Respiratory pathogen trends in queensland, australia between 2018 and 2021: A statewide cohort study before and after the initial COVID-19 outbreak

Article

Sweeny, Amy L., Gerrard, John, Alcorn, Kylie, Grant, Gary, Huang, Ya-Ling, Gerhardy, Benjamin, Keijzers, Gerben and COVERED-COVID study research investigators. 2025. "Respiratory pathogen trends in queensland, australia between 2018 and 2021: A statewide cohort study before and after the initial COVID-19 outbreak." Archives of Medical Research. 56 (3). https://doi.org/10.1016/j.arcmed.2024.103144
Article Title

Respiratory pathogen trends in queensland, australia between 2018 and 2021: A statewide cohort study before and after the initial COVID-19 outbreak

ERA Journal ID15295
Article CategoryArticle
AuthorsSweeny, Amy L., Gerrard, John, Alcorn, Kylie, Grant, Gary, Huang, Ya-Ling, Gerhardy, Benjamin, Keijzers, Gerben and COVERED-COVID study research investigators
Journal TitleArchives of Medical Research
Journal Citation56 (3)
Article Number103144
Number of Pages10
Year2025
PublisherElsevier
Place of PublicationUnited States
ISSN0188-4409
1873-5487
Digital Object Identifier (DOI)https://doi.org/10.1016/j.arcmed.2024.103144
Web Address (URL)https://www.sciencedirect.com/science/article/pii/S0188440924001954
Abstract

Background
The SARS-CoV-2 pandemic and accompanying public health measures disrupted the normal transmission of respiratory viral pathogens. Less is known about the effects on bacterial pathogens.
Aims
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).
Methods
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.
Results
Over 260,000 viral PCRs and 180,000 cultures were analyzed. Decreases in influenza and RSV were observed in 2020 from 10.8 to 1.1 and 9.5 to 2.5 per 100 tests, respectively; S. pneumoniae decreased from 1.7 to 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 to 1.8 in 2020 and 1.6 in 2021. After restrictions eased, RSV rates increased to levels higher than before the pandemic.
Conclusions
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.

KeywordsCOVID-19; Epidemiology; Microbial; Virus; Respiratory
Contains Sensitive ContentDoes not contain sensitive content
ANZSRC Field of Research 2020420501. Acute care
420299. Epidemiology not elsewhere classified
420699. Public health not elsewhere classified
Byline AffiliationsSchool of Nursing and Midwifery
Centre for Health Research
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