Rapid molecular diagnostics for detection of extensively drug-resistant Salmonella Typhi

Abstract

Background: Salmonella enterica serovar Typhi results in >160 000 deaths annually. In endemic regions, infections disproportionately affect infants and children. Current diagnostics rely on culture-based approaches that lack sensitivity and require infrastructure and skills that are not always possible in developing regions.

Objectives: We developed a suite of rapid, sensitive and specific molecular diagnostic tools to detect S. Typhi, and markers of extensive antimicrobial resistance (AMR), with the capacity to be used in low- and middle-income countries (LMIC).

Methods: Singleplex and multiplex PCR assays, recombinase polymerase amplification with lateral flow detection (RPA-LF) assays and loop-mediated isothermal amplification (LAMP) assays were developed, targeting markers consistent with Salmonella Typhi and makers of extensive AMR (blaCTX-M-15 and qnrS1). Assays were tested across four banks of samples (n = 115 total) to assess sensitivity, specificity and limit of detection.

Results: Singleplex and multiplex PCR assays demonstrated excellent sensitivity (100%) and specificity (96%-100%) for detection of XDR S. Typhi and extensive AMR, particularly the H58 clade deletion and STY4669 genes of S. Typhi. Similarly, sensitivity and specificity were also observed for RPA-LF assays (100% sensitivity, 96%-100% specificity) and LAMP assays (100% sensitivity, 87.5%-100% specificity) for all targets.

Conclusions: These tools are timely, providing a range of options for targeted detection of XDR S. Typhi in the laboratory or nearer to the point of care. These assays have the potential to improve resistance-guided therapy for S. Typhi, which is important given the increasing prevalence of XDR S. Typhi in endemic regions of Pakistan, and increasing case reports globally.