Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains

[1]  N. Nagarajan,et al.  Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore , 2022, Emerging infectious diseases.

[2]  Natalia Khalatyan,et al.  Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates , 2022, BMC Infectious Diseases.

[3]  Jing Wu,et al.  Sequence-Based Genomic Analysis Reveals Transmission of Antibiotic Resistance and Virulence among Carbapenemase-Producing Klebsiella pneumoniae Strains , 2022, mSphere.

[4]  Rong Zhang,et al.  Molecular epidemiology of carbapenem-resistant hypervirulent Klebsiella pneumoniae in China , 2022, Emerging microbes & infections.

[5]  Rong Zhang,et al.  Molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in China, 2016-20. , 2022, Lancet. Infectious Diseases (Print).

[6]  K. Holt,et al.  ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting , 2021, medRxiv.

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

[8]  Ashok Kumar,et al.  Extensively Drug-Resistant Hypervirulent Klebsiella pneumoniae From a Series of Neonatal Sepsis in a Tertiary Care Hospital, India , 2021, Frontiers in Medicine.

[9]  Y. Duan,et al.  Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data , 2021, bioRxiv.

[10]  E. van Nimwegen,et al.  Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species , 2021, eLife.

[11]  L. Bobay,et al.  Impact of homologous recombination on core genome phylogenies , 2020, BMC Genomics.

[12]  Alex Diaz-Papkovich,et al.  A review of UMAP in population genetics , 2020, Journal of human genetics.

[13]  T. Naas,et al.  Emergence of New Non–Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae Isolates, France , 2020, Emerging infectious diseases.

[14]  K. Bush,et al.  Epidemiology of β-Lactamase-Producing Pathogens , 2020, Clinical Microbiology Reviews.

[15]  N. P. H. Lan,et al.  Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia , 2019, Genome Medicine.

[16]  J. E. Choby,et al.  Hypervirulent Klebsiella pneumoniae – clinical and molecular perspectives , 2020, Journal of internal medicine.

[17]  T. M. Venancio,et al.  Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes , 2019, The FEBS journal.

[18]  T. M. Venancio,et al.  Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes , 2019, bioRxiv.

[19]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[20]  N. Thomson,et al.  Complement Susceptibility in Relation to Genome Sequence of Recent Klebsiella pneumoniae Isolates from Thai Hospitals , 2018, mSphere.

[21]  K. Holt,et al.  Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae , 2018, bioRxiv.

[22]  S. Partridge,et al.  Mobile Genetic Elements Associated with Antimicrobial Resistance , 2018, Clinical Microbiology Reviews.

[23]  K. Holt,et al.  Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae , 2018, Genome Medicine.

[24]  Mark A. Miller,et al.  Identification of Biomarkers for Differentiation of Hypervirulent Klebsiella pneumoniae from Classical K. pneumoniae , 2018, Journal of Clinical Microbiology.

[25]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction , 2018, ArXiv.

[26]  U. Garza-Ramos,et al.  Hypervirulence and hypermucoviscosity: Two different but complementary Klebsiella spp. phenotypes? , 2017, Virulence.

[27]  Robert A. Weinstein,et al.  The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace , 2017, The Journal of infectious diseases.

[28]  Ruobing Wang,et al.  High Prevalence of Hypervirulent Klebsiella pneumoniae Infection in China: Geographic Distribution, Clinical Characteristics, and Antimicrobial Resistance , 2016, Antimicrobial Agents and Chemotherapy.

[29]  Huang Gao,et al.  Database resources of the National Center for Biotechnology Information , 2015, Nucleic Acids Res..

[30]  Amy K. Cain,et al.  The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource , 2015, Genome Medicine.

[31]  Xiumei Xiao,et al.  Clinical and molecular characteristics of multi-clone carbapenem-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae isolates in a tertiary hospital in Beijing, China. , 2015, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

[32]  P. Andersen,et al.  Mapping the Evolution of Hypervirulent Klebsiella pneumoniae , 2015, mBio.

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

[34]  T. Russo,et al.  Hypervirulent Klebsiella pneumoniae , 2014, Open forum infectious diseases.

[35]  R. Evans.  European Centre for Disease Prevention and Control. , 2014, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

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

[37]  Ricardo J. G. B. Campello,et al.  Density-Based Clustering Based on Hierarchical Density Estimates , 2013, PAKDD.

[38]  J. Iredell,et al.  Genetic Contexts of blaNDM-1 , 2012, Antimicrobial Agents and Chemotherapy.

[39]  Thomas L. Madden,et al.  Domain enhanced lookup time accelerated BLAST , 2012, Biology Direct.

[40]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[41]  Hongbin Zha,et al.  Riemannian Manifold Learning , 2008, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[42]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .