Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping

Frontiers in Microbiology

Microbiology

Christoph Högenauer¹  Gebhard Feierl²  Eva Leitner²  Franz F. Reinthaler²  Christian Petternel²  Herbert Galler²  Kathrin A. Herzog-Obereder³  Elisabeth Tatscher³  Sandra Raffl⁴  Amar Cosic⁵  Ellen L. Zechner⁶  Sabine Kienesberger⁶ 

[1] BioTechMed-Graz, Graz, Austria;Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria;Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria;Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria;Institute of Molecular Biosciences, University of Graz, Graz, Austria;Institute of Molecular Biosciences, University of Graz, Graz, Austria;BioTechMed-Graz, Graz, Austria;Institute of Molecular Biosciences, University of Graz, Graz, Austria;BioTechMed-Graz, Graz, Austria;Field of Excellence BioHealth, University of Graz, Graz, Austria;

关键词: bacterial phylogeny;    Klebsiella oxytoca;    taxonomic classification;    necrotizing enterocolitis;    bacterial cytotoxicity;    intestinal disease;   

DOI  :  10.3389/fmicb.2021.692453

 received in 2021-04-08, accepted in 2021-05-28,  发布年份 2021

来源: Frontiers

【 摘 要 】

Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (blaOXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting blaOXY and accessory genes defined here.

【 授权许可】

Unknown   
Copyright © 2021 Cosic, Leitner, Petternel, Galler, Reinthaler, Herzog-Obereder, Tatscher, Raffl, Feierl, Högenauer, Zechner and Kienesberger.

【 图 表 】

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