Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss

Abstract

The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages-20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae-were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I-III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.

Keywords: adaptive environment; bacteriophages; evolution; genomes; staphylococcus.

Figure 1

Phylogeny of 188 S. aureus phages and the Erwinia phage, phiEa2809, based on 681,666 single-nucleotide polymorphisms. The inner ring is colored according to the organism; the middle ring, according to the geographic region; and the outer ring, according to the structural type.

Figure 2

Mosaic structure of the lineage I phage SapYZU11. Functional modules are annotated with different colors. ORFs are shown as arrows, indicating the transcription direction, and the colors of the arrows represent different fragments. Gene color code: virulence determinants, white; holin gene, pink; lysin gene, red; genes associated with lysogeny, purple; bla, green; DNA packaging genes, blue; genes associated with DNA metabolism, yellow; and genes encoding hypothetical proteins, brown.

Figure 3

Mosaic structure of the clade IIa phage, SapYZU15.

Figure 4

Mosaic structure of the clade IIb phage, phiSA_BS2.

Figure 5

Mosaic structure of the clade IIc phage, 676Z.

Figure 6

Comparative structural analysis of clades IIIa–IIIe.

Figure 7

Comparative structural analysis of phage 187 against prophages 4 and 6 of the S. aureus isolate, RJ1267. Areas shaded in gray represent regions with >95% nucleotide sequence identity.

Figure 8

Comparative structural analysis of phage 2368A against a prophage of Staphylococcal pseudintermedius strain SP_11306_4. Areas shaded in gray represent regions with >95% nucleotide sequence identity.

Figure 9

Heat map showing the distribution of holin, lysin, and DNA packaging genes in S. aureus phages. The pattern of gene presence (colored blocks) or absence (white) is shown.