(P315) Systematic review of the applications for individual clinical management and care of whole genome sequencing for human pathogens

Background

Whole genome sequencing (WGS) has been valuable for a range of public health applications, including monitoring antimicrobial resistance, variant tracking, surveillance and outbreak investigation. In the field of sexually transmitted infections (STIs), WGS has provided valuable insights into transmission within high-risk sexual networks. However, it’s still unclear whether WGS can inform real-time clinical risk assessment and patient management during STI-related care. We conducted a systematic review of applications of WGS for human pathogens involving individual clinical management.



Methods

Six databases were searched to identify English articles published between 01/01/2010 and 10/11/2021 that reported on real- or near real-time human pathogen WGS as a clinical intervention. No geographical restrictions were applied, and all study types were included. Findings were analysed using narrative synthesis. Quality was assessed using an adapted Critical Appraisal Skills Tool.



Results

9,204 articles were identified, and 4,948 remained following de-duplication. Seven quantitative articles reported real- or near real-time applications to inform tuberculosis (n=6) and gonorrhoea (n=1) clinical management (Table 1). WGS data were used as an adjunct to clinical and epidemiological data to perform contact-tracing (n=2), identify cross-contamination (n=1) or antimicrobial susceptibility testing (n=5). Applications included confirming or disproving suspected transmission links, confirming treatment choice, or optimising treatment selection. WGS was used as a complementary tool to provide enhanced partner notification among individuals diagnosed with gonorrhoea in sexual health clinics. WGS was proposed to aid individualised care, by distinguishing re-infection from the same source from an acquisition from a new source, and identifying individuals with whom multiple index patients (who are genetically linked) report sexual contact with. However, most studies had significant risk of bias and other quality limitations, and there was no cost-effectiveness assessment. Ethical concerns around deductive disclosure were largely not addressed in the reviewed literature.



Conclusions

Despite great promise, there was a scarcity of published literature on using WGS to inform individual patient management in the field of STIs, and most human pathogens. While there was some evidence of feasibility in using WGS to provide individualised tuberculosis treatment, research is needed on the potential role of WGS for patient care in sexual health services.