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

Amy L Sweeny; John Gerrard; Kylie Alcorn; Gary Grant; Ya-Ling Huang; Benjamin Gerhardy; Gerben Keijzers; COVERED-COVID study research investigators

doi:10.1016/j.arcmed.2024.103144

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

Arch Med Res. 2024 Dec 22;56(3):103144. doi: 10.1016/j.arcmed.2024.103144. Online ahead of print.

Authors

Amy L Sweeny¹, John Gerrard², Kylie Alcorn³, Gary Grant⁴, Ya-Ling Huang⁵, Benjamin Gerhardy⁶, Gerben Keijzers⁷; COVERED-COVID study research investigators

Affiliations

¹ Department of Emergency Medicine, Gold Coast Hospital and Health Service, Southport Queensland, Australia; Menzies Health Institute Queensland, Griffith University, Queensland, Australia; Bond University, Faculty of Health Sciences and Medicine, Australia. Electronic address: amy.sweeny@health.qld.gov.au.
² Queensland Health, Office of the Chief Health Officer, Australia; Infectious Diseases Department, Gold Coast Hospital and Health Service, Australia.
³ Infectious Diseases Department, Gold Coast Hospital and Health Service, Australia; Griffith University School of Medicine and Dentistry, Australia.
⁴ Griffith University School of Pharmacy and Medical Sciences, Australia.
⁵ Department of Emergency Medicine, Gold Coast Hospital and Health Service, Southport Queensland, Australia; Faculty of Nursing, University of Southern Queensland, Queensland, Australia.
⁶ Nepean Blue Mountains Local Health District, Nepean Hospital, Australia.
⁷ Department of Emergency Medicine, Gold Coast Hospital and Health Service, Southport Queensland, Australia; Menzies Health Institute Queensland, Griffith University, Queensland, Australia.

PMID: 39718274
DOI: 10.1016/j.arcmed.2024.103144

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.

Keywords: COVID-19; Epidemiology; Microbial; Respiratory; Virus.