Loop-mediated isothermal amplification as a diagnostic tool for rapid identification of enteric bacterial pathogens from stool samples

Abstract

Molecular assays, which are commonly based on multiplex PCR techniques, are increasingly being used to diagnose bacterial gastroenteritis due to faster results and more straightforward workflows compared to conventional culture. Many culture-dependent methods and semi-automated PCR assays, are labour-intensive and require technical expertise. Therefore, assays that are easy to perform and allow for the timely identification of the most common enteric bacterial pathogens may be of interest. This study investigated a molecular assay based on loop-mediated isothermal amplification (LAMP) for the rapid identification of several common bacterial pathogens. A total of 204 stool samples were analysed. The sensitivity and specificity of the assay, compared to the BD MAX™ Enteric Bacterial Panel PCR as the reference method, were as follows: 88.35 % and 99.04 % for Campylobacter spp., 88 % and 100 % for Salmonella spp., and 71.43 % and 100 % for Shiga toxins (stx), respectively. Overall sensitivity of the LAMP assay was 89.81 % for samples with PCR Ct values ≤40, and 95.14 % when using a Ct cut-off ≤35, respectively. More samples tested positive for C. jejuni, C. coli and stx1 by LAMP than by culture. There was 100 % concordance between the two methods for stx2 and Y. enterocolitica. Four out of 25 Salmonella cases were identified by culture but not by LAMP. With a test run time of 30 min and a few minutes for sample preparation, the LAMP assay could be useful for diagnosing bacterial gastrointestinal pathogens in individual cases where specific therapeutic decisions are required.