Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

[1]  L. Comstock,et al.  Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering , 2021, bioRxiv.

[2]  R. Tamayo,et al.  Site-Specific Recombination - How Simple DNA Inversions Produce Complex Phenotypic Heterogeneity in Bacterial Populations. , 2020, Trends in genetics : TIG.

[3]  G. Dantas,et al.  Antimicrobial resistance in enteric bacteria: current state and next-generation solutions , 2020, Gut microbes.

[4]  Robert D. Finn,et al.  A unified catalog of 204,938 reference genomes from the human gut microbiome , 2020, Nature Biotechnology.

[5]  H. Schulenburg,et al.  The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution. , 2020, Trends in microbiology.

[6]  R. Tamayo,et al.  Enhancing bacterial survival through phenotypic heterogeneity , 2020, PLoS pathogens.

[7]  Christine J. Boinett,et al.  Commensal E. coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei , 2019, Nature Microbiology.

[8]  R. Xavier,et al.  Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools , 2019, PloS one.

[9]  J. Rossen,et al.  Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates. , 2019, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[10]  Andrew C. Tolonen,et al.  Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut , 2019, Science.

[11]  Meng Liu,et al.  ICEberg 2.0: an updated database of bacterial integrative and conjugative elements , 2018, Nucleic Acids Res..

[12]  A. Shen,et al.  Genome-wide detection of conservative site-specific recombination in bacteria , 2018, PLoS genetics.

[13]  E. Pamer,et al.  The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens , 2017, Immunological reviews.

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

[15]  J. Martínez,et al.  Fitness costs associated with the acquisition of antibiotic resistance. , 2017, Essays in biochemistry.

[16]  Raymond Lo,et al.  CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database , 2016, Nucleic Acids Res..

[17]  M. Touchon,et al.  Identification of protein secretion systems in bacterial genomes , 2015, Scientific Reports.

[18]  Hervé Ménager,et al.  MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems , 2014, PloS one.

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

[20]  E. Urbán,et al.  The prevalence of antibiotic resistance genes in Bacteroides fragilis group strains isolated in different European countries. , 2013, Anaerobe.

[21]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

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

[23]  Wolf-Dietrich Hardt,et al.  Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae , 2012, Proceedings of the National Academy of Sciences.

[24]  Zhen Xu,et al.  ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria , 2011, Nucleic Acids Res..

[25]  E. Urbán,et al.  Investigation of the prevalence of tetQ, tetX and tetX1 genes in Bacteroides strains with elevated tigecycline minimum inhibitory concentrations. , 2011, International journal of antimicrobial agents.

[26]  A. Roberts,et al.  Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. , 2011, FEMS microbiology reviews.

[27]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[28]  E. Urbán,et al.  ESCMID Study group on Antimicrobial resistance in anaerobic bacteria , 2011 .

[29]  M. W. van der Woude,et al.  Phase variation : how to create and coordinate population diversity , 2011 .

[30]  Stefan Niemann,et al.  Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes , 2011 .

[31]  Stephen D. Bentley,et al.  Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis , 2010, Microbiology.

[32]  Diarmaid Hughes,et al.  Antibiotic resistance and its cost: is it possible to reverse resistance? , 2010, Nature Reviews Microbiology.

[33]  D. Snydman,et al.  Lessons learned from the anaerobe survey: historical perspective and review of the most recent data (2005-2007). , 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[34]  L. Comstock,et al.  A Family of Transcriptional Antitermination Factors Necessary for Synthesis of the Capsular Polysaccharides of Bacteroides fragilis , 2009, Journal of bacteriology.

[35]  G. Church,et al.  Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora , 2009, Science.

[36]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[37]  L. Paoletti,et al.  Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis , 2008, Proceedings of the National Academy of Sciences.

[38]  L. Comstock,et al.  Niche-Specific Features of the Intestinal Bacteroidales , 2007, Journal of bacteriology.

[39]  Hannah M. Wexler,et al.  Bacteroides: the Good, the Bad, and the Nitty-Gritty , 2007, Clinical Microbiology Reviews.

