Bacterial and Fungal Co-Infections and Superinfections in a Cohort of COVID-19 Patients: Real-Life Data from an Italian Third Level Hospital

Abstract

The use of immune suppressive drugs combined with the natural immune suppression caused by SARS-CoV-2 can lead to a surge of secondary bacterial and fungal infections. The aim of this study was to estimate the incidence of superinfections in hospitalized subjects with COVID-19. We carried out an observational retrospective single center cohort study. We enrolled patients admitted at the "Garibaldi" hospital for ≥72 h, with a confirmed diagnosis of COVID-19. All patients were routinely investigated for bacterial, viral, and fungal pathogens. A total of 589 adults with COVID-19 were included. A total of 88 infections were documented in different sites among 74 patients (12.6%). As for the etiology, 84 isolates were bacterial (95.5%), while only 4 were fungal (4.5%). A total of 51 episodes of hospital-acquired infections (HAI) were found in 43 patients, with a bacterial etiology in 47 cases (92.2%). Community-acquired infections (CAIs) are more frequently caused by Streptococcus pneumoniae, while HAIs are mostly associated with Pseudomonas aeruginosa. A high rate of CAIs and HAIs due to the use of high-dose corticosteroids and long hospital stays can be suspected. COVID-19 patients should be routinely evaluated for infection and colonization. More data about antimicrobial resistance and its correlation with antibiotic misuse in COVID-19 patients are required.

Keywords: COVID-19; bacterial; coinfections; community-acquired infection (CAI); fungal; hospital-acquired infection (HAI); superinfections.

Figure 1

Etiology of bacterial and fungal infections, differentiated by their origin. Community-acquired infections (points) are only bacterial in etiology, while hospital-acquired infections (stripes), more frequent than CAIs, are both bacterial and fungal. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; CAI, community-acquired infection; HAI, hospital-acquired infection.

Figure 2

Etiology of CAIs by site of infection. Twenty-three cases of pneumonia were caused by Streptococcus pneumoniae (sparse points), three cases were due to Moraxella catarrhalis (thick points), and one patient had a Haemophilus influenzae (slant stripes) pneumonia. All the BSIs were caused by MRSA (checks). UTIs were caused by Escherichia coli (horizontal stripes) in four cases and Proteus mirabilis (black) in one case. Abbreviations: MRSA, methicillin-resistant S. aureus; BSI, bloodstream infection; UTI, urinary tract infection.

Figure 3

Etiology of HAIs by site of infection. A total of 18 cases of pneumonia were caused by Pseudomonas aeruginosa (horizontal stripes), 13 cases were due to Escherichia coli (sparse points), 6 patients had a Klebsiella spp. (checks) pneumonia, and MRSA (large slant stripes) and Aspergillus fumigatus (vertical stripes) caused 2 cases of pneumonia each. BSIs were caused by Klebsiella spp. (checks) in two cases, MRSA (slant stripes) in three cases, and by Candida albicans (close slant stripes). UTIs were caused by Escherichia coli in three cases and Pseudomonas aeruginosa in one case. One case of IAI was caused by C. albicans. Abbreviations: spp., species plures; MRSA, methicillin-resistant S. aureus; BSI, bloodstream infection; UTI, urinary tract infection; IAI, intra-abdominal infections.

Figure 4

Total use of antibiotics belonging to a restricted list in COVID-19 wards, during the first year of the pandemic (Days 2020) compared with total use within the same wards during the two pre-pandemic years (days 2018, days 2019). Y axis is in logarithmic scale. It can be noticed that in 2020 the use of each antibiotic was constant or even lower than the years before, despite an increase in beds, apart from dalbavancin and ertapenem. Both antibiotics are easily managed in a day hospital setting, as they have, respectively, weekly and daily intake.