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Once episomal, the hybrid molecule replicates like a normal viral genome would, and if it has retained a cos site, the concatameric hybrid DNA can be packaged into phage heads by the cos-type packaging machinery and transferred to new host cells (Fig 2). Because aberrant excision is rare, and the bacterial DNA that can be transferred is restricted, specialized transduction is believed to make only a small contribution to all phage-mediated gene transfer. [...]to offset the predictably catastrophic effects (splitting the viral genome in two) of in situ DNA packaging, in situ theta replication creates multiple integrated genomes so that both in situ DNA packaging and phage maturation can proceed in parallel. SaPI-encoded small terminases then form hetero-oligomers with phage large terminases to form new terminase enzymes that recognize SaPI pac sites (instead of phage pac sites), enabling SaPIs to hijack the phage packaging machinery to encapsidate their own genomes into infective phage-derived particles that are transferred at extremely high frequencies, both intra- and intergenerically (Fig 3) [21, 22]. [...]SaPI-like elements appear to be widespread, as phage-inducible chromosomal islands (PICIs) have now been discovered in both gram-positive and gram-negative bacteria [23, 24]. [...]an important distinction is that although phage pseudo-pac sites appear to be located in random positions, SaPI pseudo-pac sites are often linked to and direct the unidirectional packaging of S. aureus genes that are associated with virulence and disease. [...]although they are relatively small pathogenicity islands (generally 14–16 kb), island-mediated generalized transduction links the SaPIs to a much broader repertoire of virulence determinants than they can carry themselves.

Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.

It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus , where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica . We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution. It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.

Prophages are quiescent viruses located in the chromosomes of bacteria. In the human pathogen, Staphylococcus aureus , prophages are omnipresent and are believed to be responsible for the spread of some antibiotic resistance genes. Here we demonstrate that release of phages from a subpopulation of S. aureus cells enables the intact, prophage-containing population to acquire beneficial genes from competing, phage-susceptible strains present in the same environment. Phage infection kills competitor cells and bits of their DNA are occasionally captured in viral transducing particles. Return of such particles to the prophage-containing population can drive the transfer of genes encoding potentially useful traits such as antibiotic resistance. This process, which can be viewed as ‘auto-transduction’, allows S. aureus to efficiently acquire antibiotic resistance both in vitro and in an in vivo virulence model (wax moth larvae) and enables it to proliferate under strong antibiotic selection pressure. Our results may help to explain the rapid exchange of antibiotic resistance genes observed in S. aureus . Prophages are quiescent bacterial viruses that, when activated, produce viral particles and kill their host cells. Here, Haaber et al . show that these viral particles can mediate the transfer of antibiotic resistance genes from neighbouring cells back to the remaining prophage-containing cells.

Phage satellites are defined as viruses that have a life cycle dependent on a helper virus. Thus, they are often considered as parasites of parasites, although recent work suggests it may be more accurate to consider them as symbionts that evolved along a parasitism–mutualism continuum. Over the past years, multiple studies have examined the fascinating life cycle of these elements, focusing on the characterization of the molecular mechanisms they use to hijack the helper phage machinery for their own packaging and transfer. As some phage satellites encode toxins and other virulence and resistance genes, the impact of these elements on bacterial virulence has also been extensively analysed. Recent studies suggest that satellites have unprecedented roles in the ecology and evolution of bacteria and their mobile genetic elements. In this Review, we explore the genetics and the life cycle of these elements, with special emphasis on the new mechanisms involved in their spread in nature. We discuss the unexpected impact of these elements on the evolution of other mobile genetic elements and their host bacteria, and examine their potential origins. In this Review, Penadés et al. explore the genetics, potential origins and life cycle of phage satellites, and they discuss the impact of these elements on the evolution of other mobile genetic elements and their host bacteria.

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage e xcision followed by DNA r eplication and p ackaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 ts c 2 29 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program. We find that P22 ts c 2 29 excises early after induction, but P22 delays excision to just before it is detrimental to phage production. This allows P22 to engage in lateral transduction. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation. During the transition from lysogeny (a stable association between a phage and its bacterial host) to the lytic cycle, prophage excision can be followed or preceded by DNA replication and packaging. Here, the authors show that prophage excision is delayed in Salmonella phage P22, thus allowing the packaging and transfer of large fragments of host DNA via lateral transduction.

Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.

Conjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilisable and non-transmissible plasmids coincides with the average size of phages (~40 kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission. Many plasmids can be transferred between bacterial cells via conjugation; however, the mechanisms underlying the transfer of non-conjugative plasmids are less clear. Here, Humphrey et al. show that staphylococcal phages and a family of pathogenicity islands (PICIs) can mediate intra- and inter-species plasmid transfer via generalised transduction.

Bacteriophages are the main vehicle for gene swapping in bacteria, notoriously of pathogenicity islands and antibiotic resistance genes. Chen et al. noticed that the Staphylococcus aureus prophages do not excise from their host's genome until very late in their life cycles (see the Perspective by Davidson). Thus, the phage DNA is amplified while embedded in the bacterial chromosome. The resulting concatemers are processively packed into virus capsules while still integrated in the host chromosome. Each virion is only set loose when the capsule has reached physical capacity—a process called “headful” packaging. In situ amplification maximizes viral replication, and the headful mechanism means adjacent bacterial-host DNA also gets grabbed to fill the capsule. This process ensures that host genes are transmitted along with the phage. Science , this issue p. 207 ; see also p. 152 Staphylococcus aureus phages amplify and package while chromosomally integrated such that host DNA becomes incorporated in the virus particle. Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of Staphylococcus aureus engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program. Here, DNA packaging initiates in situ from integrated prophages, and large metameric spans including several hundred kilobases of the S. aureus genome are packaged in phage heads at very high frequency. In situ replication before DNA packaging creates multiple prophage genomes so that lateral-transducing particles form during normal phage maturation, transforming parts of the S. aureus chromosome into hypermobile regions of gene transfer.

The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we found that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful lifestyle. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci.