Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 12, 2018

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

• Public Health England Team Describes Metagenomic Sequencing Strategy to ID Viral Pathogens  
  Heger M. GenomeWeb, Jul 11, 2018.
• FDA revises Zika testing for blood donations to allow pooled screening  
  Schnirring L. CIDRAP, Jul 5, 2018.
• UK Study Suggests Need for Faster Viral Meningitis Diagnosis  
  Johnson M. GenomeWeb, Jul 6, 2018.
• Duke 'Exposome' Project Nears Commercialization, Spawns Startup  
  Johnson M. GenomeWeb, Jun 27, 2018.
• Polio outbreaks in the DRC threaten eradication effort  
  Roberts L. Science, Jul 6, 2018.
• The Case for Approving a Drug Never to Be Used (We Hope)  
  Wilson FP. MedPage Today, Jul 9, 2018.
• Experts warn of increasing cases of 'red meat allergy' from tick bites  
  Kelly L. Washington Times, Jul 5, 2018.

EVENTS / TRAINING / WEB RESOURCES

• Tracking projects with Gmail tags: Collaborating through email  
  (blog post) Carpenter A. CellProfiler, Jul 9, 2018.

POLICY

• Building Capacity for a Global Genome Editing Observatory: Conceptual Challenges.  
  Hurlbut J Benjamin et al. Trends in biotechnology 2018 Jul (7) 639-641
• Biologists raise alarm over changes to biopiracy rules.  
  Kupferschmidt Kai et al. Science (New York, N.Y.) 2018 Jul (6397) 14

CONCEPTS / COMMENTS

• What if they don’t have tuberculosis? The consequences and trade-offs involved in false-positive diagnoses of tuberculosis  
  Houben RM, et al. Clin Infect Dis, Jul 5, 2018. 
• Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research  
  Schloss PD. mBio May/June 2018 9:e00525-18.

METHODS / TOOLS

• INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance.  
  Borges Vítor et al. Genome medicine 2018 Jun (1) 46
• Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples.  
  Kafetzopoulou LE, et al. bioRxiv, Jun 25, 2018.
• Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community  
  Perras A, et al. bioRxiv, Jul 10, 2018.
• NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform  
  Calus ST, et al. bioRxiv, Jul 4, 2018.
• Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.  
  Poon Art F Y et al. Retrovirology 2018 Jul (1) 47
• Complete Genome Sequences of Zika Virus Strains Used for the Formulation of CBER/FDA RNA Reference Reagents and Lot Release Panels for Nucleic Acid Technology Testing.  
  Volkova Evgeniya et al. Genome announcements 2018 Jul (27)

EVOLUTION / ECOLOGY / POPULATIONS

• Proximity to other commercial turkey farms affects colonization onset, genotypes and antimicrobial resistance profiles of Campylobacter in turkeys: suggestive evidence from a paired-farm model.  
  Niedermeyer Jeffrey A et al. Applied and environmental microbiology 2018 Jul
• Whole genome sequencing of antimicrobial-resistant Shigella sonnei associated with infection acquired from international and domestic setting reveals gene allelic variants that predict Global Lineages  
  Abelman RL, et al. bioRxiv, Jul 3, 2018.
• Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses.  
  Campioni Fábio et al. Scientific reports 2018 Jul (1) 10478
• Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh.  
  Hossain Zenat Zebin et al. Letters in applied microbiology 2018 Jul
• Molecular characterization of Vibrio cholerae responsible for cholera epidemics in Uganda by PCR, MLVA and WGS.  
  Bwire Godfrey et al. PLoS neglected tropical diseases 2018 06 (6) e0006492
• Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains.  
  Schuenemann Verena J et al. PLoS neglected tropical diseases 2018 06 (6) e0006447
• Full genome and phylogenetic analysis of hepatitis B virus genotype F in Mexican isolates.  
  Fragoso-Fonseca David Esaú et al. Archives of virology 2018 Jul (7) 1981-1984
• Genetic diversity, phylogeography and molecular clock of the Lutzomyia longipalpis complex (Diptera: Psychodidae).  
  Pech-May Angélica et al. PLoS neglected tropical diseases 2018 Jul (7) e0006614

