Assessment of Nucleic Acid Amplification Testing (NAAT) Implementation for Tuberculosis Diagnosis in Cross River State Government Hospitals

Nucleic acid amplification testing (NAAT), particularly the Xpert MTB/RIF and its successor Xpert Ultra platforms, has transformed tuberculosis (TB) diagnosis by providing same-day results with simultaneous rifampicin resistance detection. However, implementation barriers frequently limit their impact in Nigerian state-level health facilities. This study assessed NAAT implementation quality and operational challenges for TB diagnosis in government hospitals across Cross River State, South-South Nigeria. A mixed-methods design was employed, combining facility surveys at 12 NAAT-equipped sites, review of GeneXpert utilization records from 2022 to 2024, and in-depth interviews with laboratory coordinators and program managers. Overall GeneXpert test positivity was 23.4%, with average cartridge stockout periods of 18 days per quarter at rural sites. Machine downtime due to module failure or power interruptions affected testing continuity in 67% of facilities for a mean of 12 weeks per year. Sample referral delays reduced the clinical utility of NAAT results in 38% of diagnosed cases. Staff reported inadequate training refreshers in maintenance and error code troubleshooting. These findings reveal systemic operational barriers that significantly reduce the clinical impact of NAAT deployment in Cross River State, and highlight specific targets for supply chain and maintenance system improvements. Keywords: NAAT, Xpert MTB/RIF, tuberculosis diagnosis, implementation, Cross River State.