What has molecular epidemiology ever done for wildlife disease research? Past contributions and future directions

Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

(2014) Hon S. Ip et al.   JOURNAL OF VIROLOGICAL METHODS

Vaccine-induced Rabies in a Red Fox (Vulpes vulpes): Isolation of Vaccine Virus in Brain Tissue and Salivary Glands

(2014) Peter Hostnik et al.   JOURNAL OF WILDLIFE DISEASES

PHYLOGENETIC COMPARISON OF AVIAN HAEMOSPORIDIAN PARASITES FROM RESIDENT AND MIGRATORY BIRDS IN NORTHERN JAPAN

(2014) Aya Yoshimura et al.   JOURNAL OF WILDLIFE DISEASES

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

(2014) Rowland R. Kao et al.   TRENDS IN MICROBIOLOGY

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Polar Bear Encephalitis: Establishment of a Comprehensive Next-generation Pathogen Analysis Pipeline for Captive and Free-living Wildlife

(2013) C.A. Szentiks et al.   JOURNAL OF COMPARATIVE PATHOLOGY

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

(2013) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Diagnostic Applications of High-Throughput DNA Sequencing

(2012) Scott D. Boyd   Annual Review of Pathology-Mechanisms of Disease

Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak

(2012) Sonia M. Hernandez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogeographic distribution of very virulent infectious bursal disease virus isolates in the Iberian Peninsula

(2012) Martí Cortey et al.   AVIAN PATHOLOGY

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

Phylogeography of foot-and-mouth disease virus serotype O in Ecuador

(2012) Luiz Max Fagundes de Carvalho et al.   INFECTION GENETICS AND EVOLUTION

Single Nucleotide Polymorphisms in the Mycobacterium bovis Genome Resolve Phylogenetic Relationships

(2012) D. Joshi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Epidemiological Dynamics and Phylogeography of Influenza Virus in Southern China

(2012) Xiaowen Cheng et al.   JOURNAL OF INFECTIOUS DISEASES

Immunogenicity and tolerability of a multicomponent meningococcal serogroup B (4CMenB) vaccine in healthy adolescents in Chile: a phase 2b/3 randomised, observer-blind, placebo-controlled study

(2012) María Elena Santolaya et al.   LANCET

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

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

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contact with Domestic Dogs Increases Pathogen Exposure in Endangered African Wild Dogs (Lycaon pictus)

(2012) Rosie Woodroffe et al.   PLoS One

Immunogenetic Variation and Differential Pathogen Exposure in Free-Ranging Cheetahs across Namibian Farmlands

(2012) Aines Castro-Prieto et al.   PLoS One

BCG Vaccination Reduces Risk of Tuberculosis Infection in Vaccinated Badgers and Unvaccinated Badger Cubs

(2012) Stephen P. Carter et al.   PLoS One

Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

(2012) Brendan D. Cowled et al.   PLoS One

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

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine

Geographical association between the genotype of bovine tuberculosis in found dead badgers and in cattle herds

(2012) A. V. Goodchild et al.   VETERINARY RECORD

Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock

(2012) L. B. Price et al.   mBio

Epidemiology and Molecular Relationships of Cryptosporidium spp. in People, Primates, and Livestock from Western Uganda

(2012) Stephanie J. Salyer et al.   PLoS Neglected Tropical Diseases

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

(2012) Roman Biek et al.   PLoS Pathogens

Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies

(2012) Daniel G. Streicker et al.   PLoS Pathogens

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

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

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

Global trends in molecular epidemiology of HIV-1 during 2000–2007

(2011) Joris Hemelaar et al.   AIDS

A National Agenda for the Future of Pathology in Personalized Medicine

(2011) Peter J. Tonellato et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

(2011) B. Hu et al.   Briefings in Functional Genomics

Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis

(2011) Y. Feng et al.   CLINICAL MICROBIOLOGY REVIEWS

Reduced Effect of Tasmanian Devil Facial Tumor Disease at the Disease Front

(2011) RODRIGO HAMEDE et al.   CONSERVATION BIOLOGY

Molecular phylogeography of the Chagas’ disease vector Triatoma infestans in Argentina

(2011) A R Pérez de Rosas et al.   HEREDITY

Microbial Genomics and Infectious Diseases

(2011) David A. Relman   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

Role of stochastic processes in maintaining discrete strain structure in antigenically diverse pathogen populations

