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Public Health Genomics Knowledge Base (v1.0)



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Advanced Molecular Detection: Weekly Clips

About Advanced Molecular Detection Clips

Advanced Molecular Detection(AMD) Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged.

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Spotlight

Genetic diversity of Plasmodium falciparum parasite by microsatellite markers after scale-up of insecticide-treated bed nets in western Kenya. An initial study of genetic diversity of Plasmodium falciparum in Asembo, western Kenya showed that the parasite maintained overall genetic stability 5 years after insecticide-treated bed net (ITN) introduction in 1997.... This study showed the P. falciparum high genetic diversity and parasite population resilience on samples collected 10 years apart and in different areas in western Kenya. The results highlight the need for long-term molecular monitoring after implementation and use of combined and intensive prevention and intervention measures in the region.

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Host-Microbe Interactions

NEWS

• Meet the Necrobiome: The Waves of Microbes That Will Eat Your Corpse 
  Yong E. Atlantic, Dec 10, 2015.
• Synthetic Long Reads Identify Diverse Bacterial Species in Human Gut Microbiome 
  GenomeWeb, Dec 14, 2015.
• UK Team Develops Fast, Cost-Effective NGS-Based Tuberculosis Test 
  Heger M. GenomeWeb, Dec 15, 2015.
• Citizen Sequencers: Taking Oxford Nanopore's MinION to the Classroom and Beyond 
  Krol A. Bio-IT World, Dec 9, 2015.
• Congress Reaches Agreement on Budget to Boost NIH Funding by $2B 
  GenomeWeb, Dec 16, 2015.
• Researchers Assess Variant Calling Pipelines Using Genome in a Bottle 'Gold Standard' 
  Heger M. GenomeWeb, Dec 15, 2015.
• Sequencing Study Tracks Roots of TB Emergence to East Africa 
  GenomeWeb, dec 10, 2015.
• German Group Develops On-Chip RPA Arrays for Isothermal Detection of Viruses, Bacteria 
  Johnson M. GenomeWeb, Dec 16, 2015.

EVENTS / TRAINING / WEB RESOURCES

• SRA Toolkit: the SRA database at your fingertips 
  (blog post) NCBI, Dec 11, 2015.
• Fine-tune your web-based search results with SRA Run Selector 
  (blog post) NCBI, Dec 11, 2015.
• New NCBI Insights blog posts highlight SRA Toolkit, Run Selector 
  (blog post) NCBI News, Dec 11, 2015.
• List of Community Software Tools for Next Generation Sequencing 
  (web page) NCBI-Hackathons, updated Dec 9, 2015.
• NCBI Learn 
  (website) Webinars, tutorials, documentation.
• New Educational Module from the Bioethics Commission on Privacy in Ethics and Ebola Now Available 
  (blog post) Pike E. blog.Bioethics.gov, Dec 11, 2015.

CONCEPTS / COMMENTS

• Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond 
  Colijn C, Cohen T. Lancet, Dec 3, 2015.
• Principle of proportionality in genomic data sharing. 
  Wright Caroline F et al. Nature reviews. Genetics 2016 Jan (1) 1-2
• Antiviral Innate Immunity through the lens of Systems Biology. 
  Tripathi Shashank et al. Virus research 2015 Dec

METHODS / TOOLS

• Systematic comparison of variant calling pipelines using gold standard personal exome variants. 
  Hwang Sohyun et al. Scientific reports 2015 17875
• Sequence database versioning for command line and Galaxy bioinformatics servers. 
  Dooley Damion et al. Bioinformatics (Oxford, England) 2015 Dec
• markophylo: Markov chain analysis on phylogenetic trees. 
  Dang Utkarsh J et al. Bioinformatics (Oxford, England) 2015 Sep
• BamHash: a checksum program for verifying the integrity of sequence data. 
  Óskarsdóttir Arna et al. Bioinformatics (Oxford, England) 2015 Sep
• Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland. 
  Reuter Sandra et al. Genome research 2015 Dec

