MLST revisited: the gene-by-gene approach to bacterial genomics

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology

(2013) Marcos Pérez-Losada et al.   INFECTION GENETICS AND EVOLUTION

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

(2013) A. J. Cody et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

(2013) Josephine M Bryant et al.   LANCET

Updating benchtop sequencing performance comparison

(2013) Sebastian Jünemann et al.   NATURE BIOTECHNOLOGY

Bacterial genomes in epidemiology--present and future

(2013) N. J. Croucher et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

High-throughput microbial population genomics using the Cortex variation assembler

(2012) Zamin Iqbal et al.   BIOINFORMATICS

Evolutionary and genomic insights into meningococcal biology

(2012) Holly B Bratcher et al.   Future Microbiology

Meticillin-resistant Staphylococcus aureus (MRSA): global epidemiology and harmonisation of typing methods

(2012) Stefania Stefani et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Genome Sequence of the Halotolerant Staphylococcus sp. Strain OJ82, Isolated from Korean Traditional Salt-Fermented Seafood

(2012) J.-S. Sung et al.   JOURNAL OF BACTERIOLOGY

Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp. Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation

(2012) Teik-Min Chong et al.   JOURNAL OF BACTERIOLOGY

Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods

(2012) K. A. Jolley et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria

(2012) J. S. Bennett et al.   MICROBIOLOGY-SGM

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

(2012) Xosé M. Fernández-Suárez et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics of Prokaryotic Ribosomal Proteins

(2012) Natalya Yutin et al.   PLoS One

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

(2012) Y. Cui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus

(2012) P. R. McAdam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Livestock-associated Staphylococcus aureus: origin, evolution and public health threat

(2012) J. Ross Fitzgerald   TRENDS IN MICROBIOLOGY

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter

(2012) Samuel K. Sheppard et al.   Genes

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Coagulase-negative staphylococci: update on the molecular epidemiology and clinical presentation, with a focus on Staphylococcus epidermidis and Staphylococcus saprophyticus

(2011) M. Widerström et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin

(2011) Deborah C. Holt et al.   Genome Biology and Evolution

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Bacterial epidemiology and biology - lessons from genome sequencing

(2011) Julian Parkhill et al.   GENOME BIOLOGY

Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology

(2010) Pierre-Edouard Fournier et al.   Annual Review of Microbiology

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

(2010) Mark J Pallen et al.   CURRENT OPINION IN MICROBIOLOGY

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

Genomic variation and evolution of Staphylococcus aureus

(2009) Jodi A. Lindsay   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Population structure of Streptococcus oralis

(2009) T. Do et al.   MICROBIOLOGY-SGM

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Development of an unambiguous and discriminatory multilocus sequence typing scheme for the Streptococcus zooepidemicus group

(2008) K. Webb et al.   MICROBIOLOGY-SGM

Emerging patterns in the comparative analysis of phylogenetic community structure

(2008) S. M. VAMOSI et al.   MOLECULAR ECOLOGY

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis

(2008) C. O. Buckee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY