Respiratory Pathogen Trends in Queensland, Australia Between 2018-2021: A Statewide Cohort Study Before and After the Initial COVID-19 Outbreak

The SARS-CoV-2 pandemic and accompanying public health measures disrupted the normal transmission of respiratory viral pathogens. Less is known about the effects of bacterial pathogens. To assess the impact of public health restrictions on common respiratory pathogens (influenza viruses, respiratory syncytial virus (RSV) and the following bacterial pathogens: Streptococcus pneumoniae (S. pneumoniae), Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus). This statewide cohort study used respiratory specimen result data from 237 health facilities in Queensland, Australia, collected between January 2018 and June 2021. Trends and weekly positive rates per 100 tests/cultures for weeks 11-27 (with 95% confidence intervals) were compared between pre-pandemic (2018/2019), early pandemic restrictions (2020), and easing of restrictions (2021) periods. Over 260,000 viral PCRs and 180,000 cultures were analyzed. Decreases in influenza and RSV were observed in 2020 from 10.8–1.1 and 9.5–2.5 per 100 tests, respectively; S. pneumoniae decreased from 1.7–1.1 per 100 cultures. Influenza levels remained low until the end of the study period. There was no change in the detection of S. aureus or P. aeruginosa per 100 cultures, but cultures positive for K. pneumoniae increased from 1.2 in 2018/2019–1.8 in 2020 and 1.6 in 2021. After restrictions eased, RSV rates increased to levels higher than before the pandemic. Transmission of droplet-spread pathogens decreased after the introduction of public health restrictions due to the COVID-19 pandemic. The increase in K. pneumoniae, often associated with nosocomial infections, warrants further investigation.