Analysis of ICU resistome dynamics in patients, staff and environment for the identification of predictive biomarkers of sepsis and early mortality.

Antimicrobial resistance (AMR) is a global crisis, posing a critical challenge to healthcare systems, particularly in intensive care units (ICUs), where multidrug-resistant organisms (MDROs) threaten patient survival. This study offers a unique, real-world perspective on AMR dynamics by analyzing 96 metagenomic samples from three key sources: oropharyngeal and rectal swabs of deceased ICU patients (both postadmission and antemortem), healthcare workers, and high-touch ICU surfaces. Findings revealed the ICU environment as a major AMR reservoir, with oropharyngeal swabs carrying the highest AMR burden. While healthcare staff facilitated MDRO spread, they were not primary sources. Staff microbiomes' MDRO pattern closely resembled environmental samples. Key AMR species included B. fragilis, E. coli, S. pneumoniae, S. aureus, with P. aeruginosa persisting on high-touch surfaces. Tetracycline resistance was the most prevalent, with common resistances comprising 36.1% of all detected AMR markers. Staff microbial community exhibited higher resistance to macrolides, fluoroquinolones, lincosamides, and cephamycins. A 10-day survival threshold distinguished early (EM) and late mortality (LM) groups. EM patients exhibited unique AMR species in the oropharynx, suggesting respiratory-driven infections, while LM patients showed greater gut-associated resistance. Higher rectal AMR counts correlated with prolonged survival. Notably, four key MDROs (L. monocytogenes, M. tuberculosis, S. haemolyticus, and S. agalactiae) were enriched in sepsis patients, suggesting early risk markers. Fewer new resistances emerged in rectal than oropharyngeal swabs, likely due to antibiotic selection pressure. Vancomycin and levofloxacin, frequently co-administered, exerted stronger selective pressure in the oropharynx, possibly explaining the high MRSA prevalence in patient and environmental samples.