Complete Genome Sequence of Bacteriophage SM9-3Y Infecting Serratia marcescens.

Serratia marcescens is an important opportunistic organism that causes nosocomial infections. Bacteriophage therapy has the potential to control S. marcescens infection. We present here the complete genome sequence of a lytic S. marcescens bacteriophage, SM9-3Y, which is a linear double-stranded DNA genome of 39,631 bp with 50.7% G+C content.

GENOME ANNOUNCEMENT

Serratia marcescens is a Gram-negative bacillus belonging to the family Enterobacteriaceae. This opportunistic organism has been responsible for nosocomial infections of the respiratory tract, urinary tract, and bloodstream (1, 2). In addition, outbreaks of β-lactamase-producing S. marcescens in hospital settings have been frequently reported, making chemotherapy against S. marcescens infection difficult (3–5). Phage therapy presents a possible approach to controlling infections caused by multidrug-resistant S. marcescens.

Bacteriophage SM9-3Y was isolated from raw sewage collected from the First Affiliated Hospital of Jilin University, and it formed clear plaques. Bacteriophage SM9-3Y was propagated on 8 out of 25 tested clinical strains. The morphology of phage particles was measured using transmission electron microscopy. SM9-3Y showed a 48 ± 0.4-nm icosahedral capsid with a short tail and was assigned to the family Podoviridae. Phage DNA was sequenced at Suzhou Genewiz Biological Technology Co., Ltd. (Suzhou, China), using an Illumina MiSeq 250-bp paired-end run with a 546-bp insert library. A total of 3,095,936 reads (928,780,800 bp) were trimmed and assembled using SSPACE and GapFiller (BaseClear). Open reading frame (ORF) prediction and annotation were performed using Glimmer version 3.02 (6) and protein BLAST (7) and were subsequently confirmed using the Rapid Annotation using Subsystem Technology (RAST) server (8). tRNAscan-SE was employed to predict the presence of tRNA genes (9), but no putative genes coding for tRNAs were discovered in phage SM9-3Y.

The genome of phage SM9-3Y consists of 39,631 bp of linear double-stranded DNA (dsDNA) flanked by terminal repeats of 300 bp, with a G+C content of 50.7%. The genome of phage SM9-3Y shares high nucleotide identity (96%) with Serratia phage 2050H2. Of the 48 ORFs predicted, 17 encoded hypothetical proteins. The remaining 31 ORFs were categorized into 5 functional groups, that is, DNA metabolism (exonuclease, DNA-directed RNA polymerase, DNA ligase, endonuclease, DNA primase/helicase, and DNA polymerase), phage structure (head-to-tail joining protein, capsid and scaffold protein, minor capsid protein, tail tubular proteins, internal virion proteins, and tail fiber protein), packaging (DNA-packaging protein A, DNA-packaging protein B, and HNH endonuclease), lytic features (N-acetylmuramoyl-l-alanine amidase, holin, i-spanin, and o-spanin), and additional functions (S-adenosyl-l-methionine hydrolase, protein kinase, dGTP triphosphohydrolase inhibitor, bacterial RNA polymerase inhibitor, and HNS binding protein).

Accession number(s).

The genome sequence of phage SM9-3Y has been deposited in GenBank under the accession number KX778611. The version described here is KX778611.3.