Snapshot of COVID-19 superinfections in Marseille hospitals: where are the common pathogens?

Abstract

Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42,468 patients who had been diagnosed with 261 subjects who had tested Covid-19 negative between 26 February 2020 and 1 May 2021. In addition, 4,059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients (p<0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving E. coli (p<0.0001) and Klebsiella pneumoniae (p=0.027) when compared to controls. In respiratory specimens Haemophilus influenzae (p<0.0001) was more frequent in controls, while Streptococcus pneumoniae (p<0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, were more frequent among COVID-19 patients. Finally, we observed a high frequency of Enterococcus faecalis bacteraemia among COVID-19 patients, which were mainly ICUacquired and associated with a longer timescale to acquisition.

Pseudomonas aeruginosa Bloodstream Infections in SARS-CoV-2 Infected Patients: A Systematic Review

“…The COVID-19 patients had a higher prevalence of HA-BSIs, overall 72.2% vs. 48.2% and 39.5% in non-COVID-19 and influenza patient controls, respectively. Among these, P. aeruginosa BSI was significantly more common in non-COVID-19 patients than in controls ( p = 0.002), both in medicine wards and in ICUs, and it was more common in the respiratory samples than in blood ones [ 62 ]. In addition, Meschiari et al noticed a reduction in the prevalence of P. aeruginosa susceptible strains during the pandemic [ 63 ].…”

Reinfection with SARS‐CoV‐2 Omicron BA.4 and BA.5 variants

“…Our laboratory has extensively and continuously screened SARS-CoV-2 infections by real-time reverse transcription-polymerase chain reaction (RT-PCR) and performed SARS-CoV-2 genotyping since February 2020, when the virus emerged in France, making it possible to calculate the rate of reinfection during the whole pandemic period (Table S1). 1,4,6,7 A computerized alert based on our laboratory information system was applied to identify patients reinfected with Omicron BA.4 or BA.5. Criteria for defining reinfections are described in Table 1.…”