Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Dec 6, 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
• Events / Training / Web Resources
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Nanopore Platform Developers Aim to Bring Multiplex MDx Testing to Point of Care
  O'Connor L. 360dx, Nov 29, 2018.
• Drug-Resistant Infections Targeted by FIND's New Diagnostics Initiative
  360dx, Nov 27, 2018.
• Metagenomic Sequencing Approach Proposed for Respiratory Tract Infection Detection
  GenomeWeb, Nov 28, 2018.
• Genetic relic of the 'black death' may offer clues in treating liver disease
  Ricks C. MedicalXpress, Dec 3, 2018.
• Universal flu vaccine is ‘an alchemist's dream’
  Cohen J. Science, Dec 7, 2018.
• Four small cities may have played an outsize role in spreading deadly flu
  Garcia de Jesus EI. Science, Dec 4, 2018.
• A shot-in-the-dark email leads to a century-old family treasure — and hope of cracking a deadly flu’s secret
  Branswell H. STAT, Dec 5, 2018.
• This Gene Can Make Viruses Invisible to the Immune System — Up to a Point
  Saplakoglu Y. Live Science, Nov 30, 2018.
• The silent epidemic killing more people than HIV, malaria or TB
  Graber-Stiehl I. Nature, Dec 6, 2018.
• Bacterial defence molecules target viral DNA
  Clokie MR. Nature, Dec 5, 2018.
• Malaria Drug Resistance Genetic Features Profiled in Southeast Asia
  GenomeWeb, Dec 4, 2018.

EVENTS / TRAINING / WEB RESOURCES

• Adapting flatfile parsers for GenBank’s new accession formats
  (announcement) NCBI Insights, Dec 3, 2018.

POLICY

• UN treaty agrees to limit gene drives but rejects a moratorium
  Callaway E. Nature, Nov 30, 2018.

CONCEPTS / COMMENTS

• Readiness for Responding to a Severe Pandemic 100 Years After 1918.
  Jester Barbara et al. American journal of epidemiology 2018 Aug  
• Global molecular epidemiology of HIV-1: the chameleon challenge.
  Paraskevis Dimitrios et al. The Lancet. Infectious diseases 2018 Nov

METHODS / TOOLS

• Building a local community of practice in scientific programming for life scientists.
  Stevens Sarah L R et al. PLoS biology 2018 Nov (11) e2005561
• Strategies and opportunities for promoting bioinformatics in Zimbabwe.
  Shoko Ryman et al. PLoS computational biology 2018 Nov (11) e1006480
• Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.
  Baichoo Shakuntala et al. BMC bioinformatics 2018 Nov (1) 457
• Evaluating the performance of tools used to call minority variants from whole genome short-read data.
  Said Mohammed Khadija et al. Wellcome open research 2018 21
• DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.
  Asgari Ehsaneddin et al. Bioinformatics (Oxford, England) 2018 Nov
• Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes.
  van Hemert Formijn et al. Computational and mathematical methods in medicine 2018 6490647
• Genome analysis of Mycobacterium avium subspecies hominissuis strain 109.
  Matern William M et al. Scientific data 2018 Dec 180277
• Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques.
  Boldogkoi Zsolt et al. Scientific data 2018 Nov 180266

EVOLUTION / ECOLOGY / POPULATIONS

• Genetic characteristics of Bacillus anthracis isolated from northwestern China from 1990 to 2016.
  Zhang Huijuan et al. PLoS neglected tropical diseases 2018 Nov (11) e0006908
• Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.
  Wyres Kelly L et al. The Journal of antimicrobial chemotherapy 2018 Dec
• Predicting Intraserotypic Recombination in Enterovirus 71.
  Woodman Andrew et al. Journal of virology 2018 Nov
• Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing.
  New David et al. Medical mycology 2018 Nov
• Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa.
  Jeffries Claire L et al. Wellcome open research 2018 113

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.
  Méric Guillaume et al. Nature communications 2018 Nov (1) 5034
• Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA .
  LaBreck Patrick T et al. Frontiers in microbiology 2018 2664
• Novel type of pilus associated with a Shiga-toxigenic E. coli hybrid pathovar conveys aggregative adherence and bacterial virulence.
  Lang Christina et al. Emerging microbes & infections 2018 Dec (1) 203
• Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.
  Schubert Benjamin et al. Nature microbiology 2018 Dec
• Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.
  Golparian Daniel et al. Scientific reports 2018 Dec (1) 17596
• Mechanistic Basis for Decreased Antimicrobial Susceptibility in a Clinical Isolate of Neisseria gonorrhoeae Possessing a Mosaic-Like mtr Efflux Pump Locus.
  Rouquette-Loughlin Corinne E et al. mBio 2018 Nov (6) 
• The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background
  Zhu L, et al. Nat Commun, Dec 4, 2018.
• The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background.
  Zhu Lei et al. Nature communications 2018 Dec (1) 5158
• Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain.
  Samarasinghe Sumudu R et al. BMC genomics 2018 Nov (1) 843

DETECTION / DIAGNOSIS

• Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study.
  Imai Kazuo et al. Frontiers in microbiology 2018 2748
• Diagnosis of Human Immunodeficiency Virus Infection.
  Parekh Bharat S et al. Clinical microbiology reviews 2019 Jan (1)  
• Contribution of Environment Sample-Based Detection to Ebola Outbreak Management.
  Kapetshi Jimmy et al. The Journal of infectious diseases 2018 Nov (suppl_5) S292-S296
• Laboratory challenges of Plasmodium species identification in Aceh Province, Indonesia, a malaria elimination setting with newly discovered P. knowlesi.
  Coutrier Farah N et al. PLoS neglected tropical diseases 2018 Nov (11) e0006924 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks.
  Ezeoke Ifeoma et al. PloS one 2018 (11) e0202615
• Outbreak of Yersiniabactin-Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit.
  Wisgrill Lukas et al. The Pediatric infectious disease journal 2018 Nov 
• Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective.
  Rumore Jillian et al. BMC genomics 2018 Dec (1) 870 
• An Outbreak of Salmonella Agbeni Infections Linked to Turtle Exposure — United States, 2017
  Koski L. MMWR, Dec 7, 2018.  
• Ebola Virus Infection Associated with Transmission from Survivors 
  Den Boon S, et al. Emerg Infect Dis 2019: Feb 17;25(2). 
• Molecular and epidemiologic investigation of a rhinovirus outbreak in a neonatal intensive care unit.
  El Idrissi Kenza Rahmouni et al. Infection control and hospital epidemiology 2018 Dec 1-3
• Hepatitis C virus transmission in a Dutch haemodialysis unit: detailed outbreak investigation using NS5A gene sequencing.
  Heikens E et al. The Journal of hospital infection 2018 Nov

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A Bacteriophage T4 Nanoparticle-Based Dual Vaccine against Anthrax and Plague.
  Tao Pan et al. mBio 2018 Oct (5)
• Universal Influenza Vaccines: Progress in Achieving Broad Cross-Protection In Vivo.
  Epstein Suzanne L et al. American journal of epidemiology 2018 Dec (12) 2603-2614

HOST-MICROBE INTERACTIONS

• VDR polymorphism, gene expression and vitamin D levels in leprosy patients from North Indian population.
  Singh Itu et al. PLoS neglected tropical diseases 2018 Nov (11) e0006823
• Host and viral determinants of influenza A virus species specificity.
  Long Jason S et al. Nature reviews. Microbiology 2018 Nov
• Genetic variations in human papillomavirus and cervical cancer outcomes.
  Rader Janet S et al. International journal of cancer 2018 Dec

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.