Mapping the genomics of sexually transmitted infections
A team of researchers are finding ways to improve diagnostic testing and genomic tracking of sexually transmitted infections in Australia.
Over the last 15 years, the rates of sexually transmitted infections (STIs), like syphilis, have been rising in Australia.
Current routine diagnostic testing provides very little information and evolutions of the bacteria driving the syphillis epidemic, Treponema pallidum. That’s where genomic sequencing comes in.
Detailed diagnostic surveillance, including genomic sequencing is important to the prevention, treatment and control of infectious diseases, but can be difficult for some STIs like syphilis, explains University of Melbourne Dr Shivani Pasricha, a Postdoctoral Fellow in the Williamson Laboratory at the Doherty Institute.
“When an infectious disease outbreak occurs, diagnostic testing and information from genomic sequencing enables a much greater understanding of how, when and where the outbreaks have stemmed from and how they are spreading,” explains Dr Pasricha.
“One of the main problems of STIs, is that a number of the bacteria, like Treponema pallidum and Mycoplasma genitalium don’t culture in the lab, making genomic characterisation challenging,” says Dr Pasricha.
So, the team posed the question – how can we get around this?
“We wanted to use a method to sequence from clinical samples to improve our diagnostic testing so we didn’t have to culture anything, so it wouldn’t be a barrier,” says Dr Pasricha.
The team turned to an area they were more than familiar with – whole genome sequencing.
In 2021, Professor Williamson received funding to see if it was possible to sequence syphilis genomes. Using a hybridisation capture approach (‘target enrichment’), the team were able to extract the genetic material of syphilis from clinical samples, ready for sequencing.
“If you tried to sequence the sample straight away, you’ll mostly get human genome and very little of the bacterial DNA,” explains Dr Pasricha.
“This method allowed us to just pull out the bacterial material and obtain high-quality data for analysis.”
Using this method, the team successfully processed and sequenced over 450 Australian syphilis samples from 2005 to 2020, and the findings were published in Lancet Microbe.
“We were able to see the rise in syphilis cases was not due to one distinct outbreak but driven by multiple different lineages. We were also able to correlate lineages with different risk profiles,” says Dr Pasricha.
Being able to use genomics for surveillance of STI outbreaks in Australia could change the game.
“It will provide us with so much more information about how the pathogen is changing, whether it is developing a resistance to certain antibiotics and will inform how we should be best using our antimicrobial therapy,” explains Dr Pasricha.
And they are hopeful that this method could be applied to other unculturable STIs, such as Mycoplasma genitalium and Chlamydia trachomatis.
“We hope that such methods can be integrated into routine diagnostic testing of not just STIs but all infectious diseases.”
Built with Shorthand