richard W Truman
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LO, USA
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria - Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
| |
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
7
|
Panzenhagen PHN, Cabral CC, Suffys PN, Franco RM, Rodrigues DP, Conte-Junior CA. Comparative genome analysis and characterization of the Salmonella Typhimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach. Lett Appl Microbiol 2018; 66:352-359. [PMID: 29397031 DOI: 10.1111/lam.12859] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/11/2018] [Accepted: 01/20/2018] [Indexed: 02/03/2023]
Abstract
Salmonella pathogenicity relies on virulence factors many of which are clustered within the Salmonella pathogenicity islands. Salmonella also harbours mobile genetic elements such as virulence plasmids, prophage-like elements and antimicrobial resistance genes which can contribute to increase its pathogenicity. Here, we have genetically characterized a selected S. Typhimurium strain (CCRJ_26) from our previous study with Multiple Drugs Resistant profile and high-frequency PFGE clonal profile which apparently persists in the pork production centre of Rio de Janeiro State, Brazil. By whole-genome sequencing, we described the strain's genome virulent content and characterized the repertoire of bacterial plasmids, antibiotic resistance genes and prophage-like elements. Here, we have shown evidence that strain CCRJ_26 genome possible represent a virulence-associated phenotype which may be potentially virulent in human infection. SIGNIFICANCE AND IMPACT OF THE STUDY Whole-genome sequencing technologies are still costly and remain underexplored for applied microbiology in Brazil. Hence, this genomic description of S. Typhimurium strain CCRJ_26 will provide help in future molecular epidemiological studies. The analysis described here reveals a quick and useful pipeline for bacterial virulence characterization using whole-genome sequencing approach.
Collapse
Affiliation(s)
- P H N Panzenhagen
- Food Science Program, Chemistry Institute, University Federal of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Food Technology, Faculty of Veterinary Medicine, Federal Fluminense University (UFF), Niterói, Rio de Janeiro, Brazil
| | - C C Cabral
- Department of Food Technology, Faculty of Veterinary Medicine, Federal Fluminense University (UFF), Niterói, Rio de Janeiro, Brazil.,Faculty of Veterinary Medicine, Severino Sombra University (USS), Vassouras, Rio de Janeiro, Brazil
| | - P N Suffys
- Laboratory of Molecular Biology and Diagnosis of Infectious Diseases, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - R M Franco
- Department of Food Technology, Faculty of Veterinary Medicine, Federal Fluminense University (UFF), Niterói, Rio de Janeiro, Brazil
| | - D P Rodrigues
- National Reference Laboratory Diagnosis of Enteric Bacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - C A Conte-Junior
- Food Science Program, Chemistry Institute, University Federal of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Food Technology, Faculty of Veterinary Medicine, Federal Fluminense University (UFF), Niterói, Rio de Janeiro, Brazil.,National Institute of Quality Control in Health, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| |
Collapse
|
8
|
Fontes ANB, Lima LNGC, Mota RMS, Almeida RLF, Pontes MA, Gonçalves HDS, Frota CC, Vissa VD, Brennan PJ, Guimaraes RJPS, Kendall C, Kerr LRFS, Suffys PN. Genotyping of Mycobacterium leprae for better understanding of leprosy transmission in Fortaleza, Northeastern Brazil. PLoS Negl Trop Dis 2017; 11:e0006117. [PMID: 29244821 PMCID: PMC5747459 DOI: 10.1371/journal.pntd.0006117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 12/29/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022] Open
Abstract
Leprosy is endemic in large part of Brazil with 28,761 new patients in 2015, the second largest number worldwide and reaches 9/10.000 in highly endemic regions and 2.7/10.000 in the city of Fortaleza, Ceará, Northeast Brazil. For better understanding of risk factors for leprosy transmission, we conducted an epidemiologic study supplemented by 17 locus VNTR and SNP 1-4 typing of Mycobacterium leprae in skin biopsy samples from new multibacillary (MB) patients diagnosed at a reference center in 2009 and 2010. Among the 1,519 new patients detected during the study period, 998 (65.7%) were MB and we performed DNA extraction and genotyping on 160 skin biopsy samples, resulting in 159 (16%) good multilocus VNTR types. Thirty-eight of these patients also provided VNTR types from M. leprae in nasal swabs. The SNP-Type was obtained for 157 patients and 87% were of type 4. Upon consideration all VNTR markers, 156 different genotypes and three pairs with identical genotypes were observed; no epidemiologic relation could be observed between individuals in these pairs. Considerable variability in differentiating index (DI) was observed between the different markers and the four with highest DI [(AT)15, (TA)18, (AT)17 and (GAA)21] frequently demonstrated differences in copy number when comparing genotypes from both type of samples. Excluding these markers from analysis resulted in 83 genotypes, 20 of which included 96 of the patients (60.3%). These clusters were composed of two (n = 8), three (n = 6), four (n = 1), five (n = 2), six (n = 1), 19 (n = 1) and 23 (n = 23) individuals and suggests that recent transmission is contributing to the maintenance of leprosy in Fortaleza. When comparing epidemiological and clinical variables among patients within clustered or with unique M. leprae genotypes, a positive bacterial index in skin biopsies and knowledge of working with someone with the disease were significantly associated with clustering. A tendency to belong to a cluster was observed with later notification of disease (mean value of 3.4 months) and having disability grade 2. A tendency for lack of clustering was observed for patients who reported to have lived with another leprosy case but this might be due to lack of inclusion of household contacts in the study. Although clusters were spread over the city, kernel analysis revealed that some of the patients belonging to the two major clusters were spatially related to some neighborhoods that report poverty and high disease incidence in children. Finally, inclusion of genotypes from nasal swabs might be warranted. A major limitation of the study is that sample size of 160 patients from a two year period represents only 15% of the new patients and this could have weakened statistical outcomes. This is the first molecular epidemiology study of leprosy in Brazil and although the high clustering level suggests that recent transmission is the major cause of disease in Fortaleza; the existence of two large clusters needs further investigation.
Collapse
Affiliation(s)
- Amanda N. B. Fontes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Rosa M. S. Mota
- Department of Statistics and Applied Mathematics, Federal University of Ceará, Fortaleza, Brazil
| | - Rosa L. F. Almeida
- Post Graduation Program of Public Health, University of Fortaleza, Fortaleza, CE, Brazil
| | - Maria A. Pontes
- Reference Center on Dermatology Dona Libânia, State Health Office, Fortaleza, Brazil
| | | | | | - Varalakshmi D. Vissa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | - Patrick J. Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | | | - Carl Kendall
- Department of Global Community Health and Behavioral Sciences, Tulane School of Public Health and Tropical Medicine, New Orleans, United States
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Ligia R. F. S. Kerr
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Philip N. Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
- Department of Biomedical Sciences, Mycobacteriology Unit, Tropical Institute of Medicine, Antwerp, Belgium
- * E-mail:
| |
Collapse
|
9
|
Lima LNGC, Fontes ANB, Li W, Suffys PN, Vissa VD, Mota RMS, Almeida RLF, Pontes MA, Gonçales HDS, Frota CC, Rodrigues LC, Kendall C, Kerr LRFS. Intrapatient comparison of Mycobacterium leprae by VNTR analysis in nasal secretions and skin biopsy in a Brazilian leprosy endemic region. LEPROSY REV 2016; 87:486-500. [PMID: 30226353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
BACKGROUND This study compares the strains of genotypes of M. leprae from nasal secretions (NS) and skin biopsy (SB) in the same patient, supplementing conventional epidemiology to gain insight into the infection of leprosy in Fortaleza, Brazil. METHODS The sample consisted of 38 newly diagnosed leprosy patients attending the National Reference Center of Dermatology Dona Libania (CDERM), in Fortaleza, who tested positive for M. leprae by PCR in DNA extracts of nasal secretions. DNA was also extracted from skin biopsy (SB) scrapings of each patient and used for multiplex PCR amplification of M. leprae VNTR loci. The number of repeats at 15 loci were determined by the fragment length analysis method. RESULTS Locus VNTR genotypes were achieved in 38 NS, and in 38 SB specimens. M. leprae strains differed in their genotypes in paired specimens in all but two of 38 patients. The genotype similarity in the remainder ranged from 53% to 87%. CONCLUSION M. leprae 15 VNTR loci genotypes of paired nasal and biopsy skin samples from five patients were identical, while as many as seven loci differed in the 33 other patients. When the NS and biopsy genotypes were pooled and compared, it was found that there was a great variability among different VNTR markers. It is important to investigate other molecular markers suitable for typing genetic variations of the bacilli.
Collapse
|
10
|
Lima LNGC, Fontes ANB, Li W, Suffys PN, Vissa VD, Mota RMS, Almeida RLF, Pontes MA, Gonçalves HDS, Frota CC, Rodrigues LC, Kendall C, Kerr LRFS. Intrapatient comparison of Mycobacterium leprae by VNTR analysis in nasal secretions and skin biopsy in a Brazilian leprosy endemic region. LEPROSY REV 2016. [DOI: 10.47276/lr.87.4.486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
11
|
Sacchi FPC, Praça RM, Tatara MB, Simonsen V, Ferrazoli L, Croda MG, Suffys PN, Ko AI, Andrews JR, Croda J. Prisons as reservoir for community transmission of tuberculosis, Brazil. Emerg Infect Dis 2015; 21:452-5. [PMID: 25642998 PMCID: PMC4344267 DOI: 10.3201/eid2103.140896] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We conducted a population-based study of tuberculosis (TB) cases in Dourados, Brazil, to assess the relationship between incarceration and TB in the general population. Incarceration was associated with TB in an urban population; 54% of Mycobacterium tuberculosis strains were related to strains from persons in prisons. TB control in prisons is critical for reducing disease prevalence.
