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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., 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.

The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18 000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6 % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis. Fil: van Tonder, Andries. Wellcome Genome Campus; Fil: Gladstone, Rebecca A.. Wellcome Genome Campus; Fil: Lo, Stephanie W.. Wellcome Genome Campus; Fil: Nahm, Moon H.. University Of Alabama At Birmingahm. School Of Medicine; Estados Unidos Fil: du Plessis, Mignon. National Institute For Communicable Diseases; Sudáfrica. University of the Witwatersrand; Sudáfrica Fil: Cornick, Jennifer. Malawi Liverpool Wellcome Trust; Malaui Fil: Kwambana Adams, Brenda. Vaccines And Immunity Theme; Gambia Fil: Madhi, Shabir A.. University of the Witwatersrand; Sudáfrica Fil: Hawkins, Paulina A.. University Of Emory. Rollins School Of Public Health; Estados Unidos Fil: Benisty, Rachel. Ben Gurion University of the Negev; Israel Fil: Dagan, Ron. Ben Gurion University of the Negev; Israel Fil: Everett, Dean. University of Edinburgh; Reino Unido Fil: Antonio, Martin. Vaccines And Immunity Theme; Gambia Fil: Klugman, Keith P.. University Of Emory. Rollins School Of Public Health; Estados Unidos Fil: von Gottberg, Anne. National Institute For Communicable Diseases; Sudáfrica. University of the Witwatersrand; Sudáfrica Fil: Breiman, Robert F.. University Of Emory. Rollins School Of Public Health; Estados Unidos. University of Edinburgh; Reino Unido Fil: McGee, Lesley. Centers for Disease Control and Prevention; Estados Unidos Fil: Bentley, Stephen D.. Wellcome Genome Campus; . University Of Emory. Emory College Of Arts And Sciences.; Estados Unidos Fil: Faccone, Diego Francisco. Administracion Nacional de Laboratorios E Institutos de Salud "dr. Carlos G. Malbran". Instituto Nacional de Epidemiologia. Departamento de Investigacion.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

Streptococcus parauberis is a pathogen of streptococcosis in turbot Scophthalmus maximus and the Japanese flounder Paralichthys olivaceus. S. parauberis isolates from diseased Japanese flounder have been classified into several serological phenotypes. In this study we analyzed the DNA sequence of the genetic locus for capsular polysaccharide (CPS) biosynthesis of S. parauberis KRS02083 (subserotype Ia), NUF1003 (subserotype Ib), NUF1071 (subserotype Ic), NUF1032 (serotype II), 2007-1 (nontypeable/PFGE cluster I) and NUF1095 (nontypeable/PFGE cluster III) to elucidate the genetic basis for serological diversity. As a result, three kinds of cps locus were revealed among serotypes and subserotypes, namely the loci for subserotype Ia, subserotypes Ib/Ic and serotype II. The genetic structure of cps loci suggests that the capsules of S. parauberis are synthesized through the Wzy-dependent pathway. Subserotypes Ib and Ic possessed the same genetic structure, although single-base substitution at several regions or insertion of an IS (insertion sequence) element was found in subserotype Ic. The nontypeable strains, which agglutinated with both serotypes I and II antisera, possessed the same genetic structure as subserotype Ib/Ic or serotype II with single-base substitution at several regions., Fish Pathology, 50(4), pp.192-199; 2015