Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil.

Lack of routine surveillance in countries endemic for bovine tuberculosis (TB) and limited laboratory support contributes to the inability to differentiate the Mycobacterium tuberculosis Complex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing of Mycobacterium bovis isolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission of M. bovis is ongoing at distinct sites. Moreover, the M. bovis epidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from other M. bovis clades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for the M. bovis Marajó strain. In conclusion, this study contributes with data regarding the identification of a novel M. bovis phylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB

Epidemiologia molecular da tuberculose no Brasil: uma perspectiva da pesquisa translacional

Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brasil

Molecular epidemiology of tuberculosis in Brazil: a translational research perspective*

Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brasil

Tuberculosis drug resistance profiling based on machine learning: a literature review

Liverpool John Moores University. Faculty of Engineering and Technology. Liverpool, United KingdomFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Programa de Pós-graduação em Pesquisa Clínica e Doenças Infecciosas. Rio de Janeiro, RJ, Brazil / Stellenbosch University. Faculty of Medicine and Health Sciences. Division of Molecular Biology and Human Genetics. South African Medical Research Council Centre for Tuberculosis Research. Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research. Cape Town, South AfricaTuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is one of the top 10 causes of death worldwide. Drug-resistant tuberculosis (DR-TB) poses a major threat to the World Health Organization's "End TB" strategy which has defined its target as the year 2035. In 2019, there were close to 0.5 million cases of DRTB, of which 78% were resistant to multiple TB drugs. The traditional culture-based drug susceptibility test (DST - the current gold standard) often takes multiple weeks and the necessary laboratory facilities are not readily available in low-income countries. Whole genome sequencing (WGS) technology is rapidly becoming an important tool in clinical and research applications including transmission detection or prediction of DR-TB. For the latter, many tools have recently been developed using curated database(s) of known resistance conferring mutations. However, documenting all the mutations and their effect is a time-taking and a continuous process and therefore Machine Learning (ML) techniques can be useful for predicting the presence of DR-TB based on WGS data. This can pave the way to an earlier detection of drug resistance and consequently more efficient treatment when compared to the traditional DST

Identificación genotípica de miembros del complejo Mycobacterium avium aislados de infecciones pulmonares en el Estado de Pará, Brasil

Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade Federal do Pará. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade Federal do Pará. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.INTRODUÇÃO: O complexo Mycobacterium avium (MAC) compreende micobactérias de crescimento lento, naturalmente encontradas no meio ambiente, capazes de causar infecções em diversas espécies de seres vivos, incluindo aves, suínos e humanos. Tais infecções podem ser assintomáticas, clinicamente significantes e, em alguns casos, fatais. No entanto, existe a necessidade de se disponibilizarem técnicas que ofereçam uma identificação conclusiva de bactérias estreitamente relacionadas. As técnicas de biologia molecular se apresentam como ferramentas promissoras para uma identificação mais precisa. MATERIAIS E MÉTODOS: Neste trabalho foram avaliados os marcadores moleculares RNAr 16S, hsp65 e rpoB aplicados à distinção de membros do MAC isolados no Laboratório de Micobactérias do Instituto Evandro Chagas. RESULTADOS: Amostras de MAC colhidas em 15 pacientes foram previamente avaliadas pelo método de análise de polimorfismo de fragmentos de restrição do gene hsp65 (PRA-hsp65), que forneceu três diferentes perfis: (I) BstEII: 235/115/100, HaeIII:145/130/60; (II) BstEII:235/210, HaeIII:130/105; e (III) : 235/210, HaeIII:145/130. Árvores filogenéticas foram construídas após análise do RNAr 16S, em que as amostras foram distribuídas em dois grupos, semelhante ao encontrado na análise de hsp65. Entretanto, os resultados de rpoB foram discordantes daqueles das outras árvores, devido à modificação de topologia. CONCLUSÃO: Os achados deste estudo sugerem que diferentes forças evolucionárias podem estar atuando sobre o gene rpoB, e, desta forma, é necessário que se tenha precaução ao estabelecer esse alvo para fins taxonômicos. Adicionalmente, recomenda-se que mais de um marcador, incluindo o RNAr 16S, seja avaliado para a identificação micobacteriana.INTRODUCTION: The Mycobacterium avium complex (MAC) is a group of slow-growing mycobacteria naturally found in the environment capable of causing infections in a wide variety of living species, including birds, swines and humans. These infections can be asymptomatic, clinically significant and, in some cases, fatal. There is a demand for techniques that are capable of conclusively identifying closely related bacteria. Molecular biological techniques are promising tools for a more precise identification. MATERIAL AND METHODS: In this study, we evaluated the ability of 16S rRNA, hsp65 and rpoB molecular markers to distinguish between members of the MAC isolated in the Mycobacteria Laboratory at the Instituto Evandro Chagas. RESULTS: MAC samples collected from 15 patients were previously evaluated using an hsp65 gene restriction fragment length polymorphism analytical method (RFLP-hsp65), and they showed three different profiles: (I) BstEII: 235/115/100, HaeIII: 145/130/60; (II) BstEII: 235/210, HaeIII: 130/105; and (III) BstEII: 235/210, HaeIII: 145/130. We constructed phylogenetic trees using 16S rRNA analysis in which the samples were distributed into two groups, similarly to those found in the hsp65 analysis. However, the results from the rpoB analysis disagreed with those of the other trees due to changes in topology. CONCLUSION: The findings from this study warrant that various evolutionary forces may be acting on the rpoB gene. Thus, it is necessary to be cautious when using this target for taxonomic analyses. Additionally, we recommend that multiple markers (including16S rRNA) be evaluated when identifying mycobacteria

Mycobacterium tuberculosis spoligotypes and drug-resistant characterization from Beira compared to genotypes circulating in Mozambique

INTRODUCTION: Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug resistant (DR) strains from Beira, Mozambique comparing them with genotypes in the country. METHODS: We performed spoligotyping of 79 M. tuberculosis suspected of DR-TB compared all spoligotype patterns published on the international database and PubMed. RESULTS: Both in Beira and Mozambique (n=578), the main clades were Latin-American-Mediterranean, East-African-Indian, Beijing and T, with no extensively DR TB cases. CONCLUSIONS: Beira and Mozambique share the same population genetic structure of M. tuberculosis

Frecuencia y distribución anual de resistencia de la tuberculosis en la red de laboratorios de salud pública del Estado de Pará, Brasil

