Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Apr 26, 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
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• UK Effort to Sequence 3K Bacterial Genomes Nears Goal  
  Butkus B. GenomeWeb, Apr 23, 2018.
• Hospitals and device makers still struggle to rid medical scopes of infectious bacteria  
  Terhune C. Los Angeles Times, Apr 23, 2018.
• Shoebox-sized lab can diagnose infectious diseases from a drop of blood  
  Branswell H. STAT, Apr 25, 2018.
• Food Bugs to Meet Sequencers  
  GenomeWeb, Apr 26, 2018.
• Study Shows cccDNA Detection With Digital PCR Sensitively Detects Hepatitis B Virus  
  Johnson A. GenomeWeb, Apr 26, 2018.
• Transmitting HIV Is a Crime in Most States. Is HCV Next?  
  Salzman S. MedPage Today, Apr 22, 2018.
• Flu virus finally sequenced in its native form  
  Callaway E. Nature, Apr 20, 2018.
• FDA approves rapid diagnostic test for Candida auris  
  Dall C. CIDRAP, Apr 23, 2018.
• DNA Analysis Of Ancient Excrement Reveals The Diets Of Centuries Past  
  Chen A. NPR, Apr 25, 2018.

EVENTS / TRAINING / WEB RESOURCES

• MicrobeTRACE: A CDC open source application that integrates epidemiologic and pathogen sequence data to help infer and visualize transmission networks.  
  (wiki) CDC, GitHub.com.
• NCBI to help with Rocky Mountain Genomics HackCon at University of Colorado BioFrontiers Institute June 18 – 23, 2018  
  (event) NCBI insights, Apr 20, 2018.
• NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser  
  (announcement) NCBI, Apr 24, 2018.
• The HHS Data Science CoLab  
  (announcement) HHS, applications due Apr 27, 2018.
• Public Health England reference collections  
  (database) Sanger Institute.
• Where to find images.  
  Milne R. Nat Research Microbiol Commun.

CONCEPTS / COMMENTS

• Complexity and biosemiotics in evolutionary ecology of zoonotic infectious agents.  
  Kosoy Michael et al. Evolutionary applications 2018 Apr (4) 394-403 

METHODS / TOOLS

• Comparative study of sequence aligners for detecting antibiotic resistance in bacterial metagenomes.  
  McCall C et al. Letters in applied microbiology 2018 Mar (3) 162-168
• The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces  
  Whon TW, et al. Sci Data, Apr 24, 2018.
• Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes.  
  Wick Ryan R et al. Journal of clinical microbiology 2018 Apr
• ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications.  
  Verhoeven Joost Theo Petra et al. Canadian journal of microbiology 2018 Apr
• Use of external quality control material for HIV-1 RNA testing to assess the comparability of data generated in separate laboratories and the stability of HIV-1 RNA in samples after prolonged storage.  
  Jennings Cheryl et al. Journal of clinical microbiology 2018 Apr 

EVOLUTION / ECOLOGY / POPULATIONS

• Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes. 
  Potgieter Sarah et al. Water research 2018 Mar 406-419
• Molecular Evidence of Rickettsia in Human and Dog Blood in Bangkok.  
  Mongkol Nanthanida et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2018 Apr
• Zika Virus MB16-23 in Mosquitoes, Miami-Dade County, Florida, USA, 2016.  
  Mutebi John-Paul et al. Emerging infectious diseases 2018 Apr (4) 
• Mapping the Evolutionary Potential of RNA Viruses.  
  Dolan Patrick T et al. Cell host & microbe 2018 Apr (4) 435-446
• Detection of numerous HIV-1/MO recombinants in France.  
  De Oliveira Fabienne et al. AIDS (London, England) 2018 Apr
• Stochastic processes constrain the within and between host evolution of influenza virus.  
  McCrone John T et al. eLife 2018 Apr

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Antibiotic resistance and molecular characteristics of Staphylococcus aureus isolated from backyard-raised pigs and pig workers.  
  Momoh Asabe Halimat et al. Tropical animal health and production 2018 Apr
• Carbapenem-Resistant E. cloacae in Southwest China: Molecular Analysis of Resistance and Risk Factors for Infections Caused by NDM-1-Producers. 
  Jia Xiaojiong et al. Frontiers in microbiology 2018 658
• Significance of Coexisting Mutations on Determination of the Degree of Isoniazid Resistance in Mycobacterium tuberculosis Strains.  
  Karunaratne Galbokka Hewage Roshanthi Eranga et al. Microbial drug resistance (Larchmont, N.Y.) 2018 Apr
• Experimental Adaptive Evolution of Simian Immunodeficiency Virus SIVcpz to Pandemic Human Immunodeficiency Virus Type 1 by Using a Humanized Mouse Model.  
  Sato Kei et al. Journal of virology 2018 02 (4)
• Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel.  
  Chow Nancy A et al. Genome announcements 2018 Apr (15) 

