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

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.

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

“…K. oxytoca has been detected in the faeces of a subset of preterm infants via cultivation or shotgun metagenomics, but its association with preterm-associated infections is unknown [1,17,70]. At the DNA level, bacteria characterized phenotypically as K. oxytoca actually represent six phylogroups/distinct species: Ko1, K. michiganensis; Ko2, K. oxytoca; Ko3, Klebsiella spallanzanii; Ko4, Klebsiella pasteurii; Ko6, K. grimontii; Ko8, K. huaxiensis [71][72][73][74][75]. K. michiganensis and K. oxytoca are distinguishable based on the bla OXY gene they carry (bla OXY-1 and bla OXY-2 , respectively) [71].…”

“…K. grimontii was recently described to accommodate Ko6 strains based on rpoB, gyrA and rrs gene sequences [73]. All six members of the complex can be differentiated by matrix-assisted laserdesorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS) [75], but reference databases currently in routine clinical use lack reference spectra for the different species to allow identification beyond K. oxytoca. Consequently, reports on complex members other than K. oxytoca have only recently begun to appear in the literature [73][74][75][76][77].…”

Klebsiella indica sp. nov., isolated from the surface of a tomato

“…This Klebsiella-Raoultella clade further divided into three sub-clades, including two Klebsiella sub-clades and one Raoultella sub-clade. A distinct branch was obtained for strain TOUT106 T on the border of Klebsiella sub-clade II, which comprised K. oxytoca NCTC132727 T and K. michiganensis DSM25444 T , and four recently described species K. grimontii 06D021 T , K. huaxiensis WCHKl090001 T , K. pasteurii SB6412 T and K. spallanzanii SB6411 T [6][7][8]. The genomic DNA G+C content of strain TOUT106 T was 53.53 mol%, which is well within the range (i.e., 53-58 mol%) of the genus Klebsiella [1].…”

“…Strain TOUT106 T is negative for the Voges-Proskauer test, for which the majority of members of Klebsiella are usually positive [1]. Two recently described species, K. spallanzanii and K. huaxensis, also showed a negative Voges-Proskauer test result [6,8]. Strain TOUT106 T showed negative urease activity, while the majority of Klebsiella members are urease-positive [1], except K. michiganensis, K. pastuerii, K. grimontii and K. huaxensis [3,[6][7][8].…”

“…Recently, four novel species of the genus have been described viz., Klebsiella michiganensis [3], Klebsiella quasipneumoniae [4], Klebsiella africana [5] and Klebsiella huaxiensis [6]. The strains previously identified as Klebsiella oxytoca phylogroup Ko6 have been reclassified into a new species Klebsiella grimontii [7], Ko3 as Klebsiella spallanzanii and Ko4 as Klebsiella pasteurii [8]. Members of this genus have been isolated from varied sources including clinical specimens [4][5][6][7][8], soil [9,10], water samples [11], household toothbrush holder [3] and mammalian gut [12].…”