Network-wide analysis of the Serosep EntericBio Gastro Panel 2 for the detection of enteric pathogens in Public Health Wales microbiology laboratories.

A retrospective data analysis of 34 months (spanning 2016-2020) of 961573 diagnostic results obtained before and after nucleic acid amplification testing (NAAT) implementation, across the Public Health Wales microbiology network. This is the first network-wide analysis of the implementation of enteric NAAT in diagnostic microbiology. To assess the outcome of replacing microscopy and bacterial culture with NAAT as the primary test in the diagnosis of: spp. sp., spp. Shiga toxin-producing (STEC) spp. and infections. Following NAAT introduction, bacterial culture was performed as a secondary test, to provide further information from NAAT positive samples for epidemiological purposes. Primary detection rates and overall bacterial culture rates were calculated for each target pathogen using both testing regimes (Stage I) including a comparison of in-patient and out-patient diagnoses (Stage II). Stage I analysis showed that the primary detection rate significantly increased for spp. (<0.0001), sp. (=0.0151), spp. (<0.0001), STEC (<0.0001), spp. (<0.0001) and (<0.0001) when using NAAT compared to microscopy or bacterial culture. A significant decrease was seen in the overall rate of spp. isolation by bacterial culture (<0.0001), whilst other targets remained unaffected. Stage II analysis showed that NAAT positive out-patient samples were more likely to be supplemented by a positive bacterial culture than NAAT positive in-patient samples for spp. (<0.0001) sp. (=0.0004) and STEC (=0.0039). However, spp. was more frequently isolated from NAAT positive in-patient samples (=0.0005). A notable increase was seen for detection from in-patient samples (=0.0002). Reference laboratory data showed the NAAT assay can detect at least 53 serotypes of STEC but may not be able to detect some of the rarer species of seen in human infections. The implementation of NAAT has significantly increased the primary detection rate of all target enteric pathogens in Wales and information gleaned previously from direct culture is largely unaffected.