Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 27, 2017

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.

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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

• 'Editathon' Looks to Improve Wikipedia for Computational Biology  
  Versel N. GenomeWeb, Jul 24, 2017.
• Nanopore Sequencing, PCR Platforms Evaluated for Rapid Pneumonia Diagnosis in UK Study  
  Karow J. GenomeWeb, Jul 24, 2017.
• Researchers Find MRSA Genesis Occurred Years Before Clinical Introduction of Methicillin  
  GenomeWeb, Jul 24, 2017.
• Sanger Institute Wins Grant for Antibiotic Resistance Surveillance  
  GenomeWeb, Jul 21, 2017.
• Nanopore Sequencing, PCR Platforms Evaluated for Rapid Pneumonia Diagnosis in UK Study  
  Karow J. GenomeWeb, Jul 24, 2017.
• Child Lives with HIV for Years Without Treatments  
  Grant B. The Scientist, Jul 24, 2017.
• CDC keeping a watchful eye on Candida auris  
  Dall C. CIDRAP, Jul 20, 2017.
• Adapted blood test predicts risk for anemia following malaria treatment  
  Healio, Jul 14, 2017.
• Microbiota Manipulations  
  Williams R. The Scientist, Jul 17, 2017.

EVENTS / TRAINING / WEB RESOURCES

• WikiProject Computational Biology/ISCB competition announcement 2017-18  
  (announcement) Wikipedia, Jul 21, 2017. The International Society for Computational Biology (ISCB) announces its 6th annual international competition to improve the coverage on Wikipedia of any aspect of computational biology.
• Unleashing the potential of infectious disease genomics  
  (blog post) PHG Foundation, Jul 6, 2017.

POLICY

• Global action plan on HIV drug resistance 2017–2021  
  (report) WHO, Jul 2017.
• HIV drug resistance report 2017  
  (report) WHO, Jul 2017.

CONCEPTS / COMMENTS

• Metagenomics: The Next Culture-Independent Game Changer.  
  Forbes Jessica D et al. Frontiers in microbiology 2017 1069
• A promising means of pest control meets some evolutionary truths  
  Economist, Juul 22, 2017.

METHODS / TOOLS

• Best Practice Data Life Cycle Approaches for the Life Sciences  
  Griffin PC, et al. bioRxiv, Jul 24, 107.
• FaStore - a space-saving solution for raw sequencing data  
  Roguski L, et al. bioRxiv, Jul 25, 2017.
• Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture.  
  Azman Syafiq Kamarul et al. BMC bioinformatics 2017 Jul (1) 353
• A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation  
  McCloskey RM, Poon A. bioRxiv, Jul 19, 2017.

EVOLUTION / ECOLOGY / POPULATIONS

• Finished Whole-Genome Sequences of Clostridium butyricum Toxin Subtype E4 and Clostridium baratii Toxin Subtype F7 Strains.  
  Halpin Jessica L et al. Genome announcements 2017 Jul (29) 
• Molecular evolution of two asymptomatic echovirus 6 strains that constitute a novel branch of recently epidemic echovirus 6 in China.  
  Sun Hao et al. Virology journal 2017 Jul (1) 140
• Circulation and diagnostics of Puumala virus in Norway: nephropatia epidemica incidence and rodent population dynamics.  
  Milhano Natacha et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2017 Aug (8) 732-742
• Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra.  
  Rawson Jonathan M O et al. Journal of molecular biology 2017 Jul (15) 2290-2307
• Epidemiology, Evolution, and Pathogenesis of H7N9 Influenza Viruses in Five Epidemic Waves since 2013 in China.  
  Su Shuo et al. Trends in microbiology 2017 Jul
• Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana.  
  Tirera Sourakhata et al. PLoS neglected tropical diseases 2017 Jul (7) e0005764
• Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats.  
  Dario Maria Augusta et al. PLoS neglected tropical diseases 2017 Jul (7) e0005790
• A study of ticks and tick-borne livestock pathogens in Pakistan.  
  Karim Shahid et al. PLoS neglected tropical diseases 2017 Jun (6) e0005681

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.  
  Stoesser N et al. Scientific reports 2017 Jul (1) 5917
• Genomic characterization of novel IncFII-type multidrug resistant plasmids p0716-KPC and p12181-KPC from Klebsiella pneumoniae.  
  Feng Jiao et al. Scientific reports 2017 Jul (1) 5830
• Persistent bacterial infections and persister cells.  
  Fisher Robert A et al. Nature reviews. Microbiology 2017 Aug (8) 453-464
• Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration.  
  Lees John A et al. eLife 2017 Jul
• Evolution of Acinetobacter baumannii In Vivo: International Clone II, More Resistance to Ceftazidime, Mutation in ptk.  
  Hua Xiaoting et al. Frontiers in microbiology 2017 1256
• Next-generation sequencing to monitor the spread of antimicrobial resistance.  
  Otto Michael et al. Genome medicine 2017 Jul (1) 68
• Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice.  
  Harkins Catriona P et al. Genome biology 2017 Jul (1) 130
• Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci.  
  O'Toole Ronan F et al. Genomics 2017 Jul
• An infant with acute gastroenteritis caused by a secondary infection with a Rotarix-derived strain.  
  Sakon Naomi et al. European journal of pediatrics 2017 Jul
• Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam.  
  Day Jeremy N et al. PLoS neglected tropical diseases 2017 Jun (6) e0005628
• Contemporary status of insecticide resistance in the major Aedes vectors of arboviruses infecting humans.  
  Moyes Catherine L et al. PLoS neglected tropical diseases 2017 Jul (7) e0005625

