Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant...

Area of Science:

• Clinical microbiology
• Genomic epidemiology
• Infectious disease surveillance

Background:

• Healthcare-associated infections pose a significant threat, driven by multi-drug resistant (MDR) bacteria.
• Rapid identification of transmission is crucial for effective infection control.

Purpose of the Study:

• To evaluate the feasibility and impact of prospective whole-genome sequencing (WGS) for surveillance of MDR bacteria in a hospital setting.
• To identify transmission events and inform infection prevention strategies.

Main Methods:

• Prospective collection of bacterial isolates (MRSA, VRE, CRAB, ESBL-E, CPE) from blood, sterile sites, and screening specimens.
• Whole-genome sequencing (WGS) for in silico multi-locus sequence typing (MLST) and resistance gene profiling.
• Core genome single nucleotide polymorphism (SNP) analysis to detect transmission clusters.
• Integration of clinical metadata and automated reporting to infection control teams.

Main Results:

• Over 4 years, 2660 isolates were sequenced, including significant numbers of CPE, ESBL-E, MRSA, and VRE.
• Genomic analysis identified 76 distinct transmission clusters, with 43 contained within the study hospitals, indicating ongoing local transmission.
• 33 clusters suggested inter-hospital or community transmission.
• Demonstrated impact on infection control policy in one hospital by identifying negligible transmission of specific MRSA strains.

Conclusions:

• Routine WGS for MDR pathogens is feasible in clinical laboratories.
• WGS-based surveillance enables targeted infection prevention and control interventions.
• Genomic surveillance enhances the ability to manage and mitigate the spread of resistant bacteria in healthcare settings.