[Evaluation of molecular diagnosis of tuberculosis and resistance to rifampicin with GeneXpert® MTB/RIF in Algeria]. / Évaluation du GeneXpert® MTB/RIF dans le diagnostic moléculaire de la tuberculose et de la résistance à la rifampicine en Algérie.

Objective: 1) To evaluate the contribution of the GeneXpert® MTB/RIF (GX) test in the diagnosis of pulmonary and extra-pulmonary tuberculosis compared to culture. 2) To compare the rifampicin results resistance obtained by GX with the phenotypic sensitivity test. Materials and methods: Retrospective study carried out over a period of five years, from May 2017 to June 2022 at the microbiology laboratory of the Central army Hospital Mohamed Seghir Nekkache, Algiers (Algeria). The pulmonary and extrapulmonary clinical specimens were collected, cultivated, tested by GX PCR and direct examination by Ziehl-Neelsen staining. The study of sensitivity to antituberculosis drugs was performed according to the proportion method on liquid medium Bactec MGIT 960 (or on solid medium Lowenstein-Jensen at the Algerian Pasteur Institute). Results: 310 samples were included in the final analysis of the study, of which 156 were of pulmonary origin and 154 of extrapulmonary origin. Mycobacterium tuberculosis complex (MTBC) was detected in 95 samples from 88 tuberculosis patients (sex ratio 2,03 and middle age 37 years) with 49 cases of pulmonary tuberculosis and 39 cases of extra-pulmonary tuberculosis. For 2 cases, the GX was positive while the culture was negative and for 11 cases, the GX was negative while the culture was positive. Thus, in our study and compared to culture, GX showed an overall sensitivity of 88.2%, a specificity of 98.6%, a positive predictive value (PPV) of 96.4% and a negative predictive value (NPV) of 95.2%. The analysis of the data according to the type of samples, the sensitivity, specificity, PPV and NPV of GX for the pulmonary and extrapulmonary samples were 96.3% vs. 77.0%, 98.0% vs. 99.1%, 96.2% vs. 96.5% and 98.0% vs. 92.7% respectively. The sensitivity of GX for disco-vertebral, lymph node, meningeal and pleural tuberculosis were 100%, 90.0%, 71.4% and 57.1% respectively. The sensitivity of GX for pulmonary tuberculosis compared to microscopy was 96% vs. 68%. The comparison of the results of detection of resistance to rifampicin by GX and by phenotypic methods showed perfect agreement. Discussion and conclusion: A good sensitivity of GX compared to microscopy was revealed. The GX is a useful tool for the diagnosis of pulmonary tuberculosis, especially in smear-negative cases. The sensitivity of GX in extrapulmonary tuberculosis varied depending on the location of the infection. A negative result by GX does not exclude tuberculosis and cases of resistance to RIF detected by GX must be confirmed by phenotypic method.

Genetic diversity of Mycobacterium tuberculosis strains isolated in Algeria: Results of spoligotyping.

OBJECTIVE/BACKGROUND: Molecular typing tools, including spoligotyping, are currently widely used in the monitoring and study of the dynamics of tuberculosis epidemics. METHODS: A study of the molecular profile of a sample of 129 Myobacterium tuberculosis strains isolated during 2011 was carried out in the National Reference Laboratory for Tuberculosis and Mycobacteria at the Pasteur Institute of Algeria. This sample was selected at random from a set of 350 strains isolated from tuberculosis patients from central and eastern areas of the country. RESULTS: Genotypic analysis helped to clarify the frequencies of the different genotypes in the current study population: H family, 29%; LAM family, 26%; T family, 25%; S family, 5%, and other genomic families, including orphan strains, 15%. CONCLUSION: The study of strains isolated between January and December 2011 has allowed insight into the frequency of different genomic families and the importance of existing clusters in the population of central and eastern Algeria.

Mycobacterium tuberculosis genotype Beijing: About 15 strains and their part in MDR-TB outbreaks in Algeria.

Within the framework of epidemiological surveillance by molecular typing tools conducted in the NRL on multi-resistant strains, the application of spoligotyping on a group of 390 strains consisting of 389 DR-MTB strains and 1 susceptible strain isolated from patients made it possible to detect the presence of 15 strains belonging to the Beijing genotype. All 15 strains were genotyped by MTBDRplus. Among the 15 strains, 11 were typed by RFLP and 9 by MIRU-VNTR. After analysis of the profiles obtained by the software MIRU-VNTRplus, two spoligotypes (st No. 1 and st No. 265) and four RFLP profiles and a complete identity profile by MIRU-VNTR, information collected on patients allowed the research team to detect a family tie among patients of three different families, as well as one nosocomial TB transmission. The percentage of Beijing strains found among the patients in this study was 3.8%; this figure does not reflect the reality because it was calculated from an essay on MDR-TB. To get an idea of the prevalence of Beijing TB strains in this country, a more extensive study is currently being considered.