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

Carla Rodrigues,João A Lopes,Clara Sousa,Luísa Peixe,Ângela Novais,Pieter C Dorrestein

doi:10.1128/msystems.00386-19

Carla Rodrigues, João A Lopes + Show 4 more

Open Access

https://doi.org/10.1128/msystems.00386-19

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Abstract

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.

Highlights

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
Our approach was validated on a collection of 154 well-characterized MDR K. pneumoniae isolates that had been involved in local or nationwide epidemics in different countries from Europe and South America spanning a long period of time (2002 to 2015)
These isolates were selected to capture a diversity of capsular types harbored by the main diverse K. pneumoniae lineages from different clonal groups (CG) that had been involved in human clinical infections and in the expansion of extended-spectrum ␤-lactamases and/or carbapenemases (Table 1)

Summary

Introduction

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. 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. K-type prediction based on allelic variation of loci (e.g., wzi or wzc) within the capsule biosynthetic pathway (cps locus) constitute more rapid and simple approaches (14, 15), but the characterization of the whole cps and rfb (O-antigen biosynthesis) locus by whole-genome sequencing (WGS) improved accessibility and precision, especially through user-friendly Web-based platforms, such as Kaptive (http://kaptive.holtlab.net) (7, 16) These in silico studies and others uncovered a series of novel cps loci and at least 161 presumptive phenotypically distinct capsular types (designated KL to differentiate from the reference K types) (7, 16–18). These data revealed the usefulness of K variation as an epidemiological marker for strain subtyping, encouraging the development of reliable, fast, and highthroughput tools for K typing (7, 17, 19–21)

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