Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Mar 30, 2017

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

• NIH Names Semifinalists in $20M Antibiotic Resistance Dx Competition  
   GenomeWeb, Mar 28, 2017.
• CDC updates flaccid myelitis testing, expands search for clues  
   Schnirring L. CIDRAP, Mar 28, 2017.
• The Quest to Kill the Superbug That Can Survive in Outer Space  
   Stirone S. The Atlantic, Mar 28, 2017.
• #AprilFoolome: scientists suggest funny -omes  
   Nat Microbiol, Apr 1, 2017

EVENTS / TRAINING / WEB RESOURCES

• 6th Applied Bioinformatics and Public Health Microbiology  
  (conference) Wellcome Genome Campus, Hinxton, Cambridge UK, May 17-19, 2017.

CONCEPTS / COMMENTS

• The Real Threat to National Security: Deadly Disease  
  Osterholm MT, Olshaker M. New York Times, Mar 24, 2017.
• Why prokaryotes have pangenomes  
  McInerney JO, et al. Nat Microbiol, Mar 28, 2016.

METHODS / TOOLS

• swga: A primer design toolkit for selective whole genome amplification.  
  Clarke Erik L et al. Bioinformatics (Oxford, England) 2017 Feb
• Portable devices and mobile instruments for infectious diseases point-of-care testing.  
  Bissonnette Luc et al. Expert review of molecular diagnostics 2017 Mar
• On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data  
  Arredondo-Alonso S, et al. bioRxiv, Mar 28, 2017.
• Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.  
  Judge Kim et al. Microbial genomics 2016 Sep (9) e000085
• Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.  
  Page Andrew J et al. Microbial genomics 2016 Aug (8) e000083
• A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens.  
  Katz Lee S et al. Frontiers in microbiology 2017 375 
• De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.  
  Dudchenko Olga et al. Science (New York, N.Y.) 2017 Mar
• NGMASTER:in silico multi-antigen sequence typing for Neisseria gonorrhoeae.  
  Kwong Jason C et al. Microbial genomics 2016 Aug (8) e000076
• NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.  
  Sahl Jason W et al. Microbial genomics 2016 Aug (8) e000074
• Integrating Patient And Whole Genome Sequencing Data To Provide Insights Into The Epidemiology Of Seasonal Influenza A(H3N2) Viruses  
  Goldstein EJ, et al. bioRxiv, Mar 28, 2017.
• Defining HIV-1 transmission clusters based on sequence data: a systematic review and perspectives.  
  Hassan Amin S et al. AIDS (London, England) 2017 Mar
• New approaches for characterization of the genetic stability of vaccine cell lines.  
  Ng Siemon et al. Human vaccines & immunotherapeutics 2017 Feb 1-4

EVOLUTION / ECOLOGY / POPULATIONS

• Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain 
  Dunne KA, et al. Microbial Genomics, Mar 23, 2017.
• Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.
  Zangenah Salah et al. Scientific reports 2016 Mar 22919
• Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence
  Xie X, et al. Vet Microbio, Mar 18, 2017.
• Long-range dispersal moved Francisella tularensis into Western Europe from the East.
  Dwibedi Chinmay et al. Microbial genomics 2016 Dec (12) e000100
• Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis.
  Lees John A et al. Microbial genomics 2017 Jan (1) e000103
• Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity.
  Chapple Stephanie N J et al. Microbial genomics 2016 Jul (7) e000067
• Massive dispersal of Coxiella burnetii among cattle across the United States.
  Olivas Sonora et al. Microbial genomics 2016 Aug (8) e000068
• A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus.
  Gonçalves da Silva Anders et al. Microbial genomics 2017 Jan (1) e000105
• Molecular epidemiology of Pseudomonas aeruginosa bloodstream infection isolates in a non-outbreak setting.
  McCarthy Kate L et al. Journal of medical microbiology 2017 Mar (2) 154-159
• Multiregional dissemination of KPC-producing Klebsiella pneumoniae ST258/ST512 genotypes in Poland, 2010-14.
  Baraniak Anna et al. The Journal of antimicrobial chemotherapy 2017 Mar
• Genomic characterization of Nontuberculous Mycobacteria.
  Fedrizzi Tarcisio et al. Scientific reports 2017 Mar 45258
• Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats.
  Yinda Claude Kwe et al. BMC genomics 2017 Mar (1) 249
• Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade 2.3.4.4 Outbreaks.
  Hill Nichola J et al. Emerging infectious diseases 2017 Apr (4) 654-657
• Characterization of Highly Pathogenic Avian Influenza Virus A(H5N6), Japan, November 2016.
  Okamatsu Masatoshi et al. Emerging infectious diseases 2017 Apr (4) 691-695
• Three Divergent Subpopulations of the Malaria Parasite Plasmodium knowlesi.
  Divis Paul C S et al. Emerging infectious diseases 2017 Apr (4) 616-624

