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bioRxiv2018

Klebsiella huaxiensis sp. nov., recovered from human urine

A Klebsiella strain, WCHKl090001, was recovered from a human urine sample in China in 2017. Phylogenetic analysis based on gyrA and rpoB housekeeping genes revealed that the strain was distinct from any previously described species of the genus Klebsiella though it was clustered with the Klebsiella oxytoca phylogroup including Klebsiella grimontii, Klebsiella michiganensis, and Klebsiella oxytoca. The whole genome sequence of strain WCHKl090001 has an up to 87.18% average nucleotide identity with those of type strains of all known Klebsiella species. In silico DNA-DNA hybridization (isDDH) values between strain WCHKl090001 and type strains of all known Klebsiella species range from 22.3 to 35.2%. Strain WCHKl090001 could be distinguished from species of the Klebsiella oxytoca phylogroup by its negative Voges-Proskauer reaction. Genotypic and phenotypic characteristics from this study indicate that strain WCHKl090001 should be considered to represent a novel species of the genus Klebsiella, for which the name Klebsiella huaxiensis sp. nov. is proposed. The type strain is WCHKl090001T (=GDMCC1.1379T = CCTCC AB 2018106 T).

microbiology↗

bioRxiv2017

New kids on the block: Intercontinental dissemination and transmission of newly emerging lineages of multi-drug resistant Escherichia coli with highly dynamic resistance gene acquisition.

The increase in infections as a result of multi-drug resistant strains of Escherichia coli is a global health crisis. The emergence of globally disseminated lineages of E. coli carrying ESBL genes has been well characterised. An increase in strains producing carbapenemase enzymes and mobile colistin resistance is now being reported, but to date there is little genomic characterisation of such strains. Routine screening of patients within an ICU of West China Hospital identified a number of E. coli carrying the blaNDM-5 carbapenemase gene, found to be two distinct clones, E. coli ST167 and ST617. Interrogation of publically available data shows isolation of ESBL and carbapenem resistant strains of both lineages from clinical cases across the world. Further analysis of a large collection of publically available genomes shows that ST167 and ST617 have emerged in distinct patterns from the ST10 clonal complex of E. coli, but share evolutionary events involving switches in LPS genetics, intergenic regions and anaerobic metabolism loci. These may be evolutionary events which underpin the emergence of carbapenem resistance plasmid carriage in E. coli.

microbiology↗