Annual trends in Mycobacterium tuberculosis detection and rifampicin resistance at a regional referral hospital in Northern Ghana, 2019–2024

Background Tuberculosis (TB) remains an important public health problem in Ghana, while rifampicin-resistant TB (RR-TB) poses an additional challenge to TB control. Routine molecular diagnostic data can provide useful information on temporal patterns of TB detection and drug resistance, particularly in regions where population-based surveillance data are limited. However, findings from referral facilities may be influenced by referral patterns and access to diagnostic services and should therefore be interpreted within their health-system context. We conducted a cross-sectional study using historical GeneXpert MTB/RIF data collected from January 2019 to December 2024 at the Upper East Regional Hospital (UERH), a regional referral facility in Bolgatanga, Ghana. Data were extracted from GeneXpert laboratory and TB programme registers for patients tested for presumptive TB. MTB detection and rifampicin resistance were determined from GeneXpert MTB/RIF results. Temporal differences in categorical outcomes were assessed using Pearson's chi-square test of independence. Multivariable logistic regression was used to identify factors independently associated with rifampicin resistance. A total of 6,897 GeneXpert MTB/RIF tests were included. The mean age of the tested population was 44.6 ± 20.4 years, and 56.7% were male. MTB was detected in 1,083 tests (15.7%). MTB detection varied significantly across study years (χ² = 28.46, p < 0.001), with positivity ranging from 9.8% in 2022 to 20.9% in 2021. Among MTB-positive tests, 192/1,083 (17.7%) showed rifampicin resistance. The annual proportion of rifampicin resistance ranged from 9.5% in 2020 to 23.1% in 2023 and varied significantly across years (χ² = 27.13, p < 0.001). Low MTB bacterial load was significantly more frequent among rifampicin-resistant cases. In multivariable analysis, female sex was associated with higher odds of rifampicin resistance after adjustment for age and MTB bacterial-load category (aOR = 1.44, 95% CI: 1.02-2.02; p = 0.037), while low MTB bacterial load was independently associated with rifampicin resistance after adjustment for age and sex (aOR = 9.62, 95% CI: 5.77-16.04; p < 0.001). MTB detection and rifampicin resistance showed substantial year-to-year variation among patients tested at UERH during 2019-2024. The 17.7% rifampicin-resistance proportion represents a hospital-based estimate among MTB-positive GeneXpert-tested cases and should not be interpreted as the population prevalence of RR-TB in the Upper East Region. The observed pattern nevertheless warrants further investigation to determine the contribution of referral patterns, targeted testing, previous treatment, and other programme factors to the high proportion of rifampicin resistance observed at this referral facility.