Abstract
Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host’s genome by co-opting the host’s XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UPϕ901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UPϕ901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call ‘UPϕ viruses’, also harbors two or more novel genes of unknown function.
Highlights
Phages are often described by their potential to kill their hosts
We describe a new filamentous phage, UP/901, which we originally found integrated in a clinical isolate of Escherichia coli from urine
We confirmed by PCR that the phage is shed from infected bacteria, as centrifuged culture supernatant treated with DNase is positive for UP/901 DNA (Fig. 1A) but negative for bacterial genomic DNA (Fig. 1B)
Summary
Phages are often described by their potential to kill their hosts. Obligately lytic phages kill their hosts following infection, whereas temperate phages may lie dormant as prophages within lysogenized bacteria for several generations before entering a lytic cycle. While killing by phages has immediate consequences for bacterial ecology and has led to the revival of phage therapy for treating bacterial infections (Kortright et al 2019), many phages carry genes that alter bacterial behavior (Mai-Prochnow et al 2015; Warwick-Dugdale et al 2019) The effects of these phage-encoded genes range from modifying photosynthesis in cyanobacteria (Sieradzki et al 2019) to producing toxins in potential pathogens (Waldor and Mekalanos 1996). The majority of characterized inoviruses maintain productive infections over multiple bacterial generations, without killing their hosts In many cases, these phages integrate as tandem repeats (e.g. Derbise et al 2007) into their hosts’ genomes at a locus called the dif site (Mai-Prochnow et al 2015).
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