Bacterial and viral co-infections in patients with severe SARS-CoV-2 pneumonia admitted to a French ICU

Abstract

Background Data on the prevalence of bacterial and viral co-infections among patients admitted to the ICU for acute respiratory failure related to SARS-CoV-2 pneumonia are lacking. We aimed to assess the rate of bacterial and viral co-infections, as well as to report the most common micro-organisms involved in patients admitted to the ICU for severe SARS-CoV-2 pneumonia. Patients and methods In this monocenter retrospective study, we reviewed all the respiratory microbiological investigations performed within the first 48 h of ICU admission of COVID-19 patients (RT-PCR positive for SARS-CoV-2) admitted for acute respiratory failure. Results From March 13th to April 16th 2020, a total of 92 adult patients (median age: 61 years, 1st–3rd quartiles [55–70]; males: n = 73/92, 79%; baseline SOFA: 4 [3–7] and SAPS II: 31 [21–40]; invasive mechanical ventilation: n = 83/92, 90%; ICU mortality: n = 45/92, 49%) were admitted to our 40-bed ICU for acute respiratory failure due to SARS-CoV-2 pneumonia. Among them, 26 (28%) were considered as co-infected with a pathogenic bacterium at ICU admission with no co-infection related to atypical bacteria or viruses. The distribution of the 32 bacteria isolated from culture and/or respiratory PCRs was as follows: methicillin-sensitive Staphylococcus aureus (n = 10/32, 31%), Haemophilus influenzae (n = 7/32, 22%), Streptococcus pneumoniae (n = 6/32, 19%), Enterobacteriaceae (n = 5/32, 16%), Pseudomonas aeruginosa (n = 2/32, 6%), Moraxella catarrhalis (n = 1/32, 3%) and Acinetobacter baumannii (n = 1/32, 3%). Among the 24 pathogenic bacteria isolated from culture, 2 (8%) and 5 (21%) were resistant to 3rd generation cephalosporin and to amoxicillin–clavulanate combination, respectively. Conclusions We report on a 28% rate of bacterial co-infection at ICU admission of patients with severe SARSCoV-2 pneumonia, mostly related to Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae and Enterobacteriaceae. In French patients with confirmed severe SARSCoV-2 pneumonia requiring ICU admission, our results encourage the systematic administration of an empiric antibiotic monotherapy with a 3rd generation cephalosporin, with a prompt de-escalation as soon as possible. Further larger studies are needed to assess the real prevalence and the predictors of co-infection together with its prognostic impact on critically ill patients with severe SARS-CoV-2 pneumonia.

Bacterial coinfection in critically ill COVID-19 patients with severe pneumonia

“…If the high rate of coinfection with S. aureus has been well described in Flu [ 4 ], first reported cohorts do not mention bacterial co-infection as a common feature of COVID-19 with pneumonia [ 5 ]. Our findings are consistent with those of two recent series which focused on the early bacterial coinfection associated with SARS-CoV-2 pneumonia, and highlighted that S. aureus was one of the main identified microorganism, using molecular diagnostic tests alone or in association with conventional tests [ 6 , 7 ]. Interestingly, procalcitonin level did not differ between the patients with and without associated bacterial coinfection, as already reported by Kreitmann et al [ 7 ] raising the question of the usefulness of this biomarker to help for identifying early bacterial coinfection during COVID-19 pneumonia.…”

High rate of infections during ICU admission of patients with severe SARS-CoV-2 pneumonia: A matter of time?

“… 1 In contrast, other authors, applying molecular screening for co-infection, described co-infection rates as high as 28% and 41% in two ICUs. 2 , 3 In other meta-analysis, 4 secondary bacterial infection during admission on hospitalized adult patients was identified in 14.3% of COVID-19 patients (95% CI 9.6–18.9%), although this prevalence might not reflect the rates in ICUs. In this work, we want to report our findings in a Spanish ICU with high incidence of both co-infection and secondary infections during the first wave of the pandemic.…”

“…Even though the AspICU algorithm to diagnose invasive pulmonary aspergillosis in critically ill patients requires a positive respiratory culture to identify Aspergillus , the real prevalence remains elusive because of the current absence of a standardized definition for non-proven disease in non-neutropenic critically ill patients. 8 , 9 Nine multidrug-resistant strains were isolated, which represented 6% of microbial isolates: extended-spectrum beta-lactamase E. coli (4); multi-resistant P. aeruginosa (2), and methicillin-resistant S. aureus (3).…”

Will coronavirus disease (COVID-19) have an impact on antimicrobial resistance?

“…infection in an immunocompetent COVID-19 patient [ 15 ]. However, other studies from France and Spain did not show an increase in infections with multidrug-resistant bacteria [ 16 , 17 ], and one Italian study even saw a reduction in Clostridioides difficile infections in hospitalised patients [ 18 ]. In a rapid review, Fattorini et al found that only 1.3% of 522 COVID-19 patients in intensive care units (ICUs), and apparently no COVID-19 patients in other units, developed a healthcare-associated superinfection with antimicrobial-resistant bacteria [ 19 ].…”