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Advanced Molecular Detection Clips

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About Advanced Molecular Detection Clips

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 infectious disease 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. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.

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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

• Ebola Re-emergence in Liberia Involved Virus With Reduced Evolutionary Rate, Study Suggests 
  Anderson A. GenomeWeb, Apr 29, 2016.
• 3-D printers, lab-grown 'mini brains' used to study Zika's effect 
  Healio Infectious Disease News, Apr 29, 2016.
• Genetic detectives: how scientists use DNA to track disease outbreaks 
  Martin ET. The Conversation, Apr 29, 2016.
• MRSA Genomes Scrutinized for Clues to Routine Surveillance 
  GenomeWeb, May 5, 2016.
• Earth: Home to 1 Trillion Microbial Species 
  Offord C. The Scientist, May 4, 2016.
• Gamer-Sourced Diagnostic 
  GenomeWeb, May 3, 2016.
• Figshare launches 'academic Pinterest' 
  Research Information, Mar 24, 2016.
• Why Are Your Gut Microbes Different From Mine? 
  Yong E. Atlantic, Apr 28, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Microbiota at Work 
  (special issue) Science, Apr 28, 2016.

POLICY

• Policy: Security spending must cover disease outbreaks 
  Yamada T, et al. Nature, May 3, 2016.

CONCEPTS / COMMENTS

• Towards biome-specific analysis of meta-omics data. 
  Darzi Youssef et al. The ISME journal 2016 May (5) 1025-8
• Archaeological occurrences and historical review of the human amoeba, Entamoeba histolytica, over the past 6000years. 
  Le Bailly Matthieu et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr

METHODS / TOOLS

• IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. 
  Mysara Mohamed et al. BMC bioinformatics 2016 (1) 192
• Visual programming for next-generation sequencing data analytics. 
  Milicchio Franco et al. BioData mining 2016 16
• Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe 
  Aanensen D, et al. mBio, May 5, 2016.
• Incorporating microbiota data into epidemiologic models: examples from vaginal microbiota research. 
  van de Wijgert Janneke H et al. Annals of epidemiology 2016 Apr

EVOLUTION / ECOLOGY / POPULATIONS

• First molecular detection and phylogenetic analysis of Anaplasma phagocytophilum in shelter dogs in Seoul, Korea. 
  Lee Sukyee et al. Ticks and tick-borne diseases 2016 Apr
• The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. 
  Karkey Abhilasha et al. PLoS neglected tropical diseases 2016 Jan (1) e0004346
• Molecular detection and characterization of Anaplasma platys in dogs and ticks in Cuba. 
  Silva Claudia Bezerra da et al. Ticks and tick-borne diseases 2016 Apr
• Origin of modern syphilis and emergence of a contemporary pandemic cluster 
  Arora N, et al. bioRxiv, Apr 29, 2016.
• Characterization of novel human papillomavirus types 157, 158 and 205 from healthy skin and recombination analysis in genus γ-Papillomavirus. 
  Bolatti Elisa M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Norovirus epidemics caused by new GII.2 chimera viruses in 2012-2014 in Japan. 
  Motomura Kazushi et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Reduced evolutionary rate in reemerged Ebola virus transmission chains 
  Blackley DJ, et al. Sci Adv, Apr 29, 2016.
• Enterovirus D68 Infections Associated with Severe Respiratory Illness in Elderly Patients and Emergence of a Novel Clade in Hong Kong. 
  Lau Susanna K P et al. Scientific reports 2016 25147
• Multiple Introductions of Dengue 2 Virus Strains into Saudi Arabia from 1992 to 2014. 
  El-Kafrawy Sherif A et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2016 May
• Molecular Characterization of Two Major Dengue Outbreaks in Costa Rica. 
  Soto-Garita Claudio et al. The American journal of tropical medicine and hygiene 2016 May
• Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes. 
  Carissimo Guillaume et al. PloS one 2016 (5) e0153881
• Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever. 
  Engelthaler David M et al. mBio 2016 (2) 
• Genetic micro-heterogeneity of Leishmania major in emerging foci of zoonotic cutaneous leishmaniasis in Tunisia. 
  Attia Hanene et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Intergenic VNTR Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes. 
  Zhu Luchang et al. Infection and immunity 2016 May
• Silenced vanA gene cluster on a transferable plasmid cause outbreak of vancomycin variable enterococci. 
  Sivertsen Audun et al. Antimicrobial agents and chemotherapy 2016 May
• Correlation of rpsU Gene Sequence Clusters and Biochemical Properties, Gc-Ms Spectra and Resistance Profiles of Clinical Burkholderia Spp. Isolates. 
  Ostermann Maria Franziska et al. European journal of microbiology & immunology 2016 Mar (1) 25-39
• Imbalanced presence of Borrelia burgdorferi s.l. multilocus sequence types in clinical manifestations of Lyme borreliosis. 
  Coipan E Claudia et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. 
  Liu Shiyou et al. BMC genomics 2016 (1) 316 
• Current progress in the biology of members of the Sporothrix schenckii complex following the genomic era. 
  Mora-Montes Héctor M et al. FEMS yeast research 2015 Sep (6)
• Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes. 
  Mondelaers Annelies et al. PloS one 2016 (4) e0154101

