Genome Sequence Survey Identifies Unique Sequences and Key Virulence Genes with Unusual Rates of Amino Acid Substitution in Bovine Staphylococcus aureus

Abstract

Staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. We here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, RF122, and the recently sequenced human-associated clones, Mu50 and N315, of Staphylococcus aureus. A shotgun sequence survey of ϳ10% of the RF122 genome identified numerous unique sequences and those with elevated rates of nonsynonymous substitution. Taken together, these analyses show that there are notable differences in the genomes of bovine mastitis-associated and human clones of S. aureus and provide a framework for the identification of specific factors associated with host specificity in this major human and animal pathogen.Staphylococcus aureus is a widely distributed animal and human pathogen. Phenotypic analyses of S. aureus strains isolated from human and bovine hosts have revealed important differences between the two populations of isolates, but the underlying genetic basis for the variation among S. aureus strains remains unknown (10,14,15). Multilocus enzyme electrophoretic analysis of 2,077 S. aureus isolates from bovine, ovine, and human hosts showed that only 6 of the 33 clusters included isolates from more than one host species (11). Population genetic analysis of 357 S. aureus isolates recovered from cases of bovine mastitis from global sources suggested that only eight clones represented 90% of the isolates, and these clones rarely overlapped with those responsible for human disease (5). To begin identifying the nature and scope of the genetic differences between the bovine and human staphylococcal genomes, we present here a comparative analysis of the genome content of the common bovine S. aureus clone RF122 (4) and the recently sequenced human pathogenic clones Mu50 and N315 (6).A random shotgun genomic library was prepared as described previously (7), with the exception that RF122 genomic DNA was mechanically sheared with a Hydroshear device (GeneMachines, San Carlos, Calif.). The first 850 random shotgun clones of RF122, encoding 285,077 unique bases and representing approximately 10% of the total genome, were sequenced by using dideoxy terminator chemistry on ABI 3700 DNA sequencers (ABI, Foster City, Calif.) and assembled into 600 contigs consisting of one to six sequences and ranging in size from 82 to 1,828 bases using phredPhrap (P. Green, University of Washington, Seattle) (details of individual genes, gene names, and categories are available at http://www.cbc.umn .edu/ResearchProjects/AGAC/Staph/staphhome.html). The average GC content of the initial sequences was 33.95%, closely approximating the GC content of the completed S. aureus genomes (6). The range of GC contents of individual contigs was 21 to 73%. Fourteen contigs had GC contents greater than 45%. Of these, two had no significant hits (P Ͻ e-15) to any GenBank submission based on tBLASTn searches, five had significant homology to S. aureus genomic DNA, and one was homologous to an S. aureus plasmid (1). The remaining five contig...

Bap-dependent biofilm formation by pathogenic species of Staphylococcus: evidence of horizontal gene transfer?

“…This difference between the human and ruminant mastitis isolates suggests that these strains are not clonally related, and that specific host-dependent pathogenic factors may have evolved independently in both humans and ruminants. This diversity between isolates from different hosts corroborates the results of Herron et al (2002), who, in a preliminary analysis of the genome of a common clone of bovine S. aureus, showed the presence of numerous genes and sequences that differentiate this bovine isolate from previously characterized human S. aureus strains. These differences indicate that a rational and effective strategy to control intramammary infections caused by bovine-specific isolates may be advantageous.…”

The icaA gene in staphylococci from bovine mastitis

“…The pia1/2 failed to recognize the ica in the S. sciuri strains, possibly due to its having a lower homology with S. epidermidis and S. aureus, as shown in Figure 1. Previously, gene diversity has been demonstrated between bovine and human strains of S. aureus [26] and this might also be possible for the ica operon which has been considered to be highly conserved [11]. Our finding that S. sciuri (#V290) was ica positive with fcv primers but was not a biofilm producer might be explained by its not having a complete gene, or because its regulon was not able to produce a biofilm.…”

Multilocus Sequence Typing of Staphylococcus aureus Isolated from High-Somatic-Cell-Count Cows and the Environment of an Organic Dairy Farm in the United Kingdom

“…The detection of previously undescribed alleles may help to explain the seemingly improved ability of some STs of S. aureus compared with those of other more human-associated strains to persist and cause disease following invasion of the mammary gland. Indeed, a bovine mastitis-associated S. aureus clone (RF122) has recently been demonstrated to have elevated rates of nonsynonymous substitutions compared with the sequences of human-associated clones Mu50 and N315, which may relate to host specificity (10).…”