Evaluation of molecular detection of extrapulmonary tuberculosis and resistance to rifampicin with GeneXpert® MTB/RIF

Med Mal Infect. 2016 Feb;46(1):20-4. doi: 10.1016/j.medmal.2015.10.012. Epub 2015 Dec 2.


Objective: We aimed to evaluate the GeneXpert® MTB/RIF test for the diagnosis of extrapulmonary tuberculosis. The test simultaneously detects Mycobacterium tuberculosis complex and resistance to rifampicin.

Methods: We analyzed 153 clinical samples collected in a tertiary hospital in Sfax, Tunisia, between 2013 and 2014. We performed the GeneXpert® test, a Ziehl-Neelsen and auramine-rhodamine staining, conventional culture on MGIT 960 and LJ media, and we tested the resistance to anti-tuberculosis drugs on MGIT 960 and LJ media for each sample. Diagnosis was based on clinical, radiological, microbiological, pathological, and therapeutic data.

Results: We considered that 59 patients out of 153 presented with tuberculosis. PCR was positive in 50 samples and all of these samples were susceptible to rifampicin. Sensitivity, specificity, positive predictive value, and negative predictive value of the GeneXpert® test were 84.7%, 96.8%, 94.3%, and 91%, respectively, compared with diagnosis. We observed a statistically significant difference between the direct test and the GeneXpert® test, and between culture and the GeneXpert® test. No statistically significant difference was observed between pathological results and the GeneXpert® test. Sensitivity of the GeneXpert® test was 87.5% in biopsies, 80% in pus and abscesses, and 66.7% in biological fluids. All strains were susceptible to rifampicin with culture and GeneXpert® test.

Conclusion: The GeneXpert® test helped detect a higher proportion of M. tuberculosis complex. It does not replace conventional diagnostic methods but it is a useful addition to achieve better sensitivity and obtain rapid results.

Keywords: Complexe Mycobacterium tuberculosis; Extrapulmonary tuberculosis; GeneXpert(®) MTB/RIF; Mycobacterium tuberculosis complex; Resistance to rifampicin; Résistance à la rifampicine; Tuberculose extra-pulmonaire.

Publication types

  • Evaluation Study

MeSH terms

  • Abscess / microbiology
  • Antitubercular Agents / pharmacology*
  • Biopsy
  • Body Fluids / microbiology
  • DNA, Bacterial / genetics*
  • Drug Resistance / genetics*
  • Female
  • HIV Seronegativity
  • Humans
  • Male
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / isolation & purification*
  • Polymerase Chain Reaction / methods*
  • Predictive Value of Tests
  • Retrospective Studies
  • Rifampin / pharmacology*
  • Sensitivity and Specificity
  • Staining and Labeling
  • Suppuration / microbiology
  • Tuberculosis / diagnosis*
  • Tuberculosis / microbiology
  • Tuberculosis, Multidrug-Resistant / microbiology


  • Antitubercular Agents
  • DNA, Bacterial
  • Rifampin