During the COVID-19 pandemic, PANDORA-ID-NET researchers were awarded a $65,000 grant from the British Society for Microbial Chemistry to undertake a project looking at the impact of COVID-19 on transmission of hospital acquired infections and antimicrobial resistance in Sudan and Zambia. The study was undertaken by Dr Linzy Elton, Professor Tim McHugh, Dr Mags Thomason, Dr Isobel Honeyborne and Mrs Kerry Roulston from UCL (UK), Dr Muzamil Mahdi Abdel Hamid and Dr Hana Elbadawi from the Institute of Endemic Diseases (Sudan) and Dr John Tembo from HerpeZ (Zambia).


Project set up

Patients who develop serious illness due to COVID-19 are more likely to have bacterial co-infections and the World Health Organization therefore recommends treatment with antibiotics. As a result, many countries are observing a change in antimicrobial stewardship, in addition to changes in infection prevention and control practices such as the use of personal protective equipment, on COVID-19 wards. Few data on COVID-19 and its impact on antimicrobial resistance (AMR) have come from low and middle-income countries (LMICs). As these countries often have higher rates of AMR, and COVID-19 cases are still increasing across many sub-Saharan African countries, it is vital to report on how COVID-19 is affecting antimicrobial stewardship, to direct clinical practice moving forward.


What we did

This pilot study, based in hospitals in Khartoum, Sudan and Lusaka, Zambia compared the secondary bacterial infections acquired by patients with COVID-19 on COVID-19 and COVID-19 negative patients on non-COVID-19 wards, using microbiological and sequencing methods to identify species, as well as identifying AMR transmission patterns using phylogenetic analysis. This project enabled an Oxford Nanopore Sequencing platform to be set up in Sudan (one had recently been installed in Zambia), with UCL providing sequencing training. These platforms and the training programme enabled the teams in both countries to not only undertake sequencing for this project, but also set up a sequencing pipeline for the identification of multi-drug resistant bacteria in clinical settings.



The study found that significantly more patients on COVID-19 wards had multi-drug resistant infections in both Sudan and Zambia. Multi-drug-resistant bacteria are resistant to at least one drug in three or more antibiotic classes, which makes them 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 worrying for patient outcomes. The study 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 from COVID-19 patients significantly higher than from COVID-19 negative patients. 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. 

As a result of this study, Infection Prevention and Control policies have been modified for COVID-19 wards in the hospitals involved in both countries. 

The manuscript describing the results of this study was published in Annals of Clinical Microbiology and Antimicrobials and is Open Access. You can find the link to the published paper here.


Scientific communications

You can access the Oxford Nanopore Technologies sequencing tutorial videos on our sequencing page, or on PANDORA-ID-NET's YouTube channel.

You can watch the progress of the project on Twitter (@AmrCovid).

As part of this project we have written three blogs on the BSAC website, one outlining the project itself, one describing the results we found and one summarising the paper that was published

Principle investigator Dr Linzy Elton has also written an introduction to the project and a plain language summary of the paper published on her blog.