Coinfections in Patients Hospitalized with COVID-19: A Descriptive Study from the United Arab Emirates

Abstract

Microbial coinfections in COVID-19 patients carry a risk of poor outcomes. This study aimed to characterize the clinical and microbiological profiles of coinfections in patients with COVID-19. Methods: A retrospective review of the clinical and laboratory records of COVID-19 patients with laboratory-confirmed infections with bacteria, fungi, and viruses was conducted. Only adult COVID-19 patients hospitalized at participating health-care facilities between February 1 and July 31, 2020 were included. Data were collected from the centralized electronic system of Dubai Health Authority hospitals and Sheikh Khalifa General Hospital Umm Al Quwain. Results: Of 29,802 patients hospitalized with COVID-19, 392 (1.3%) had laboratoryconfirmed coinfections. The mean age of patients with coinfections was 49.3±12.5 years, and a majority were male (n=330 of 392, 84.2%). Mean interval to commencement of empirical antibiotics was 1.2±3.6) days postadmission, with ceftriaxone, azithromycin, and piperacillin-tazobactam the most commonly used. Median interval between admission and first positive culture (mostly from blood, endotracheal aspirates, and urine specimens) was 15 (IQR 8-25) days. Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli were predominant in first positive cultures, with increased occurrence of Stenotrophomonas maltophilia, methicillin-resistant Staphylococcus aureus, Acinetobacter baumannii, Candida auris, and Candida parapsilosis in subsequent cultures. The top three Gram-positive organisms were Staphylococcus epidermidis, Enterococcus faecalis, and Staphylococcus aureus. There was variability in levels of sensitivity to antibiotics and isolates harboring mecA, ESBL, AmpC, and carbapenemase-resistance genes were prevalent. A total of 130 (33.2%) patients died, predominantly those in the intensive-care unit undergoing mechanical ventilation or extracorporeal membrane oxygenation. Conclusion:Despite the low occurrence of coinfections among patients with COVID-19 in our setting, clinical outcomes remained poor. Predominance of Gram-negative pathogens, emergence of Candida species, and prevalence of isolates harboring drug-resistance genes are of concern.

Evaluation of Bacterial Coinfection and Antibiotic Resistance in Patients with COVID-19 Under Mechanical Ventilation

“…Patients with confirmed SARS-CoV-2 are principally at risk of emerging superinfections, particularly those caused by Gram-negative bacteria with MDR infections [ 21 ]. However, the pattern of coinfections and the microbiological profile in these cases remain an essential information gap in the literature [ 22 ]. To reveal this aspect, we investigated microbiologic data from 22 severe COVID-19 patients under mechanical ventilation.…”

“…was observed in 18.2% of cases. Senok et al in evaluation of Dubai Health Authority hospitals and Sheikh Khalifa General Hospital Umm Al Quwain patients stated that predominance of Gram-negative pathogens, emergence of Candida species, and prevalence of isolates harboring drug-resistance genes are of concern [ 33 ]. Eventually, a widespread consumption of antimicrobials, the immune dysregulation, and less adherence to the infection control and prevention measures are the main reasons of the high incidence of bacterial and fungal infections in severe COVID-19 cases [ 34 ].…”

Pathogenesis of Respiratory Viral and Fungal Coinfections

“… Candida auris is a multidrug-resistant fungal pathogen classified as an “urgent threat” by the U.S. Centers for Disease Control and Prevention (CDC) due to its ability to cause life-threatening systemic infections in critically ill patients. Several outbreaks of C. auris infection in COVID-19 patients have been reported ( 144 – 149 ), in some cases associated with corticosteroid treatment ( 150 – 154 ). C. auris is difficult to identify by standard laboratory methods, which can lead to misidentification, causing outbreaks in health care settings often associated with high mortality.…”

Methicillin-resistant Staphylococcus aureus lung infection in coronavirus disease 2019: how common?

“…With regard to secondary infections in hospitalized patients, S. aureus was the most frequent causative agent of VABP (4/11, 36%) [ 1 ]. In a multicenter retrospective study conducted in the United Arab Emirates, Senok et al [ 26 ] registered 392 co-infections among 29 802 hospitalized patients with COVID-19, with S. aureus being isolated from lower respiratory tract specimens in 8/392 cases of coinfections (2%). Several other organisms (e.g., Pseudomonas aeruginosa , Enterobacterales ) were more frequently isolated than S. aureus , but it should be noted that this count also included infections other than pneumonia [ 26 ].…”