Respiratory pathogen trends coinciding with the early public health response to limit transmission of SARS-Coronavirus-2.

Abstract

The SARS-Coronavirus-2 pandemic disrupted normal transmission of many viral respiratory pathogens. We analysed a state-wide dataset of microbiological results from public hospitals in Queensland, Australia. Following declaration of the pandemic and subsequent non-pharmaceutical interventions (NPIs), we observed decreases in influenza and respiratory syncytial virus (RSV) consistent with other studies. However, upon easing intrastate border and crowd gathering restrictions, RSV levels surged to unseasonally high levels; influenza levels did not. Among bacterial pathogens, we observed a decrease in detection of S. pneumoniae of 35% (95% confidence interval: 22% to 47%). No change in detection of S. aureus or P. aeruginosa per 100 cultures was evident, but cultures positive for K. pneumoniae increased from 1.21 (1.10-1.32) per 100 cultures pre-pandemic to 1.80 (1.58-2.02) in 2020 and 2021. We suggest that early NPIs limited transmission of all droplet-spread pathogens. However, later less-restrictive NPIs allowed RSV, (with a reproductive number greater than influenza or the Delta strain of SARS-CoV-2 but lower than the Omicron strain), to re-emerge. The increase in K. pneumoniae, commonly implicated in hospital-acquired infections, requires further investigation.