Determination of the diagnostic accuracy of nanopore sequencing using bronchoalveolar lavage fluid samples from patients with sputum-scarce pulmonary tuberculosis

Abstract

PurposeThe early and efficient diagnosis of patients suspected of having pulmonary tuberculosis (PTB) remains challenging. This study aimed to evaluate the accuracy of nanopore sequencing for PTB diagnosis using bronchoalveolar lavage fluid (BALF) samples and compared it with other techniques such as acid-fast bacilli smear, culture, Xpert MTB/RIF, and CapitalBio Mycobacterium reverse transcription–polymerase chain reaction (MTB RT–PCR). MethodsWe retrospectively analyzed the clinical data of 195 patients with suspected PTB who were admitted to our hospital. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) of these assays were calculated and compared. ResultsThe overall sensitivity, specificity, PPV, NPV, and AUC of nanopore sequencing were 90.70%, 84.85%, 92.13%, 82.35%, and 0.88; those of acid-fast bacilli smear were 12.40%, 98.48%, 94.12%, 36.52%, and 0.55; those of culture were 36.43%, 100%, 100%, 44.59%, and 0.68; those of Xpert MTB/RIF were 41.09%, 100%, 100%, 46.48%, and 0.71; and those of CapitalBio MTB RT–PCR were 34.88%, 98.48%, 97.83%, 43.62%, and 0.67, respectively. ConclusionThe nanopore sequencing assay using BALF samples showed the best diagnostic accuracy for sputum-scarce PTB. Moreover, it can improve the clinical diagnosis of PTB.