Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jan 11, 2018

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. View Data Selection Criteria

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Advanced Molecular Detection Clips Content

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

NEWS

• Silicon gains ground in quantum-computing race  
  Castelvecchi D. Nature, Jan 10, 2018.
• Harvard-Led Team Develops Handheld Device for DNA, RNA Amplification, Detection  
  Gilmore J. 360dx, Jan 10, 2018.
• Mysterious explosion of a deadly plague may come down to a sugar in ice cream  
  Mole B. ArsTechnica, Jan 10, 2018.
• ‘What the hell is going on?’ Polio cases are vanishing in Pakistan, yet the virus won't go away  
  Roberts L. Science, Jan 11, 2018.
• Scientists Continue to Use Outdated Methods  
  Offord C. The Scientist, Jan 9, 2018.
• Scientists race to find genetic clues as malaria decimates rare Hawaiian honeycreepers  
  Donahue MZ. Smithsonian Insider, Jan 9, 2018.

CONCEPTS / COMMENTS

• Ten simple rules for biologists learning to program.  
  Carey Maureen A et al. PLoS computational biology 2018 Jan (1) e1005871
• Chasing Seasonal Influenza - The Need for a Universal Influenza Vaccine.  
  Paules Catharine I et al. The New England journal of medicine 2018 Jan (1) 7-9
• Plague in Madagascar - A Tragic Opportunity for Improving Public Health.  
  Mead Paul S et al. The New England journal of medicine 2018 Jan (2) 106-108
• Exploring the Brave New World of Metagenomics  
  (blog post) Koonin E. NLM, Jan 9, 2018.
• Precision medicine using microbiota.  
  Jobin Christian et al. Science (New York, N.Y.) 2018 01 (6371) 32-34

METHODS / TOOLS

• A Primer on Microbial Bioinformatics for non-bioinformaticians.  
  Carriço J A et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Jan
• Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory  
  Crisan A, et al. PeerJ, Jan 10, 2018.
• Real-time search of all bacterial and viral genomic data  
  Bradley P, et al. bioRxiv, Dec 15, 2018.
• NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform  
  Calus ST, et al. bioRxiv, Jan 7, 2018.
• MentaLiST - A fast MLST caller for large MLST schemes.  
  Feijao Pedro et al. Microbial genomics 2018 Jan
• TreeTime: Maximum-likelihood phylodynamic analysis  
  Segulenko P, et al. Virus Evol, Jan 1, 2018.
• TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses  
  Tranchant-Dubreuil C, et al. bioRxiv, Jan 10, 2018.
• QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.  
  Skums Pavel et al. Bioinformatics (Oxford, England) 2018 Jan (1) 163-170 
• Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays  
  Sasani TA, et al. bioRxiv, Jan 9, 2018.
• Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission.  
  Wong Wesley et al. PLoS computational biology 2018 Jan (1) e1005923

EVOLUTION / ECOLOGY / POPULATIONS

• High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping.  
  Schroeder Max R et al. Genome announcements 2018 Jan (1) 
• Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers.  
  Llewellyn Anna C et al. PloS one 2017 (12) e0189937
• Vibrio cholerae genomic diversity within and between patients.  
  Levade Inès et al. Microbial genomics 2017 Dec (12)
• The paradox of HBV evolution as revealed from a 16th century mummy.  
  Patterson Ross Zoe et al. PLoS pathogens 2018 Jan (1) e1006750
• Swarm incursions of reassortants of highly pathogenic avian influenza virus strains H5N8 and H5N5, clade 2.3.4.4b, Germany, winter 2016/17.  
  Pohlmann Anne et al. Scientific reports 2018 Jan (1) 15

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Molecular characterization of IMP-1-producing Enterobacter cloacae complex isolates in Tokyo.  
  Aoki Kotaro et al. Antimicrobial agents and chemotherapy 2018 Jan
• Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus.  
  Fowler Philip W et al. Cell chemical biology 2018 Jan
• Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad.  
  Diallo Kanny et al. BMC genomics 2017 May (1) 398
• Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence.  
  Thibeaux Roman et al. Microbial genomics 2018 Jan
• Signatures of selection at drug resistance loci in Mycobacterium tuberculosis  
  Mortimer TD, et al. bioRxiv, Jan 8, 2018.
• Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades.  
  Bainomugisa Arnold et al. Microbial genomics 2018 Jan
• Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses.  
  Goldstein Emily J et al. Microbial genomics 2017 Dec
• HIV-1 viraemia and drug resistance amongst female sex workers in Soweto, South Africa: A cross sectional study.  
  Coetzee Jenny et al. PloS one 2017 (12) e0188606
• Molecular identification of sulfadoxine-pyrimethamine resistance in malaria infected women who received intermittent preventive treatment in the Democratic Republic of Congo.  
  Ruh Emrah et al. Malaria journal 2018 Jan (1) 17
• Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival.  
  Zackay Arie et al. PLoS genetics 2018 Jan (1) e1007133

DETECTION / DIAGNOSIS

• Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection.  
  Etchebarne Brett E et al. Frontiers in microbiology 2017 2211
• Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples.  
  Andersen Sandra Christine et al. Genes 2018 Jan (1)
• Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace.  
  Kan Biao et al. Frontiers of medicine 2018 Jan
• Culture-independent approaches to chlamydial genomics.  
  Taylor-Brown Alyce et al. Microbial genomics 2018 Jan
• Development of molecular methods for the rapid detection of antibiotic susceptibility of Mycoplasma bovis.  
  Sulyok Kinga M et al. Veterinary microbiology 2018 Jan 47-57
• Establishing Ebola Virus Disease (EVD) diagnostics using GeneXpert technology at a mobile laboratory in Liberia: Impact on outbreak response, case management and laboratory systems strengthening.  
  Raftery Philomena et al. PLoS neglected tropical diseases 2018 Jan (1) e0006135  
• Molecular subtyping of European swine influenza viruses and scaling to high-throughput analysis.  
  Bonin Emilie et al. Virology journal 2018 Jan (1) 7

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017.  
  Brandwagt Diederik et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jan (1) 
• Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.  
  Kwong Jason C et al. PeerJ 2018 e4210 
• Measles Outbreak Prevention and Control among Adults: Lessons from an Importation Outbreak in Yunnan Province, China, 2015.  
  Zhao Zhixian et al. Human vaccines & immunotherapeutics 2018 Jan 0

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Discovery of Next-Generation Antimicrobials through Bacterial Self-Screening of Surface-Displayed Peptide Libraries.  
  Tucker Ashley T et al. Cell 2018 Jan
• Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures  
  Lamendella R, et al. mSphere, Jan 10, 2018.
• Deep Sequencing Shows Low Level Oncogenic Hepatitis B Virus Variants Persisting Post-Liver Transplant Despite Potent Anti-HBV Prophylaxis.  
  Lau Keith Ck et al. Journal of viral hepatitis 2018 Jan

HOST-MICROBE INTERACTIONS

• Microbiome at the Frontier of Personalized Medicine.  
  Kashyap Purna C et al. Mayo Clinic proceedings 2017 Dec (12) 1855-1864
• Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility.  
  Graspeuntner Simon et al. PloS one 2018 (1) e0191047
• The role of the gut microbiome in systemic inflammatory disease.  
  Clemente Jose C et al. BMJ (Clinical research ed.) 2018 Jan j5145
• The germ-organ theory of non-communicable diseases.  
  Byndloss Mariana X et al. Nature reviews. Microbiology 2018 Jan
• Microbial modulation of cardiovascular disease.  
  Brown J Mark et al. Nature reviews. Microbiology 2018 Jan
• Increased HIV-1 superinfection risk in carriers of specific human leukocyte antigen alleles.  
  Vesa Jouni et al. AIDS (London, England) 2017 May (8) 1149-1158
• Putative biomarkers for cervical cancer: SNVs, methylation and expression profiles.  
  Cardoso Maria de Fátima Senra et al. Mutation research 2017 Jul 161-173

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