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

Staphylococcus aureus 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 S. aureus virulence, including the type VII secretion system (T7SS), which is comprised of twelve genes, six of which form the T7SS core and are conserved across S. aureus strains. In this study, we conducted comparative genome analyses of five S. aureus 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 ɸSa3 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 confirms S. aureus genome plasticity. Unexpectedly, strain CBS2016-05 was found to encode a pseudo-T7SS that had lost five of the conserved core genes (esxA, esaA, essA, esaB and essB) and contained a 5’ truncated essC. Since these genes are essential for the function of the T7SS protein transport machinery, which plays a key role in S. aureus virulence, CBS2016-05 probably compensates by recruiting other export mechanisms and/or alternative virulence factors, such as neutralizing immunity proteins. This study unravels genome rearrangements in S. aureus isolated from PCs and reports the first S. aureus isolate lacking conserved T7SS core genes.