Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms

Abstract

Staphylococcus pseudintermedius is historically understood as a prevalent commensal and pathogen of dogs, though modern clinical diagnostics reveal an expanded host-range that includes humans. It remains unclear whether differentiation across S. pseudintermedius populations is driven primarily by niche-type or host-species. We sequenced 501 diagnostic and commensal isolates from a hospital, veterinary diagnostic laboratory, and within households in the American Midwest, and performed a comparative genomics investigation contrasting human diagnostic, animal diagnostic, human colonizing, pet colonizing, and household-surface S. pseudintermedius isolates. Though indistinguishable by core and accessory gene architecture, diagnostic isolates harbor more encoded and phenotypic resistance, whereas colonizing and surface isolates harbor similar CRISPR defense systems likely reflective of common household phage exposures. Furthermore, household isolates that persist through anti-staphylococcal decolonization report elevated rates of base-changing mutations in – and parallel evolution of – defense genes, as well as reductions in oxacillin and trimethoprim-sulfamethoxazole susceptibility. Together we report parallel niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation.

Pathogenic Potential of Coagulase-Positive Staphylococcus Strains Isolated from Aviary Capercaillies and Free-Living Birds in Southeastern Poland

“…The sensitivity of the MALDI TOF method for identifying S. pseudintermedius has been estimated at 78%, and its specificity at 97% [7]. However, in recently published research by Sawhney et al (2023), a comparative analysis of the effectiveness of whole genome sequencing (WGS) and MALDI-TOF MS in identifying staphylococci from the SIG group among 493 strains of S. pseudintermedius and 7 strains of S. delphini showed that MALDI-TOF provides 99.8% and 100% precision in identifying an isolate as S. pseudintermedius and S. delphini, respectively [39]. In our study, log(score) values for S. pseudintermedius and S. delphini isolates obtained in MALDI-TOF mass spectrometry were higher than 2.0, which indicates a high probability of correct identification to the species level (Table 2).…”

“…pseudintermedius virulence factors, like those produced by S. aureus, promote colonisation and infection [19]. Reports indicate that S. pseudintermedius is an opportunistic pathogen that can cause infections of the skin (purulent dermatitis, otitis externa, wound infections, or abscesses), and other tissues and body cavities [19,39,51,52]. The ability to haemolyse blood cells by producing cytolysins is a feature observed in various species of staphylococci.…”

“…These are important factors in the pathogenicity of these bacteria [10]. The pathogenic potential of S. pseudintermedius is determined by virulence factors including coagulase, protein A, protease, enterotoxins, TSST-1 (toxic shock syndrome toxin), exfoliative toxin SIET, and cytolysins, i.e., leukotoxin Luk-I and haemolysins [19,39]. PCR analysis for virulence determinants of strains isolated from capercaillies and free-living birds showed that genes involved in avoidance and invasion (hla and hlb) were the most common in S. aureus isolates.…”