Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus <i>coagulans</i>

Abstract

Staphylococcus schleiferi is an opportunistic pathogen in humans and dogs. Recent taxonomic reassignment of its subspecies (<i>S. schleiferi</i> subsp. <i>schleiferi</i> and <i>S. schleiferi</i> subsp. <i>coagulans</i>) into two separate species (<i>S. schleiferi</i> and <i>S. coagulans</i>) lacks supporting data for diagnostic implications and clinical relevance. We aimed to confirm the reclassification of <i>S. schleiferi</i> by using genomic and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data for a large set of isolates from humans and animals to investigate their molecular epidemiology and clinical relevance. Routine MALDI-TOF analysis and Illumina sequencing were performed on 165 <i>S. schleiferi</i> isolates from the Netherlands. With 33 publicly available genomes, the study included 198 genomes from 149 dogs, 34 humans, and 15 other sources. The Type Strain Genome Server was used to identify species in the genomes, and the MALDI-TOF MS database was extended to improve species differentiation. MALDI-TOF did not discriminate between <i>S. schleiferi</i> and <i>S. coagulans.</i> Genome phylogeny distinguished the two species in two monophyletic clusters. <i>S. schleiferi</i> isolates originated from humans, while <i>S. coagulans</i> isolates were found in animals and three human isolates clustering with the animal isolates. The sialidase B gene (<i>nanB</i>) was a unique marker gene for <i>S. schleiferi</i>, whereas the <i>chrA</i> gene was exclusive for <i>S. coagulans</i>. The <i>mecA</i> gene was exclusively detected in <i>S. coagulans</i>, as were the <i>lnu</i>(A), <i>blaZ</i>, <i>erm</i>(B/C), <i>tet</i>(O/M), and <i>aac</i>(6')-<i>aph</i>(2'') genes. The MALDI-TOF database extension did not improve differentiation between the two species. Even though our whole-genome sequencing-based approach showed clear differentiation between these two species, it remains critical to identify <i>S. schleiferi</i> and <i>S. coagulans</i> correctly in routine diagnostics. <b>IMPORTANCE</b> This study clearly shows that <i>S. schleiferi</i> is a concern in human hospital settings, whereas <i>S. coagulans</i> predominantly causes infections in animals. <i>S. coagulans</i> is more resistant to antibiotics and can sometimes transmit to humans via exposure to infected dogs. Even though genome-based methods can clearly differentiate the two species, current diagnostic methods used routinely in clinical microbiology laboratories cannot distinguish the two bacterial species.