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Mapping of pathogens and antibiotic resistance genes in a hospital reservoir

Mapping of pathogens and antibiotic resistance genes in a hospital reservoir

While disinfection is the key to infection control, colonization, and resistance patterns of hospital microorganisms remain underestimated. A new paper in Nature Medicine, with a contribution of Bioinformatics Group Leader - Prof. Paweł Łabaj as a MetaSUB consortium member, may underline the importance of describing clusters of antibiotic resistance in hospitals and define the feasibility of systematic research to focus resources on infection prevention.

The global outbreak of antibiotic resistance is once again drawing attention to the control and prevention of infections in hospitals where hospital-acquired infections (HAIs) are a major challenge. The hospital environment is another key, alongside human-to-human transfer, a node in the transmission network, and there is growing evidence that it is a habitat for opportunistic antibiotic-resistant pathogens that contribute to the formation of HAIs. As a result, microbiological ecology and uncharacterized genetic resources of hospital environments are interesting for both infection epidemics and microbiology.

The first extensive genomic characteristics of microbiomes, pathogens, and antibiotic resistance cassettes are described in the Nature Medicine publication in a tertiary-care hospital from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Long-read sequencing techniques introduce new opportunities for pathogen and resistance monitoring. Deep shotgun metagenomics showed marked ecological niches for microorganisms and antibiotic resistance genes, characterized by biofilm formation and human microbiological environment with corresponding spatiotemporal variability patterns.

Fig. 1: Sampling locations and an analysis scheme a) Samples were taken from various places such as bed rails, tables, bedside tables, door handles, tap taps, pulsometers; b) nalysis scheme for samples collected from selected sites subjected to cell culture, ectraction and sequencing (shotgun metagenomic sequencing, Illumina platform andquasi-metagenomics, GridION). (Chng, K.R., Li, C., Bertrand, D. et al.)

 

 

 

 

 

Quasi-metagenomics using nanopore technology has supplied thousands of genomes with complex, phage and plasmid sequences, featuring resilient and movable diversity and dynamic architecture in the hospital setting. Phylogenetics has found multi-drug resistant strains to be widespread and stable to colonize in many places. Clinical comparison with hospital isolates showed that such microorganisms can survive in hospitals over a longer-term (>8 years) to opportunistically infect the patient.

 

References

1) Chng, K.R., Li, C., Bertrand, D. et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med (2020). https://doi.org/10.1038/s41591-020-0894-4