VOLUME 19 (Supplement)

Alternative respiratory specimens for GeneXpert-based tuberculosis (TB) and COVID-19 diagnosis in selected cities of Laguna, Philippines, amid and post-pandemic

Diagnosis of tuberculosis (TB) and coronavirus disease (COVID-19) relies on the collection of standard specimens, yet obtaining these remains a persistent challenge in practice. TB testing typically relies on sputum, which requires patient ability to expectorate or to cough up from the lungs, while nasopharyngeal and oropharyngeal swabbing for COVID-19 can be uncomfortable or even painful. Exploring alternative specimens provides practical options in cases when standard specimen collection is not feasible, enabling timely diagnosis, patient-centered care, and offering a potential for dual testing from a single specimen. The Cepheid GeneXpert® technology supports this approach by providing a platform capable of diagnosing both TB and COVID-19.

This study evaluated the diagnostic performance of Xpert® MTB/RIF Ultra using oropharyngeal swabs (OPS) and Xpert® Xpress SARS-CoV-2 using sputum for the respective diagnosis of TB and COVID-19. Study participants presenting with signs and symptoms of either or both diseases were enrolled from selected sites in Laguna from August 2022 to September 2024. Both standard and alternative specimens were collected and tested using their corresponding diagnostic assays: Xpert® MTB/RIF Ultra and Xpert® Xpress SARS-CoV-2, with reference standards culture and conventional real-time reverse transcriptase polymerase chain reaction (RT-PCR) for TB and COVID-19, respectively. Diagnostic accuracy parameters were analyzed and compared across specimen types.

A total of 111 study participants were enrolled into these screening cohorts: 69 with TB, 4 with COVID-19, and 38 with co-infection wherein, 107 OPS specimens were analyzed using Xpert® MTB/RIF Ultra, and 35 sputum specimens were tested with Xpert® Xpress SARS-CoV-2.

Using sputum TB culture (n=24) as reference standard in diagnosing TB, OPS (n=14) in saline tested positive in Xpert® MTB/RIF Ultra yielded a sensitivity of 58.33% (95% CI: 48.52–68.14), specificity of 86.30% (95% CI: 79.46-93.14), positive predictive value (PPV) of 58.33% (95% CI: 48.52–68.14), and negative predictive value (NPV) of 86.30% (95% CI: 79.46-93.14).

Comparable studies have reported sensitivity of 36% (95% CI: 26–48) to 91% (95% CI: 80–98) and specificity of 66% (95% CI: 52–78) to 100.00% (95% CI: 97–100) in adults (Church et al., 2024).

Meanwhile, all 5 COVID-19 positive samples (Xpert® Xpress SARS-CoV-2 sputum positive vs OPS positive in RT-PCR) yielded a sensitivity of 100.00% (95% CI: 100–100), specificity of 90.00% (95% CI: 80.06–99.94), PPV of 62.50% (95% CI: 46.46–78.54), and NPV of 100.00% (95% CI: 100–100). These findings were higher compared with prior findings reporting 67% sensitivity (MacLean et al., 2023).

The use of OPS for TB diagnosis with Xpert® MTB/RIF Ultra and sputum for COVID-19 diagnosis with Xpert® Xpress SARS-CoV-2 showed diagnostic performance comparable to that of standard specimens. These alternative specimens may serve as reliable options, especially in situations where collecting standard specimens is difficult. Notably, sputum may be a practical dual-use specimen for diagnosing both TB and COVID-19 during emergency responses such as pandemics. Nevertheless, standard specimens remain the preferred choice whenever feasible due to their established diagnostic accuracy.