Abstract
The microbiome of hospital environments is increasingly recognised as a reservoir for clinically relevant pathogens, yet the ecological mechanisms that shape the persistence of the pathogen are poorly understood. Here, we ask whether the community structure plays a role in determining the persistence of the pathogen and if it metabolically supports them to thrive in the harsh conditions of hospitals. We used shotgun metagenomic data from hospital and other urban built environments to explore and compare their microbial diversity. Utilising co-occurrence networks, we reveal that hospital communities harbour unique microbial interactions, dominated by phylogenetically and functionally diverse keystone pathogens. Integrating metabolic modelling with microbial associations, we demonstrate that hospital consortia provide significantly higher metabolic support to pathogens relative to other environments, quantified by a novel Pathogen Support Index. These findings highlight the computational framework for elucidating pathogen ecology in urban microbiomes and suggest potential avenues for intervention to mitigate infection risks in healthcare settings.
Our analysis is distributed into four major parts
- Compare microbial diversity in hospital environments with other built environments
- Inferring microbial associations in built environments and identifying their ecological inference
- Identifying metabolic cross-feeding enabling microbial associations
- Explore the role of microbial communities in the pathogen persistence
Here we have the overview of our workflow
Cite:
Sengupta, P., Kapse, V. S., Raman, K. (2025) Microbial Communities Facilitate Pathogen Persistence in Hospital Environments. https://github.com/RamanLab/Hospital_Microbiome