Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 11, 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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Technology, Trace Back: Keys to Tracking Foodborne Outbreaks
  Walker M. MedPage Today, Oct 6, 2018.
• Groups Report Progress, Challenges in Using Metagenomic Sequencing for Infectious Disease Dx
  Heger M. GenomeWeb, Oct 8, 2018.
• Researchers Develop Low-Cost Pan-HPV MDx Using Enzyme-DNA Nanostructures
  Johnson M. GenomeWeb, Oct 5, 2018.
• Space Oddities: Changing Microbiomes in the Final Frontier
  Walker M. MedPage Today, Oct 4, 2018.
• Filed Under: Cyclospora; Foodborne Disease
  Soucheray S. CIDRAP, Oct 5, 2018.
• A Frozen Idea To Save Helpful Germs From Disasters
  Schreiber M. NPR, Oct 4, 2018.

CONCEPTS / COMMENTS

• How big data is changing science
  Chivers T. Mosaic, October 2, 2018.
• Horsepox: Framing a dual use research of concern debate.
  Coyne Carolyn B et al. PLoS pathogens 2018 Oct (10) e1007344
• Preserving microbial diversity.
  Bello Maria G Dominguez et al. Science (New York, N.Y.) 2018 Oct (6410) 33-34
• Classification, Ontology, and Precision Medicine
  Haendel MA, et al. New Engl J Med, Oct 11, 2018.
• Ten simple rules for scientists: Improving your writing productivity.
  Peterson Todd C et al. PLoS computational biology 2018 Oct (10) e1006379

METHODS / TOOLS

• VIRULIGN: fast codon-correct alignment and annotation of viral genomes.
  Libin Pieter et al. Bioinformatics (Oxford, England) 2018 Oct
• FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
  Quan J, et al. bioRxiv, Sep 27, 2018.
• BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results.
  Blanco-Míguez Aitor et al. PloS one 2018 (10) e0205286
• Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow.
  Douglas Gavin M et al. Methods in molecular biology (Clifton, N.J.) 2018 131-141
• Detection of mixed-strain infections by FACS and ultra-low input genome sequencing.
  Džunková Mária et al. Gut microbes 2018 Oct 1-5
• 'How to do it' - a molecular investigation of a hospital outbreak.
  Nutman Amir et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Oct
• Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk.
  Xu Yifei et al. Frontiers in microbiology 2018 2225
• Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets.
  Hoggard Michael et al. Frontiers in microbiology 2018 2208
• ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.
  Rosenfeld Aaron M et al. Frontiers in immunology 2018 2107

EVOLUTION / ECOLOGY / POPULATIONS

• Mosaic Plasmids are Abundant and Unevenly Distributed Across Prokaryotic Taxa.
  Pesesky MW, et al. bioRxiv, Sep 26, 2018.
• Evolution of influenza genome diversity during infection in immunocompetent patients
  Pichon M, et al. bioRxiv, Oct 4, 2018.
• Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan.
  Ko Hui-Ying et al. PLoS neglected tropical diseases 2018 Oct (10) e0006827
• Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations.
  Thiele Elizabeth A et al. PLoS neglected tropical diseases 2018 Oct (10) e0006747

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• WGS analysis of a penicillin-resistant Neisseria meningitidis strain containing a chromosomal ROB-1 β-lactamase gene.
  Tsang Raymond S W et al. The Journal of antimicrobial chemotherapy 2018 Oct
• Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying bla NDM in Enterobacteriaceae Isolates in Geographically Widespread Areas.
  Wang Ya et al. Frontiers in microbiology 2018 2272
• Emergence of enteroaggregative Escherichia coli within the ST131 lineage as a cause of extraintestinal infections
  Boll EJ, et al. bioRxiv, Oct 5, 2018.
• Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus
  Lipworth SI, et al. bioRxiv, Sep 28, 2018.
• Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles
  Shaw LP, et al. bioRxiv, Oct 5, 2018.
• Genetic characterization of measles virus genotype D6 subacute sclerosing panencephalitis case, Alberta, Canada.
  Pabbaraju K et al. Journal of neurovirology 2018 Oct
• HIV-1C proviral DNA for detection of drug resistance mutations.
  Huruy Kahsay et al. PloS one 2018 (10) e0205119

DETECTION / DIAGNOSIS

• Direct PCR amplification of 16S rRNA genes offers accelerated bacterial identification using the MinION™ nanopore sequencer
  Kai S, et al. bioRxiv, Oct 5, 2018.
• The clinical utility of point-of-care tests for influenza in ambulatory care: A systematic review and meta-analysis.
  Lee Joseph J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct 
• Immunosignature Analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).
  Günther Oliver P et al. Molecular neurobiology 2018 Oct

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit.
  Madigan Theresa et al. Infection control and hospital epidemiology 2018 Oct 1-7
• Outbreak of Salmonella Chailey Infections Linked To Precut Coconut Pieces - United States and Canada, 2017.
  Luna Sarah et al. MMWR. Morbidity and mortality weekly report 2018 Oct (39) 1098-1100  
• Multihospital Outbreak of a Middle East Respiratory Syndrome Coronavirus Deletion Variant, Jordan: A Molecular, Serologic, and Epidemiologic Investigation.
  Payne Daniel C et al. Open forum infectious diseases 2018 May (5) ofy095
• Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study.
  Kusejko Katharina et al. Virus evolution 2018 Jul (2) vey024
• Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey.
  Chow Nancy A et al. The Lancet. Infectious diseases 2018 Oct 
• Notes from the Field: Multiple Cyclosporiasis Outbreaks - United States, 2018.
  Casillas Shannon M et al. MMWR. Morbidity and mortality weekly report 2018 Oct (39) 1101-1102  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• New Vaccine Technologies to Combat Outbreak Situations.
  Rauch Susanne et al. Frontiers in immunology 2018 1963

HOST-MICROBE INTERACTIONS

• Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia.
  Scott William K et al. PLoS genetics 2018 Oct (10) e1007667
• Single-cell virus sequencing of influenza infections that trigger innate immunity
  Russell AB, et al. bioRxiv, Oct 7, 2018.
• Host Genetic Polymorphisms Influencing Susceptibility to Dengue.
  Gupta Sudheer et al. DNA and cell biology 2018 Oct (10) 805-807
• IFNL3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma.
  Bibert Stéphanie et al. AIDS (London, England) 2018 Sep
• Gut Microbiota Diversity across Ethnicities in the United States
  bioRxiv, Oct 3, 2018.
• Methods and Strategies to Examine the Human Breastmilk Microbiome.
  LeMay-Nedjelski Lauren et al. Methods in molecular biology (Clifton, N.J.) 2018 63-86

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.