Published in BMC Genomics on December 13, 2012
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol (2013) 1.86
Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS One (2014) 1.78
Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One (2014) 1.47
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics (2014) 1.36
Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics (2015) 1.27
WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare? Pathogens (2014) 1.02
Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis. Genome Biol Evol (2014) 0.98
Genomic signature of multidrug-resistant Salmonella enterica serovar typhi isolates related to a massive outbreak in Zambia between 2010 and 2012. J Clin Microbiol (2014) 0.97
Internet-based solutions for analysis of next-generation sequence data. J Clin Microbiol (2013) 0.96
Complete sequence of pABTJ2, a plasmid from Acinetobacter baumannii MDR-TJ, carrying many phage-like elements. Genomics Proteomics Bioinformatics (2014) 0.89
Genome sequencing and genomic characterization of a tigecycline-resistant Klebsiella pneumoniae strain isolated from the bile samples of a cholangiocarcinoma patient. Gut Pathog (2014) 0.88
Genome analysis of 17 extensively drug-resistant strains reveals new potential mutations for resistance. Genome Announc (2014) 0.88
Characterization of a novel composite staphylococcal cassette chromosome mec (SCCmec-SCCcad/ars/cop) in the neonatal sepsis-associated Staphylococcus capitis pulsotype NRCS-A. Antimicrob Agents Chemother (2013) 0.88
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes (Basel) (2014) 0.87
It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source. J Clin Microbiol (2015) 0.87
Advances in translational bioinformatics and population genomics in the Asia-Pacific. BMC Genomics (2012) 0.86
Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics (2015) 0.84
Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014. PLoS One (2015) 0.81
Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence. BMC Genomics (2015) 0.81
Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. BMC Evol Biol (2016) 0.81
Genomic and Phenomic Study of Mammary Pathogenic Escherichia coli. PLoS One (2015) 0.81
Whole-Genome Comparison Uncovers Genomic Mutations between Group B Streptococci Sampled from Infected Newborns and Their Mothers. J Bacteriol (2015) 0.81
PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing. Sci Rep (2016) 0.80
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. PLoS One (2016) 0.79
Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates. BMC Genomics (2014) 0.78
Genomic dissection of travel-associated extended-spectrum-beta-lactamase-producing Salmonella enterica serovar typhi isolates originating from the Philippines: a one-off occurrence or a threat to effective treatment of typhoid fever? J Clin Microbiol (2014) 0.78
Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104. Appl Environ Microbiol (2016) 0.78
Simultaneous Presence of Insertion Sequence Excision Enhancer and Insertion Sequence IS629 Correlates with Increased Diversity and Virulence in Shiga Toxin-Producing Escherichia coli. J Clin Microbiol (2015) 0.78
Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections. PLoS One (2016) 0.78
Parallel Evolution in Streptococcus pneumoniae Biofilms. Genome Biol Evol (2016) 0.76
GcoGSA-BA: a global core genome SNP analysis for Bacillus anthracis. Health Secur (2015) 0.75
Capsule Switching and Antimicrobial Resistance Acquired during Repeated Streptococcus pneumoniae Pneumonia Episodes. J Clin Microbiol (2015) 0.75
Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. BMC Genomics (2017) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
The variant call format and VCFtools. Bioinformatics (2011) 25.88
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio (2012) 6.50
Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio (2011) 4.70
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open (2012) 3.93
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A (2012) 3.42
Bacterial epidemiology and biology--lessons from genome sequencing. Genome Biol (2011) 2.18
High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease. Clin Infect Dis (2012) 1.47
Choosing an appropriate bacterial typing technique for epidemiologic studies. Epidemiol Perspect Innov (2005) 1.13
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio (2012) 6.50
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio (2011) 4.70
beta-Lactamases among extended-spectrum beta-lactamase (ESBL)-resistant Salmonella from poultry, poultry products and human patients in The Netherlands. J Antimicrob Chemother (2005) 3.82
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill (2015) 3.13
International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin. J Infect Dis (2011) 2.70
Global monitoring of Salmonella serovar distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: results of quality assured laboratories from 2001 to 2007. Foodborne Pathog Dis (2011) 2.56
World Health Organization ranking of antimicrobials according to their importance in human medicine: A critical step for developing risk management strategies for the use of antimicrobials in food production animals. Clin Infect Dis (2009) 2.54
