Whole genome sequencing and de novo assembly of Staphylococcus pseudintermedius: a pangenome approach to unravelling pathogenesis of canine pyoderma

Background Staphylococcus pseudintermedius is the main aetiological agent of canine pyoderma. Whole genome sequencing is the most comprehensive way of obtaining relevant genomic information about micro‐organisms. Hypothesis/Objectives Oxford Nanopore technology enables quality sequencing and de novo assembly of the whole genome of S. pseudintermedius. Whole genome analysis of S. pseudintermedius may help to better understand the pathogenesis of canine pyodermas. Methods and materials Twenty‐two strains of S. pseudintermedius isolated from the skin of five healthy dogs and 33 strains isolated from skin of 33 dogs with pyoderma were analysed. DNA was extracted and sequenced using Oxford Nanopore MinION, a new technology that delivers longer reads in a hand‐held device. The pangenome was analysed and visualised with Anvi’o 6.1. Results Nanopore technology allowed the sequencing and de novo assembly of the genomes of 55 S. pseudintermedius strains isolated from healthy dogs and from dogs with pyoderma. The average genome size of S. pseudintermedius was 2.62 Mbp, with 48% being core genome. Pyoderma isolates contained a higher number of antimicrobial resistance genes, yet the total number of virulence factors genes did not change between isolates from healthy dogs and from dogs with pyoderma. Genomes of meticillin‐resistant S. pseudintermedius (MRSP) strains were larger than those of meticillin‐susceptible (MSSP) strains (2.80 Mbp versus 2.59 Mbp), as a consequence of a greater presence of antimicrobial resistance genes, phages and prophages. Conclusions and clinical importance This technique allows much more precise and easier characterisation of canine S. pseudintermedius populations and may lead to a better understanding of the pathogenesis of canine pyodermas. Résumé Contexte Staphylococcus pseudintermedius est le principal agent étiologique de la pyodermite canine. Le séquençage du génome entier est le moyen le plus complet d'obtenir des informations génomiques pertinentes sur les micro‐organismes. Hypothèse/Objectifs La technologie Oxford Nanopore permet un séquençage de qualité et un assemblage de novo de l'ensemble du génome de S. pseudintermedius. L'analyse du génome entier de S. pseudintermedius peut aider à mieux comprendre la pathogénie des pyodermites canines. Méthodes et materiel Vingt‐deux souches de S. pseudintermedius isolées de la peau de cinq chiens sains et 33 souches isolées de la peau de 33 chiens atteints de pyodermite ont été analysées.