Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 9, 2019

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

• How genetically engineered viruses — and a rotten eggplant — prolonged a teenager’s life
  Boodman E. STAT, May 8, 2019.

EVENTS / TRAINING / WEB RESOURCES

• How to communicate uncertainty about facts, numbers, science?
  (Twitter thread) Spiegelhalter D. May 8, 2019.

POLICY

• Stopping the Gaps in Epidemic Preparedness.
  Farrar Jeremy J et al. The New England journal of medicine 2019 May (19) 1788-1789 

CONCEPTS / COMMENTS

• Microbial evolutionary medicine: from theory to clinical practice.
  Andersen Sandra B et al. The Lancet. Infectious diseases 2019 Apr
• Two Health or Not Two Health? That Is the Question.
  Hanage William P et al. mBio 2019 04 (2)
• The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise.
  Fitak Robert R et al. The Journal of heredity 2019 May (3) 261-274 
• Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology.
  Lakdawala Seema S et al. Journal of molecular biology 2019 Apr
• Ethical issues in HIV phylogenetics and molecular epidemiology.
  Mehta Sanjay R et al. Current opinion in HIV and AIDS 2019 May (3) 221-226
• The pros, cons, and many unknowns of probiotics
  Suez J, et al. Nat Med, May 6, 2019.

METHODS / TOOLS

• Application of Machine Learning in Microbiology.
  Qu Kaiyang et al. Frontiers in microbiology 2019 827
• Performance of neural network basecalling tools for Oxford Nanopore sequencing
  Wick RR, et al. bioRxiv, May 6, 2019.
• BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing.
  Khachatryan Lusine et al. BMC genomics 2019 May (1) 338
• AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential.
  Alanjary Mohammad et al. Nucleic acids research 2019 Apr
• Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases.
  Alamil M et al. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2019 Jun (1775) 20180258
• Ten quick tips for biocuration.
  Tang Y Amy et al. PLoS computational biology 2019 May (5) e1006906
• An Overview of PulseNet USA Databases.
  Tolar Beth et al. Foodborne pathogens and disease 2019 May  
• A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
  Fonseca Vagner et al. PLoS neglected tropical diseases 2019 May (5) e0007231
• DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics
  Mendes CI, et al. bioRxiv, May 6, 2019.
• Using Earth Mover’s Distance for Viral Outbreak Investigations
  Melnyk A, et al. bioRxiv, May 6, 2019. 

EVOLUTION / ECOLOGY / POPULATIONS

• Remarkable genome stability among emm1 group A Streptococcus in Belgium over 19 years.
  Coppens Jasmine et al. Genome biology and evolution 2019 May
• Arboviral screening of invasive Aedes species in northeastern Turkey: West Nile virus circulation and detection of insect-only viruses.
  Akiner Mustafa M et al. PLoS neglected tropical diseases 2019 May (5) e0007334
• Identification of a New HCV Subtype 6xg Among Injection Drug Users in Kachin, Myanmar.
  Ye Mei et al. Frontiers in microbiology 2019 814
• A brief history of bird flu.
  Lycett Samantha J et al. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2019 Jun (1775) 20180257
• Would you like to purchase a rodent with dermatophytes?
  Tekin Hasan Gökcer et al. Mycoses 2019 May

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals.
  McMillan Elizabeth A et al. Frontiers in microbiology 2019 832
• Large-Scale Genomic Analyses and Toxinotyping of Clostridium perfringens Implicated in Foodborne Outbreaks in France.
  Mahamat Abdelrahim Abakabir et al. Frontiers in microbiology 2019 777
• Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada.
  Ceric Olgica et al. BMC veterinary research 2019 May (1) 130 
• A megaplasmid family responsible for dissemination of multidrug resistance in Pseudomonas
  Cazares A, et al. bioRxiv, May 8, 2019.
• Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate.
  Carroll Laura M et al. mBio 2019 May (3)

DETECTION / DIAGNOSIS

• Point-of-care tests to reduce the burden of sexually transmitted infections.
  Peeling Rosanna Wai Wan et al. The Lancet. Infectious diseases 2019 Apr
• Simple assay to detect Central Asia Outbreak clade of Mycobacterium tuberculosis Beijing genotype.
  Shitikov Egor et al. Journal of clinical microbiology 2019 May
• Clinical impact and cost-effectiveness of genotype testing at HIV diagnosis in the United States.
  Hyle Emily P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 May 
• Viral Metagenomics on Cerebrospinal Fluid.
  Edridge Arthur W D et al. Genes 2019 Apr (5)
• Visualization of Microbes by 16S in situ Hybridization in Term and Preterm Placentae without Intraamniotic Infection.
  Seferovic Maxim D et al. American journal of obstetrics and gynecology 2019 May
• Refining wet lab experiments with in silico searches: A rational quest for diagnostic peptides in visceral leishmaniasis.
  Bremer Hinckel Bruno Cesar et al. PLoS neglected tropical diseases 2019 May (5) e0007353

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Molecular epidemiology study on a nosocomial Moraxella catarrhalis outbreak in a neurological rehabilitation unit.
  P Warnke et al. The Journal of hospital infection 2019 May 
• Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates.
  Smith Anthony M et al. Foodborne pathogens and disease 2019 May 
• Molecular identification of the source of an uncommon tularaemia outbreak, Germany, autumn 2016.
  Jacob Daniela et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 May (18)
• Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018.
  Dangel Alexandra et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 May (18)
• Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review.
  van der Werf Marieke J et al. Frontiers in public health 2019 87 
• Risk of HIV transmission through condomless sex in serodifferent gay couples with the HIV-positive partner taking suppressive antiretroviral therapy (PARTNER): final results of a multicentre, prospective, observational study.
  Rodger Alison J et al. Lancet (London, England) 2019 May 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Antisense peptide nucleic acids as a potential anti-infective agent.
  Lee Hyung Tae et al. Journal of microbiology (Seoul, Korea) 2019 May
• Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus
  Dedrick RM, et al. Nat Med, May 8, 2019.
• Endemic outbreaks due to the re-emergence of classical swine fever after accidental introduction of modified live LOM vaccine on Jeju Island, South Korea.
  Jang Guehwan et al. Transboundary and emerging diseases 2019 Mar (2) 634-639 

HOST-MICROBE INTERACTIONS

• Homozygosity for TYK2 P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry
  Kerner G, et al. Proc Nat Acad Sci, May 8, 2019.
• Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.
  Haran John P et al. mBio 2019 May (3)
• Association of Oral Human Papillomavirus DNA Persistence With Cancer Progression After Primary Treatment for Oral Cavity and Oropharyngeal Squamous Cell Carcinoma.
  Fakhry Carole et al. JAMA oncology 2019 May

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB