Direct sequencing technologies for bacterial sexually transmitted infections

Abstract

There is an important role for direct sequencing of patient samples to complement traditional culture-based methods for bacterial sexually transmitted infections (STIs), effectively overcoming limitations posed by fastidious or unculturable pathogens such as Neisseria gonorrhoeae, Treponema pallidum, Mycoplasma genitalium and Chlamydia trachomatis. Metagenomic techniques can enable profiling of antimicrobial resistance (AMR), strain typing and microbiome analysis in the absence of a cultured isolate, contributing critical information to understanding epidemiological trends and guiding targeted therapies. Despite significant advancements, challenges persist, such as cost, bioinformatics complexity and ethical considerations. The paper discusses current applications, technological innovations, and future prospects for integrating metagenomics into routine bacterial STI surveillance, emphasising the need to identify cost and time-effective workflows and enhanced accessibility of genomic data. By addressing these challenges, direct sequencing promises to fill critical gaps in AMR monitoring and pathogen typing, offering new avenues for enhancing public health strategies in combating bacterial STIs worldwide.