Rapid bacterial identification and resistance detection using a low complexity molecular diagnostic platform in Zimbabwe - Study dataset and codebook

Only samples with available reference standard results were included in the analysis. Data captured on paper-based forms was entered into electronic case report forms (ODK Collect). Specificity and sensitivity for BCID2 were calculated in comparison to the reference standards, with performance measures calculated using the Wilson score.

Biomedical scientists using BCID2 completed a system usability survey (SUS). RESULTS: Positive results were recorded in 780/2,023 (38.5%) blood cultures, within which 377 (48.3%) had reference results and so were included in analysis. Neonatal samples were most frequent (182, 48.3%), then paediatric (150, 39.8%), then adults (18, 4.8%) and unknown (27, 7.2%).

Specificity exceeded 95% throughout. Sensitivity ranged from 50% ( A. calcoaceticus-baumanii complex, Proteus spp.) to 100% ( S. pneumoniae , Salmonella spp). Using BCID2, CTX-M was detected in 111/175 (74.5%) Enterobacterales, from which 5/111 also had NDM and VIM detected.

NDM-5 was detected in 2/5 NDM samples using sequencing. In total 3/23 S. aureus isolates were methicillin resistant, from which one was confirmed using phenotypic antimicrobial susceptibility testing. Usability was good (SUS score = 79.5).

CONCLUSION: Rapid molecular tests have potential to improve turn-around time and quality of sepsis diagnostics. However, specific work-flows are critical to supplement molecular tests with minimal phenotypic tests for optimal clinical decision-making.