Comparative analysis of IR-Biotyper, MLST, cgMLST, and WGS for clustering of vancomycin-resistant Enterococcus...

Area of Science:

• Microbiology and Infectious Diseases
• Genomic Epidemiology
• Healthcare Epidemiology

Background:

• Healthcare-associated infections (HAIs) caused by vancomycin-resistant Enterococcus faecium (VREFM) present a significant clinical challenge.
• Accurate and rapid determination of bacterial isolate relatedness is crucial for effective outbreak management in healthcare settings.
• Neonatal intensive care units (NICUs) are particularly vulnerable to VREFM outbreaks due to susceptible patient populations.

Purpose of the Study:

• To evaluate the efficacy of the IR-Biotyper for confirming VREFM nosocomial outbreaks in a NICU setting.
• To compare the performance of IR-Biotyper against established methods like multilocus sequencing typing (MLST), core-genome MLST (cgMLST), and whole-genome sequencing (WGS).
• To determine an optimal clustering cutoff for the IR-Biotyper and assess its within-run precision.

Main Methods:

• Analysis of twenty VREFM isolates from four neonates and ten control isolates using IR-Biotyper, MLST, cgMLST, and WGS.
• IR-Biotyper analysis performed on bacterial colonies after 24-hour incubation.
• Determination of optimal IR-Biotyper clustering cutoff by comparing results with WGS data; assessment of clustering concordance using adjusted Rand and Wallace indices.

Main Results:

• MLST and cgMLST identified sequence types and complex types consistent with a VREFM outbreak, predominantly ST17 and CT6553, which were confirmed by WGS.
• The proposed optimal clustering cutoff range for the IR-Biotyper was determined to be 0.106-0.111.
• Despite lower within-run precision, the IR-Biotyper demonstrated favorable clustering concordance with WGS, meeting criteria for real-time screening and showing high discriminatory power.

Conclusions:

• The IR-Biotyper successfully confirmed a nosocomial VREFM outbreak in a NICU, demonstrating promising results compared to MLST.
• The IR-Biotyper shows potential as a valuable real-time screening tool for detecting VREFM-related nosocomial outbreaks.
• Further improvements in within-run precision are recommended for the IR-Biotyper, but its high discriminatory power and concordance with WGS are significant advantages.