Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 22, 2019

Advanced Molecular Detection Clips Content

• News
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Taiwanese Team Explores New Sequencing Chemistry to Power Novel Single-Molecule Platform
  Han AP. GenomeWeb, Aug 19, 2019.
• Optofluidic Chip Integrates Nanopores, Electrical Feedback to Control Single-Molecule Delivery 
  Gilmore J. GenomeWeb, Aug 16, 2019.
• A Tissue Sample From 1966 Held Traces of Early HIV
  Yong E. Atlantic, Aug 16, 2019.
• Could the world see a resurgence of polio? Experts fear a cautionary tale in measles
  Branswell H. STAT, Aug 19, 2019.

POLICY

• Diagnosis, management and prevention of Candida auris in hospitals: Position statement of the Australasian Society for Infectious Diseases.
  Ong Chong W et al. Internal medicine journal 2019 Aug 

CONCEPTS / COMMENTS

• Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases.
  Rojek Amanda M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Aug
• Improving the estimation of the global burden of antimicrobial resistant infections.
  Limmathurotsakul Direk et al. The Lancet. Infectious diseases 2019 Aug
• Solving the species problem in viral taxonomy: recommendations on non-Latinized binomial species names and on abandoning attempts to assign metagenomic viral sequences to species taxa.
  Van Regenmortel Marc H V et al. Archives of virology 2019 Sep (9) 2223-2229

METHODS / TOOLS

• Long-read amplicon denoising.
  Kumar Venkatesh et al. Nucleic acids research 2019 Aug
• Impact of nucleic acid extraction platforms on hepatitis virus genome detection.
  Pauly Matthew D et al. Journal of virological methods 2019 Aug 113715  
• Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases.
  Theys Kristof et al. Frontiers in public health 2019 208

EVOLUTION / ECOLOGY / POPULATIONS

• Genetic diversity, virulence factors and farm-to-table spread pattern of Vibrio parahaemolyticus food-associated isolates.
  Yang Chao et al. Food microbiology 2019 Dec 103270 
• Molecular Characterization and Phylogenetic Analysis of Enteroviruses and Hepatitis A Viruses in Sewage Samples, Northern Italy, 2016.
  Pellegrinelli Laura et al. Food and environmental virology 2019 Aug 
• Molecular characterization and evolutionary dynamics of measles virus sequences isolated from children in Lagos and Ibadan, South Western, Nigeria.
  Faneye Adedayo Omotayo et al. Journal of infection and public health 2019 Aug
• Detection of classic and cryptic Strongyloides genotypesby deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities.
  Beknazarova Meruyert et al. PLoS neglected tropical diseases 2019 Aug (8) e0007241 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates.
  Feldgarden Michael et al. Antimicrobial agents and chemotherapy 2019 Aug  
• Toxins of Toxin/Antitoxin Systems are Inactivated Primarily Through Promoter Mutations.
  Fernandez-Garcia Laura et al. Journal of applied microbiology 2019 Aug
• Genomic investigation of Staphylococcus aureus recovered from Gambian women and newborns following an oral dose of intra-partum azithromycin.
  Bojang Abdoulie et al. The Journal of antimicrobial chemotherapy 2019 Aug
• Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion.
  Dunai Anett et al. eLife 2019 Aug
• Big data analysis of all bacterial genomes establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria
  Botelho J, et al. bioRxiv, Aug 17, 2019.
• Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis.
  Cohen Keira A et al. Thorax 2019 Sep (9) 882-889
• Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019 
  Takashita E, et al. Emerg Infect Dis, Nov 2019.
• Effect of the baseline Y93H resistance-associated substitution in HCV genotype 3 for direct-acting antiviral treatment: real-life experience from a multicenter study in Sweden and Norway.
  Kjellin Midori et al. Scandinavian journal of gastroenterology 2019 Aug 1-9 

