Nanopore Sequencing May Improve the Accuracy of Pulmonary Tuberculosis Diagnoses

Pulmonary Tuberculosis . Chest X-ray : interstitial infiltration at left upper lung due to Mycobacterium Tuberculosis infection
Researchers assessed the diagnostic accuracy of nanopore sequencing for the early identification of pulmonary tuberculosis.

The use of nanopore sequencing for the early identification of pulmonary tuberculosis (TB) infection had superior diagnostic accuracy compared with both Mycobacterium tuberculosis (MTB) culture analyses and Xpert MTB/rifampin (RIF) assays, according to results of a study published in International Journal of Infectious Diseases.

In this retrospective study, researchers obtained clinical data from 164 patients who were tested for suspected pulmonary TB infection via nanopore sequencing between July and November 2021. Patient data were obtained from the TB Diagnosis and Treatment Center of Zhejiang province of the Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine. Included patients also underwent TB testing via acid-fast bacilli (AFB) smear, MTB culture, and Xpert MTB/RIF. The researchers calculated the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and the area under the curve (AUC) for all 4 testing methods, and the diagnostic accuracy of each test was compared.

After 7 patients with incomplete data were excluded, the final study population comprised 164 patients. Of these patients, the mean age was 51 years, 56.1% were men, and none were positive for HIV infection.

The sensitivity and specificity of pulmonary TB testing via nanopore sequencing was 94.8% and 97.9%, respectively. Compared with nanopore sequencing, AFB smear, MTB culture analysis, and Xpert MTB/RIF assay had significantly decreased sensitivity (27.6%, 57.8%, and 62.9%, respectively); however, the specificity of MTB culture analysis (100.0%) and Xpert MTB/RIF assay (97.9%) were similar.

Further analysis showed that the PPV and NPV of nanopore sequencing were 99.1% and 88.7%, respectively. For AFB smear, MTB culture analysis, and Xpert MTB/RIF assay, the respective PPVs and NPVs were as follows: 84.2% and 33%; 100.0% and 49.5%; and 99.1% and 88.7%.

Overall, nanopore sequencing had a superior diagnostic performance (AUC, 0.96) compared with AFB smear (AUC, 0.58), MTB culture analysis (AUC, 0.79), and Xpert MTB/RIF assay (AUC, 0.80).

Owing to these findings, the researchers noted that the diagnostic accuracy of nanopore sequencing was significantly increased compared with both MTB culture analysis and Xpert MTB/RIF assay (P <.05). Among all pulmonary TB testing methods, AFB smear exhibited the lowest diagnostic accuracy.

Study limitations included potential selection bias, the absence of MTB resistance-related outcomes, and that non-MTB-related data were not assessed. This study also was conducted in an area with an increased TB burden, thus these results may not be generalizable to other regions.

The researchers concluded “if applicable, this study recommends nanopore sequencing as an effective alternative to Xpert MTB/RIF for the initial detection of [pulmonary] TB infection…”


Yu G, Shen Y, Zhong F, et al. Diagnostic accuracy of nanopore sequencing using respiratory specimens in the diagnosis of pulmonary tuberculosis. Int J Infect Dis. Published online June 6, 2022. doi: 10.1016/j.ijid.2022.06.001

This article originally appeared on Infectious Disease Advisor