Multi-species host range of staphylococcal phages isolated from wastewater

Pauline C Göller,Annika Naumann,Ekaterina Khatchatourova,Martin J Loessner,Dominic Lorgé,Felipe Hernandes Coutinho,Elena Gómez-Sanz,Natasa Radulovic,Tabea Elsener,Viona Bernardi,Nesrine Amri

doi:10.1038/s41467-021-27037-6

Pauline C Göller, Annika Naumann + Show 9 more

Open Access

https://doi.org/10.1038/s41467-021-27037-6

Copy DOI

Abstract

The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.

Highlights

The host range of bacteriophages defines their impact on bacterial communities and genome diversity
Using a network-based approach, we further demonstrate that staphylococcal hosts of different species, ecosystems, or antibiotic resistance phenotypes are closely connected through a multitude of phages
Of the initial 30 coagulase-negative staphylococci (CoNS) enrichment hosts, 22 strains were phage susceptible, in contrast to only four of the 16 coagulase-positive staphylococci (CoPS) hosts. This outline resulted in the isolation of 136 phages on CoNS and 19 on CoPS (Supplementary Table 2)

Summary

Introduction

The host range of bacteriophages defines their impact on bacterial communities and genome diversity. A few network studies from a compilation of published data or marine viruses find that phages can infect a multitude of hosts and that different phage types predate each bacterial species[5,6,7] Such interactions have profound implications on how phages influence bacterial community composition and ecology[8,9], or facilitate horizontal gene transfer (HGT)[10,11,12]. Bacteria of the genus Staphylococcus are part of the natural skin microbiota of mammals and represent life-threatening pathogens due to their increasing virulence and antibiotic resistance repertoire Based on their ability to produce coagulase, staphylococci are divided into the traditionally more pathogenic coagulase-positive staphylococci (CoPS), with S. aureus as the major species, and coagulase-negative staphylococci (CoNS), such as S. epidermidis. CoNS are increasingly recognized as major nosocomial pathogens with limited treatment options due to a large proportion of antibiotic-resistant strains[14]

Methods

Results

Conclusion