Advanced Molecular Detection Clips ► Public Health Genomics Knowledge Base (v1.0)

Public Health Genomics Knowledge Base (v1.0)

Advanced Molecular Detection Clips

About Advanced Molecular Detection Clips

Advanced Molecular Detection(AMD) Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged.

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Spotlight

Multi-Center Evaluation of the Xpert Norovirus Assay for Detection of Norovirus GI and GII in Fecal Specimens. Norovirus is the most common cause of sporadic gastroenteritis and outbreaks worldwide. The rapid identification of norovirus has important implications for infection prevention measures, and may reduce the need for additional diagnostic testing. The Xpert Norovirus Assay recently received FDA clearance for the detection and differentiation of norovirus genogroups I and II (GI and GII), which account for the vast majority of infections. In this study, we evaluated the performance of the Xpert Norovirus Assay with both fresh, prospectively collected (n=914) and frozen, archived (n=489) fecal specimens. A Centers for Disease Control (CDC) composite reference method was used as the gold standard for comparison. For both prospective and frozen specimens, the Xpert Norovirus Assay showed a positive percent agreement (PPA) and negative percent agreement (NPA) of 98.3% and 98.1% for GI, and 99.4% and 98.2% for GII, respectively. Norovirus prevalence in the prospective specimens (collected from March to May of 2014) was 9.9% (n=90), with the majority of positives caused by genogroup II (82%, n=74). The positive predictive value (PPV) of the Xpert Norovirus Assay was 75% for GI whereas it was 86.5% for GII positive specimens. The negative predictive value (NPV) for GI and GII was 100% and 99.9%, respectively.

Advanced Molecular Detection Clips Content

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

NEWS

• FDA Kicks Off Closed Beta of Platform to Advance NGS Test Standards, Bioinformatics Approaches 
  Ray T. GenomeWeb, Nov 13, 2015.
• Lab-Made Coronavirus Triggers Debate 
  Akst J. The Scientist, Nov 16, 2015.
• Colour-changing dressing 'fights antibiotic resistance' 
  BBC News, Nov 15, 2015.
• New meningitis strains could thrive following vaccine success 
  Callaway E. Nature, Nov 10, 2015.
• Toward Eliminating Poliovirus--In the Lab 
  Shaikh-Lesko R. The Scientist, Nov 16, 2015.
• Genetic Analysis Indicates Likely Person-to-Person Transmission of Avian Flu 
  GenomeWeb, Nov 19, 2015.
• Group Demos Nanopore Technology for Pathogen Identification 
  Heger M. GenomeWeb, Nov 18, 2015.
• Hepatitis A may have small animal origins: University of Bonn researchers 
  Outbreak News Today, Nov 4, 2015.

EVENTS / TRAINING / WEB RESOURCES

• NCBI to hold three-day genomics hackathon in January 
  (event) NCBI News, Nov 13, 2015.

POLICY

• The Public Health Evidence for FDA Oversight of Laboratory Developed Tests: 20 Case Studies
  Office of the Commissioner, FDA, Nov 16, 2015.

CONCEPTS / COMMENTS

• How the Western diet has derailed our evolution. 
  Velazquez-Manoff M. Nautilus, Nov 12, 2015.
• Biological research: Rethink biosafety. 
  Trevan Tim et al. Nature 2015 Nov (7577) 155-8
• Clinical implications of and lessons learnt from external assessment of Mers-CoV diagnostics. 
  Pas Suzan D et al. Expert review of molecular diagnostics 2015 Nov
• Global research priorities for infections that affect the nervous system. 
  John Chandy C et al. Nature 2015 Nov (7578) S178-86
• Commentary: Continuing Challenges for the Clinical Laboratory for the Detection of Carbapenem-Resistant Enterobacteriaceae. 
  Humphries Romney M et al. Journal of clinical microbiology 2015 Oct

METHODS / TOOLS

• Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications 
  Gu W, et al. bioRxiv, Nov 14, 2015. doi: http://dx.doi.org/10.1101/031708
• DataJoint: managing big scientific data using MATLAB or Python 
  Yatsenko D, et al. bioRxiv, Nov 14, 2015. doi: http://dx.doi.org/10.1101/031658
• TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing. 
  Sekizuka Tsuyoshi et al. PloS one (11) e0142951
• Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria. 
  Famulare Michael et al. International health 2015 Mar (2) 130-8
• Probing the virus host interaction in high containment: an approach using pooled short hairpin RNA. 
  Filone Claire Marie et al. Assay and drug development technologies (1) 34-43
• Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. 
  Conceição-Neto Nádia et al. Scientific reports 2015 16532
• Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. 
  Nayfach Stephen et al. PLoS computational biology 2015 Nov (11) e1004573
• Safeguarding CRISPR-Cas9 gene drives in yeast. 
  DiCarlo James E et al. Nature biotechnology 2015 Nov
• Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform. 
  Xu Wenjie et al. Methods in molecular biology (Clifton, N.J.) 2016 57-65

EVOLUTION / ECOLOGY / POPULATIONS

• Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014. 
  Chowdhury Fahima et al. PLoS neglected tropical diseases 2015 Nov (11) e0004183
• CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping. 
  Karah Nabil et al. PloS one 2015 (2) e0118205
• Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. 
  Trovão Nídia Sequeira et al. Molecular biology and evolution 2015 Sep
• Ebolavirus Evolution: Past and Present. 
  de La Vega Marc-Antoine et al. PLoS pathogens 2015 Nov (11) e1005221
• Prevalence and molecular characterizations of enterovirus D68 among children with acute respiratory infection in China between 2012 and 2014. 
  Xiao Qiuyan et al. Scientific reports 16639
• Insights into the Molecular Evolution of Dengue virus Type 4 in Puerto Rico over Two Decades of Emergence. 
  Martin Estelle et al. Virus research 2015 Nov (CDC Author)
• Nuclear Markers Reveal Predominantly North to South Gene Flow in Ixodes scapularis, the Tick Vector of the Lyme Disease Spirochete. 
  Van Zee Janice et al. PloS one 2015 (11) e0139630 (CDC Author)
• Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection 
  Mesquita RD, et al. PNAS, Oct 6, 2015.

