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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China
Jilin Yang1, Lingyi Li2, Xiaolin Zhu1
1Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People's Republic of China.
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.
Insights
Surface pathogens in ICUs threaten elderly patients. Metagenomic sequencing revealed high pathogen and resistance gene abundance on frequently touched surfaces, highlighting mNGS as a key surveillance tool.
Area of Science:
- Environmental microbiology
- Hospital-acquired infections
- Genomics and sequencing technologies
Background:
- Intensive care unit (ICU) surface pathogens pose a global health risk, particularly to immunocompromised elderly individuals.
- Metagenomic next-generation sequencing (mNGS) offers an unbiased approach for environmental microbiological surveillance.
Purpose of the Study:
- To investigate microbial communities in Chinese geriatric ICUs over a six-month period.
- To analyze pathogen profiles and drug resistance genes in environmental samples and compare them with patient cultures.
- To assess the utility of mNGS for hospital environmental monitoring.
Main Methods:
- A six-month study (January-July 2022) in geriatric ICUs.
- Regular monitoring of multiple surfaces at three-month intervals using mNGS.
- Comparison of pathogen and drug resistance gene profiles between environmental and patient samples.
Main Results:
- Microbial composition was stable over time but varied significantly across different surfaces.
- High-contact surfaces harbored pathogenic microorganisms, including *Acinetobacter baumannii* (CRAB), *Pseudomonas aeruginosa*, and *Enterococcus faecium*.
- mNGS detected viruses, fungi, and parasites; abundant drug resistance genes were found in most environmental samples.
Conclusions:
- ICU microbial composition remained constant, with floors showing highest diversity and abundance.
- Drug-resistant genes in the ICU environment may transfer to patients.
- mNGS is a powerful emerging tool for microbiological surveillance of hospital environments.
