Integrating tuberculosis and COVID-19 molecular testing in Lima, Peru: a cross-sectional, diagnostic accuracy study

Abstract

Background: Integrated molecular testing could be an opportunity to detect and provide care for both tuberculosis and COVID-19. Many high tuberculosis burden countries, such as Peru, have existing GeneXpert systems for tuberculosis testing with GeneXpert Xpert MTB/RIF Ultra (Xpert Ultra), and a GeneXpert SARS-CoV-2 assay, GeneXpert Xpert Xpress SARS-CoV-2 (Xpert Xpress), is also available. We aimed to assess the feasibility of integrating tuberculosis and COVID-19 testing using one sputum specimen with Xpert Ultra and Xpert Xpress in Lima, Peru.

Methods: In this cross-sectional, diagnostic accuracy study, we recruited adults presenting with clinical symptoms or suggestive history of tuberculosis or COVID-19, or both. Participants were recruited from a total of 35 primary health facilities in Lima, Peru. Participants provided one nasopharyngeal swab and one sputum sample. For COVID-19, we tested nasopharyngeal swabs and sputum using Xpert Xpress; for tuberculosis, we tested sputum using culture and Xpert Ultra. We compared diagnostic accuracy of sputum testing using Xpert Xpress with nasopharyngeal swab testing using Xpert Xpress. Individuals with positive Xpert Xpress nasopharyngeal swab results were considered COVID-19 positive, and a positive culture indicated tuberculosis. To assess testing integration, the proportion of cases identified in sputum by Xpert Xpress was compared with Xpert Xpress on nasopharyngeal swabs, and sputum by Xpert Ultra was compared with culture.

Findings: Between Jan 11, 2021, and April 26, 2022, we recruited 600 participants (312 [52%] women and 288 [48%] men). In-study prevalence of tuberculosis was 13% (80 participants, 95% CI 11-16) and of SARS-CoV-2 was 35% (212 participants, 32-39). Among tuberculosis cases, 13 (2·2%, 1·2-3·7) participants were concurrently positive for SARS-CoV-2. Regarding the diagnostic yield of integrated testing, Xpert Ultra detected 96% (89-99) of culture-confirmed tuberculosis cases (n=77), and Xpert Xpress-sputum detected 67% (60-73) of COVID-19 cases (n=134). All five study staff reported that integrated molecular testing was easy and acceptable.

Interpretation: The diagnostic yield of Xpert Xpress on sputum was moderate, but integrated testing for tuberculosis and COVID-19 with GeneXpert was feasible. However, systematic testing for both diseases might not be the ideal approach for everyone presenting with presumptive tuberculosis or COVID-19, as concurrent positive cases were rare during the study period. Further research might help to identify when integrated testing is most worthwhile and its optimal implementation.

Funding: Canadian Institutes of Health Research and International Development Research Centre.

Translation: For the Spanish translation of the abstract see Supplementary Materials section.

Figure 1

Study procedures Each participant provided one nasopharyngeal swab and one sputum sample. During the phone call, we asked whether the participant was living at time of follow-up, was hospitalised since enrolling in the study, had received a diagnosis of tuberculosis or COVID-19 after enrolling in our study, or had any current symptoms, and how their overall physical and mental health were compared with usual health.

Figure 2

Boxplots of cough duration stratified by disease condition Tuberculosis was defined by culture positivity (n=80). COVID-19 was defined by a positive test result on Xpert Xpress with nasopharyngeal swabs (n=212). Concurrent tuberculosis and COVID-19 was defined as concurrent tuberculosis culture and a positive result on Xpert Xpress with nasopharyngeal swabs or sputum (n=13).

Figure 3

Venn diagram of Xpert Xpress results for SARS-CoV-2 detection with nasopharyngeal swabs and sputum Numbers in the figure correspond to the number of individuals with positive test results on either nasopharyngeal swab (n=67), sputum (n=13), or both (n=134). Here, data from individuals with any missing test results were excluded from the figure.