Complete Genome Sequence of Klebsiella pneumoniae Siphophage Seifer

Carbapenemase-producing Klebsiella pneumoniae poses a significant public health threat due to its resistance to antibiotics. Siphophage Seifer was isolated and characterized as part of an effort to develop phage therapeutics to control this pathogen. This report describes the complete genome sequence of phage Seifer, which is a distant member of the χ-like siphovirus phage cluster. ABSTRACT Carbapenemase-producing Klebsiella pneumoniae poses a significant public health threat due to its resistance to antibiotics. Siphophage Seifer was isolated and characterized as part of an effort to develop phage therapeutics to control this pathogen. This report describes the complete genome sequence of phage Seifer, which is a distant member of the χ-like siphovirus phage cluster.

[1]  J. Gill,et al.  Complete Genome Sequence of Sin4, a Siphophage Infecting Carbapenemase-Producing Klebsiella pneumoniae , 2019, Microbiology Resource Announcements.

[2]  J. Gill,et al.  Complete Genome Sequence of Klebsiella pneumoniae Phage Sweeny , 2019, Microbiology Resource Announcements.

[3]  Marius van den Beek,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update , 2018, Nucleic Acids Res..

[4]  The Uniprot Consortium.  UniProt: the universal protein knowledgebase , 2018, Nucleic acids research.

[5]  Lukas Zimmermann,et al.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.

[6]  D. Nelson,et al.  Complete Genome Sequence of Klebsiella pneumoniae Phages SopranoGao, MezzoGao, and AltoGao , 2017, Genome Announcements.

[7]  Adam P Arkin,et al.  PaperBLAST: Text Mining Papers for Information about Homologs , 2017, mSystems.

[8]  D. Bikard,et al.  PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data , 2017, Scientific Reports.

[9]  Genome Sequence of Escherichia coli Tailed Phage Utah , 2017, Genome Announcements.

[10]  S. Seo,et al.  Multicenter Clinical and Molecular Epidemiological Analysis of Bacteremia Due to Carbapenem-Resistant Enterobacteriaceae (CRE) in the CRE Epicenter of the United States , 2017, Antimicrobial Agents and Chemotherapy.

[11]  J. Cahill,et al.  Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Siphophage Sushi , 2015, Genome Announcements.

[12]  J. Davison.  Pre-early functions of bacteriophage T5 and its relatives , 2015, Bacteriophage.

[13]  Jonathan Wilksch,et al.  Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health , 2015, Proceedings of the National Academy of Sciences.

[14]  S. Casjens,et al.  Genome Sequence of Salmonella Phage χ , 2014, Genome Announcements.

[15]  Xi Li,et al.  Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment , 2014, Genome Announcements.

[16]  S. Casjens,et al.  Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. , 2014, Virology.

[17]  S. Casjens,et al.  Genome Sequence of Salmonella Phage 9NA , 2014, Genome Announcements.

[18]  Sarah S. Lewis,et al.  Rising Rates of Carbapenem-Resistant Enterobacteriaceae in Community Hospitals: A Mixed-Methods Review of Epidemiology and Microbiology Practices in a Network of Community Hospitals in the Southeastern United States , 2014, Infection Control & Hospital Epidemiology.

[19]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[20]  M. Belfort,et al.  Homing endonucleases: from genetic anomalies to programmable genomic clippers. , 2014, Methods in molecular biology.

[21]  A. Davidson,et al.  Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components , 2013, Journal of Virology.

[22]  R. Hendrix,et al.  A balanced ratio of proteins from gene G and frameshift-extended gene GT is required for phage lambda tail assembly. , 2013, Journal of molecular biology.

[23]  Leighton Pritchard,et al.  Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology , 2013, PeerJ.

[24]  Monica C Munoz-Torres,et al.  Web Apollo: a web-based genomic annotation editing platform , 2013, Genome Biology.

[25]  Hakdong Shin,et al.  Complete genome sequence analysis of bacterial-flagellum-targeting bacteriophage chi , 2013, Archives of Virology.

[26]  Gupta Ekta,et al.  Klebsiella pneumoniae Antimicrobial Drug Resistance, United States, 1998–2010 , 2013, Emerging infectious diseases.

[27]  K. Rajakumar,et al.  Isolation and Characterisation of Lytic Bacteriophages of Klebsiella pneumoniae and Klebsiella oxytoca , 2012, Current Microbiology.

[28]  Grace C. Lee,et al.  Treatment of Klebsiella Pneumoniae Carbapenemase (KPC) infections: a review of published case series and case reports , 2012, Annals of Clinical Microbiology and Antimicrobials.

[29]  J. Gill,et al.  The Caulobacter crescentus phage phiCbK: genomics of a canonical phage , 2012, BMC Genomics.

[30]  M. Bassetti,et al.  Predictors of mortality in bloodstream infections caused by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: importance of combination therapy. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[31]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[32]  Z. Deng,et al.  Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Multidrug-Resistant Strain Isolated from Human Sputum , 2012, Journal of bacteriology.

[33]  D. Morgan,et al.  Emergence of Klebsiella pneumoniae Carbapenemase-Producing Bacteria , 2011, Southern medical journal.

[34]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[35]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[36]  E. Summer.  Preparation of a phage DNA fragment library for whole genome shotgun sequencing. , 2009, Methods in molecular biology.

[37]  T. Itoh,et al.  MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

[38]  Ry Young,et al.  Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. , 2007, Journal of molecular biology.

[39]  S. Salzberg,et al.  Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake , 2007, Genome Biology.

[40]  C. Struve,et al.  Pathogenic potential of environmental Klebsiella pneumoniae isolates. , 2004, Environmental microbiology.

[41]  E. Verdin,et al.  Sirtuins: Sir2-related NAD-dependent protein deacetylases , 2004, Genome Biology.

[42]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[43]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[44]  A. Krogh,et al.  Prediction of lipoprotein signal peptides in Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[45]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[46]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[47]  R. Podschun,et al.  Klebsiella spp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors , 1998, Clinical Microbiology Reviews.

[48]  E. Stadtman,et al.  Regulation of glutamine synthetase. XII. Electron microscopy of the enzyme from Escherichia coli. , 1968, Biochemistry.