DETECTION / DIAGNOSIS

• Serogenotyping and antimicrobial susceptibility testing of Salmonella spp. isolated from retail meat samples in Lagos, Nigeria. 
  Stella Smith et al. Molecular and cellular probes 2016 Apr
• Detection of amino acid substitutions in the GyrA protein of fluoroquinolone-resistant typhoidal Salmonella isolates using high-resolution mass spectrometry. 
  Hassing Robert-Jan et al. International journal of antimicrobial agents 2016 Mar
• Using a practical molecular capsular serotype prediction strategy to investigate Streptococcus pneumoniae serotype distribution and antimicrobial resistance in Chinese local hospitalized children. 
  Jin Ping et al. BMC pediatrics 2016 (1) 53
• A Novel Peptidomic Approach to Strain Typing of Clinical Acinetobacter baumannii Isolates Using Mass Spectrometry. 
  Wang Honghui et al. Clinical chemistry 2016 Apr
• Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children. 
  Andersen Heidi et al. Journal of clinical microbiology 2016 Apr
• Comparison of molecular detection methods for pertussis in children during a state-wide outbreak. 
  Qin X et al. Annals of clinical microbiology and antimicrobials 2016 (1) 28 
• Development of a reverse transcription loop-mediated isothermal amplification assay for the detection of vesicular stomatitis New Jersey virus: Use of rapid molecular assays to differentiate between vesicular disease viruses. 
  Fowler Veronica L et al. Journal of virological methods 2016 Apr 123-131
• New molecular detection methods of malaria parasites with multiple genes from genomes. 
  Gupta Himanshu et al. Acta tropica 2016 Apr 15-22
• Integration of Multiplex Bead Assays for Parasitic Diseases into a National, Population-Based Serosurvey of Women 15-39 Years of Age in Cambodia.
  Priest Jeffrey W et al. PLoS neglected tropical diseases 2016 May (5) e0004699 
• An Innovative Field-Applicable Molecular Test to Diagnose Cutaneous Leishmania Viannia spp. Infections. 
  Saldarriaga Omar A et al. PLoS neglected tropical diseases 2016 Apr (4) e0004638

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Next generation sequencing confirms presumed nosocomial transmission of LA-MRSA in the Netherlands. 
  Bosch Thijs et al. Applied and environmental microbiology 2016 Apr
• Systematic surveillance detects multiple silent introductions and household transmission of methicillin-resistant Staphylococcus aureus USA300 in the east of England. 
  Toleman Michelle S et al. The Journal of infectious diseases 2016 Apr
• Translating phylogeny into action for HIV surveillance. 
  Gardy Jennifer L et al. The lancet. HIV 2016 May (5) e196-7 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Synthetic biology platform technologies for antimicrobial applications. 
  Braff Dana et al. Advanced drug delivery reviews 2016 Apr

HOST-MICROBE INTERACTIONS

• Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study. 
  Arboleya Silvia et al. International journal of molecular sciences (5)
• Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. 
  Zhernakova Alexandra et al. Science (New York, N.Y.) 2016 Apr (6285) 565-9
• Microbiome sequencing: challenges and opportunities for molecular medicine. 
  Clavel Thomas et al. Expert review of molecular diagnostics 2016 Apr
• Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection. 
  Montassier Emmanuel et al. Genome medicine 2016 (1) 49
• Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection. 
  Seekatz Anna Maria et al. Genome medicine 2016 (1) 47
• Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections. 
  Singh Pallavi et al. Annals of epidemiology 2016 Apr
• Population-level analysis of gut microbiome variation. 
  Falony Gwen et al. Science (New York, N.Y.) 2016 Apr (6285) 560-4
• Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. 
  Vatanen Tommi et al. Cell 2016 Apr
• Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease 
  Chu H, et al. Science, May 5, 2016.
• Epidemiology and the microbiome 
  Foxman B, et al, Annals of Epidemiology, May 2016
• Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. 
  Klemm Elizabeth J et al. Nature microbiology 2016 Mar (3)
• 25-Hydroxy Vitamin D, Vitamin D Receptor and Toll-like Receptor 2 Polymorphisms in Spinal Tuberculosis: A Case-Control Study. 
  Panwar Ajay et al. Medicine 2016 Apr (17) e3418
• HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women. 
  Mirabello Lisa et al. Journal of the National Cancer Institute 2016 Sep (9)
• Demographic and immune-based selection shifts before and after European contact inferred from 50 ancient and modern exomes from the Northwest Coast of North America 
  Lindo J, et al. bioRxiv, Apr 29, 2016.

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.