Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jan 30, 2020

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
• Host-Microbe Interactions

NEWS

• DNA sleuths read the coronavirus genome, tracing its origins and looking for dangerous mutations
  Begley S. STAT, Jan 24, 2020.
• Scientists are unraveling the Chinese coronavirus with unprecedented speed and openness
  Johnson C. Washington Post, Jan 24, 2020.
• Coronavirus Genome Sequencing Finds Distinct Genetic Differences From 2003 SARS Virus
  GenomeWeb, Jan 29, 2020.
• Coronavirus latest: Australian lab first to grow virus outside China
  Nature, Jan 27, 2020.
• Why snakes probably aren't spreading the new China virus
  Callaway E, Cyranoski D. Nature, Jan 23, 2020.
• Could Novel Coronavirus Become Low-Level Pandemic?
  Walker M. MedPage Today, Jan 24, 2020.
• CDC Provides Test Protocol for Novel Coronavirus, Preps Kits for Local Use
  Johnson M. GenomeWeb, Jan 27, 2020.
• With Wuhan Virus Genetic Code in Hand, Scientists Begin Work on a Vaccine
  (Reuters) New York Times, Jan 25, 2020.
• Promising Vaccine Candidate
  GenomeWeb, Jan 29, 2020.
• TB vaccines can vary greatly, study finds. But does that mean some are less protective?
  Boodman E. STAT, Jan 28, 2020.
• Study Finds No Association Between Herpes Virus and Alzheimer's
  Zimmer K. The Scientist, Jan 23, 2020.
• UK Newborn Trial to Assess PCR Test for Antibiotic-Induced Hearing Loss
  GenomeWeb, Jan 27, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Genomic analysis of nCoV spread. Situation report 2020-01-23.
  (interactive report) Bedford T, et al. NextStrain, Jan 23, 2020.
• ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
  Lavender Christopher A et al. PLoS computational biology 2020 Jan (1) e1007571
• An educational guide for nanopore sequencing in the classroom.
  Salazar Alex N et al. PLoS computational biology 2020 Jan (1) e1007314

CONCEPTS / COMMENTS

• A Novel Coronavirus Emerging in China - Key Questions for Impact Assessment.
  Munster Vincent J et al. The New England journal of medicine 2020 Jan
• Rapid outbreak response requires trust
  (editorial) Nature, Jan 22, 2020.
• Phylogenomic analysis of Neisseria gonorrhoeae: a promising tool for tracking putative gonococcal sexual networks.
  Jolly Ann M et al. The Lancet. Infectious diseases 2020 Jan

METHODS / TOOLS

• Using R and Bioconductor in Clinical Genomics and Transcriptomics.
  Sepulveda Jorge L et al. The Journal of molecular diagnostics : JMD 2020 Jan (1) 3-20 
• A new method for inferring timetrees from temporally sampled molecular sequences.
  Miura Sayaka et al. PLoS computational biology 2020 Jan (1) e1007046
• EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing.
  Perini Matteo et al. Scientific reports 2020 Jan (1) 1307
• QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data.
  Anyansi Christine et al. BMC genomics 2020 Jan (1) 80

EVOLUTION / ECOLOGY / POPULATIONS

• Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population.
  Kirchberger Paul C et al. Environmental microbiology 2020 Jan
• Genomic analysis of Mycobacterium tuberculosis isolates and construction of a Beijing lineage reference genome.
  Wang Woei-Fuh et al. Genome biology and evolution 2020 Jan 
• Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
  Lu R, et al. Lancet, Jan 30, 2020. 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• The O-Antigen Epitope Governs Susceptibility to Colistin in Salmonella enterica.
  Ricci Vito et al. mBio 2020 Jan (1)
• The epidemic of multidrug resistant tuberculosis in China in historical and phylogenetic perspectives.
  Zhou Yang et al. The Journal of infection 2020 Jan

DETECTION / DIAGNOSIS

• Characterization of antimicrobial resistance genes from Neisseria gonorrhoeae positive remnant Aptima urine specimens.
  Parmar Nidhi R et al. Future microbiology 2020 Jan
• Resistance Sniffer: An online tool for prediction of drug resistance patterns of Mycobacterium tuberculosis isolates using next generation sequencing data.
  Muzondiwa Dillon et al. International journal of medical microbiology : IJMM 2020 Jan 151399

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak.
  Elliott Thomas M et al. BMC infectious diseases 2020 Jan (1) 72 
• Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei.
  Roberts Leah W et al. Nature communications 2020 Jan (1) 466 
• Phylogenomic analysis of Neisseria gonorrhoeae transmission to assess sexual mixing and HIV transmission risk in England: a cross-sectional, observational, whole-genome sequencing study.
  Town Katy et al. The Lancet. Infectious diseases 2020 Jan
• A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster.
  Chan Jasper Fuk-Woo et al. Lancet (London, England) 2020 Jan 
• Temporal Changes in HIV Transmission Patterns among Young Men Who Have Sex with Men, United States, 2009-2016.
  Panneer Nivedha et al. Journal of acquired immune deficiency syndromes (1999) 2020 Jan 

HOST-MICROBE INTERACTIONS

• Association of toll-like receptor 10 polymorphisms with pediatric pneumococcal meningitis.
  Xiang Qiaoyan et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2020 Jan
• Immune correlates of tuberculosis disease and risk translate across species
  Ahmed M, et al. Sci Transl Med, Jan 29, 2020.
• Age-specific incidence of influenza A responds to change in virus subtype dominance.
  Gagnon Alain et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jan
• Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis.
  Lee Allen A et al. Inflammatory bowel diseases 2020 Jan
• CFTR dysregulation drives active selection of the gut microbiome.
  Meeker Stacey M et al. PLoS pathogens 2020 Jan (1) e1008251
• The predictive power of the microbiome exceeds that of genome-wide association studies in the discrimination of complex human disease
  Tierney BT, et al. bioRxiv, Jan 2, 2020.

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.