Open Access Highly Accessed Research article

Molecular analysis of Mycobacterium isolates from extrapulmonary specimens obtained from patients in Mexico

Cosme Alvarado-Esquivel1*, Nora García-Corral2, David Carrero-Dominguez3, José Antonio Enciso-Moreno4, Teodoro Gurrola-Morales5, Leopoldo Portillo-Gómez6, Rudi Rossau7 and Wouter Mijs7

Author affiliations

1 Department of Microbiology, Faculty of Medicine, Juárez University of Durango State, Durango, Mexico

2 Department of Pharmacology, Faculty of Medicine, Juárez University of Durango State, Durango, Mexico

3 Regional Laboratory of Epidemiological Reference, Mexican Social Security Institute, Guadalajara, Mexico

4 Medical Research Unit, Mexican Social Security Institute, Zacatecas, México

5 Department of Pathology, Faculty of Medicine, Juárez University of Durango State, Durango, Mexico

6 Department of Microbiology and Parasitology, University Center of Health Sciences, University of Guadalajara, Guadalajara, Mexico

7 R&D Diagnostics, Innogenetics NV, Gent, Belgium

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Citation and License

BMC Clinical Pathology 2009, 9:1  doi:10.1186/1472-6890-9-1

Published: 9 March 2009



Little information is available on the molecular epidemiology in Mexico of Mycobacterium species infecting extrapulmonary sites in humans. This study used molecular methods to determine the Mycobacterium species present in tissues and body fluids in specimens obtained from patients in Mexico with extrapulmonary disease.


Bacterial or tissue specimens from patients with clinical or histological diagnosis of extrapulmonary tuberculosis were studied. DNA extracts from 30 bacterial cultures grown in Löwenstein Jensen medium and 42 paraffin-embedded tissues were prepared. Bacteria were cultured from urine, cerebrospinal fluid, pericardial fluid, gastric aspirate, or synovial fluid samples. Tissues samples were from lymph nodes, skin, brain, vagina, and peritoneum. The DNA extracts were analyzed by PCR and by line probe assay (INNO-LiPA MYCOBACTERIA v2. Innogenetics NV, Gent, Belgium) in order to identify the Mycobacterium species present. DNA samples positive for M. tuberculosis complex were further analyzed by PCR and line probe assay (INNO-LiPA Rif.TB, Innogenetics NV, Gent, Belgium) to detect mutations in the rpoB gene associated with rifampicin resistance.


Of the 72 DNA extracts, 26 (36.1%) and 23 (31.9%) tested positive for Mycobacterium species by PCR or line probe assay, respectively. In tissues, M. tuberculosis complex and M. genus were found in lymph nodes, and M. genus was found in brain and vagina specimens. In body fluids, M. tuberculosis complex was found in synovial fluid. M. gordonae, M. smegmatis, M. kansasii, M. genus, M. fortuitum/M. peregrinum complex and M. tuberculosis complex were found in urine. M. chelonae/M. abscessus was found in pericardial fluid and M. kansasii was found in gastric aspirate. Two of M. tuberculosis complex isolates were also PCR and LiPA positive for the rpoB gene. These two isolates were from lymph nodes and were sensitive to rifampicin.


1) We describe the Mycobacterium species diversity in specimens derived from extrapulmonary sites in symptomatic patients in Mexico; 2) Nontuberculous mycobacteria were found in a considerable number of patients; 3) Genotypic rifampicin resistance in M. tuberculosis complex infections in lymph nodes was not found.