Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil.

Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).

Use of amplified Mycobacterium tuberculosis direct test in respiratory samples from HIV-infected patients in Brazil.

OBJECTIVE: To compare the accuracy of the amplified Mycobacterium tuberculosis direct (AMTD) test with reference methods for the laboratory diagnosis of tuberculosis in HIV-infected patients. METHODS: This was a study of diagnostic accuracy comparing AMTD test results with those obtained by culture on Löwenstein-Jensen (LJ) medium and by the BACTEC Mycobacteria Growth Indicator Tube 960 (BACTEC MGIT 960) system in respiratory samples analyzed at the Bioassay and Bacteriology Laboratory of the Oswaldo Cruz Foundation Evandro Chagas Clinical Research Institute in the city of Rio de Janeiro, Brazil. RESULTS: We analyzed respiratory samples collected from 118 patients, of whom 88 (74.4%) were male. The mean age was 36.6 ± 10.6 years. Using the AMTD test, the BACTEC MGIT 960 system, and LJ culture, we identified M. tuberculosis complex in 31.0%, 29.7%, and 27.1% of the samples, respectively. In comparison with LJ culture, the AMTD test had a sensitivity, specificity, positive predictive value, and negative predictive value of 87.5%, 89.4%, 75.7%, and 95.0%, respectively, for LJ culture, whereas, in comparison with the BACTEC MGIT 960 system, it showed values of 88.6%, 92.4%, 83.8%, and 94.8%, respectively. CONCLUSIONS: The AMTD test showed good sensitivity and specificity in the population studied, enabling the laboratory detection of M. tuberculosis complex in paucibacillary respiratory specimens.

Use of amplified Mycobacterium tuberculosis direct test in respiratory samples from HIV-infected patients in Brazil / Utilização do amplified Mycobacterium tuberculosis direct test em amostras respiratórias de pacientes HIV positivos no Brasil

OBJECTIVE: To compare the accuracy of the amplified Mycobacterium tuberculosis direct (AMTD) test with reference methods for the laboratory diagnosis of tuberculosis in HIV-infected patients. METHODS: This was a study of diagnostic accuracy comparing AMTD test results with those obtained by culture on Löwenstein-Jensen (LJ) medium and by the BACTEC Mycobacteria Growth Indicator Tube 960 (BACTEC MGIT 960) system in respiratory samples analyzed at the Bioassay and Bacteriology Laboratory of the Oswaldo Cruz Foundation Evandro Chagas Clinical Research Institute in the city of Rio de Janeiro, Brazil. RESULTS: We analyzed respiratory samples collected from 118 patients, of whom 88 (74.4%) were male. The mean age was 36.6 ± 10.6 years. Using the AMTD test, the BACTEC MGIT 960 system, and LJ culture, we identified M. tuberculosis complex in 31.0%, 29.7%, and 27.1% of the samples, respectively. In comparison with LJ culture, the AMTD test had a sensitivity, specificity, positive predictive value, and negative predictive value of 87.5%, 89.4%, 75.7%, and 95.0%, respectively, for LJ culture, whereas, in comparison with the BACTEC MGIT 960 system, it showed values of 88.6%, 92.4%, 83.8%, and 94.8%, respectively. CONCLUSIONS: The AMTD test showed good sensitivity and specificity in the population studied, enabling the laboratory detection of M. tuberculosis complex in paucibacillary respiratory specimens. .

OBJETIVO: Comparar a acurácia do teste amplified Mycobacterium tuberculosis direct (AMTD) com métodos de referência para o diagnóstico laboratorial de tuberculose em pacientes HIV positivos. MÉTODOS: Estudo de acurácia diagnóstica comparando os resultados do teste AMTD com os de cultura em Löwenstein-Jensen (LJ) e de BACTEC Mycobacteria Growth Indicator Tube 960 (sistema BACTEC MGIT 960) em amostras respiratórias analisadas no Laboratório de Bacteriologia e Bioensaios do Instituto de Pesquisa Clínica Evandro Chagas da Fundação Oswaldo Cruz, no Rio de Janeiro (RJ). RESULTADOS: Foram analisadas amostras respiratórias de 118 pacientes, dos quais 88 (74,4%) eram do sexo masculino. A média de idade foi de 36,6 ± 10,6 anos. O complexo M. tuberculosis foi identificado em 31,0%, 29,7% e 27,1% das amostras através do teste AMTD, sistema BACTEC MGIT 960 e LJ, respectivamente. Na comparação com a cultura em LJ, o teste AMTD apresentou sensibilidade, especificidade, valor preditivo positivo e valor preditivo negativo de 87,5%, 89,4%, 75,7% e 95,0%, respectivamente, enquanto na comparação com o sistema BACTEC MGIT 960, os valores foram de 88,6%, 92,4%, 83,8% e 94,8%, respectivamente. CONCLUSÕES: O teste AMTD mostrou boa sensibilidade e especificidade na população estudada, possibilitando a detecção laboratorial do complexo M. tuberculosis em espécimes respiratórios paucibacilares. .

