相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Database resources of the National Center for Biotechnology Information
Eric W. Sayers et al.
NUCLEIC ACIDS RESEARCH (2020)
Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria
Julia Vergalli et al.
NATURE REVIEWS MICROBIOLOGY (2020)
The role of hosts, plasmids and environment in determining plasmid transfer rates: A meta-analysis
Richard J. Sheppard et al.
PLASMID (2020)
Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
Leah W. Roberts et al.
NATURE COMMUNICATIONS (2020)
Genomic Epidemiology of Complex, Multispecies, Plasmid-Borne blaKPC Carbapenemase in Enterobacterales in the United Kingdom from 2009 to 2014
Nicole Stoesser et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2020)
Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Daniel R. Evans et al.
ELIFE (2020)
Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae
Christoph M. Ernst et al.
NATURE MEDICINE (2020)
Multidrug-Resistant Bacterial Infections in US Hospitalized Patients, 2012-2017
John A. Jernigan et al.
NEW ENGLAND JOURNAL OF MEDICINE (2020)
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Kern Rei Chng et al.
NATURE MEDICINE (2020)
Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae
Sophia David et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Emmanuel Paradis et al.
BIOINFORMATICS (2019)
Horizontal transfer of antibiotic resistance genes in clinical environments
Nicole A. Lerminiaux et al.
CANADIAN JOURNAL OF MICROBIOLOGY (2019)
Tracking the spread of carbapenem-resistant Enterobacteriaceae (CRE) through clinical cultures alone underestimates the spread of CRE even more than anticipated
Bruce Y. Lee et al.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY (2019)
Ultrafast search of all deposited bacterial and viral genomic data
Phelim Bradley et al.
NATURE BIOTECHNOLOGY (2019)
Interactions between plasmids and other mobile genetic elements affect their transmission and persistence
Francisco Dionisio et al.
PLASMID (2019)
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes
Ankita Kothari et al.
MBIO (2019)
Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Update on Therapeutic Options
Chau-Chyun Sheu et al.
FRONTIERS IN MICROBIOLOGY (2019)
TASmania: A bacterial Toxin-Antitoxin Systems database
Hatice Akarsu et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
Sophia David et al.
NATURE MICROBIOLOGY (2019)
Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals
Jennifer H. Han et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2019)
Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years
Jane W. Marsh et al.
MBIO (2019)
Treatment Options for Carbapenem-resistant Gram-negative Bacterial Infections
Yohei Doi
CLINICAL INFECTIOUS DISEASES (2019)
ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database
Joao L. Reis-Cunha et al.
PLOS ONE (2019)
Assessing genetic diversity and similarity of 435 KPC-carrying plasmids
Christian Brandt et al.
SCIENTIFIC REPORTS (2019)
Characteristics of Carbapenemase-Producing Enterobacteriaceae in Wastewater Revealed by Genomic Analysis
Ryota Gomi et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2018)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches
A. C. Schurch et al.
CLINICAL MICROBIOLOGY AND INFECTION (2018)
Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste
Nachiket P. Marathe et al.
ENVIRONMENT INTERNATIONAL (2018)
Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance
D. G. Joakim Larsson et al.
ENVIRONMENT INTERNATIONAL (2018)
Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae
M. Rozwandowicz et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2018)
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Ruobing Wang et al.
NATURE COMMUNICATIONS (2018)
Vital Signs: Containment of Novel Multidrug-Resistant Organisms and Resistance Mechanisms — United States, 2006–2017
Kate Russell Woodworth et al.
MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2018)
Association Between Carbapenem Resistance and Mortality Among Adult, Hospitalized Patients With Serious Infections Due to Enterobacteriaceae: Results of a Systematic Literature Review and Meta-analysis
Amber Martin et al.
OPEN FORUM INFECTIOUS DISEASES (2018)
A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control
V. Decraene et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2018)
Synergistic Activity of Colistin-Containing Combinations against Colistin-Resistant Enterobacteriaceae
Thea Brennan-Krohn et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2018)
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks
Ryan R. Wick et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
Anna E. Sheppard et al.