Collapse
|
12
|
Araújo CP, Osório ALAR, Jorge KSG, Ramos CAN, Souza Filho AF, Vidal CES, Vargas APC, Roxo E, Rocha AS, Suffys PN, Fonseca AA, Silva MR, Barbosa Neto JD, Cerqueira VD, Araújo FR. Direct detection of Mycobacterium tuberculosis complex in bovine and bubaline tissues through nested-PCR. Braz J Microbiol 2014; 45:633-40. [PMID: 25242951 PMCID: PMC4166292 DOI: 10.1590/s1517-83822014000200035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 03/14/2014] [Indexed: 11/22/2022] Open
Abstract
Post-mortem bacterial culture and specific biochemical tests are currently performed to characterize the etiologic agent of bovine tuberculosis. Cultures take up to 90 days to develop. A diagnosis by molecular tests such as PCR can provide fast and reliable results while significantly decreasing the time of confirmation. In the present study, a nested-PCR system, targeting rv2807, with conventional PCR followed by real-time PCR, was developed to detect Mycobacterium tuberculosis complex (MTC) organisms directly from bovine and bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other Actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. Regarding the analytical sensitivity, DNA of the M. bovis AN5 strain was detected up to 1.5 pg by nested-PCR, whereas DNA of M. tuberculosis H37Rv strain was detected up to 6.1 pg. The nested-PCR system showed 100% analytical specificity for MTC when tested with DNA of reference strains of non-tuberculous mycobacteria and closely-related Actinomycetales. A clinical sensitivity level of 76.7% was detected with tissues samples positive for MTC by means of the culture and conventional PCR. A clinical specificity of 100% was detected with DNA from tissue samples of cattle with negative results in the comparative intradermal tuberculin test. These cattle exhibited no visible lesions and were negative in the culture for MTC. The use of the nested-PCR assay to detect M. tuberculosis complex in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis.
Collapse
Affiliation(s)
- Cristina P Araújo
- Programa de Pós-Graduação em Ciência Animal Faculdade de Medicina Veterinária e Zootecnia Universidade Federal de Mato Grosso do Sul Campo GrandeMS Brazil Programa de Pós-Graduação em Ciência Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Ana Luiza A R Osório
- Programa de Pós-Graduação em Ciência Animal Faculdade de Medicina Veterinária e Zootecnia Universidade Federal de Mato Grosso do Sul Campo GrandeMS Brazil Programa de Pós-Graduação em Ciência Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Klaudia S G Jorge
- Programa de Pós-Graduação em Ciência Animal Faculdade de Medicina Veterinária e Zootecnia Universidade Federal de Mato Grosso do Sul Campo GrandeMS Brazil Programa de Pós-Graduação em Ciência Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Carlos A N Ramos
- Faculdade de Medicina Veterinária e Zootecnia Universidade Federal de Mato Grosso do Sul Campo GrandeMS Brazil Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Antonio F Souza Filho
- Programa de Pós-Graduação em Ciência Animal Faculdade de Medicina Veterinária e Zootecnia Universidade Federal de Mato Grosso do Sul Campo GrandeMS Brazil Programa de Pós-Graduação em Ciência Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Carlos E S Vidal
- Programa de Pós-Graduação em Medicina Veterinária Universidade Federal de Santa Maria Santa MariaRS Brazil Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Agueda P C Vargas
- Programa de Pós-Graduação em Medicina Veterinária Universidade Federal de Santa Maria Santa MariaRS Brazil Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Eliana Roxo
- Instituto Biológico de São Paulo São PauloSP Brazil Instituto Biológico de São Paulo, São Paulo, SP, Brazil
| | - Adalgiza S Rocha
- Fundação Oswaldo Cruz Rio de JaneiroRJ Brazil Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Philip N Suffys
- Fundação Oswaldo Cruz Rio de JaneiroRJ Brazil Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Antônio A Fonseca
- Laboratório Nacional Agropecuário Pedro LeopoldoMG Brazil Laboratório Nacional Agropecuário, Pedro Leopoldo, MG, Brazil
| | - Marcio R Silva
- Embrapa Gado de Leite Juiz de ForaMG Brazil Embrapa Gado de Leite, Juiz de Fora, MG, Brazil
| | - José D Barbosa Neto
- Universidade Federal do Pará CastanhalPA Brazil Universidade Federal do Pará, Castanhal, PA, Brazil
| | - Valíria D Cerqueira
- Universidade Federal do Pará CastanhalPA Brazil Universidade Federal do Pará, Castanhal, PA, Brazil
| | - Flábio R Araújo
- Embrapa Gado de Corte Campo GrandeMS Brazil Embrapa Gado de Corte, Campo Grande, MS, Brazil
| |
Collapse
|
13
|
de Freitas FAD, Bernardo V, Gomgnimbou MK, Sola C, Siqueira HR, Pereira MAS, Fandinho FCO, Gomes HM, Araújo MEI, Suffys PN, Marques EA, Albano RM. Multidrug resistant Mycobacterium tuberculosis: a retrospective katG and rpoB mutation profile analysis in isolates from a reference center in Brazil. PLoS One 2014; 9:e104100. [PMID: 25093512 PMCID: PMC4122415 DOI: 10.1371/journal.pone.0104100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/07/2014] [Indexed: 01/27/2023] Open
Abstract
Background Multidrug resistance is a critical factor in tuberculosis control. To gain better understanding of multidrug resistant tuberculosis in Brazil, a retrospective study was performed to compare genotypic diversity and drug resistance associated mutations in Mycobacterium tuberculosis isolates from a national reference center. Methods and Findings Ninety-nine multidrug resistant isolates from 12 Brazilian states were studied. Drug-resistance patterns were determined and the rpoB and katG genes were screened for mutations. Genotypic diversity was investigated by IS6110-RFLP and Luminex 47 spoligotyping. Mutations in rpoB and katG were seen in 91% and 93% of the isolates, respectively. Codon 315 katG mutations occurred in 82.8% of the isolates with a predominance of the Ser315Thr substitution. Twenty-five isolates were clustered in 11 groups with identical IS6110-RFLP patterns while 74 showed unique patterns with no association between mutation frequencies or susceptibility profiles. The most prevalent spoligotyping lineages were LAM (47%), T (17%) and Haarlen (12%). The Haarlen lineage showed a higher frequency of codon 516 rpoB mutations while codon 531 mutations prevailed in the other isolates. Conclusions Our data suggest that there were no major multidrug resistant M. tuberculosis strains transmitted among patients referred to the reference center, indicating an independent acquisition of resistance. In addition, drug resistance associated mutation profiles were well established among the main spoligotyping lineages found in these Brazilian multidrug resistant isolates, providing useful data for patient management and treatment.
Collapse
Affiliation(s)
- Flávia A. D. de Freitas
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vagner Bernardo
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie– Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie– Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Hélio R. Siqueira
- Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia A. S. Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fátima C. O. Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcelo E. I. Araújo
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Philip N. Suffys
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Elizabeth A. Marques
- Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|
14
|
Alzamora Filho F, Vasconcellos SE, Gomes HM, Cavalcante MP, Suffys PN, Costa JN. Múltiplas estirpes de isolados de Mycobacteriumbovis identificados por tipagem molecular em bovinos abatidos em matadouros-frigoríficos. Pesq Vet Bras 2014. [DOI: 10.1590/s0100-736x2014000200001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O objetivo do presente trabalho foi utilizar métodos bacteriológicos e moleculares para a identificação do Mycobacteriumbovis em lesões observadas em carcaças de bovinos durante a inspeção postmortem de rotina em matadouros-frigoríficos com serviço de inspeção oficial. Foi acompanhado o abate e a inspeção de 825.394 bovinos, sadios ao exame ante mortem pelo serviço de inspeção oficial em dez matadouros-frigoríficos do estado da Bahia. Carcaça de 180 bovinos apresentaram lesões sugestivas de tuberculose e por outras linfadenites. No isolamento bacteriano, 25 amostras apresentaram crescimento disgônico de colônias de coloração creme-amareladas em meio de cultura Stonebrink-Leslie. Desses isolados, 14 foram identificados como M. bovis PCR multiplex e pela técnica do spoligotyping foram discriminados oito diferentes espoligotipos do M. bovis, sendo sete descritos na literatura e um novo spoligotipo sem descrição anterior. O espoligotipo majoritário foi o SB0121, com cinco amostras, sendo descrito no Brasil e em outros países, seguidos por dois clusters, SB295 e SB1055, com dois isolados cada. O espoligotipo SB1145 e SB1648 foram referidos apenas no Brasil e Dinamarca, respectivamente. O espoligotipo SB140 já foi encontrado no Brasil, Argentina, Uruguai e Paraguai. Estes resultados demonstram que os espoligotipos obtidos são compartilhados, até o momento, entre estados brasileiros e entre países da América Latina e Europa. Sendo assim, a discriminação molecular de isolados de M. bovis através do Spoligotyping constitui-se numa ferramenta para estudos epidemiológicos da tuberculose bovina no Estado da Bahia.
Collapse
|
15
|
Perizzolo PF, Dalla Costa ER, Ribeiro AW, Spies FS, Ribeiro MO, Dias CF, Unis G, Almeida da Silva P, Gomes HM, Suffys PN, Rossetti MLR. Characteristics of multidrug-resistant Mycobacterium tuberculosis in southern Brazil. Tuberculosis (Edinb) 2012; 92:56-9. [DOI: 10.1016/j.tube.2011.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/08/2011] [Accepted: 09/20/2011] [Indexed: 11/30/2022]
|
16
|
Abadia E, Zhang J, Ritacco V, Kremer K, Ruimy R, Rigouts L, Gomes HM, Elias AR, Fauville-Dufaux M, Stoffels K, Rasolofo-Razanamparany V, Garcia de Viedma D, Herranz M, Al-Hajoj S, Rastogi N, Garzelli C, Tortoli E, Suffys PN, van Soolingen D, Refrégier G, Sola C. The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: providing guidelines for Quality Assurance when working on membranes. BMC Infect Dis 2011; 11:110. [PMID: 21527037 PMCID: PMC3107175 DOI: 10.1186/1471-2334-11-110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 04/28/2011] [Indexed: 11/25/2022] Open
Abstract
Background The classical spoligotyping technique, relying on membrane reverse line-blot hybridization of the spacers of the Mycobacterium tuberculosis CRISPR locus, is used world-wide (598 references in Pubmed on April 8th, 2011). However, until now no inter-laboratory quality control study had been undertaken to validate this technique. We analyzed the quality of membrane-based spoligotyping by comparing it to the recently introduced and highly robust microbead-based spoligotyping. Nine hundred and twenty-seven isolates were analyzed totaling 39,861 data points. Samples were received from 11 international laboratories with a worldwide distribution. Methods The high-throughput microbead-based Spoligotyping was performed on CTAB and thermolyzate DNA extracted from isolated Mycobacterium tuberculosis complex (MTC) strains coming from the genotyping participating centers. Information regarding how the classical Spoligotyping method was performed by center was available. Genotype discriminatory analyses were carried out by comparing the spoligotypes obtained by both methods. The non parametric U-Mann Whitney homogeneity test and the Spearman rank correlation test were performed to validate the observed results. Results Seven out of the 11 laboratories (63 %), perfectly typed more than 90% of isolates, 3 scored between 80-90% and a single center was under 80% reaching 51% concordance only. However, this was mainly due to discordance in a single spacer, likely having a non-functional probe on the membrane used. The centers using thermolyzate DNA performed as well as centers using the more extended CTAB extraction procedure. Few centers shared the same problematic spacers and these problematic spacers were scattered over the whole CRISPR locus (Mostly spacers 15, 14, 18, 37, 39, 40). Conclusions We confirm that classical spoligotyping is a robust method with generally a high reliability in most centers. The applied DNA extraction procedure (CTAB or thermolyzate) did not affect the results in this study. However performance was center-dependent, suggesting that training is a key component in quality assurance of spoligotyping. Overall, no particular spacer yielded a higher degree of deviating results, suggesting that errors occur randomly either in the process of re-using membranes, or during the reading of the results and transferring of data from the film to a digital file. Last, the performance of the microbead-based method was excellent as previously shown by Cowan et al. (J. Clin. Microbiol. 2004) and Zhang et al. (J. Med. Microbiol. 2009) and demonstrated the proper detection of spacer 15 that is known to occasionally give weak signals in the classical spoligotyping.
Collapse
Affiliation(s)
- Edgar Abadia
- Institute of Genetics and Microbiology UMR8621, CNRS Université Paris-Sud 11 Universud, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Vasconcellos SEG, Huard RC, Niemann S, Kremer K, Santos AR, Suffys PN, Ho JL. Distinct genotypic profiles of the two major clades of Mycobacterium africanum. BMC Infect Dis 2010; 10:80. [PMID: 20350321 PMCID: PMC2859774 DOI: 10.1186/1471-2334-10-80] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 03/29/2010] [Indexed: 12/03/2022] Open
Abstract
Background Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis (TB) and a member of the M. tuberculosis complex (MTC). Additional MTC species that cause TB in humans and other mammals include Mycobacterium africanum and Mycobacterium bovis. One result of studies interrogating recently identified MTC phylogenetic markers has been the recognition of at least two distinct lineages of M. africanum, known as West African-1 and West African-2. Methods We screened a blinded non-random set of MTC strains isolated from TB patients in Ghana (n = 47) for known chromosomal region-of-difference (RD) loci and single nucleotide polymorphisms (SNPs). A MTC PCR-typing panel, single-target standard PCR, multi-primer PCR, PCR-restriction fragment analysis, and sequence analysis of amplified products were among the methods utilized for the comparative evaluation of targets and identification systems. The MTC distributions of novel SNPs were characterized in the both the Ghana collection and two other diverse collections of MTC strains (n = 175 in total). Results The utility of various polymorphisms as species-, lineage-, and sublineage-defining phylogenetic markers for M. africanum was determined. Novel SNPs were also identified and found to be specific to either M. africanum West African-1 (Rv1332523; n = 32) or M. africanum West African-2 (nat751; n = 27). In the final analysis, a strain identification approach that combined multi-primer PCR targeting of the RD loci RD9, RD10, and RD702 was the most simple, straight-forward, and definitive means of distinguishing the two clades of M. africanum from one another and from other MTC species. Conclusion With this study, we have organized a series of consistent phylogenetically-relevant markers for each of the distinct MTC lineages that share the M. africanum designation. A differential distribution of each M. africanum clade in Western Africa is described.
Collapse
Affiliation(s)
- Sidra E Gonçalves Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil 4365, Rio de Janeiro, Brazil
| | | | | | | | | | | | | |
Collapse
|
18
|
Teixeira RLF, Silva FP, Silveira AR, Cabello PH, Mendonça-Lima L, Rabahi MF, Kritski AL, Mello FCQ, Suffys PN, de Miranda AB, Santos AR. Sequence analysis of NAT2 gene in Brazilians: identification of undescribed single nucleotide polymorphisms and molecular modeling of the N-acetyltransferase 2 protein structure. Mutat Res 2010; 683:43-49. [PMID: 19909761 DOI: 10.1016/j.mrfmmm.2009.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 09/30/2009] [Accepted: 10/16/2009] [Indexed: 05/28/2023]
Abstract
N-Acetyltransferase 2 (NAT2) metabolizes a variety of xenobiotics that includes many drugs, chemicals and carcinogens. This enzyme is genetically variable in human populations and polymorphisms in the NAT2 gene have been associated with drug toxicity and efficacy as well as cancer susceptibility. Here, we have focused on the identification of NAT2 variants in Brazilian individuals from two different regions, Rio de Janeiro and Goiás, by direct sequencing, and on the characterization of new haplotypes after cloning and re-sequencing. Upon analysis of DNA samples from 404 individuals, six new SNPs (c.29T>C, c.152G>T, c.203G>A, c.228C>T, c.458C>T and c.600A>G) and seven new NAT2 alleles were identified with different frequencies in Rio de Janeiro and Goiás. All new SNPs were found as singletons (observed only once in 808 genes) and were confirmed by three independent technical replicates. Molecular modeling and structural analysis suggested that p.Gly51Val variant may have an important effect on substrate recognition by NAT2. We also observed that amino acid change p.Cys68Tyr would affect acetylating activity due to the resulting geometric restrictions and incompatibility of the functional group in the Tyr side chain with the admitted chemical mechanism for catalysis by NATs. Moreover, other variants, such like p.Thr153Ile, p.Thr193Met, p.Pro228Leu and p.Val280Met, may lead to the presence of hydrophobic residues on NAT2 surface involved in protein aggregation and/or targeted degradation. Finally, the new alleles NAT2*6H and NAT2*5N, which showed the highest frequency in the Brazilian populations considered in this study, may code for a slow activity. Functional studies are needed to clarify the mechanisms by which new SNPs interfere with acetylation.
Collapse
Affiliation(s)
- Raquel L F Teixeira
- Laboratory of Human Genetics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Dalla Costa ER, Ribeiro MO, Silva MSN, Arnold LS, Rostirolla DC, Cafrune PI, Espinoza RC, Palaci M, Telles MA, Ritacco V, Suffys PN, Lopes ML, Campelo CL, Miranda SS, Kremer K, da Silva PEA, Fonseca LDS, Ho JL, Kritski AL, Rossetti MLR. Correlations of mutations in katG, oxyR-ahpC and inhA genes and in vitro susceptibility in Mycobacterium tuberculosis clinical strains segregated by spoligotype families from tuberculosis prevalent countries in South America. BMC Microbiol 2009; 9:39. [PMID: 19228426 PMCID: PMC2650697 DOI: 10.1186/1471-2180-9-39] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 02/19/2009] [Indexed: 11/17/2022] Open
Abstract
Background Mutations associated with resistance to rifampin or streptomycin have been reported for W/Beijing and Latin American Mediterranean (LAM) strain families of Mycobacterium tuberculosis. A few studies with limited sample sizes have separately evaluated mutations in katG, ahpC and inhA genes that are associated with isoniazid (INH) resistance. Increasing prevalence of INH resistance, especially in high tuberculosis (TB) prevalent countries is worsening the burden of TB control programs, since similar transmission rates are noted for INH susceptible and resistant M. tuberculosis strains. Results We, therefore, conducted a comprehensive evaluation of INH resistant M. tuberculosis strains (n = 224) from three South American countries with high burden of drug resistant TB to characterize mutations in katG, ahpC and inhA gene loci and correlate with minimal inhibitory concentrations (MIC) levels and spoligotype strain family. Mutations in katG were observed in 181 (80.8%) of the isolates of which 178 (98.3%) was contributed by the katG S315T mutation. Additional mutations seen included oxyR-ahpC; inhA regulatory region and inhA structural gene. The S315T katG mutation was significantly more likely to be associated with MIC for INH ≥2 μg/mL. The S315T katG mutation was also more frequent in Haarlem family strains than LAM (n = 81) and T strain families. Conclusion Our data suggests that genetic screening for the S315T katG mutation may provide rapid information for anti-TB regimen selection, epidemiological monitoring of INH resistance and, possibly, to track transmission of INH resistant strains.
