Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 25, 2019

Advanced Molecular Detection Clips Content

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

NEWS

• What happens when a deadly disease is eradicated? Scientists sequence and destroy
  Butler D. Science, Jul 24, 2019.
• Archaic TB test for cows could finally be put out to pasture 
  Nature, Jul 17, 2019.
• NIH awards contract for acute flaccid myelitis natural history study
  NIH, Jul 23, 2019.
• Experts call for action on chronic wasting disease
  Soucheray S. CIDRAP, Jul 23, 2019.
• Deadly fungal disease may be linked to climate change, study suggests
  Sun LH. Washington Post, Jul 23, 2019.
• Visceral Leishmaniasis Tests Lack Accuracy, Study Finds
  360dx, Jul 18, 2019.
• You're very easy to track down, even when your data has been anonymized
  Jee C. MIT Tech Rev, Jul 23, 2019.

CONCEPTS / COMMENTS

• You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details.
  Treangen Todd J et al. EMBO reports 2018 12 (12)
• Cholera: recent updates.
  Weil Ana A et al. Current opinion in infectious diseases 2018 10 (5) 455-461
• The 1918 influenza pandemic: 100 years of questions answered and unanswered
  Taubenberger J, et al. Sci Transl Med, Jul 24, 2019.
• On the Emergence of Candida auris: Climate Change, Azoles, Swamps, and Birds
  Casadevall A, et al. mBio, Jul 23, 2019.
• Accelerated evolution and spread of multidrug-resistant Plasmodium falciparum takes down the latest first-line antimalarial drug in southeast Asia
  Menard D, Fidock DA. Lancet Infect Dis, Jul 22, 2019.
• An innovative way to publish
  (editorial) Nature, Jul 23, 2019.

METHODS / TOOLS

• A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples.
  Deng Ling et al. Viruses 2019 Jul (7)
• Direct Sequencing of RNA with MinION Nanopore: Detecting Mutations based on Associations
  Harel N, et al. bioRxiv, Jul 21, 2019.
• Phylogenetic Concepts and Tools Applied to Epidemiologic Investigations of Infectious Diseases.
  Janies Daniel et al. Microbiology spectrum 2019 Jul (4) 
• Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks.
  Bloomfield Samuel et al. PloS one 2019 (7) e0214169
• Misclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies
  Bandoy DJ, et al. medRxiv, Jul 6, 2019.

EVOLUTION / ECOLOGY / POPULATIONS

• High colonization rate of a novel carbapenem-resistant Klebsiella lineage among migratory birds at Qinghai Lake, China.
  Liao Xiaoping et al. The Journal of antimicrobial chemotherapy 2019 Jul
• Whole Genome Sequencing Characterization of Shiga Toxin-Producing Escherichia coli Isolated from Flour from Swiss Retail Markets.
  Boss Renate et al. Journal of food protection 2019 Jul 1398-1404
• Genomic Evolution of Staphylococcus aureus During Artificial and Natural Colonization of the Human Nose.
  Goyal Manisha et al. Frontiers in microbiology 2019 1525
• Molecular detection and genetic characterisation of pathogenic Theileria, Anaplasma and Ehrlichia species among apparently healthy sheep in central and western Kenya.
  Ringo Aaron E et al. The Onderstepoort journal of veterinary research 2019 Jun (1) e1-e8
• Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
  Seiler Enrico et al. PLoS computational biology 2019 Jul (7) e1007208
• Nationwide Molecular Epidemiology of Measles Virus in Japan Between 2008 and 2017.
  Seki Fumio et al. Frontiers in microbiology 2019 1470
• Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies
  Giovanetti M, et al. bioRxiv, Jul 23, 2019.
• Deep sequencing of 2009 influenza A/H1N1 virus isolated from volunteer human challenge study participants and natural infections.
  Xiao Yongli et al. Virology 2019 Aug 96-107
• The structure of the influenza A virus genome.
  Dadonaite Bernadeta et al. Nature microbiology 2019 Jul
• Enterovirus-D68 (EV-D68) in pediatric patients with respiratory infection: The circulation of a new B3 clade in Italy.
  Piralla Antonio et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 91-96
• Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago.
  Sameroff Stephen et al. Scientific reports 2019 Jul (1) 10421
• Novel hepatitis D-like agents in vertebrates and invertebrates.
  Chang Wei-Shan et al. Virus evolution 2019 Jul (2) vez021
• Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study
  Hamilton WL, et al. Lancet Infect Dis, Jul 22, 2019.
• Recombinant vector vaccine evolution.
  Bull James J et al. PLoS computational biology 2019 Jul (7) e1006857

