Implications of empirical testing and treatment for atypical bacteria in patients hospitalized with COVID, influenza, or RSV: a retrospective observational cohort study

PURPOSE: Patients admitted with viral respiratory tract infections are at risk ofbacterial co-infections that may exacerbate disease severity. Detection of atypical bacteria requires specific laboratory diagnostic modality and specific antibiotics. METHODS: In this retrospective regionwide cohort study we included all patients admitted to a hospital in the Central Denmark Region with COVID-19, influenza A, influenza B, or Respiratory Syncytial Virus (RSV) from February 2019 to February 2024. Firstly, we investigated the number of patients testing positive for atypical bacterial co-infection. Secondly, we evaluated associations with diagnostic testing for these atypical bacteria, and the use and associations with administration of empirical treatment with clarithromycin. RESULTS: During the study period a total of 19,651 patients were admitted with one of the viral respiratory tract infections. Only 21 patients tested positive for atypical bacterial co-infection, corresponding to 0.1% of those tested (n = 2,369). Empirical clarithromycin was administered to 859 (4.4%) patients. Still 17 out of the 21 patients (81.0%) with atypical bacterial co-infection did not receive clarithromycin before the result of diagnostic test was available. CONCLUSIONS: Our findings do not support routine testing for atypical bacterial co-infection and use of empirical treatment for atypical pneumonia in this population.