Pathogen genome bioinformatics.

Recent advances in DNA sequencing technology have made the whole-genome sequencing of pathogens in a clinically relevant turn-around time both technically and economically feasible. The DNA sequencing of pathogens with epidemic potential offers new and exciting opportunities for high-resolution public health surveillance. This chapter outlines major methods and bioinformatics tools for pathogen genome characterization, the identification of infectious disease clusters, as well as for genomics-guided biosurveillance. Existing challenges are also considered.

[1]  R. Siezen,et al.  High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster , 2010, Journal of Clinical Microbiology.

[2]  Yuhong Yang.  Can the Strengths of AIC and BIC Be Shared , 2005 .

[3]  Stefan Niemann,et al.  Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study , 2013, PLoS medicine.

[4]  Nuno A. Fonseca,et al.  Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.

[5]  G. Dougan,et al.  Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology , 2012, PLoS pathogens.

[6]  N. Loman,et al.  Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. , 2011, The Journal of antimicrobial chemotherapy.

[7]  D. Bessen.  Population genomics: an investigative tool for epidemics. , 2012, The American journal of pathology.

[8]  Gavin MacBeath,et al.  Receptor Tyrosine Kinases Fall into Distinct Classes Based on Their Inferred Signaling Networks , 2013, Science Signaling.

[9]  Casey S. Greene,et al.  Chapter 2: Data-Driven View of Disease Biology , 2012, PLoS Comput. Biol..

[10]  C. Robert,et al.  Real-Time Sequencing To Decipher the Molecular Mechanism of Resistance of a Clinical Pan-Drug-Resistant Acinetobacter baumannii Isolate from Marseille, France , 2012, Antimicrobial Agents and Chemotherapy.

[11]  Jonathan R. Iredell,et al.  Pathogen profiling for disease management and surveillance , 2007, Nature Reviews Microbiology.

[12]  Marc A. Suchard,et al.  SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics , 2011, Bioinform..

[13]  Daniel J. Wilson,et al.  Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study , 2013, The Lancet. Infectious diseases.

[14]  T. Dallman,et al.  Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak , 2012, Journal of Clinical Microbiology.

[15]  W. Heneine,et al.  Ancient co-speciation of simian foamy viruses and primates , 2005, Nature.

[16]  W. M. Dunne,et al.  Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory , 2012, European Journal of Clinical Microbiology & Infectious Diseases.

[17]  Julian Parkhill,et al.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. , 2012, The New England journal of medicine.

[18]  M. Kulldorff,et al.  A Space–Time Permutation Scan Statistic for Disease Outbreak Detection , 2005, PLoS medicine.

[19]  D. Relman,et al.  Microbial genomics and infectious diseases. , 2011, The New England journal of medicine.

[20]  T. Walker,et al.  Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[21]  G. Getz,et al.  PathSeq: software to identify or discover microbes by deep sequencing of human tissue , 2011, Nature Biotechnology.

[22]  Steven J. M. Jones,et al.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. , 2011, The New England journal of medicine.

[23]  M. Gilmour,et al.  Public Health Genomics and the New Molecular Epidemiology of Bacterial Pathogens , 2013, Public Health Genomics.

[24]  C. Bertelli,et al.  Rapid bacterial genome sequencing: methods and applications in clinical microbiology. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[25]  N. Loman,et al.  A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. , 2013, JAMA.

[26]  Enrico Coiera,et al.  Biosurveillance of emerging biothreats using scalable genotype clustering , 2009, J. Biomed. Informatics.

[27]  Julian Parkhill,et al.  Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks , 2013 .

[28]  J. Musser,et al.  A Genomic Day in the Life of a Clinical Microbiology Laboratory , 2013, Journal of Clinical Microbiology.

[29]  Julian Parkhill,et al.  Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data , 2013, BMC Infectious Diseases.

[30]  S. Althomsons,et al.  Using Routinely Reported Tuberculosis Genotyping and Surveillance Data to Predict Tuberculosis Outbreaks , 2012, PloS one.

[31]  D. Falush.  Toward the Use of Genomics to Study Microevolutionary Change in Bacteria , 2009, PLoS genetics.

[32]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[33]  Michael J. Becich,et al.  Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics , 2012, Journal of pathology informatics.