Genome Comparison of an Ancestral Isolate and a Modern Isolate of Mycobacterium tuberculosis of the Beijing Lineage from São Paulo, Brazil

Submitted by sandra infurna ([email protected]) on 2016-03-31T11:53:07Z No. of bitstreams: 1 sidra_vasconcellos_etal_IOC_2015.pdf: 154933 bytes, checksum: 4c0416a8ad804bc5b55bf7e401d4f3fc (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-03-31T12:08:13Z (GMT) No. of bitstreams: 1 sidra_vasconcellos_etal_IOC_2015.pdf: 154933 bytes, checksum: 4c0416a8ad804bc5b55bf7e401d4f3fc (MD5)Made available in DSpace on 2016-03-31T12:08:13Z (GMT). No. of bitstreams: 1 sidra_vasconcellos_etal_IOC_2015.pdf: 154933 bytes, checksum: 4c0416a8ad804bc5b55bf7e401d4f3fc (MD5) Previous issue date: 2015Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada à Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil.Universidade Estadual do Norte Fluminense. Laboratório de Biologia do Reconhecimento. Campos de Goytacazes, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada à Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada à Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada à Micobactérias. Rio de Janeiro, RJ, Brasil.Mycobacterium tuberculosis of the Bejing subtype (MtbB) is transmitted efficiently in high burden countries for this genotype. A higher virulence was associated with isolates of the “modern” Beijing genotype sub-lineages when compared to “ancient” ones. Here, we report the full genomes of the strain representing these two genotypes from Brazil, a country with a low incidence of MtbB

Frequency of the Mycobacterium tuberculosis RDRio genotype and its association with multidrug-resistant tuberculosis

Submitted by Sandra Infurna ([email protected]) on 2020-03-28T16:58:25Z No. of bitstreams: 1 PhilipNSuffys_SEGVasconcelos_etal_IOC_2019.pdf: 2891235 bytes, checksum: 2bb6f334e755ecd55c7914668a54beb7 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2020-03-28T17:10:51Z (GMT) No. of bitstreams: 1 PhilipNSuffys_SEGVasconcelos_etal_IOC_2019.pdf: 2891235 bytes, checksum: 2bb6f334e755ecd55c7914668a54beb7 (MD5)Made available in DSpace on 2020-03-28T17:10:51Z (GMT). No. of bitstreams: 1 PhilipNSuffys_SEGVasconcelos_etal_IOC_2019.pdf: 2891235 bytes, checksum: 2bb6f334e755ecd55c7914668a54beb7 (MD5) Previous issue date: 2019Universidade Federal de Minas Gerais. Faculdade de Medicina. Laboratório de Pesquisa em Micobactérias. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Universidade Federal de Minas Gerais. Faculdade de Medicina. Laboratório de Pesquisa em Micobactérias. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Faculdade de Medicina. Laboratório de Pesquisa em Micobactérias. Belo Horizonte, MG, Brasil.Fundação Ezequiel Dias. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Escola de Veterinária. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Universidade Federal de Minas Gerais. Faculdade de Farmácia. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Faculdade de Medicina. Laboratório de Pesquisa em Micobactérias. Belo Horizonte, MG, Brasil.Background: In recent decades, Mycobacterium tuberculosis with the RDRio genotype, frequently isolated from tuberculosis patients in Rio de Janeiro, has become part of the Latin American – Mediterranean (LAM) family and has been associated with multidrug-resistant tuberculosis (MDR-TB). The aim of this study was to investigate the frequency of M. tuberculosis RDRio in the state of Minas Gerais, Brazil, and its relationship with MDR-TB. Methods: For convenience, 172 susceptible and 63 MDR M. tuberculosis isolates were taken from pulmonary samples from patients diagnosed between January 2007 and December 2011. The DNA extracted from these isolates was analyzed by spoligotyping, PCR-RFLP to characterize fbpC103/Ag85C103, multiplex PCR to detect RDRio and RD174, and MIRU-VNTR 24 loci. Results: Among the 235 isolates, the RDRio pattern was identified in 122 (51.9%) isolates (IC 0.45–0.58), with 100 (42.5%) wild-type and 13 (5.5%) mixed pattern isolates, whereas RD174 was identified in 93 of the 122 RDRio positive samples (76.3%). The LAM family and the LAM9 lineage were the most frequently identified among the isolates in this study. Among the 63 MDR isolates, 41 (65.1%) were RDRio and 28 (44.4%) RD174. Conclusion: The association of both deletions with MDR proved to be statistically significant, corroborating the few reports that have associated RDRio with MDR