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic insights into the rapid emergence and evolution of MDR in Staphylococcus pseudintermedius. 
  McCarthy Alex J et al. The Journal of antimicrobial chemotherapy 2015 Apr (4) 997-1007
• Characterization of worldwide Helicobacter pylori strains reveals genetic conservation and essentiality of serine protease HtrA. 
  Tegtmeyer Nicole et al. Molecular microbiology 2015 Nov
• High Prevalence of Intermediate Leptospira spp. DNA in Febrile Humans from Urban and Rural Ecuador. 
  Chiriboga Jorge et al. Emerging infectious diseases 2015 Dec (12) 2141-7
• Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study 
  Liu YY, et al. Lancet Infect Dis, Nov 18, 2015.
• Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. 
  Sanborn Keri B et al. Retrovirology (1) 96

DETECTION / DIAGNOSIS

• Raman spectroscopy-based identification of nosocomial outbreaks of the clonal bacterium Escherichia coli. 
  Kusters J G et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Nov
• Multi locus variable-number tandem repeat (MLVA) typing tools improved the surveillance of Salmonella enteritidis: a 6 years retrospective study. 
  Bertrand Sophie et al. PloS one 2015 (2) e0117950
• Emerging methodologies for pathogen identification in positive blood culture testing. 
  Dubourg Grégory et al. Expert review of molecular diagnostics 2015 Nov 1-15
• Complete deletion of the fucose operon in Haemophilus influenzae is associated with a cluster in MLSA-phylogenetic group II related to Haemophilus haemolyticus: implications for identification and typing. 
  de Gier Camilla et al. Journal of clinical microbiology 2015 Sep
• Recognition of Streptococcus pseudoporcinus Colonization in Women as a Consequence of using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Group B Streptococcus Identification. 
  Suwantarat Nuntra et al. Journal of clinical microbiology 2015 Oct
• Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections. 
  Vincent Jean-Louis et al. Critical care medicine 2015 Nov (11) 2283-91
• Validation of a loop-mediated isothermal amplification assay for rapid diagnosis of pertussis infection in nasopharyngeal samples. 
  Brotons Pedro et al. Expert review of molecular diagnostics 2015 Nov 1-6
• Genomic Pathogen Typing Using Solid-State Nanopores. 
  Squires Allison H et al. PloS one (11) e0142944
• Evaluation of the Biofire FilmArray Biothreat E-test (v2.5) for rapid identification of Ebola virus disease in heat-treated blood samples obtained in Sierra Leone and United Kingdom. 
  Weller Simon A et al. Journal of clinical microbiology 2015 Nov
• Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1-4. 
  Hu Sheng-Feng et al. BMC microbiology (1) 265
• Simultaneous Detection of Major Drug Resistance Mutations of HIV-1 Subtype B Viruses from Dried Blood Spot Specimens by Multiplex Allele-specific Assay. 
  Zhang Guoqing et al. Journal of clinical microbiology 2015 Nov (CDC Author)
• Multi-Center Evaluation of the Xpert Norovirus Assay for Detection of Norovirus GI and GII in Fecal Specimens. 
  Gonzalez Mark D et al. Journal of clinical microbiology 2015 Nov (CDC Author)
• Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria. 
  Daniels Rachel et al. Journal of visualized experiments : JoVE (105)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Clinical and Molecular Epidemiology of Childhood Invasive nontypeable Haemophilus influenzae Disease in England and Wales. 
  Collins Sarah et al. The Pediatric infectious disease journal 2015 Nov
• Nosocomial transmission of avian influenza A (H7N9) virus in China: epidemiological investigation. 
  Fang Chun-Fu et al. BMJ (Clinical research ed.) h5765
• Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks. 
  Penedos Ana Raquel et al. PloS one (11) e0143081
• Long-term transmission of measles virus in Central and continental Western Europe. 
  Santibanez S et al. Virus genes 2015 Feb (1) 2-11
• Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States. 
  Whiteside Y Omar et al. AIDS (London, England) 2015 Nov (18) 2517-22 (CDC Author)
• A Large Outbreak of Hepatitis C Virus Infections in a Hemodialysis Clinic. 
  Nguyen Duc B et al. Infection control and hospital epidemiology 2015 Nov 1-9 (CDC Author)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces. 
  Zaura Egija et al. mBio 2015 (6)
• Identification of mutations in the HVR1 and PKR-BD regions in HCV-infected patients resistant to PEG-IFNα/RBV therapy. 
  Holysz M et al. Journal of applied genetics 2015 Aug (3) 403-9

HOST-MICROBE INTERACTIONS

• Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria 
  Nayfach S, Pollard KS. bioRxiv, Nov 14, 2015. doi: http://dx.doi.org/10.1101/031757
• Hepatitis B virus genotype, mutations, human leukocyte antigen polymorphisms and their interactions in hepatocellular carcinoma: a multi-centre case-control study. 
  Wen Juan et al. Scientific reports 16489
• Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. 
  McLaren Paul J et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Nov