Kevin Chau, a PhD student in the first cohort of our National PhD Training Programme in AMR Research, has contributed to the pandemic response as part of the Modernising Medical Microbiology team at the John Radcliffe Hospital in Oxford. In this blog post, he describes the experience.
The swift spread of SARS-CoV-2 (the virus causing Covid-19) meant a rapid research response was essential to understand the novel coronavirus and to control it.
As part of the Modernising Medical Microbiology Covid-response team, I contributed to setting-up and running a liquid handling robotics lab to process thousands of blood samples for coronavirus antibody testing every day. Under the supervision of robotics expert Dr Alison Howarth (from Oxford University’s Structural Genomics Consortium), I programmed, maintained and troubleshooted the liquid handler while working in the robot team.
The robot itself doesn’t measure anything, but performs a vital processing step to array samples from difficult-to-handle clinical tubes into an efficient format where they can be analysed en masse by researchers – specifically, for the presence of Covid-19 antibodies (i.e. whether someone has been infected by the virus or not).
Thanks to a massive joint effort, we converted a disused storeroom laboratory into a safe and fully operational robotics laboratory in just nine days – a task which would normally take months. Previous manual processing was slow and labour-intensive, which bottlenecked testing capacity, but the functional robotics laboratory has increased processing speed from hundreds of samples per day to thousands. Skills developed from analysing antibiotic prescribing data during my PhD have also come in handy for helping to script R code to track the large numbers of samples being arrayed, which has required some complicated data handling.
The samples we prepared were used in one of the largest healthcare worker testing programmes for Covid-19 to date, comprising 11,000 staff at Oxford University Hospitals, as well as an Office for National Statistics (ONS) study, which looked at how many people across England tested positive for Covid-19, helping to inform public health strategy around the lockdown. By estimating the proportion of people in different groups (e.g. hospital staff and households in England) who have been infected with Covid-19, these studies have helped to identify risk factors for infection, quantify the number of asymptomatic infections and produce valuable epidemiological data.
I have also contributed to sample handling for a head-2-head evaluation of major serology tests in conjunction with Public Health England and many other groups. Evaluating how well different antibody tests perform also helps decide which test is the most appropriate for widespread use.
We were able to mount a rapid research response by working closely with infectious disease doctors, epidemiologists, biomedical scientists, engineers and biosafety officers (and many more!), demonstrating how a combined interdisciplinary effort is vital to combating complex public health emergencies like the Covid-19 pandemic. The same complexity is inherent in the rising problem of drug-resistant infections, and reinforces the importance of interdisciplinary collaboration, as the Medical Research Foundation has encouraged with its national PhD training programme in antimicrobial resistance.
Along with the camaraderie that comes with working alongside colleagues in the NHS and academia, the knowledge that our combined hard work has directly contributed to advising government, and the local and national Covid-19 response, is extremely rewarding.
I’m grateful to the Medical Research Foundation for enabling me to help in the response to Covid-19 while studying on their PhD programme, and look forward to applying the new skills I have learned to help tackle antimicrobial resistance. My PhD looks at the prevalence of antimicrobial resistance in sewage and how it may be used for surveillance, and it will be really interesting to see how this has changed due to the pandemic. For example, the lockdown drastically altered everyday life causing: (i) reduced GP/hospital visits which may have resulted in reduced antibiotic prescribing, and (ii) significantly reduced population movement changing sewer inputs – both potentially affecting sewage composition. There’s also greater interest within the science community around the surveillance of sewage, as researchers have found evidence for the use of sewage for large-scale surveillance of Covid-19 – another area which would be fascinating to get involved in during my PhD.
This blog article is written and submitted by Kevin Chau, who is a Medical Research Foundation 2018-2019 core-funded PhD student at the University of Oxford.
Kevin is studying within the REHAB AMR consortium and is undertaking a PhD on ‘Wastewater influent and population-level surveillance of antimicrobial resistance in Enterobacteriaceae in Oxfordshire using whole genome sequencing’, supervised by Prof Derrick Crook & Dr Nicole Stoesser, Nuffield Dept. Medicine, University of Oxford and Dr Daniel Read, UK Centre for Ecology & Hydrology .