Refining the definition of the avian pathogenic Escherichia coli (APEC) pathotype through inclusion of high-risk clonal groups

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

(2021) Leonardos Mageiros et al.   Nature Communications

The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes

(2021) Jai W. Mehat et al.   AVIAN PATHOLOGY

Whole genome sequencing analysis of avian pathogenic Escherichia coli from China

(2021) Xuhua Chen et al.   VETERINARY MICROBIOLOGY

In silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data

(2020) Anna Maria Malberg Tetzschner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

(2019) Zhemin Zhou et al.   GENOME RESEARCH

Estimating Pangenomes with Roary

(2019) Farrah Sitto et al.   MOLECULAR BIOLOGY AND EVOLUTION

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

(2018) Zhemin Zhou et al.   GENOME RESEARCH

Characterization of Escherichia coli causing cellulitis in broilers

(2018) Louise Ladefoged Poulsen et al.   VETERINARY MICROBIOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Evaluation of Escherichia coli isolates from healthy chickens to determine their potential risk to poultry and human health

(2017) Zachary R. Stromberg et al.   PLoS One

Pathology and Molecular Characterization ofEscherichia ColiAssociated With the Avian Salpingitis-Peritonitis Disease Syndrome

(2016) Rikke Heidemann Olsen et al.   AVIAN DISEASES

Comparative genomics of European avian pathogenic E. Coli (APEC)

(2016) Guido Cordoni et al.   BMC GENOMICS

Diversity of Escherichia coli strains involved in vertebral osteomyelitis and arthritis in broilers in Brazil

(2016) Juliana Fortes Vilarinho Braga et al.   BMC Veterinary Research

Structure and genetics of the O-antigens of Escherichia coli O182–O187

(2016) Sof’ya N. Senchenkova et al.   CARBOHYDRATE RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Development of an Allele-Specific PCR Assay for Simultaneous Sero-Typing of Avian Pathogenic Escherichia coli Predominant O1, O2, O18 and O78 Strains

(2014) Shaohui Wang et al.   PLoS One

Overlapped Sequence Types (STs) and Serogroups of Avian Pathogenic (APEC) and Human Extra-Intestinal Pathogenic (ExPEC) Escherichia coli Isolated in Brazil

(2014) Renato Pariz Maluta et al.   PLoS One

Comparison of Multilocus Sequence Analysis and Virulence Genotyping of Escherichia coli from Live Birds, Retail Poultry Meat, and Human Extraintestinal Infection

(2013) Jessica L. Danzeisen et al.   AVIAN DISEASES

Molecular and Phenotypic Characterization of Escherichia coli Isolated from Broiler Chicken Flocks in Egypt

(2013) Ashraf H. M. Hussein et al.   AVIAN DISEASES

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

Genetic diversity and virulence profiles of Escherichia coli causing salpingitis and peritonitis in broiler breeders

(2012) Teresa Pires-dos-Santos et al.   VETERINARY MICROBIOLOGY

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

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Examination of the Source and Extended Virulence Genotypes of Escherichia coli Contaminating Retail Poultry Meat

(2009) Timothy J. Johnson et al.   Foodborne Pathogens and Disease

Plasmid-Borne Virulence-Associated Genes Have a Conserved Organization in Virulent Strains of Avian Pathogenic Escherichia coli

(2009) K. A. Tivendale et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mutational and transcriptional analyses of an avian pathogenic Escherichia coli ColV plasmid

(2008) Jerod A Skyberg et al.   BMC MICROBIOLOGY

Identification of Minimal Predictors of Avian Pathogenic Escherichia coli Virulence for Use as a Rapid Diagnostic Tool

(2008) T. J. Johnson et al.   JOURNAL OF CLINICAL MICROBIOLOGY