Date Published: July 5, 2019
Publisher: Public Library of Science
Author(s): Alfred Fillol-Salom, Ahlam Alsaadi, Jorge A. Moura de Sousa, Li Zhong, Kevin R. Foster, Eduardo P. C. Rocha, José R. Penadés, Hanne Ingmer, Jakob Haaber, Michael Otto.
Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.
Temperate bacteriophages (phages) have a dual life cycle. They reside in the bacterial chromosome as prophages until induction initiates lytic replication, where phage structural proteins are produced, phage DNA is packaged into virions, and the cell ultimately lyses releasing the phage progeny. Prophages are common in bacteria and almost half of the bacterial genomes carry prophages with pathogens more likely being lysogens than non-pathogens . For the Gram-positive, human pathogen, Staphylococcus aureus, essentially all clinical strains carry between 1 and 4 prophages  and for the Gram-negative pathogen, Salmonella enterica serovar Typhimurium, prophages are present in the majority of strains [3,4]. While prophage induction obviously can reduce host viability through lytic replication [5,6] and negatively impact host fitness either by providing a metabolic cost  or by disrupting host genes upon integration [4,7], there are also examples of mutualistic interactions between temperate phages and their hosts . Foremost, prophages provide immunity to attack from related phages by expressing the phage repressor protein that controls the transition between temperate and lytic replication [5,9]. They can also express a variety of adaptive accessory genes [8,10], and for bacterial pathogens, prophage encoded virulence factors contribute to colonization and pathogenesis [4,8,11]. Despite these mutalistic interactions, phages are largely considered parasites in a continous arms race with the host  where the constant attack from phages have led to the evolution of an impressive arsenal of anti-phage systems .
Generalized transduction has long been used as a tool for genetic engineering  and, at the same time, is considered a major driver of bacterial evolution [9,14,16,34–36]. Yet, we know relatively little of the process under natural conditions. Here we have examined the impact of generalized transduction on the interactions between temperate, transducing phages and two important bacterial pathogens, namely the Gram-positive S. aureus and the Gram-negative S. enterica Typhimurium. We find that with the examined pathogens and conditions, transduction and lysogeny contribute synergistically to the survival of transducing phages and their hosts. This is because transductants that are lysogens receive the genetic information without enduring mortality by the surrounding phage virions, leading to rapid spread of a trait when there is selection for it. In the rare cases where transductants are not becoming lysogens we anticipate that the cells have become resistant to phage attack by another mechanism. Once lysogens have established, they can exchange genetic material via transducing particles without the risk of being killed by the phage. In our experiments we monitored transfer of plasmid-encoded antibiotic resistance markers suggesting that transfer occurs by generalized rather than lateral transduction, a process which just recently was demonstrated to enable lysogens to transfer chromosomal markers positioned downstream of the phage integration site at very high frequencies . We predict that if we were to monitor such markers even greater transfer frequencies would be observed.