Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens
暂无分享,去创建一个
V. Cooper | D. Van Tyne | Jieshi Chen | A. Dubrawski | M. Mustapha | D. Evans | A. Sundermann | M. Griffith | L. Harrison | Vatsala Rangachar Srinivasa | V. Rangachar Srinivasa
[1] R. Bhattacharyya,et al. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance , 2022, Genome Medicine.
[2] Christina A. Cuomo,et al. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance , 2021, Genome Medicine.
[3] Jane W. Marsh,et al. Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance , 2021, bioRxiv.
[4] R. Kouyos,et al. Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage , 2021, bioRxiv.
[5] B. Cooper,et al. Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalised patients , 2021, Nature Microbiology.
[6] P. Lapierre,et al. Nanopore MinION Sequencing Reveals Possible Transfer of blaKPC–2 Plasmid Across Bacterial Species in Two Healthcare Facilities , 2020, Frontiers in Microbiology.
[7] R. Kaas,et al. ResFinder 4.0 for predictions of phenotypes from genotypes , 2020, The Journal of antimicrobial chemotherapy.
[8] Jane W. Marsh,et al. Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital , 2020, eLife.
[9] L. Harrison,et al. Clinical and Genomic Epidemiology of Carbapenem-Nonsusceptible Citrobacter spp. at a Tertiary Health Care Center over 2 Decades , 2020, Journal of Clinical Microbiology.
[10] Samuel Kaski,et al. Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium , 2020, mBio.
[11] F. Balloux,et al. Large-scale network analysis captures biological features of bacterial plasmids , 2019, bioRxiv.
[12] Jane W. Marsh,et al. Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years , 2019, mBio.
[13] Jane W. Marsh,et al. Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole Genome Sequencing-Based Surveillance. , 2019, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[14] Andreas Keller,et al. Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates , 2019, Briefings Bioinform..
[15] M. Gut,et al. Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing , 2019, mSphere.
[16] P. Bork,et al. Interactive Tree Of Life (iTOL) v4: recent updates and new developments , 2019, Nucleic Acids Res..
[17] G. Snyder,et al. Automated data mining of the electronic health record for investigation of healthcare-associated outbreaks , 2019, Infection Control & Hospital Epidemiology.
[18] Andrew D. S. Cameron,et al. Horizontal transfer of antibiotic resistance genes in clinical environments. , 2019, Canadian journal of microbiology.
[19] Á. San Millán. Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context. , 2018, Trends in microbiology.
[20] Jian Yang,et al. VFDB 2019: a comparative pathogenomic platform with an interactive web interface , 2018, Nucleic Acids Res..
[21] Keith A Jolley,et al. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.
[22] James Robertson,et al. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies , 2018, Microbial genomics.
[23] C. Deming,et al. Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance , 2018, mBio.
[24] L. Schouls,et al. Outbreak of NDM-1-Producing Klebsiella pneumoniae in a Dutch Hospital, with Interspecies Transfer of the Resistance Plasmid and Unexpected Occurrence in Unrelated Health Care Centers , 2017, Journal of Clinical Microbiology.
[25] Ryan R. Wick,et al. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.
[26] Jia Jun Lee,et al. Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches. , 2016, The Journal of antimicrobial chemotherapy.
[27] David K. Karig,et al. Antibiotics as a selective driver for conjugation dynamics , 2016, Nature Microbiology.
[28] Andrew J. Page,et al. Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.
[29] Torsten Seemann,et al. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[30] Ole Lund,et al. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.
[31] Derrick E. Wood,et al. Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.
[32] J. Chun,et al. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. , 2014, International Journal of Systematic and Evolutionary Microbiology.
[33] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[34] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[35] A. Sundsfjord,et al. A Long-Term Low-Frequency Hospital Outbreak of KPC-Producing Klebsiella pneumoniae Involving Intergenus Plasmid Diffusion and a Persisting Environmental Reservoir , 2013, PloS one.
[36] S. Rasmussen,et al. Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.
[37] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[38] Mitchell J. Sullivan,et al. Easyfig: a genome comparison visualizer , 2011, Bioinform..
[39] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[40] Tatiana Tatusova,et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..
[41] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[42] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.