Performance of Xpert MTB/RIF and sputum microscopy compared to sputum culture for diagnosis of tuberculosis in seven hospitals in Indonesia

Anis Karuniawati, Erlina Burhan, Eko Budi Koendhori, Desvita Sari, Budi Haryanto, Titik Nuryastuti, A. A.A.Yuli Gayatri, Uleng Bahrun, R. Lia Kusumawati, Retna Indah Sugiyono, Nugroho Harry Susanto, Aly Diana, Herman Kosasih, Adhella Menur Naysilla, Dewi Lokida, Aaron Neal, Sophia Siddiqui, Chuen Yen Lau, Muhammad Karyana

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


Introduction: Tuberculosis (TB) is a major public health concern in Indonesia, where the incidence was 301 cases per 100,000 inhabitants in 2020 and the prevalence of multi-drug resistant (MDR) TB is increasing. Diagnostic testing approaches vary across Indonesia due to resource limitations. Acid-fast bacilli (AFB) smear is widely used, though Xpert MTB/RIF has been the preferred assay for detecting TB and rifampicin resistance since 2012 due to higher sensitivity and ability to rapidly identify rifampicin resistance. However, <1,000 Xpert instruments were available in Indonesia as of 2020 and the Xpert supply chain has suffered interruptions. Methods: We compared the performance of Xpert MTB/RIF and AFB smear to facilitate optimization of TB case identification. We analyzed baseline data from a cohort study of adults with pulmonary TB conducted at seven hospitals across Indonesia. We evaluated sensitivity and specificity of AFB smear and Xpert MTB/RIF using Mycobacterium tuberculosis (Mtb) culture as the gold standard, factors associated with assay results, and consistency of Xpert MTB/RIF with drug susceptibility test (DST) in detecting rifampicin resistance. Results: Sensitivity of AFB smear was significantly lower than Xpert MTB/RIF (86.2 vs. 97.4%, p-value <0.001), but specificity was significantly better (86.7 vs. 73.3%, p-value <0.001). Performance varied by hospital. Positivity rate for AFB smear and Mtb culture was higher in subjects with pulmonary cavities and in morning sputum samples. Consistency of Xpert MTB/RIF with DST was lower in those with rifampicin- sensitive TB by DST. Discussion: Additional evaluation using sputa from primary and secondary Indonesian health centers will increase the generalizability of the assessment of AFB smear and Xpert MTB/RIF performance, and better inform health policy. Clinical trial registration: [], identifier [NCT027 58236].

Original languageEnglish
Article number909198
JournalFrontiers in Medicine
Publication statusPublished - 20 Jan 2023


  • diagnosis
  • DST
  • mycobacteria
  • rifampicin
  • sputum culture
  • sputum microscopy
  • tuberculosis
  • Xpert MTB/RIF


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