Novel Approach for Differentiating Shigella Species and Escherichia coli by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Khot, Prasanna D.; Fisher, Mark A.

doi:10.1128/jcm.01526-13

Cited by 128 publications

(106 citation statements)

References 28 publications

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“…However, the current IVD and RUO systems and databases cannot differentiate E. coli from Shigella or E. coli from STEC or other E. coli pathotypes and cannot identify Salmonella to the serotype (276). The technology is rapidly approaching these targets, through special extraction protocols and selection of stable, pathogen-specific biomarkers (289)(290)(291)(292), which can be internally verified by individual laboratories. In addition, one or both of the IVD MALDI-TOF systems can be used to identify the other enteric pathogens described in this article, with the exceptions of B. cereus, P. shigelloides, E. albertii, and P. alcalifaciens.…”

Section: Maldi-tof Msmentioning

confidence: 99%

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

2015

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SUMMARY Bacterial gastroenteritis is a disease that is pervasive in both the developing and developed worlds. While for the most part bacterial gastroenteritis is self-limiting, identification of an etiological agent by bacterial stool culture is required for the management of patients with severe or prolonged diarrhea, symptoms consistent with invasive disease, or a history that may predict a complicated course of disease. Importantly, characterization of bacterial enteropathogens from stool cultures in clinical laboratories is one of the primary means by which public health officials identify and track outbreaks of bacterial gastroenteritis. This article provides guidance for clinical microbiology laboratories that perform stool cultures. The general characteristics, epidemiology, and clinical manifestations of key bacterial enteropathogens are summarized. Information regarding optimal specimen collection, transport, and processing and current diagnostic tests and testing algorithms is provided. This article is an update of Cumitech 12A (P. H. Gilligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, Laboratory diagnosis of bacterial diarrhea, 1992).

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Section: Maldi-tof Msmentioning

confidence: 99%

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

2015

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“…The differentiation of E. coli and Shigella species was targeted by Khot et al using a set of strains originating from a wide geographical region (13). The spectral data acquired on a Microflex instrument were analyzed with ClinProTools to establish groupidentifying models using fully automated or manual methods or a hybrid approach.…”

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confidence: 99%

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

et al. 2015

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eThe integration of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been integrated into the routine diagnostic workflow of many industrial, pharmaceutical, and medical microbiology laboratories. It has already been thoroughly evaluated for the identification of clinically relevant bacterial species, including anaerobes, Gram-positive rods and cocci, Enterobacteriaceae, and miscellaneous Gram-negative (including nonfermentative) rods, with adequate to excellent results (1, 2).Species identification, however, is only a first step in the diagnostic workflow. The ability to quickly and reliably distinguish or "type" related bacterial isolates is essential for bacterial transmission studies and larger-scale epidemiological surveillance projects. "Conventional" phenotyping methods, such as multiple-susceptibility testing, phage typing, serotyping, biochemical typing, and several others, have been important contributors to our understanding of the epidemiology of community-and health careassociated infections. However, these methods all have practical limitations which render them largely unsuitable for comprehensive bacterial population analyses as well as for scientifically less ambitious but critical infection surveillance. Furthermore, most phenotypic methods have been developed for individual bacterial taxa and are not transferable to other taxa without considerable adaptation.Hence, over the past 2 decades, phenotyping has been largely replaced by "molecular" genotyping. Clonal reproduction by binary fission imprints the evolutionary history of the organism in genotypic markers amenable to analysis by nucleic acid-mediated methods. However, in practice, the ease with which recombination, transfection, and transformation can take place in bacteria necessitates that data from multiple genetic markers are analyzed in defining a "precise" genotype and even then there is no guarantee that an adequate natural taxonomy will be derived. Polyphasic taxonomy currently uses combinations of different phenotypic and/or genotypic data sets to define genera, species, and entities at or below the subspecies level. Still, all these approaches remain time-consuming and relatively...

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“…All classification algorithms that were generated and tested identified Hib among the H. influenzae isolates, with variations in sensitivity and specificity. The ClinProTools model had the best and most robust results, performing similarly to or better than models based on this software in previous studies (23)(24)(25).…”

Section: Discussionmentioning

confidence: 94%

“…A few recent studies have also been published that use ClinProTools software for bacterial classification, for example, for the differentiation of Shigella species from E. coli and Streptococcus pneumoniae from Streptococcus mitis (23,24). These studies also used ethanol-formic acid extraction.…”

Section: Discussionmentioning

confidence: 99%

Identification of Haemophilus influenzae Type b Isolates by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

et al. 2015

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dHaemophilus influenzae type b (Hib) is, in contrast to non-type b H. influenzae, associated with severe invasive disease, such as meningitis and epiglottitis, in small children. To date, accurate H. influenzae capsule typing requires PCR, a time-consuming and cumbersome method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) provides rapid bacterial diagnostics and is increasingly used in clinical microbiology laboratories. Here, MALDI-TOF MS was evaluated as a novel approach to separate Hib from other H. influenzae. PCR-verified Hib and non-Hib reference isolates were selected based on genetic and spectral characteristics. Mass spectra of reference isolates were acquired and used to generate different classification algorithms for Hib/non-Hib differentiation using both ClinProTools and the MALDI Biotyper software. A test series of mass spectra from 33 Hib and 77 non-Hib isolates, all characterized by PCR, was used to evaluate the algorithms. Several algorithms yielded good results, but the two best were a ClinProTools model based on 22 separating peaks and subtyping main spectra (MSPs) using MALDI Biotyper. The ClinProTools model had a sensitivity of 100% and a specificity of 99%, and the results were 98% reproducible using a different MALDI-TOF MS instrument. The Biotyper subtyping MSPs had a sensitivity of 97%, a specificity of 100%, and 93% reproducibility. Our results suggest that it is possible to use MALDI-TOF MS to differentiate Hib from other H. influenzae. This is a promising method for rapidly identifying Hib in unvaccinated populations and for the screening and surveillance of Hib carriage in vaccinated populations. Haemophilus influenzae type b (Hib) has been, and in some regions still is, the dominating cause of severe invasive disease associated with the species H. influenzae. More specifically, it is (or used to be) a feared cause of meningitis and epiglottitis in small children (1, 2). The conjugate vaccines against Hib that were introduced in the early 1990s have resulted in a steep decline in invasive Hib disease (1, 3-5). However, Hib still causes 5 to 10% of invasive H. influenzae disease in Sweden, and occasional cases of fully vaccinated children with invasive Hib disease have been reported in several countries (6, 7). Hib is estimated to cause a substantial number of infections and deaths among young children each year on a global basis (8). PCR is at present required for accurate Hib capsule typing (9-11) but is a relatively time-consuming and laborious method. Agglutination with antisera is an alternative method used for capsular typing. Even though this is a faster method than PCR, studies have shown that its accuracy is comparatively poor (12).Early studies have suggested that the Hib population consists of two genetically distinct clusters (13,14). This population structure was later confirmed using multilocus sequence typing (MLST), since practically all Hib isolates that had been submitted to the MLST database from all over the world cou...

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Novel Approach for Differentiating Shigella Species and Escherichia coli by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Cited by 128 publications

References 28 publications

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

Identification of Haemophilus influenzae Type b Isolates by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

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