Prevalence of respiratory pathogens in COVID patients

Abstract

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. meningitidisand 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.

The Rapid Rebound of Invasive Meningococcal Disease in France at the End of 2022

“…4 It is noteworthy that the diminution of circulation of bacterial isolates is expected to reduce not only the incidence of the disease but also that of asymptomatic carriage. 7 A further decline in IMD may have also occurred subsequent to the reduction in the circulation of influenza viruses, 18 as also suggested by our data, which shows a significant correlation between the number of IMD and flu-like cases. Secondary bacterial infections (including IMD) generally occur a few days after the peak of flu-like cases 9 and was already described during the flu pandemic of 1918.…”

Recent increase of atypical forms of invasive meningococcal disease

“…Indeed, meningococcal isolates circulated at low levels during the COVID-19 pandemic [22]. Similar low circulation of Hemophilus in unezae, Streptococcus pneumoniae and in uenza A virus was reported among COVID-19 patients in France in 2020 and 2021, suggesting a modi cation of the nasopharyngeal microbiota [22]. Moreover, non-hyperinvasive clonal complexes are more frequent in carriage and should be expected to recolonize rapidly the nasopharynx and can still be involved in IMD cases [4].…”

“…The emergence of those new genotypes may have been potentiated by an "immunity gap" in the herd immunity of the population during the NPIs, due to the reduced circulation of historical hyperinvasive isolates [12,21]. Indeed, meningococcal isolates circulated at low levels during the COVID-19 pandemic [22]. Similar low circulation of Hemophilus in unezae, Streptococcus pneumoniae and in uenza A virus was reported among COVID-19 patients in France in 2020 and 2021, suggesting a modi cation of the nasopharyngeal microbiota [22].…”

Recent increase in atypical presentations of invasive meningococcal disease in France

“…The emergence of those new genotypes may have been potentiated by an "immunity gap" in the herd immunity of the population during the NPIs, due to the reduced circulation of historical hyperinvasive isolates [12,24]. Indeed, meningococcal isolates circulated at low levels during the COVID-19 pandemic [25]. Similar low circulation of Haemophilus influenzae, Streptococcus pneumoniae and influenza A virus was reported among COVID-19 patients in France in 2020 and 2021, suggesting a modification of the nasopharyngeal microbiota [25].…”

“…Indeed, meningococcal isolates circulated at low levels during the COVID-19 pandemic [ 25 ]. Similar low circulation of Haemophilus influenzae , Streptococcus pneumoniae and influenza A virus was reported among COVID-19 patients in France in 2020 and 2021, suggesting a modification of the nasopharyngeal microbiota [ 25 ]. Moreover, non-hyperinvasive clonal complexes are more frequent in carriage and should be expected to recolonize rapidly the nasopharynx and can still be involved in IMD cases [ 4 ].…”