Comparação do teste amplified mycobacterium tuberculosis direct com métodos de referência para detecção de mycobacterium tuberculosis em espécimes respiratórios de pacientes HIV positivo / Comparison of amplified mycobacterium tuberculosis direct test with reference methods for detection of mycobacterium tuberculosis in respiratory specimens of HIV positive patients

O diagnóstico rápido da tuberculose (TB) é fundamental para a redução da taxa detransmissão da doença e conseqüentemente do número de pessoas infectadas peloindivíduo doente além de possibilitar a prevenção do óbito e as seqüelas causadaspela progressão da doença sem tratamento. A baciloscopia possui baixasensibilidade e o maior problema da cultura para micobactérias é o longo tempo de incubação necessário, até oito semanas. Novos testes, apesar do custo elevado, podem representar um avanço no combate à doença. O teste AmplifiedMycobacterium tuberculosis Direct (MTD; Gen-Probe; San Diego, CA) é capaz dedetectar o rRNA do complexo M. tuberculosis em aproximadamente 3 horas, porémé necessário um melhor entendimento da performance deste teste para clientelapaucibacilar, que é o caso de pacientes HIV positivo, já que a qualidade de suasamostras normalmente dificulta o diagnóstico laboratorial tanto pela baciloscopiaquanto pela cultura. Este estudo foi realizado no Laboratório de Bacteriologia eBioensaios do Instituto de Pesquisa Clínica Evandro Chagas da Fundação OswaldoCruz e tem como objetivo comparar o teste Amplified Mycobacterium tuberculosisDirect com métodos de referência para o diagnóstico laboratorial de tuberculose empacientes HIV positivo na forma de um estudo retrospectivo de acurácia diagnósticacomparando os resultados do MTD com cultura em LJ e BACTEC MGIT 960. Foramanalisadas amostras respiratórias de 118 pacientes, 74,4% do sexo masculino, eidade média de 36,61 ± 10,6 anos. O MTD identificou 31% das amostras comocomplexo M. tuberculosis (M.tb). Entre as culturas em BACTEC MGIT 960, 29,7 por centoforam isolados como M.tb e as culturas em LJ isolaram 27,1%...

Rapid diagnosis of tuberculosis (TB) is important to reduce the rate of diseasetransmission and the number of infected people, enabling prevention of death andsequel caused by disease progression without treatment. The bacilloscopy has lowsensitivity and mycobacteria culture takes long incubation time, up to eight weeks.New tests, despite the high cost, may represent a breakthrough in combating thedisease. The Amplified Mycobacterium tuberculosis Direct Test (MTD, Gen-Probe,San Diego, CA) is capable of detecting the rRNA of the M. tuberculosis in about 3hours, but a better understanding of the performance of this test in paucibacillaryclientele is needed, which is the case of HIV positive patients, since the quality oftheir samples usually difficult both for the laboratory diagnosis by smear and culture.This study was conducted at the Laboratory of Bacteriology and bioassays of theClinical Research Institute Evandro Chagas, Oswaldo Cruz Foundation, and aims tocompare the Amplified Mycobacterium tuberculosis Direct Test with referencemethods for the laboratory diagnosis of tuberculosis in HIV positive patients with aretrospective study of diagnostic accuracy by comparing the results of MTD with LJand BACTEC MGIT 960. We analyzed respiratory samples from 118 patients, 74.4%, mean age 36.61 ± 10.6 years...