A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex

Pavlovic, Melanie; Konrad, Regina; Iwobi, Azuka; Sing, Andreas; Busch, Ulrich; Huber, Ingrid

doi:10.1111/j.1574-6968.2011.02479.x

Cited by 82 publications

(41 citation statements)

References 18 publications

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“…instead of Enterobacter kobei). Our result is in agreement with what reported by other previous studies, in which MALDI-TOF MST accurately detects Enterobacter cloacae complex although it may not discriminate some species within this complex [25][26][27].…”

Section: Discussionsupporting

confidence: 83%

Identification and antimicrobial susceptibility testing of microorganisms from positive blood cultures by a combined lysis-centrifugation method with MALDI-TOF MS and VITEK2 System

Rodio

Febbraro

Puggioni

et al. 2017

APALM

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Background: Rapid identification and the application of antimicrobial susceptibility testing (AST) to microorganisms causing bloodstream infections is pivotal to guide antimicrobial therapy. This study aims to: 1) utilize the Lysis-Centrifugation Method (LCM) not only for identification of microorganisms from positive blood culture bottles, but also for direct AST full panel by Vitek ® 2 system (bioMérieux, Inc. France) and by disc diffusion plate (Kirby Bauer Method) and 2) analyze the accuracy of these combined methods.Methods: 124 mono-microbial positive blood culture bottles were included in this study. An aliquot was subjected to LCM and used for the identification by the MALDI-TOF System. Moreover the microbial pellet was used for direct AST testing full panel by VITEK Results: 123 isolates were correctly identified to the species level and 1 isolate was identified to the genus level. Comparing the two utilized AST methods, it was observed that Gram-positive isolates showed an agreement rate of 96.6% (58/60). Enterococcus faecalis was the only microorganism with a major error rate of 0.6% (2/324) related to erythromycin. Among the Gram-negative, the overall agreement rate was 93.3 (56/60). Klebsiella pneumoniae, Escherichia coli and Enterobacter spp. were the major cause of minor error rates (0.6%, 4/709) and major error rates (1.1%, 8/709). Among the yeasts, results showed an agreement rate of 100% (4/4). Conclusions:Our simple and cost-effective sample preparation method is very useful for rapid identification as well as AST of microorganisms directly from positive blood culture bottles in a clinical setting.

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Section: Discussionsupporting

confidence: 83%

Identification and antimicrobial susceptibility testing of microorganisms from positive blood cultures by a combined lysis-centrifugation method with MALDI-TOF MS and VITEK2 System

Rodio

Febbraro

Puggioni

et al. 2017

APALM

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“…Although an obvious demarcation is shown in the dendrogram, differentiation on the basis of the reference library was not possible. Correspondingly, it has been reported for certain members of the family Enterobacteriaceae that the discriminatory power of MALDI-TOF protein profiling can be insufficient for closely related species (He et al 2010;Pavlovic et al 2012).…”

Section: Taxonomic Characterisationmentioning

confidence: 95%

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium

Behrendt

Augustin

Spröer

et al. 2015

Antonie van Leeuwenhoek

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In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.

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“…(108,109). Finally, Pavlovic et al demonstrated that MALDI-TOF MS did not allow differentiation between different tested species of Enterobacter (110).…”

Section: Detection Of Growthmentioning

confidence: 99%

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

et al. 2015

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SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

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A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex

Cited by 82 publications

References 18 publications

Identification and antimicrobial susceptibility testing of microorganisms from positive blood cultures by a combined lysis-centrifugation method with MALDI-TOF MS and VITEK2 System

Identification and antimicrobial susceptibility testing of microorganisms from positive blood cultures by a combined lysis-centrifugation method with MALDI-TOF MS and VITEK2 System

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

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