Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 8, 2019

Advanced Molecular Detection Clips Content

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

NEWS

• Point-of-Care Molecular Test Adoption: Insights From a Health System's Experience
  Johnson M. GenomeWeb,Aug 7, 2019.
• Molecular Testing for Flu Catching up, But Still Lagging Far Behind RIDTs
  O'Connor L. GenomeWeb, Aug 5, 2019.
• Cancer therapy returns to original target: HIV
  Cohen M. Science, Aug 9, 2019.

CONCEPTS / COMMENTS

• Next-Generation Sequencing in Clinical Microbiology: Are We There Yet?
  Mitchell Stephanie L et al. Clinics in laboratory medicine 2019 Sep (3) 405-418 
• Human bornavirus research: Back on track!
  Rubbenstroth Dennis et al. PLoS pathogens 2019 Aug (8) e1007873

METHODS / TOOLS

• Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  Latorre-Perez A, et al. bioRxiv, Aug 5, 2019.
• Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
  Hicks AL, et al. bioRxiv, Aug 7, 2019.
• Global genomic population structure of Clostridioides difficile
  Frentrup M, et al. bioRxiv, Aug 6, 2019.
• An interactive data visualisation application to investigate nosocomial transmission of infections.
  Smith Catherine M et al. Wellcome open research 2019 100

EVOLUTION / ECOLOGY / POPULATIONS

• Co-circulation and persistence of multiple A/H3N2 influenza variants in China.
  Shi Weifeng et al. Emerging microbes & infections 2019 (1) 1157-1167 
• Global patterns of avian influenza A(H7): virus evolution and zoonotic threats.
  Naguib Mahmoud M et al. FEMS microbiology reviews 2019 Aug
• Epidemiology of measles cases and phylogenetic analysis of the virus circulated in the Federation of Bosnia and Herzegovina during 2018: implications for elimination efforts.
  Salimovic-Bešic Irma et al. Medicinski glasnik : official publication of the Medical Association of Zenica-Doboj Canton, Bosnia and Herzegovina 2020 Feb (1)
• Genetic Variability of Chikungunya Virus in Southern Mexico.
  Galan-Huerta Kame A et al. Viruses 2019 Aug (8)
• The evolutionary dynamics of DENV 4 genotype I over a 60-year period.
  Sang Shaowei et al. PLoS neglected tropical diseases 2019 Jul (7) e0007592
• Dengue genetic divergence generates within-serotype antigenic variation, but serotypes dominate evolutionary dynamics
  Bell SM, et al. eLife, Aug 6, 2019.
• The transmission dynamic of Madariaga Virus by bayesian phylogenetic analysis: Molecular surveillance of an emergent pathogen.
  Benvenuto Domenico et al. Microbial pathogenesis 2019 Jul 80-86
• Genome of Alaskapox Virus, A Novel Orthopoxvirus Isolated from Alaska.
  Gigante Crystal M et al. Viruses 2019 Aug (8) 
• Molecular typing of clinical and environmental isolates of Cryptococcus gattii species complex from Southern California, United States.
  Hurst Steven et al. Mycoses 2019 Aug 
• Development of a Next Generation DNA Sequencing-based Multi Detection Assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies.
  Abbasi Ibrahim et al. Acta tropica 2019 Jul 105101

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain.
  Botelho João et al. Emerging microbes & infections 2019 (1) 1186-1194
• Local outbreak of extended spectrum beta lactamase SHV2a producing Pseudomonas aeruginosa reveals the emergence of a new specific sub-lineage of the international ST235 high risk clone.
  Royer Guilhem et al. The Journal of hospital infection 2019 Jul
• Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.
  Mourkas Evangelos et al. Environmental microbiology 2019 Aug
• Novel quinolone resistance determinant, qepA8, in Shigella flexneri isolated in the United States, 2016
  Webb HE, et al. bioRxiv, Aug 6, 2019. 
• Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
  Danko DC, et al. bioRxiv, Aug 5, 2019.

DETECTION / DIAGNOSIS

• Comparison of respiratory pathogen yields from Nasopharyngeal/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya.
  Nyawanda Bryan O et al. Scientific reports 2019 Aug (1) 11237 
• A two-step approach for the investigation of a Clostridium difficile outbreak by molecular methods.
  Krutova Marcela et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Jul 
• Enteropathogens in pediatric gastroenteritis: comparison of routine diagnostic and molecular methods.
  Tilmanne Anne et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Jul 
• A diagnostic evaluation of a molecular assay used for testing and treating anorectal chlamydia and gonorrhoea infections at the point-of-care in Papua New Guinea.
  Badman S G et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 May (5) 623-627  
• Identification and Discrimination of Chlamydia trachomatis Ocular and Urogenital Strains and Major Phylogenetic Lineages by CtGEM Typing, A Double-Locus Genotyping Method.
  Holt Deborah C et al. Methods in molecular biology (Clifton, N.J.) 2019 87-122
• Multilocus Sequence Typing (MLST) of Chlamydiales.
  Jelocnik Martina et al. Methods in molecular biology (Clifton, N.J.) 2019 69-86
• Whole-Genome Sequencing of Chlamydia trachomatis Directly from Human Samples.
  Brown Amanda Claire et al. Methods in molecular biology (Clifton, N.J.) 2019 45-67
• Rapid Detection of Peste des Petits Ruminants Virus (PPRV) Nucleic Acid Using a Novel Low-Cost Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Future Use in Nascent PPR Eradication Programme.
  Mahapatra Mana et al. Viruses 2019 Jul (8)
• Prediction of the Spatial Origin of Puumala Virus Infections Using L Segment Sequences Derived from a Generic Screening PCR.
  Weiss Sabrina et al. Viruses 2019 Jul (8)
• Role of Nucleic Acid Amplification assays in monitoring treatment response in Chagas disease: Usefulness in clinical trials.
  Sulleiro Elena et al. Acta tropica 2019 Jul 105120

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A nonclonal outbreak of vancomycin-sensitive Enterococcus faecalis bacteremia in a neonatal intensive care unit.
  Kotsanas Despina et al. Infection control and hospital epidemiology 2019 Aug 1-7 
• Multicenter Outbreak of Gram-Negative Bloodstream Infections in Hemodialysis Patients.
  Novosad Shannon A et al. American journal of kidney diseases : the official journal of the National Kidney Foundation 2019 Jul  
• Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities.
  Zakham F et al. New microbes and new infections 2019 Sep 100582 
• Hepatitis A outbreak among men who have sex with men (MSM) in England, 2016-2018: The contribution of past and current vaccination policy and practice.
  Plunkett James et al. Vaccine: X 2019 Apr 100014 
• Phylogenetic Analysis of Hepatitis B Virus among Household Members with HBV Chronic Infection.
  Sali Shahnaz et al. Avicenna journal of medical biotechnology (3) 221-228
• GII.17 norovirus infections in outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan during two decades.
  Iritani Nobuhiro et al. Journal of medical virology 2019 Aug

HOST-MICROBE INTERACTIONS

• Commensal Neisseria Kill Neisseria gonorrhoeae through a DNA-Dependent Mechanism.
  Kim Won Jong et al. Cell host & microbe 2019 Jul

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.