During the COVID-19 pandemic in 2020, our team at the Centre for Clinical Microbiology was asked for help by our infectious disease clinical colleagues at the Royal Free Hospital, in London. They’d noticed that on the COVID-19 wards, patients were catching a different set of bacterial infections, which had different resistances to antibiotics, than before the pandemic. The aim of that study was to identify, using sequencing, whether the bacteria were related, and whether they were sharing AMR genes. We wanted to see if the same thing was happening in our African partner sites, HerpeZ (Zambia) and IEND (Sudan).
When we looked at the literature, we saw that patients who develop a severe illness due to COVID-19 (i.e. patients who get sick enough to require ventilators) are more likely to be admitted to hospital and catch bacterial infections while on the ward. Because they are more at risk of catching bacterial infections, the WHO recommends rapid treatment with antibiotics, which can mean they are treated before the tests have been done to confirm what organism is causing their illness. When we started this study, there were few reports from resource-constrained settings in this area.
We enrolled patients from COVID-19-positive wards and COVID-19-negative wards if their doctors thought they might have caught a bacterial infection whilst they were in hospital. Patients’ infection sites were swabbed and their samples were analysed to identify what species was causing their infection and some of these samples were sequenced.
We found that patients who had COVID-19 were significantly more likely to catch a multi-drug-resistant bacterial infection (this was found in both countries). The total number of patients who caught a bacterial infection whilst in hospital (both susceptible and resistant) increased significantly on COVID-19 wards in Sudan. We found the opposite in Zambia though. When we looked at the genome of the bacteria, we found significantly more β-lactam genes per isolate on COVID-19 wards in both countries.
When we analysed our results, we decided that the changes in bacterial infections and AMR patterns we saw in COVID-19 patients likely resulted from many different factors. These may include patient factors (such as underlying health conditions), types of drugs the patients were treated with, and also differing emphases on infection prevention and control in the wards. As a result of this study, the hospitals in both countries adapted their COVID-19 infection prevention and control policies.
This project was made possible through an unrestricted grant from Pfizer.