Whole Genome Sequencing as a Tool for Identifying Phenotypic Properties and Underlying Genetic Mechanisms in <i>Staphylococcus pseudintermedius</i>

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci and no antibiotic resistance plasmids have been identified in this organism. Due to conflicting reports of antibiotic resistance in clinical MRSP isolates, we hypothesized that genes encoding resistance are carried on mobile genetic elements known to encode variable degrees of resistance which are difficult to identify using standard molecular techniques. Whole genome sequencing was performed on six MRSP isolates, including 3 genomes that were completed and circularized using a combination of short reads, long molecule reads and optical genome maps.

A total of nine plasmids, six of which contain known antibiotic resistance genes, were identified from five genomes using a novel plasmid identification pipeline. Resistance to antibiotics was predicted from genes carried in each isolate, yet did not match susceptibility profiles generated using standard assays. Genes encoding resistance to chloramphenicol and gentamicin were located on mobile elements and displayed delayed resistance in in-vitro susceptibility tests. When cultured in these antibiotics and re-tested they displayed significant antibiotic resistance, suggesting standard assay testing time points may be too short to detect certain types of antibiotic resistance.

These findings suggest that horizontal transfer of clinically relevant genes is common in S. pseudintermedius, and that genome sequencing can be used to identify mobile genetic elements. Predicting phenotypes from underlying genome data can reveal potential for antibiotic resistance not identified using standardized assays.