Multidrug resistant bacterial infections in severely ill COVID-19 patients admitted in a national referral and teaching hospital, Kenya
Authors: Mutua Jeniffer Munyiva , Mwaniki John Njeru , Musyoki Abednego Moki 
Published: October 2022

Abstract
Background: Bacterial infections are a common complication in patients with seasonal viral respiratory tract infections and are associated with poor prognosis, increased risk of ICU admission and 29-55% mortality. Yet, there is limited data on the burden of bacterial infections among COVID-19 patients in Africa, where underdeveloped healthcare systems are likely to play a pertinent role in the epidemiology of the COVID-19 pandemic. Here, we evaluated the etiologies, Antimicrobial Resistance profiles, risk factors, and outcomes of bacterial infections in severely ill COVID-19 patients admitted to in a tertiary national teaching and referral hospital in Kenya.
Methods: A descriptive cross-sectional study design on severely ill COVID-19 patients at Kenyatta National Hospital between October and December 2021 was adopted. A structured questionnaire and case report forms were used to collect patients’ sociodemographic, clinical presentation and outcomes respectively. Blood, nasal/oropharyngeal swabs and tracheal aspirate samples were collected based on the decision of the treating physician and transported to microbiology laboratory for immediate processing following the standard bacteriological procedures.
Results: At least one bacterial infection was found in 44.2% (53/120) patients sampled. A mortality rate of 31.7% (38/120) was found. The majority of pathogens were from upper respiratory tract (62.7%, 42/67), with gram-negative bacteria as the most dominant isolates (73.1%, 49/67). Male were about three times more likely to acquire bacterial infection than females (aOR = 2.61, 95% CI: 1.2 – 5.65, p = 0.015). Those aged between 25 to 40 years (aOR = 0.13, 95% CI: 0.02 – 0.6, p =0.009), vaccinated (aOR = 0.2, 95%CI: 0.05 – 0.83, p = 0.027) and admitted to the Infectious Disease Unit (IDU) ward (aOR = 3.27, 95%CI: 1.08 – 6.89, p=0.031), for those admitted for a short length of stay (0 -5 days) (aOR=14.28, 95% CI:3.25 - 62.76, p<0.001) were more likely to have a positive outcome. The majority of bacteria isolates (64.3%, 46/67) were multidrug-resistant (MDR), mostly attributable to gram negative bacteria (GNB) (69.6%, 32/46). The predominant MDR phenotypes were found in Enterococcus cloacae (42.9%, 3/7), Klebsiella pneumonia (25%, 4/16), and Escherichia coli (40%, 2/5) and mostly involved cefotaxime, ceftriaxone, gentamicin, ciprofloxacin, aztreonam and trimethoprim/sulfamethoxazole.
Conclusion: Our findings highlight a high prevalence of bacterial infections in hospitalized COVID-19 patients during the peak of the pandemic, with males more likely to be infected, while those in advanced age, not vaccinated, admitted to the critical care unit, and those with prolonged length of hospital stay showing a poor hospitalization outcome. The observed high multidrug-resistant infections are unacceptably high, emphasizing the need to monitor the effectiveness of the existing infection control strategies at KNH-IDU and adherence to antimicrobial stewardship in line with local and global AMR control action plans.