DETECTION / DIAGNOSIS

• Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin-producing Escherichia coli.
  Greig David R et al. GigaScience 2019 Aug (8)
• Application of digital PCR and next generation sequencing in the etiology investigation of a foodborne disease outbreak caused by Vibrio parahaemolyticus.
  Li Ying et al. Food microbiology 2019 Dec 103233
• Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing
  Gargis AS, et al. bioRxiv, Aug 15, 2019. 
• Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing.
  Artaza-Irigaray Cristina et al. Diagnostic pathology 2019 Apr (1) 31
• Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease.
  Schibler Manuel et al. Genes 2019 Aug (8)
• Identification of Candida auris using the updated 8.01 VITEK®2 yeast identification system: a multi-laboratory evaluation study.
  Ambaraghassi Georges et al. Journal of clinical microbiology 2019 Aug  
• Simultaneous detection of four protozoan parasites on leafy greens using a novel multiplex PCR assay.
  Shapiro Karen et al. Food microbiology 2019 Dec 103252 
• Using detergent-enhanced LAMP for African trypanosome detection in human cerebrospinal fluid and implications for disease staging.
  Grab Dennis J et al. PLoS neglected tropical diseases 2019 Aug (8) e0007631

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Frequent MRSA Introductions into an Inner-City Jail: Indications of Community Transmission Networks.
  Popovich Kyle J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Aug
• Outbreak of Escherichia coli O157:H7 Infections Linked to Mechanically Tenderized Beef and the Largest Beef Recall in Canada, 2012.
  Currie Andrea et al. Journal of food protection 2019 Aug 1532-1538 
• Genomic sequencing of a national emm66 group A streptococci (GAS) outbreak among people who inject drugs and the homeless community in England and Wales, January 2016-May 2017.
  Bubba Laura et al. The Journal of infection 2019 Aug
• Bayesian reconstruction of a vancomycin-resistant Enterococcus transmission route using epidemiologic data and genomic variants from whole genome sequencing.
  Fujikura Y et al. The Journal of hospital infection 2019 Aug
• Local outbreak of Clostridioides difficile PCR-Ribotype 018 investigated by multi locus variable number tandem repeat analysis, whole genome multi locus sequence typing and core genome single nucleotide polymorphism typing.
  Gateau Cécile et al. Anaerobe 2019 Aug 102087
• Outbreak of Salmonella Newport Infections with Decreased Susceptibility to Azithromycin Linked to Beef Obtained in the United States and Soft Cheese Obtained in Mexico -- United States, 2018-2019
  Plumb ID, et al. MMWR, Aug 23, 2019.  
• Toward an understanding of group A streptococcal transmission dynamics using national-level surveillance.
  Flores Anthony R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Aug 
• Parechovirus A infections in healthy Australian children during the first 2-years of life: a community-based longitudinal birth cohort study.
  Wang Claire Y T et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Aug
• Progress Toward Poliomyelitis Eradication ? Afghanistan, January 2018?May 2019
  Martinez M, et al. MMWR, Aug 23, 2019.  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Safety and immunogenicity of an anti-Middle East respiratory syndrome coronavirus DNA vaccine: a phase 1, open-label, single-arm, dose-escalation trial.
  Modjarrad Kayvon et al. The Lancet. Infectious diseases 2019 Jul

HOST-MICROBE INTERACTIONS

• Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi.
  Kamoto Kelita et al. PLoS neglected tropical diseases 2019 Aug (8) e0007603
• Different Associations between DC-SIGN Promoter-336G/A ( rs4804803 ) Polymorphism with Severe Dengue in Asians and South-Central Americans: a Meta-Analysis.
  Ren Jiangping et al. International journal of environmental research and public health 2019 04 (8)
• Distinct serum biosignatures are associated with different tuberculosis treatment outcomes.
  Ronacher Katharina et al. Tuberculosis (Edinburgh, Scotland) 2019 Aug 101859
• Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples
  Baumgartner M, et al. bioRxiv, Aug 20, 2019.
• Application of machine learning techniques for creating urban microbial fingerprints.
  Ryan Feargal Joseph et al. Biology direct 2019 Aug (1) 13
• Parasite-microbe-host interactions and cancer risk.
  Dheilly Nolwenn M et al. PLoS pathogens 2019 Aug (8) e1007912

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.