Abstract
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 < 0.05), indicating reduced microbiome diversity. Multivariable Cox regression analysis identified APACHE II score (hazard ratio [HR] = 1.04, P = 0.029) and maximum bacterial load (HR = 1.67, P = 0.046) as independent risk factors for ICU mortality. This study highlights changes in microbiome composition across epidemic phases, which may inform treatment strategies.IMPORTANCEWith the development of next-generation sequencing technology, it is increasingly being applied in clinical practice, especially in evaluating the prognosis of severe infections and co-infections. This study characterized the composition of microorganisms in the lower respiratory tract of ventilator-associated pneumonia (VAP) patients across three phases of the COVID-19 epidemic. Our study emphasizes that the relative abundance of bacteria, fungi, and viruses in bronchoalveolar lavage fluid of VAP patients may vary with the progression of the local epidemic and host immune status. These findings provide a mechanistic basis for optimizing targeted therapies in VAP management during infectious disease outbreaks.