Secondary Bacterial and Fungal Infections in Hospitalized Patients With COVID-19

Healthcare professional in protective mask pointing at laptop. Senior doctor is assisting female nurse in corridor during COVID-19 pandemic. They are in hospital during state of emergency.
A team of researchers sought to identify the incidence, antimicrobial susceptibilities, and outcomes associated with bacterial and fungal secondary infections in a large cohort of patients with COVID-19.

During the peak of the pandemic, 17% of patients hospitalized with COVID-19 in New York City developed secondary bacterial or fungal infections, according to a retrospective cohort study published in Open Forum Infectious Diseases.

Investigators studied patients aged 18 years and older who presented to the emergency department and were hospitalized with COVID-19 for more than 24 hours between March 2, 2020, and May 31, 2020, at a quaternary medical center in New York City. During the study period, 3028 patients were admitted with COVID-19; among those patients, 899 positive cultures were identified in 516 patients (17%).

Community-associated coinfections were defined as positive culture isolates within the initial 3 days of hospitalization or within 5 days before admission from an outpatient or emergency department visit. The study authors identified 221 cultures from 183 patients (6%), with the majority isolated from urine (51%), blood (31%), and the respiratory tract (12%). Escherichia coli (31%) and Staphylococcus aureus (11%) were the most common organisms identified.

Health care-associated infections were defined as positive cultures obtained after day 3 of hospitalization. The researchers identified 678 isolates in 350 patients (12%) with the median onset of infection on hospital day 16. Among these isolates, 385 (57%) were Gram-negative bacteria, 167 (25%) were Gram-positive bacteria, and 126 (19%) were fungi.

There were 133 bacteremia isolates in 94 patients with a median hospital admission of 23 days. It was noted that Enterobacterales was the most common cause of bacteremia occurring after hospital day 28 (33%). There were 298 respiratory isolates in 207 patients, with the majority classified as ventilator associated (83%). There were 216 urinary isolates with Enterobacterales species and enterococci as the most common pathogens (81%).

Among all patients, 2015 (67%) were exposed to at least 1 antibiotic dose. The most commonly used agents included broad-spectrum penicillins (65%), cephalosporins (59%), anti-staphylococcal agents with activity against methicillin-resistant S aureus (56%), and tetracyclines (26%). Methicillin-resistant S aureus was identified in 33% of S aureus isolates, and vancomycin-resistant Enterococcus was identified in 36% of enterococci isolates. The researchers noted that most antimicrobial-resistant isolates occurred after hospital day 28.

The investigators identified the following risk factors to be associated with health care-related infection: significantly older age and male sex; intensive care unit stay (odds ratio [OR], 4.140; 95% CI, 2.534-6.764; P <.001); need for invasive mechanical ventilation (OR, 6.044; 95% CI, 3.667-9.961; P <.001); and need for steroid administration (OR, 1.910; 95% CI, 1.419-2.571; P <.001).

This study had some limitations. It did not evaluate the appropriateness of changing antimicrobial agents, and it did not evaluate the duration of antibiotic treatment and its relationship to the development of resistance.

“Antimicrobial stewardship principles are of utmost importance early and throughout the hospitalization in these patients, and antimicrobials must be limited to suspected or confirmed bacterial infections. Additional studies are needed to evaluate the long-term consequences of steroid use, our antimicrobial decision-making, and ways to optimize antimicrobial use in patients hospitalized with COVID-19,” study authors concluded.


Kubin CJ, McConville TH, Dietz D, et al. Characterization of bacterial and fungal infections in hospitalized patients with COVID-19 and factors associated with healthcare-associated infections. Open Forum Infect Dis. 2021;8(6):ofab201. doi:10.1093/ofid/ofab201