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.  
  Musicha Patrick et al. The Journal of antimicrobial chemotherapy 2017 Mar
• Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species. 
  Zangenah S et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Apr (4) 657-662
• The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes.  
  Seth-Smith Helena M B et al. Genome biology and evolution 2017 Mar
• Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody  
  Dingens AS, et al. bioRxiv, mar 18, 2017.
• FunResDB-A web resource for genotypic susceptibility testing of Aspergillus fumigatus.  
  Weber Michael et al. Medical mycology 2017 Mar

DETECTION / DIAGNOSIS

• Pathogen Identification in Suspected Cases of Pyogenic Spondylodiscitis.  
  Sheikh Ahmad Farajzadeh et al. Frontiers in cellular and infection microbiology 2017 60
• Defining a core genome multilocus sequence typing scheme for the global epidemiology of Vibrio parahaemolyticus.  
  Gonzalez-Escalona Narjol et al. Journal of clinical microbiology 2017 Mar
• Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Klebsiella pneumoniae. 
  Zhou Haijian et al. Frontiers in microbiology 2017 371
• Same-day identification and antibiotic susceptibility testing on positive blood cultures: a simple and inexpensive procedure.  
  Maelegheer K et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Apr (4) 681-687
• Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial.  
  Witney Adam A et al. BMC medicine 2017 Mar (1) 71
• Evaluation of Automated Molecular Testing Rollout for Tuberculosis Diagnosis Using Routinely Collected Surveillance Data — Uganda, 2012–2015
  Scott C, et al. MMWR, March 31, 2017  
• Asymptomatic infection and unrecognised Ebola virus disease in Ebola-affected households in Sierra Leone: a cross-sectional study using a new non-invasive assay for antibodies to Ebola virus.  
  Glynn Judith R et al. The Lancet. Infectious diseases 2017 Feb
• Hepatitis B serological markers and plasma DNA concentrations: baseline results from the DART trial.  
  Price Huw et al. AIDS (London, England) 2017 Mar
• Molecular identification of unusual Mycetoma agents isolated from patients in Venezuela.  
  Rojas Olga C et al. Mycoses 2017 Feb (2) 129-135
• Contribution of real-time PCR to Plasmodium species identification and to clinical decisions: a nationwide study in a non-endemic setting.  
  Grossman T et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Apr (4) 671-675 
• Development of a rapid loop-mediated isothermal amplification assay for diagnosis and assessment of cure of Leishmania infection.  
  Verma Sandeep et al. BMC infectious diseases 2017 Mar (1) 223
• Rapid Surveillance for Vector Presence (RSVP): Development of a novel system for detecting Aedes aegypti and Aedes albopictus.  
  Montgomery Brian L et al. PLoS neglected tropical diseases 2017 Mar (3) e0005505

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Outbreak of Campylobacteriosis Following a Dairy Farm Visit: Confirmation by Genotyping.  
  Lahti Elina et al. Foodborne pathogens and disease 2017 Mar
• Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.  
  Cowley Lauren A et al. Microbial genomics 2016 Sep (9) e000084
• Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network.  
  Dallman Tim et al. Microbial genomics 2016 Aug (8) e000070
• Declaring a tuberculosis outbreak over with genomic epidemiology.  
  Hatherell Hollie-Ann et al. Microbial genomics 2016 May (5) e000060
• Transmission of Hepatitis A Virus through Combined Liver-Small Intestine-Pancreas Transplantation.  
  Foster Monique A et al. Emerging infectious diseases 2017 Apr (4) 590-596

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Quantifying The Fitness Benefit And Cost Of Cefixime Resistance In Neisseria gonorrhoeae To Inform Prescription Policy  
  Whittles LK, et al. biRxiv, Mar 28, 2017.
• A Novel Pan-Genome Reverse Vaccinology Approach Employing a Negative-Selection Strategy for Screening Surface-Exposed Antigens against leptospirosis.  
  Zeng LingBing et al. Frontiers in microbiology 2017 396
• Arm Paralysis After Routine Childhood Vaccinations: Application of Advanced Molecular Methods to the Causality Assessment of an Adverse Event After Immunization.  
  Shaw Jana et al. Journal of the Pediatric Infectious Diseases Society 2017 Jan  

HOST-MICROBE INTERACTIONS

• Remodeling of the gut microbiota and structural shifts in Preeclampsia patients in South China.  
  Liu J et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Apr (4) 713-719
• Improvement of abnormal vaginal flora in Ugandan women by self-testing and short use of intravaginal antimicrobials.  
  Donders G et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Apr (4) 731-738
• Bacteria-Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality.  
  Scanlan Pauline D et al. Trends in microbiology 2017 Mar
• The blood DNA virome in 8,000 humans.  
  Moustafa Ahmed et al. PLoS pathogens 2017 Mar (3) e1006292
• RNA viruses drove adaptive introgressions between Neanderthals and modern humans  
  Enard D, Petrov DA. bioRxiv, Mar 24, 107.

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB