Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 18, 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

• The RNA Age: A Primer  
   Williams R. The Scientist, May 11, 2017.
• David Lipman Leaves NCBI  
   GenomeWeb, Mayy 16, 2017.
• British scientists survey infectious bacteria by having people walk outside in socks  
   Guarino B. Washington Post, May 12, 2017.
• Metagenomic Analysis Tool Taxonomer IDs Multiple Pathogens From Clinical Samples  
   Curtin C. GenomeWeb, May 12, 2017.
• DNA Sequencing Finds Uncommon Klebsiella Strain Circulating Among Houston Patients  
   GenomeWeb, May 16, 2017.
• She’s got a radical approach for the age of superbugs: Don’t fight infections. Learn to live with them  
   McFarling U. STAT, May 12, 2017.
• Ebola vaccine could get first real-world test in emerging outbreak  
   Maxmen A. Nature, May 12, 2017.
• WHO confirms 2nd Ebola case in DRC; 17 suspected  
   Soucheray S. CIDRAP, May 15, 2017.
• Diseased Microbiome Varies From Condition to Condition  
   Curtin C. GenomeWeb, May 15, 2017.
• Creative Minds: The Human Gut Microbiome’s Top 100 Hits  
   Collins F. NIH Director's Blog, May 18, 2017.

EVENTS / TRAINING / WEB RESOURCES

• Microbial Genomics and Metagenomics in Human Health and Disease  
  (special issue) J Biotechnol, May 20, 2017.
• What's next for whole genome sequencing?: Moving from research to diagnostics and beyond
  (webinar) Science, Jun 1, 2017, noon-1:00 EDT

CONCEPTS / COMMENTS

• Unravelling pathogenetic mechanisms of epidemic lineages.  
  Oppegaard Oddvar et al. Virulence 2017 May 0
• Disease Resistance and the Definition of Genetic Enhancement  
  So D, et al. Front Genet, Apr 2017.

METHODS / TOOLS

• The challenge of detecting indels in bacterial genomes from short-read sequencing data.  
  Steglich Matthias et al. Journal of biotechnology 2017 May 11-15
• FTA Cards Facilitate Storage, Shipment, and Detection of Arboviruses in Infected Aedes aegypti Collected in Adult Mosquito Traps.  
  Hall-Mendelin Sonja et al. The American journal of tropical medicine and hygiene 2017 May (5) 1241-1243
• Reverse Genetics of Zika Virus.  
  Shan Chao et al. Methods in molecular biology (Clifton, N.J.) 2017 47-58
• Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning.  
  Cuypers Lize et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 May 15-23
• A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples.  
  Huson Daniel H et al. Journal of biotechnology 2017 May 45-50

EVOLUTION / ECOLOGY / POPULATIONS

• Invasive Serotype 35B Pneumococci Including an Expanding Serotype Switch Lineage, United States, 2015–2016 
  Chochua S, et al. Emerg Infect Dis, Jun 2017. 
• Molecular characterization of Mycoplasma pneumoniae infections in two rural populations of Thailand from 2009-2012.
  Whistler Toni et al. Journal of clinical microbiology 2017 May 
• Resurgence of rabies in Hungary during 2013-2014: An attempt to track the origin of identified strains.
  Hornyák Á et al. Transboundary and emerging diseases 2017 May
• Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin.
  Quinteros José A et al. Veterinary microbiology 2016 Dec 27-38
• Discovery of a Novel Canine Respiratory Coronavirus Support Genetic Recombination among Betacoronavirus1.
  Lu Shuai et al. Virus research 2017 May
• Genetic and Epidemiologic Trends of Norovirus Outbreaks in the US Demonstrated Emergence of Novel GII.4 Recombinant Viruses, 2013-2016.
  Cannon Jennifer L et al. Journal of clinical microbiology 2017 May 
• Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing.
  Cramaro Wibke J et al. Parasites & vectors 2017 Feb (1) 71

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Enhanced Nasopharyngeal Infection and Shedding Associated with an Epidemic Lineage of emm3 group A Streptococcus.  
  Afshar Baharak et al. Virulence 2017 May 0
• Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307  
  Long SW, et al. mBio, May 16, 2017.
• A Clostridioides difficile bacteriophage genome encodes functional binary toxin-associated genes.  
  Riedel Thomas et al. Journal of biotechnology 2017 May 23-28
• Genomic evolution of bacterial populations under coselection by antibiotics and phage.  
  Cairns Johannes et al. Molecular ecology 2017 Apr (7) 1848-1859
• Bifidobacterium bacteremia - clinical characteristics and a genomic approach to assess pathogenicity.  
  Esaiassen Eirin et al. Journal of clinical microbiology 2017 May
• Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.  
  Long S Wesley et al. mBio 2017 May (3)
• Clinical and bacteriological characteristics associated with clustering of multidrug-resistant tuberculosis.  
  J-Y Feng J-Y et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2017 May
• Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes.  
  Liu Yang et al. Nature 2017 May
• Genetic Variability of Myxoma Virus Genomes.  
  Braun Christoph et al. Journal of virology 2017 Feb (4)
• Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes.  
  Gomes Ana Rita et al. International journal for parasitology. Drugs and drug resistance 2017 Mar (2) 174-180
• Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure  
  Benavente ED, et al. PLoS One, May 11, 2017.
• Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance.  
  Cerqueira Gustavo C et al. Genome biology 2017 Apr (1) 78