This study was supported by the Instituto Evandro Chagas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and the Programa de Pós-graduação em Biologia Parasitária/Universidade Estadual do Pará.Universidade do Estado do Pará. Programa de Pós-graduação em Biologia Parasitária da Amazônia. Belém, PA, Brasil.Universidade do Estado do Pará. Programa de Pós-graduação em Biologia Parasitária da Amazônia. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Laboratório de Geoprocessamento. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.This study described the frequency and variety of multidrug-resistant tuberculosis (MDR-TB) cases in Pará State, Brazil. In order to record the epidemiology and spacial distribution of the disease, antimicrobial susceptibility testing (AST) and the proportion method were used. The AST was performed on 848 samples at the Instituto Evandro Chagas and a central public health laboratory in that State. Of all patients enrolled in the study, 358 (42.2%) were resistant to at least one antituberculosis (anti-TB) drug. The percentage of primary, acquired resistance and combined MDR-TB was 30.4%, 69.3% and 42.2% respectively. MDR-TB was detected in 223 (26.3%) samples. Primary MDR-TB was found in 14% of previously treated patients, while 48% exhibited acquired resistance and 62% exhibited combined resistance. Of all age groups, from 25 to 36 years old (mean age 38.7 ± 15) showed the highest proportion of resistant cases (26.3%). Seven cities in the State presented 59.6% of the cases documented in the study. These findings reflect the poor quality of the healthcare for patients in these cities. We further suggest that clinicians need to observe their patients more directly during treatment and test them more often for anti-TB drug sensitivity. The number of TB cases in Pará did not vary significantly during the period studied, but researchers did notice a slight increase in the proportion of drug-resistant cases related to the total number of cases reported in Pará. This change in the resistance rates reflects the need to improve the quality of health services for TB care. A concentration of TB cases was observed in some municipalities and in the neighborhoods of the Belém City.Este estudo descreveu a frequência e variedade de casos de tuberculose multirresistente (TBMR) no Estado do Pará, Brasil. A fim de registrar a epidemiologia e a distribuição espacial da doença, foram utilizados testes de suscetibilidade antimicrobiana (TSA) e do método proporcional (MP). O TSA foi realizado em 848 amostras no Instituto Evandro Chagas e em um laboratório central de saúde pública naquele Estado. De todos os pacientes incluídos no estudo, 358 (42,2%) eram resistentes a pelo menos um medicamento antituberculose (anti-TB). A porcentagem das resistências primária, adquirida e TBMR foi de 30,4%, 69,3% e 42,2%, respectivamente. A TBMR foi detectada em 223 (26,3%) amostras. A TBMR primária foi encontrada em 14% dos pacientes tratados anteriormente, enquanto que 48% apresentaram a resistência adquirida e 62% exibiram resistência combinada. De todos os grupos etários, o de 25-36 anos (média de idade de 38,7 ± 15) apresentou a maior proporção de casos resistentes (26%). Sete cidades do Estado apresentaram 59,6% dos casos documentados no estudo. Estes resultados refletem a baixa qualidade dos cuidados de saúde com os doentes nestas cidades. Observa-se ainda, a necessidade de maiores cuidados dos médicos para com os pacientes durante o tratamento e realização, com maior frequência, dos testes de sensibilidade aos medicamentos anti-TB. O número de casos de TB no Pará não variou significativamente durante o período estudado, porém os pesquisadores notaram um ligeiro aumento na proporção de casos resistentes aos medicamentos relacionados com o número total de casos notificados no Estado. Esta mudança nas taxas de resistência reflete a necessidade de melhorar a qualidade dos serviços de saúde para a atenção à TB. A concentração de casos de tuberculose foi observada em alguns municípios e nos bairros da Cidade de Belém

Factors associated with Tuberculosis outcome in a hyperendemic city in the North of Brazil

This research was supported by funding from Evandro Chagas Institute (IEC), Secretariat for Science, Technology, Innovation and Strategic Health Inputs (SCTIE), Brazilian Ministry of Health (MS). Yan Corrêa Rodrigues scholarship is funded by PDPG—Pós-Doutorado Estratégico (PDPGPOSDOC), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/Edital 16/2022).State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil.State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil.State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil.State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil.Department of Health of Pará State. EpiSUS Intermediário. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Programa de Epidemiologia e Vigilância Sanitária. Ananindeua, PA, Brasil.State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil / Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Stellenbosch University. Faculty of Medicine and Health Sciences. Division of Molecular Biology and Human Genetics. Stellenbosch, South Africa.State University of Pará. Program in Parasitic Biology in the Amazon Region. Belém, PA, Brazil / Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ananindeua city, State of Pará, North of Brazil, is a hyperendemic area for tuberculosis (TB), with a cure rate below the recommendation by the Brazilian Ministry of Health. We aimed to describe: (I) the TB incidence coefficient of Ananindeua municipality comparatively against Brazilian data; (II) TB treatment outcomes; (III) to compare the socioeconomic and epidemiological characteristics of abandonment versus cure outcome; and (IV) to evaluate the risk factors associated with TB treatment abandonment in Ananindeua city, from 2017 to 2021. This is a retrospective, descriptive, and crosssectional epidemiological study which used secondary TB entries. Data were analyzed by linear regression, descriptive statistics, and associations were made using the Chi-square test and G-test, followed by univariate and multivariate logistic regression analyses. Cure rates ranged from 28.7% to 70.1%, abandonment between 7.3% and 11.8%, deaths from the disease ranged from 0% to 1.6%, and drug-resistant tuberculosis (TB-DR) rates had frequencies from 0% to 0.9%. Patient transfer rates to other municipalities were between 4.9% and 12.5%. The multivariate analysis showed that alcohol is almost 2 times more likely to lead an individual to abandon treatment and use of illicit drugs was almost 3 times more likely. Individuals between 20 and 59 years of age were also more likely to abandon treatment almost twice as often. Finally, data obtained in the present report is of great relevance to strengthen epidemiological surveillance and minimize possible discrepancies between the information systems and the reality of public health in high endemicity areas

