Epidemics & Pandemics

Epidemics and pandemics are global health challenges characterised by the rapid spread of infectious diseases, impacting communities on a massive scale. The most recent, having a global impact, was COVID-19.

COVID-AMR

Study to determine the impact of COVID-19 infection control and prevention measures on the control of AMR within inpatient wards 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. 

This pilot study, based in hospitals in Sudan and Zambia, will identify infection prevention and control (IPC) guidelines for COVID-19 and non-COVID-19 wards. We will then compare the secondary bacterial infections acquired by patients, as well as from the ward environment, on COVID-19 and non-COVID-19 wards, using microbiological and sequencing methods to identify species, as well as identifying AMR transmission patterns using phylogenetic analysis. 

This project will enable an Oxford Nanopore Sequencing platform to be set up in Sudan (one has recently been installed in Zambia), with UCL providing sequencing training. These platforms and the training programme will enable 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 results of this study will provide evidence that can inform policy on IPC measures put in place on COVID-19 wards. You can follow the progress of our study on twitter (@AmrCovid). Link to our paper below

A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings.Elton L, Abdel Hamid MM, Tembo J, Elbadawi H, Maluzi K, Abdelraheem MH, Cullip T, Kabanda C, Roulston K, Honeyborne I, Thomason MJ, Elhag K, Mohammed A, Adam A, Mulonga K, Sikakena K, Matibula P, Kabaso M, Nakazwe R, Fwoloshi S, Zumla A, McHugh TD.Ann Clin Microbiol Antimicrob. 2023 Apr 13;22(1):25. doi: 10.1186/s12941-023-00575-1.PMID: 37055793

RAPIDCoV

Cross-sectional evaluation of rapid antibody tests for the diagnosis and management of COVID-19 in sub-Saharan Africa

Objectives: To conduct a diagnostic validation study of SARS-CoV-2 diagnostic kits.

Methods: We compared SARS-CoV-2 diagnostic test results from 3 RT-PCR assays used by the Zambian government between November 2020 and February 2021 (Panther Fusion assay, Da An Gene’s 2019-nCoV RNA kit and Maccura’s PCR Kit) with the Altona RealStar RT-PCR kit which served as the gold standard. We also evaluated results from rapid antigen testing and whether comorbidities were linked with increased odds of infection.

Results: We recruited 244 participants, 61% (149/244) were positive by at least 1 PCR assay. Da An Gene, Maccura, and Panther Fusion assays had sensitivities of 0.0% (95% confidence interval [CI] 0%-41%), 27.1% (95% CI 15%-42%), and 76% (95% CI 65%-85%), respectively, but specificity was low (<85% for all 3 assays). HIV and TB were not associated with SARS-CoV-2, whereas female sex (OR 0.5 [0.3-0.9], p = 0.026) and chronic pulmonary disease (0.1 [0.0-0.8], p = 0.031) were associated with lower odds of SARS-CoV-2 infection. Of 44 samples, 84% sequenced were Beta variant.

Conclusions: The RT-PCR assays evaluated did not meet WHO recommended minimum sensitivity of 80%. Local diagnostic validation studies should be embedded within preparedness plans for future outbreaks to improve the public health response.

PUBLICATIONS

A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings. Elton L, Abdel Hamid MM, Tembo J, Elbadawi H, Maluzi K, Abdelraheem MH, Cullip T, Kabanda C, Roulston K, Honeyborne I, Thomason MJ, Elhag K, Mohammed A, Adam A, Mulonga K, Sikakena K, Matibula P, Kabaso M, Nakazwe R, Fwoloshi S, Zumla A, McHugh TD.Ann Clin Microbiol Antimicrob. 2023 Apr 13;22(1):25. doi: 10.1186/s12941-023-00575-1.PMID: 37055793

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