DETECTION / DIAGNOSIS

• Advances in point-of-care technologies for molecular diagnostics.  
  Zarei Mohammad et al. Biosensors & bioelectronics 2017 Jul 494-506
• Strengthening the laboratory diagnosis of infections caused by pathogenic Corynebacterium species in the Vaccine era.  
  Rajamani Sekar Suresh Kumar et al. Letters in applied microbiology 2017 Jul
• Recent advances in the development and use of molecular tests to predict antimicrobial resistance in Neisseria gonorrhoeae.  
  Donà Valentina et al. Expert review of molecular diagnostics 2017 Jul
• Acid-fast bacterium detection and identification from paraffin-embedded tissues using a PCR-pyrosequencing method.  
  Bao Jian R et al. Journal of clinical pathology 2017 Jul
• Ten years transmission of the new variant of Chlamydia trachomatis in Sweden: prevalence of infections and associated complications.  
  Dahlberg Jenny et al. Sexually transmitted infections 2017 Jul
• Culture-Independent Detection of Nontuberculous Mycobacteria in Clinical Respiratory Samples.  
  Scoleri Gianny P et al. Journal of clinical microbiology 2016 Sep (9) 2395-8
• Improved detection of genus-specific Alphavirus using a generic TaqMan® assay.  
  Giry Claude et al. BMC microbiology 2017 Jul (1) 164
• The role of supplementary environmental surveillance to complement acute flaccid paralysis surveillance for wild poliovirus in Pakistan - 2011-2013. 
  Cowger Tori L et al. PloS one 2017 (7) e0180608 
• Comparative Study and Analytical Verification of PCR Methods for the Diagnosis of Congenital Chagas Disease.  
  Cura Carolina Inés et al. The Journal of molecular diagnostics : JMD 2017 Jul 
• Analytical sensitivity and specificity of a loop-mediated isothermal amplification (LAMP) kit prototype for detection of Trypanosoma cruzi DNA in human blood samples.  
  Besuschio Susana A et al. PLoS neglected tropical diseases 2017 Jul (7) e0005779
• 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.  
  Hernandez-Castro Luis E et al. PLoS neglected tropical diseases 2017 Jul (7) e0005710

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Outbreak of Salmonella enteritidis PT14b gastroenteritis at a restaurant in England: the use of molecular typing to achieve a successful prosecution. 
  Chatt C et al. Public health 2017 Jul 51-58
• Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.  
  Brodrick Hayley J et al. Genome medicine 2017 Jul (1) 70
• Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns  
  Donker T, et al. Microbial Genomics, Jul 4, 2017.
• Notes from the Field: Cluster of Acute Flaccid Myelitis in Five Pediatric Patients - Maricopa County, Arizona, 2016.  
  Iverson Sally A et al. MMWR. Morbidity and mortality weekly report 2017 Jul (28) 758-760 
• Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1.  
  Charpentier Elena et al. Emerging infectious diseases 2017 Aug (8) 1237-1245

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Neuraminidase-based recombinant virus-like particles protect against lethal avian influenza A(H5N1) virus infection in ferrets.  
  Smith Gale E et al. Virology 2017 Sep 90-97 
• DNA-immunisation with dengue virus E protein domains I/II, but not domain III, enhances Zika, West Nile and Yellow Fever virus infection.  
  Slon Campos Jose L et al. PloS one 2017 (7) e0181734

HOST-MICROBE INTERACTIONS

• Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis.  
  Virtanen Seppo et al. PloS one 2017 (7) e0181477
• The Human Virome - Implications for Clinical Practice in Transplantation Medicine.  
  Tan Susanna K et al. Journal of clinical microbiology 2017 Jul
• Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles.  
  Robinson James et al. PLoS genetics 2017 Jun (6) e1006862
• Genetic polymorphisms of the IL6 and NOD2 genes are risk factors for inflammatory reactions in leprosy.  
  Sales-Marques Carolinne et al. PLoS neglected tropical diseases 2017 Jul (7) e0005754
• The impact of genetic variation in IL28B, IFNL4 and HLA genes on treatment responses against chronic hepatitis C virus infection.  
  Sakhaee Fatemeh et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jul
• Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease.  
  Chu Hiutung et al. Genome medicine 2017 Jul (1) 69

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.