Determinants of Phage Host Range in Staphylococcus Species

Abstract

Bacteria in the genus Staphylococcus are important targets for phage therapy due to their prevalence as pathogens and increasing antibiotic resistance. Here we review Staphylococcus outer surface features and specific phage resistance mechanisms that define the host range, the set of strains that an individual phage can potentially infect. Phage infection goes through five distinct phases: attachment, uptake, biosynthesis, assembly, and lysis. Adsorption inhibition, encompassing outer surface teichoic acid receptor alteration, elimination, or occlusion, limits successful phage attachment and entry. Restriction-modification systems (in particular, type I and IV systems), which target phage DNA inside the cell, serve as the major barriers to biosynthesis as well as transduction and horizontal gene transfer between clonal complexes and species. Resistance to late stages of infection occurs through mechanisms such as assembly interference, in which staphylococcal pathogenicity islands siphon away superinfecting phage proteins to package their own DNA. While genes responsible for teichoic acid biosynthesis, capsule, and restriction-modification are found in most Staphylococcus strains, a variety of other host range determinants (e.g., clustered regularly interspaced short palindromic repeats, abortive infection, and superinfection immunity) are sporadic. The fitness costs of phage resistance through teichoic acid structure alteration could make staphylococcal phage therapies promising, but host range prediction is complex because of the large number of genes involved, and the roles of many of these are unknown. In addition, little is known about the genetic determinants that contribute to host range expansion in the phages themselves. Future research must identify host range determinants, characterize resistance development during infection and treatment, and examine population-wide genetic background effects on resistance selection.

Keywords: CRISPR; host range; phage resistance; phage therapy; staphylococci.

FIG 1

Stages of phage infection and corresponding examples of resistance mechanisms at each stage. Examples not yet identified in the staphylococci are listed in red.

FIG 2

(A) Structure of the staphylococcal cell envelope. Lipoteichoic acid is shown in orange (glycerol phosphate), a surface protein is in black, wall teichoic acid is in orange (glycerol phosphate) and yellow (ribitol phosphate), capsule is in blue, and cell wall carbohydrates are in green (N-acetylglucosamine [GlcNAc]) and purple (N-acetylmuramic acid [MurNAc]). Staphylococcal phages bind WTA and/or its ribitol phosphate modifications (i.e., GlcNAc). (B) Outline of the wall teichoic acid (WTA) biosynthesis pathway, with the proteins corresponding to each step listed in the blue arrows. Abbreviations are defined as follows: C₅₅-P, undecaprenyl phosphate; GlcNAc, N-acetylglucosamine; UDP-GlcNAc, uridine-5-diphosphate-N-acetylglucosamine; ManNAc, N-acetylmannosamine; UDP-ManNAc, uridine-5-diphosphate-N-acetylmannosamine; Gro-P, glycerol phosphate; CDP-Gro, cytidyl diphosphate-glycerol; Rbo-P, ribitol phosphate; CDP-Rbo, cytidyl diphosphate-ribitol; ABC, ATP-binding cassette; and LCP, LytR-CpsA-Psr.

FIG 3

Phage host range for an individual strain is the combination of multiple factors that have different levels of conservation within the species. This is illustrated by a hypothetical phylogenetic tree. Mechanisms can be present throughout strains (1, most conserved; red), present in many strains but with considerable allelic variation (2, conserved but polymorphic; shades of green), or present in a few strains, possibly with allelic variation (3a to 3c, less conserved with potential polymorphism; blue, purple, and yellow, respectively). Branches where mechanisms evolved by mutation or homologous recombination, in the case of mechanisms 1 and 2, or were acquired by HGT, in the case of mechanisms 3a to 3c, are annotated with colored stars. The table on the right summarizes the mechanisms (1 to 3c) present in each strain (strains A to J) using shaded boxes with corresponding colors. Strain J has a mutation that results in the null phenotype for the red mechanism. Host range is the result of the combination of mechanisms present, so strains A to C as well as F, H, and I would be predicted to have identical host ranges, but phage-specific factors could also introduce variability.