Longitudinal analysis of resistance dynamics in oropharyngeal and rectal swab microbiota: a comparison of post-admission and antemortem samples in ICU patients, healthcare staff, and the hospital environment

A longitudinal study was conducted involving 69 ICU patients admitted between February 13 and June 22, 2023. Oropharyngeal and rectal swabs were collected every three days to capture both the post-admission and antemortem microbiota of 20 deceased patients. Additionally, eight samples from healthcare staff were included in the study who were involved in continuous patient care, along with samples from 23 key hospital surfaces within the ICU environment. In total, 96 shotgun metagenomes were analyzed. Our study aimed to comprehensively evaluate overlapping and distinct antimicrobial resistance (AMR) patterns across various reservoirs by comparing samples from patients, healthcare staff, and the ICU environment. Furthermore, we sought to assess the impact of excessive antibiotic use on microbiota diversity, with a particular focus on short-chain fatty acid (SCFA)-producing bacteria and to investigate how antibiotic-induced stress affects microbial community resilience and the emergence of new resistances in oropharyngeal and rectal swabs from critically ill patients.