Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany

[1]  S. Beatson,et al.  Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27 , 2018, The Journal of antimicrobial chemotherapy.

[2]  S. Fuchs,et al.  Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario , 2018, Front. Microbiol..

[3]  L. Kreienbrock,et al.  Cefotaxime-resistant E. coli in dairy and beef cattle farms-Joint analyses of two cross-sectional investigations in Germany. , 2017, Preventive veterinary medicine.

[4]  O. Lund,et al.  Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids. , 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[5]  J. Ellis,et al.  Plasmid‐mediated resistance to cephalosporins and quinolones in Escherichia coli from American crows in the USA , 2017, Environmental microbiology.

[6]  F. Velkers,et al.  Dynamics of CMY-2 producing E. coli in a broiler parent flock. , 2017, Veterinary microbiology.

[7]  A. Carattoli,et al.  Plasmids Carrying blaCMY -2/4 in Escherichia coli from Poultry, Poultry Meat, and Humans Belong to a Novel IncK Subgroup Designated IncK2 , 2017, Front. Microbiol..

[8]  J. Pitout,et al.  Escherichia coli ST131: a multidrug-resistant clone primed for global domination , 2017, F1000Research.

[9]  G. Valenza,et al.  Molecular characterisation of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from hospital and ambulatory patients in Germany. , 2017, Veterinary microbiology.

[10]  H. Rohde,et al.  First report of Escherichia coli co-producing NDM-1 and OXA-232. , 2016, Diagnostic microbiology and infectious disease.

[11]  U. Roesler,et al.  Extended-Spectrum-Beta-Lactamase- and Plasmid-Encoded Cephamycinase-Producing Enterobacteria in the Broiler Hatchery as a Potential Mode of Pseudo-Vertical Transmission , 2016, Applied and Environmental Microbiology.

[12]  S. Börjesson,et al.  Introduction of quinolone resistant Escherichia coli to Swedish broiler population by imported breeding animals. , 2016, Veterinary microbiology.

[13]  A. Friedrich,et al.  Virulence, Antimicrobial Resistance Properties and Phylogenetic Background of Non-H7 Enteropathogenic Escherichia coli O157 , 2016, Front. Microbiol..

[14]  A. Mellmann,et al.  Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting , 2016, Journal of Clinical Microbiology.

[15]  D. Trott,et al.  Dynamics of extended-spectrum cephalosporin resistance in pathogenic Escherichia coli isolated from diseased pigs in Quebec, Canada. , 2016, International journal of antimicrobial agents.

[16]  Annemarie Käsbohrer,et al.  Prevalence of mcr-1 in E. coli from Livestock and Food in Germany, 2010–2015 , 2016, PloS one.

[17]  J. Knobloch,et al.  Colonization with third-generation cephalosporin-resistant Enterobacteriaceae on hospital admission: prevalence and risk factors. , 2016, The Journal of antimicrobial chemotherapy.

[18]  L. Kreienbrock,et al.  Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. , 2016, International journal of antimicrobial agents.

[19]  V. Bortolaia,et al.  Host-Specific Patterns of Genetic Diversity among IncI1-Iγ and IncK Plasmids Encoding CMY-2 β-Lactamase in Escherichia coli Isolates from Humans, Poultry Meat, Poultry, and Dogs in Denmark , 2016, Applied and Environmental Microbiology.

[20]  J. Wain,et al.  Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK. , 2016, The Journal of antimicrobial chemotherapy.

[21]  E. S. Berg,et al.  Plasmid and Host Strain Characteristics of Escherichia coli Resistant to Extended-Spectrum Cephalosporins in the Norwegian Broiler Production , 2016, PloS one.

[22]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[23]  B. Berenger,et al.  Detection, Characterization, and Typing of Shiga Toxin-Producing Escherichia coli , 2016, Front. Microbiol..

[24]  L. Kreienbrock,et al.  Cefotaxime-resistant Escherichia coli in broiler farms-A cross-sectional investigation in Germany. , 2016, Preventive veterinary medicine.

[25]  A. Manges.  Escherichia coli and urinary tract infections: the role of poultry-meat. , 2016, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[26]  John H. E. Nash,et al.  Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources , 2016, Genome Announcements.

[27]  T. Rogers,et al.  Identification of emergent blaCMY-2-carrying Proteus mirabilis lineages by whole-genome sequencing , 2015, New microbes and new infections.

[28]  Jian Sun,et al.  Prevalence of extended-spectrum cephalosporin-resistant Escherichia coli in a farrowing farm: ST1121 clone harboring IncHI2 plasmid contributes to the dissemination of blaCMY-2 , 2015, Front. Microbiol..

[29]  T. Dallman,et al.  Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance , 2015, Journal of Clinical Microbiology.

[30]  Ting Huang,et al.  Dissemination of the chromosomally encoded CMY-2 cephalosporinase gene in Escherichia coli isolated from animals. , 2015, International journal of antimicrobial agents.

[31]  F. Aarestrup,et al.  Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data , 2015, Journal of Clinical Microbiology.

[32]  H. Uphoff,et al.  Extended-spectrum beta-lactamase-producing Shiga toxin gene (stx1)-positive Escherichia coli O91:H14 carrying blaCTX-M-15 on an IncI1-ST31 plasmid isolated from a human patient in Germany. , 2015, International journal of medical microbiology : IJMM.

[33]  E. Denamur,et al.  Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. , 2015, Microbiology.

[34]  Rob J. L. Willems,et al.  Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages , 2014, PLoS genetics.

[35]  H. Hasman,et al.  Spread of extended spectrum cephalosporinase-producing Escherichia coli clones and plasmids from parent animals to broilers and to broiler meat in a production without use of cephalosporins. , 2014, Foodborne pathogens and disease.

[36]  D. Paterson,et al.  Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst Escherichia coli. , 2014, International journal of antimicrobial agents.

[37]  L. Kreienbrock,et al.  Prevalence and potential risk factors for the occurrence of cefotaxime resistant Escherichia coli in German fattening pig farms--a cross-sectional study. , 2014, Preventive veterinary medicine.

[38]  L. Kreienbrock,et al.  Extended-spectrum beta-lactamases (ESBL)/AmpC beta-lactamases-producing Escherichia coli in German fattening pig farms: a longitudinal study. , 2014, Berliner und Munchener tierarztliche Wochenschrift.

[39]  M. Norström,et al.  Emergence of AmpC-producing Escherichia coli in the broiler production chain in a country with a low antimicrobial usage profile. , 2014, Veterinary microbiology.

[40]  Xavier Bertrand,et al.  Escherichia coli ST131, an Intriguing Clonal Group , 2014, Clinical Microbiology Reviews.

[41]  J. Iredell,et al.  Complete Sequencing of IncI1 Sequence Type 2 Plasmid pJIE512b Indicates Mobilization of blaCMY-2 from an IncA/C Plasmid , 2014, Antimicrobial Agents and Chemotherapy.

[42]  V. Bortolaia,et al.  High diversity of plasmids harbouring blaCMY-2 among clinical Escherichia coli isolates from humans and companion animals in the upper Midwestern USA. , 2014, The Journal of antimicrobial chemotherapy.

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

[44]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[45]  Juan Wang,et al.  Complete nucleotide sequence of a conjugative IncF plasmid from an Escherichia coli isolate of equine origin containing blaCMY-2 within a novel genetic context. , 2014, FEMS microbiology letters.

[46]  Ole Lund,et al.  Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli , 2014, Journal of Clinical Microbiology.

[47]  Aaron E. Darling,et al.  A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data , 2014, Bioinform..

[48]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[49]  L. Price,et al.  The Epidemic of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx , 2013, mBio.

[50]  C. Schapendonk,et al.  Identical plasmid AmpC beta-lactamase genes and plasmid types in E. coli isolates from patients and poultry meat in the Netherlands. , 2013, International journal of food microbiology.

[51]  Y. Pfeifer,et al.  Prevalence of extended-spectrum-β-lactamase-producing Escherichia coli and spread of the epidemic clonal lineage ST131 in nursing homes in Hesse, Germany. , 2013, The Journal of antimicrobial chemotherapy.

[52]  W. Rabsch,et al.  Presence of β-lactamases in extended-spectrum-cephalosporin-resistant Salmonella enterica of 30 different serovars in Germany 2005-11. , 2013, The Journal of antimicrobial chemotherapy.

[53]  L. Kreienbrock,et al.  Longitudinal Monitoring of Extended-Spectrum-Beta-Lactamase/AmpC-Producing Escherichia coli at German Broiler Chicken Fattening Farms , 2013, Applied and Environmental Microbiology.

[54]  M. Mulvey,et al.  Molecular epidemiology of extended-spectrum β-lactamase-, AmpC β-lactamase- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolated from Canadian hospitals over a 5 year period: CANWARD 2007-11. , 2013, The Journal of antimicrobial chemotherapy.

[55]  Jens Stoye,et al.  Updating benchtop sequencing performance comparison , 2013, Nature Biotechnology.

[56]  A. Friedrich,et al.  Overview of molecular typing methods for outbreak detection and epidemiological surveillance. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[57]  E. Denamur,et al.  The CTX-M-15-Producing Escherichia coli Clone O25b: H4-ST131 Has High Intestine Colonization and Urinary Tract Infection Abilities , 2012, PloS one.

[58]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[59]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[60]  Eric S. Lander,et al.  Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 , 2012, Proceedings of the National Academy of Sciences.

[61]  Ole Lund,et al.  Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria , 2012, Journal of Clinical Microbiology.

[62]  S. Lallechère,et al.  Cephalosporin and fluoroquinolone combinations are highly associated with CTX-M β-lactamase-producing Escherichia coli: a case-control study in a French teaching hospital. , 2011, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[63]  F. de la Cruz,et al.  Plasmid segregation without partition , 2011, Mobile genetic elements.

