The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic

Abstract

Background The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). Methods This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. Results Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. Conclusion During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.

Candent issues in pneumonia. Reflections from the Fifth Annual Meeting of Spanish Experts 2023

“…Thanks to introduction of syndromic panels [ 19 ], proportion of pneumonia caused by identified bacteria grew from 15-30% to 62-71%, compared to classic methods, such as cultures [ 20 , 21 ]. Also, the impact of COVID-19 made Haemophilus influenzae and Staphylococcus aureus were more frequent than Streptococcus pneumoniae [ 22 ].…”

Effect of Age, Sex, and COVID-19 Vaccination History on All-Cause Mortality: Unexpected Outcomes in a Complex Biological and Social System

“…The proportion of other viruses was 14% lower and the proportion of bacterial-and viral co-detections was reduced by half. Streptococcus pneumoniae in the pre-COVID was largely replaced by Staphylococcus aureus in the COVID cohort, however Adenovirus, Parainfluenza virus and several bacteria showed little change in the proportion of detections [110]. Such selective shifts cannot be explained by the imposition of protective measures.…”

Impact of normalized COVID-19 prevention and control measures on lower respiratory tract infection pathogenesis in hospitalized children

“…Notably, the incidence of LRTIs was significantly reduced after the COVID-19 outbreak, suggesting the effectiveness of COVID-19 prevention and control measures in reducing childhood respiratory infections ( 16 , 19 ). Detection rates for different pathogens show significantly variation with age, with the highest rates, particularly for viral infections ( 17 – 21 ), occurring before the age of 3 years, this is attributed to lower immunity and increased environmental contact in young children, coupled with challenges in adhering to preventive measures liking handwashing and mask-wearing ( 18 , 19 ). While the incidence rate of LRTI usually decreases with age, the incidence rate of LRTI increases significantly at the age of 3 years, which may be due to the fact that children begin to learn in early childhood settings at this age ( 22 ).…”

“…Before and during the COVID-19 pandemic, there was no statistically significant difference in the incidence of LRTIs among children in summer ( Figure 1 ), but there was no statistically significant difference in the rate of pathogen positivity compared with that in autumn ( Table 1 ), and the difference in seasonal incidence was attributed to the change in temperature in autumn and winter, which is favorable for pathogen multiplication, and the peak of pathogen infection started in autumn ( 25 ). The increase in the pathogen-positive detection rate may be due to the systematic training of all sampling personnel in health care facilities on respiratory specimen collection during the COVID-19 pandemic, and the prevention and control measures that allowed children to attend the hospital relatively late ( 17 ).…”