Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Sep 13, 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

• FDA Mulls Guidelines for NGS-Based Infectious Disease Diagnostics
  Heger M. GenomeWeb, Sep 12, 2018.
• Sandia Researchers Combine Molecular, Immunoassays for Syndromic Testing
  Johnson M. GenomeWeb, Sep 10, 2018.
• Just Breathe: In Pursuit Of A Malaria Breathalyzer
  Nicolaus D. DiagnosticsWorld, Sep 12, 2018.
• UK Team Demos Nanopore Metagenomic Sequencing for Respiratory Infection Dx
  Heger M. GenomeWeb, Sep 6, 2018.
• Report ties 2 US cases of MCR-1 to problematic GI scope
  Dall C. CIDRAP, Sep 11, 2018.
• Fast-acting flu drug shows strong potential, but clinical trial results also raise concerns
  Branswell H. STAT, Sep 10, 2018.
• Probiotics’ Effects on the Microbiome Vary Widely
  Olena A. The Scientist, Sep 6, 2018.
• Google unveils search engine for open data
  Castelvecchi D. Nature, Sep 5, 2018.

CONCEPTS / COMMENTS

• From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
  Balloux Francois et al. Trends in microbiology 2018 Sep

METHODS / TOOLS

• Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals.
  Reeves Lawrence E et al. PLoS neglected tropical diseases 2018 Aug (8) e0006767
• RefSeq database growth influences the accuracy of k-mer-based species identification
  Nasko DJ, et al. bioRxiv, Apr 18, 2018.
• The effects of random taxa sampling schemes in Bayesian virus phylogeography.
  Magee Daniel et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Oct 225-230

EVOLUTION / ECOLOGY / POPULATIONS

• Pseudomonas -Specific NGS Assay Provides Insight Into Abundance and Dynamics of Pseudomonas Species Including P. aeruginosa in a Cooling Tower.
  Pereira Rui P A et al. Frontiers in microbiology 2018 1958
• Molecular Epidemiology, Ecology, and Evolution of Group A Streptococci.
  Bessen Debra E et al. Microbiology spectrum 2018 Sep (5) 
• Mycobacterium decipiens sp. nov., a new species closely related to the Mycobacterium tuberculosis complex.
  Brown-Elliott Barbara A et al. International journal of systematic and evolutionary microbiology 2018 Sep
• Characterisation of the HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread
  Nazziwah J, et al. bioRxiv, Sep 7, 2018.
• Phylogenomic analysis unravels evolution of yellow fever virus within hosts.
  Chen Chen et al. PLoS neglected tropical diseases 2018 Sep (9) e0006738
• Genomics and evolution of Pneumocystis species.
  Cissé Ousmane H et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Aug 308-320
• Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients.
  Nkhoma Standwell C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Aug 414-424
• Detection OF Wolbachia in field-collected mosquito vector, Aedes aegypti
  Carvajal T, et al. bioRxiv, Sep 4, 2018.
• Morphometric and genetic variation in eight breeds of Ethiopian camels (Camelus dromedarius).
  Legesse Y W et al. Journal of animal science 2018 Sep 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Mosaic Drug Efflux Gene Sequences from Commensal Neisseria Can Lead to Low-Level Azithromycin Resistance Expressed by Neisseria gonorrhoeae Clinical Isolates.
  Shafer William M et al. mBio 2018 Sep (5)
• Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA.
  Tagg Kaitlin A et al. The Journal of antimicrobial chemotherapy 2018 Sep 
• Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
  Wyres KL, et al. bioRxiv, Sep 12, 2018.
• Antimicrobial resistance plasmid reservoir in food and food-producing animals.
  Madec Jean-Yves et al. Plasmid 2018 Sep
• Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra-Deep Pyrosequencing in A Turkish Cohort.
  Sili Uluhan et al. Current HIV research 2018 Sep
• How Respiratory Syncytial Virus Genotypes Influence the Clinical Course in Infants Hospitalized for Bronchiolitis.
  Midulla Fabio et al. The Journal of infectious diseases 2018 Sep
• The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri.
  Liechti Nicole et al. BMC genomics 2018 Sep (1) 654

DETECTION / DIAGNOSIS

• Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
  Charalampous T, et al. bioRxiv, Aug 9, 2018.
• Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue.
  Katz Samantha S et al. PloS one 2018 (9) e0203632 
• Modelling-based evaluation of the costs, benefits and cost-effectiveness of multipathogen point-of-care tests for sexually transmitted infections in symptomatic genitourinary medicine clinic attendees.
  Huntington Susie E et al. BMJ open 2018 Sep (9) e020394
• Identification and capsular serotype sequetyping of Streptococcus pneumoniae strains
  Siles LG, et al. bioRxiv, Sep 12, 2018.
• Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors
  Dalmat RR, et al. bioRxiv, Sep 12, 2018.
• Rapid diagnosis of Zika virus through saliva and urine by Loop-mediated isothermal amplification (LAMP).
  Castro Talita et al. Journal of oral microbiology 2018 (1) 1510712
• Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing
  Leon KE, et al. bioRxiv, Sep 12, 2018.
• Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza.
  Zhang Hanyuan et al. Analytical chemistry 2018 Aug (15) 9583-9590
• Mosquito excreta: A sample type with many potential applications for the investigation of Ross River virus and West Nile virus ecology.
  Ramírez Ana L et al. PLoS neglected tropical diseases 2018 Aug (8) e0006771
• Recent advances in the molecular diagnosis of mucormycosis.
  Dadwal Sanjeet S et al. Expert review of molecular diagnostics 2018 Sep
• Direct nucleic acid analysis of mosquitoes for high fidelity species identification and detection of Wolbachia using a cellphone.
  Bhadra Sanchita et al. PLoS neglected tropical diseases 2018 Aug (8) e0006671
• Screening for Pfhrp2/3-Deleted Plasmodium falciparum, Non-falciparum, and Low-Density Malaria Infections by a Multiplex Antigen Assay.
  Plucinski Mateusz M et al. The Journal of infectious diseases 2018 Sep 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Transmission of Mobile Colistin Resistance (mcr-1) by Duodenoscope.
  Shenoy Erica S et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Sep 
• Elizabethkingia anophelis and Association with Tap Water and Handwashing, Singapore.
  Yung Chee-Fu et al. Emerging infectious diseases 2018 Sep (9) 1730-1733
• Assessing the utility of minority variant composition in elucidating RSV transmission pathways
  Githinji G, et al. bioRxiv, Sep 12, 2018.
• Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission
  Thompson R, et al. bioRxiv, Sep 12, 2018.
• Case-Control Study of Cryptosporidium Transmission in Bangladeshi Households.
  Korpe Poonum S et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Sep

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A single-dose plasmid-launched live-attenuated Zika vaccine induces protective immunity.
  Zou Jing et al. EBioMedicine 2018 Sep
• Association of Rapid Molecular Testing With Duration of Respiratory Isolation for Patients With Possible Tuberculosis in a US Hospital.
  Chaisson Lelia H et al. JAMA internal medicine 2018 Aug

HOST-MICROBE INTERACTIONS

• Genome-wide microRNA analysis of HPV-positive self-samples yields novel triage markers for early detection of cervical cancer.
  Snoek Barbara C et al. International journal of cancer 2018 Sep
• Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities.
  Glanzmann Brigitte et al. Genes and immunity 2018 Sep
• Gut microbiota in HIV-infected individuals linked to coronary heart disease.
  Kehrmann J et al. The Journal of infectious diseases 2018 Sep
• Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn's Disease Cohort
  Sprockett D, et al. bioRxiv, Sep 10, 2018.

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.