Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 31, 2019

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

• Zoonotic Disease Research Program Shut Down
  Makowski E. The Scientist, Oct 28, 2019.
• Lyme Disease Test Could Enable 15-Minute Results at the Point of Care
  O'Connor L. 360dx, Oct 21, 2019.
• Is Crispr the Next Antibiotic?
  Sheikh K. New York Times, Oct 28, 2019.
• Backgrounder: NIH Collaboration on Gene-Based Cures for SCD and HIV
  NIH, Oct 23, 2019.
• How measles infections can wipe away immunity to other diseases
  Branswell H. STAT, Oct 31, 2019.
• Inexpensive LAMP-Based Schistosome Tests Could Help Eradication Efforts
  Johnson M. GenomeWeb, Oct 29, 2019.
• Massachusetts General Hospital oversaw trial that led to the first death from a fecal transplant, a new paper shows
  Sheridan K. STAT, Oct 30, 2019.

EVENTS / TRAINING / WEB RESOURCES

• Reframing Resistance
  (report) Wellcome Trust, Oct 29, 2019.
• The Convergence of Infectious Diseases and Noncommunicable Diseases: Proceedings of a Workshop Prepublication The Convergence of Infectious Diseases and Noncommunicable Diseases
  (workshop report) NASEM, 2019.
• An Expanded Platform for Young Scientists
  (editorial) Imperiale MJ, Blader IJ. mSphere, Oct 18, 2019.
• Public Health Alliance for Genomic Epidemiology
  Twitter account: @pha4ge

CONCEPTS / COMMENTS

• Fecal Microbiota Transplantation for Dysbiosis--Predictable Risks
  Blaser MJ. New Engl J Med, Oct 30, 2019.

METHODS / TOOLS

• treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.
  Wang Li-Gen et al. Molecular biology and evolution 2019 Oct
• Living Trees: High Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees.
  Hu Dalong et al. Molecular biology and evolution 2019 Oct
• Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets
  Cozzuto L, et al. bioRxiv, Oct 28, 2019.
• An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples
  Kuhring M, et al. bioRxiv, Oct 24, 2019.
• Pangenomic read mapping
  Anari SS, et al. bioRxiv, Oct 24, 2019.
• Accurate and Complete Genomes from Metagenomes
  Chen LX, et al. bioRxiv, Oct 29, 2019.
• CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
  Alcock Brian P et al. Nucleic acids research 2019 Oct

EVOLUTION / ECOLOGY / POPULATIONS

• Whole Genome Sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada.
  Tsang Raymond S W et al. Canadian journal of microbiology 2019 Oct
• National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016.
  Fu Xuemin et al. Virologica Sinica 2019 Oct 
• Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018.
  Deng Yi-Mo et al. Emerging infectious diseases 2020 Jan (1)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure.
  Kime Louise et al. mBio 2019 10 (5)
• Transmission and evolution of OXA-48-producing Klebsiella pneumoniae ST11 in a single hospital in Taiwan.
  Lu Min-Chi et al. The Journal of antimicrobial chemotherapy 2019 Oct
• Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent.
  Britto Carl D et al. The Journal of antimicrobial chemotherapy 2019 Oct
• International Spread of Multidrug-Resistant Campylobacter coli in Men who have Sex with Men in Washington State and Quebec, 2015-2018.
  Greninger Alexander L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Oct
• Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei.
  Chung The Hao et al. Nature communications 2019 Oct (1) 4828
• Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa.
  Brown Tyler S et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Oct 

DETECTION / DIAGNOSIS

• A review of a 13-month period of FilmArray Meningitis/Encephalitis panel implementation as a first-line diagnosis tool at a university hospital.
  Boudet Agathe et al. PloS one 2019 (10) e0223887 
• A Multiplexed Serologic Test for Diagnosis of Lyme Disease for Point-of-Care Use.
  Arumugam Siddarth et al. Journal of clinical microbiology 2019 Oct
• Genotyping of Mycobacterium tuberculosis Rifampin Resistance Associated Mutations Using Data From Xpert® MTB/RIF Ultra Enables Large-Scale Tuberculosis Molecular Epidemiology Studies.
  Weinrick Brian et al. Journal of clinical microbiology 2019 Oct
• Automatic identification of individual rpoB gene mutations responsible for rifampin resistance in Mycobacterium tuberculosis using melting temperature signatures generated by the Xpert® MTB/RIF Ultra* assay.
  Cao Yuan et al. Journal of clinical microbiology 2019 Sep

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Whole genome sequencing detects minimal clustering among Escherichia coli Sequence Type 131 H30 isolates collected from U.S. children's hospitals
  Miles-Jay A, et al. medRxiv, Oct 29, 2019.
• Ethnically diverse urban transmission networks of Neisseria gonorrhoeae without evidence of HIV serosorting.
  Dave Jayshree et al. Sexually transmitted infections 2019 Oct
• Community outbreak of hepatitis A disproportionately affecting men who have sex with men in Toronto, Canada, January 2017-November 2018.
  Sachdeva H et al. Canada communicable disease report = Releve des maladies transmissibles au Canada 2019 Oct (10) 262-268
• Genetic Epidemiology reveals three chronic reservoir areas with recurrent population mobility challenging poliovirus eradication in Pakistan.
  Akhtar Ribqa et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Oct 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing.
  Hamilton Thomas A et al. Nature communications 2019 Oct (1) 4544
• Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant.
  DeFilipp Zachariah et al. The New England journal of medicine 2019 Oct 

HOST-MICROBE INTERACTIONS

• Association of CR2 genotypes with the acquisition of HIV infection in a trial of recombinant glycoprotein 120 Vaccine.
  Meza Giovanna et al. AIDS (London, England) 2019 Oct
• Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies.
  Perelygina Ludmila et al. PLoS pathogens 2019 Oct (10) e1008080 
• Secretor Status is Associated with Susceptibility to Disease in a Large GII.6 Norovirus Foodborne Outbreak.
  Sharma Sumit et al. Food and environmental virology 2019 Oct
• Untapped "-omics": the microbial metagenome, estrobolome, and their influence on the development of breast cancer and response to treatment.
  Komorowski A S et al. Breast cancer research and treatment 2019 Oct
• The microbiota regulate neuronal function and fear extinction learning.
  Chu Coco et al. Nature 2019 10 (7779) 543-548
• The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease.
  van Rijn Anneloes L et al. PloS one 2019 (10) e0223952

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.