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomics of vancomycin-resistant Enterococcus faecium.
  Gorrie Claire et al. Microbial genomics 2019 Jul
• Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages
  Beale MA, et al. Nat Commun, Jul 22, 2019.
• Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia .
  Naidenov Bryan et al. Frontiers in microbiology 2019 1446
• Rapid Characterization of Virulence Determinants in Helicobacter pylori Isolated from Non-Atrophic Gastritis Patients by Next-Generation Sequencing.
  Imkamp Frank et al. Journal of clinical medicine 2019 Jul (7)
• Association of Enterovirus D68 with Acute Flaccid Myelitis, Philadelphia, Pennsylvania, USA, 2009–2018 
  Uprety P, et al. Emerg Infect Dis, Sep 2019.
• Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study
  van der Pluijm R, et al. Lancet Infect Dis, Jul 22, 2019.
• Cutaneous leishmaniasis in the 21st century: from the laboratory to the bedside.
  Barkati Sapha et al. Current opinion in infectious diseases 2019 Jul
• Characterizing the molecular and metabolic mechanisms of insecticide resistance in Anopheles gambiae in Faranah, Guinea.
  Stica Caleb et al. Malaria journal 2019 Jul (1) 244  

DETECTION / DIAGNOSIS

• Antimycobacterial Susceptibility Testing of Nontuberculous Mycobacteria.
  Brown-Elliott Barbara A et al. Journal of clinical microbiology 2019 Jul 
• Potential occupational and respiratory hazards in a Minnesota cannabis cultivation and processing facility.
  Couch James R et al. American journal of industrial medicine 2019 Jul  
• Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.
  Sheahan Taylor et al. PloS one 2019 (7) e0219961
• Erysipelothrix rhusiopathiae endocarditis diagnosed by broad range 16s rRNA PCR gene sequencing.
  Balkhair A et al. IDCases 2019 e00584 
• Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology.
  Pérez-Sautu Unai et al. Emerging microbes & infections 2019 (1) 1054-1065
• A defined antigen skin test for the diagnosis of bovine tuberculosis.
  Srinivasan Sreenidhi et al. Science advances 2019 Jul (7) eaax4899
• European Echinococcus multilocularis Identified in Patients in Canada.
  Massolo Alessandro et al. The New England journal of medicine 2019 Jul (4) 384-385 
• Targeting a highly repeated germline DNA sequence for improved real-time PCR-based detection of Ascaris infection in human stool.
  Pilotte Nils et al. PLoS neglected tropical diseases 2019 Jul (7) e0007593

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases.
  Gerner-Smidt Peter et al. Frontiers in public health 2019 172  
• Differentiating Epidemic from Endemic or Sporadic Infectious Disease Occurrence.
  Riley Lee W et al. Microbiology spectrum 2019 Jul (4) 
• Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case.
  Francés-Cuesta Carlos et al. Forensic science international. Genetics 2019 Jul 141-146 
• Genomics for molecular epidemiology and detecting transmission of carbapenemase-producing Enterobacterales in Victoria, Australia, 2012-2016.
  Sherry Norelle L et al. Journal of clinical microbiology 2019 Jul 
• An Outbreak of KPC-Producing Klebsiella pneumoniae Linked with an Index Case of Community-Acquired KPC-Producing Isolate: Epidemiological Investigation and Whole Genome Sequencing Analysis.
  Song Je Eun et al. Microbial drug resistance (Larchmont, N.Y.) 2019 Jul
• Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.
  Li Tony et al. Journal of clinical microbiology 2019 Jul 
• Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016.
  Alkam Duah et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Jul 103965 

HOST-MICROBE INTERACTIONS

• Role of the Microbiota in the Modulation of Vaccine Immune Responses.
  Ciabattini Annalisa et al. Frontiers in microbiology 2019 1305
• Classification of individuals and the potential to detect sexual contact using the microbiome of the pubic region.
  Williams Diana W et al. Forensic science international. Genetics 2019 07 177-187

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.