Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting

Abstract INTRODUCTION: Nontuberculous mycobacteria (NTM) species, as human pathogens, are increasing in the world, as is the difficulty of accurately identifying them. Differential diagnosis, especially between the M. tuberculosis complex and NTM species, and the characterization of NTM species is important. This study aimed to evaluate the performance of a molecular system based on multiplex real-time PCR with high-resolution melting (HRM) for the identification and differentiation of NTM species of clinical importance of an endemic area for tuberculosis in northeastern Brazil. METHODS: The technical protocol of the molecular system was based on multiplex real-time PCR-HRM, and evaluated the sensitivity and specificity of the detection of NTM species in mycobacterial clinical isolates from the studied region. The gold standard method was specific gene sequencing. RESULTS: The sensitivity and specificity of multiplex real-time PCR-HRM modified for differentiation between NTM and M. tuberculosis were 90% and 100%, respectively. The PCR-HRM sensitivities for the characterization of NTM species (M. kansasii, M. abscesses, M. avium, and M. fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively. CONCLUSIONS The multiplex real-time PCR-HRM modified assay has the potential to rapidly and efficiently identify nontuberculous mycobacteria of clinical importance, which is crucial for immediate implementation of the appropriate therapy and thus avoiding complications and sequelae in patients.

Fatores associados ao abandono e ao óbito de casos de tuberculose drogarresistente (TBDR) atendidos em um centro de referência no Rio de Janeiro, Brasil / Factores asociados al abandono y al fallecimiento por casos de tuberculosis farmacorresistente (TBFR), atendidos en un centro de referencia en Río de Janeiro, Brasil / Factors associated with loss to follow-up and death in cases of drug-resistant tuberculosis (DR-TB) treated at a reference center in Rio de Janeiro, Brazil

Resumo: A tuberculose drogarresistente (TBDR) representa hoje uma grave ameaça aos avanços no controle da tuberculose (TB) no Brasil e no mundo. Neste estudo, investigam-se fatores associados ao abandono e ao óbito de casos em tratamento para TBDR, em um centro de referência terciária do Município do Rio de Janeiro, Brasil. Trata-se de um estudo de coorte retrospectiva, a partir dos casos notificados no Sistema de Informação de Tratamentos Especiais de Tuberculose (SITETB), no período de 1º de janeiro de 2012 a 31 de dezembro de 2013. Um total de 257 pacientes foi notificado no SITETB e iniciou o tratamento para TBDR. Desse total, 139 (54,1%) tiveram sucesso terapêutico como desfecho, 54 (21%) abandonaram o tratamento e 21 (8,2%) evoluíram para óbito. Após análise de regressão logística multinomial múltipla, a faixa etária acima de cinquenta anos foi observada como único fator de proteção ao abandono, ao passo que ter menos de oito anos de escolaridade e reingresso após abandono foram considerados como fatores de risco. Reingresso após abandono, recidiva e falência indicaram fatores de risco. Nossos dados reforçam a concepção de que o abandono do tratamento de tuberculose resistente é um sério problema de saúde pública, sendo necessário um adequado acompanhamento no tratamento de pacientes com esse histórico e com baixa escolaridade. Além disso, uma rede de apoio social ao paciente é imprescindível para que desfechos desfavoráveis sejam evitados.

Resumen: La tuberculosis farmacorresistente (TBFR) representa hoy una grave amenaza para los avances en el control de la tuberculosis (TB) en Brasil y en el mundo. En este estudio, se investigan factores asociados al abandono y al óbito de casos en tratamiento para TBDR, dentro de un centro de referencia de carácter terciario del municipio de Río de Janeiro, Brasil. Se trata de un estudio de cohorte retrospectiva, a partir de los casos notificados en el Sistema de Información de Tratamientos Especiales de Tuberculosis (SITETB), durante el período del 1 de enero de 2012 al 31 de diciembre de 2013. Un total de 257 pacientes fue notificado en el SITETB y comenzó el tratamiento para TBDR. De ese total, 139 (un 54,1%) tuvieron éxito terapéutico como desenlace, 54 (un 21%) abandonaron el tratamiento y un 21 (8,2%) evolucionaron hacia óbito. Tras el análisis de regresión logística multinomial múltiple, la franja de edad por encima de cincuenta años se observó como el único factor de protección al abandono, al mismo tiempo que tener menos de ocho años de escolaridad y reingresar en el sistema educativo tras el abandono fueron considerados como factores de riesgo. Reingreso tras abandono, recidiva e insolvencia indicaron factores de riesgo. Nuestros datos refuerzan la concepción de que el abandono del tratamiento de tuberculosis resistente es un serio problema de salud pública, siendo necesario un adecuado acompañamiento en el tratamiento de pacientes con este historial y con baja escolaridad. Además, una red de apoyo social entorno al paciente es imprescindible para que los desenlaces desfavorables sean evitados.

