Dataset Information

Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

ABSTRACT: Klebsiella pneumoniae and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination of K. pneumoniae and K. variicola by MALDI-TOF MS.

SUBMITTER: Dinkelacker AG

PROVIDER: S-EPMC6204683 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Dinkelacker Ariane G AG Vogt Sophia S Oberhettinger Philipp P Mauder Norman N Rau Jörg J Kostrzewa Markus M Rossen John W A JWA Autenrieth Ingo B IB Peter Silke S Liese Jan J

Journal of clinical microbiology 20181025 11

<i>Klebsiella pneumoniae</i> and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical <i>Klebsiella</i> isolates in comparison to whole-genome seq ...[more]

PMID: 30135233

Similar Datasets

Project description:Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.

Project description:Genomics-based population analysis of multidrug-resistant (MDR) Klebsiella pneumoniae motivated a renewed interest on the capsule as an evolutionary and virulence marker of clinically relevant strains. Whole-genome sequencing (WGS)-based approaches have provided great insights into the genetic variability of the capsular locus, but genotypic-biochemical capsular (K)-type correlations are lacking, hindering the establishment of a reliable framework for K-type characterization and typing. To fill this gap, we combined molecular, comparative genomics, and multivariate data analysis tools with biochemical data on the capsular locus to support the usefulness of Fourier transform infrared (FT-IR) spectroscopy as a reliable K typing tool. To validate our approach, we used a representative collection of well-defined MDR K. pneumoniae lineages involved in local or nationwide epidemics in multiple countries. With this, we demonstrate a high accuracy and resolution of our FT-IR-based spectroscopy approach for K-type discrimination that is even higher than that provided by WGS. Moreover, the specific associations established between certain K types and specific K. pneumoniae lineages with high clinical relevance, together with the accuracy, simplicity, short time to result, and inexpensive features of the method, support the value of the developed FT-IR-based approach for an easy, fast, and cost-effective strain typing. This fulfills a still unmet need for tools to support real-time monitoring and control of K. pneumoniae infections. In addition, the genotypic-biochemical correlations established provide insights on sugar composition/structure of newly defined K. pneumoniae capsular types.IMPORTANCE Klebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity.

Dataset Information

Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Publications

Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets