Complete Genome Sequence of IME13, a Stenotrophomonas maltophilia Bacteriophage with Large Burst Size and Unique Plaque Polymorphism

Abstract

Stenotrophomonas maltophilia bacteriophage IME13 is a virulent phage with a large burst size, exceeding 3,000, much larger than that of any other stenotrophomonas phage reported before. It showed effective lysis of Stenotrophomonas maltophilia. Additionally, the phage IME13 developed at least three obviously different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Here we announce its complete genome and describe major findings from its annotation.

GENOME ANNOUNCEMENT

Stenotrophomonas maltophilia has emerged as an important opportunistic pathogen in the debilitated host (2), while emergence of antibiotic resistance in Stenotrophomonas maltophilia is getting more problematic (9). Bacteriophage therapy is now considered a good alternative biocontrol method to inhibit the pathogen (11). Because bacteriophage treatment gained the status of “generally recognized as safe” by the U.S. FDA in 2006 (6) and it has a long history in some eastern European countries such as Georgia and Poland (8), the phage therapy approach could be useful for inhibiting pathogenic Stenotrophomonas.

Stenotrophomonas maltophilia bacteriophage IME13 was isolated from hospital sewage using a strain of clinically isolated Stenotrophomonas maltophilia. The one-step growth curve showed it had a very big burst size which exceeded 3,000 (data not shown). A Stenotrophomonas maltophilia phage of such a big burst size had not yet been reported (3–5, 7). Meantime, the phage appeared as at least three obviously different sizes of plaques on a double-layer Luria broth agar plate, a phenomenon that we had never observed on other phages.

Genomic DNA was extracted from the stock by the proteinase K/SDS method (10). Whole-genome sequencing of this organism was performed with the Genome Sequencer FLX System Titanium (42× coverage), and the raw sequences were primarily assembled using the 454 Newbler 2.5 assembler. The prediction of open reading frames (ORFs) was performed using the RAST annotation server (1) and Kodon (Applied Math, Sint-Martens-Latem, Belgium).

The complete genome of phage IME13 revealed a length of 162,327 bp, with a G+C content of 41.2%, 182 ORFs and 15 tRNAs. A total of 95 of the ORFs were annotated as known genes, probably due to insufficient database information about the functional genes of Stenotrophomonas phage genomes.

This genome contains functional genes related to phage structure and packaging (major capsid and scaffold protein, membrane protein), tail structure for host interaction (tail fiber protein, tail sheath protein, tail pin, baseplate tail tube cap, tail assembly protein, and tail completion protein), head (prohead assembly protein, precursor of head vertex subunit, head assembly chaperone protein, head completion protein), replication/transcription (primase/helicase, DNA topoisomerase, DNA polymerase, DNA polymerase clamp loader, DNA ligase, RNA ligase, double-stranded DNA binding protein, single-stranded DNA-binding protein, dCMP deaminase, dCTP pyrophosphatase, thymidylate synthase, replication factor C small subunit/sliding clamp DNA polymerase accessory protein, RNA polymerase binding protein, DNA-directed RNA polymerases, exonuclease A, DNA homing endonuclease, recombination-related endonuclease, RNase H, endo-DNase, terminase, 3′-phosphatase, 5′-polynucleotide kinase, and transcription regulator), host lysis (lysin, holin protein, host nucleoid disrupting protein, host ATPase affecting protein, lysis inhibition regulator membrane protein, Alc inhibitor of host transcription), and additional functions (thioredoxin, deoxycytidylate 5-hydroxymethyltransferase, nicotinamide phosphoribosyl transferase, ribonucleotide reductase of class III, dNMP kinase, guanosine-3, adenosylribosyltransferase, ribonucleotide reductase of class Ia aerobic thymidine kinase, anti-sigma 70 protein, UDP-galactopyranose mutase, N-acetylmuramoyl-l-alanine amidase, dihydrofolate reductase). The complete genome analysis of this phage provides a new insight into its characteristics and interactions with Stenotrophomonas maltophilia.

Nucleotide sequence accession number.

The complete genome sequence of Stenotrophomonas phage IME13 was submitted to GenBank under the accession number JX306041.