Seasonal Genomic Dynamics of Multidrug-Resistant Pathogens in ICU Environments and Perspectives on Phage-Based Interventions

Abstract

Background: The emergence of multidrug-resistant (MDR) pathogens in intensive care units (ICUs) has become a pressing global health issue, contributing to mortality rates exceeding 40%. Among these, carbapenem-resistant Klebsiella pneumoniae and Acinetobacter baumannii are especially problematic. Seasonal fluctuations in resistance patterns have been observed, yet the genomic mechanisms underlying these trends remain insufficiently characterized. Objective: This study investigated the seasonal variation in resistance gene prevalence among ICU-derived bacterial isolates and elucidates the genomic features contributing to antimicrobial resistance. Methods: Environmental and clinical samples were collected from ICU settings over multiple seasons using a systematic, stratified approach. Whole-genome sequencing was conducted on isolates via Illumina and Nanopore platforms. Resistance genes were annotated using CARD, VFDB, and BiocideResistance databases. Statistical associations were assessed using logistic regression and generalized linear mixed models, while phylogenetic trees evaluated clonal relationships. Results: The blaCTX-M-3 gene was detected in 100% of autumn isolates (n=52), showing a statistically significant association with increased bed turnover and prolonged disinfection intervals (p=0.003). During winter, 75% of isolates (n=50) tested positive for qacEΔ1, correlating with elevated multidrug resistance indices (p=0.01) and patterns consistent with clonal expansion based on whole-genome SNP profiling. These winter strains also exhibited enhanced biofilm formation capacity (OD595=0.67 ± 0.11) and upregulation of efflux pump transcripts (2.3-fold increase vs summer; p=0.02), supporting environmental adaptation under low-temperature stress. Notably, aac(6’)-Ib7, an aminoglycoside-modifying enzyme gene, was the most frequently detected resistance determinant, present in 68% of isolates, highlighting substantial antibiotic selection pressure. Conclusion: This study reveals distinct seasonal genomic patterns in ICU drug-resistant pathogens and emphasizes the necessity for adaptive infection control strategies. Targeted disinfection, antibiotic stewardship, and consideration of phage therapy as a complementary strategy particularly during winter may help mitigate the spread of high-risk resistant clones, though further in vitro and in vivo validation is required.