ABSTRACT
The last both authors contributed equally Purpose To design clinical and public health policies, including immunization, during the COVID-19 pandemic, it is critical to monitor not only infections due to SARS-CoV-2 but other pathogens as well. We evaluated interim results from the first year of a multi-site study of community-acquired pneumonia (CAP) and early onset hospital-acquired pneumonia (HAP) in Germany to assess the contribution of different pathogens over time. Methods This multicenter trial is being conducted from January 2021 to December 2023 at three hospitals in Thuringia: Jena University Hospital (1396 beds), SRH Hospitals Gera (951 beds) and Suhl (653 beds). Adult hospitalized patients with CAP/early onset HAP are identified by a screening algorithm which includes assessment by a study physician. Study procedures included: health data collection, urine specimens (using S. pneumoniae serotype-specific urinary antigen detection assays (UAD-1/2) and BinaxNOW), and nasopharyngeal swabs (analyzed by multiplex microbiological analysis), disease severity assessments, mortality (follow-up to day 90), pathogen spectrum, and quality of life (follow-up to day 180). Results Within the first year (2021), 760 patients (58 % male, 70 % >= 60 years) were enrolled. ICU admission occurred in 16.1 % of cases, and 9.2 % required mechanical ventilation. Pathogens were identified for 553 cases. SARS-CoV-2 was identified in 78.4 % in the first half of the year while S. pneumoniae was detected in 6 cases (2.1 %;2/6 as a co-infection (0.7 %)). Other respiratory viruses were detected in 18 of 338 cases, of which 15 (4.2 %) were coinfections with SARS-CoV-2. In the second half of 2021, SARS-CoV-2 was identified in 58.3 % of cases, however, other pathogens occurred more frequently including S. pneumoniae 10.2 % (n/N = 34/333;13/34 as a co-infection with SARS-CoV-2 (3.9 %)) and other respiratory viruses 11.4 % (n/N = 41/360;11/41 as a co-infection with SARS-CoV-2 (3.0 %)). Influenza was not detected. Conclusion While SARS-CoV-2 remained the most common pathogen among patients with CAP/early onset HAP during the study year, other pathogens reemerged during the second half of 2021. Correspondingly, co-infections with SARS-CoV-2 increased, with pneumococci as the leading pathogen.