Publication date: Sep 19, 2025
Ventilator-associated pneumonia (VAP) is a major cause of morbidity in critically ill patients, and the SARS-CoV-2 infection has influenced the lung microbiome. This study aimed to examine the lower respiratory tract microbiome in VAP patients during different phases of the Shanghai COVID-19 epidemic. A total of 175 patients were included and divided into pre-epidemic (Pre), during-epidemic (Dur), and post-epidemic (Post) groups for analysis. Bronchoalveolar lavage fluid and serum were analyzed using next-generation sequencing. The intensive care unit (ICU) mortality rates were 48. 3% (Pre group), 60. 3% (Dur group), and 28. 8% (Post group). Cytokine levels were lower in the Post group compared to the Pre group. Acinetobacter, Candida, and Herpes Simplex Virus 1 (HSV-1) were the most frequently detected organisms. The prevalence of Klebsiella pneumoniae, Enterococcus faecium, Aspergillus fumigatus, and HSV-1 was higher in the Dur group. α-Diversity of bacteria was significantly lower in the Dur group (P
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| Concepts | Keywords |
|---|---|
| Acinetobacter | COVID-19 |
| Fungi | microbiome |
| Optimizing | next-generation sequencing technology |
| Pneumonia | species richness |
| Shanghai | ventilator-associated pneumonia |
Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | ventilator-associated pneumonia |
| disease | MESH | COVID-19 |
| disease | MESH | morbidity |
| disease | MESH | critically ill |
| pathway | REACTOME | SARS-CoV-2 Infection |
| drug | DRUGBANK | Enterococcus faecium |
| disease | IDO | bacteria |
| disease | MESH | infections |
| disease | MESH | co-infections |
| disease | IDO | host |
| disease | MESH | infectious disease |
| pathway | REACTOME | Infectious disease |