A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings.

BACKGROUND: Patients who develop severe illness due to COVID-19 are more likely to be admitted to hospital and acquire bacterial co-infections, therefore the WHO recommends empiric treatment with antibiotics. Few reports have addressed the impact of COVID-19 management on emergence of nosocomial antimicrobial resistance (AMR) in resource constrained settings. This study aimed to ascertain whether being admitted to a COVID-19 ward (with COVID-19 infection) compared to a non-COVID-19 ward (as a COVID-19 negative patient) was associated with a change in the prevalence of bacterial hospital acquired infection (HAI) species or resistance patterns, and whether there were differences in antimicrobial stewardship (AMS) and infection prevention and control (IPC) guidelines between COVID-19 and non-COVID-19 wards. The study was conducted in Sudan and Zambia, two resource constrained settings with differing country-wide responses to COVID-19. METHODS: Patients suspected of having hospital acquired infections were recruited from COVID-19 wards and non-COVID-19 wards. Bacteria were isolated from clinical samples using culture and molecular methods and species identified. Phenotypic and genotypic resistance patterns were determined by antibiotic disc diffusion and whole genome sequencing. Infection prevention and control guidelines were analysed for COVID-19 and non-COVID-19 wards to identify potential differences. RESULTS: 109 and 66 isolates were collected from Sudan and Zambia respectively. Phenotypic testing revealed significantly more multi-drug resistant isolates on COVID-19 wards in both countries (Sudan p = 0.0087, Zambia p = 0.0154). The total number of patients with hospital acquired infections (both susceptible and resistant) increased significantly on COVID-19 wards in Sudan, but the opposite was observed in Zambia (both p = ≤ 0.0001). Genotypic analysis showed significantly more ß-lactam genes per isolate on COVID-19 wards (Sudan p = 0.0192, Zambia p = ≤ 0.0001). CONCLUSIONS: Changes in hospital acquired infections and AMR patterns were seen in COVID-19 patients on COVID-19 wards compared to COVID-19 negative patients on non-COVID-19 wards in Sudan and Zambia. These are likely due to a potentially complex combination of causes, including patient factors, but differing emphases on infection prevention and control, and antimicrobial stewardship policies on COVID-19 wards were highlighted.

The impact of COVID-19 infection prevention and control measures on transmission of hospital-acquired infections and antimicrobial resistance in Africa

Background Patients who develop serious illness due to COVID-19 are more likely to have bacterial coinfections, for which WHO recommends treatment with antibiotics. As a result, many countries are observing a change in antimicrobial stewardship (AMS), in addition to changes in infection prevention and control (IPC) practices such as the use of personal protective equipment, on COVID-19 wards. Few data on COVID-19 and its impact on nosocomial infections and antimicrobial resistance (AMR) are available from low and middle-income countries (LMICs). As these countries often have high rates of AMR, it is vital to report the effects of COVID-19 on AMS so as to inform clinical practice and IPC guidelines. This study aims to compare prevalence of AMR in COVID-19 wards with general non-COVID-19 hospital wards. Methods This pilot hospital-based study is being conducted in two sites in both Sudan and Zambia. IPC and AMS guidelines for COVID-19 and non-COVID-19 wards were identified for each institution. This study is comparing bacterial isolates and AMR patterns of nosocomial associated infections acquired on COVID-19 and non-COVID-19 wards were compared, using microbiological and sequencing methods. A total of 200 patients have been recruited: 100 per country, 50 COVID-19 patients and 50 non-COVID-19 patients. AMR transmission patterns are being identified using Oxford Nanopore Technologies sequencing for phylogenetic analysis. Results The study began recruiting in May 2021 and completed recruitment of patients in October 2021. The majority of microbiological laboratory work will be completed within Q3 2021, with analysis of the results and sequencing completed in Q4 2021. A half-way point summary analysis of the data suggests differences in patient profiles, both between COVID-19 and non-COVID-19 wards at both sites, as well as differences between the two countries. Preliminary analysis also suggests a significant difference between the prevalence of MDR infections in Gram-negatives seen between COVID-19 (53% in Sudan and 83% in Zambia) and non-COVID-19 (14% Sudan, 33% Zambia) (t-test, P=0.0032 Sudan, P=0.0455 Zambia) ward patients in both countries (see Figure 1).Figure 1. Percentage of Gram-negative bacteria isolated from patients on COVID-19 and non-COVID-19 wards in Sudan and Zambia, showing significant difference between the wards in both countries (t-test, P = 0.0032 Sudan, P = 0.0455 Zambia). Conclusions The study is providing evidence to inform policy on IPC and AMS measures to be implemented on COVID-19 wards. In addition, the outcomes of the study will be used to create a pragmatic sequencing pipeline for potential AMR outbreaks suitable for use in LMICs clinical settings.