Lytic and genomic properties of spontaneous host-range Kayvirus mutants prove their suitability for upgrading phage therapeutics against staphylococci

Tibor Botka,Pavla Havlíčková,Martin Benešík,Roman Pantůček,Vladislav Jakubů,Marian Varga,Ivana Koláčková,Jiří Doškař,Petr Petráš,Martina Florianová,Renáta Karpíšková,Vladislava Růžičková,Ivana Mašlaňová,Helena Žemličková

doi:10.1038/s41598-019-41868-w

Abstract

Lytic bacteriophages are valuable therapeutic agents against bacterial infections. There is continual effort to obtain new phages to increase the effectivity of phage preparations against emerging phage-resistant strains. Here we described the genomic diversity of spontaneous host-range mutants of kayvirus 812. Five mutant phages were isolated as rare plaques on phage-resistant Staphylococcus aureus strains. The host range of phage 812-derived mutants was 42% higher than the wild type, determined on a set of 186 methicillin-resistant S. aureus strains representing the globally circulating human and livestock-associated clones. Comparative genomics revealed that single-nucleotide polymorphisms from the parental phage 812 population were fixed in next-step mutants, mostly in genes for tail and baseplate components, and the acquired point mutations led to diverse receptor binding proteins in the phage mutants. Numerous genome changes associated with rearrangements between direct repeat motifs or intron loss were found. Alterations occurred in host-takeover and terminal genomic regions or the endolysin gene of mutants that exhibited the highest lytic activity, which implied various mechanisms of overcoming bacterial resistance. The genomic data revealed that Kayvirus spontaneous mutants are free from undesirable genes and their lytic properties proved their suitability for rapidly updating phage therapeutics.

Highlights

Lytic bacteriophages are valuable therapeutic agents against bacterial infections
Mutants of phage 812 exhibiting a broader host range were isolated as rare plaques on various S. aureus strains resistant to the parental phage (Fig. 1)
As the phage 812a-derived mutants did not exhibit a satisfactory lytic effect on livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) (LA-MRSA) strains (Supplementary Table S1), a new lineage of mutants represented by phage 812h1 was selected from wild-type phage 812 on phage-resistant LA-MRSA strains (Fig. 1)

Summary

Introduction

Lytic bacteriophages are valuable therapeutic agents against bacterial infections. There is continual effort to obtain new phages to increase the effectivity of phage preparations against emerging phageresistant strains. The genes for host recognition, attachment, and infection are often affected by SNPs or major re-arrangements[11,14,15] The fixation of these genome changes by natural selection enables the phages to recognize new hosts[16] and avoid anti-phage systems[17] such as the type II R-M system Sau3AI in kayviruses[18]. Due to their polyvalence, kayviruses are valuable agents which can be used to treat infections caused by a broad range of S. aureus and even non-S. aureus staphylococcal species[1,3,7]. Spontaneous mutants of phage 812 exhibiting a broad host range on recently circulating methicillin-resistant Staphylococcus aureus (MRSA) strains were isolated. With respect to interest in using the mutants in phage therapy, we focused on deep sequence analysis of their genomes, characterization of genomic variations, and exclusion of potential risks for phage therapy as required by pharmaceuticals authorities[31]

Methods

Results

Conclusion