Computational protocol: Complete Genome Sequence of the Streptococcus suis Temperate Bacteriophage ϕNJ2

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Protocol publication

[…] Streptococcus suis infection is considered to be a major problem in the swine industry worldwide. S. suis can cause severe invasive infections in piglets, e.g., meningitis, arthritis, and sepsis (). S. suis can also cause disease in humans. Humans are at risk mainly after contact with contaminated pigs or pig meat (, ).Due to their highly specific host recognition, bacteriophages have potential as therapeutic agents in the treatment of infections (, ). Until now, only one lytic bacteriophage specific for S. suis has been described (). In addition, several prophages could be identified in the whole genome sequences of various S. suis isolates (–). So far, however, the lytic capacities of these prophages are unknown.Here, we report the full genome sequence of a novel temperate bacteriophage induced from the S. suis isolate NJ2. NJ2 was isolated from a diseased pig in China, and its temperate phage, designated ϕNJ2, was isolated from the host strain after induction with mitomycin C. The bacteriophages obtained were used for the isolation of the phage DNA. The genomic DNA of the bacteriophage ϕNJ2 was isolated using SDS-proteinase K and phenol-chloroform extraction methods (). Genome deep-sequencing was performed using paired-end libraries (sets of two 150-bp sequences obtained with Nextera tagmentation sequencing kits [Epicentre, Madison, WI]) on an Illumina MiSeq sequencer. The quality filtered reads were subsequently assembled de novo using the ABySS algorithm (abyss-pe version 1.3.3), and the overall phage genome coverage was approximately 680-fold. Putative open reading frames (ORFs) were identified by GeneMarkS (). BLASTP analyses of the putative ORFs against the NCBI nonredundant proteins (NR) database and Pfam analysis ( were used to assess their putative functions. The prediction of tRNA sequences was carried out using the tRNAscan-SE 1.23 software ().The phage ϕNJ2 contains a circular double-stranded DNA genome of 37,282 bp with a G+C content of 39%. A total of 56 ORFs were predicted. Thirty-one of the ORFs (55%) encoded hypothetical proteins, clearly indicating the novelty of the ϕNJ2 phage. Based on Pfam homology searches, the putative functions of the putative ORFs could be categorized into five functional modules comprising proteins for (i) lysogeny (putative recombinase), (ii) DNA replication and modification (putative endodeoxyribonuclease RusA, putative C-5 cytosine-specific DNA methylase, and putative MazG nucleotide pyrophosphohydrolase), (iii) head and tail morphogenesis (phage tail protein and minor capsid protein), (iv) packaging (putative phage portal protein and putative terminase of large subunit and small subunit), and (v) host lysis (putative holin and phage amidase protein). No tRNA sequences could be identified.The phage ϕNJ2 genome showed a high level of similarity (68% query coverage, displaying 84 to 97% identity) to sequences present in the S. suis isolate ST1, whereas it showed almost no similarity (less than 1% query coverage) to the lytic S. suis phage SMP (). […]

Pipeline specifications

Software tools GeneMarkS, BLASTP, tRNAscan-SE
Databases Pfam
Applications Genome annotation, WGS analysis
Organisms Streptococcus suis, Homo sapiens
Diseases Arthritis, Meningitis
Chemicals Mitomycin