The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains

Abstract

Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.

Keywords: Myoviridae; coliphages; comparative analysis; depolymerase.

Figure 1

Virion morphology of phage phiC120 observed by transmission electron microscopy. The bars represent length in nanometers.

Figure 2

Graphic representation of genome organization of phage phiC120. Putative ORFs are indicated as arrows, where the orientation indicates the direction of transcription. GC content is indicated in black.

Figure 3

Comparative genomic analysis of phiC120 genome and other similar phages. (A) Progressive Mauve alignment was used to determine blocks of homolog genomic regions (showed in different colors) and identify genomic rearrangements. (B) Comparison of the genome structure of phiC120 using Easyfig. Lines between genome maps indicate the level of identity in genes sharing orientation (blue/turquoise) or with inverted orientation (red/orange). GenBank accession numbers: phiC120, KY703222.1; RB69, AY303349.1; phiE142, KU255730.1; Escherichia coli O157 typing phage 3 (O157tp3), NC_041863.1; Escherichia phage vB_EcoM_WFK,; Shigella phage Shf125875, MK373775.1.

Figure 4

Phylogenetic tree using the major capsid protein (g23) genes of phiC120 and representative members of different genera of Tevenvirinae subfamily to investigate the possible genus which phiC120 belongs.

Figure 5

Phylogenetic tree of TerL subunit protein of phiC120 and representative phages with known packaging mechanisms. Brackets indicate clusters of phages, that follow a similar packaging strategy.