Genetic clustering of tuberculosis in an indigenous community of Brazil

We conducted a population-based study of tuberculosis (TB) from 2009 to 2015 in an indigenous community of Brazil, the largest in the country, to investigate risk factors associated with recent TB transmission. The clinical isolates of Mycobacterium tuberculosis were genotyped by IS6110-RFLP (restriction fragment length polymorphism) and spoligotyping analysis. Among 67 isolates typed by RFLP, 69% fell into fifteen clusters, and 91% of TB cases with shared IS6110-RFLP pattern were diagnosed within 2 years of another case in the cluster. Individual risk factors associated with genetic clustering were domestic overcrowding (odds ratio [OR]: 6.10; 95% confidence interval [CI]: 1.50-24.88) and low social class (OR: 3.72; 95% CI: 1.00-13.98). Most reported contacts (76%) were identified within the household of the index TB case, but most of the genetic clustering of M. tuberculosis occurred outside of household (79%). Expanded contacts investigation and prophylaxis outside of household should be considered as a priority for TB control programs in this population

Investigating drug resistance of Mycobacterium leprae in the Comoros: an observational deep-sequencing study

International audienceBackground: Despite strong leprosy control measures, including effective treatment, leprosy persists in the Comoros. As of May, 2022, no resistance to anti-leprosy drugs had been reported, but there are no nationally representative data. Post-exposure prophylaxis (PEP) with rifampicin is offered to contacts of patients with leprosy. We aimed to conduct a countrywide drug resistance survey and investigate whether PEP led to the emergence of drug resistance in patients with leprosy.Methods: In this observational, deep-sequencing analysis we assessed Mycobacterium leprae genomes from skin biopsies of patients in Anjouan and Mohéli, Comoros, collected as part of the ComLep (NCT03526718) and PEOPLE (NCT03662022) studies. Skin biopsies that had sufficient M leprae DNA (>2000 bacilli in 2 μl of DNA extract) were assessed for the presence of seven drug resistance-associated genes (ie, rpoB, ctpC, ctpI, folP1, gyrA, gyrB, and nth) using Deeplex Myc-Lep (targeted next generation deep sequencing), with a limit of detection of 10% for minority M leprae bacterial populations bearing a polymorphism in these genes. All newly registered patients with leprosy for whom written informed consent was obtained were eligible for inclusion in the survey. Patients younger than 2 years or with a single lesion on the face did not have biopsies taken. The primary outcome of our study was the proportion of patients with leprosy (ie, new cases, patients with relapses or reinfections, patients who received single (double) dose rifampicin-PEP, or patients who lived in villages where PEP was distributed) who were infected with M leprae with a drug-resistant mutation for rifampicin, fluoroquinolone, or dapsone in the Comoros.Findings: Between July 1, 2017, and Dec 31, 2020, 1199 patients with leprosy were identified on the basis of clinical criteria, of whom 1030 provided a skin biopsy. Of these 1030 patients, 755 (73·3%) tested positive for the M leprae-specific repetitive element-quantitative PCR (qPCR) assay. Of these 755 patients, 260 (34·4%) were eligible to be analysed using Deeplex Myc-Lep. 251 (96·5%) were newly diagnosed with leprosy, whereas nine (3·4%) patients had previously received multidrug therapy. 45 (17·3%) patients resided in villages where PEP had been administered in 2015 or 2019, two (4·4%) of whom received PEP. All seven drug resistance-associated targets were successfully sequenced in 216 samples, 39 samples had incomplete results, and five had no results. No mutations were detected in any of the seven drug resistance-related genes for any patient with successfully sequenced results.Interpretation: This drug resistance survey provides evidence to show that M leprae is fully susceptible to rifampicin, fluoroquinolones, and dapsone in the Comoros. Our results also show, for the first time, the applicability of targeted sequencing directly on skin biopsies from patients with either paucibacillary or multibacillary leprosy. These data suggest that PEP had not selected rifampicin-resistant strains, although further support for this finding should be confirmed with a larger sample size

