Prevalence of Respiratory Pathogens in COVID Patients

Author(s): Johnny Michel, Maria-Alexandra Stoica, Myriam Aouiti-Trabelsi, Fabienne DE Oliveira, Eva Hong, Luc-Marie Joly, Ala-Eddine Deghmane, Jean-Christophe Plantier, Muhamed-Kheir Taha

Background: Management of a novel respiratory virus causing severe pneumonitis included the use of antibiotics to prevent bacterial co-infections and secondary infections. However, the impact of this antibiotic use on the selection of resistant bacterial isolates needs to be evaluated.

Methods: We conducted a single-center retrospective study from November 14, 2020 to December 31, 2021 to assess the prevalence of several members of the nasopharyngeal microbiota from PCR-positive SARS-CoV-2 subjects. The study population corresponded to 1030 nasopharyngeal swabs positive for SARS-CoV-2 at the university hospital of Rouen site in symptomatic patients aged 16 years and older. Real-time PCR was used to detect the presence of Haemophilus influenzae, Streptococcus pneumonia, Neisseria meningitidis and influenza A virus. An analysis of the ftsI gene was further used to analyze beta-lactam resistance in H. influenzae.

Results: The results reveled less than expected carriage rate with 5% for H. influenzae, 1.2% for N. meningitidis and 3.7% for S. pneumoniae and an absence of influenza A. On the other hand, there was a significant difference (p<0.01) between the "carriage" and "no carriage" groups on age, sex, oxygen therapy and orotracheal intubation, implying a more severe evolution of the COVID-19 in carriers. Analysis of the ftsI gene reveals 26% of predicted resistance to amoxicillin without resistance to third generation cephalosporins.

Conclusions: COVID-19 pandemic has disrupted bacterial and viral epidemiology, leading to lower circulation of several respiratory pathogens.