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) , Davide Sassera (2) , Jukka Corander (5, 6, 9) , Edward J. Feil (4) , Sylvain Brisse (3)

1 Fondazione IRCCS Policlinico San Matteo [Pavia]
2 UNIPV - Università degli Studi di Pavia = University of Pavia
3 Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens
4 University of Bath [Bath]
5 The Wellcome Trust Sanger Institute [Cambridge]
6 UiO - University of Oslo
7 SCU - Sichuan University [Chengdu]
8 UNIMI - Università degli Studi di Milano = University of Milan
9 Helsingin yliopisto = Helsingfors universitet = University of Helsinki

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.

Mots clés: Klebsiella oxytoca complex; MALDI-ToF mass spectrometry; blaOXY; genome sequencing; phylogeny; taxonomy

Domaines: Biochimie, Biologie Moléculaire; Biodiversité; Santé publique et épidémiologie

Cristina Merla, Carla Rodrigues, Virginie Passet, Marta Corbella, Harry A. Thorpe, et al.. Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.. Frontiers in Microbiology, 2019, 10, pp.2360. ⟨10.3389/fmicb.2019.02360⟩. ⟨pasteur-03329680⟩