Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings
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ABSTRACT:
SUBMITTER: Zendri F
PROVIDER: S-EPMC10869444 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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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.
| S-EPMC7093823 | biostudies-literature
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.
| S-EPMC8473902 | biostudies-literature
Project description:Early use of infection control methods is critical for preventing the spread of antimicrobial resistance. Whole-genome sequencing (WGS) is considered the gold standard for investigating outbreaks; however, the turnaround time is usually too long for clinical decision-making and the method is also costly. The aim of this study was to evaluate the performance of Fourier transform infrared (FTIR) and artificial intelligence tools as a first-line typing tool for typing carbapenemase-producing Klebsiella pneumoniae (CPK) in the hospital setting. For this purpose, we analyzed 365 CPK isolates from two tertiary hospitals in Spain in parallel by applying unsupervised principal component analysis (PCA) and supervised algorithms (artificial neural network [ANN], support vector machine [SVM] linear, SVM radial basis function in the IR Biotyper software, and random forest in the Clover MSDAS software). Concordance with FTIR clustering considering the sequence type (ST) and the clonal cluster, obtained by cgMLST for reference purposes, was measured using the adjusted Wallace index (AWI), yielding values of 0.611 and 0.652, respectively. Different regions of the spectra were studied in relation to repeatability and reproducibility, and the polysaccharides region proved the best for FTIR differential analysis. The best results for accuracy were obtained using the ANN algorithm in the IR Biotyper software, with 80.5% of correct prediction. Regarding accuracy, the poorest results were obtained for isolates belonging to ST392 (55.5%) and the best results for ST307 (94.4%). The findings demonstrate the utility of the FTIR method as a rapid, inexpensive, first-line typing tool for detecting CPK, preserving WGS for confirmation and further characterization.
| S-EPMC11784409 | biostudies-literature
Project description:The Fourier transform infrared (FT-IR) signals obtained from bacterial samples are specific and reproducible, making FT-IR an efficient tool for bacterial typing at a subspecies level. However, the typing accuracy could be affected by many factors, including sample preparation and spectral acquisition. Here, we present a unified protocol for bacterial typing based on FT-IR spectroscopy. We describe sample preparation from bacterial culture and FT-IR spectrum collection. We then detail FT-IR spectrum preprocessing and multivariate analysis of spectral data for bacterial typing.
| S-EPMC10130498 | biostudies-literature
Project description:Fourier transform infrared (FT-IR) spectroscopy (IR Biotyper; Bruker) allows highly discriminatory fingerprinting of closely related bacterial strains. In this study, FT-IR spectroscopy-based capsular typing of Streptococcus pneumoniae was validated as a rapid, cost-effective, and medium-throughput alternative to the classical phenotypic techniques. A training set of 233 strains was defined, comprising 34 different serotypes and including all 24 vaccine types (VTs) and 10 non-vaccine types (NVTs). The acquired spectra were used to (i) create a dendrogram where strains clustered together according to their serotypes and (ii) train an artificial neural network (ANN) model to predict unknown pneumococcal serotypes. During validation using 153 additional strains, we reached 98.0% accuracy for determining serotypes represented in the training set. Next, the performance of the IR Biotyper was assessed using 124 strains representing 59 non-training set serotypes. In this setting, 42 of 59 serotypes (71.1%) could be accurately categorized as being non-training set serotypes. Furthermore, it was observed that comparability of spectra was affected by the source of the Columbia medium used to grow the pneumococci and that this complicated the robustness and standardization potential of FT-IR spectroscopy. A rigorous laboratory workflow in combination with specific ANN models that account for environmental noise parameters can be applied to overcome this issue in the near future. The IR Biotyper has the potential to be used as a fast, cost-effective, and accurate phenotypic serotyping tool for S. pneumoniae.
| S-EPMC9297836 | biostudies-literature
Project description:Members of the Enterobacter (E.) cloacae complex have emerged as important pathogens frequently encountered in nosocomial infections. Several outbreaks with E. cloacae complex have been reported in recent years, especially in neonatal units. Fast and reliable strain typing methods are crucial for real-time surveillance and outbreak analysis to detect pathogen reservoirs and transmission routes. The aim of this study was to evaluate the performance of Fourier-transform infrared (FTIR) spectroscopy as a fast method for typing of clinical E. cloacae complex isolates, when whole genome sequencing (WGS) analysis was used as reference. First, the technique was used retrospectively on 24 first isolates of E. cloacae complex strains from neonatal patients and showed good concordance with SNP-based clustering [adjusted rand index (ARI) = 0.818] and with the sequence type (ST) (ARI = 0.801). 29 consecutive isolates from the same patients were shown by WGS analysis to almost always belong to the same SNP cluster as the first isolates, which was only inconsistently recognized by FTIR spectroscopy. Training of an artificial neural network (ANN) with all FTIR spectra from sequenced strains markedly improved the recognition of related and unrelated isolate spectra. In a second step, FTIR spectroscopy was applied on 14 strains during an outbreak with E. cloacae complex and provided fast typing results that were confirmed by WGS analysis. In conclusion, FTIR spectroscopy is a promising tool for strain typing of clinical E. cloacae complex strains. Discriminatory power can be improved by implementing an ANN for spectrum analysis. Due to its low costs and fast turnaround times, the method presents a valuable tool for real-time surveillance as well as outbreak analysis.
| S-EPMC6851243 | biostudies-literature
Project description:Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.
| S-EPMC9218594 | biostudies-literature
Project description: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.
| S-EPMC6204683 | biostudies-literature
Project description:Fourier-transform infrared (FTIR) spectroscopy characterization is a powerful and easy-to-use technique frequently employed for the characterization and fingerprinting of materials. Although MXenes are a large and fastest growing family of inorganic 2D materials, the lack of systematic FTIR spectroscopy studies hinders its application to MXenes and often leads to misinterpretation of the results. In this study, we report experimental and calculated FTIR spectra of 12 most typical carbide and carbonitride MXenes with different compositions (5 transition metals) and all four basic structures, including Ti2CT x , Nb2CT x , Mo2CT x , V2CT x , Ti3C2T x , Ti3CNT x , Mo2TiC2T x , Mo2Ti2C3T x , Nb4C3T x , V4C3T x , Ta4C3T x , and Mo4VC4T x . The measurements were performed on delaminated MXene flakes incorporated in KBr pellets in the 4000-400 cm-1 range. We provide detailed instructions for sample preparation, data collection, and interpretation of FTIR spectra of MXenes. Background correction and spectra smoothing are applied to obtain clear FTIR peaks corresponding to bond vibrations in MXenes. Density functional theory calculations were used for the precise assignment of all characteristic FTIR peaks and an in-depth analysis of the vibration modes. This work aims to provide the 2D material community with the FTIR spectroscopy technique as a reliable method for identifying and analyzing MXenes.
| S-EPMC11393797 | biostudies-literature
Project description:Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.
| S-EPMC10581122 | biostudies-literature