Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8.

Vera Morozova,Yuliya Kozlova,Alevtina Bardasheva,Ivan Baykov,Olga Bokovaya,Tatyana Ushakova,Elena Ryabchikova,Artem Tikunov,Ekaterina Zelentsova,Nina Tikunova,Igor Babkin

doi:10.3390/v11121115

Abstract

Klebsiella pneumoniae is a common pathogen, associated with a wide spectrum of infections, and clinical isolates of K. pneumoniae often possess multiple antibiotic resistances. Here, we describe a novel lytic N4-like bacteriophage KP8, specific to K. pneumoniae, including its genome, partial structural proteome, biological properties, and proposed taxonomy. Electron microscopy revealed that KP8 belongs to the Podoviridae family. The size of the KP8 genome was 73,679 bp, and it comprised 97 putative open reading frames. Comparative genome analysis revealed that the KP8 genome possessed the highest similarity to the genomes of Enquatrovirus and Gamaleyavirus phages, which are N4-like podoviruses. In addition, the KP8 genome showed gene synteny typical of the N4-like podoviruses and contained the gene encoding a large virion-encapsulated RNA polymerase. Phylogenetic analysis of the KP8 genome revealed that the KP8 genome formed a distinct branch within the clade, which included the members of Enquatrovirus and Gamaleyavirus genera besides KP8. The average evolutionary divergences KP8/Enquatrovirus and KP8/Gamaleyavirus were 0.466 and 0.447 substitutions per site (substitutes/site), respectively, similar to that between Enquatrovirus and Gamaleyavirus genera (0.468 substitutes/site). The obtained data suggested that Klebsiella phage KP8 differs from other similar phages and may represent a new genus within the N4-like phages.

Highlights

Klebsiella pneumoniae is a Gram-negative, non-motile, non-sporulating bacterium belonging to the Klebsiella genus of the Enterobacteriaceae family
The strain K. pneumoniae CEMTC 356 was used as a host strain for isolation of the bacteriophage
Phylogenetic analysis showed that the CEMTC 356 wzi gene sequence differed from all available wzi genes of Klebsiella reference strains (Figure 1), so the host strain had a Klebsiella capsular types (K-types) different from previously found K-types

Summary

Introduction

Klebsiella pneumoniae is a Gram-negative, non-motile, non-sporulating bacterium belonging to the Klebsiella genus of the Enterobacteriaceae family. Members of the Klebsiella genus are widespread in nature and found in soil, sewage, plants, and the intestinal tract of humans and animals. K. pneumoniae is a common pathogen, associated with a wide spectrum of infections, such as pneumonia, urinary tract infections, intra-abdominal infections, bloodstream infections, meningitis, and pyogenic liver abscesses [1]. The Klebsiella capsular polysaccharides are one of the major factors of virulence [2] and currently more than 80 variants of Klebsiella capsular types (K-types) are known [3]. Each K-type is associated with particular genes in the cluster of capsular synthesis (cps). The cps cluster has a mosaic structure with a group of six conserved genes (galF, orf, wzi, wza, wzb, and wzc) at the Viruses 2019, 11, 1115; doi:10.3390/v11121115 www.mdpi.com/journal/viruses

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