Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 3, 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
• Host-Microbe Interactions

NEWS

• The US opioid epidemic is driving a spike in infectious diseases
  Reardon S. Nature, Jun 28, 2019.
• For the First Time, Researchers Eliminated HIV From the Genomes of Living Animals
  Park A. TIME, Jul 2, 2019.
• Vanderbilt Sample Prep Method May Enable Whole-Blood Malaria Drug Resistance Test at Point of Care
  Johnson M. GenomeWeb, Jul 2, 2019.

EVENTS / TRAINING / WEB RESOURCES

• New BLAST results for specialized searches now available for testing
  (announcement) NCBI, Jun 28, 2019.
• Microbial Virulence in the Cloud hackathon August 13 – 15 2019
  (announcement) NCBI, free registration due Jul 11, 2019, by 3 pm ET
• Scientific Community Image Forum 
  (online discussion forum) image.sc

CONCEPTS / COMMENTS

• How to support open-source software and stay sane
  Nowogrodzki A. Nature, Jul 1, 2019.
• Outbreak response as an essential component of vaccine development.
  Hatchett Richard et al. The Lancet. Infectious diseases 2019 Jun

METHODS / TOOLS

• Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study.
  Moossavi Shirin et al. BMC microbiology 2019 Jun (1) 145
• Challenges and recommendations to improve the installability and archival stability of omics computational tools.
  Mangul Serghei et al. PLoS biology 2019 Jun (6) e3000333
• Systematic benchmarking of omics computational tools.
  Mangul Serghei et al. Nature communications 2019 03 (1) 1393
• FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files.
  Roser Leandro Gabriel et al. BMC bioinformatics 2019 Jun (1) 361
• Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.
  Lima Leandro et al. Briefings in bioinformatics 2019 Jun
• Use and abuse of correlation analyses in microbial ecology.
  Carr Alex et al. The ISME journal 2019 Jun
• Design and Implementation of Data Exchange Formats for Molecular Detection of Drug-Resistant Tuberculosis.
  Bonney Wilfred et al. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2019 686-695 
• The human gut virome database
  Gregory AC, et al. bioRxiv, Jul 2, 2019.
• A database for ITS2 sequences from nematodes
  Workentine ML, et al. bioRxiv, Jul 2, 2019.
• Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?
  Davies Angela C et al. PLoS computational biology 2019 Jun (6) e1006746

EVOLUTION / ECOLOGY / POPULATIONS

• One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia.
  Barkham Timothy et al. PLoS neglected tropical diseases 2019 Jun (6) e0007421
• Whole-genome sequencing reveals Listeria monocytogenes diversity and allows identification of long-term persistent strains in Brazil.
  Camargo Anderson C et al. Environmental microbiology 2019 Jun
• Differentiating New from Newly Detected: Melioidosis in Yap, Federated States of Micronesia.
  Nolen Leisha D et al. The American journal of tropical medicine and hygiene 2019 Jul 
• Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm
  Eckstrom K, Barlow J. bioRxiv, Jul 3, 2019.
• Genetic diversity and host adaptation of avian H5N1 influenza viruses during human infection.
  Welkers Matthijs R A et al. Emerging microbes & infections 2019 (1) 262-271
• Middle East respiratory syndrome coronavirus infection in non-camelid domestic mammals.
  Kandeil Ahmed et al. Emerging microbes & infections 2019 (1) 103-108
• Genetic variability of the measles virus hemagglutinin gene in B3 genotype strains circulating in Northern Italy.
  Ciceri Giulia et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Jun 103943

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi.
  Lima Nicholas Costa Barroso et al. BMC genomics 2019 Jun (1) 530
• SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia.
  Forde Brian M et al. Scientific reports 2019 Jul (1) 9436
• A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort.
  Telele Nigus Fikrie et al. BMC infectious diseases 2019 Jul (1) 569 

DETECTION / DIAGNOSIS

• HIV-1 drug resistance surveillance among parturient women on anti-retroviral therapy in the Eastern Cape, South Africa: Implications for elimination of mother-to-child transmission.
  Adeniyi Oladele Vincent et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 Jun 89-95
• Coccidioidomycosis Detection Using Targeted Plasma and Urine Metabolic Profiling.
  Jasbi Paniz et al. Journal of proteome research 2019 Jun
• Detection of Single-Nucleotide Polymorphism Markers of Antimalarial Drug Resistance Directly from Whole Blood.
  Leelawong Mindy et al. The Journal of molecular diagnostics : JMD 2019 Jul (4) 623-631

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Foodborne Botulism Outbreak Associated with Commercial Nacho Cheese Sauce from a Gas Station Market.
  Rosen Hilary E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jun 
• Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation.
  Besser John M et al. Foodborne pathogens and disease 2019 Jun  
• Sources of Airborne Norovirus in Hospital Outbreaks.
  Alsved Malin et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jun

HOST-MICROBE INTERACTIONS

• Natural Clostridioides difficile toxin immunization in colonized infants.
  Kociolek Larry K et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jun
• HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response.
  Hamdane Nourdine et al. Gastroenterology 2019 06 (8) 2313-2329.e7
• Multi-lineage evolution in viral populations driven by host immune systems
  Marchi J, et al. bioRxiv, Jun 21, 2019.
• Interplay Between the Host, the Human Microbiome, and Drug Metabolism.
  Nichols Robert G et al. Human genomics 2019 Jun (1) 27

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.