MICROBIAL GENOMICS (2018)
SynerClust: a highly scalable, synteny-aware orthologue clustering tool
Christophe H. Georgescu et al.
MICROBIAL GENOMICS (2018)
Epidemiology of Carbapenem-Resistant Enterobacteriaceae Infections: Report from the China CRE Network
Yawei Zhang et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2018)
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
James Robertson et al.
MICROBIAL GENOMICS (2018)
Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection
Li-Guan Li et al.
ISME JOURNAL (2017)
European Nucleotide Archive in 2016
Ana Luisa Toribio et al.
NUCLEIC ACIDS RESEARCH (2017)
Carbapenem-resistant Enterobacteriaceae in the community: a scoping review
Ana M. Kelly et al.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS (2017)
The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace
Latania K. Logan et al.
JOURNAL OF INFECTIOUS DISEASES (2017)
Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: Plasmids promote the immigration of other plasmids but repress co-colonizing plasmids
Joao Alves Gama et al.
PLASMID (2017)
Co-resident plasmids travel together
Joao Alves Gama et al.
PLASMID (2017)
Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks
Gustavo C. Cerqueira et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak
Evan S. Snitkin et al.
SCIENCE TRANSLATIONAL MEDICINE (2017)
Persistence and reversal of plasmid-mediated antibiotic resistance
Allison J. Lopatkin et al.
NATURE COMMUNICATIONS (2017)
Therapeutic options for carbapenem-resistant Enterobacteriaceae infections
Enrico Maria Trecarichi et al.
VIRULENCE (2017)
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Ryan R. Wick et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
The impact of insertion sequences on bacterial genome plasticity and adaptability
Joachim Vandecraen et al.
CRITICAL REVIEWS IN MICROBIOLOGY (2017)
Concentration and Variety of Carbapenemase Producers in Recreational Coastal Waters Showing Distinct Levels of Pollution
Raphael P. Paschoal et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2017)
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Martin Hunt et al.
MICROBIAL GENOMICS (2017)
Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients
Claire L. Gorrie et al.
CLINICAL INFECTIOUS DISEASES (2017)
Counting the cost of an outbreak of carbapenemase-producing Enterobacteriaceae: an economic evaluation from a hospital perspective
J. A. Otter et al.
CLINICAL MICROBIOLOGY AND INFECTION (2017)
Potential economic burden of carbapenem-resistant Enterobacteriaceae (CRE) in the United States
S. M. Bartsch et al.
CLINICAL MICROBIOLOGY AND INFECTION (2017)
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary et al.
NUCLEIC ACIDS RESEARCH (2016)
Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC
Anna E. Sheppard et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2016)
Verification of an Automated, Digital Dispensing Platform for At-Will Broth Microdilution-Based Antimicrobial Susceptibility Testing
Kenneth P. Smith et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2016)
Multiple Variants of Klebsiella pneumoniae Producing Carbapenemase in One Patient
Michael R. Mulvey et al.
NEW ENGLAND JOURNAL OF MEDICINE (2016)
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
James P. J. Hall et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131
Timothy J. Johnson et al.
MSPHERE (2016)
Identification of protein secretion systems in bacterial genomes
Sophie S. Abby et al.
SCIENTIFIC REPORTS (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
Klebsiella pneumoniae Carbapenemase (KPC)-Producing K-pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing
Amy J. Mathers et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2015)
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential
Chandan Pal et al.
BMC GENOMICS (2015)
In Vivo Horizontal Gene Transfer of the Carbapenemase OXA-48 During a Nosocomial Outbreak
Stephan Goettig et al.
CLINICAL INFECTIOUS DISEASES (2015)
The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae
Amy J. Mathers et al.
CLINICAL MICROBIOLOGY REVIEWS (2015)
Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins
Michael Knopp et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition
Susu He et al.
MBIO (2015)
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Xavier Didelot et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Treatment Options for Carbapenem-Resistant Enterobacteriaceae Infections
Haley J. Morrill et al.
OPEN FORUM INFECTIOUS DISEASES (2015)
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
The Transporter Classification Database
Milton H. Saier et al.
NUCLEIC ACIDS RESEARCH (2014)
Database resources of the National Center for Biotechnology Information
Abigail Acland et al.
NUCLEIC ACIDS RESEARCH (2014)
Pfam: the protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2014)
Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome
Tue Sparholt Jorgensen et al.
PLOS ONE (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems
Sophie S. Abby et al.
PLOS ONE (2014)
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae
Sean Conlan et al.
SCIENCE TRANSLATIONAL MEDICINE (2014)
Outbreak Caused by an Ertapenem-Resistant, CTX-M-15-Producing Klebsiella pneumoniae Sequence Type 101 Clone Carrying an OmpK36 Porin Variant
Aggeliki Poulou et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2013)
Broad-host-range IncP-1 plasmids and their resistance potential
Magdalena Popowska et al.
FRONTIERS IN MICROBIOLOGY (2013)
Genetic Features of the Widespread Plasmid Coding for the Carbapenemase OXA-48
Laurent Poirel et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2012)
CD-HIT: accelerated for clustering the next-generation sequencing data
Limin Fu et al.
BIOINFORMATICS (2012)
Carbapenemases in Klebsiella pneumoniae and Other Enterobacteriaceae: an Evolving Crisis of Global Dimensions
L. S. Tzouvelekis et al.
CLINICAL MICROBIOLOGY REVIEWS (2012)
Spread of an OmpK36-modified ST15 Klebsiella pneumoniae variant during an outbreak involving multiple carbapenem-resistant Enterobacteriaceae species and clones
A. Novais et al.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2012)
Finished bacterial genomes from shotgun sequence data
Filipe J. Ribeiro et al.
GENOME RESEARCH (2012)
Outbreak of Carbapenem-Resistant Enterobacteriaceae at a Long-Term Acute Care Hospital: Sustained Reductions in Transmission through Active Surveillance and Targeted Interventions
Amit S. Chitnis et al.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY (2012)
Identification of acquired antimicrobial resistance genes
Ea Zankari et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing
Evan S. Snitkin et al.
SCIENCE TRANSLATIONAL MEDICINE (2012)
Functional Characterization of Tn4401, a Tn3-Based Transposon Involved in blaKPC Gene Mobilization
Gaelle Cuzon et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2011)
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Guillaume Marcais et al.
BIOINFORMATICS (2011)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation
Julien Guglielmini et al.
PLOS GENETICS (2011)
Horizontal gene exchange in environmental microbiota
Rustam I. Aminov
FRONTIERS IN MICROBIOLOGY (2011)
Does the Wide Use of Quaternary Ammonium Compounds Enhance the Selection and Spread of Antimicrobial Resistance and Thus Threaten Our Health?
Kristin Hegstad et al.
MICROBIAL DRUG RESISTANCE (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
Resistance Plasmid Families in Enterobacteriaceae
Alessandra Carattoli
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock et al.
BIOINFORMATICS (2009)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Attributable Mortality Rate for Carbapenem-Resistant Klebsiella pneumoniae Bacteremia
Abraham Borer et al.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY (2009)
Genetic structures at the origin of acquisition of the β-lactamase blaKPC gene
Thierry Naas et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2008)
Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria
P. M. Bennett
BRITISH JOURNAL OF PHARMACOLOGY (2008)
Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system
Serge V. Nekrasov et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
Johan Goris et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2007)
Evolution of mutation rates in bacteria
E Denamur et al.
MOLECULAR MICROBIOLOGY (2006)
ISfinder: the reference centre for bacterial insertion sequences
P. Siguier et al.
NUCLEIC ACIDS RESEARCH (2006)
Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH
C Hunte et al.
NATURE (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
Versatile and open software for comparing large genomes
S Kurtz et al.
GENOME BIOLOGY (2004)
Toxins-antitoxins: Plasmid maintenance, programmed cell death, and cell cycle arrest
F Hayes
SCIENCE (2003)
Extended-spectrum β-lactamases in the 21st century:: Characterization, epidemiology, and detection of this important resistance threat
PA Bradford
CLINICAL MICROBIOLOGY REVIEWS (2001)
分享论文
