Overestimated discriminatory power of MALDI-TOF mass spectrometry for typing of carbapenem-resistant Klebsiella pneumoniae clones.

Fei Jiang,Ping Ma,Bing Gu,Ziyan Kong,Haiquan Kang,Chen Cheng

doi:10.1017/s0950268819002097

Abstract

Homology surveillance of carbapenem-resistant Klebsiella pneumoniae (CRKP) is critical to monitor and prevent outbreaks of nosocomial infections. In the present study, a matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF MS)-based method was evaluated as a rapid tool for typing CRKP in comparison with pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST). Drug-resistant phenotypes and genotypes of 44 CRKP isolates were detected by microdilution broth method and polymerase chain reaction, and typed by PFGE, MLST and MALDI-TOF MS. Simpson's Index of Diversity was used to evaluate taxonomic diversity, Adjusted Rand Index (ARI) for congruence between the typing methods and Wallace coefficients (W) for the ability of either method to predict each other. Forty-four CRKP isolates of 15 sequence types (STs) produced either NDM-1 (n = 16), NDM-5 (n = 9) or KPC-2 (n = 19) carbapenemases. PFGE differentiated these isolates into 16 distinct types, and two deoxyribonucleic acid profiles were assigned to ST337 and ST11, respectively. MALDI-TOF MS failed to clearly delineate between clusters on dendrograms based on principal components analysis and main spectrum profile. The chosen parameters resulted in a maximum ARI of 0.310 (95% CI 0.088-0.531) between MALDI-TOF MS typing and the PFGE reference, indicating a low ability of the former to correctly identify related isolates. Likewise, the maximum W coefficient of 0.367 (95% CI 0.203-0.532) showed that MALDI-TOF MS had a lower predictive power than PFGE. We conclude that MALDI-TOF MS lacks the discriminatory power necessary for clone assignment of CRKP isolates and consequently cannot be considered as a rapid and creditable method for this purpose.

Highlights

Klebsiella pneumoniae is one of the most common pathogens associated with community-acquired and hospital-acquired infections
Phylogenetic trees derived from the pulsed-field gel electrophoresis (PFGE) analysis separated all 44 carbapenem-resistant K. pneumoniae (CRKP) isolates into 16 clusters (PC1–PC16) according to 80% similarity while multilocus sequence typing (MLST) differentiated all isolates into 15 clusters
By Simpson’s DI scores, MALDI-TOF MS (DI = 0.614, 95% CI 0.522–0.707) was less discriminating than PFGE (DI = 0.805, 95% CI 0.721–0.890) and MLST (DI = 0.791, 95% CI 0.704–0.877)

Summary

Introduction

Klebsiella pneumoniae is one of the most common pathogens associated with community-acquired and hospital-acquired infections. The mortality in patients with carbapenem-resistant K. pneumoniae (CRKP) infection has been increasing [1 2]. According to national bacterial resistance monitoring data of China Antimicrobial Surveillance Network, the detection rate of CRKP increased from 5% in 2008 to 25% in 2018. The increasing number of nosocomial outbreaks due to CRKP worldwide has presented great challenges for clinical treatment, prevention and control of such infections [3,4,5,6]. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) are widely used techniques for molecular typing of bacteria. Whole genome sequencing is increasingly replacing PFGE and MLST as a gold standard for molecular typing of bacteria [7], it is, in keeping with the foregoing techniques, time-consuming and expensive and not suitable for real-time surveillance of nosocomial infections

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