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage. 
  Octavia Sophie et al. Journal of clinical microbiology 2015 Nov (11) 3507-14
• Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples. 
  Nicholson Ainsley C et al. Genome announcements 2015 (6)
• Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410 - another successful pandemic clone? 
  Schaufler Katharina et al. FEMS microbiology ecology 2015 Dec
• Molecular characterisation of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from hospital and ambulatory patients in Germany. 
  Pietsch Michael et al. Veterinary microbiology 2015 Nov
• An Epizootiological Report of the Re-emergence and Spread of a Lineage of Virulent Newcastle Disease Virus into Eastern Europe. 
  Fuller C et al. Transboundary and emerging diseases 2015 Dec
• Importation and Recombination Are Responsible for the Latest Emergence of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus in China. 
  Zhao Kuan et al. Journal of virology 2015 Oct (20) 10712-6
• Population genomics of intrapatient HIV-1 evolution. 
  Zanini Fabio et al. eLife 2015 Dec
• Molecular evolution and intra-clade recombination of Enterovirus D68 during the 2014 outbreak in the United States. 
  Tan Yi et al. Journal of virology 2015 Dec
• Evolution and Spread of Ebola Virus in Liberia, 2014-2015. 
  Ladner Jason T et al. Cell host & microbe 2015 Dec (6) 659-69
• Clonal population expansion in an outbreak of Plasmodium falciparum on the northwest coast of Ecuador. 
  Sáenz Fabián E et al. Malaria journal (1) 497
• Comparison of Leishmania killicki (syn. L. tropica) and Leishmania tropica Population Structure in Maghreb by Microsatellite Typing. 
  Chaara Dhekra et al. PLoS neglected tropical diseases 2015 Dec (12) e0004204
• Genetic diversity of Plasmodium falciparum parasite by microsatellite markers after scale-up of insecticide-treated bed nets in western Kenya. 
  Gatei Wangeci et al. Malaria journal (1) 495 (CDC Author)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015 
  Hasman H, et al. Euro Surveill. 2015;20(49):pii=30085.
• Whole-genome sequence analysis and exploration of the zoonotic potential of a rat-borne Bartonella elizabethae. 
  Tay S T et al. Acta tropica 2015 Dec
• Decreased susceptibility to chlorhexidine among nosocomial Staphylococcus aureus at Texas Children's Hospital: Clinical and Molecular Features. 
  McNeil J Chase et al. Antimicrobial agents and chemotherapy 2015 Dec

DETECTION / DIAGNOSIS

• Molecular tests for the detection of antimicrobial resistant Neisseria gonorrhoeae: when, where, and how to use? 
  Low Nicola et al. Current opinion in infectious diseases 2015 Dec
• On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria. 
  Kunze A et al. Analytical chemistry 2015 Dec
• Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study 
  Pankhurst LJ, et al. Lancet, Dec 3, 2015.
• Detection of rare drug resistance mutations by digital PCR in a human influenza A virus model system and clinical samples. 
  Whale Alexandra S et al. Journal of clinical microbiology 2015 Dec
• Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection 
  Berg MG, et al. PLoS Pathogens, Dec 11, 2015.
• Application of PCR and High-Resolution Melting for Rapid Identification of Yeasts Routinely Isolated in a Clinical Microbiology Laboratory. 
  Ninghui Guo et al. Annals of clinical and laboratory science 2015 Nov (6) 680-5
• Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. 
  Greninger Alexander L et al. Genome medicine 2015 (1) 113

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• HIV infection and hepatitis C virus genotype 1a are associated with phylogenetic clustering among people with recently acquired hepatitis C virus infection. 
  Bartlett Sofia R et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Nov
• Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny. 
  Maurer-Stroh Sebastian et al. Diagnostic microbiology and infectious disease 2015 Nov
• Hospital outbreak of pulmonary and cutaneous zygomycosis due to contaminated linen items from substandard laundry. 
  Cheng Vincent C C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Dec

HOST-MICROBE INTERACTIONS

• Epidemiologic, Virologic, and Host Genetic Factors of Norovirus Outbreaks in Long-term Care Facilities. 
  Costantini Veronica P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Oct (CDC Author)
• Human papillomavirus genotype and oropharynx cancer survival in the United States of America. 
  Goodman Marc T et al. European journal of cancer (Oxford, England : 1990) 2015 Dec (18) 2759-67 (CDC Author)
• Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide. 
  Chen Alyce A et al. Journal of virology 2015 Oct (20) 10680-7
• The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni. 
  Clayton Katie A et al. Parasites & vectors (1) 632

Public Health Genomics Knowledge Base (v1.0)