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Analysis of Streptococcus pneumoniae using Fourier-transformed infrared spectroscopy allows prediction of capsular serotype.

ABSTRACT: Determination of the capsule type of clinical isolates of Streptococcus pneumoniae is a prerequisite for epidemiological studies and further vaccine development. The Quellung reaction for serotyping is expensive and mostly done in reference centres. We wanted to evaluate whether Fourier-transformed infrared (FT-IR) spectroscopy is suitable for capsular type analysis and prediction of pneumococcal serotypes. We used the IR-Biotyper™ (Bruker) to create a database containing the spectra of 120 strains from invasive disease. The strains covered the 24 vaccine serotypes contained in the 13-valent conjugate vaccine (PCV13) and the 23-valent polysaccharide vaccine (PSV23). Hierarchical clustering analysis was performed. Finally, two different classification sets were created (PCV13 and PSV23). They were used to predict the serotype of 168 different challenge strains (invasive and non-invasive disease) covering 48 different serotypes (vaccine and non-vaccine types). FT-IR spectra from pneumococci (1300-800 cm^-1) clustered along their serotype as determined by the Quellung reaction (120 strains, 24 different serotypes). Strains with unknown serotype fell within the cluster of the correct serotype, as long as the latter was represented in the database (168 strains, 48 different serotypes). Concordance between the Quellung reaction and FT-IR spectroscopy was excellent (kappa ??0.75). FT-IR spectroscopy is a fast and cost-effective method to predict the capsular serotype of pneumococci.

SUBMITTER: Burckhardt I

PROVIDER: S-EPMC6778537 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Analysis of Streptococcus pneumoniae using Fourier-transformed infrared spectroscopy allows prediction of capsular serotype.

Burckhardt Irene I Sebastian Kerstin K Mauder Norman N Kostrzewa Markus M Burckhardt Florian F Zimmermann Stefan S

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 20190709 10

Determination of the capsule type of clinical isolates of Streptococcus pneumoniae is a prerequisite for epidemiological studies and further vaccine development. The Quellung reaction for serotyping is expensive and mostly done in reference centres. We wanted to evaluate whether Fourier-transformed infrared (FT-IR) spectroscopy is suitable for capsular type analysis and prediction of pneumococcal serotypes. We used the IR-Biotyper™ (Bruker) to create a database containing the spectra of 120 stra ...[more]

PMID: 31286288

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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.

Project description:BackgroundChina is one of ten countries with the highest prevalence rate of pneumococcal infections. However, there is limited serotype surveillance data for Streptococcus pneumoniae, especially from the community or rural regions, partly due to limited serotyping capacity because Quellung serotyping is only available in few centers in China. The aim of this study was to develop a simple, practical and economic pneumococcal serotype prediction strategy suitable for future serotype surveillance in China.MethodsIn this study, 193 S. pneumoniae isolates were collected from hospitalized children, 96.9 % of whom were < 5 years old. The cpsB sequetyping, complemented by selective and modified USA CDC sequential multiplex-PCR, was performed on all the isolates, and serotypes 6A-6D specific PCRs were done on all serogroup 6 isolates. Based on systematic analysis of available GenBank cpsB sequences, we established a more comprehensive cpsB sequence database than originally published for cpsB sequetyping. Antibiotic susceptibility of all isolates was determined using the disk diffusion or E-test assays.ResultsWe built up a comprehensive S. pneumoniae serotype cpsB sequetyping database for all the 95 described serotypes first, and then developed a simple strategy for serotype prediction based on the improved cpsB sequetyping and selective multiplex-PCR. Using the developed serotype prediction strategy, 191 of 193 isolates were successfully "serotyped", and only two isolates were "non-serotypeable". Sixteen serotypes were identified among the 191 "serotypeable" isolates. The serotype distribution of the isolates from high to low was: 19 F (34.7 %), 23 F (17.1 %), 19A (11.9 %), 14 (7.3 %), 15B/15C (6.7 %), 6B (6.7 %), 6A (6.2 %), 9 V/9A (1.6 %); serotypes 6C, 3, 15 F/15A, 23A and 20 (each 1.1 %); serotypes 10B, 28 F/28A and 34 (each 0.5 %). The prevalence of parenteral penicillin resistance was 1.0 % in the non-meningitis isolates and 88.6 % in meningitis isolates. The total rate of multidrug resistance was 86.8 %.ConclusionsThe integrated cpsB sequetyping supplemented with selective mPCR and serotypes 6A-6D specific PCRs "cocktail" strategy is practical, simple and cost-effective for use in pneumococcal infection serotype surveillance in China. For hospitalized children with non-meningitis penicillin-susceptible pneumococcal infections, clinicians still can use narrow-spectrum and cheaper penicillin, using the parenteral route, rather than using broader-spectrum and more expensive antimicrobials.

Dataset Information

Analysis of Streptococcus pneumoniae using Fourier-transformed infrared spectroscopy allows prediction of capsular serotype.

Publications

Analysis of Streptococcus pneumoniae using Fourier-transformed infrared spectroscopy allows prediction of capsular serotype.

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