title: Evaluation of the GeneXpert MTB/RIF assay on extrapulmonary and respiratory samples other than sputum: a low burden country experience.
abstract: The aim of this study was to assess the performance of the GeneXpert MTB/RIF assay on extrapulmonary (EP) and respiratory (non-sputum) clinical samples of patients suspected of having tuberculosis (TB) from Queensland, Australia. A total of 269 EP and respiratory (non-sputum) clinical samples collected from Qld patients who were suspected of having TB were subjected to the GeneXpert MTB/RIF analysis, Ziehl-Neelsen (ZN) staining, Mycobacterium tuberculosis (MTB) culture and drug susceptibility testing. Phenotypic and genotypic data were compared. The overall performance analysis of the GeneXpert MTB/RIF assay for detection of MTB complex demonstrated sensitivity of 89%, specificity of 95%, PPV of 89% and NPV of 95% using culture as a reference standard. The GeneXpert MTB/RIF analysis of acid-fast bacilli (AFB) smear positive samples and AFB smear negative samples showed sensitivities of 100% and 77%, respectively. Looking at individual EP and respiratory (non-sputum) sample types, the sensitivity ranged from 60% to 100% although the specificity ranged from 33% to 100% with the specificity of lymph node tissue biopsy being the lowest. The GeneXpert MTB/RIF assay detected 11% more TB cases than culture and 27% more cases than ZN microscopy. Due to insufficient numbers of presenting rifampicin resistance cases, performance analysis of the GeneXpert MTB/RIF assay on rifampicin resistance could not be carried out. The GeneXpert MTB/RIF assay is potentially valuable for TB diagnosis in the majority of the EP and respiratory (other than sputum) samples in our setting. Although the GeneXpert MTB/RIF assay provides rapid diagnostic results, the overall sensitivity to rule out the disease is suboptimal for some specimen types. Performance varied according to specimen type and AFB smear status. The sensitivity and specificity of lymph node tissue was 63% and 33%. Care must be taken when using the GeneXpert MTB/RIF assay for detection of MTB in lymph node tissue samples. All samples should be cultured regardless of the GeneXpert MTB/RIF assay result.
authors.affiliation: Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland Health, Qld, Australia. Electronic address: sushil.pandey@health.qld.gov.au.
authors.forename: Sushil
authors.initials: S
authors.lastname: Pandey
authors.affiliation: Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland Health, Qld, Australia.
authors.forename: Jacob
authors.initials: J
authors.lastname: Congdon
authors.affiliation: Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland Health, Qld, Australia.
authors.forename: Bradley
authors.initials: B
authors.lastname: McInnes
authors.affiliation: Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland Health, Qld, Australia.
authors.forename: Alina
authors.initials: A
authors.lastname: Pop
authors.affiliation: Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland Health, Qld, Australia.
authors.forename: Christopher
authors.initials: C
authors.lastname: Coulter
mesh_terms: D024881:Drug Resistance, Bacterial / Q000187:drug effects*; D005838:Genotype; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics; D012293:Rifampin / Q000494:pharmacology*; D012680:Sensitivity and Specificity; D013183:Sputum / Q000187:drug effects* / Q000378:metabolism; D014376:Tuberculosis / Q000175:diagnosis* / Q000188:drug therapy / Q000473:pathology*
chemical_list: D012293:Rifampin
keywords: GeneXpert MTB/RIF; Mycobacterium tuberculosis; culture; extrapulmonary