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Etiologic Agents of Non-COVID Community-Acquired Pneumonia Requiring Hospitalization – Analyzing Changes Over Time

Published online by Cambridge University Press:  23 June 2026

Nak-Hyun Kim
Affiliation:
Seoul National University Bundang Hospital
Danielle Cook
Affiliation:
University of Utah
Nora Fino
Affiliation:
University of Utah
Claire Ciarkowski
Affiliation:
University of Utah
Tejal Gandhi
Affiliation:
University of Michigan Medical School
Lindsay Petty
Affiliation:
Michigan Medicine
Scott Flanders
Affiliation:
Michigan Medicine
Jennifer Horowitz
Affiliation:
DIvision of Hospital Medicine, Michigan Medicine
David Ratz
Affiliation:
University of Michigan
Ashwin Gupta
Affiliation:
University of Michgian/VA Ann Arbor Healthcare System
Preeti Misra
Affiliation:
Trinity Health Livonia Hospital
Anurag Malani
Affiliation:
Trinity Health Michigan
Valerie Vaughn
Affiliation:
University of Utah School of Medicine

Abstract

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Background: Community-acquired pneumonia (CAP), a heterogeneous clinical entity with a wide range of inciting pathogens, remains a significant cause of morbidity and mortality worldwide. The recent COVID-19 pandemic and subsequent shifts in clinical and diagnostic practices necessitate an updated understanding of the contemporary epidemiologic and etiologic landscape for non-COVID CAP. Method: This retrospective cohort study included adult patients hospitalized with CAP between January 1, 2017, and December 31, 2024, across 68 hospitals participating in the Michigan Hospital Medicine Safety consortium. Eligible patients included hospitalized adults with a pneumonia discharge code, symptoms and imaging consistent with pneumonia, and receipt of antibiotic treatment on hospital day 1 or 2. Patients admitted to intensive care, those with concomitant infections, positive SARS-CoV-2 tests, or severe immunosuppression were excluded. Diagnostic testing methods and the pathogens detected were reviewed and summarized by year. Result: A total of 62,340 patients were included. Mean age was 69.0 ±15.9 years, and 50.3% (31,359) were male. 94.0% (58,613) received a chest X-ray and 53.1% (33,084) received a CT, with use of CTs increasing over time. Microbiological evaluation was performed in 92.8% (57,820) of patients, with a median 4 [IQR 2-6] etiologic tests per patient. Blood cultures were the most common microbiologic test (74.7%; 46,566) with use slightly decreasing over the study period. In contrast, the use of molecular respiratory pathogen assays increased substantially from 28.2% in 2017 to 77.1% in 2024 (overall performed in 55.6%, 34,655). Over the entire study period, one or more pathogens were detected in 15.9% (9,915) of patients: 10.5% (6,515) had a bacterial pathogen, 6.3% (3,908) had a viral pathogen, and 0.8% (508) had both. The most common pathogens were Streptococcus pneumoniae (2.6%), influenza virus (2.6%), Pseudomonas aeruginosa (1.6%), and human rhinovirus (1.4%). Conclusion: The 2019 CAP guideline recommendations to limit traditional bacterial tests to severe CAP patients appear to have had minimal impact on diagnostic practices. Despite a substantial post-pandemic increase in molecular diagnostic use, pathogen detection rates remained low, revealing an etiology in only a minority of patients. These findings underscore the need for a reassessment of the diagnostic approach to optimize resource allocation and ensure high-value testing in hospitalized CAP patients.

Multiple graphs depict trends in radiologic, etiologic, and respiratory virus/pathogen PCR tests over the years 2017 to 2024.

A table showing the detection of pathogens in patients over several years.

Information

Type
Diagnostic Stewardship
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
© The Author(s), 2026. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America