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

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

NEWS

• CRISPR/Cas9 Excises HIV From T Cells But May Cause Virus to Develop Resistance to Editing 
  Han AP. GenomeWeb, Apr 7, 2016.
• Next-generation genetics offer new way to combat hospital infections 
  Porterfield A. Genetic Literacy Project, Apr 6, 2016.
• Antibiotic Resistance Not Spread through Gene Swapping 
  GEN News, Apr 12, 2016.
• New TB Drug Resistance Genes Identified as Researchers Scour Mycobacteria Genomes 
  GenomeWeb, Apr 11, 2016.
• A New Tree 
  GenomeWeb, Apr 12, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Translating the microbiome: health and disease 
  (special issue) Genome Med, Apr 4, 2016.
• Scientific Data to publish a wider range of research advancing data sharing and reuse 
  (announcement) Hufton A. Scientific Data, Apr 11, 2016.
• What bacterial genome assemblers are people using? 
  (blog post) Seemann T. The Genome Factory, Apr 11, 2016.
• Genomic Data Visualization in Python: From deep sequencing to insights 
  (blog post) Full Stack Data Scientist, Mar 16, 2016.

CONCEPTS / COMMENTS

• The virome: a missing component of biological interaction networks in health and disease 
  Handley SA. Genome Med, Apr 1, 2016.
• The golden era of biomedical informatics has begun 
  Moore JH, Holmes JH. BioData Mining, Apr 11, 2016.

METHODS / TOOLS

• It’s all relative: analyzing microbiome data as compositions 
  Gloor GB, et al. Ann Epidemiol, Apr 2, 2016.
• Compositional Data Analysis of the Microbiome: Fundamentals, Tools, and Challenges 
  Tsilimigras MC, Fodor AA. Ann Epidemiol, Mar 31, 2016.
• Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System. 
  Steuerman Yael et al. PLoS computational biology 2016 Apr (4) e1004856
• Viral quasispecies complexity measures. 
  Gregori Josep et al. Virology 2016 Apr 227-237
• BaitFisher: A software package for multi-species target DNA enrichment probe design. 
  Mayer Christoph et al. Molecular biology and evolution 2016 Mar
• MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. 
  Kumar Sudhir et al. Molecular biology and evolution 2016 Mar
• Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees. 
  Kenah Eben et al. PLoS computational biology 2016 Apr (4) e1004869
• Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. 
  Schloss Patrick D et al. PeerJ 2016 e1869
• SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. 
  Whiteside Matthew D et al. BMC microbiology 2016 (1) 65

EVOLUTION / ECOLOGY / POPULATIONS

• A new view of the tree of life 
  Hug LA, et al. Nat Microbiol, Apr 11, 2016.
• Analysis of clinical Bordetella pertussis isolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States of America 
  Otero G, et al. bioRxiv, Apr 9, 2016.
• Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis. 
  Gyuranecz Miklós et al. Veterinary microbiology 2016 Apr 8-12
• A glimpse into evolution and dissemination of multidrug-resistant Acinetobacter baumannii isolates in East Asia: a comparative genomics study. 
  Feng Ye et al. Scientific reports 2016 24342
• Phylogeographic analysis of the 2000-2002 foot-and-mouth disease epidemic in Argentina. 
  Brito Barbara et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr 93-99
• Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic. 
  Fischer Cristine D B et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Phylogenetic analysis of a newfound bat-borne hantavirus supports a laurasiatherian host association for ancestral mammalian hantaviruses. 
  Witkowski Peter T et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Multispecies reassortant bovine rotavirus strain carries a novel simian G3-like VP7 genotype. 
  Malik Yashpal Singh et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar 63-72
• Genomic Characterization of Yogue, Kasokero, Issyk-Kul, Keterah, Gossas, and Thiafora Viruses: Nairoviruses Naturally Infecting Bats, Shrews, and Ticks. 
  Walker Peter J et al. The American journal of tropical medicine and hygiene 2015 Nov (5) 1041-51
• Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. 
  Gardner Shea N et al. PloS one 2016 (4) e0152604
• Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. 
  Ma Liang et al. Nature communications 2016 10740

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Molecular characterization and phylogeny of Shiga toxin-producing E. coli (STEC) isolates obtained from two Dutch regions using whole genome sequencing. 
  Ferdous Mithila et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Apr
• Insertion sequence ISRP10 inactivation of the oprD gene in imipenem-resistant Pseudomonas aeruginosa clinical isolates. 
  Sun Qinghui et al. International journal of antimicrobial agents 2016 Mar
• Epidemiology of Campylobacter jejuni infections in Sweden, November 2011-October 2012: is the severity of infection associated with C. jejuni sequence type? 
  Harvala Heli et al. Infection ecology & epidemiology 2016 31079
• Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada. 
  Duvvuri Venkata R et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Apr
• Comparison of transcriptomes of wild-type and isothiazolone-resistant Pseudomonas aeruginosa by using RNA-seq. 
  Zhou Gang et al. Molecular biology reports 2016 Apr
• Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. 
  Sheppard Anna E et al. Antimicrobial agents and chemotherapy 2016 Apr
• Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. 
  Desjardins Christopher A et al. Nature genetics 2016 Apr
• Increasing clinical severity during a dengue virus type 3 Cuban epidemic: deep sequencing of evolving viral populations. 
  Rodriguez-Roche Rosmari et al. Journal of virology 2016 Feb

