Comparative genome analyses of Staphylococcus aureus from platelet concentrates reveal rearrangements involving loss of type VII secretion genes

<i>Staphylococcus aureus</i> has been involved in transfusion-transmitted fatalities associated with platelet concentrates (PCs) due to its heightened pathogenicity enhanced by genome-encoded virulence and antibiotic resistance genes. This may be facilitated by mobile genetic elements (MGEs) that can cause rearrangements. Several factors contribute to <i>S. aureus</i> virulence, including the type VII secretion system (T7SS), composed of six core genes conserved across <i>S. aureus</i> strains. In this study, we conducted comparative genome analyses of five <i>S. aureus</i> isolates from PCs (CI/BAC/25/13 /W, PS/BAC/169/17 /W and PS/BAC/317/16 /W were detected during PCs screening with the BACT/ALERT automated culture system, and ATR-20003 and CBS2016-05 were missed during screening and caused septic transfusion reactions). Multiple alignments of the genomes revealed evidence of rearrangements involving phage Sa3int in PS/BAC/169/17 /W and PS/BAC/317/16 /W. While the former had undergone translocation of its immune evasion cluster (IEC), the latter had lost part of the phage, leaving behind the IEC. This observation highlights <i>S. aureus</i> genome plasticity. Unexpectedly, strain CBS2016-05 was found to encode a pseudo-type VII secretion system (T7SS) that had lost five of the conserved core genes (<i>esxA</i>, <i>esaA, essA, esaB</i> and <i>essB</i>) and contained a 5' truncated <i>essC</i>. Since these genes are essential for the function of the T7SS protein transport machinery, which plays a key role in <i>S. aureus</i> virulence, CBS2016-05 probably compensates by recruiting other export mechanisms and/or alternative virulence factors, such as neu-tralizing immunity proteins. This study unravels genome rearrangements in <i>S. aureus</i> isolated from PCs and reports the first <i>S. aureus</i> isolate lacking conserved T7SS core genes.