Collapse
Affiliation(s)
- Elis R Dalla Costa
- State Foundation for Production and Research in Health (FEPPS), Porto Alegre, Brazil.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Ritacco V, López B, Cafrune PI, Ferrazoli L, Suffys PN, Candia N, Vásquez L, Realpe T, Fernández J, Lima KV, Zurita J, Robledo J, Rossetti ML, Kritski AL, Telles MA, Palomino JC, Heersma H, van Soolingen D, Kremer K, Barrera L. Mycobacterium tuberculosis strains of the Beijing genotype are rarely observed in tuberculosis patients in South America. Mem Inst Oswaldo Cruz 2008; 103:489-92. [PMID: 18797764 DOI: 10.1590/s0074-02762008000500014] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 07/04/2008] [Indexed: 11/21/2022] Open
Abstract
The frequency of the Beijing genotype of Mycobacterium tuberculosis as a cause of tuberculosis (TB) in South America was determined by analyzing genotypes of strains isolated from patients that had been diagnosed with the disease between 1997 and 2003 in seven countries of the subcontinent. In total, 19 of the 1,202 (1.6%) TB cases carried Beijing isolates, including 11 of the 185 patients from Peru (5.9%), five of the 512 patients from Argentina (1.0%), two of the 252 Brazilian cases (0.8%), one of the 166 patients from Paraguay (0.6%) and none of the samples obtained from Chile (35), Colombia (36) and Ecuador (16). Except for two patients that were East Asian immigrants, all cases with Beijing strains were native South Americans. No association was found between carrying a strain with the Beijing genotype and having drug or multi-drug resistant disease. Our data show that presently transmission of M. tuberculosis strains of the Beijing genotype is not frequent in Latin America. In addition, the lack of association of drug resistant TB and infection with M. tuberculosis of the Beijing genotype observed presently demands efforts to define better the contribution of the virulence and lack of response to treatment to the growing spread of Beijing strains observed in other parts of the world.
Collapse
Affiliation(s)
- Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos Malbrá, Buenos Aires, Argentina.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Oelemann MC, Fontes ANB, Pereira MADS, Bravin Y, Silva G, Degrave W, Carvalho ACC, Brito RC, Kritski AL, Suffys PN. Typing of Mycobacterium tuberculosis strains isolated in Community Health Centers of Rio de Janeiro City, Brazil. Mem Inst Oswaldo Cruz 2008; 102:455-62. [PMID: 17612765 DOI: 10.1590/s0074-02762007005000034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 03/12/2007] [Indexed: 11/21/2022] Open
Abstract
Fingerprinting of Mycobacterium tuberculosis strains from tuberculosis (TB) patients attended in Community Health Centers (CHCs) of Rio de Janeiro was performed to verify possible risk factors for TB transmission. A prospective community-based study was performed during the period of July 1996 to December 1996 by collecting sputum samples of 489 patients in 11 different CHCs in four different planning areas (APs) of the city. Bacteriological, clinical, and epidemiological information was collected and M. tuberculosis genotypes defined after restriction fragment length polymorphism (IS6110-RFLP) and double repetitive element (DRE) fingerprinting of RFLP-clustered cases. Risk factors for TB transmission were looked for using three levels of cluster stringency. Among 349 (71%) positive cultures obtained, IS6110-RFLP typing could be performed on strains from 153 different patients. When using identity of RFLP patterns as cluster definition, 49 (32%) of the strains belonged to a cluster and none of the clinical or epidemiologic characteristics was associated with higher clustering levels. However, higher clustering level was observed in the AP including the central region of the city when compared to others. This strongly suggests that more recent transmission occurs in that area and this may be related with higher incidence of TB and HIV in this region.
Collapse
Affiliation(s)
- Maraníbia C Oelemann
- Departamento de Micobacterioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Teixeira RLF, Miranda AB, Pacheco AG, Lopes MQP, Fonseca-Costa J, Rabahi MF, Melo HM, Kritski AL, Mello FCQ, Suffys PN, Santos AR. Genetic profile of the arylamine N-acetyltransferase 2 coding gene among individuals from two different regions of Brazil. Mutat Res 2007; 624:31-40. [PMID: 17509624 DOI: 10.1016/j.mrfmmm.2007.03.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 01/11/2007] [Accepted: 03/01/2007] [Indexed: 05/15/2023]
Abstract
Arylamine N-acetyltranferase 2 is the main enzyme responsible for the isoniazid metabolization into hepatotoxic intermediates and the degree of hepatotoxicity severity has been attributed to genetic variability in the NAT2 gene. The main goal of this study was to describe the genetic profile of the NAT2 gene in individuals from two different regions of Brazil: Rio de Janeiro and Goiás States. Therefore, after preparation of DNA samples from 404 individuals, genotyping of the coding region of NAT2 was performed by direct PCR sequencing. Thirteen previously described SNPs were detected in these Brazilian populations, from which seven: 191 G>A; 282 C>T; 341 T>C; 481 C>T; 590 G>A; 803 A>G and 857 G>A are the most frequent in other populations. The presence of so-called ethnic-specific SNPs in our population is in accordance with the Brazilians' multiple ancestry. Upon allele and genotype analysis, the most frequent NAT2 alleles were respectively NAT2*5B (33%), NAT2*6A (26%) and NAT2*4 (20%) being NAT2*5/*5 the more prevalent genotype (31.7%). These results clearly demonstrate the predominance in the studied Brazilian groups of NAT2 alleles associated with slow over the fast and intermediate acetylator genotypes. Additionally, in Rio de Janeiro, a significantly higher frequency of intermediate acetylation status was found when compared to Goiás (42.5% versus 25%) (p=0.05), demonstrating that different regions of a country with a population characterized by a multi-ethnic ancestry may present a large degree of variability in NAT2 allelic frequencies. This finding has implications in the determination of nationwide policies for use of appropriate anti-TB drugs.
Collapse
Affiliation(s)
- Raquel L F Teixeira
- Laboratory of Molecular Biology Applied to Mycobacteria, Department of Mycobacteriosis, IOC/Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, CEP 21040-900, Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Lazzarini LCO, Huard RC, Boechat NL, Gomes HM, Oelemann MC, Kurepina N, Shashkina E, Mello FCQ, Gibson AL, Virginio MJ, Marsico AG, Butler WR, Kreiswirth BN, Suffys PN, Lapa E Silva JR, Ho JL. Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol 2007; 45:3891-902. [PMID: 17898156 PMCID: PMC2168543 DOI: 10.1128/jcm.01394-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current study evaluated Mycobacterium tuberculosis isolates from Rio de Janeiro, Brazil, for genomic deletions. One locus in our panel of PCR targets failed to amplify in approximately 30% of strains. A single novel long sequence polymorphism (>26.3 kb) was characterized and designated RD(Rio). Homologous recombination between two similar protein-coding genes is proposed as the mechanism for deleting or modifying 10 genes, including two potentially immunogenic PPE proteins. The flanking regions of the RD(Rio) locus were identical in all strains bearing the deletion. Genetic testing by principal genetic group, spoligotyping, variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR), and IS6110-based restriction fragment length polymorphism analysis cumulatively support the idea that RD(Rio) strains are derived from a common ancestor belonging solely to the Latin American-Mediterranean spoligotype family. The RD(Rio) lineage is therefore the predominant clade causing tuberculosis (TB) in Rio de Janeiro and, as indicated by genotypic clustering in MIRU-VNTR analysis, the most significant source of recent transmission. Limited retrospective reviews of bacteriological and patient records showed a lack of association with multidrug resistance or specific risk factors for TB. However, trends in the data did suggest that RD(Rio) strains may cause a form of TB with a distinct clinical presentation. Overall, the high prevalence of this genotype may be related to enhanced virulence, transmissibility, and/or specific adaptation to a Euro-Latin American host population. The identification of RD(Rio) strains outside of Brazil points to the ongoing intercontinental dissemination of this important genotype. Further studies are needed to determine the differential strain-specific features, pathobiology, and worldwide prevalence of RD(Rio) M. tuberculosis.
Collapse
Affiliation(s)
- Luiz Claudio Oliveira Lazzarini
- Department of Medicine, Division of International Medicine and Infectious Diseases, Cornell University, Joan and Sanford I Weill Medical College, New York, NY 10021, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Senna SG, Gomes HM, Ribeiro MO, Kristki AL, Rossetti MLR, Suffys PN. In house reverse line hybridization assay for rapid detection of susceptibility to rifampicin in isolates of Mycobacterium tuberculosis. J Microbiol Methods 2006; 67:385-9. [PMID: 16814419 DOI: 10.1016/j.mimet.2006.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 04/14/2006] [Indexed: 11/29/2022]
Abstract
We developed a Reverse Hybridization Assay (RHA) slightly modified from the Rifoligotyping assay and analyzed the presence of mutations in a specific region of rpoB gene in 157 isolates (90 rifampin-resistant and 67 rifampin sensitive) of Mycobacterium tuberculosis from patients attended in South and Southeast region of Brazil. Comparing to standardized drug susceptibility testing results, the sensitivity and specificity of the RHA was respectively 93% (95% IC: 86.6%-97.2%) and 100% respectively. Additionally, a high agreement (kappa coefficient 95%) between the RHA assay and sequencing was obtained. Among the 90 rifampicin-resistant isolates, RHA identified point mutations in the following codons: 42 isolates (46.6%) in 531; 29 isolates (32.2%) in 526, 6 isolates (6.7%) in 516, 3 isolates (3.3%) in 522, 2 isolates (2.2%) in 515, 514, 513 and 1 isolate (1.1%) in 511, 524 and 525. Mutations in different codons were simultaneously identified in 8 isolates (8.9%). The RHA used in the present study had a high accuracy and can be rapidly performed. However, more reproducible hybridization conditions should be looked for to increase reliability of mutant probe interpretation.