[40]  S. Levy,et al.  Molecular Mechanisms of Antibacterial Multidrug Resistance , 2007, Cell.

[41]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[42]  F. Yoshimura,et al.  Bacteroides fragilis BmeABC efflux systems additively confer intrinsic antimicrobial resistance. , 2006, The Journal of antimicrobial chemotherapy.

[43]  R. Villemur,et al.  Phase variation and antigenic variation , 2005 .

[44]  É. Hegedűs,et al.  Survivability of vancomycin resistant enterococci and fitness cost of vancomycin resistance acquisition , 2005, Journal of Clinical Pathology.

[45]  Yanping Wang,et al.  Human intestinal bacteria as reservoirs for antibiotic resistance genes. , 2004, Trends in microbiology.

[46]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[47]  M. W. van der Woude,et al.  Phase and Antigenic Variation in Bacteria , 2004, Clinical Microbiology Reviews.

[48]  D. Livermore,et al.  Enhancement of host fitness by the sul2-coding plasmid p9123 in the absence of selective pressure. , 2004, The Journal of antimicrobial chemotherapy.

[49]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[50]  E. Murphy.  Nucleotide sequence of a spectinomycin adenyltransferase AAD(9) determinant from Staphylococcus aureus and its relationship to AAD(3″) (9) , 2004, Molecular and General Genetics MGG.

[51]  Yanping Wang,et al.  A Newly Discovered Bacteroides Conjugative Transposon, CTnGERM1, Contains Genes Also Found in Gram-Positive Bacteria , 2003, Applied and Environmental Microbiology.

[52]  K. Hughes,et al.  Flagellar Phase Variation in Salmonella enterica Is Mediated by a Posttranscriptional Control Mechanism , 2003, Journal of bacteriology.

[53]  E. Böttger,et al.  Fitness Cost of Chromosomal Drug Resistance-Conferring Mutations , 2002, Antimicrobial Agents and Chemotherapy.

[54]  Laurie E. Comstock,et al.  Extensive surface diversity of a commensal microorganism by multiple DNA inversions , 2001, Nature.

[55]  H. Vlamakis,et al.  Evidence for Extensive Resistance Gene Transfer amongBacteroides spp. and among Bacteroides and Other Genera in the Human Colon , 2001, Applied and Environmental Microbiology.

[56]  E. R. Rocha,et al.  Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. , 2000, FEMS microbiology letters.

[57]  O. Berg,et al.  Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. , 2000, Science.

[58]  B. Levin,et al.  The biological cost of antibiotic resistance. , 1999, Current opinion in microbiology.

[59]  I. Henderson,et al.  Molecular switches — the ON and OFF of bacterial phase variation , 1999, Molecular microbiology.

[60]  S. Schrag,et al.  Reducing antibiotic resistance , 1996, Nature.

[61]  P. Klemm,et al.  Localization of promoters in the fim gene cluster and the effect of H-NS on the transcription of fimB and fimE. , 1994, FEMS microbiology letters.

[62]  R. Jotwani,et al.  Pathogenicity of Bacteroides fragilis Group in Rat Intra‐Abdominal Abscesses , 1992, Microbiology and immunology.

[63]  M. Ehrenberg,et al.  Kinetic properties of Escherichia coli ribosomes with altered forms of S12. , 1992, Journal of molecular biology.

[64]  F. L. Macrina,et al.  Nucleotide sequence of ermFU, a macrolide-lincosamide-streptogramin (MLS) resistance gene encoding an RNA methylase from the conjugal element of Bacteroides fragilis V503. , 1991, Nucleic acids research.

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

[66]  E. Baron,et al.  The bacteriology of gangrenous and perforated appendicitis--revisited. , 1990, Annals of surgery.

[67]  J. Abraham,et al.  An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[68]  L. E. Bryan,et al.  Mechanism of Aminoglycoside Antibiotic Resistance in Anaerobic Bacteria: Clostridium perfringens and Bacteroides fragilis , 1979, Antimicrobial Agents and Chemotherapy.