DETECTION / DIAGNOSIS

• Molecular Surveillance of Cronobacter spp. Isolated from a Wide Variety of Foods from 44 Different Countries by Sequence Typing of 16S rRNA, rpoB and O-Antigen Genes.  
  Miranda Nancy et al. Foods (Basel, Switzerland) 2017 May (5)
• High-Resolution Melting Curve Analysis of the 16S Ribosomal Gene to Detect and Identify Pathogenic and Saprophytic Leptospira Species in Colombian Isolates.  
  Peláez Sánchez Ronald G et al. The American journal of tropical medicine and hygiene 2017 May (5) 1031-1038
• Impact of "a" Determinant Mutations on Detection of Hepatitis B Surface Antigen (HBsAg) in HBV Strains from Chinese Patients with Occult Hepatitis B.  
  Huang Xiangyan et al. Journal of medical virology 2017 May
• High-throughput whole genome sequencing of Porcine reproductive and respiratory syndrome virus from cell culture materials and clinical specimens using next-generation sequencing technology.  
  Zhang Jianqiang et al. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2017 Jan (1) 41-50
• Development of a rapid HRM qPCR for the diagnosis of the four most prevalent Plasmodium lineages in New Zealand.  
  Schoener E R et al. Parasitology research 2017 May
• Defining the next generation of Plasmodium vivax diagnostic tests for control and elimination: Target product profiles.  
  Ding Xavier C et al. PLoS neglected tropical diseases 2017 Apr (4) e0005516 
• Development of molecular diagnostic protocols for detecting three types of Entamoeba from diarrheal and asymptomatic pigs and environmental moist soils.  
  Hirashima Yoshimasa et al. Parasitology research 2017 May

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Increased Risk for Meningococcal Disease among Men who have Sex with Men in the United States, 2012-2015.  
  Folaranmi Temitope A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 May 
• Identification of a major Listeria monocytogenes outbreak clone linked to soft cheese in Northern Italy - 2009-2011.  
  Amato Ettore et al. BMC infectious diseases 2017 May (1) 342
• Characterization of the Salmonella enterica Serotype Isangi Isolated from Patients for the First Time in China.  
  Li Xin-Peng et al. Foodborne pathogens and disease 2017 May
• Acquisition and Transmission of Streptococcus pneumoniae is Facilitated During Rhinovirus Infection in Families with Children.  
  Karppinen Sinikka et al. American journal of respiratory and critical care medicine 2017 May
• Evolution of Drug-resistant Acinetobacter baumannii After DCD Renal Transplantation.  
  Jiang Hong et al. Scientific reports 2017 May (1) 1968
• Invasive Nontuberculous Mycobacterial Infections among Cardiothoracic Surgical Patients Exposed to Heater-Cooler Devices(1).  
  Lyman Meghan M et al. Emerging infectious diseases 2017 May (5) 796-805 
• A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012.  
  Castley Alison et al. PloS one 2017 (5) e0170601
• Notes from the Field: Ongoing Transmission of Candida auris in Health Care Facilities — United States, June 2016–May 2017
  Tsay S, et al. MMWR, May 19, 2017. 
• Using Molecular Characterization to Support Investigations of Aquatic Facility–Associated Outbreaks of Cryptosporidiosis — Alabama, Arizona, and Ohio, 2016
  Hlavsa M, et al. MMWR, May 19, 2017. 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A proposed analytic framework for determining the impact of an antimicrobial resistance intervention.  
  Grohn Yrjo T et al. Animal health research reviews 2017 May 1-25

HOST-MICROBE INTERACTIONS

• Genetic Polymorphisms Associated with Liver Disease Progression in HIV/HCV-Coinfected Patients.  
  Medrano Luz M et al. AIDS reviews (1) 3-15
• IFITM3, TLR3, and CD55 Genes SNPs and Cumulative Ge-netic Risks for Severe Outcomes in Chinese Patients with H7N9 / H1N1pdm09 Influenza. 
  Lee Nelson et al. The Journal of infectious diseases 2017 May
• Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.  
  Pannaraj Pia S et al. JAMA pediatrics 2017 May

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