Collapse
|
25
|
Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, de Viedma DG, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ly HM, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006; 6:23. [PMID: 16519816 PMCID: PMC1468417 DOI: 10.1186/1471-2180-6-23] [Citation(s) in RCA: 777] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 03/06/2006] [Indexed: 12/04/2022] Open
Abstract
Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
Collapse
Affiliation(s)
- Karine Brudey
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | | | - Leen Rigouts
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Wolfgang M Prodinger
- Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Andrea Gori
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Sahal A Al-Hajoj
- Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
| | - Liselotte Aristimuño
- Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
| | - Jyoti Arora
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Lothar Binder
- Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
| | | | - Angel Cataldi
- Instituto de Biotecnologia INTA, Castelar, Argentina
| | - Soonfatt Cheong
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Roland Diel
- University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
| | | | - Jason T Evans
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | | | - Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Dario Garcia de Viedma
- Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
| | - Carlo Garzelli
- Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
| | - Lidia Gazzola
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Harrison M Gomes
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Peter M Hawkey
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | - Paul D van Helden
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Gurujaj V Kadival
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | | | - Kristin Kremer
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Milan Kubin
- Municipal Institute of Hygiene, Prague, Czech Republic
| | - Savita P Kulkarni
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | - Benjamin Liens
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Troels Lillebaek
- Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
| | - Ho Minh Ly
- Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Christian Martin
- Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
| | - Igor Mokrousov
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Olga Narvskaïa
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Yun Fong Ngeow
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Ludmilla Naumann
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Stefan Niemann
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Ida Parwati
- Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
| | - Zeaur Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | | | | | | | - Sabine Rüsch-Gerdes
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Anna Sajduda
- Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
| | - Sofia Samper
- Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Igor G Shemyakin
- State Research Center for Applied Microbiology, Obolensk, Russian Federation
| | | | - Akos Somoskovi
- Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
| | - Robin A Skuce
- Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
| | - Dick van Soolingen
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Streicher
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Philip N Suffys
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Enrico Tortoli
- Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
| | | | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Tommie C Victor
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Robin M Warren
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Sook Fan Yap
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Khadiza Zaman
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | - Françoise Portaels
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| |
Collapse
|
26
|
Leite CQF, da Silva Rocha A, de Andrade Leite SR, Ferreira RMC, Suffys PN, de Souza Fonseca L, Saad MHF. A comparison of mycolic acid analysis for nontuberculous mycobacteria identification by thin-layer chromatography and molecular methods. Microbiol Immunol 2005; 49:571-8. [PMID: 16034199 DOI: 10.1111/j.1348-0421.2005.tb03642.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The development of fast, inexpensive, and reliable tests to identify nontuberculous mycobacteria (NTM) is needed. Studies have indicated that the conventional identification procedures, including biochemical assays, are imprecise. This study evaluated a proposed alternative identification method in which 83 NTM isolates, previously identified by conventional biochemical testing and in-house M. avium IS1245-PCR amplification, were submitted to the following tests: thin-layer chromatography (TLC) of mycolic acids and PCR-restriction enzyme analysis of hsp65(PRA). High-performance liquid chromatography (HPLC) analysis of mycolic acids and Southern blot analysis for M. avium IS1245 were performed on the strains that evidenced discrepancies on either of the above tests. Sixty-eight out of 83 (82%) isolates were concordantly identified by the presence of IS1245 and PRA and by TLC mycolic acid analysis. Discrepant results were found between the phenotypic and molecular tests in 12/83 (14.4%) isolates. Most of these strains were isolated from non-sterile body sites and were most probably colonizing in the host tissue. While TLC patterns suggested the presence of polymycobacterial infection in 3/83 (3.6%) cultures, this was the case in only one HPLC-tested culture and in none of those tested by PRA. The results of this study indicated that, as a phenotypic identification procedure, TLC mycolic acid determination could be considered a relatively simple and cost-effective method for routine screening of NTM isolates in mycobacteriology laboratory practice with a potential for use in developing countries. Further positive evidence was that this method demonstrated general agreement on MAC and M. simiae identification, including in the mixed cultures that predominated in the isolates of the disseminated infections in the AIDS patients under study. In view of the fact that the same treatment regimen is recommended for infections caused by these two species, TLC mycolic acid analysis may be a useful identification tool wherever molecular methods are unaffordable.
Collapse
|
27
|
Parreiras PM, Lobato FCF, Alencar AP, Figueiredo TD, Gomes HM, Boéchat N, Lage AP, Assis RA, Pereira MAS, Souza PR, Mota PMPC, Suffys PN. Drug susceptibility of Brazilian strains of Mycobacterium bovis using traditional and molecular techniques. Mem Inst Oswaldo Cruz 2004; 99:749-52. [PMID: 15654433 DOI: 10.1590/s0074-02762004000700015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Transmission of Mycobacterium bovis from cattle to humans has been reported and can cause tuberculosis (Tb) and a problem in certain risk populations. Therefore, knowledge of resistance of M. bovis towards antibiotics used for therapy of human Tb could help avoiding cure delay and treatment cost increase when dealing with drug resistant organisms. We therefore evaluated the susceptibility of M. bovis isolates towards streptomycin, isoniazide, rifampicin, ethambutol, and ethionamide, the first line antibiotics for human Tb. Therefore, 185 clinical samples from cattle with clinical signs of tuberculosis were processed and submitted to culturing and bacterial isolates to identification and drug susceptibility testing using the proportion method. Among 89 mycobacterial strains, 65 were identified as M. bovis and none were resistant to any of the antibiotics used. Confirmation of present results by future studies, enrolling a large number of isolates and designed to properly represent Brazilian regions, may favor the idea of using isoniazide preventive therapy as part of a Tb control strategy in special situations. Also, nucleic acids from bacterial isolates were submitted to rifoligotyping, a recently described reverse hybridization assay for detection of mutations causing resistance towards rifampicin. Concordance between the conventional and the molecular test was 100%, demonstrating the use of such methodology for rapid evaluation of drug susceptibility in M. bovis.
Collapse
Affiliation(s)
- Patrícia M Parreiras
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Departamento de Medicina Tropical, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Mokrousov I, Bhanu NV, Suffys PN, Kadival GV, Yap SF, Cho SN, Jordaan AM, Narvskaya O, Singh UB, Gomes HM, Lee H, Kulkarni SP, Lim KC, Khan BK, van Soolingen D, Victor TC, Schouls LM. Multicenter evaluation of reverse line blot assay for detection of drug resistance in Mycobacterium tuberculosis clinical isolates. J Microbiol Methods 2004; 57:323-35. [PMID: 15134881 DOI: 10.1016/j.mimet.2004.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Revised: 01/20/2004] [Accepted: 02/10/2004] [Indexed: 10/26/2022]
Abstract
A multicenter study was conducted with the objective to evaluate a reverse line blot (RLB) assay to detect resistance to rifampin (RIF), isoniazid (INH), streptomycin (STR), and ethambutol (EMB) in clinical isolates of Mycobacterium tuberculosis. Oligonucleotides specific for wild type and mutant (drug resistance linked) alleles of the selected codons in the genes rpoB, inhA, ahpC, rpsL, rrs, embB, were immobilized on a nylon membrane. The RLB assay conditions were optimized following analysis of DNA samples with known sequences of the targeted genes. For validation of the method at different geographical locations, the membranes were sent to seven laboratories in six countries representing the regions with high burdens of multudrug-resistant tuberculosis. The reproducibility of the assay for detection of rpoB genotypes was initially evaluated on a blinded set of twenty reference DNA samples with known allele types and overall concordant results were obtained. Further mutation analysis was performed by each laboratory on the local strains. Upon RLB analysis of 315 clinical isolates from different countries, 132 (85.2%) of 155 RIF-resistant and 28 (51.0%) of 55 EMB-resistant isolates were correctly identified, showing applicability of the assay when targeting the rpoB hot-spot region and embB306. Mutations in the inhA and ahpC promoter regions, conferring resistance to INH, were successfully identified in respectively 16.9% and 13.2% of INH-resistant strains. Likewise, mutations in rrs513 and rpsL88 that confer resistance to STR were identified in respectively 15.1% and 10.7% of STR-resistant strains. It should be mentioned that mutation analysis of the above targets usually requires rather costly DNA sequencing to which the proposed RLB assay presents rapid and inexpensive alternative. Furthermore, the proposed method requires the same simple equipment as that used for spoligotyping and permits simultaneous analysis of up to 40 samples. This technique is a first attempt to combine different targets in a single assay for prediction of antituberculosis drugs resistance. It is open to further development as it allows easy incorporation of new probes for detection of mutations in other genes associated with resistance to second-line (e.g., fluoroquinolones) and new antituberculosis compounds.
Collapse
Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Pignataro P, Rocha ADS, Nery JAC, Miranda A, Sales AM, Ferrreira H, Valentim V, Suffys PN. Leprosy and AIDS: two cases of increasing inflammatory reactions at the start of highly active antiretroviral therapy. Eur J Clin Microbiol Infect Dis 2004; 23:408-11. [PMID: 15112073 DOI: 10.1007/s10096-004-1131-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reported here are the cases of two HIV-positive patients with skin lesions suggestive of leprosy, based on clinical and pathological analysis, which worsened during the few weeks following initiation of highly active antiretroviral therapy. The lesions improved after a few weeks of multidrug therapy for leprosy. Mycobacterium leprae was confirmed by polymerase chain reaction analysis of blood in case 1 and of a biopsy sample in case 2. Neither Mycobacterium avium complex nucleic acid, which is usually associated with immune restoration syndrome, nor mycobacterial cutaneous manifestations were detected in either case.
Collapse
Affiliation(s)
- P Pignataro
- Leprosy Laboratory, Department of Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil 4365, Manguinhos, CEP 21045-900 Rio de Janeiro, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Dang DA, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Kassa-Kelembho E, Ho ML, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol 2003; 41:1963-70. [PMID: 12734235 PMCID: PMC154710 DOI: 10.1128/jcm.41.5.1963-1970.2003] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present update on the global distribution of Mycobacterium tuberculosis complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for M. tuberculosis complex, including Mycobacterium bovis, from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, a number of major and minor visual rules were also defined. A total of six major rules (A to F) with the precise description of the extra missing spacers (minor rules) were used to define 36 major clades (or families) of M. tuberculosis. Some major clades identified were the East African-Indian (EAI) clade, the Beijing clade, the Haarlem clade, the Latin American and Mediterranean (LAM) clade, the Central Asian (CAS) clade, a European clade of IS6110 low banders (X; highly prevalent in the United States and United Kingdom), and a widespread yet poorly defined clade (T). When the visual rules defined above were used for an automated labeling of the 813 shared types to define nine superfamilies of strains (Mycobacterium africanum, Beijing, M. bovis, EAI, CAS, T, Haarlem, X, and LAM), 96.9% of the shared types received a label, showing the potential for automated labeling of M. tuberculosis families in well-defined phylogeographical families. Intercontinental matches of shared types among eight continents and subcontinents (Africa, North America, Central America, South America, Europe, the Middle East and Central Asia, and the Far East) are analyzed and discussed.
Collapse
Affiliation(s)
- Ingrid Filliol
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Santos AR, Suffys PN, Vanderborght PR, Moraes MO, Vieira LMM, Cabello PH, Bakker AM, Matos HJ, Huizinga TWJ, Ottenhoff THM, Sampaio EP, Sarno EN. Role of tumor necrosis factor-alpha and interleukin-10 promoter gene polymorphisms in leprosy. J Infect Dis 2002; 186:1687-91. [PMID: 12447749 DOI: 10.1086/345366] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2002] [Revised: 08/23/2002] [Indexed: 11/03/2022] Open
Abstract
Single-nucleotide polymorphisms within the genes coding for tumor necrosis factor (TNF)-alpha and interleukin (IL)-10 have been associated with several infectious diseases. To determine whether such polymorphisms are associated with leprosy, genotyping was performed at the -308 and -238 positions of the promoter of the TNF-alpha gene in 210 and 191 patients with multibacillary (MB) leprosy, respectively; 90 and 79 patients with paucibacillary (PB) leprosy; and 92 control subjects. For the -592 and -819 positions within the promoter of the IL-10 gene, 143 patients with MB leprosy, 79 patients with PB leprosy, and 62 control subjects were included in the analysis. TNF2 allele frequency was significantly higher among control subjects than among all patients with leprosy or in the MB group (P<.05 and P<.01). For the IL-10 gene, the frequency of the homozygous -819TT genotype was significantly higher among patients than among control subjects. These data indicate that a relationship exists between TNF-alpha and IL-10 promoter polymorphisms and the development of PB leprosy.
Collapse
Affiliation(s)
- Adalberto R Santos
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Anh DD, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Källenius G, Kassa-Kelembho E, Koivula T, Ly HM, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N. Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg Infect Dis 2002; 8:1347-9. [PMID: 12453368 PMCID: PMC2738532 DOI: 10.3201/eid0811.020125] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We present a short summary of recent observations on the global distribution of the major clades of the Mycobacterium tuberculosis complex, the causative agent of tuberculosis. This global distribution was defined by data-mining of an international spoligotyping database, SpolDB3. This database contains 11708 patterns from as many clinical isolates originating from more than 90 countries. The 11708 spoligotypes were clustered into 813 shared types. A total of 1300 orphan patterns (clinical isolates showing a unique spoligotype) were also detected.
Collapse
Affiliation(s)
- Ingrid Filliol
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | - Dick van Soolingen
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Kristin Kremer
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | - Karin Brudey
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | | | - Debby V. Cousins
- Australian Reference Laboratory for Bovine Tuberculosis, Department of Agriculture, South Perth, Australia
| | | | | | | | | | | | | | - Max Gordon
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | | | - Herre Heersma
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | | | - Tuija Koivula
- Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Ho Minh Ly
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Gerald Martin
- Bundesinstitut für gesundheitlichenVerbraucherschutz und Veterinärmedizin, Jena, Germany
| | - Peter Moström
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | - Igor Mokrousov
- Pasteur Institute of Saint Petersburg, Saint Petersburg, Russia
| | | | - Olga Narvskaya
- Pasteur Institute of Saint Petersburg, Saint Petersburg, Russia
| | | | | | - Jean W Pape
- Les Centres Gheskio, Institut National de Laboratoire et de Recherche, Port-au- Prince, Haïti
- Cornell University, Ithaca, New York, USA
| | | | | | | | - Fritz Stauffer
- Bundesstaatliche bakteriologisch-serologische Untersuchungsanstalt Wien, Austria
| | | | | | | | | | | | - Christophe Sola
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | - Nalin Rastogi
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| |
Collapse
|
33
|
da Silva Rocha A, Werneck Barreto AM, Dias Campos CE, Villas-Bôas da Silva M, Fonseca L, Saad MH, Degrave WM, Suffys PN. Novel allelic variants of Mycobacteria isolated in Brazil as determined by PCR-restriction enzyme analysis of hsp65. J Clin Microbiol 2002; 40:4191-6. [PMID: 12409396 PMCID: PMC139659 DOI: 10.1128/jcm.40.11.4191-4196.2002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human isolates of Mycobacterium collected in 16 different states of Brazil were submitted to PCR-restriction analysis (PRA) of a 439-bp fragment of the hsp65 gene with HaeIII and BstEII. Fourteen allelic variants not described in clinical isolates so far were observed among 36 (10%) of 356 Brazilian strains, including a new pattern for Mycobacterium scrofulaceum, M. intracellulare, and M. flavescens, two new patterns for M. fortuitum, three new patterns each for M. gordonae and M. terrae, and one new pattern for M. avium complex-like strains. Two unidentified strains each also presented a new pattern, strongly suggesting that Mycobacterium genotypes are distributed biogeographically. The PRA procedure was also performed with 43 reference isolates belonging to 34 species, adding a further six new patterns to the identification algorithm. A database containing the normalized restriction patterns of both enzymes was constructed. Patterns available on the Internet can be introduced into this database, which will make possible the comparison of genotypes from isolates from different parts of the world.
Collapse
Affiliation(s)
- A da Silva Rocha
- Biochemistry and Molecular Biology Departmentand, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Suffys PN, da Silva Rocha A, de Oliveira M, Campos CE, Barreto AM, Portaels F, Rigouts L, Wouters G, Jannes G, van Reybroeck G, Mijs W, Vanderborght B. Rapid identification of Mycobacteria to the species level using INNO-LiPA Mycobacteria, a reverse hybridization assay. J Clin Microbiol 2001; 39:4477-82. [PMID: 11724865 PMCID: PMC88569 DOI: 10.1128/jcm.39.12.4477-4482.2001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
INNO-LiPA Mycobacteria (LiPA; Innogenetics, Zwijnaarde, Belgium) is a kit for the simultaneous detection and identification of Mycobacterium species in culture and identifies the Mycobacterium tuberculosis complex, the M. avium complex (MAC), and the following Mycobacterium species: M. kansasii, M. avium, M. intracellulare, M. scrofulaceum, M. gordonae, M. xenopi, and the M. chelonae-M. abscessus complex. The assay, which targets the 16S-23S rRNA spacer region, was evaluated on 157 mycobacterial strains that had been identified by conventional techniques and PCR-restriction enzyme analysis of the hsp65 gene (PRA). Forty-seven reference strains consisting of 37 different species and 110 human clinical isolates were submitted to the test, and all were hybridized with the Mycobacterium genus probe (MYC) on the LiPA strip (100% sensitivity). Ninety-four isolates hybridized to their corresponding species- or complex-specific probes; only one isolate phenotypically identified as M. gordonae did not react with its specific probe (99.4% accuracy). Thirty-seven MAC strains were phenotypically identified to the complex level and to the species level by LiPA as M. avium (n = 18) or M. intracellulare (n = 7) or as belonging to the M. avium-M. intracellulare-M. scrofulaceum complex (n = 12). Of the last 12 strains, 10 had M. avium PRA patterns and 2 had M. intracellulare PRA patterns. Three isolates that had been identified as a single species by conventional identification were proven to be mixed cultures by the LiPA assay. The whole procedure can be performed in 1 working day, starting with the supernatant of a small amount of bacterial mass that had been treated by freezing and then boiling.
Collapse
Affiliation(s)
- P N Suffys
- Biochemistry and Molecular Biology Department, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Santos AR, Balassiano V, Oliveira ML, Pereira MA, Santos PB, Degrave WM, Suffys PN. Detection of Mycobacterium leprae DNA by polymerase chain reaction in the blood of individuals, eight years after completion of anti-leprosy therapy. Mem Inst Oswaldo Cruz 2001; 96:1129-33. [PMID: 11784934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Thirty eight patients with indeterminate leprosy (HI), at least 4 to 6 years after discharge from multibacillary (MB) or paucibacillary (PB) schemes of anti leprosy multidrug therapy (MDT), were submitted to traditional diagnostic procedures for leprosy and to polymerase chain reaction (PCR) analysis of different clinical samples for detection of Mycobacterium leprae DNA. No significant difference was observed for any of the parameters analyzed between PB or MB schemes of treatment and no indications were found for more efficient outcome of HI using the MB scheme. Remarkably, 18 (54.5%) of the individuals were PCR positive in at least one of the samples: positivity of PCR was highest in blood samples and four individuals were PCR positive in blood and some other sample. Upon comparison of PCR results with clinical and histopathological parameters, no correlation was found between PCR-positivity and eventual relapse. This is the first report on detection of M. leprae DNA in PB patients, more than half a decade after completion of MDT, suggesting that live bacilli are present and circulating much longer than expected, although reinfection of the individuals can not be excluded. Overall, we feel that because of the high sensitivity of the assay, extreme care should be taken about association of PCR results, efficacy of treatment and disease status.
