Detecting sexual bridges: Whole genome sequencing to enable rapid surveillance of sexually transmitted infections amongst high and low risk population

Lead Research Organisation: St George's University of London
Department Name: Institute of Population Health


Sexually transmitted infections (STIs) such as Chlamydia and Gonorrhoea are a global health issue and untreated infection can result in serious health complications, disproportionately affecting women. In low and middle income countries (LMICs), testing and surveillance of STIs may not be universally available and there is often poor regulation of antibiotics, driving antimicrobial resistance (AMR). In Latin America and Ecuador in particular, STI testing is usually limited to HIV and Syphilis and few prevalence data are available for other bacterial STIs. Additionally, in Ecuador sex work is legal (conditional on regular HIV and Syphilis testing) and female sex workers (FSW) are likely to represent a large proportion of the at risk population as they may engage in risky behaviour such as inconsistent condom use and multiple sexual partners.
Understanding patterns of transmission for different strains of STIs and identifying 'transmission bridges', i.e. specific infection strains passing from high risk groups such as FSW and men-who-have-sex-with-men (MSM) to other population groups, may provide early warning signs of outbreaks and spread of AMR. Infection surveillance systems that incorporate DNA sequencing methods, can help to inform public health bodies by identifying different clusters of infections and AMR, in a timely manner. However, in order to successfully sequence bacteria, large volumes of DNA are required alongside removal of host and other contaminating DNA, meaning microbiological culture is often essential. For infections such as Chlamydia, culture is not feasible as is it technically difficult and expensive. Alternative techniques that allow sequencing directly from clinical samples without culture, require the development of DNA enrichment and amplification methods. New technologies exist that allow for field-based rapid DNA sequencing from clinical samples and may allow for real-time surveillance systems, but require optimisation.
This project aims to demonstrate a system of surveillance that can be used to visualize and quickly identify sexual transmission networks and possible sexual transmission bridges between high risk groups and the general population, by combining phylogenetic analysis with epidemiological data. The work aims ultimately to inform public health control and prevention strategies and answer the following questions:
1. Can a targeted enrichment and amplification method be optimised to allow sequencing of NG and CT bacterial DNA directly from clinical samples?
2. Can existing DNA sequencing devices be optimised to enhance rapid surveillance of STIs?
3. Can sequencing technology be used to identify clusters and bridging between FSW, non sex worker and high-risk other populations?
To answer these questions, laboratory based techniques and a combination of bioinformatics and epidemiological analysis will be used. Strain types will be identified via sequencing and their relatedness investigated by constructing phylogenies to identify possible transmission events.
Samples (vaginal, rectal and pharyngeal swabs) will be collected from FSW from two regions of Ecuador. Females attending antenatal clinics in these two regions will also have samples collected (vaginal and pharyngeal swabs). All swabs will be tested for 4 key bacterial STIs: CT, NG, MG and TV using PCR. A questionnaire will be provided to all groups to identify different factors such as previous antibiotic exposure, partners in the preceding months and other health morbidities. These data will be essential for identifying possible links between infection status and risk factors and developing the molecular epidemiology of the project.
Optimisation of a direct DNA sequencing method will be established using techniques such as "bait" capture, amongst others. Based on previous data from the region as well as worldwide prevalence estimates of STIs and associated AMR, CT and NG will be the focus.


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Description School visit (workshop) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Participated in a half day school workshop which aimed to inspire the next generation of public health professionals. The workshop was entitled: 'Outbreak control: an introduction to careers in public health'. In two separate sessions, groups of 30 pupils were guided through five interactive demonstrations, featuring props such as marbles and mosquitos, to allow school students to be introduced to the work of epidemiologists, statisticians and lab scientists in an outbreak situation. Following the workshop there was an opportunity for the students to ask questions and understand possible career options in different fields. The school and pupils reported positive feedback from the sessions and were interested in different job and career opportunities in science that they had not before considered.
Year(s) Of Engagement Activity 2020