Factors Associated with Tuberculosis Outcome in a Hyperendemic City in the North of Brazil

Ananindeua city, State of Pará, North of Brazil, is a hyperendemic area for tuberculosis (TB), with a cure rate below the recommendation by the Brazilian Ministry of Health. We aimed to describe: (I) the TB incidence coefficient of Ananindeua municipality comparatively against Brazilian data; (II) TB treatment outcomes; (III) to compare the socioeconomic and epidemiological characteristics of abandonment versus cure outcome; and (IV) to evaluate the risk factors associated with TB treatment abandonment in Ananindeua city, from 2017 to 2021. This is a retrospective, descriptive, and cross-sectional epidemiological study which used secondary TB entries. Data were analyzed by linear regression, descriptive statistics, and associations were made using the Chi-square test and G-test, followed by univariate and multivariate logistic regression analyses. Cure rates ranged from 28.7% to 70.1%, abandonment between 7.3% and 11.8%, deaths from the disease ranged from 0% to 1.6%, and drug-resistant tuberculosis (TB-DR) rates had frequencies from 0% to 0.9%. Patient transfer rates to other municipalities were between 4.9% and 12.5%. The multivariate analysis showed that alcohol is almost 2 times more likely to lead an individual to abandon treatment and use of illicit drugs was almost 3 times more likely. Individuals between 20 and 59 years of age were also more likely to abandon treatment almost twice as often. Finally, data obtained in the present report is of great relevance to strengthen epidemiological surveillance and minimize possible discrepancies between the information systems and the reality of public health in high endemicity areas

Factors Associated with Tuberculosis Outcome in a Hyperendemic City in the North of Brazil

Ananindeua city, State of Pará, North of Brazil, is a hyperendemic area for tuberculosis (TB), with a cure rate below the recommendation by the Brazilian Ministry of Health. We aimed to describe: (I) the TB incidence coefficient of Ananindeua municipality comparatively against Brazilian data; (II) TB treatment outcomes; (III) to compare the socioeconomic and epidemiological characteristics of abandonment versus cure outcome; and (IV) to evaluate the risk factors associated with TB treatment abandonment in Ananindeua city, from 2017 to 2021. This is a retrospective, descriptive, and cross-sectional epidemiological study which used secondary TB entries. Data were analyzed by linear regression, descriptive statistics, and associations were made using the Chi-square test and G-test, followed by univariate and multivariate logistic regression analyses. Cure rates ranged from 28.7% to 70.1%, abandonment between 7.3% and 11.8%, deaths from the disease ranged from 0% to 1.6%, and drug-resistant tuberculosis (TB-DR) rates had frequencies from 0% to 0.9%. Patient transfer rates to other municipalities were between 4.9% and 12.5%. The multivariate analysis showed that alcohol is almost 2 times more likely to lead an individual to abandon treatment and use of illicit drugs was almost 3 times more likely. Individuals between 20 and 59 years of age were also more likely to abandon treatment almost twice as often. Finally, data obtained in the present report is of great relevance to strengthen epidemiological surveillance and minimize possible discrepancies between the information systems and the reality of public health in high endemicity areas