UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales

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.

Keywords: bacteriophage; bladder; inovirus; prophage.

Figure 1.

Phage DNA confirmation. PCR results using (A) UPϕ or (B) 16S primers after DNase treatment to remove bacterial genomic DNA from filtrates of UMB0901, UMB1220, UMB1526, and UMB5814 cultures. The + control lane was from UMB0901 colony PCR.

Figure 2.

Comparison of UPϕ901 to related inoviruses. Roman numerals are the names for core inovirus genes common in M13 and the Lineavirus members. Ypfφ genes labeled as in Derbise et al. (2007). Genes shaded gray are darker if they are more similar to the sequence from the UPϕ901 prophage in UMB0901.

Figure 3.

Cladograms of UPϕ prophages in GenBank assemblies (A) and their hosts (B). The outer ring is the host species, the middle ring is the sample material, and the inner ring is the source environment. Black arrows indicate (A) UPϕ901 and (B) UMB0901. Samples sizes shown in parentheses in the legend. Trees are based on amino acid sequences of core genes. Bootstrap support is shown by the size of black dots with at least 51 per cent support. High-resolution trees with scale bars and bootstrap supports are in Supplementary Fig. S3.

Figure 4.

Number of unique amino acid sequence variants for each UPϕ gene used to build trees.