The COVID-19 pandemic has provided new challenges when it comes to antimicrobial stewardship, and it is vitally important to strike the balance right between protecting patients and staff from COVID-19 but also guarding them against hospital-acquired infections. This is especially important in low- and middle-income countries, where deaths associated with AMR are projected to be higher than anywhere else in the world, according to the 2016 Review on antimicrobial resistance. Whilst there have been reviews, there has been little primary data on the effects of COVID-19 infection prevention and control policies on AMR, especially in resource-constrained settings, and this is why, thanks to funding from BSAC, we set out to determine the impact of COVID-19 on AMR and prevalence of hospital-acquired bacterial infections in Sudan and Zambia. The sites involved are part of the PANDORA-ID-NET consortium and the two countries had different approaches to lockdown measures. Whilst we were primarily comparing COVID-19 wards and non-COVID-19 control wards, we wanted to see whether there were differences between the countries too.

To conduct our study, patients admitted to hospitals in Sudan and Zambia, and who were suspected of having hospital-acquired infections, were recruited from COVID-19 wards and non-COVID-19 wards. Swabs were taken from the patients’ infection sites and cultured, so we could identify the species and also what antibiotics they were resistant to. We then used whole genome sequencing to identify what resistance genes they had. We also collected infection prevention and control guidelines used both nationally and specifically from each hospital to see whether there was any COVID-19 guidance that might be having an effect on the types of infections and the resistance we saw. The logistics of working under COVID-19 restrictions meant that our site training was all online, and as a result, we have published the sequencing tutorial videos on YouTube and our TGHN Hub page, which have received tens of thousands of views.

Most concerningly, we found that significantly more patients on COVID-19 wards had multi-drug resistant infections in both countries. Multi-drug-resistant bacteria are resistant to at least one drug in three or more antibiotic classes, which means they are going to be much harder to treat. Considering that these patients were already seriously ill with COVID-19, and research in Israel has shown that having a bacterial infection alongside COVID-19 increases the risk of dying nearly 3 fold, this is potentially very worrying for patient outcomes. We found high levels of both phenotypic and genotypic resistance in both countries, especially to β-lactams, with the number of β-lactamase genes per bacterial isolate on COVID-19 wards significantly higher than the non-COVID-19 wards. Whilst we did not find any specific infection prevention and control policies introduced for the COVID-19 wards, there were some changes to the antibiotics that were prescribed to COVID-19 patients (especially so in Sudan). It is likely that these guideline changes had an effect on the resistances seen, but it is a complex picture and further work must be done to fully understand this.

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Linzy Elton is a postdoctoral researcher at the Centre for Clinical Microbiology at UCL, where she focusses on AMR, tuberculosis and developing sequencing pipelines for resource limited settings. She has worked on research projects in a number of countries, including Egypt, Tanzania and Uganda. She also worked as a scientific officer on a game reserve in South Africa, tracking and monitoring the health of the animals including lions, elephants, and black and white rhino. Whilst her background is in parasitology (focusing on helminths and specifically the prevalence and control of schistosomiasis), she completed her PhD on the role of biofilms in the transmission of Yersinia pestis in fleas and lice.