Abstract: Drug-resistant tuberculosis (DR-TB) poses a serious threat to tuberculosis (TB) control in Brazil and worldwide. The current study investigated factors associated with loss to follow-up and death in the course of treatment for DR-TB in a tertiary reference center in the city of Rio de Janeiro, Brazil. This was a retrospective cohort study of cases reported to the Information System on Special Treatments for Tuberculosis (SITETB) from January 1, 2012, to December 31, 2013. A total of 257 patients were reported to the SITETB and initiated treatment for DR-TB. Of this total, 139 (54.1%) achieved treatment success as the outcome, 54 (21%) were lost to follow-up, and 21 (8.2%) died. Following a multiple multinomial logistic regression analysis, the age bracket older than 50 years was the only protective factor against loss to follow-up, whereas less than eight years of schooling and reentry after loss to follow-up were considered risk factors. Reentry after loss to follow-up, relapse, and treatment failure appeared as risk factors. Our data reinforce the concept that loss to follow-up in drug-resistant tuberculosis is a serious public health problem, and that adequate follow-up of treatment is necessary in patients with this history and low schooling. A social support network for patients is also indispensable for avoiding unfavorable outcomes.

Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity

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.

Nontuberculous mycobacteria in respiratory samples from patients with pulmonary tuberculosis in the state of Rondonia, Brazil

The main cause of pulmonary tuberculosis (TB) is infection with Mycobacterium tuberculosis (MTB). We aimed to evaluate the contribution of nontuberculous mycobacteria (NTM) to pulmonary disease in patients from the state of Rondônia using respiratory samples and epidemiological data from TB cases. Mycobacterium isolates were identified using a combination of conventional tests, polymerase chain reaction-based restriction enzyme analysis of hsp65 gene and hsp65 gene sequencing. Among the 1,812 cases suspected of having pulmonary TB, 444 yielded bacterial cultures, including 369 cases positive for MTB and 75 cases positive for NTM. Within the latter group, 14 species were identified as Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium intracellulare, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium asiaticum, Mycobacterium tusciae, Mycobacterium porcinum, Mycobacterium novocastrense, Mycobacterium simiae, Mycobacterium szulgai, Mycobacterium phlei and Mycobacterium holsaticum and 13 isolates could not be identified at the species level. The majority of NTM cases were observed in Porto Velho and the relative frequency of NTM compared with MTB was highest in Ji-Paraná. In approximately half of the TB subjects with NTM, a second sample containing NTM was obtained, confirming this as the disease-causing agent. The most frequently observed NTM species were M. abscessus and M. avium and because the former species is resistant to many antibiotics and displays unsatisfactory cure rates, the implementation of rapid identification of mycobacterium species is of considerable importance.

Primeiro isolamento de Mycobacterium kyorinense em espécime clínico no Brasil / First isolation of Mycobacterium kyorinense in a clinical specimen in Brazil

Os testes bioquímicos realizados, o seqüenciamento de diferentes alvos genéticos e a construção de uma árvore concatenada, construída a través do método Neighbor-Joining, permitiram a identificação das cepas brasileiras como M. kyorinense.

Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil

A single strain of Mycobacterium abscessus subsp. bolletii, characterised by a particular rpoB sequevar and two highly related pulsed field gel electrophoresis patterns has been responsible for a nationwide outbreak of surgical infections in Brazil since 2004. In this study, we developed molecular tests based on polymerase chain reaction restriction-enzyme analysis (PRA) and sequencing for the rapid identification of this strain. Sequences of 15 DNA regions conserved in mycobacteria were retrieved from GenBank or sequenced and analysed in silico. Single nucleotide polymorphisms specific to the epidemic strain and located in enzyme recognition sites were detected in rpoB, the 3' region of the 16S rDNA and gyrB. The three tests that were developed, i.e., PRA-rpoB, PRA-16S and gyrB sequence analysis, showed 100%, 100% and 92.31% sensitivity and 93.06%, 90.28% and 100% specificity, respectively, for the discrimination of the surgical strain from other M. abscessus subsp. bolletii isolates, including 116 isolates from 95 patients, one environmental isolate and two type strains. The results of the three tests were stable, as shown by results obtained for different isolates from the same patient. In conclusion, due to the clinical and epidemiological importance of this strain, these tests could be implemented in reference laboratories for the rapid preliminary diagnosis and epidemiological surveillance of this epidemic strain.