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Feb 8, 2018 - controlled trimmed reads were assembled with MITObim version 1.8 software. The cover- age was on the order of 1,000, and one contig was ...
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crossm Complete Genome Sequence of the Myoviral Bacteriophage YS35, Which Causes the Lysis of a Multidrug-Resistant Pseudomonas aeruginosa Strain Sheng Yu,a Honglan Huang,a Yuchong Hao,a Hongyan Shi,a Chunyan Zhao,a Yanbo Suna a

Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun, People’s Republic of China

ABSTRACT The lytic bacteriophage YS35, which is capable of lysing multidrug-resistant Pseudomonas aeruginosa strains, was isolated from a sewage sample. Here, we describe the complete genome sequence of this myoviral bacteriophage, which contains 93,296 bp of double-stranded DNA and has a 49.4% G⫹C content.

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seudomonas aeruginosa strains are glucose-nonfermenting Gram-negative opportunistic pathogens that cause health care-associated infections (1). Moreover, the growing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains is considered a tremendous threat to global public health (2, 3). Recently, the application of phage-based products to treat P. aeruginosa infections in vitro and in vivo has been reported (4). We isolated the lytic bacteriophage YS35 from a sewage sample collected at the First Affiliated Hospital of Jilin University, China, using the MDR P. aeruginosa strain DH35 isolated from a patient with chronic pulmonary infection. The bacteriophage YS35 belongs to the Myoviridae family based on the morphological features determined using transmission electron microscopy. Genomic DNA of phage YS35 was extracted from purified phage stock using a phenol extraction method (5). Whole-genome sequencing was conducted using the Illumina HiSeq 4000 platform at Hangzhou Lianchuan Biotechnology Co., Ltd. (Hangzhou, China). Qualitycontrolled trimmed reads were assembled with MITObim version 1.8 software. The coverage was on the order of 1,000⫻, and one contig was obtained. Potential open reading frames (ORFs) were identified with GeneMarkS version 4.17 (6), and the functions of the ORFs were predicted using BLASTp searches against the nonredundant NCBI database. tRNAscan-SE version 1.3.1 (7) was employed to predict tRNAs. The YS35 genome comprises 93,296 bp of linear double-stranded DNA with a G⫹C content of 49.3% and 13 tRNAs. In total, 172 ORFs were predicted, only 28 of which had a putative function. Furthermore, 52 ORFs are rightward oriented, while 120 ORFs are leftward oriented. According to a BLASTn analysis, the nearest neighbors (query coverage range from 95% to 97%, identity range from 98% to 99%) of phage YS35 are Pseudomonas phages vB_PaeM C2-10 Ab02, phage vB_PaeM C2-10 Ab10, phage vB_PaeM C2-10 Ab1, phage vB_PaeM C2-10 Ab8, and phage vB_PaeM C2-10 Ab15. These five phages, which were isolated in Abidjan, Côte d’Ivoire, are similar to PAK_P1, which was isolated in France. Therefore, the phage YS35 is closely associated with PAK_P1-like virus. The comprehensive analysis of the genes and proteins encoded by phage YS35 can provide new insight into phage-bacteria coevolution and strategies for the therapeutic use of bacteriophages. Accession number(s). The complete genome sequence of bacteriophage YS35 has been deposited in GenBank under accession number MF974178. Volume 6 Issue 6 e01395-17

Received 6 November 2017 Accepted 22 December 2017 Published 8 February 2018 Citation Yu S, Huang H, Hao Y, Shi H, Zhao C, Sun Y. 2018. Complete genome sequence of the myoviral bacteriophage YS35, which causes the lysis of a multidrug-resistant Pseudomonas aeruginosa strain. Genome Announc 6:e01395-17. https://doi.org/10.1128/ genomeA.01395-17. Copyright © 2018 Yu et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Yanbo Sun, [email protected].

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Yu et al.

ACKNOWLEDGMENTS We thank Hangzhou Lianchuan Biotechnology Co., Ltd., for supporting the data analysis. This research was supported by the Innovative Training Project for college students sponsored by Jilin University, China (grant 090017).

REFERENCES 1. Peña C, Gómez-Zorrilla S, Suarez C, Dominguez MA, Tubau F, Arch O, Oliver A, Pujol M, Ariza J. 2012. Extensively drug-resistant Pseudomonas aeruginosa: risk of bloodstream infection in hospitalized patients. Eur J Clin Microbiol Infect Dis 31:2791–2797. https://doi.org/10.1007/s10096 -012-1629-3. 2. Buhl M, Peter S, Willmann M. 2015. Prevalence and risk factors associated with colonization and infection of extensively drug-resistant Pseudomonas aeruginosa: a systematic review. Expert Rev Anti Infect Ther 13: 1159 –1170. https://doi.org/10.1586/14787210.2015.1064310. 3. Obritsch MD, Fish DN, MacLaren R, Jung R. 2005. Nosocomial infections due to multidrug-resistant Pseudomonas aeruginosa: epidemiology and treatment options. Pharmacotherapy 25:1353–1364. https:// doi.org/10.1592/phco.2005.25.10.1353.

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4. Pires DP, Vilas Boas DV, Sillankorva S, Azeredo J. 2015. Phage therapy: a step forward in the treatment of Pseudomonas aeruginosa infections. J Virol 89:7449 –7456. https://doi.org/10.1128/JVI.00385-15. 5. Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 6. Besemer J, Lomsadze A, Borodovsky M. 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. https://doi.org/10.1093/nar/29.12.2607. 7. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964.

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