Pigs as source of methicillin-resistant Staphylococcus aureus CC398 infections in humans, Denmark. Emerg Infect Dis (2008) 2.52
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother (2012) 2.23
Results of use of WHO Global Salm-Surv external quality assurance system for antimicrobial susceptibility testing of Salmonella isolates from 2000 to 2007. J Clin Microbiol (2008) 2.02
Association between antimicrobial resistance in Escherichia coli isolates from food animals and blood stream isolates from humans in Europe: an ecological study. Foodborne Pathog Dis (2011) 1.99
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol (2013) 1.86
The Salmonella enterica pan-genome. Microb Ecol (2011) 1.76
IS21-558 insertion sequences are involved in the mobility of the multiresistance gene cfr. Antimicrob Agents Chemother (2006) 1.74
Human deaths and third-generation cephalosporin use in poultry, Europe. Emerg Infect Dis (2013) 1.66
Salmonella serovars from humans and other sources in Thailand, 1993-2002. Emerg Infect Dis (2004) 1.65
tcrB, a gene conferring transferable copper resistance in Enterococcus faecium: occurrence, transferability, and linkage to macrolide and glycopeptide resistance. Antimicrob Agents Chemother (2002) 1.63
Benchmarking of methods for genomic taxonomy. J Clin Microbiol (2014) 1.51
GenePublisher: Automated analysis of DNA microarray data. Nucleic Acids Res (2003) 1.45
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics (2012) 1.43
WHO global salm-surv external quality assurance system (EQAS): an important step toward improving the quality of Salmonella serotyping and antimicrobial susceptibility testing worldwide. Microb Drug Resist (2002) 1.38
In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards. Clin Infect Dis (2012) 1.28
An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol (2006) 1.28
Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. MBio (2013) 1.27
Molecular characterization and antimicrobial susceptibility of Salmonella isolates from infections in humans in Henan Province, China. J Clin Microbiol (2008) 1.25
Zinc resistance of Staphylococcus aureus of animal origin is strongly associated with methicillin resistance. Vet Microbiol (2011) 1.24
Broiler chickens, broiler chicken meat, pigs and pork as sources of ExPEC related virulence genes and resistance in Escherichia coli isolates from community-dwelling humans and UTI patients. Int J Food Microbiol (2010) 1.24
Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics (2012) 1.23
International collaborative study on the occurrence of plasmid-mediated quinolone resistance in Salmonella enterica and Escherichia coli isolated from animals, humans, food and the environment in 13 European countries. J Antimicrob Chemother (2011) 1.22
Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J (2011) 1.22
Prevalence and characterization of human Shigella infections in Henan Province, China, in 2006. J Clin Microbiol (2010) 1.22
Escherichia coli isolates from broiler chicken meat, broiler chickens, pork, and pigs share phylogroups and antimicrobial resistance with community-dwelling humans and patients with urinary tract infection. Foodborne Pathog Dis (2010) 1.18
External quality assurance system for antibiotic resistance in bacteria of animal origin in Europe (ARBAO-II), 2003. Vet Microbiol (2006) 1.18
A virulent parent with probiotic progeny: comparative genomics of Escherichia coli strains CFT073, Nissle 1917 and ABU 83972. Mol Genet Genomics (2010) 1.17
Molecular characterization and antimicrobial susceptibility testing of Escherichia coli isolates from patients with urinary tract infections in 20 Chinese hospitals. J Clin Microbiol (2011) 1.16
Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A (2013) 1.15
Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism. Immunology (2010) 1.15
Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs. J Antimicrob Chemother (2012) 1.11
Relationship between copper, glycopeptide, and macrolide resistance among Enterococcus faecium strains isolated from pigs in Denmark between 1997 and 2003. Antimicrob Agents Chemother (2005) 1.10
Emergence of multidrug-resistant salmonella concord infections in Europe and the United States in children adopted from Ethiopia, 2003-2007. Pediatr Infect Dis J (2009) 1.08
Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- and Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals. J Antimicrob Chemother (2009) 1.06
First description of meticillin-resistant Staphylococcus aureus (MRSA) CC30 and CC398 from swine in Portugal. Int J Antimicrob Agents (2009) 1.06
Antimicrobial-resistant Shigella infections from Iran: an overlooked problem? J Antimicrob Chemother (2012) 1.04
Danish integrated antimicrobial resistance monitoring and research program. Emerg Infect Dis (2007) 1.04
Molecular characterization of extended-spectrum cephalosporinase-producing Salmonella enterica serovar Choleraesuis isolates from patients in Thailand and Denmark. J Clin Microbiol (2009) 1.03
Multidrug resistance among different serotypes of clinical Salmonella isolates in Taiwan. Diagn Microbiol Infect Dis (2006) 1.02
Prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in Danish slaughter pigs and retail meat identified by selective enrichment and association with cephalosporin usage. J Antimicrob Chemother (2011) 1.02
