Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

[1]  K. Ko,et al.  Plasmid analysis of Escherichia coli isolates from South Korea co-producing NDM-5 and OXA-181 carbapenemases. , 2019, Plasmid.

[2]  S. Peacock,et al.  Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: A Mathematical Early Modeling Study of Cost-effectiveness , 2019, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[3]  P. Owlia,et al.  Frequency Distribution, Genotypes and the most Prevalent Sequence Types of New Delhi Metallo-beta-lactamase-Producing Escherichia coli among Clinical Isolates around the World; A Review. , 2019, Journal of global antimicrobial resistance.

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

[5]  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.

[6]  Shangshang Qin,et al.  Early emergence of OXA-181-producing Escherichia coli ST410 in China. , 2018, Journal of global antimicrobial resistance.

[7]  A. Sumi,et al.  Prevalence of Extended-Spectrum Beta-Lactamase and Carbapenemase Genes in Clinical Isolates of Escherichia coli in Myanmar: Dominance of blaNDM-5 and Emergence of blaOXA-181. , 2018, Microbial drug resistance.

[8]  Keith A Jolley,et al.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.

[9]  Julian Parkhill,et al.  Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens , 2018, Microbiology.

[10]  H. Hasman,et al.  Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones , 2018, mSphere.

[11]  Kathryn E Holt,et al.  Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens , 2018, Science.

[12]  G. Tsafnat,et al.  Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database , 2018, The Journal of antimicrobial chemotherapy.

[13]  H. Hasman,et al.  Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM-5 on an IncF Multidrug Resistance Plasmid and blaOXA-181 on an IncX3 Plasmid , 2018, Genome Announcements.

[14]  I. Van Walle,et al.  PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance , 2017, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[15]  Julian Parkhill,et al.  ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.

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

[17]  M. Gwinn,et al.  Integrating Advanced Molecular Technologies into Public Health , 2016, Journal of Clinical Microbiology.

[18]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[19]  Andrew J. Page,et al.  Multilocus sequence typing by blast from de novo assemblies against PubMLST , 2016, J. Open Source Softw..

[20]  K. Holt,et al.  Identification of Klebsiella capsule synthesis loci from whole genome data , 2016, bioRxiv.

[21]  Khalil Abudahab,et al.  Microreact: visualizing and sharing data for genomic epidemiology and phylogeography , 2016, Microbial genomics.

[22]  M. Kulldorff,et al.  Statistical detection of geographic clusters of resistant Escherichia coli in a regional network with WHONET and SaTScan , 2016, Expert review of anti-infective therapy.

[23]  Jia Jun Lee,et al.  Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches. , 2016, The Journal of antimicrobial chemotherapy.

[24]  P. Ashton,et al.  Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales. , 2016, The Journal of antimicrobial chemotherapy.

[25]  T. Dallman,et al.  Use of whole-genome sequencing for the public health surveillance of Shigella sonnei in England and Wales, 2015. , 2016, Journal of medical microbiology.

[26]  Julian Parkhill,et al.  Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.

[27]  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.

[28]  Claire Jenkins,et al.  Identification of Salmonella for public health surveillance using whole genome sequencing , 2016, PeerJ.

[29]  Henk C den Bakker,et al.  Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. , 2016, Annual review of food science and technology.

[30]  Simon R. Harris,et al.  SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.

[31]  L. Martínez-Martínez,et al.  First identification of NDM-5 associated with OXA-181 in Escherichia coli from Egypt , 2016, Emerging Microbes & Infections.

[32]  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.

[33]  Jacqueline A. Keane,et al.  Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, Genome Biology.

[34]  Paul Turner,et al.  Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events , 2015, Nature Genetics.

[35]  Z. Zong,et al.  First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing , 2015, Antimicrobial Agents and Chemotherapy.

[36]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[37]  C. Kiffer,et al.  A space–time model for carbapenemase-producing Klebsiella pneumoniae (KPC) cluster quantification in a high-complexity hospital , 2015, Epidemiology and Infection.

[38]  Jacqueline A. Keane,et al.  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.

[39]  Sharon J. Peacock,et al.  Whole-genome sequencing to control antimicrobial resistance , 2014, Trends in genetics : TIG.

[40]  J. Rolain,et al.  Carbapenemase genes and genetic platforms in Gram-negative bacilli: Enterobacteriaceae, Pseudomonas and Acinetobacter species. , 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

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

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

[43]  B. Limbago,et al.  Carbapenem-Resistant Klebsiella pneumoniae Producing New Delhi Metallo-β-Lactamase at an Acute Care Hospital, Colorado, 2012 , 2014, Infection Control & Hospital Epidemiology.

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

[45]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[46]  S. Molnár,et al.  First description of bla(NDM-1), bla(OXA-48), bla(OXA-181) producing Enterobacteriaceae strains in Romania. , 2013, International journal of medical microbiology : IJMM.

[47]  J. Rolain,et al.  ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes , 2013, Antimicrobial Agents and Chemotherapy.

[48]  Julian Parkhill,et al.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study , 2013, The Lancet. Infectious Diseases.

[49]  G. Peirano,et al.  Surveillance and Molecular Epidemiology of Klebsiella pneumoniae Isolates That Produce Carbapenemases: First Report of OXA-48-Like Enzymes in North America , 2012, Antimicrobial Agents and Chemotherapy.

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

[51]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[52]  P. Nordmann,et al.  NDM-1, OXA-48 and OXA-181 carbapenemase-producing Enterobacteriaceae in Sultanate of Oman. , 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[53]  M. Falagas,et al.  Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. , 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[54]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[55]  Robert A. Bonomo,et al.  Carbapenems: Past, Present, and Future , 2011, Antimicrobial Agents and Chemotherapy.

[56]  Nicola K. Petty,et al.  BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons , 2011, BMC Genomics.

[57]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

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

[59]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[60]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[61]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

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

[63]  F. Rodríguez-Valera,et al.  Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of Acinetobacter baumannii , 2005, Journal of Clinical Microbiology.

[64]  Sylvain Brisse,et al.  Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates , 2005, Journal of Clinical Microbiology.

[65]  H. Grundmann,et al.  Development of a Multilocus Sequence Typing Scheme for the Opportunistic Pathogen Pseudomonas aeruginosa , 2004, Journal of Clinical Microbiology.

[66]  T. F. O'Brien,et al.  WHONET: an information system for monitoring antimicrobial resistance. , 1995, Emerging infectious diseases.

[67]  C. Dolea,et al.  World Health Organization , 1949, International Organization.