Re: ‘Multicentre study evaluating matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibility’ by Shang et al.

Abstract

We read with interest the article by Cheng et al. [[1]Cheng Y.H. Perng C.L. Jian M.J. Cheng Y.H. Lee S.Y. Sun J.R. et al.Multicentre study evaluating matrix-assisted laser desorption ionizationetime of flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibility.Clin Microbiol Infect. 2019; 25: 340-345Abstract Full Text Full Text PDF PubMed Scopus (21) Google Scholar]. This work with regard to the identification of Elizabethkingia species has come at a time when there is a gradual rise in the reporting of Elizabethkingia cases and outbreaks in journals from various parts of the world. We would like to add a few comments to this article. Elizabethkingia is an important emerging pathogen, particularly in healthcare settings. Antimicrobial resistance may vary depending on the species as well as the region and time of bacterial isolation. However, it is not easy to identify the species. Along with phenotypic identification methods such as API 20NE and VITEK 2; Phoenix 100 ID/AST (Becton Dickinson [BD], San Diego, CA, USA) has also been used by certain studies for identification of Elizabethkingia spp. Although it includes E. meningoseptica and E. miricola in its database, Phoenix 100 also has not proved to be reliable for Elizabethkingia identification [2Lin J.N. Lai C.H. Yang C.H. Huang Y.H. Lin H.F. Lin H.H. Comparison of four automated microbiology systems with 16S rRNA gene sequencing for identification of Chryseobacterium and Elizabethkingia species.Sci Rep. 2017; 7: 13824Crossref PubMed Scopus (30) Google Scholar, 3Filho E.B. Marson F.A.L. Levy C.E. Challenges in the identification of Chryseobacterium indologenes and Elizabethkingia meningoseptica in cases of nosocomial infections and patients with cystic fibrosis.New Microbe. New Infect. 2017; 20: 27-33Crossref PubMed Scopus (8) Google Scholar]. In addition, there is evidence of discrepancies in 16S rRNA results because of a few misidentified E. meningoseptica strains in GenBank, which later were identified as E. anophelis by whole-genome sequencing [[4]Lau S.K.P. Wu A.K.L. Teng J.L.L. Tse H. Curreem S.O.T. Tsui S.K.W. et al.Evidence for Elizabethkingia anophelis transmission from mother to infant, Hong Kong.Emerg Infect Dis. 2015; 21: 232-241Crossref PubMed Scopus (53) Google Scholar]. These misidentified strains in the GenBank need to be corrected for reliable 16S rRNA gene sequencing results. Further, only two similar studies have been conducted where the existing database of matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), irrespective of the type of machine used, was amended with species-specific mass spectra from E. anophelis isolates [5Lau S.K.P. Chow W.N. Foo C.H. Curreem S.O.T. Lo G.C.S. Teng J.L.L. et al.Elizabethkingia anopheles bacteremia is associated with clinically significant infections and high mortality.Sci Rep. 2016; 6: 26045Crossref PubMed Scopus (107) Google Scholar, 6Han M.S. Kim H. Lee Y. Kim M. Ku N.S. Choi J.Y. et al.Relative prevalence and antimicrobial susceptibility of clinical isolates of Elizabethkingia species based on 16S rRNA gene sequencing.J Clin Microbiol. 2017; 55: 274-280Crossref PubMed Scopus (72) Google Scholar]. The amended database identified all the Elizabethkingia species (E. meningoseptica, E. anophelis, E. miricola) accurately; however, the major limitation of these expanded databases is that they are not widely available and are meant for research use only. Hence, to be useful for routine clinical microbiologic purposes, there is a need for database upgrades for VITEK 2 and MALDI-TOF MS because they are the most widely used in routine scenarios. Nicholson et al. [[7]Nicholson A.C. Gulvik C.A. Whitney A.M. Humrighouse B.W. Graziano J. Emery B. et al.Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.Antonie Van Leeuwenhoek. 2018; 111: 55-72PubMed Google Scholar], using whole-genome sequencing, optical mapping and MALDI-TOF MS (Bruker Daltonics, Bremen, Germany), recently proposed three novel species under the genus Elizabethkingia: E. bruuniana sp. nov., E. ursingii sp. nov. and Elizabethkingia occulta sp. nov. The Bruker biotyper was used along with the US Centers for Disease Control and Prevention's (CDC) publically available online database (https://microbenet.cdc.gov/), which offers free access to main spectral profiles from the CDC's bacterial collections. It was found that the Bruker and CDC's MicrobeNet database, used together, can reliably identify E. meningoseptica and E. anophelis but cannot distinguish between E. miricola, E. ursingii, E. bruuniana and E. occulta using direct-transfer protocols. Finally, accurate identification along with confirmation is crucial before reporting cases and outbreaks of unusual pathogens such as Elizabethkingia species. Hence, peer reviewers and journal editors must cautiously look for identification confirmation results by 16S rRNA gene sequencing or whole-genome sequencing before publishing reports describing outbreaks of particular Elizabethkingia species. This may prevent false reporting as well as pseudo-outbreaks of this emerging organism. All authors report no conflicts of interest relevant to this article. Multicentre study evaluating matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibilityClinical Microbiology and InfectionVol. 25Issue 3PreviewRapid identification of Elizabethkingia species is essential because these species show variations in antibiotic susceptibility and clinical outcomes. Many recent inaccuracies in Elizabethkingia identification by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) have been noted. Accordingly, in this study, we evaluated the use of MALDI-TOF MS with an amended database to identify isolates of Elizabethkingia anophelis, E. miricola and E. meningoseptica. We then investigated the antimicrobial susceptibility of Elizabethkingia. Full-Text PDF Open Archive‘Multicentre study evaluating matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibility’ – Author's replyClinical Microbiology and InfectionVol. 25Issue 3PreviewWe appreciate the constructive feedback from Rahim et al. [1] and are grateful for the opportunity to reply. Our responses to the comments are as follows. Full-Text PDF Open Archive