Evaluation of Xpert MTB/RIF assay accuracy for diagnosing TB and detecting rifampin resistance in patients with very low bacterial loads results: a retrospective study in Hunan, China

There is widespread use of Xpert MTB/RIF for tuberculosis (TB) diagnosis and rifampin resistance (RIF-R) detection. Despite this, concerns have been raised about false-positive results, which are more prevalent in patients with very low bacterial loads. We performed a retrospective analysis of 717 patients at Hunan Chest Hospital from January 2022 to January 2023, all of whom had Xpert MTB/RIF results indicating very low bacterial loads. The accuracy of Xpert in diagnosing TB was evaluated against a composite reference standard (CRS), which classified cases via symptom, liquid culture, imaging assessments, immunological tests, and therapeutic response. In addition, rifampicin resistance was adjudicated using a composite reference standard of pDST and rpoB sequencing, with pDST as the primary reference for Xpert MTB/RIF results and sequencing used to resolve discrepancies. Of 717 patients with Xpert detected very low bacterial loads, 175 (24.4%) yielded positive cultures, while 16 cases identified as non-tuberculous mycobacteria (NTM). The positive predictive value (PPV) of Xpert for bacteriologically confirmed TB was 90.8% (159/175). For 542 culture-negative patients, Xpert’s PPV was 81.7% (443/542) in clinically diagnosed TB (80.4% pulmonary TB, 88.9% extrapulmonary TB). In 121 patients with pDST, Xpert for RIF-R had 68.4% sensitivity (13/19), 88.2% specificity (90/102), respectively. Among the 6 patients who were RIF-R by pDST but rifampin susceptible by Xpert, four cases harbored mutations inside the 81-bp Rifampicin Resistance-Determining Region (RRDR) region of rpoB. Xpert demonstrates good performance in diagnosing TB among the patients with results showing very low bacterial loads, especially in the culture-positive group and extrapulmonary tuberculosis group. However, its performance in detecting rifampicin resistance is not reliable. Our findings emphasize that Xpert results showing very low bacterial loads should be confirmed when diagnosing rifampin resistance tuberculosis.