Application of the Bruker IR Biotyper for Strain Typing During An Outbreak

Abstract

Background Molecular typing methods such as whole genome sequencing are relatively time-consuming and expensive. Here we demonstrate the effectiveness of the Bruker IR biotyper in strain typing. Methods Isolates of multi-resistant Enterobacteriacae from clinical samples were typed using the Bruker IR Biotyper. The relationships between isolates were analysed using the Bruker IR biotyper software (version 2.1.0.195). Results On dendrogram analysis, the 13 E. coli isolates mostly clustered independently with all 5 replicates. Two isolates (RFH035 and RFH007) clustered together, their replicates spanning across 3 clusters, indicating that they are the same isolate. This was confirmed on Principle Component Analysis (PCA). EightK. pneumoniaeisolates segregated into 7 clusters. Two isolates (RFH033 and RFH006) clustered together initially but separated on the PCA plot. Discussion RFH035 and RFH007 both came from patients infected with NDM-producing E. coli. Their PFGE profiles are indistinguishable. Both patients were admitted to hospital and were on the same ward simultaneously, reflecting the co-clustering seen with the Bruker IR biotyper. Both RFH033 and 006 were NDM producers, but RFH033 co-produced OXA48. They had almost indistinguishable VNTR profiles with only one difference. This relatedness but difference in resistance profile is reflected in the close relationship seen on dendrogram but separation by PCA seen with the Bruker IR biotyper. The Bruker IR biotyper is therefore able to reliably demonstrate relatedness and discrimination between strains of E. coli and K. pneumoniae. This methodology has much faster turnaround times than conventional methodology, and therefore has the potential to inform outbreak management in a more timely manner.