A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae

[1]  M. Stares,et al.  The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping , 2021, Cell host & microbe.

[2]  Timothy L. Tickle,et al.  Multivariable association discovery in population-scale meta-omics studies , 2021, bioRxiv.

[3]  Konrad Zych,et al.  Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox , 2020, Genome Biology.

[4]  Scarlet S. Shell,et al.  Regulation of mRNA Stability During Bacterial Stress Responses , 2020, Frontiers in Microbiology.

[5]  P. Kochanek,et al.  Depletion of gut microbiota is associated with improved neurologic outcome following traumatic brain injury , 2020, Brain Research.

[6]  Donovan H. Parks,et al.  A complete domain-to-species taxonomy for Bacteria and Archaea , 2020, Nature Biotechnology.

[7]  D. Caudell,et al.  Animal Model To Study Klebsiella pneumoniae Gastrointestinal Colonization and Host-to-Host Transmission , 2020, Infection and Immunity.

[8]  R. Frozza,et al.  The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication , 2020, Frontiers in Endocrinology.

[9]  E. Quigley,et al.  The microbiome and inflammatory bowel disease. , 2020, The Journal of allergy and clinical immunology.

[10]  Antibiotic resistance threats in the United States, 2019 , 2019 .

[11]  Jacobo de la Cuesta-Zuluaga,et al.  Struo: a pipeline for building custom databases for common metagenome profilers , 2019, bioRxiv.

[12]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[13]  Richard J. Goater,et al.  Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread , 2019, Nature Microbiology.

[14]  Y. Taur,et al.  Genome-Wide Screening for Enteric Colonization Factors in Carbapenem-Resistant ST258 Klebsiella pneumoniae , 2019, mBio.

[15]  K. Faber,et al.  Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases , 2019, Front. Immunol..

[16]  Jin-Town Wang,et al.  A Novel Role for the Klebsiella pneumoniae Sap (Sensitivity to Antimicrobial Peptides) Transporter in Intestinal Cell Interactions, Innate Immune Responses, Liver Abscess, and Virulence , 2018, The Journal of infectious diseases.

[17]  G. Barlow,et al.  Obesity, diabetes, and the gut microbiome: an updated review , 2018, Expert review of gastroenterology & hepatology.

[18]  Shaolin Wang,et al.  Emerging Carriage of NDM-5 and MCR-1 in Escherichia coli From Healthy People in Multiple Regions in China: A Cross Sectional Observational Study , 2018, EClinicalMedicine.

[19]  C. Deming,et al.  Expanded skin virome in DOCK8-deficient patients , 2018, Nature Medicine.

[20]  Y. Carmeli,et al.  Estimating the number of infections caused by antibiotic-resistant Escherichia coli and Klebsiella pneumoniae in 2014: a modelling study. , 2018, The Lancet. Global health.

[21]  Wei Chen,et al.  Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis , 2018, Front. Microbiol..

[22]  H. Gilbert,et al.  Biochemistry of complex glycan depolymerisation by the human gut microbiota , 2018, FEMS microbiology reviews.

[23]  J. Lucet,et al.  Infection prevention and control measures and tools for the prevention of entry of carbapenem-resistant Enterobacteriaceae into healthcare settings: guidance from the European Centre for Disease Prevention and Control , 2017, Antimicrobial Resistance & Infection Control.

[24]  Johannes Söding,et al.  MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.

[25]  M. Brittnacher,et al.  Comprehensive Arrayed Transposon Mutant Library of Klebsiella pneumoniae Outbreak Strain KPNIH1 , 2017, Journal of bacteriology.

[26]  C. Deming,et al.  Whole-Genome Sequencing Overrules a Suspected Case of Carbapenem-Resistant Enterobacter cloacae Transmission , 2017, Journal of Clinical Microbiology.

[27]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[28]  T. Bollenbach,et al.  Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment. , 2017, Cell systems.

[29]  N. Beeching,et al.  Guidelines for the prevention and treatment of travelers’ diarrhea: a graded expert panel report , 2017, Journal of travel medicine.

[30]  S. Abramson,et al.  Short- and long-term effects of oral vancomycin on the human intestinal microbiota , 2016, The Journal of antimicrobial chemotherapy.

[31]  S. Lynch,et al.  The Human Intestinal Microbiome in Health and Disease. , 2016, The New England journal of medicine.

[32]  Luis Pedro Coelho,et al.  Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper , 2016, bioRxiv.

[33]  S. Yooseph,et al.  Microbial diversity in individuals and their household contacts following typical antibiotic courses , 2016, Microbiome.

[34]  P. V. van Genderen,et al.  Prolonged carriage and potential onward transmission of carbapenemase-producing Enterobacteriaceae in Dutch travelers. , 2016, Future microbiology.

