Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens

[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.