Evaluation of a Novel MALDI Biotyper Algorithm to Distinguish Mycobacterium intracellulare From Mycobacterium chimaera.

Markus Timke,Markus Kostrzewa,Niels K Helstrom,L Elaine Epperson,David Durbin,Michael Strong,Paul Godo,Nabeeh A Hasan,Gongyi Shi,Max Salfinger

doi:10.3389/fmicb.2018.03140

Abstract

Accurate and timely mycobacterial species identification is imperative for successful diagnosis, treatment, and management of disease caused by nontuberculous mycobacteria (NTM). The current most widely utilized method for NTM species identification is Sanger sequencing of one or more genomic loci, followed by BLAST sequence analysis. MALDI-TOF MS offers a less expensive and increasingly accurate alternative to sequencing, but the commercially available assays used in clinical mycobacteriology cannot differentiate between Mycobacterium intracellulare and Mycobacterium chimaera, two closely related potentially pathogenic species of NTM that are members of the Mycobacterium avium complex (MAC). Because this differentiation of MAC species is challenging in a diagnostic setting, Bruker has developed an improved spectral interpretation algorithm to differentiate M. chimaera and M. intracellulare based on differential spectral peak signatures. Here, we utilize a set of 185 MAC isolates that have been characterized using rpoB locus sequencing followed by whole genome sequencing in some cases, to test the accuracy of the Bruker subtyper software to identify M. chimaera (n = 49) and M. intracellulare (n = 55). 100% of the M. intracellulare and 82% of the M. chimaera isolates were accurately identified using the MALDI Biotyper algorithm. This subtyper module is available with the MALDI Biotyper Compass software and offers a promising mechanism for rapid and inexpensive species determination for M. chimaera and M. intracellulare.

Highlights

From the initial strain collection, 185 isolates were identified by rpoB amplicon sequencing as one of the three prominent clinical Mycobacterium avium complex (MAC) species, 74 M. avium, M. intracellulare, and M. chimaera
These 185 strains were analyzed using MALDI-TOF MS at National Jewish Health, in Denver, Colorado, United States and the data were re-analyzed in Bremen, Germany, yielding identical results according to the Biotyper 4.0 software
Our findings indicate that a call of M. chimaera by the Bruker subtyping algorithm tested here is correct every time for a positive predictive value of 100%

Summary

Introduction

Species identification of bacteria is honed to strain-specific and subspecies distinctions in many cases (Neville et al, 2011; Huang et al, 2018) as well as the characterization of nonbacterial organisms such as fungi (Chalupova et al, 2014; Levesque et al, 2015) These approaches are relatively rapid, inexpensive, and accurate for use in clinical diagnostics (Neville et al, 2011), environmental sample analysis, food safety, and other applications (Carbonnelle et al, 2011; Florio et al, 2018). Bruker Daltonik (Bremen, Germany) developed a commercially available algorithm to differentiate M. chimaera and M. intracellulare from each other using only MALDI-TOF peak data This algorithm was found to perform well against 59 bacterial isolates of European origin using the internal transcribed spacer (ITS) sequence to identify species (Pranada et al, 2017). Sequence from the rpoB locus was used to determine species, but in 16 discrepant cases, the isolates were whole genome sequenced and species identity was determined using phylogenomics

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