DETECTION / DIAGNOSIS

• Pathogen detection in the CRISPR-Cas era.  
  Sashital Dipali G et al. Genome medicine 2018 Apr (1) 32
• Multicentre study evaluating matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibility.  
  Cheng Yun-Hsiang et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Apr
• Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy.  
  Britto Carl D et al. PLoS neglected tropical diseases 2018 Apr (4) e0006408
• Performance of the Trioplex real-time RT-PCR assay for detection of Zika, dengue, and chikungunya viruses.  
  Santiago Gilberto A et al. Nature communications 2018 Apr (1) 1391 
• The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs.  
  Keske Siran et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Apr (4) 779-783 
• Comparison of an in vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing.  
  Tzou Philip L et al. Journal of clinical microbiology 2018 Apr
• Ebolavirus diagnosis made simple, comparable and faster than molecular detection methods: preparing for the future.  
  James Ameh S et al. Virology journal 2018 Apr (1) 75
• Rapid and reliable diagnostic method to detect Zika virus by real-time fluorescence reverse transcription loop-mediated isothermal amplification.  
  Guo Xu-Guang et al. AMB Express 2018 Apr (1) 60
• Detection of Candida species in pregnant Chinese women with a molecular beacon method.  
  Zhai Yanhong et al. Journal of medical microbiology 2018 Apr
• Molecular diagnosis of Strongyloides stercoralis among transplant candidates.  
  Paula Fabiana M et al. Transplant infectious disease : an official journal of the Transplantation Society 2018 Apr e12909

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis.  
  Leong Kelvin W C et al. Scientific reports 2018 Apr (1) 6274
• Protracted Outbreak of Salmonella Newport Infections Linked to Ground Beef: Possible Role of Dairy Cows - 21 States, 2016-2017.  
  Marshall Katherine E Heiman et al. MMWR. Morbidity and mortality weekly report 2018 Apr (15) 443-446  
• A case of haemolytic uraemic syndrome (HUS) revealed an outbreak of Shiga toxin-2-producing Escherichia coli O26:H11 infection in a nursery, with long-lasting shedders and person-to-person transmission, Italy 2015.  
  Scavia Gaia et al. Journal of medical microbiology 2018 Apr
• Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis.  
  Yang Chongguang et al. The Lancet. Infectious diseases 2018 Apr
• A 2015 outbreak of flea-borne rickettsiosis in San Gabriel Valley, Los Angeles County, California.  
  Nelson Kimberly et al. PLoS neglected tropical diseases 2018 Apr (4) e0006385  
• HIV-1 transmission networks across Cyprus (2010-2012).  
  Kostrikis Leondios G et al. PloS one 2018 (4) e0195660
• Zoonotic origin and transmission of Middle East respiratory syndrome coronavirus in the UAE.  
  Paden C R et al. Zoonoses and public health 2018 05 (3) 322-333 
• Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.  
  Garcia-Hermoso Dea et al. mBio 2018 Apr (2)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A world without bacterial meningitis: how genomic epidemiology can inform vaccination strategy.  
  Rodrigues Charlene M C et al. F1000Research 2018 401
• Predicting Influenza H3N2 Vaccine Efficacy from Evolution of the Dominant Epitope.  
  Bonomo Melia E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Apr
• MicroRNA-Based Attenuation of Influenza Virus across Susceptible Hosts.  
  Waring Barbara M et al. Journal of virology 2018 01 (2)

HOST-MICROBE INTERACTIONS

• Use of Genetic Testing for Primary Immunodeficiency Patients.  
  Heimall Jennifer R et al. Journal of clinical immunology 2018 Apr
• Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection.  
  Midani Firas S et al. The Journal of infectious diseases 2018 Apr
• Genome-Wide Analysis to Identify HLA Factors Potentially Associated With Severe Dengue.  
  Gupta Sudheer et al. Frontiers in immunology 2018 728
• Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α + thalassaemia.  
  Opi D Herbert et al. eLife 2018 Apr

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