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. 2019 Oct 25:10:2360.
doi: 10.3389/fmicb.2019.02360. eCollection 2019.

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

Cristina Merla  1   2 , Carla Rodrigues  3 , Virginie Passet  3 , Marta Corbella  1 , Harry A Thorpe  4 , Teemu V S Kallonen  5   6 , Zhiyong Zong  7 , Piero Marone  1 , Claudio Bandi  8   9 , Davide Sassera  10 , Jukka Corander  5   6   11 , Edward J Feil  4 , Sylvain Brisse  3
Affiliations

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

Cristina Merla et al. Front Microbiol. .

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.

Keywords: Klebsiella oxytoca complex; MALDI-ToF mass spectrometry; blaOXY; genome sequencing; phylogeny; taxonomy.

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Figures

FIGURE 1
FIGURE 1
Maximum likelihood phylogenetic tree inferred based on the concatenated nucleotide sequence alignments of 3,814 core genes. The tree was rooted using K. pneumoniae DSM 30104T (=ATCC 13883T). Taxonomic groups are indicated in front of the branches. Branch lengths represent the number of nucleotide substitutions per site (scale, 0.01 substitution per site). Bootstrap values are indicated at major nodes. Strain labels are given as Strain Bank ID (e.g., SB73) followed by original strain name, followed by the phylogroup. A “T” after the strain name indicates that the strain is the type strain of its taxon.
FIGURE 2
FIGURE 2
Phylogenetic relationships (neighbor-joining method, Jukes-Cantor correction) based on the concatenated sequences of gyrA and rpoB genes. The tree was rooted using K. pneumoniae DSM 30104T (=ATCC 13883T). Taxonomic groups are indicated in front of the branches. Bootstrap proportions obtained after 1000 replicates are indicated at the nodes. Branch lengths represent the number of nucleotide substitutions per site (scale, 0.01 substitution per site). Strain labels are given as Strain Bank ID (e.g., SB73) followed by original strain name, followed by phylogroup. A “T” after the strain name indicates that the strain is the type strain of its taxon.
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