Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing

Novais, Ângela; Freitas, Ana R.; Rodrigues, Carla; Peixe, Luı́sa

doi:10.1007/s10096-018-3431-3

Cited by 112 publications

(97 citation statements)

References 181 publications

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“…Differentiation of K types by FT-IR spectroscopy. FT-IR spectroscopy detects variation of the vibrational modes of chemical bonds that are exposed to infrared radiation, and when applied to bacterial cells, it provides a highly specific wholeorganism fingerprint that reflects their biochemical composition (22). The methodology we used is simple and inexpensive, since one bacterial colony is directly applied to an instrument with small amounts of consumables and low maintenance (see Materials and Methods for further details).…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, the time to result is very short, since one isolate can be typed in ca. 5 to 10 min at a lower cost (from 30%) than with competing DNA-based methods (22). Hence, we evaluated the ability of this methodology to differentiate the 19 K. pneumoniae K types or other surface structures.…”

Section: Resultsmentioning

confidence: 99%

“…Fourier transform infrared (FT-IR) spectroscopy has been shown to detect surface phenotypic differences linked to a variable composition on glycan structures that form part of the O and K antigens, depending on the bacterial species (22)(23)(24)(25). Considering that the capsule is the outermost structure of K. pneumoniae, we hypothesize that FT-IR spectroscopy is a reliable tool to detect variations on K. pneumoniae capsule composition, as observed for other capsulated bacteria (26,27).…”

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confidence: 87%

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A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool

et al. 2020

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 87%

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A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool

et al. 2020

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“…The same spectral region was previously reported to be highly discriminatory for several bacterial species including other relevant clinical or food pathogens such as Escherichia coli, Acinetobacter baumannii, Salmonella enterica, Staphylococcus aureus or Streptococcus pneumoniae 24–26,34,35 . Some of these studies have also pointed-out a correlation with variation on bacterial serogroups or capsules, supporting the importance of surface polysaccharides as discriminatory biomarkers 22 .…”

Section: Discussionmentioning

confidence: 87%

“…Fourier transform infrared (FT-IR) spectroscopy has been shown to detect surface phenotypic differences linked to a variable composition on glycan structures that form part of the O and K antigens, depending on the bacterial species 22–25 . Considering that the capsule is the outermost structure of Kp , we hypothesize that FT-IR spectroscopy is a reliable tool to detect variations on Kp capsule composition, as observed for other capsulated bacteria 26,27 .…”

Section: Introductionmentioning

confidence: 99%

On the front line of Klebsiella pneumoniae surface structures understanding: establishment of Fourier Transform Infrared (FT-IR) spectroscopy as a capsule typing method

Rodrigues

Sousa

Lopes

et al. 2019

Preprint

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Genomics-based population analysis of multidrug resistant (MDR) Klebsiella pneumoniae (Kp) motivated a renewed interest on capsule (K) types given their importance as evolutionary and virulence markers of clinically relevant strains. However, there is a gap between genotypic based predictions and information on capsular polysaccharide structure and composition. We used molecular genotypic, comparative genomics, biochemical and phenotypic data on the cps locus to support the usefulness of Fourier-Transform Infrared (FT-IR) spectroscopy as a phenotypic approach for K-type characterization and identification. The approach was validated with a collection of representative MDR Kp isolates from main lineages/Clonal Groups (CGs) involved in local or nationwide epidemics in 6 European and South American countries. FT-IR-based K-type assignments were compared with those obtained by genotypic methods and WGS (cps operon), and further complemented with data on the polysaccharide composition and structure of known K-types.We demonstrate that our FT-IR-based spectroscopy approach can discriminate all 21 K-types identified with a resolution comparable (or even higher) to that provided by WGS, considered gold-standard methodology. Besides contributing to enlighten K-type diversity among a significant MDR Kp collection, the specific associations between certain K-types and Kp lineages identified in different geographic regions over time support the usefulness of our FT-IR-based approach for strain typing. Additionally, we demonstrate that FT-IR discriminatory ability is correlated with variation on the structure/composition of known K-types and, supported on WGS data, we were able to predict the sugar composition and chemical structure of new KL-types. Our data revealed an unprecedent resolution at a quick and low-cost rate of Kp K-types at the phenotypic level. Our FT-IR spectroscopy-based approach might be extremely useful not only as a cost-effective Kp typing tool, but also to improve our understanding on sugar-based coating structures of high relevance for strain evolution and host adaptation.

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Chemical sensing of common microorganisms found in biopharmaceutical industries using MIR laser spectroscopy and multivariate analysis

Carrión‐Roca,

Colón‐Mercado,

Castro‐Suarez

et al. 2024

Journal of Biophotonics

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Mid‐infrared laser spectroscopy was used to investigate common bacteria encountered in biopharmaceutical industries. The study involved the detection of bacteria using quantum cascade laser spectroscopy coupled to a grazing angle probe (QCL‐GAP). Substrates similar to surfaces commonly used in biopharmaceutical industries were used as support media for the samples. Reflectance measurements were assisted by Multivariate Analysis (MVA) to assemble a powerful spectroscopic technique with classification and identification resources. The species analyzed, Staphylococcus aureus, Staphylococcus epidermidis, and Micrococcus luteus, were used to challenge the technique's capability to discriminate from microorganisms of the same family. Principal Components Analysis and Partial Least Squares‐Discriminant Analysis differentiated between the bacterial species, using QCL‐GAP‐MVA as the reference. Spectral differences in the bacterial membrane were used to determine if these microorganisms were present in the samples analyzed. Results herein provided effective discrimination for the bacteria under study with high sensitivity and specificity.

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Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing

Cited by 112 publications

References 181 publications

A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool

A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool

On the front line of Klebsiella pneumoniae surface structures understanding: establishment of Fourier Transform Infrared (FT-IR) spectroscopy as a capsule typing method

Chemical sensing of common microorganisms found in biopharmaceutical industries using MIR laser spectroscopy and multivariate analysis

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