Multidrug resistant bacterial infections in severely ill COVID-19 patients admitted in a national referral and teaching hospital, Kenya

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 intensive care unit 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.

Methods: A descriptive cross-sectional study design was adopted in severely ill COVID-19 patients at Kenyatta National Hospital, Kenya, from October to December 2021. We used a structured questionnaire and case report forms to collect sociodemographics, clinical presentation, and hospitalization outcome data. Blood, nasal/oropharyngeal swabs and tracheal aspirate samples were collected based on the patient's clinical presentation and transported to the Kenyatta National Hospital microbiology laboratory for immediate processing following the standard bacteriological procedures.

Results: We found at least one bacterial infection in 44.2% (53/120) of the patients sampled, with a 31.7% mortality rate. Pathogens were mainly from the upper respiratory tract (62.7%, 42/67), with gram-negative bacteria dominating (73.1%, 49/67). Males were about three times more likely to acquire bacterial infection (p = 0.015). Those aged 25 to 44 years (p = 0.009), immunized against SARS-CoV-2 (p = 0.027), and admitted to the infectious disease unit ward (p = 0.031) for a short length of stay (0-5 days, p < 0.001) were more likely to have a positive outcome. Multidrug-resistant isolates were the majority (64.3%, 46/67), mainly gram-negative bacteria (69.6%, 32/46). The predominant multidrug-resistant phenotypes were in Enterococcus cloacae (42.9%, 3/7), Klebsiella pneumonia (25%, 4/16), and Escherichia coli (40%, 2/5).

Conclusion: Our findings highlight a high prevalence of multidrug-resistant bacterial infections in severely ill COVID-19 patients, with male gender as a risk factor for bacterial infection. Elderly Patients, non-SARS-CoV-2 vaccination, intensive care unit admission, and long length of hospital stay were associated with poor outcomes. There is a need to emphasize strict adherence to infection and prevention at KNH-IDU and antimicrobial stewardship in line with local and global AMR control action plans.

Keywords: Bacterial infections; COVID-19; Multidrug resistant; SARS-CoV-2; Severely ill patients.

Fig. 1

Bacterial infections and their etiologies in COVID-19-positive patients admitted at KNH-IDU. COVID-19 Coronavirus Disease-2019, URTI Upper Respiratory Tract Infections, LRTIs Lower Respiratory Tract Infections, BSI Blood Stream Infections

Fig. 2

AMR profiles for gram-negative bacteria in COVID-19 patients to IDU at KNH. AMR Antimicrobial resistant, AMC amoxicillin/clavulanate, SAM ampicillin/sulbactam, TZP piperacillin/tazobactam, CTX cefotaxime, CAZ ceftazidime, CRO ceftriaxone, FEP cefepime, ATM aztreonam, MEM meropenem, AMK amikacin, GEN gentamicin, CIP ciprofloxacin, SXT trimethoprim/sulfamethoxazole

Fig. 3

AMR profiles for gram-positive bacteria in COVID-19 patients in KNH-IDU. AMR Antimicrobial resistant, BP benzylpenicillin, ERY erythromycin, LVX levofloxacin, LZD linezolid, TEC teicoplanin, VAN vancomycin, TET tetracycline, TGC tigecycline