Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

Cristina Merla,Jukka Corander,Sylvain Brisse,Edward J Feil,Harry A Thorpe,Virginie Passet,Carla Rodrigues,Teemu V S Kallonen,Piero Marone,Claudio Bandi,Marta Corbella,Zhiyong Zong,Davide Sassera

doi:10.3389/fmicb.2019.02360

Abstract

Klebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4 and Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), K. oxytoca (Ko2), K. huaxiensis (Ko8), and K. grimontii (Ko6). The average nucleotide identity (ANI) of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human feces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4, and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T and DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T and DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow feces, and farm surfaces, while strains of K. pasteurii were found in fecal carriage from humans, cows, and turtles.

Highlights

The genus Klebsiella, a member of the Enterobacteriaceae family, includes Gram-negative, non-motile and non-spore-forming capsulated bacteria
The phylogenomic analysis based on the concatenation of 3,814 core genes (Figure 1) showed six distinct and highly supported branches
The thirteen Ko4 strains were clustered with Ko4 reference strain SG266 (SB3355) and this group was related to, but clearly distinct from, K. grimontii (Ko6)

Summary

Introduction

The genus Klebsiella, a member of the Enterobacteriaceae family, includes Gram-negative, non-motile (except K. aerogenes) and non-spore-forming capsulated bacteria. K. oxytoca carries a chromosomally encoded β-lactamase gene (blaOXY) that confers resistance to amino- and carboxypenicillins (Fournier and Roy, 1997). This gene was shown to have diversified in parallel to housekeeping genes, and variants were classified into seven groups (blaOXY−1 to blaOXY−7) (Granier et al, 2003a,b; Fevre et al, 2005; Izdebski et al, 2015). The aim of this work was to define the taxonomic status of K. oxytoca phylogroups Ko3 and Ko4 and provide identification biomarkers for all members of the K. oxytoca species complex

Objectives

Methods

Results