Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

Rapid molecular diagnostics for extensively-drug resistant Salmonella Typhi (82796)

Jacob Tickner 1 2 , Nicole Ertl 1 2 , Saba Riaz 3 , Adam Irwin 1 2 , David Whiley 1 2 4 , Emma Sweeney 1 2
  1. UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
  2. Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, Queensland, Australia
  3. Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Punjab, Pakistan
  4. Microbiology Department, Pathology Queensland, Brisbane, Queensland, Australia

Salmonella Typhi infections are a major problem globally, with over 20 million cases of typhoid diagnosed every year [1]. This pathogen has become remarkably resistant to a range of antibiotics, complicating the successful and timely treatment of these potentially life-threatening infections [2]. Increasing reports of multi-drug resistant and extensively drug-resistant (XDR) Salmonella Typhi have escalated this pathogen to “high” on the World Health Organizations priority pathogens list. The “gold standard” for diagnosis of Salmonella infections in high income settings is blood culture, which often takes >48 hours for identification of the infection and determination of antimicrobial resistance. Diagnostic methods are at best limited or otherwise not available in low resource settings, where these infections are disproportionately prevalent. Enhanced diagnostics that can simultaneously diagnose Salmonella Typhi infections as well as identify antimicrobial resistance determinants are urgently needed [3].

In this study, we developed a range of rapid diagnostic tests to detect XDR Salmonella Typhi alongside key markers for ciprofloxacin and ceftriaxone resistance. Sixteen clinical XDR Salmonella Typhi isolates were tested via real-time PCR and isothermal amplification (RPA and LAMP) detection assays, alongside targeted amplicon sequencing and whole-genome sequencing. All XDR Salmonella Typhi isolates (16/16) were positive for two Typhi-specific detection genes, as well as a Typhi H58 clade-specific target, while antimicrobial resistance genes for ciprofloxacin and ceftriaxone could be detected in 75% of isolates (12/16). Negligible cross reactivity was observed in Typhi-negative banks of Salmonella species-positive (n=68), and non-Salmonella species-positive (n=22) clinical isolates. Whole genome sequencing confirmed the XDR Salmonella Typhi isolates as members of the currently disseminating H58 clade that displays extensive antimicrobial resistance, confirmed by the presence of a clade-specific deletion and multiple antimicrobial resistance determinants [4].

These assays will enable the rapid detection of XDR Salmonella Typhi in laboratories, or closer to the point of care, and empower clinicians to select the most appropriate antimicrobial treatment thereby improving patient-centered care.

  1. Centers for Disease Control and Prevention , National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) , Division of Foodborne, Waterborne, and Environmental Diseases (DFWED)
  2. Marchello, C. S., et al. (2020). A Systematic Review on Antimicrobial Resistance among Salmonella Typhi Worldwide. The American Journal of Tropical Medicine and Hygiene, 103(6), 2518–2527. https://doi.org/10.4269/ajtmh.20-0258.
  3. Mather, R. G., et al. (2019). Redefining typhoid diagnosis: what would an improved test need to look like?. BMJ global health, 4(5), e001831. https://doi.org/10.1136/bmjgh-2019-001831
  4. Klemm, E. J., et al. (2018). Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins. mBio, 9(1), e00105-18. https://doi.org/10.1128/mBio.00105-18