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Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae

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Abstract

Enterococcus phage Nonaheksakonda was isolated from wastewater, using a vancomycin-resistant strain of the opportunistic pathogen Enterococcus faecalis (VRE) as a host. Nonaheksakonda is a lytic phage infecting E. faecalis V583 and clinical isolates with at least four different multi-locus sequence types (MLSTs). The genome is a 41.9-kb double-stranded DNA molecule (34.6% GC) with 74 coding sequences. Comparative analysis revealed only one close relative, Enterococcus phage heks. All other phages had low protein similarity and shared less than 54% nucleotide sequence identity with phage Nonaheksakonda. The most similar phages were all classified and unclassified efquatroviruses. We propose that the phages Nonaheksakonda and heks represent a novel genus within the family Siphoviridae, order Caudovirales, for which we propose the name “Nonaheksakondavirus”.

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Acknowledgements

The authors thank senior scientist Henrik Hasman (Statens Serum Insittut, SSI) for supplying us with clinical isolates of Enterococcus faecalis, and Aalborg Forsyning Wastewater Treatment Plant East, a member of the Danish Water and Wastewater Association (DANVA), who supplied us with wastewater samples.

Funding

This research was funded by Villum Experiment Grant 17595, Aarhus University Research Foundation AUFF Grant E-2015-FLS-7-28 to Witold Kot, and Lars Hestbjerg Hansen’s Human Frontier Science Program Grant: RGP0024/2018.

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Authors and Affiliations

  1. Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark

    Nikoline S. Olsen, Katrine Johansen Nielsen, Maja Plöger, Witold Kot & Lars Hestbjerg Hansen

  2. Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark

    Nikoline S. Olsen

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  1. Nikoline S. Olsen
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  2. Katrine Johansen Nielsen
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Contributions

All authors contributed to the study conception and design. Nikoline S. Olsen and Katrine Johansen Nielsen contributed equally. Material preparation, data collection and analysis were performed by Nikoline S. Olsen and Katrine Johansen Nielsen. The first draft of the manuscript was written by Katrine Johansen Nielsen, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Nikoline S. Olsen or Lars Hestbjerg Hansen.

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Conflict of interest

The authors declare no conflicts of interest or competing interests.

Availability of data and material

The full genome sequences of Enterococcus phage Nonaheksakonda (MK125140) is available in the NCBI GenBank database.

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Supplementary Information

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705_2020_4905_MOESM1_ESM.pdf

Supplementary file1 Online resource 1: Putative functions and percent amino acid sequence identity (BLASTp) for 10 of the Nonaheksakonda coding sequences (CDS). Online resource 2: BLASTn hits for phage Nonaheksakonda with >35% nucleotide similarity. Online resource 3: Similarity heatplot (Gegenees, BLASTx algorithm) (PDF 414 KB)

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Olsen, N.S., Nielsen, K.J., Plöger, M. et al. Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae. Arch Virol 166, 593–599 (2021). https://doi.org/10.1007/s00705-020-04905-y

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