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing.  
  Cuypers Wim L et al. Microbial genomics 2018 Jul
• Gonorrhoea treatment failure caused by a Neisseria gonorrhoeae strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018.  
  Eyre David W et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jul (27)
• Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis.  
  Carter Laurenda et al. International journal of food microbiology 2018 Jun 31-39
• High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis.  
  Depledge Daniel P et al. The Journal of infectious diseases 2018 Jul
• Detection of minority drug resistant mutations in Malawian HIV-1 subtype C-positive patients initiating and on first-line antiretroviral therapy. 
  Zhou Zhiyong et al. African journal of laboratory medicine 2018 (1) 708 
• Human Herpes Virus 6 (HHV-6) - Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing  
  Sharp C, et al. bioRxiv, Jul 5, 2018.
• High proportion of multiple copies of Plasmodium falciparum Plasmepsin-2 gene in African isolates: Is piperaquine resistance emerging in Africa? 
  Leroy D, et al. bioRxiv, Jul 3, 2018.

DETECTION / DIAGNOSIS

• Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania.  
  Sonda Tolbert et al. Antimicrobial resistance and infection control 2018 72
• Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality.  
  Dekker John P et al. Journal of clinical microbiology 2018 Jul
• Interlaboratory Evaluation of the U.S. Food and Drug Administration Escherichia coli Identification Microarray for Profiling Shiga Toxin-Producing Escherichia coli.  
  Patel Isha R et al. Journal of food protection 2018 Jul 1275-1282 
• Rapid detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification assay.  
  Yuan Xin et al. Medicine 2018 Jun (25) e10806
• Epidemiology of rubella infection and genotyping of rubella virus in Cote d'Ivoire, 2012-2016.  
  Kadjo Herve A et al. Journal of medical virology 2018 Jul 
• Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples.  
  Sauvage Virginie et al. PloS one 2018 (3) e0194366
• Development of multiplex real time reverse transcriptase PCR assay for simultaneous detection of Zika, Dengue, Yellow Fever and Chikungunya Viruses in a single tube.  
  Wu Wenhui et al. Journal of medical virology 2018 Jul
• Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda.  
  Boyce Ross M et al. Scientific reports 2018 Jul (1) 10159
• Field evaluation of a real time loop-mediated isothermal amplification assay (RealAmp) for malaria diagnosis in Cruzeiro do Sul, Acre, Brazil.  
  Viana Giselle Maria Rachid et al. PloS one 2018 (7) e0200492 
• Improved diagnosis of active Schistosoma infection in travellers and migrants using the ultra-sensitive in-house lateral flow test for detection of circulating anodic antigen (CAA) in serum.  
  van Grootveld Rebecca et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Jul

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Sharing more than friendship - transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015.  
  Grönthal Thomas et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jul (27)
• Persistence of an outbreak of gonorrhoea with high-level resistance to azithromycin in England, November 2014‒May 2018.  
  Smolarchuk Christa et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jun (23)
• Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States.  
  Séraphin Marie Nancy et al. The American journal of tropical medicine and hygiene 2018 Jul
• Two concurrent outbreaks of hepatitis A highlight the risk of infection for non-immune travellers to Morocco, January to June 2018.  
  Gassowski Martyna et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jul (27)
• Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing.  
  Cowell Annie N et al. Genome medicine 2018 Jul (1) 52

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Eradication genomics—lessons for parasite control  
  Cotton JA, et al. Science, Jul 13, 2018.

HOST-MICROBE INTERACTIONS

• Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand.  
  Kisuse Juma et al. Frontiers in microbiology 2018 1345

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.