Prevalence of antimicrobial resistance among bacterial pathogens isolated from cattle in different European countries: 2002-2004. Acta Vet Scand (2008) 1.02
International spread of bla(CMY-2)-mediated cephalosporin resistance in a multiresistant Salmonella enterica serovar Heidelberg isolate stemming from the importation of a boar by Denmark from Canada. Antimicrob Agents Chemother (2004) 1.00
Streptogramin resistance among Enterococcus faecium isolated from production animals in Denmark in 1997. Microb Drug Resist (2002) 1.00
Characterization of isolates of Salmonella enterica serovar Stanley, a serovar endemic to Asia and associated with travel. J Clin Microbiol (2012) 1.00
Characterization of antimicrobial resistance in Salmonella enterica food and animal isolates from Colombia: identification of a qnrB19-mediated quinolone resistance marker in two novel serovars. FEMS Microbiol Lett (2010) 1.00
Antimicrobial susceptibility and serovars of Salmonella from chickens and humans in Ibadan, Nigeria. J Infect Dev Ctries (2010) 0.99
Risk factors and epidemiology of the ten most common Salmonella serovars from patients in Thailand: 2002-2007. Foodborne Pathog Dis (2009) 0.98
Antimicrobial resistance and molecular epidemiology of Salmonella Rissen from animals, food products, and patients in Thailand and Denmark. Foodborne Pathog Dis (2008) 0.98
Susceptibility of Escherichia coli and Enterococcus faecium isolated from pigs and broiler chickens to tetracycline degradation products and distribution of tetracycline resistance determinants in E. coli from food animals. Vet Microbiol (2003) 0.97
The attribution of human infections with antimicrobial resistant Salmonella bacteria in Denmark to sources of animal origin. Foodborne Pathog Dis (2007) 0.97
First description of an oxyimino-cephalosporin-resistant, ESBL-carrying Escherichia coli isolated from meat sold in Denmark. J Antimicrob Chemother (2006) 0.97
First description of blaCTX-M-1-carrying Escherichia coli isolates in Danish primary food production. J Antimicrob Chemother (2006) 0.96
Shigella from humans in Thailand during 1993 to 2006: spatial-time trends in species and serotype distribution. Foodborne Pathog Dis (2008) 0.95
The proteome of seed development in the model legume Lotus japonicus. Plant Physiol (2009) 0.94
Occurrence of integrons and antimicrobial resistance genes among Salmonella enterica from Brazil. J Antimicrob Chemother (2006) 0.94
Microbiologic and clinical features of Salmonella species isolated from bacteremic children in eastern Democratic Republic of Congo. Pediatr Infect Dis J (2010) 0.94
Occurrence of antimicrobial resistance among bacterial pathogens and indicator bacteria in pigs in different European countries from year 2002 - 2004: the ARBAO-II study. Acta Vet Scand (2008) 0.94
Diversity and stability of plasmids from glycopeptide-resistant Enterococcus faecium (GRE) isolated from pigs in Denmark. Microb Drug Resist (2005) 0.93
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics (2009) 0.93
Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast (2004) 0.92
Extended-spectrum beta-lactamases, food, and cephalosporin use in food animals. Clin Infect Dis (2007) 0.92
Antimicrobial susceptibility and tetracycline resistance determinant genotyping of Gallibacterium anatis. Vet Microbiol (2010) 0.92
Bifidobacterium bifidum actively changes the gene expression profile induced by Lactobacillus acidophilus in murine dendritic cells. PLoS One (2010) 0.92
WHO Global Salm-Surv external quality assurance system for serotyping of Salmonella isolates from 2000 to 2007. J Clin Microbiol (2009) 0.92
Clonal diversity of Staphylococcus aureus originating from the small ruminants goats and sheep. Vet Microbiol (2011) 0.92
Molecular characterization and occurrence of extended-spectrum beta-lactamase resistance genes among Salmonella enterica serovar Corvallis from Thailand, Bulgaria, and Denmark. Microb Drug Resist (2006) 0.92
Occurrence of integrons and resistance genes among sulphonamide-resistant Shigella spp. from Brazil. J Antimicrob Chemother (2005) 0.91
Antimicrobial resistance in Salmonella spp. recovered from patients admitted to six different hospitals in Tehran, Iran from 2007 to 2008. Folia Microbiol (Praha) (2012) 0.91
Study of methicillin resistant Staphylococcus aureus (MRSA) in Danish pigs at slaughter and in imported retail meat reveals a novel MRSA type in slaughter pigs. Vet Microbiol (2011) 0.90
Prevalence and characterization of cephalosporin resistance in nonpathogenic Escherichia coli from food-producing animals slaughtered in Poland. Microb Drug Resist (2011) 0.90
Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo. J Infect Dev Ctries (2013) 0.89
IS6100-mediated genetic rearrangement within the complex class 1 integron In104 of the Salmonella genomic island 1. J Antimicrob Chemother (2010) 0.89
Establishing streptomycin epidemiological cut-off values for Salmonella and Escherichia coli. Microb Drug Resist (2011) 0.88
Complete genes may pass from food to human blood. PLoS One (2013) 0.87
Vancomycin-resistant Enterococcus faecalis isolates from a Danish patient and two healthy human volunteers are possibly related to isolates from imported turkey meat. J Antimicrob Chemother (2008) 0.87
Antimicrobial drug resistance of Salmonella isolates from meat and humans, Denmark. Emerg Infect Dis (2007) 0.87