Collapse
Affiliation(s)
- A R Santos
- Setor de Hanseníase, Departamento de Medicina Tropical, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil
| | | | | | | | | | | | | |
Collapse
|
36
|
Moraes MO, Duppre NC, Suffys PN, Santos AR, Almeida AS, Nery JA, Sampaio EP, Sarno EN. Tumor necrosis factor-alpha promoter polymorphism TNF2 is associated with a stronger delayed-type hypersensitivity reaction in the skin of borderline tuberculoid leprosy patients. Immunogenetics 2001; 53:45-7. [PMID: 11261930 DOI: 10.1007/s002510000295] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- M O Moraes
- Tropical Medicine Department, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Sarno EN, Santos AR, Jardim MR, Suffys PN, Almeida AS, Nery JA, Vieira LM, Sampaio EP. Pathogenesis of nerve damage in leprosy: genetic polymorphism regulates the production of TNF alpha. LEPROSY REV 2000; 71 Suppl:S154-8; discussion S158-60. [PMID: 11201873 DOI: 10.5935/0305-7518.20000087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Studies carried out over the last decade have strongly suggested that TNF alpha both overtly participates in the cell-mediated immune response against Mycobacterium leprae, and is overproduced during reaction. In addition, reactions are intimately related to the onset of nerve damage. Finally, TNF alpha has been implicated in the pathogenesis of many human and experimental autoimmune peripheral neuropathies that, as in leprosy, result in demyelination and axonal lesions. Because of recent findings associating human TNF alpha mutant alleles at the -308 position with increased production of TNF alpha in many immunological and infectious diseases, an investigation of the role of TNF2 in predisposing leprosy patients to reaction has been undertaken. Analysis of 300 patients with leprosy--210 multibacillary and 90 paucibacillary--has shown that the percentage of reactional patients was similar among both carriers and non-carriers of the TNF2 allele. However, a separate analysis of 57 carriers of TNF2 found that reactions occurred much more frequently among heterozygous than among homozygous patients. Moreover, the frequency of neuritis was somewhat greater among the heterozygous patients than among the non-carriers. Enhanced serum levels of TNF alpha have been noted in both TNF-1 and TNF-2 mutant patients in the course of leprosy reaction. Our observations to date suggest that other factors not related to the presence of the mutant gene may lead to the TNF alpha hyper-responsiveness observed during reaction.
Collapse
Affiliation(s)
- E N Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Loureiro MM, de Moraes BA, Quadra MR, Pinheiro GS, Suffys PN, Asensi MD. Molecular epidemiology of methicillin resistant Staphylococcus aureus isolated from newborns in a hospital in Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz 2000; 95:777-82. [PMID: 11080760 DOI: 10.1590/s0074-02762000000600005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Methicillin resistant Staphylococcus aureus (MRSA) is an organism that is frequently transmitted in hospitals and perinatal units. The MRSA is considered a public health problem in neonatology because of its strong potential for dissemination in the wards associated with high rates of morbidity and mortality. In this study we describe the bacteriological, epidemiological and molecular characteristics of MRSA isolated from anterior nares and blood cultures of newborns hospitalized in a public maternity hospital in the city of Rio de Janeiro, Brazil. The frequency of MRSA isolated from nasal swabs of newborns was 47.8% (43/90). The genetic analysis of MRSA strains from anterior nares, showed 8 different pulsed field gel electrophoresis patterns (PFGE). Upon analysis of PFGE patterns of the 12 MRSA strains isolated from blood cultures, 8 different patterns were observed, 9 (75%) strains were genetic related to nasal secretion isolates patterns. In conclusion, our data demonstrate the importance of screening of newborns for the presence of MRSA in Brazilian hospitals and the usefulness of genetic typing of these pathogen during epidemiologic studies. This should lead to a better knowledge on the significancy and spreading of MRSA in the hospitals.
Collapse
Affiliation(s)
- M M Loureiro
- Laboratório de Enterobactérias, Departamento de Bacteriologia, Instituto Oswaldo Cruz, 21045-900 Rio de Janeiro, RJ, Brasil
| | | | | | | | | | | |
Collapse
|
39
|
Santos AR, Almeida AS, Suffys PN, Moraes MO, Filho VF, Mattos HJ, Nery JA, Cabello PH, Sampaio EP, Sarno EN. Tumor necrosis factor promoter polymorphism (TNF2) seems to protect against development of severe forms of leprosy in a pilot study in Brazilian patients. Int J Lepr Other Mycobact Dis 2000; 68:325-7. [PMID: 11221098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
40
|
Suffys PN, Ivens de Araujo ME, Rossetti ML, Zahab A, Barroso EW, Barreto AM, Campos E, van Soolingen D, Kremer K, Heersma H, Degrave WM. Usefulness of IS6110-restriction fragment length polymorphism typing of Brazilian strains of Mycobacterium tuberculosis and comparison with an international fingerprint database. Res Microbiol 2000; 151:343-51. [PMID: 10919514 DOI: 10.1016/s0923-2508(00)00157-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Strains of Mycobacterium tuberculosis isolated from 219 different tuberculosis patients, 115 from patients residing in Rio de Janeiro, 79 from Rio Grande do Sul and the remaining from other regions of the country, were analyzed by IS6110-restriction fragment length polymorphism fingerprinting. The IS6110-DNA patterns from these strains were highly polymorphic: 174 different patterns were observed and 25 patterns were shared by 70 isolates (32%). Most strains (93.4%) had multicopy patterns and only 17% of clustered strains had less than six IS6110 copies. Strain clustering was significantly higher for isolates from Rio Grande do Sul (36.7%) in comparison with strains from Rio de Janeiro (22.6%), but only when using high stringency during cluster analysis. Upon screening of an international database containing 3,970 fingerprints of M. tuberculosis strains, 15% of the patterns of Brazilian strains (21% of the strains) were identical to a fingerprint of an isolate from another country and one particular eight-band pattern forming the largest Brazilian cluster was detected in seven additional countries, suggesting that international transmission of tuberculosis from and to Brazil could be occurring frequently. Alternatively,preferential use of certain IS6110 integration sites could also be important in high-copy number strains, having important consequences for the use of databases for epidemiological studies on a large scale.
Collapse
Affiliation(s)
- P N Suffys
- Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
da Silva Rocha A, da Costa Leite C, Torres HM, de Miranda AB, Pires Lopes MQ, Degrave WM, Suffys PN. Use of PCR-restriction fragment length polymorphism analysis of the hsp65 gene for rapid identification of mycobacteria in Brazil. J Microbiol Methods 1999; 37:223-9. [PMID: 10480266 DOI: 10.1016/s0167-7012(99)00062-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Polymerase chain reaction amplification of part of the gene coding for the heat shock protein hsp65 followed by restriction enzyme analysis (PRA) is a recently described tool for rapid identification of mycobacteria. In this study, the speed and simplicity of PRA for identification of isolates of mycobacteria from patients with clinical symptoms of tuberculosis was evaluated and compared with identification results obtained by commercially available methods. Established PRA patterns were observed for nineteen isolates of Mycobacterium tuberculosis, eleven belonging to the complex M. avium-intracellulare, four of M. kansasii, one of M. fortuitum, one of M. abscessus, three of M. gordonae and one of the recently described species M. lentiflavum, as identified by commercially available methods. Two isolates of M. fortuitum and one of M. gordonae had unique and so far undescribed PRA patterns, suggesting geographically-related intra-species variation within the hsp65 sequence. We propose the inclusion of these new patterns in the PRA identification algorithm and have defined more accurately the molecular weight values of the restriction fragments. This is the first report on the isolation of M. lentiflavum in Brazil suggesting that identification by means of PRA could be useful for detection of mycobacterial species that are usually unnoticed. Where the use of several commercial techniques in combination was necessary for correct identification, PRA demonstrated to be a simple technique with good cost-benefit for characterization of all mycobacterial isolates in this study.
Collapse
Affiliation(s)
- A da Silva Rocha
- Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | | | | | | |
Collapse
|
42
|
Santos AR, Degrave WM, Suffys PN. Use of polymerase chain reaction (PCR) in leprosy research. Indian J Lepr 1999; 71:101-10. [PMID: 10439331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- A R Santos
- Dept. of Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | |
Collapse
|
43
|
Ivens-de-Araujo ME, Fandinho FC, Werneck-Barreto AM, Gonçalves-Veloso V, Grinstejn B, Lourenço MK, Werneck-Barroso E, Degrave WM, Suffys PN. DNA fingerprinting of Mycobacterium tuberculosis from patients with and without AIDS in Rio de Janeiro. Braz J Med Biol Res 1998; 31:369-72. [PMID: 9698784 DOI: 10.1590/s0100-879x1998000300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Isolates of Mycobacterium tuberculosis derived from patients with AIDS from a single hospital in Rio de Janeiro were typed using a standardized RFLP technique detecting IS6110 polymorphism. Nineteen isolates were obtained from 15 different patients. Eleven distinct IS6110 patterns were found, with 4 banding patterns shared by 2 patients. The clustering value of 53% was much higher in comparison with clustering of M. tuberculosis strains from TB patients without clinical signs for HIV infection from randomly selected health centers. We present these results as preliminary data on M. tuberculosis strain polymorphism in Brazil and on the higher risk for recent transmission amongst patients with AIDS.