Molecular Typing of Mycobacterium bovis from Cattle Reared in Midwest Brazil

Submitted by Sandra Infurna ([email protected]) on 2017-03-09T13:46:12Z No. of bitstreams: 1 sidra_vasconcelos_etal_IOC_2016.pdf: 2784815 bytes, checksum: 6e67c19317c3bc5230963a00d08a0619 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2017-03-09T14:01:21Z (GMT) No. of bitstreams: 1 sidra_vasconcelos_etal_IOC_2016.pdf: 2784815 bytes, checksum: 6e67c19317c3bc5230963a00d08a0619 (MD5)Made available in DSpace on 2017-03-09T14:01:21Z (GMT). No. of bitstreams: 1 sidra_vasconcelos_etal_IOC_2016.pdf: 2784815 bytes, checksum: 6e67c19317c3bc5230963a00d08a0619 (MD5) Previous issue date: 2016Universidade Federal do Rio de Janeiro, Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil / Universidade Federal de Mato Grosso. Faculdade de Nutrição. Cuiabá, MT, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de de Biologia Molecular Aplicado a Micobactérias. Rio de Janeiro, RJ. Brasil.Ministério da Agricultura, Pecuária e Abastecimento. Laboratório Nacional Agropecuário. Pedro Leopoldo, MG, Brasil.Ministério da Agricultura, Pecuária e Abastecimento. Laboratório Nacional Agropecuário. Pedro Leopoldo, MG, Brasil.Ministério da Agricultura, Pecuária e Abastecimento. Laboratório Nacional Agropecuário. Pedro Leopoldo, MG, Brasil.Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Gado de Corte). Campo Grande, MS, Brasil.Universidade Federal do Rio de Janeiro, Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Campus Macaé. Macaé, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de de Biologia Molecular Aplicado a Micobactérias. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de de Biologia Molecular Aplicado a Micobactérias. Rio de Janeiro, RJ. Brasil / Tropical Institute of Medicine. Mycobacteriology Unit. Antwerp, Belgium.Universidade Federal de Mato Grosso. Faculdade de Nutrição. Cuiabá, MT, Brasil.Universidade Federal do Rio de Janeiro, Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil.Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), the pathogen responsible for serious economic impact on the livestock sector. In order to obtain data on isolated M. bovis strains and assist in the control and eradication program for BTB, a cross sectional descriptive molecular epidemiology study in the Brazilian Midwest was conducted. Through spoligotyping and 24-loci MIRU-VNTR methods, 37 clinical isolates of M. bovis circulating in the region were analyzed, 10 isolated from the state of Mato Grosso, 12 from the state of Mato Grosso do Sul and 15 from the state of Goiás. The spoligotyping analysis identified 10 distinct M. bovis profiles (SB0121 n = 14, SB0295 n = 6, SB0140 n = 6, SB0881 n = 3, SB1144 n = 2, SB1145 n = 2, SB0134 n = 1, SB1050 n = 1, SB1055 n = 1, SB1136 n = 1) grouped in six clusters and four orphan patterns. The MIRU-VNTR 24-loci grouped the same isolates in six clusters and 22 unique orphan patterns, showing higher discriminatory power than spoligotyping. When associating the results of both techniques, the isolates were grouped in five clusters and 24 unique M. bovis profiles. Among the 24-loci MIRU-VNTR evaluated, two, ETR-A and QUB 11b loci, showed high discriminatory ability (h = ≥ 0.50), while MIRU 16, MIRU 27, ETR-B, ETR-C, Mtub21 and QUB 26 loci showed moderate ability (h = 0.33 or h = 0.49) and were the most effective in evaluating the genotypic similarities among the clinical M. bovis isolate samples. Herein, the 29 patterns found amongst the 37 isolates of M. bovis circulating in the Brazilian Midwest can be due to the animal movement between regions, municipalities and farms, thus causing the spread of various M. bovis strains in herds from Midwest Brazil

