Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 23, 2018

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. View Data Selection Criteria

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Advanced Molecular Detection Clips Content

• News
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission

NEWS

• Brazilian Yellow Fever Outbreak Tracked With Epidemiological, Genomic Approaches
  GenomeWeb, Aug 23, 2016
• Arrival of deadly pig disease could spell disaster for China
  Normile D. Science, Aug 23, 2018.
• Ape Parasite Genomes Suggest African Origin for Human Malaria-Causing Plasmodium Vivax
  GenomeWeb, Aug 20, 2018.

CONCEPTS / COMMENTS

• Enterovirus outbreak dynamics
  Nikolay B, Cauchemez S. Science, Aug 23, 2018.
• The reemergence of yellow fever
  Barrett AD. Science, Aug 23, 2018.
• Outbreaks in a Rapidly Changing Central Africa - Lessons from Ebola.
  Munster Vincent J et al. The New England journal of medicine 2018 Aug
• A toolkit for data transparency takes shape
  Perkel JM. Nature, Aug 20, 2018.

METHODS / TOOLS

• Identification and Quantification of DNA Viral Populations in Human Urine Using Next-Generation Sequencing Approaches.
  Santiago-Rodriguez Tasha M et al. Methods in molecular biology (Clifton, N.J.) 2018 191-200
• Viral Concentration and Amplification from Human Serum Samples Prior to Application of Next-Generation Sequencing Analysis.
  Fernandez-Cassi Xavier et al. Methods in molecular biology (Clifton, N.J.) 2018 173-188
• NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics.
  Conceição-Neto Nádia et al. Methods in molecular biology (Clifton, N.J.) 2018 85-95
• Virome Sequencing of Stool Samples.
  Kramná Lenka et al. Methods in molecular biology (Clifton, N.J.) 2018 59-83
• Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.
  Milani Christian et al. Microbiome 2018 Aug (1) 145
• A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.
  Takahashi Melissa K et al. Nature communications 2018 Aug (1) 3347

EVOLUTION / ECOLOGY / POPULATIONS

• Human plague associated with Tibetan sheep originates in marmots.
  Dai Ruixia et al. PLoS neglected tropical diseases 2018 Aug (8) e0006635
• Microevolution of epidemiological highly relevant non-O157 enterohemorrhagic Escherichia coli of serogroups O26 and O111.
  Eichhorn Inga et al. International journal of medical microbiology : IJMM 2018 Aug
• Emergence of Localized Serogroup W Meningococcal Disease in the United States - Georgia, 2006-2016.
  Moore Ashley E et al. MMWR. Morbidity and mortality weekly report 2018 Aug (32) 894-897 
• Detection and Molecular Characterization of Yellow Fever Virus, 2017, Brazil.
  Figueiredo P O et al. EcoHealth 2018 Aug
• Molecular epidemiology analysis of enterovirus 71 strains isolated in Dak Lak, Vietnam, 2011-2016.
  Tuan Le Van et al. Journal of medical virology 2018 Aug
• Attenuation of highly pathogenic avian influenza A(H5N1) viruses in Indonesia following the reassortment and acquisition of genes from low pathogenicity avian influenza A virus progenitors.
  Dharmayanti Ni Luh Putu Indi et al. Emerging microbes & infections 2018 Aug (1) 147
• Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites.
  Loy Dorothy E et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Aug

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.
  Pena-Gonzalez Angela et al. mSystems (4) 
• A Population-Based Surveillance Study of Shared Genotypes of Escherichia coli Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections.
  Yamaji Reina et al. mSphere 2018 Aug (4) 
• Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.
  Mustapha Mustapha M et al. The Journal of antimicrobial chemotherapy 2018 Aug
• Spread of Carbapenem and Colistin-Resistant Klebsiella pneumoniae ST512 Clinical Isolates in Israel: A Cause for Vigilance.
  Lalaoui Rym et al. Microbial drug resistance (Larchmont, N.Y.) 2018 Aug

DETECTION / DIAGNOSIS

• BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species.
  Topaz Nadav et al. BMC infectious diseases 2018 Aug (1) 405 
• From Culturomics to Clinical Microbiology and Forward.
  Dubourg Grégory et al. Emerging infectious diseases 2018 Sep (9) 1683-1690
• Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015.
  Van Walle Ivo et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Aug (33)
• The preparation and clinical application of diagnostic DNA microarray for the detection of pathogens in intracranial bacterial and fungal infections.
  Cao Jingrong et al. Experimental and therapeutic medicine 2018 Aug (2) 1304-1310
• Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System.
  Kohl Thomas A et al. EBioMedicine 2018 Jul
• Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance.
  Yang Yang et al. BMC infectious diseases 2018 Aug (1) 406
• Simpler, Faster, and Sensitive Zika Virus Assay Using Smartphone Detection of Loop-mediated Isothermal Amplification on Paper Microfluidic Chips.
  Kaarj Kattika et al. Scientific reports 2018 Aug (1) 12438

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• XDR tuberculosis in South Africa: genomic evidence supporting transmission in communities.
  Auld Sara C et al. The European respiratory journal 2018 Aug
• Hepatitis A outbreak disproportionately affecting men who have sex with men (MSM) in the European Union and European Economic Area, June 2016 to May 2017.
  Ndumbi Patricia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Aug (33)
• Genomic and epidemiological monitoring of yellow fever virus transmission potential
  Faria NR, et al. Science, Aug 23, 2018.
• Epidemic history of hepatitis C virus genotypes and subtypes in Portugal.
  Palladino Claudia et al. Scientific reports 2018 Aug (1) 12266

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.

Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.