Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

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Shibu, P, McCuaig, F ORCID: https://orcid.org/0000-0002-6618-7539, McCartney, AL, Kujawska, M, Hall, L and Hoyles, L ORCID: https://orcid.org/0000-0002-6418-342X, 2021. Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microbial Genomics, 7 (6): 000592. ISSN 2057-5858

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Official URL: https://doi.org/10.1099/mgen.0.000592

Abstract

As part of ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. blaOXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to speciate members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7,170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of the complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

Item Type:	Journal article
Publication Title:	Microbial Genomics
Creators:	Shibu, P., McCuaig, F., McCartney, A.L., Kujawska, M., Hall, L. and Hoyles, L.
Publisher:	Microbiology Society
Date:	18 June 2021
Volume:	7
Number:	6
ISSN:	2057-5858
Identifiers:	Number Type 10.1099/mgen.0.000592 DOI 1434470 Other
Rights:	© 2021 the authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Divisions:	Schools > School of Science and Technology
Record created by:	Jonathan Gallacher
Date Added:	30 Apr 2021 13:44
Last Modified:	21 Jun 2021 10:44
URI:	https://irep.ntu.ac.uk/id/eprint/42792