Using core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide...

Area of Science:

• Microbiology
• Epidemiology
• Genomics

Background:

• Vancomycin-resistant Enterococcus faecium (VREfm) cases increased significantly at Odense University Hospital after July 2016.
• Previous detection of VREfm was sporadic before July 2016.

Purpose of the Study:

• To apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to analyze VREfm isolates.
• To compare local VREfm isolates with national cgMLST data to trace transmission routes.
• To investigate the outbreak of VREfm at a single Danish hospital.

Main Methods:

• Whole-genome sequencing was used to analyze 38 VREfm clinical isolates collected between January 2014 and June 2017.
• SeqSphere+ software was utilized for Multi-Locus Sequence Typing (MLST), cgMLST, and epidemiological curve generation.
• Admission histories and national cgMLST surveillance data were integrated to identify transmission pathways.

Main Results:

• Six sequence types (STs) were identified, with ST80, ST117, and ST203 being the most prevalent.
• cgMLST analysis resolved the 38 isolates into 18 distinct complex types (CTs), with ST80-CT993 comprising 34% of isolates.
• Epidemiological curves indicated ST80-CT993 transmission across multiple hospital departments; however, transmission from inter-hospital transfers was not detected.

Conclusions:

• High-resolution cgMLST provided detailed insights into nosocomial transmission of specific VREfm complex types.
• Comparison with national data facilitated clarification of transmission routes.
• cgMLST, combined with patient admission histories, effectively targeted epidemiological investigations and informed infection control measures, leading to outbreak containment.