Complete Genome Sequence of Bp7, an Escherichia coli Bacteriophage with a Wide Host Range

Abstract

Chicken colibacillosis is caused by some pathogenic Escherichia coli strains. Thirty-five pathogenic antibiotic-resistant E. coli strains were used in the host range detection of bacteriophage Bp7. The phage showed a wide range of E. coli hosts (46%). The complete genome of bacteriophage Bp7 was sequenced, assembled, and analyzed. The results revealed a linear double-stranded DNA sequence of 168,066 bp harboring 791 open reading frames. The major findings from its annotation are described.

GENOME ANNOUNCEMENT

Escherichia coli is one of the most significant bacterial pathogens causing chicken mortality (6), and multidrug resistance has become a serious problem (2, 3). Bacteriophage therapy is now considered a good alternative biocontrol method to inhibit the pathogen (4, 7). A multivalent virulent bacteriophage would be a good selection for phage therapy because of its wide host range.

Bacteriophage Bp7 was isolated from chicken feces. The morphology determined by transmission electron microscopy showed that Bp7 has an elongated icosahedral head and contractile sheathed tails, which indicates that it belongs to the order Caudovirales and the family Myoviridae, morphotype T4 (5).

Thirty-five pathogenic antibiotic-resistant E. coli strains were isolated from diseased chickens and were used to detect the host range of phage Bp7 by the double-layer agar plate method. The phage showed a wide host range that included pathogenic E. coli strains (46%) and most laboratory strains (including JM109, JM110, DH5α, and BL21). Genomic DNA was purified with a High Pure PCR template preparation kit (Roche). A random library of Bp7 was constructed by shotgun library method and sequenced (10-fold coverage) with an ABI Prism 3100-Avant genetic analyzer (Applied Biosystems, Foster City, CA). Putative open reading frames (ORFs) were predicted using Glimmer software (version 3.02) (8). The translated ORF products were compared with known protein sequences using BLASTP (1) and the nonredundant public GenBank database. The tRNA sequences were analyzed using the tRNAscan-SE server (9).

Bp7 had a linear double-stranded DNA of 168,066 bp with an overall G+C content of 39.49%. It harbored 791 ORFs, and the shortest ORF encoded only 36 amino acids.

Most of the proposed genes had ATG initiation codons, 7 began with GTG, and 5 began with TTG. A similarity search for homologous genome sequences was carried out. DNA sequence of Bp7 had 90% query coverage (displaying 100% identity) with bacteriophage JS98. The query coverage (displaying 98% identity) was only 12% with bacteriophage T4.

One hundred forty-one ORFs of the Bp7 genome were annotated as encoding hypothetical proteins, and 122 ORFs were annotated as known genes. These genes were clustered into three functional groups, as follows: (i) phage structure and packaging (major capsid and scaffold protein, membrane protein, tail protein, baseplate protein, spackle periplasmic protein, terminase subunits, and phage portal protein); (ii) DNA replication, transcription, and translation (DNA helicase, DNA primase, DNA polymerase, endonuclease, topoisomerase, ligase, dihydrofolate reductase, dCMP deaminase, polynucleotide kinase and phosphatase, thymidine kinase, dNMP kinase, DNA-binding transcriptional regulator, valerian ammonia acyl synthetase regulator, transcription-associated factors, thymidylate synthase, dihydrofolate reductase, glutaredoxin, thioredoxin, dTMP synthase, and dCTPase); and (iii) host lysis (endolysin, holin, perforin, cell wall hydrolase, host nucleoid-disrupting protein, and lysis inhibition auxiliary protein). No tRNA was detected.

Multivalent virulent bacteriophage Bp7 has potential as a biocontrol agent to prevent chicken colibacillosis.

Nucleotide sequence accession number.

The complete genome sequence of E. coli phage Bp7 is available in GenBank under the accession number HQ829472.