| Description |
Staphylococci commonly cause nosocomial infections, often complicated by antibiotic resistance. Staphylococcus aureus is a known opportunistic pathogen, while coagulase-negative Staphylococcus epidermidis has been assumed as a human commensal. However, it has also currently become an increasing source of infections in hospital environments complicated by biofilm formation. The acquisition of mobile genetic elements (MGEs), which are the source of pathogenicity-related genes that can spread by intra- and inter-species horizontal gene transfer, is a major contributor to the evolution of staphylococci, leading to the emergence of antibiotic-resistant strains. Temperate phages contribute to lysogenic hosts' virulence and can mediate generalized, specialized, and lateral transduction of chromosomal and MGE sequences. It can be triggered by phage infection or prophage excision caused by SOS response due to antimicrobials or another phage infection. The subsequent spread of MGEs containing resistance or virulence genes, together with strong selection, leads to the emergence of more pathogenic bacteria in hospitals. In addition to plasmids and prophages, genes for virulence and resistance factors are often carried by chromosomal islands that can be mobilized by helper temperate phages. Hence, they are called phage-inducible chromosomal islands (PICIs). PICIs can interact with the virion assembly of helper phages and alter the capsid architecture, leading to the formation of small-headed virions. This results in a reduction in the number of normal virions capable of carrying the whole helper phage genome. Infection by a small-headed virion containing a partial phage genome does not lead to a productive phage infection. In contrast, the capacity of such a particle is sufficient to carry a full-length PICI and can, therefore, be transferred to a new bacterial cell. To date, no method has been able to effectively distinguish and compare individual packaged DNAs (genophores) in phage and phage-derived small-headed particles. At the same time, it was not possible to determine the ratio between genophores of different origins, even less how it differs when the lysogenic bacterial cell is exposed to different antimicrobial agents and their combinations. Using long-read nanopore sequencing in the S. epidermidis model, we determined the origin of the packaged DNAs and the proportion of different types of genophores, where phage and PICI sequences prevailed, while plasmid and chromosomal sequences were represented marginally. The ratios appeared to vary mainly depending on the antimicrobials used for induction. We have shown that contrary to antibiotics, treatment of a bacterial strain with a lytic phage does not increase the risk of MGE spreading. Nevertheless, the combination of lytic phage with an antibiotic was the most effective in eradicating the bacterium, while the amount of released MGEs was no higher than with antibiotics alone. Our results provide a new approach to the study of the mobilome and allow us to assess the expected impact of different types of therapy of staphylococcal infections on the risk of the spread of virulence and resistance genes and thus the emergence of new pathogenic strains.
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