Antiretroviral therapy-induced paradoxical worsening of previously healed Mycobacterium haemophilum cutaneous lesions in advanced HIV infection

Submitted by Sandra Infurna ([email protected]) on 2020-03-26T20:48:24Z No. of bitstreams: 1 PhilipNSuffys_HarrisonGomes_etal_IOC_2019.pdf: 1698056 bytes, checksum: 5e736975d1ecd4bad2cdc6f2ebcc2946 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2020-03-26T20:58:16Z (GMT) No. of bitstreams: 1 PhilipNSuffys_HarrisonGomes_etal_IOC_2019.pdf: 1698056 bytes, checksum: 5e736975d1ecd4bad2cdc6f2ebcc2946 (MD5)Made available in DSpace on 2020-03-26T20:58:16Z (GMT). No. of bitstreams: 1 PhilipNSuffys_HarrisonGomes_etal_IOC_2019.pdf: 1698056 bytes, checksum: 5e736975d1ecd4bad2cdc6f2ebcc2946 (MD5) Previous issue date: 2019Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Centro de Ciências Biológicas e da Saúde. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Mycobacterium haemophilum is a nontuberculous mycobacterium that causes localized or disseminated disease, mainly in immunocompromised hosts. We report the case of a 35-year-old HIV-infected woman who presented with several enlarging cutaneous lesions over the arms and legs. Histopathological examination revealed the diagnosis of a cutaneous mycobacterial disease. Mycobacterial analyses unveiled M. haemophilum infection. Six months after completion of a successful antimycobacterial treatment, she developed an immune reconstitution inflammatory syndrome (IRIS). This paradoxical relapse presented as tenderness, redness and swelling at the precise sites of the healed lesions and took place in the setting of significant recovery of the CD4 cell count (from 05 to 318 cells/mm 3 ). Microbiological analyses of these worsening lesions were negative, and they spontaneously remitted without the initiation of a novel antimycobacterial treatment cycle. M. haemophilum infection should always be considered as a cause of skin lesions in immunocompromised subjects. Physicians should be aware of the possibility of IRIS as a complication of successful antiretroviral therapy in HIV-infected patients with M. haemophilum infection

Allele diversity of the 24-<i>loci</i> MIRU-VNTR.

<p>Allele diversity of the 24-<i>loci</i> MIRU-VNTR.</p

Molecular characterization of the 37 <i>M</i>. <i>bovis</i> isolates by spoligotyping method.

<p>Molecular characterization of the 37 <i>M</i>. <i>bovis</i> isolates by spoligotyping method.</p

Dendrogram generated by the <i>BioNumerics</i> 6.6 software (Applied Maths) based on the combination of spoligotyping and MIRU-VNTR analyses applied to the 37 <i>M</i>. <i>bovis</i> isolates, using the categorical index and unweighted pair-grouping method analysis algorithm (UPGMA).

<p>Dendrogram generated by the <i>BioNumerics</i> 6.6 software (Applied Maths) based on the combination of spoligotyping and MIRU-VNTR analyses applied to the 37 <i>M</i>. <i>bovis</i> isolates, using the categorical index and unweighted pair-grouping method analysis algorithm (UPGMA).</p

Discriminatory ability comparison among the spoligotyping and 24 MIRU-VNTR methods and the combination of both in detecting genetic similarities.

<p>Discriminatory ability comparison among the spoligotyping and 24 MIRU-VNTR methods and the combination of both in detecting genetic similarities.</p