[64]  I. Uchida,et al.  Characterization of Salmonella enterica Serovar Typhimurium Isolates Harboring a Chromosomally Encoded CMY-2 β-Lactamase Gene Located on a Multidrug Resistance Genomic Island , 2011, Antimicrobial Agents and Chemotherapy.

[65]  W. Witte,et al.  Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. , 2010, International journal of medical microbiology : IJMM.

[66]  J. Campos,et al.  AmpC beta-lactamases in Escherichia coli: emergence of CMY-2-producing virulent phylogroup D isolates belonging mainly to STs 57, 115, 354, 393, and 420, and phylogroup B2 isolates belonging to the international clone O25b-ST131. , 2010, Diagnostic microbiology and infectious disease.

[67]  V. Dobranić,et al.  Increased number of intestinal villous M cells in levamisole -pretreated weaned pigs experimentally infected with F4ac+ enterotoxigenic Escherichia coli strain , 2010, European journal of histochemistry : EJH.

[68]  K. Schønning,et al.  Prevalence and molecular characterization of clinical isolates of Escherichia coli expressing an AmpC phenotype. , 2010, The Journal of antimicrobial chemotherapy.

[69]  A. Sundsfjord,et al.  Sporadic occurrence of CMY-2-producing multidrug-resistant Escherichia coli of ST-complexes 38 and 448, and ST131 in Norway. , 2010, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[70]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[71]  E. Chachaty,et al.  Genetic Context of Plasmid-Carried blaCMY-2-Like Genes in Enterobacteriaceae , 2009, Antimicrobial Agents and Chemotherapy.

[72]  J. Madlung,et al.  Emergence of carbapenem-non-susceptible extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates at the university hospital of Tübingen, Germany. , 2009, Journal of medical microbiology.

[73]  Alessandra Carattoli,et al.  Resistance Plasmid Families in Enterobacteriaceae , 2009, Antimicrobial Agents and Chemotherapy.

[74]  George A. Jacoby,et al.  AmpC β-Lactamases , 2009, Clinical Microbiology Reviews.

[75]  Y. Arakawa,et al.  Change in the prevalence of extended-spectrum-beta-lactamase-producing Escherichia coli in Japan by clonal spread. , 2008, The Journal of antimicrobial chemotherapy.

[76]  N. Woodford,et al.  CTX-M: changing the face of ESBLs in Europe. , 2006, The Journal of antimicrobial chemotherapy.

[77]  S. C. Donaldson,et al.  Molecular Epidemiology of Ceftiofur-Resistant Escherichia coli Isolates from Dairy Calves , 2006, Applied and Environmental Microbiology.

[78]  Daniel Falush,et al.  Sex and virulence in Escherichia coli: an evolutionary perspective , 2006, Molecular microbiology.

[79]  Thomas E. Besser,et al.  Variability in the Region Downstream of the blaCMY-2 β-Lactamase Gene in Escherichia coli and Salmonella enterica Plasmids , 2006, Antimicrobial Agents and Chemotherapy.

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

[81]  L. Wieler,et al.  National antibiotic resistance monitoring in veterinary pathogens from sick food-producing animals: the German programme and results from the 2001 pilot study. , 2003, International journal of antimicrobial agents.

[82]  O. Clermont,et al.  Rapid and Simple Determination of theEscherichia coli Phylogenetic Group , 2000, Applied and Environmental Microbiology.

[83]  Alyssa C. Bumbaugh,et al.  Parallel evolution of virulence in pathogenic Escherichia coli , 2000, Nature.

[84]  G. P. Harding,et al.  A general method for detecting and sizing large plasmids. , 1995, Analytical biochemistry.

[85]  R. Clowes,et al.  Some observations on linkage effects in genetic recombination in Escherichia coli K-12. , 1954, Journal of general microbiology.

[86]  Wenjing,et al.  Infection and Drug Resistance Dovepress , 2019 .

[87]  O. Tsang,et al.  Distribution of ESBLs, AmpC &bgr;-lactamases and carbapenemases among Enterobacteriaceae isolates causing intra-abdominal and urinary tract infections in the Asia-Pacific region during 2008–14: results from the Study for Monitoring Antimicrobial Resistance Trends (SMART) , 2017, The Journal of antimicrobial chemotherapy.

[88]  L. Cerdeira,et al.  High-virulence CMY-2- and CTX-M-2-producing avian pathogenic Escherichia coli strains isolated from commercial turkeys. , 2017, Diagnostic microbiology and infectious disease.

[89]  N. Ahmed,et al.  Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410--another successful pandemic clone? , 2016, FEMS microbiology ecology.

[90]  G. Valenza,et al.  Extended-Spectrum- -Lactamase-Producing Escherichia coli as Intestinal Colonizers in the German Community , 2014 .

[91]  L. Wieler,et al.  Extended-spectrum b-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals , and their putative impact on public health : a global perspective , 2012 .

[92]  D. Paterson,et al.  Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. , 2011, The Journal of antimicrobial chemotherapy.