Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

Abstract

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant bla NDM−1-carrying Kluyvera strain 090646 T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95-96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646 T (=GDMCC 1.1872 T =KCTC 82166 T). Strain 090646 T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), Dmannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica

“…The resulting MLSA tree () strongly supported the inclusion of G163CM T within the genus Pseudocitrobacter , as it formed a monophyletic cluster with the two Pseudocitrobacte r type species, and other non-type strains. The MLSA tree displayed substantial higher confidence values for tree branches compared to the 16S rRNA tree and corroborated a previous results [2, 22], that Kluyvera is the sister genus to Pseudocitrobacter . The MLSA tree showed that G163CM T shared a more recent ancestor with P.…”

“…The higher phylogenetic resolution of the core tree based on a larger number of coding sequences, irrespective of amino acid or nucleotide level, indicates with greater confidence that P. vendiensis CPO20170097 T is closer to G163CM T . The core phylogenomic tree is consistent with the placement of the genus Pseudocitrobacter as sister group to the genus Kluyvera [2,22].…”

“…The accepted ANI value threshold for species demarcation is 96% [20], suggesting that strain G163CM T represents a new species. In addition, the ANI values of strain G163CM T and the Pseudocitrobacter type strains were within the average intra-genus range of variation (85-94%) of four other genera (Enterobacter, Escherichia, Klebsiella and Kluyvera) in the family Enterobacteriaceae [21,22], thus supporting the assignment of G163CM T to the genus Pseudocitrobacter. The digital DNA-DNA hybridization (dDDH) values, calculated using the DSMZ TYGS server [23], were 48.8% against P. faecalis CCM 8479 T and 52.4% against P. vendiensis CPO20170097 T (Table 1).…”

“…vendiensis CPO20170097 T is closer to G163CM T . The core phylogenomic tree is consistent with the placement of the genus Pseudocitrobacter as sister group to the genus Kluyvera [2, 22].…”

Antimicrobial resistance determinants in silage

“…CCTCC M2018092 41 , Pantoea agglomerans 42 , Pseudomonas fulva 43 , P. putida 44 , Serratia marcescens 45 . Additional species may join the silage from animals, soil, or water: Acinetobacter gyllenbergii 46 , Citrobacter freundii 47 , Enterobacter asburiae 48 , E. cloacae 49 , E. roggenkampii 50 , E. sichuanensis 51 , Enterococcus faecalis 52 , Klebsiella aerogenes 53 , K. oxytoca 54 , Kluyvera intermedia 55 , Lactococcus garvieae 56 , Latilactobacillus curvatus 57 , Leclercia adecarboxylata 58 , Lelliottia amnigena 59 , Limosilactobacillus reuteri 28 , Providencia rettgeri 60 , Pseudescherichia vulneris 61 , Pseudomonas oryzihabitans 62 , Rhodopseudomonas palustris 63 , Serratia sp. SCBI 64 , Staphylococcus aureus 46 , S. kloosii 65 , S. pseudoxylosus 66 , S. saprophyticus 46 , Enterococcus faecium 52 .…”