Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

Smith-Zaitlik, T, Shibu, P, McCartney, A, Foster, G, Hoyles, L ORCID: https://orcid.org/0000-0002-6418-342X and Negus, D ORCID: https://orcid.org/0000-0001-9047-4565, 2022. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. Microbiology, 168 (9). ISSN 1350-0872

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Abstract

High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterised two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.

Item Type:	Journal article
Publication Title:	Microbiology
Creators:	Smith-Zaitlik, T., Shibu, P., McCartney, A., Foster, G., Hoyles, L. and Negus, D.
Publisher:	Microbiology Society
Date:	26 September 2022
Volume:	168
Number:	9
ISSN:	1350-0872
Identifiers:	Number Type 10.1099/mic.0.001247 DOI 1591546 Other
Rights:	© Smith-Zaitlik, T., Shibu, P., Mccartney, A., Foster, G., Hoyles, L. and Negus, D. , 2022. The definitive peer reviewed, edited version of this article is published in Microbiology 168 (9), 2022, https://doi.org/10.1099/mic.0.001247. This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial 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:	Laura Ward
Date Added:	18 Aug 2022 08:37
Last Modified:	27 Sep 2022 14:08
URI:	https://irep.ntu.ac.uk/id/eprint/46888

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