Examination ofMycobacterium aviumsubspeciesparatuberculosismixed genotype infections in dairy animals using a whole genome sequencing approach

Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis

(2016) Josephine M. Bryant et al.   BMC GENOMICS

Whole-genome sequencing as standard practice for the analysis of clonality in outbreaks of meticillin-resistant Staphylococcus aureus in a paediatric setting

(2016) E. Ugolotti et al.   JOURNAL OF HOSPITAL INFECTION

Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle

(2016) Christina Ahlstrom et al.   PLoS One

Mycobacterium avium ssp . paratuberculosis detection in animals, food, water and other sources or vehicles of human exposure: A scoping review of the existing evidence

(2016) Lisa Waddell et al.   PREVENTIVE VETERINARY MEDICINE

Detailed chronological analysis of microevolution events in herds infected persistently by Mycobacterium bovis

(2016) Yurena Navarro et al.   VETERINARY MICROBIOLOGY

The isolation and molecular characterization of Mycobacterium avium subsp. paratuberculosis in Shandong province, China

(2016) Ruichao Yue et al.   Gut Pathogens

Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level

(2015) Christina Ahlstrom et al.   BMC GENOMICS

Comprehensive insights inthe Mycobacterium aviumsubsp.paratuberculosisgenome using new WGS data of sheep strain JIII-386 from Germany

(2015) Petra Möbius et al.   Genome Biology and Evolution

Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis

(2015) Célia Leão et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Typing of Mycobacterium avium Subspecies paratuberculosis Isolates from Newfoundland Using Fragment Analysis

(2015) Milka P. Podder et al.   PLoS One

Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle

(2015) Yurena Navarro et al.   VETERINARY MICROBIOLOGY

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

Evaluation of the effects of a killed whole-cell vaccine againstMycobacterium aviumsubspparatuberculosisin 3 herds of dairy cattle with natural exposure to the organism

(2013) Barbara Knust et al.   JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Stability of genotyping target sequences of Mycobacterium avium subsp. paratuberculosis upon cultivation on different media, in vitro- and in vivo passage, and natural infection

(2013) Nadine Kasnitz et al.   VETERINARY MICROBIOLOGY

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

(2013) David W. Eyre et al.   PLoS Computational Biology

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Genome-Wide Analysis of the Emerging Infection with Mycobacterium avium Subspecies paratuberculosis in the Arabian Camels (Camelus dromedarius)

(2012) Pallab Ghosh et al.   PLoS One

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

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

(2012) David W Eyre et al.   BMJ Open

Prevalence and implications of multiple-strain infections

(2011) Oliver Balmer et al.   LANCET INFECTIOUS DISEASES

Mycobacterium aviumsubsp.paratuberculosisinfection in wildlife on three deer farms with a history of Johne's disease

(2011) G Nugent et al.   NEW ZEALAND VETERINARY JOURNAL

Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence

(2010) J. W. Wynne et al.   JOURNAL OF BACTERIOLOGY

Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?

(2008) D. Dopfer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Mycobacterium avium subsp. avium distribution studied in a naturally infected hen flock and in the environment by culture, serotyping and IS901 RFLP methods

(2007) J.E. Shitaye et al.   VETERINARY MICROBIOLOGY