Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

(2016) Nicole Stoesser et al.   mBio

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

Emergence and spread of O16-ST131 and O25b-ST131 clones among faecal CTX-M-producingEscherichia coliin healthy individuals in Hunan Province, China

(2015) Yi-Ming Zhong et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

(2015) Lucy A. Weinert et al.   Nature Communications

A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131

(2014) Ritu Banerjee et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Plasmid-Mediated Resistance to Cephalosporins and Fluoroquinolones in Various Escherichia coli Sequence Types Isolated from Rooks Wintering in Europe

(2014) Ivana Jamborova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus

(2014) Abdulaziz Alqasim et al.   BMC GENOMICS

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Transfer of noncoding DNA drives regulatory rewiring in bacteria

(2014) Yaara Oren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel independent evolution of pathogenicity within the genus Yersinia

(2014) S. Reuter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global dissemination of a multidrug resistant Escherichia coli clone

(2014) N. K. Petty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

(2014) A. San Millan et al.   Nature Communications

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

(2014) Mark de Been et al.   PLoS Genetics

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

(2014) Jason W. Sahl et al.   PeerJ

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

(2013) Alan McNally et al.   Genome Biology and Evolution

Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts

(2013) A. E. Mather et al.   SCIENCE

The Epidemic of Extended-Spectrum- -Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx

(2013) L. B. Price et al.   mBio

Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections

(2012) G. Clark et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

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

(2011) Ankur Mutreja et al.   NATURE

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms

(2011) Makrina Totsika et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Regional survey of CTX-M-type extended-spectrum  -lactamases among Enterobacteriaceae reveals marked heterogeneity in the distribution of the ST131 clone

(2010) L. Xu et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Detection of pandemic B2-O25-ST131 Escherichia coli harbouring the CTX-M-9 extended-spectrum  -lactamase type in a feral urban brown rat (Rattus norvegicus)

(2010) S. Guenther et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

(2008) A. Koeppel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE