| scholarly article | Q13442814 |
| P6179 | Dimensions Publication ID | 1009583237 |
| P356 | DOI | 10.1186/S13073-014-0114-2 |
| P932 | PMC publication ID | 4295418 |
| P698 | PubMed publication ID | 25593594 |
| P5875 | ResearchGate publication ID | 270962056 |
| P50 | author | Didier Raoult | Q915676 |
| Pierre-Édouard Fournier | Q21337923 | ||
| Grégory Dubourg | Q88357378 | ||
| P2860 | cites work | Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology | Q21091008 |
| Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction | Q21093392 | ||
| Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species | Q21146381 | ||
| Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010 | Q21534928 | ||
| The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite | Q21563620 | ||
| The Genome Sequence of Mycoplasma hyopneumoniae Strain 232, the Agent of Swine Mycoplasmosis | Q22065453 | ||
| Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen | Q22065490 | ||
| Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic Strains | Q22065493 | ||
| Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete | Q22065559 | ||
| Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks | Q22066331 | ||
| Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis | Q22066387 | ||
| Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus | Q22066388 | ||
| Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 | Q22122370 | ||
| Massive gene decay in the leprosy bacillus | Q22122381 | ||
| Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 | Q22122385 | ||
| Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4 | Q22272632 | ||
| High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak | Q56797252 | ||
| Mycobacterial virulence and specialized secretion: same story, different ending | Q79888530 | ||
| Genetic methods for detection of antimicrobial resistance | Q36003062 | ||
| Cultivating the uncultivated: a community genomics perspective | Q36206955 | ||
| spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation | Q36241116 | ||
| An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis | Q36293969 | ||
| HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci | Q36529720 | ||
| Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak | Q36559099 | ||
| Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. | Q36566426 | ||
| Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene | Q36725704 | ||
| Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory | Q36826739 | ||
| 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls | Q36878347 | ||
| Graphical design of primers with PerlPrimer | Q36977397 | ||
| Bacterial genome sequencing and its use in infectious diseases | Q36982025 | ||
| Clinical and molecular epidemiology of community-onset bacteremia caused by extended-spectrum β-lactamase-producing Escherichia coli over a 6-year period | Q37001723 | ||
| Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak | Q37025859 | ||
| Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic | Q37116927 | ||
| Evolutionary history of Salmonella typhi | Q37119283 | ||
| Suicide PCR on skin biopsy specimens for diagnosis of rickettsioses | Q37156862 | ||
| Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study | Q37311483 | ||
| Towards multitarget testing in molecular microbiology | Q37382970 | ||
| Diverse sources of C. difficile infection identified on whole-genome sequencing | Q37405479 | ||
| Basic concepts of microarrays and potential applications in clinical microbiology | Q37409999 | ||
| Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. | Q37546291 | ||
| Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples | Q37546541 | ||
| High-throughput sequencing and clinical microbiology: progress, opportunities and challenges | Q37789093 | ||
| PCR-electrospray ionization mass spectrometry: the potential to change infectious disease diagnostics in clinical and public health laboratories | Q38009990 | ||
| Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches | Q38031015 | ||
| Overview of molecular typing methods for outbreak detection and epidemiological surveillance. | Q38078090 | ||
| Investigation of antibiotic resistance in the genomic era of multidrug-resistant Gram-negative bacilli, especially Enterobacteriaceae, Pseudomonas and Acinetobacter | Q38086337 | ||
| Analysis of the resistome of a multidrug-resistant NDM-1-producing Escherichia coli strain by high-throughput genome sequencing | Q38282766 | ||
| Emergence of a multidrug-resistant (ASSuTTm) strain of Salmonella enterica serovar Typhimurium DT120 in England in 2011 and the use of multiple-locus variable-number tandem-repeat analysis in supporting outbreak investigations. | Q39381296 | ||
| Use of coagulase gene (coa) repeat region nucleotide sequences for typing of methicillin-resistant Staphylococcus aureus strains | Q39461366 | ||
| Deleterious effect of ciprofloxacin on Rickettsia conorii-infected cells is linked to toxin-antitoxin module up-regulation | Q40291520 | ||
| Use of genome selected repeated sequences increases the sensitivity of PCR detection of Tropheryma whipplei. | Q40470214 | ||
| Deciphering genomic virulence traits of a Staphylococcus epidermidis strain causing native-valve endocarditis | Q40520060 | ||
| Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study | Q41082564 | ||
| Genome of a chronic osteitis-causing Clostridium tetani | Q41684254 | ||
| Development of a rapid microarray-based DNA subtyping assay for the alleles of Shiga toxins 1 and 2 of Escherichia coli | Q41817850 | ||
| Point-of-care syndrome-based, rapid diagnosis of infections on commercial ships | Q42238289 | ||
| Identification of DNA signatures suitable for use in development of real-time PCR assays by whole-genome sequence approaches: use of Streptococcus pyogenes in a pilot study | Q42280623 | ||
| Multispacer typing of Rickettsia prowazekii enabling epidemiological studies of epidemic typhus | Q42537037 | ||
| Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. | Q42645426 | ||
| MLST revisited: the gene-by-gene approach to bacterial genomics. | Q43704503 | ||
| Genomics-based design of defined growth media for the plant pathogen Xylella fastidiosa | Q44320594 | ||
| Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications | Q45237418 | ||
| Treatment of Staphylococcus aureus endocarditis with high doses of trimethoprim/sulfamethoxazole and clindamycin-Preliminary report | Q45349303 | ||
| Genomic diversity and evolution within the species Streptococcus agalactiae | Q46626837 | ||
| Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area | Q46791842 | ||
| Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors | Q50867088 | ||
| Genome-based design of a cell-free culture medium for Tropheryma whipplei | Q51834797 | ||
| Serological and molecular capsular typing, antibiotic susceptibility and multilocus sequence typing of Streptococcus pneumoniae isolates from invasive and non-invasive infections | Q54254437 | ||
| Re: Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany | Q54344428 | ||
| From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence? | Q56780177 | ||
| Solving the problem of comparing whole bacterial genomes across different sequencing platforms | Q35222674 | ||
| Pertussis outbreak, southeastern Minnesota, 2012. | Q35456030 | ||
| Chips with everything: DNA microarrays in infectious diseases | Q35661216 | ||
| Genomic islands in pathogenic and environmental microorganisms | Q35752419 | ||
| Effect of antibiotics on Staphylococcus aureus producing Panton-Valentine leukocidin | Q35758808 | ||
| Revisiting the pestilence of Helicobacter pylori: insights into geographical genomics and pathogen evolution | Q35780872 | ||
| Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. | Q35826708 | ||
| A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012. | Q35892773 | ||
| The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace | Q35905605 | ||
| Microevolution and history of the plague bacillus, Yersinia pestis | Q24558763 | ||
| Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains | Q24558855 | ||
| Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome | Q24561599 | ||
| Genotyping, Orientalis-like Yersinia pestis, and plague pandemics | Q24604095 | ||
| The risk of the hemolytic-uremic syndrome after antibiotic treatment of Escherichia coli O157:H7 infections | Q24623245 | ||
| Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics | Q24625740 | ||
| Host cell-free growth of the Q fever bacterium Coxiella burnetii | Q24656253 | ||
| Molecular identification by "suicide PCR" of Yersinia pestis as the agent of medieval black death | Q24679324 | ||
| Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms | Q24685491 | ||
| Advancements toward a systems level understanding of the human oral microbiome | Q27022745 | ||
| Whole-genome random sequencing and assembly of Haemophilus influenzae Rd | Q27860765 | ||
| Coxiella burnetii genotyping | Q28187651 | ||
| Genome and virulence determinants of high virulence community-acquired MRSA | Q28202214 | ||
| Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei | Q28212154 | ||
| Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis | Q28217152 | ||
| Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany | Q28244221 | ||
| Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction | Q28298254 | ||
| The origin of the Haitian cholera outbreak strain | Q28300132 | ||
| Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor | Q28388579 | ||
| Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax | Q28396307 | ||
| A novel multiplex real-time PCR for the identification of mycobacteria associated with zoonotic tuberculosis | Q28476488 | ||
| Molecular basis of intrinsic macrolide resistance in the Mycobacterium tuberculosis complex | Q28487335 | ||
| Standardized metadata for human pathogen/vector genomic sequences | Q28539782 | ||
| Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study | Q28709007 | ||
| MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity | Q28727934 | ||
| Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth | Q29397612 | ||
| [21] Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction | Q29544077 | ||
| The human microbiome: at the interface of health and disease | Q29614801 | ||
| Whole-genome sequencing and social-network analysis of a tuberculosis outbreak | Q29614802 | ||
| Evolution of MRSA during hospital transmission and intercontinental spread | Q29615141 | ||
| In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data | Q29618471 | ||
| Transforming clinical microbiology with bacterial genome sequencing. | Q30356166 | ||
| Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses. | Q30363330 | ||
| Bacterial strain typing in the genomic era. | Q30377265 | ||
| Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods | Q30464193 | ||
| Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data | Q30582357 | ||
| Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community | Q31009340 | ||
| Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis | Q31148694 | ||
| Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation | Q33395337 | ||
| Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumoniae | Q33521377 | ||
| High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak | Q33532309 | ||
| Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island | Q33557553 | ||
| A microbial detection array (MDA) for viral and bacterial detection | Q33756159 | ||
| BIGSdb: Scalable analysis of bacterial genome variation at the population level. | Q33767145 | ||
| A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples | Q33839439 | ||
| Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis | Q33950950 | ||
| Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012 | Q34020362 | ||
| Actionable diagnosis of neuroleptospirosis by next-generation sequencing | Q34053612 | ||
| Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. | Q34142819 | ||
| Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains | Q34230174 | ||
| Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes | Q34297810 | ||
| Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing. | Q34334717 | ||
| A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. | Q34338220 | ||
| The emergence of mecC methicillin-resistant Staphylococcus aureus | Q34391357 | ||
| A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality | Q34472139 | ||
| Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak | Q34477876 | ||
| Point-of-care laboratory of pathogen diagnosis in rural Senegal | Q34563631 | ||
| Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting | Q34597601 | ||
| Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms | Q34655405 | ||
| Single-Nucleotide-Polymorphism Genotyping of Coxiella burnetii during a Q Fever Outbreak in The Netherlands | Q34738561 | ||
| Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology | Q34822378 | ||
| Molecular evaluation of antibiotic susceptibility: Tropheryma whipplei paradigm | Q34940257 | ||
| Rapid single-colony whole-genome sequencing of bacterial pathogens | Q35076491 | ||
| Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity | Q35089471 | ||
| Metabolic pathways in the post-genome era. | Q35135595 | ||
| Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens | Q35174643 | ||
| Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak | Q35187011 | ||
| Recent advances in genomic DNA sequencing of microbial species from single cells | Q35219184 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 11 | |
| P921 | main subject | genomics | Q222046 |
| P304 | page(s) | 114 | |
| P577 | publication date | 2014-11-29 | |
| P13046 | publication type of scholarly work | review article | Q7318358 |
| P1433 | published in | Genome Medicine | Q15816848 |
| P1476 | title | Clinical detection and characterization of bacterial pathogens in the genomics era. | |
| P478 | volume | 6 |
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