# Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period

## TL;DR

This study examines the causes and outcomes of community-acquired pneumonia during the COVID-19 pandemic and evaluates the effectiveness of molecular tests in identifying pathogens.

## Contribution

The study provides insights into the clinical and microbiological characteristics of pneumonia during the pandemic and assesses a molecular diagnostic test's utility.

## Key findings

- Streptococcus pneumoniae was the most common isolate in community-acquired pneumonia cases.
- The molecular test (FilmArray) had a low positivity rate and mainly detected viral coinfections.
- A high NEWS2 score, oncohematological disease, and chronic neurological conditions were linked to worse outcomes.

## Abstract

Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30–65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis.

We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux).

From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections.

Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.