DETECTION / DIAGNOSIS

• Adaptation and Validation of E-Probe Diagnostic Nucleic Acid Analysis for Detection of Escherichia coli O157:H7 in Metagenomic Data from Complex Food Matrices. 
  Blagden Trenna et al. Journal of food protection 2016 Apr (4) 574-81
• Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. 
  Dieckmann Ralf et al. Faraday discussions 2016 Apr
• Mass Spectrometry-Based Escherichia coli H Antigen/Flagella Typing: Validation and Comparison with Traditional Serotyping. 
  Cheng Keding et al. Clinical chemistry 2016 Apr
• Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. 
  Hiergeist Andreas et al. International journal of medical microbiology : IJMM 2016 Mar 
• Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli. 
  Timmons Chris et al. Journal of microbiological methods 2016 Apr 
• Laboratory Methods for Determining Etiology of Neonatal Infection at Population-based Sites in South Asia: The ANISA Study. 
  Saha Samir K et al. The Pediatric infectious disease journal 2016 May (5 Suppl 1) S16-22 
• Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. 
  Miller Robert J H et al. BMC infectious diseases 2016 (1) 146 
• Infection with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2012–2015 
  Huang JY, et al. MMWR, Apr 15, 2016.  
• Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study. 
  Aguilera-Arreola Ma Guadalupe et al. SpringerPlus 332
• Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B. 
  Eboigbodin Kevin et al. Applied microbiology and biotechnology 2016 Apr

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Genomic resolution of outbreak-associated Legionella pneumophila serogroup 1 isolates from New York State. 
  Raphael Brian H et al. Applied and environmental microbiology 2016 Apr 
• High Incidence of Chikungunya Virus and Frequency of Viremic Blood Donations during Epidemic, Puerto Rico, USA, 2014 
  Simmons G, et al. Emerg Infect Dis 2016 Jul. 
• Colonization with methicillin-resistant Staphylococcus pseudintermedius in multi-dog households: A longitudinal study using whole genome sequencing 
  Windahl U, et al. Vet Microbiol, Apr 11, 2016.
• Epidemiological dynamics of an urban Dengue 4 outbreak in São Paulo, Brazil. 
  Villabona-Arenas Christian Julián et al. PeerJ 2016 e1892
• Prolonged intermittent virus shedding during an outbreak of canine influenza A H3N2 virus infection in dogs in three Chicago area shelters: 16 cases (March to May 2015). 
  Newbury Sandra et al. Journal of the American Veterinary Medical Association 2016 May (9) 1022-1026
• Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study 
  Poon AF, et al. Lancet HIV, Apr 7, 2015. 
• Translating phylogeny into action for HIV surveillance 
  Gardy JL. Lancet HIV, Apr 7, 2016. 
• Cryptosporidium hominis Is a Newly Recognized Pathogen in the Arctic Region of Nunavik, Canada: Molecular Characterization of an Outbreak. 
  Thivierge Karine et al. PLoS neglected tropical diseases 2016 Apr (4) e0004534

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Design and Characterization of a COBRA HA vaccine for H1N1 influenza viruses. 
  Carter Donald M et al. Journal of virology 2016 Feb
• Effectiveness of Monovalent Rotavirus Vaccine After Programmatic Implementation in Botswana: A Multisite Prospective Case-Control Study. 
  Gastañaduy Paul A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 May S161-7 
• Surveillance Systems to Track Progress Toward Polio Eradication - Worldwide, 2014-2015. 
  Snider Cynthia J et al. MMWR. Morbidity and mortality weekly report 2016 (13) 346-51  
• Mumps in the Czech Republic in 2013: Clinical Characteristics, Mumps Virus Genotyping, and Epidemiological Links. 
  Havlícková Martina et al. Central European journal of public health 2016 Mar (1) 22-8 

HOST-MICROBE INTERACTIONS

• Acute appendicitis in children is associated with a local expansion of Fusobacteria. 
  Rogers Matthew B et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Apr
• Functional characterization of Vif proteins from HIV-1 infected patients with different APOBEC3G haplotypes. 
  Reddy Kavidha et al. AIDS (London, England) 2016 Apr
• The salivary microbiome for differentiating individuals: proof of principle. 
  Leake Sarah L et al. Microbes and infection / Institut Pasteur 2016 Apr
• Clonal deleted latent membrane protein 1 variants of Epstein-Barr virus are predominant in European extranodal NK/T lymphomas and disappear during successful treatment. 
  Halabi Mohamad Adnan et al. International journal of cancer 2016 Apr
• Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching. 
  Grubaugh Nathan D et al. Cell host & microbe 2016 Mar
• Differential expression of the MERS-coronavirus receptor in the upper respiratory tract of humans and dromedary camels. 
  Widagdo W et al. Journal of virology 2016 Feb
• The Mycobacterium tuberculosis transcription machinery: ready to respond to host attacks. 
  Flentie Kelly et al. Journal of bacteriology 2016 Feb

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. 

Public Health Genomics Knowledge Base (v1.0)