Published in JAMA Intern Med on August 12, 2013
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med (2014) 2.51
The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev (2015) 2.06
Divergent, coexisting Pseudomonas aeruginosa lineages in chronic cystic fibrosis lung infections. Am J Respir Crit Care Med (2015) 2.00
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol (2015) 1.99
Rapid single-colony whole-genome sequencing of bacterial pathogens. J Antimicrob Chemother (2013) 1.66
Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infect Dis (2015) 1.54
New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. MBio (2014) 1.51
Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci U S A (2014) 1.49
Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun (2015) 1.27
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics (2014) 1.27
Whole-genome sequencing to control antimicrobial resistance. Trends Genet (2014) 1.25
Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J Antimicrob Chemother (2015) 1.22
Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing. MBio (2014) 1.12
Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection. J Clin Microbiol (2015) 1.11
Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Med (2014) 1.10
The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrob Agents Chemother (2014) 1.08
Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones? Front Microbiol (2016) 1.03
Long term effect of gut microbiota transfer on diabetes development. J Autoimmun (2014) 1.01
Clinical microbiology informatics. Clin Microbiol Rev (2014) 1.01
Whole-genome sequencing for outbreak investigations of methicillin-resistant Staphylococcus aureus in the neonatal intensive care unit: time for routine practice? Infect Control Hosp Epidemiol (2015) 1.00
Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium. J Clin Microbiol (2015) 0.99
Towards a global antibiotic resistance surveillance system: a primer for a roadmap. Ups J Med Sci (2014) 0.97
Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J Clin Microbiol (2015) 0.96
Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol (2014) 0.95
Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med (2014) 0.94
Whole-genome sequencing in bacteriology: state of the art. Infect Drug Resist (2013) 0.94
Within-host evolution of bacterial pathogens. Nat Rev Microbiol (2016) 0.94
Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing. MBio (2015) 0.93
Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. J Clin Microbiol (2014) 0.93
Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe. MBio (2016) 0.91
Rapid resistome fingerprinting and clonal lineage profiling of carbapenem-resistant Klebsiella pneumoniae isolates by targeted next-generation sequencing. J Clin Microbiol (2014) 0.90
Molecular analysis and distribution of multidrug-resistant Enterococcus faecium isolates belonging to clonal complex 17 in a tertiary care center in Mexico City. BMC Microbiol (2013) 0.86
Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England. J Infect Dis (2016) 0.86
An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food. Front Microbiol (2015) 0.85
The time is now for gene- and genome-based bacterial diagnostics: "you say you want a revolution". JAMA Intern Med (2013) 0.84
Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks. J Clin Microbiol (2015) 0.83
Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics. Tetrahedron (2015) 0.82
Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network. Genome Med (2016) 0.82
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology. Microb Genom (2016) 0.80
Meningococcal vaccine antigen diversity in global databases. Euro Surveill (2015) 0.80
Comprehensive Characterization of Escherichia coli O104:H4 Isolated from Patients in the Netherlands. Front Microbiol (2015) 0.79
A glimpse into evolution and dissemination of multidrug-resistant Acinetobacter baumannii isolates in East Asia: a comparative genomics study. Sci Rep (2016) 0.78
In Vivo and In Vitro Efficacy of Minocycline-Based Combination Therapy for Minocycline-Resistant Acinetobacter baumannii. Antimicrob Agents Chemother (2016) 0.75
K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microb Genom (2015) 0.75
Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms (2015) 0.75
Altered Outer Membrane Transcriptome Balance with AmpC Overexpression in Carbapenem-Resistant Enterobacter cloacae. Front Microbiol (2016) 0.75
Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. Front Microbiol (2016) 0.75
Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England. Sci Rep (2017) 0.75
Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microb Genom (2017) 0.75
Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing. J Clin Microbiol (2017) 0.75
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A (1998) 39.20
Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis (2010) 35.92
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
AmpC beta-lactamases. Clin Microbiol Rev (2009) 7.14
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Epidemic meningitis, meningococcaemia, and Neisseria meningitidis. Lancet (2007) 5.11
Multiplex PCR for rapid detection of genes encoding acquired metallo-beta-lactamases. J Antimicrob Chemother (2006) 4.73
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet (2012) 4.29
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open (2012) 3.93
Emerging carbapenemases: a global perspective. Int J Antimicrob Agents (2010) 3.54
The future of antibiotics and resistance. N Engl J Med (2013) 3.47
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci U S A (2012) 3.29
Molecular mechanisms disrupting porin expression in ertapenem-resistant Klebsiella and Enterobacter spp. clinical isolates from the UK. J Antimicrob Chemother (2009) 3.09
Regulation of inducible AmpC beta-lactamase expression among Enterobacteriaceae. Curr Pharm Des (1999) 2.31
Transition of Enterococcus faecium from commensal organism to nosocomial pathogen. Future Microbiol (2009) 2.06
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A (2012) 1.83
Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047. J Bacteriol (2010) 1.76
Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog (2010) 1.66
Biology and pathogenesis of the evolutionarily successful, obligate human bacterium Neisseria meningitidis. Vaccine (2009) 1.52
Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods. J Clin Microbiol (2012) 1.50
Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol (2012) 1.49
Meningococcal disease: changes in epidemiology and prevention. Clin Epidemiol (2012) 1.48
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol (2012) 1.43
Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. Microbiology (2009) 1.14
In vivo capsular switch in Streptococcus pneumoniae--analysis by whole genome sequencing. PLoS One (2012) 0.95
IMP metallo-β-lactamase-producing clinical isolates of Enterobacter cloacae in the UK. J Antimicrob Chemother (2011) 0.85
Molecular testing for infectious diseases should be done in the clinical microbiology laboratory. J Clin Microbiol (2012) 0.83
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Enterotypes of the human gut microbiome. Nature (2011) 24.36
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Prepublication data sharing. Nature (2009) 12.24
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet (2003) 9.13
Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet (2006) 8.02
How clonal is Staphylococcus aureus? J Bacteriol (2003) 7.97
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents (2006) 7.58
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2004) 7.30
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis (2012) 7.18
Melioidosis. N Engl J Med (2012) 6.94
The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A (2003) 6.79
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36
Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei. Nat Rev Microbiol (2006) 6.34
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis (2011) 6.08
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. J Bacteriol (2007) 5.88
Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol (2011) 5.60
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43
Spondylodiscitis: update on diagnosis and management. J Antimicrob Chemother (2010) 5.26
Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol (2005) 5.20
Increasing incidence of human melioidosis in Northeast Thailand. Am J Trop Med Hyg (2010) 5.10
Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04
Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet (2013) 4.75
Multiplex PCR for rapid detection of genes encoding acquired metallo-beta-lactamases. J Antimicrob Chemother (2006) 4.73
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics (2006) 4.27
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet (2012) 4.10
Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum (beta)-lactamases. J Antimicrob Chemother (2005) 4.04
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet (2013) 3.89
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol (2008) 3.85
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog (2012) 3.81
Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci U S A (2007) 3.73
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol (2009) 3.66
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol (2007) 3.62