[35]  C. Deming,et al.  Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization , 2016, mBio.

[36]  S. Conlan,et al.  Horizontal Transfer of Carbapenemase-Encoding Plasmids and Comparison with Hospital Epidemiology Data , 2016, Antimicrobial Agents and Chemotherapy.

[37]  Raymond Dalgleish,et al.  HGVS Recommendations for the Description of Sequence Variants: 2016 Update , 2016, Human mutation.

[38]  Steven Salzberg,et al.  Bracken: Estimating species abundance in metagenomics data , 2016, bioRxiv.

[39]  N. Safdar,et al.  Risk of infection following colonization with carbapenem-resistant Enterobactericeae: A systematic review. , 2016, American journal of infection control.

[40]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[41]  E. Boyd,et al.  Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo , 2016, mBio.

[42]  A. Valleriani,et al.  Bacteria differently regulate mRNA abundance to specifically respond to various stresses , 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[43]  V. Young,et al.  Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine , 2016, mSphere.

[44]  Tracy K. Teal,et al.  Intestinal microbial communities associated with acute enteric infections and disease recovery , 2015, Microbiome.

[45]  Tracy K. Teal,et al.  Intestinal microbial communities associated with acute enteric infections and disease recovery , 2015, Microbiome.

[46]  B. Henrissat,et al.  Glycan complexity dictates microbial resource allocation in the large intestine , 2015, Nature Communications.

[47]  M. Bonten,et al.  Rectal Carriage of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae in Hospitalized Patients: Selective Preenrichment Increases Yield of Screening , 2015, Journal of Clinical Microbiology.

[48]  Y. Carmeli,et al.  Spread of KPC-producing carbapenem-resistant Enterobacteriaceae: the importance of super-spreaders and rectal KPC concentration. , 2015, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[49]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[50]  R. Mackie,et al.  Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes , 2014, Proceedings of the National Academy of Sciences.

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

[52]  V. Abratt,et al.  The recA operon: A novel stress response gene cluster in Bacteroides fragilis. , 2014, Research in microbiology.

[53]  M. Esposito‐Farèse,et al.  Acquisition of carbapenemase-producing Enterobacteriaceae by healthy travellers to India, France, February 2012 to March 2013. , 2014, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[54]  T. Murray,et al.  Extended-spectrum β-lactamase-producing Klebsiella pneumoniae in the neonatal intensive care unit: does vancomycin play a role? , 2014, American journal of infection control.

[55]  C. Buffie,et al.  Microbiota-mediated colonization resistance against intestinal pathogens , 2013, Nature Reviews Immunology.

[56]  Hui Wang,et al.  Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. , 2013, The Lancet. Infectious diseases.

[57]  B. Weimer,et al.  Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens , 2013, Nature.

[58]  Tzeng-Ji Chen,et al.  Ampicillin and amoxicillin use and the risk of Klebsiella pneumoniae liver abscess in Taiwan. , 2013, The Journal of infectious diseases.

[59]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[60]  L. Ursell,et al.  Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor , 2013, Science.

[61]  A. Walker,et al.  Intestinal colonization resistance , 2013, Immunology.

[62]  M. Schumacher,et al.  Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain , 2012, Nucleic acids research.

[63]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[64]  Evan S Snitkin,et al.  Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[65]  H. Flint,et al.  Microbial degradation of complex carbohydrates in the gut , 2012, Gut microbes.

[66]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[67]  E. Pamer,et al.  Role of the commensal microbiota in normal and pathogenic host immune responses. , 2011, Cell host & microbe.

[68]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[69]  Robert A. Edwards,et al.  Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..

[70]  M. Riley,et al.  Persistence of colicinogenic Escherichia coli in the mouse gastrointestinal tract , 2009, BMC Microbiology.

[71]  M. Leclerc,et al.  Characterization of the xylan-degrading microbial community from human faeces. , 2007, FEMS microbiology ecology.

[72]  P. Legendre,et al.  vegan : Community Ecology Package. R package version 1.8-5 , 2007 .

[73]  K. Shanmugam,et al.  Pyruvate Formate Lyase and Acetate Kinase Are Essential for Anaerobic Growth of Escherichia coli on Xylose , 2004, Journal of bacteriology.

[74]  A. Stintzi,et al.  Iron Acquisition and Regulation in Campylobacter jejuni , 2004, Journal of bacteriology.

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

[76]  J. McClure,et al.  Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[77]  R. Satokari,et al.  Persistence of Colonization of Human Colonic Mucosa by a Probiotic Strain, Lactobacillus rhamnosusGG, after Oral Consumption , 1999, Applied and Environmental Microbiology.