Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

[1]  Amy K. Cain,et al.  Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center , 2019, Genome Biology.

[2]  M. Sistrom,et al.  A Curated, Comprehensive Database of Plasmid Sequences , 2019, Microbiology Resource Announcements.

[3]  Yi Guan,et al.  Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. , 2018, Molecular biology and evolution.

[4]  K. Holt,et al.  Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes , 2018, Journal of Clinical Microbiology.

[5]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[6]  Jacqueline A. Keane,et al.  Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan , 2017, Emerging infectious diseases.

[7]  R. Nakano,et al.  Role of AmpR in the High Expression of the Plasmid-Encoded AmpC β-Lactamase CFE-1 , 2017, mSphere.

[8]  Fangfang Xia,et al.  Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 , 2017, mBio.

[9]  N. Woodford,et al.  Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone , 2017, Microbial genomics.

[10]  Julian Parkhill,et al.  ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.

[11]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[12]  J. Parkhill,et al.  Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland , 2017, mBio.

[13]  Ian M. Fingerman,et al.  Database resources of the National Center for Biotechnology Information , 2010, Nucleic Acids Res..

[14]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[15]  Liang Chen,et al.  Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms , 2016, mBio.

[16]  Andrew J. Page,et al.  Multilocus sequence typing by blast from de novo assemblies against PubMLST , 2016, J. Open Source Softw..

[17]  J. Campos,et al.  The spread of KPC-producing Enterobacteriaceae in Spain: WGS analysis of the emerging high-risk clones of Klebsiella pneumoniae ST11/KPC-2, ST101/KPC-2 and ST512/KPC-3. , 2016, The Journal of antimicrobial chemotherapy.

[18]  N. Woodford,et al.  The differential importance of mutations within AmpD in cephalosporin resistance of Enterobacter aerogenes and Enterobacter cloacae. , 2016, International journal of antimicrobial agents.

[19]  J. Parkhill,et al.  The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland , 2016, Nature Microbiology.

[20]  K. Holt,et al.  Identification of Klebsiella capsule synthesis loci from whole genome data , 2016, bioRxiv.

[21]  K. Holt,et al.  The diversity of Klebsiella pneumoniae surface polysaccharides , 2016, Microbial genomics.

[22]  Julian Parkhill,et al.  Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.

[23]  David S. Wishart,et al.  PHASTER: a better, faster version of the PHAST phage search tool , 2016, Nucleic Acids Res..

[24]  F. Rimet,et al.  phylosignal: an R package to measure, test, and explore the phylogenetic signal , 2016, Ecology and evolution.

[25]  N. Woodford,et al.  Association of Novel Nonsynonymous Single Nucleotide Polymorphisms in ampD with Cephalosporin Resistance and Phylogenetic Variations in ampC, ampR, ompF, and ompC in Enterobacter cloacae Isolates That Are Highly Resistant to Carbapenems , 2016, Antimicrobial Agents and Chemotherapy.

[26]  Simon R. Harris,et al.  SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.

[27]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[28]  V. Cattoir,et al.  Complex Regulation Pathways of AmpC-Mediated β-Lactam Resistance in Enterobacter cloacae Complex , 2015, Antimicrobial Agents and Chemotherapy.

[29]  J. Parkhill,et al.  Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, bioRxiv.

[30]  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.

[31]  Andrew J. Page,et al.  Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.

[32]  Thibaut Jombart,et al.  A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae , 2015, EMBO molecular medicine.

[33]  Anna E. Sheppard,et al.  Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing , 2015, Antimicrobial Agents and Chemotherapy.

[34]  Jacqueline A. Keane,et al.  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.

[35]  C. Torres,et al.  Characterization of Beta-lactamases in Faecal Enterobacteriaceae Recovered from Healthy Humans in Spain: Focusing on AmpC Polymorphisms , 2014, Microbial Ecology.

[36]  Daniel J. Wilson,et al.  Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting , 2014, Antimicrobial Agents and Chemotherapy.

[37]  Justin Zobel,et al.  SRST2: Rapid genomic surveillance for public health and hospital microbiology labs , 2014, bioRxiv.

[38]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[39]  Ole Lund,et al.  In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.

[40]  R. Guy,et al.  English surveillance programme for antimicrobial utilisation and resistance (ESPAUR) Report 2014 , 2014 .

[41]  N. Woodford,et al.  Declining cephalosporin and fluoroquinolone non-susceptibility among bloodstream Enterobacteriaceae from the UK: links to prescribing change? , 2013, The Journal of antimicrobial chemotherapy.

[42]  J. Rolain,et al.  ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes , 2013, Antimicrobial Agents and Chemotherapy.

[43]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[44]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[45]  N. Woodford,et al.  Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. , 2011, FEMS microbiology reviews.

[46]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..

[47]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[48]  R. Howe,et al.  BSAC standardized disc susceptibility testing method (version 10). , 2011, The Journal of antimicrobial chemotherapy.

[49]  Siv G. E. Andersson,et al.  genoPlotR: comparative gene and genome visualization in R , 2010, Bioinform..

[50]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[51]  N. Woodford,et al.  Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone , 2009, Antimicrobial Agents and Chemotherapy.

[52]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[53]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[54]  J. Andrews.  BSAC standardized disc susceptibility testing method (version 8). , 2004, The Journal of antimicrobial chemotherapy.

[55]  J. Bartlett,et al.  Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. , 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[56]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[57]  J. R. Lobry,et al.  SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis , 2007 .

[58]  N. Woodford,et al.  Molecular characterization of plasmids encoding CTX-M-15 beta-lactamases from Escherichia coli strains in the United Kingdom. , 2006, The Journal of antimicrobial chemotherapy.

[59]  Patricia Siguier,et al.  ISfinder: the reference centre for bacterial insertion sequences , 2005, Nucleic Acids Res..

[60]  M. Inoue,et al.  Gene Mutations Responsible for Overexpression of AmpC β-Lactamase in Some Clinical Isolates of Enterobacter cloacae , 2005, Journal of Clinical Microbiology.

[61]  G. Rossolini,et al.  Emergence in Klebsiella pneumoniae and Enterobacter cloacae Clinical Isolates of the VIM-4 Metallo-β-Lactamase Encoded by a Conjugative Plasmid , 2004, Antimicrobial Agents and Chemotherapy.

[62]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[63]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[64]  J. Verhoef,et al.  Evidence of extensive interspecies transfer of integron-mediated antimicrobial resistance genes among multidrug-resistant Enterobacteriaceae in a clinical setting. , 2002, The Journal of infectious diseases.

[65]  G. Barnaud,et al.  Extension of resistance to cefepime and cefpirome associated to a six amino acid deletion in the H-10 helix of the cephalosporinase of an Enterobacter cloacae clinical isolate. , 2001, FEMS microbiology letters.

[66]  M. Inoue,et al.  ampR Gene Mutations That Greatly Increase Class C β-Lactamase Activity in Enterobacter cloacae , 2000, Antimicrobial Agents and Chemotherapy.

[67]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[68]  D. Livermore,et al.  Chromosomal beta-lactamase expression and antibiotic resistance in Enterobacter cloacae. , 1988, Journal of medical microbiology.