Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS

Abstract

Background Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance. Methods In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period. Results The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii , Cutibacterium acnes , Staphylococcus haemolyticus , Pseudomonas aeruginosa , and Enterococcus faecium . Acinetobacter baumannii , particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples. Conclusion The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.

Genomic characterization and outbreak investigations of methicillin-resistant Staphylococcus aureus in a county-level hospital in China

“…On the other hand, ICU patients have compromised immune function, undergo mechanical ventilation, central venous catheterization and urinary catheterization procedures, and are applied invasive devices, all of which significantly increase the risk of infections in ICU patients ( Pachori et al, 2019 ). Furthermore, factors such as inadequate equipment disinfection and sterilization, partial aerosol transmission of pathogenic bacteria, insufficient disinfection of the environment, neglect of hand hygiene, and drug-related issues further promote the spread of MRSA in hospitals ( Yang et al, 2023 ). These results highlight the need for enhanced infection prevention and control measures in county-level hospitals in China.…”