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Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

Mark de Been, Mette Pinholt, Janetta Top

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|September 25, 2015

Summary

A new core genome multilocus sequence typing (cgMLST) scheme for Enterococcus faecium provides high-resolution, standardized outbreak tracing. This method surpasses traditional MLST and matches whole-genome sequencing SNP analysis for improved surveillance of this multidrug-resistant pathogen.

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Area of Science:

Microbiology
Epidemiology
Genomics

Background:

Enterococcus faecium is a significant multidrug-resistant nosocomial pathogen.
Conventional multilocus sequence typing (MLST) offers limited resolution for tracking E. faecium outbreaks.
Whole-genome sequencing (WGS) provides high resolution but lacks standardization for interlaboratory surveillance.

Purpose of the Study:

To develop a standardized core genome MLST (cgMLST) scheme for Enterococcus faecium.
To enhance the discriminatory power and portability of molecular typing for E. faecium surveillance.

Main Methods:

Developed an E. faecium cgMLST scheme using 40 diverse genome sequences, targeting 1,423 genes.
Applied the cgMLST scheme to whole-genome sequencing data from 103 outbreak isolates across multiple European hospitals.
Compared cgMLST performance against conventional MLST and single nucleotide polymorphism (SNP)-based WGS analysis.

Main Results:

The cgMLST scheme demonstrated high discriminatory power, distinguishing epidemiologically related from unrelated isolates, including those with identical MLST sequence types (STs).
cgMLST resolution was equivalent to SNP-based WGS analysis.
The scheme proved effective in tracing outbreaks across different hospital settings and countries.

Conclusions:

The developed E. faecium cgMLST scheme offers a rapid, standardized, and high-resolution method for outbreak tracing.
This cgMLST approach overcomes limitations of traditional MLST and current WGS methods for prospective surveillance.
Facilitates improved public health response to multidrug-resistant E. faecium infections.