Advanced Molecular Detection Clips Content ► Public Health Genomics Knowledge Base (v1.0)

Public Health Genomics Knowledge Base (v1.0)

Advanced Molecular Detection Clips

About Advanced Molecular Detection Clips

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 infectious disease 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. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.

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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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• FDA approves diagnostic test for chikungunya, dengue, or Zika; CDC to distribute 
  Outbreak News Today, Mar 19, 2016.
• Researchers Sequence Chimpanzee Parasites to Learn About Evolution of Human Malaria Species 
  Newbern E. GenomeWeb, Mar 22, 2016.
• New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data 
  GenomeWeb, Mar 21, 2016.
• Team IDs Potential Gut Microbe Marker for Necrotizing Enterocolitis in Infants 
  GenomeWeb, Mar 17, 2016.
• International Research Team Develops Blood Test for Tuberculosis Risk Assessment 
  Newbern E. GenomeWeb,Mar 24, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Zika Genome Sequences Available from NCBI 
  (announcement) NCBI, Mar 17, 2016.
• Summer Institute in Statistics and Modeling in Infectious Diseases 
  (training)Univ of Washington, Seattle. Series of 2.5-day workshops (including molecular epi, contact networks, novel data streams), July 2016.
• Submitting Data to NCBI and BioSample 
  (webinar) NCBI, Apr 13, 1:00-2:00 pm.

CONCEPTS / COMMENTS

• The FAIR Guiding Principles for scientific data management and stewardship. 
  Wilkinson Mark D et al. Scientific data 160018
• An Economic Evaluation of PulseNet: A Network for Foodborne Disease Surveillance. 
  Scharff Robert L et al. American journal of preventive medicine 2016 Feb  
• Translating RNA sequencing into clinical diagnostics: opportunities and challenges. 
  Byron Sara A et al. Nature reviews. Genetics 2016 Mar
• Reimagining the Future of the Diagnosis of Viral Infections. 
  Peeling Rosanna W et al. The Journal of infectious diseases 2016 Mar

METHODS / TOOLS

• From the desktop to the grid: scalable bioinformatics via workflow conversion. 
  de la Garza Luis et al. BMC bioinformatics 2016 (1) 127
• Strain-level microbial epidemiology and population genomics from shotgun metagenomics 
  Scholz M, et al. Nat Methods, Mar 21, 2016.
• A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. 
  Bull Rowena A et al. BMC genomics 2016 (1) 247
• Phylogenetic Analysis of Poliovirus Sequences. 
  Jorba Jaume et al. Methods in molecular biology (Clifton, N.J.) 2016 227-37 
• Flexible data integration and curation using a graph-based approach. 
  Croset Samuel et al. Bioinformatics (Oxford, England) 2015 Nov

EVOLUTION / ECOLOGY / POPULATIONS

• The genomic signatures of Shigella evolution, adaptation and geographical spread. 
  The Hao Chung et al. Nature reviews. Microbiology 2016 Apr (4) 235-50
• Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis 
  Breurec P, et al. bioRxiv, Mar 19, 2016.
• Global phylogeography and evolutionary history of Shigella dysenteriae type 1 
  Njamkepo E, et al. Nat Microbiol, Mar 21, 2016.
• Molecular evidence of Burkholderia pseudomallei genotypes based on geographical distribution. 
  Zulkefli Noorfatin Jihan et al. PeerJ 2016 e1802
• Spatial Temporal Dynamics and Molecular Evolution of Re-Emerging Rabies Virus in Taiwan. 
  Lin Yung-Cheng et al. International journal of molecular sciences (3)
• Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria. 
  de Man Tom J B et al. Genome announcements 2016 (2) 
• Zika virus in the Americas: Early epidemiological and genetic findings 
  Faria NR, et al. Science, Mar 24, 2016.

