Prevalence, risk factors and outcomes of secondary infections among hospitalised patients with COVID-19 or post-COVID-19 conditions in Victoria, 2020-2023

Objectives: Estimates of secondary infections are variedly reported, with few studies done in Australia. We investigated the occurrence and impact of secondary infections complicating COVID-19 and post-COVID-19 admissions in Victoria, Australia, 2020-2023.Methods: We used linked population-wide datasets and ICD-10 codes to identify and estimate occurrence of secondary infections. Using hospital/ICU length of stay (LOS) in negative binomial regression, and mortality, we examined the impact of secondary infections.Results: Secondary infections were identified in 6·9% (13,467/194,660) of COVID-19 and post-COVID-19 admissions; 6·0% (11,651/194,660) bacterial, 0·9% (1,691/194,660) viral, and 0·2% (385/194,660) fungal. Prevalence was highest during Pre-Delta (10.4%) and Omicron-BA2 (8.1%) periods. Sepsis and pneumonia were the most reported syndromes; occurrence of sepsis declined gradually over time. The odds of secondary infections were higher among the ≥70-year-olds (adjusted odds ratio(aOR):3·76 (95%CI: 3·43-4·14; vs 20-29-year-olds), individuals with chronic conditions (aOR:3·15; 95%CI: 2·88-3·45; vs those without), the unvaccinated (aOR:1·59; 95%CI: 1·45-1·75) and the lowest socio-economic group (aOR:1·12; 95%CI: 1·05-1·19). Patients with secondary infections had 2·43 times longer hospital LOS, and 9·60 times longer ICU LOS compared to those without. Mortality risk was 2·17 times higher in those with secondary infections.Conclusion: Secondary infections occurred in 69 per 1000 COVID-19 associated hospital admissions in Victoria, mostly in high-risk groups, and were associated with severe outcomes.