(2011) C. O. Buckee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

(2011) D. A. Rasko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular evidence of shared hookworm Ancylostoma tubaeforme haplotypes between the critically endangered Iberian lynx and sympatric domestic cats

(2011) Javier Millán et al.   VETERINARY PARASITOLOGY

Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar

(2011) Amy J. Vogler et al.   PLoS Neglected Tropical Diseases

Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity

(2011) Walter M Boyce et al.   BMC ECOLOGY

ORIGINAL ARTICLE: A Multi-Subunit Chlamydial Vaccine Induces Antibody and Cell-Mediated Immunity in Immunized Koalas (Phascolarctos cinereus): Comparison of Three Different Adjuvants

(2010) Alison J. Carey et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Metagenomics and the Units of Biological Organization

(2010) W. Ford Doolittle et al.   BIOSCIENCE

Using genomic signatures for HIV-1 sub-typing

(2010) Aridaman Pandit et al.   BMC BIOINFORMATICS

Identification of Three Novel Superantigen-Encoding Genes in Streptococcus equi subsp. zooepidemicus, szeF, szeN, and szeP

(2010) R. Paillot et al.   INFECTION AND IMMUNITY

Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study

(2010) Karthikeyan K Kumarasamy et al.   LANCET INFECTIOUS DISEASES

The landscape genetics of infectious disease emergence and spread

(2010) ROMAN BIEK et al.   MOLECULAR ECOLOGY

Next-generation sequencing: adjusting to data overload

(2010) Monya Baker   NATURE METHODS

MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer

(2010) H. V. Siddle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular detection of Babesia bovis and Babesia bigemina in white-tailed deer (Odocoileus virginianus) from Tom Green County in central Texas

(2010) Patricia J. Holman et al.   VETERINARY PARASITOLOGY

Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States

(2010) Edmond J. Byrnes et al.   PLoS Pathogens

Global Emergence ofBatrachochytrium dendrobatidisand Amphibian Chytridiomycosis in Space, Time, and Host

(2009) Matthew C. Fisher et al.   Annual Review of Microbiology

Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of devil facial tumour disease

(2009) Rodrigo K. Hamede et al.   ECOLOGY LETTERS

Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella

(2009) J. T. Foster et al.   JOURNAL OF BACTERIOLOGY

Molecular Epidemiology of Simian Immunodeficiency Virus Infection in Wild-Living Gorillas

(2009) C. Neel et al.   JOURNAL OF VIROLOGY

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

(2009) Marc Monot et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus)

(2009) Marina L. Meli et al.   PLoS One

Who infects whom? Social networks and tuberculosis transmission in wild meerkats

(2009) J. A. Drewe   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-based approaches to develop vaccines against bacterial pathogens

(2009) Davide Serruto et al.   VACCINE

Genetic diversity and phylogenetic analysis of the attachment glycoprotein of phocine distemper viruses of the 2002 and 1988 epizootics

(2009) Line Nielsen et al.   VIRUS RESEARCH

The Key Role of Genomics in Modern Vaccine and Drug Design for Emerging Infectious Diseases

(2009) Kate L. Seib et al.   PLoS Genetics

Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations

(2009) Timothy Y. James et al.   PLoS Pathogens

A Population‐Based Study of the Incidence and Molecular Epidemiology of Methicillin‐ResistantStaphylococcus aureusDisease in San Francisco, 2004–2005

(2008) Catherine Liu et al.   CLINICAL INFECTIOUS DISEASES

Pandemic Human Viruses Cause Decline of Endangered Great Apes

(2008) Sophie Köndgen et al.   CURRENT BIOLOGY

Comparative genomics: the bacterial pan-genome

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

Infecting epidemiology with genetics: a new frontier in disease ecology

(2008) Elizabeth A. Archie et al.   TRENDS IN ECOLOGY & EVOLUTION

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Genetic characterisation of attenuated SAD rabies virus strains used for oral vaccination of wildlife

(2008) Lutz Geue et al.   VACCINE

Persistence and molecular evolution of Mycobacterium bovis population from cattle and wildlife in Doñana National Park revealed by genotype variation

(2008) Beatriz Romero et al.   VETERINARY MICROBIOLOGY