Virion content unpacked by long-read sequencing: stress-induced changes in transmitted staphylococcal mobilome due to phage-satellite interactions

The evolution of the virulence and antibiotic resistance of staphylococci, important opportunistic pathogens, is strongly determined by their mobilome, which can spread by phage virions or small-headed particles resulting from the hijacking of helper phage machinery by phage satellites named phage-inducible chromosomal islands (PICIs). Despite known mechanisms of the formation of transducing particles, it has not yet been possible to analyze their DNA content at the single-virion level. Using the Staphylococcus epidermidis model and long-read nanopore sequencing, we determined the sequence structure and ratio of phage and PICI genophores, plasmid, and bacterial DNA packaged in normal and small-headed virions. It was shown that the ratios vary mainly depending on the helper phage and the antimicrobial used for induction. When the effect of a strictly lytic phage and its combination with ciprofloxacin on a packaged mobilome was analyzed, no significant increase in mobilome dissemination was observed compared to antibiotics alone. Here, we demonstrate a novel approach for the analysis of transduced bacterial mobilome and show in vitro that lytic phage-based therapeutic strategies do not increase the risk of mobile genetic element transfer.