Collapse
Affiliation(s)
- M E Ivens-de-Araujo
- Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, RJ, Brasil
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
About one third of the world population is infected with tubercle bacilli, causing eight million new cases of tuberculosis (TB) and three million deaths each year. After years of lack of interest in the disease, World Health Organization recently declared TB a global emergency and it is clear that there is need for more efficient national TB programs and newly defined research priorities. A more complete epidemiology of tuberculosis will lead to a better identification of index cases and to a more efficient treatment of the disease. Recently, new molecular tools became available for the identification of strains of Mycobacterium tuberculosis (M. tuberculosis), allowing a better recognition of transmission routes of defined strains. Both a standardized restriction-fragment-length-polymorphism-based methodology for epidemiological studies on a large scale and deoxyribonucleic acids (DNA) amplification-based methods that allow rapid detection of outbreaks with multidrug-resistant (MDR) strains, often characterized by high mortality rates, have been developed. This review comments on the existing methods of DNA-based recognition of M. tuberculosis strains and their peculiarities. It also summarizes literature data on the application of molecular fingerprinting for detection of outbreaks of M. tuberculosis, for identification of index cases, for study of interaction between TB and infection with the human immuno-deficiency virus, for analysis of the behavior of MDR strains, for a better understanding of risk factors for transmission of TB within communities and for population-based studies of TB transmission within and between countries.
Collapse
Affiliation(s)
- P N Suffys
- Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brasil
| | | | | |
Collapse
|
45
|
Abstract
One of the main limitations for successful epidemiological control of leprosy is the lack of a method for its diagnosis in subclinical cases. Because of the long incubation period of the disease, liberation and spread of Mycobacterium leprae during subclinical stages-principally in cases of untreated multibacillary forms of leprosy-constitute the main source of infection. This report describes the use of the polymerase chain reaction (PCR) for the detection of M. leprae in different types of tissue samples (blood, lymph, nasal secretion and hair) from an individual who was suspected of having leprosy. Although no conclusive diagnosis could be made by traditional diagnostic methods, the individual was found to be infected with M. leprae after amplification of the bacterial DNA.
Collapse
Affiliation(s)
- A R Santos
- Department of Tropical Medicine, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | | | | | | | | | | |
Collapse
|
46
|
Santos AR, Goes Filho JT, Nery JA, Duppre NC, Gallo ME, Suffys PN, Degrave WM. Evaluation of PCR mediated DNA amplification in non-invasive biological specimens for subclinical detection of Mycobacterium leprae. FEMS Immunol Med Microbiol 1995; 11:113-20. [PMID: 7640671 DOI: 10.1111/j.1574-695x.1995.tb00097.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA from Mycobacterium leprae, present in non-invasive clinical samples from leprosy patients, such as nasal secretion and hair bulbs, was submitted to amplification by the polymerase chain reaction using a M. leprae-specific repetitive sequence as a target. After optimization of sample processing and of the PCR conditions, we were able to detect DNA from M. leprae in both types of clinical samples, even from paucibacillary leprosy patients. The use of hair bulbs and nasal secretion as clinical samples for screening of household contacts and for the evaluation of a risk population, or for the follow-up of patients under chemotherapy, and monitoring of bacterial load is discussed.
Collapse
Affiliation(s)
- A R Santos
- Department of Tropical Medicine, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | | | | | | | | | | |
Collapse
|
47
|
Santos DO, Suffys PN, Moreira AL, Bonifacio K, Salgado JL, Esquenazi D, Bertho AL, Sarno EN. Evaluation of chemiluminescence, procoagulant activity and antigen presentation by monocytes from lepromatous leprosy patients with or without reactional episodes. LEPROSY REV 1994; 65:88-99. [PMID: 7968194 DOI: 10.5935/0305-7518.19940008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this study, we evaluated the activity of peripheral blood mononuclear cells (PBMC), isolated from treated and untreated lepromatous leprosy patients, from lepromatous leprosy patients during and after reactional episodes (erythema nodosum leprosum (ENL) and reversal reaction (RR)), and from normal healthy individuals. We determined reactive oxygen intermediate (ROI) production, procoagulant activity (PCA) and HLA-DR antigen expression of monocytes, besides lymphoproliferation, both in the presence and absence of various stimulatory agents. Phorbol myristate acetate (PMA) stimulated ROI production by monocytes from all the groups studied, with patients during reactional episodes (ENL and RR) showing a significantly higher response (p < 0.009 and p < 0.00001). Irradiated Mycobacterium leprae, although having little effect when added alone, strongly suppressed PMA-stimulated ROI production. Muramyl dipeptide (MDP) had no influence on either basal or on PMA-induced ROI production. Basal monocyte PCA, as well as M. leprae or concanavalin A (ConA)-induced monocyte PCA was comparable in monocytes from all the groups studied. ConA was able to induce mitogenic activity in mononuclear cells isolated from all the groups studied. M. leprae, although stimulatory for normal individuals, did not induce lymphoproliferation in lepromatous leprosy patients, except for cells from patients during RR, which responded equally to M. leprae and to ConA. The absence of M. leprae-induced lymphoproliferation in lepromatous leprosy patients is not caused by the lack of basal HLA-DR expression, as PBMC from all individuals studied showed the same level of this antigen. Our results suggest an increase of spontaneous or PMA-induced monocyte activity, as detected by ROI production, during the reactional episode; addition of M. leprae suppressed this response. The increase in monocyte activity could be correlated with the increase of lymphoproliferation response to M. leprae during RR, but not during ENL. The importance of a possible immune suppressive action of M. leprae is discussed.
Collapse
Affiliation(s)
- D O Santos
- Department of Cellular and Molecular Biology, Federal Fluminense University, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Santos AR, De Miranda AB, Sarno EN, Suffys PN, Degrave WM. Use of PCR-mediated amplification of Mycobacterium leprae DNA in different types of clinical samples for the diagnosis of leprosy. J Med Microbiol 1993; 39:298-304. [PMID: 8411091 DOI: 10.1099/00222615-39-4-298] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA of Mycobacterium leprae, obtained by a highly efficient nucleic acid extraction procedure, was used for standardisation of the amplification of an M. leprae-specific repetitive sequence by use of the polymerase chain reaction (PCR). With pure DNA, M. leprae-specific amplification was obtained with as low as 100 ag (1 ag = 10(-18) g) of target DNA, a quantity equal to about one-tenth of the bacterial genome. Optimal processing of different types of clinical samples such as biopsy material, blood and lymph fluid, from multibacillary leprosy patients, was studied. Simple freezing-boiling cycles in the presence of Triton X100, with some additional sample-specific modifications such as pre-treatment with NaOH to eliminate PCR inhibitors, was found to be sufficient to yield amplification of bacterial DNA in samples from paucibacillary patients. Clinical samples from 27 untreated leprosy patients, covering the various clinical forms of the disease, and with a bacterial index ranging from 5+ to 0, were collected and processed for PCR analysis. After hybridisation of the amplified material with a specific sequence, 25 of 27 patients analysed gave positive results for M. leprae in at least one of the samples. The potential of PCR for the diagnosis of leprosy is discussed.
Collapse
Affiliation(s)
- A R Santos
- Department of Tropical Medicine-Leprosy Sector, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | | |
Collapse
|
49
|
Santos DO, Suffys PN, Bonifácio K, Marques MA, Sarno EN. In vitro tumor necrosis factor production by mononuclear cells from lepromatous leprosy patients and from patients with erythema nodosum leprosum. Clin Immunol Immunopathol 1993; 67:199-203. [PMID: 8500267 DOI: 10.1006/clin.1993.1065] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The production of tumor necrosis factor (TNF) by Mycobacterium leprae-stimulated phagocyte cells, isolated from lepromatous leprosy patients (LL) and normal individuals, was evaluated, using the highly TNF-sensitive mouse fibrosarcoma cell line WEHI164cl13. Mononuclear cells, isolated from all individuals studied, showed a low level of spontaneous TNF production, except for patients undergoing erythema nodosum leprosum (ENL), in which we found significantly higher levels of TNF. Addition of M. leprae to the phagocyte cell culture enhanced TNF production in all groups studied, except in the group with untreated leprosy patients. Strongest M. leprae-induced TNF release was found in mononuclear cell cultures derived from ENL patients. Patients in the postreactional state showed significantly higher TNF levels than healthy controls. These findings support the idea that TNF plays a key role in the complex symptomatology of ENL.
Collapse
Affiliation(s)
- D O Santos
- Department of Cellular and Molecular Biology, Federal Fluminense University, Niteroi, RJ, Brazil
| | | | | | | | | |
Collapse
|
50
|
de Miranda AB, Llerena Júnior J, Dallalana LT, Moura-Neto RS, Suffys PN, Degrave WM. Use of PCR for the determination of the frequency of the delta F508 mutation in Brazilian cystic fibrosis patients. Mem Inst Oswaldo Cruz 1993; 88:309-12. [PMID: 8107592 DOI: 10.1590/s0074-02761993000200022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The delta F508 mutation in the cystic fibrosis (CF) gene was studied in a population of 18 Brazilian CF patients and their 17 families by use of PCR and differential hybridization with oligonucleotides. In a total of 34 chromosomes considered, 12 (35%) carried the F508 deletion, a frequency much lower than that reported in most other populations. As a consequence, CF in Brazil would be predominantly caused by mutations different from the F508 deletion.
Collapse
Affiliation(s)
- A B de Miranda
- Instituto Oswaldo Cruz, Departamento de Bioquímica e Biologia Molecular, Rio de Janeiro, Brasil
| | | | | | | | | | | |
Collapse
|