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Functional Genome Screening to Elucidate the Colistin Resistance Mechanism. 
  Kumar Mohit et al. Scientific reports 2016 23156
• Whole genome sequencing provides insights into the genetic determinants of invasiveness in Salmonella Dublin. 
  Mohammed M et al. Epidemiology and infection 2016 Mar 1-10
• Sensitive sentinel mutation screening reveals differential underestimation of transmitted HIV drug resistance among demographic groups. 
  Li Jin-Fen et al. AIDS (London, England) 2016 Mar 
• Detection of chloroquine and artemisinin resistance molecular markers in Plasmodium falciparum: A hospital based study. 
  Ramani S et al. Tropical parasitology (1) 69-77

DETECTION / DIAGNOSIS

• Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay. 
  Benitez Alvaro J et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 298-303 
• Combined antibody and DNA detection for early diagnosis of leptospirosis after a disaster. 
  Iwasaki Hiroko et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 287-91
• Discriminative power of Campylobacter phenotypic and genotypic typing methods. 
  Duarte Alexandra et al. Journal of microbiological methods 2016 Mar
• The Impact of Multilocus Variable-Number Tandem-Repeat Analysis on PulseNet Canada Escherichia coli O157:H7 Laboratory Surveillance and Outbreak Support, 2008-2012. 
  Rumore Jillian Leigh et al. Foodborne pathogens and disease 2016 Mar 
• Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia. 
  Gyarmati P et al. Scientific reports 23532
• A blood RNA signature for tuberculosis disease risk: a prospective cohort study 
  Zak DE, et al. Lancet, Mar 23, 2016.
• Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR. 
  Burns Cara C et al. Methods in molecular biology (Clifton, N.J.) 2016 177-212 
• Multilocus microsatellite typing of Leishmania infantum isolates in monitored Leishmania/HIV coinfected patients. 
  Tomás-Pérez Míriam et al. Parasites & vectors 2015 386
• Ribosomal DNA analysis of tsetse and non-tsetse transmitted Ethiopian Trypanosoma vivax strains in view of improved molecular diagnosis. 
  Fikru Regassa et al. Veterinary parasitology 2016 Apr 15-22

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing. 
  Yang Shangxin et al. Diagnostic microbiology and infectious disease 2016 Apr (4) 337-42
• A non-autochthonous US strain of Vibrio parahaemolyticus isolated from Chesapeake Bay oysters caused the outbreak in Maryland in 2010. 
  Haendiges Julie et al. Applied and environmental microbiology 2016 Mar
• Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections. 
  Nickbakhsh S et al. Epidemiology and infection 2016 Mar 1-13
• Human Rabies - Missouri, 2014. 
  Pratt P Drew et al. MMWR. Morbidity and mortality weekly report 2016 (10) 253-6 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Characterization and complete genome sequence analysis of two Myoviral bacteriophages infecting clinical carbapenem-resistant Acinetobacter baumannii isolates. 
  Jeon Jongsoo et al. Journal of applied microbiology 2016 Mar
• Rapid and long-term immunity elicited by DNA encoded antibody prophylaxis and DNA vaccination against Chikungunya virus. 
  Muthumani Karuppiah et al. The Journal of infectious diseases 2016 Mar

HOST-MICROBE INTERACTIONS

• Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
  Ward DV, et al. Cell Rep, Mar 17, 2016.
• Metabolic crosstalk between host and pathogen: sensing, adapting and competing. 
  Olive Andrew J et al. Nature reviews. Microbiology 2016 Apr (4) 221-34
• The maternal microbiota drives early postnatal innate immune development. 
  Gomez de Agüero Mercedes et al. Science (New York, N.Y.) 2016 Mar (6279) 1296-302
• Tumour-associated and non-tumour-associated microbiota in colorectal cancer. 
  Flemer Burkhardt et al. Gut 2016 Mar
• Clinical significance of the CCR5delta32 allele in hepatitis C. 
  Morard Isabelle et al. PloS one 2014 (9) e106424
• Responder Interferon Lambda genotypes are associated with higher risk of liver fibrosis in HIV-Hepatitis C Virus Co-infection. 
  Moqueet Nasheed et al. The Journal of infectious diseases 2016 Mar

Note:  indicates that at least one CDC-affiliated author;  indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.