Strong pathogen competition in neonatal gut colonisation

[1]  Harry A. Thorpe,et al.  A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings , 2022, Nature Microbiology.

[2]  K. Holt,et al.  Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen , 2022, Nature Communications.

[3]  B. Walker,et al.  Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women , 2022, Nature Microbiology.

[4]  J. Corander,et al.  Pneumococcal within-host diversity during colonization, transmission and treatment , 2022, bioRxiv.

[5]  Wasiu A. Akanni,et al.  C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants , 2022, bioRxiv.

[6]  J. Corander,et al.  Bacterial genomic epidemiology with mixed samples , 2021, Microbial genomics.

[7]  Christine J. Boinett,et al.  High-resolution sweep metagenomics using fast probabilistic inference , 2021, Wellcome open research.

[8]  Harry A. Thorpe,et al.  One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment , 2021 .

[9]  K. Reinert,et al.  Critical Assessment of Metagenome Interpretation: the second round of challenges , 2021, Nature Methods.

[10]  Stephen C. Watts,et al.  A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex , 2021, Nature Communications.

[11]  D. Haft,et al.  AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence , 2021, Scientific Reports.

[12]  J. Corander,et al.  Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study. , 2021, The Lancet. Microbe.

[13]  J. Corander,et al.  Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study , 2021, The Lancet. Microbe.

[14]  J. Corander,et al.  Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era , 2021, Nature Communications.

[15]  J. SantaLucia,et al.  Measurement of Klebsiella Intestinal Colonization Density To Assess Infection Risk , 2021, bioRxiv.

[16]  J. Gore,et al.  Interspecies bacterial competition regulates community assembly in the C. elegans intestine , 2021, The ISME Journal.

[17]  C. Worby,et al.  StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities , 2021, bioRxiv.

[18]  J. Corander,et al.  A comprehensive and high-quality collection of Escherichia coli genomes and their genes , 2021, Microbial genomics.

[19]  K. Holt,et al.  Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity , 2021, Gut microbes.

[20]  P. Manghi,et al.  Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 , 2020, bioRxiv.

[21]  César Rodríguez,et al.  FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies , 2020, bioRxiv.

[22]  M. Hadjifrangiskou,et al.  Invasion of vaginal epithelial cells by uropathogenic Escherichia coli , 2020, Nature Communications.

[23]  C. Alteri,et al.  The oxidative fumarase FumC is a key contributor for E. coli fitness under iron-limitation and during UTI , 2020, PLoS pathogens.

[24]  K. Ng,et al.  Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition , 2020, Nature Microbiology.

[25]  Richard J. Giannone,et al.  Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans , 2019, Cell.

[26]  Kevin Vervier,et al.  Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth , 2019, Nature.

[27]  Jonathan M. Monk,et al.  Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient , 2018, Front. Microbiol..

[28]  S. Harris.  SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology , 2018, bioRxiv.

[29]  D. Rasko,et al.  Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances , 2018, mSystems.

[30]  Jukka Corander,et al.  Fast and flexible bacterial genomic epidemiology with PopPUNK , 2018, bioRxiv.

[31]  Michael Inouye,et al.  FastSpar: rapid and scalable correlation estimation for compositional data , 2018, bioRxiv.

[32]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[33]  Luis Pedro Coelho,et al.  Selective maternal seeding and environment shape the human gut microbiome , 2018, Genome research.

[34]  T. Bollenbach,et al.  Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections , 2017, Proceedings of the National Academy of Sciences.

[35]  Jukka Corander,et al.  Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131 , 2017, Genome research.

[36]  Philip D. Blood,et al.  Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software , 2017, Nature Methods.

[37]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[38]  David J. Edwards,et al.  Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[39]  Weisheng Wu,et al.  Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae , 2016, mSphere.

[40]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

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

[42]  H. Mobley,et al.  Virulence and Fitness Determinants of Uropathogenic Escherichia coli , 2015, Microbiology spectrum.

[43]  D. Monack,et al.  Intraspecies Competition for Niches in the Distal Gut Dictate Transmission during Persistent Salmonella Infection , 2014, PLoS pathogens.

[44]  Hanspeter Pfister,et al.  UpSet: Visualization of Intersecting Sets , 2014, IEEE Transactions on Visualization and Computer Graphics.

[45]  R. Edwards,et al.  Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron. , 2013, Cell host & microbe.

[46]  Jonathan Friedman,et al.  Inferring Correlation Networks from Genomic Survey Data , 2012, PLoS Comput. Biol..

[47]  Yi-Tsung Lin,et al.  Seroepidemiology of Klebsiella pneumoniae colonizing the intestinal tract of healthy chinese and overseas chinese adults in Asian countries , 2012, BMC Microbiology.

[48]  Olivier Tenaillon,et al.  The population genetics of commensal Escherichia coli , 2010, Nature Reviews Microbiology.

[49]  B. Spratt,et al.  Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. , 2003, The Journal of infectious diseases.

[50]  A. D. de Almeida,et al.  The Yersinia high-pathogenicity island is present in different members of the family Enterobacteriaceae. , 2000, FEMS microbiology letters.

[51]  B. Levin,et al.  Distribution of multilocus genotypes of Escherichia coli within and between host families , 1984, Journal of Hygiene.

[52]  B. Levin,et al.  Genetic diversity and temporal variation in the E. coli population of a human host. , 1981, Genetics.

[53]  S. Levy,et al.  Competition between congenic Escherichia coli K-12 strains in vivo , 1981, Infection and immunity.

[54]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[55]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .