Published in Annu Rev Microbiol on January 01, 2008
Global trends in typhoid and paratyphoid Fever. Clin Infect Dis (2010) 5.25
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet (2010) 4.35
The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One (2010) 4.19
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One (2009) 4.13
Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A (2008) 3.52
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet (2011) 3.44
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics (2009) 2.89
Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet (2009) 2.76
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (2012) 2.72
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res (2014) 2.54
Probable zoonotic leprosy in the southern United States. N Engl J Med (2011) 2.22
Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A (2012) 2.22
Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One (2009) 2.20
Bacterial epidemiology and biology--lessons from genome sequencing. Genome Biol (2011) 2.18
Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. PLoS Pathog (2010) 2.06
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol (2012) 2.04
Impact of recombination on bacterial evolution. Trends Microbiol (2010) 1.98
The past and future of tuberculosis research. PLoS Pathog (2009) 1.94
Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet (2010) 1.89
Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J Bacteriol (2009) 1.83
The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet (2011) 1.75
Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS One (2012) 1.75
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc Natl Acad Sci U S A (2014) 1.73
Does M. tuberculosis genomic diversity explain disease diversity? Drug Discov Today Dis Mech (2010) 1.67
Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS One (2013) 1.67
Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing. Environ Microbiol (2011) 1.64
Pre-Columbian origins for North American anthrax. PLoS One (2009) 1.63
Recombination and population structure in Salmonella enterica. PLoS Genet (2011) 1.61
High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms. PLoS One (2012) 1.59
Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol (2009) 1.58
Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. Euro Surveill (2013) 1.53
Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing. PLoS One (2013) 1.52
Landscape epidemiology of tularemia outbreaks in Sweden. Emerg Infect Dis (2009) 1.52
The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathog (2011) 1.52
Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. Biomed Res Int (2014) 1.47
Typhoid toxin provides a window into typhoid fever and the biology of Salmonella Typhi. Proc Natl Acad Sci U S A (2016) 1.43
High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect Dis (2010) 1.40
Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies. Future Microbiol (2011) 1.39
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res (2012) 1.38
Single nucleotide polymorphism typing of Mycobacterium ulcerans reveals focal transmission of buruli ulcer in a highly endemic region of Ghana. PLoS Negl Trop Dis (2010) 1.37
Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Mol Biol Evol (2010) 1.34
Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing. PLoS Pathog (2009) 1.33
Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol (2014) 1.30
Host association of Campylobacter genotypes transcends geographic variation. Appl Environ Microbiol (2010) 1.29
"Epidemic clones" of Listeria monocytogenes are widespread and ancient clonal groups. J Clin Microbiol (2013) 1.28
Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philos Trans R Soc Lond B Biol Sci (2012) 1.28
Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06. BMC Genomics (2010) 1.27
Genotype of a historic strain of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2012) 1.27
Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A (2012) 1.26
Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clin Microbiol Infect (2011) 1.26
Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair. PLoS One (2011) 1.26
Genomic diversity of Lactobacillus salivarius. Appl Environ Microbiol (2010) 1.25
Twenty years of bacterial genome sequencing. Nat Rev Microbiol (2015) 1.22
Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol (2010) 1.22
Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis (Edinb) (2012) 1.18
Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA. ISME J (2011) 1.16
Comparative review of Francisella tularensis and Francisella novicida. Front Cell Infect Microbiol (2014) 1.16
Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother (2012) 1.16
Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011-2013. Clin Microbiol Infect (2014) 1.16
The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog (2013) 1.15
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect Genet Evol (2011) 1.15
A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. J Antimicrob Chemother (2010) 1.15
Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol (2011) 1.13
Combined species identification, genotyping, and drug resistance detection of Mycobacterium tuberculosis cultures by MLPA on a bead-based array. PLoS One (2012) 1.12
Bacterial genomes in epidemiology--present and future. Philos Trans R Soc Lond B Biol Sci (2013) 1.11
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples. J Clin Microbiol (2015) 1.10
Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One (2013) 1.06
A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria. Appl Environ Microbiol (2010) 1.05
Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol (2013) 1.05
sRNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol (2012) 1.04
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS One (2011) 1.03
Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements. BMC Genomics (2014) 1.03
A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci (2015) 1.02
Ancestral lineages of human enterotoxigenic Escherichia coli. J Clin Microbiol (2010) 1.02
A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One (2014) 1.02
Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. MBio (2014) 1.00
A role for systems epidemiology in tuberculosis research. Trends Microbiol (2011) 0.99
Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa. Appl Environ Microbiol (2013) 0.98
Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci U S A (2015) 0.98
Syphilis at the crossroad of phylogenetics and paleopathology. PLoS Negl Trop Dis (2010) 0.97
Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions. Appl Environ Microbiol (2009) 0.96
Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc Natl Acad Sci U S A (2011) 0.95
One-step triplex high-resolution melting analysis for rapid identification and simultaneous subtyping of frequently isolated Salmonella serovars. Appl Environ Microbiol (2012) 0.94
Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008. Emerg Infect Dis (2010) 0.94
Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS Negl Trop Dis (2015) 0.93
Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and Schu S4. PLoS One (2010) 0.93
Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica Serovar Typhimurium. J Clin Microbiol (2012) 0.93
Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays. BMC Microbiol (2012) 0.93
rhs genes are potential markers for multilocus sequence typing of Escherichia coli O157:H7 strains. Appl Environ Microbiol (2009) 0.93
SNP-based typing: a useful tool to study Bordetella pertussis populations. PLoS One (2011) 0.93
Genetic populations of Bacillus anthracis isolates from Korea. J Vet Sci (2012) 0.93
Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains. Infect Genet Evol (2013) 0.93
Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3. PLoS One (2014) 0.92
Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes. MBio (2016) 0.92
Disrupted human-pathogen co-evolution: a model for disease. Front Genet (2014) 0.92
Francisella tularensis molecular typing using differential insertion sequence amplification. J Clin Microbiol (2011) 0.92
Evolutionary and genomic insights into meningococcal biology. Future Microbiol (2012) 0.90
Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle, and koalas. J Clin Microbiol (2013) 0.89