Advanced Molecular Detection Clips Content || Public Health Genomics Knowledge Base (v1.2)

Public Health Genomics Knowledge Base (v1.2)



August 4-11, 2016 

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

NEWS

• FDA temporarily halts blood donation in two Florida counties over Zika fears 
  Sun LH. Washington Post, Jul 28, 2016.
• The best drug to fight Zika may already be approved and out there, study suggests 
  Joseph A. STAT, Jul 28, 2016.
• NIH begins testing investigational Zika vaccine in humans 
  (press release) NIH, Aug 3, 2016.
• US Public Health Laboratories Prepare Zika Virus Dx Strategy as Infections Increase 
  O'Connor L. GenomeWeb, Aug 4, 2016.
• Zika-specific complications hamper development of new diagnostics 
  Healio, Aug 3, 2016.
• One-hour test detects MRSA, CoNS 
  Healio, Aug 2, 2016.
• New Lyme Disease Test Developed by Summer Student 
  Rood J. The Scientist, Aug 1, 2016.
• Fecal Transplant Pill Fails Trial 
  Akst J.The Scientist, Aug 1, 2016.
• Back from vacation? Your gut bacteria picked up souvenirs, too 
  Knight M. Genetic Literacy Project, Aug 1, 2016.
• Human Functional Genomics Project Begins Unraveling Links Between Genes, Immune Response 
  Newbern E. GenomeWeb, Jul 28, 2016.
• Methods for More Accurate Microbiome Studies Could Impact Future Therapeutic Use 
  Johnson M. GenomeWeb, Jul 26, 2016.
• Introducing the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) 
  (blog post) Pallen MJ. PHG Foundation, Jul 27, 2016.
• Emerging Infections: A National Patient Safety Challenge 
  (blog post) Cleeman JI. AHRQ, Jul 26, 2016.

EVENTS / TRAINING / WEB RESOURCES

• How to Build Bioinformatic Pipelines Using Galaxy 
  Perkel JM. The Scientist, Aug 1, 2016.

POLICY

• Ethics Reporting in Biospecimen and Genetic Research: Current Practice and Suggestions for Changes 
  Chin WW, et al. PLoS Biol, Aug 2, 2016.
• Gene Drives on the Horizon: Advancing Science, Navigating Uncertainty, and Aligning Research with Public Values 
  (report) National Academies Press, 2016.

CONCEPTS / COMMENTS

• Microbial bioinformatics 2020. 
  Pallen Mark J et al. Microbial biotechnology 2016 Jul
• Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. 
  Van Voorhis Wesley C et al. PLoS pathogens 2016 Jul (7) e1005763
• Tempo and mode of genome evolution in a 50,000-generation experiment. 
  Tenaillon Olivier et al. Nature 2016 Aug

METHODS / TOOLS

• DUDes: a top-down taxonomic profiler for metagenomics. 
  Piro Vitor C et al. Bioinformatics (Oxford, England) 2016 Aug (15) 2272-80
• ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database.
  Yang Ying et al. Bioinformatics (Oxford, England) 2016 Aug (15) 2346-51
• SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.
  Lopez-Maestre Hélène et al. Nucleic acids research 2016 Jul
• Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene. 
  Allen Heather K et al. BMC research notes 2016 (1) 380

EVOLUTION / ECOLOGY / POPULATIONS

• Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis. 
  Orata Fabini D et al. International journal of systematic and evolutionary microbiology 2016 Jul 
• Whole-genome sequencing reveals transmission of Staphylococcus aureus from humans to green monkeys in The Gambia. 
  Senghore Madikay et al. Applied and environmental microbiology 2016 Jul
• Phylogenetic and geographic patterns of bartonella host shifts among bat species. 
  McKee Clifton D et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jul
• Full-Genome Sequence of a Neuroinvasive West Nile Virus Lineage 2 Strain from a Fatal Horse Infection in South Africa. 
  Mentoor Juliet L D et al. Genome announcements 2016 (4) 
• Spike gene deletion quasispecies in serum of patient with acute MERS-CoV infection. 
  Lu Xiaoyan et al. Journal of medical virology 2016 Aug 
• Characterization of VP1 sequence of Coxsackievirus A16 isolates by Bayesian evolutionary method. 
  Zhao Guolian et al. Virology journal 2016 130
• New Perspectives on Ebola Virus Evolution. 
  Brown Celeste J et al. PloS one 2016 (8) e0160410
• Virulence and Evolution of West Nile Virus, Australia, 1960-2012. 
  Prow Natalie A et al. Emerging infectious diseases 2016 Aug (8) 1353-62 
• Genotypes of Cryptosporidium spp., Enterocytozoon bieneusi and Giardia duodenalis in dogs and cats in Shanghai, China. 
  Xu Hailing et al. Parasites & vectors 2016 121 
• Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum. 
  Peel Alison J et al. Scientific data 2016 160049

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Human Functional Genomics Project Begins Unraveling Links Between Genes, Immune Response 
  Newbern E. GenomeWeb, Jul 28, 2016.
• Increased plasmid copy number is essential for Yersinia T3SS function and virulence. 
  Wang He et al. Science (New York, N.Y.) 2016 Jul (6298) 492-5
• Antimicrobial Resistance, Virulence Profile, and Molecular Characterization of Listeria monocytogenes Isolated from Ready-to-eat Food in China, 2013-2014. 
  Yan Shao Fei et al. Biomedical and environmental sciences : BES 2016 Jun (6) 448-52
• South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study 
  The HC, et al. PLoS Med, Aug 2, 2016.
• Resistant mechanisms and molecular epidemiology of imipenem-resistant Acinetobacter baumannii. 
  Xiao Shu-Zhen et al. Molecular medicine reports 2016 Jul
• Emergence of Mycoplasma genitalium strains showing mutations associated with macrolide and fluoroquinolone resistance in the region Dresden, Germany. 
  Dumke Roger et al. Diagnostic microbiology and infectious disease 2016 Jul
• Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection. 
  Kim So Yeon et al. Emerging infectious diseases 2016 Oct (10)
• HIV DNA is frequently present within pathologic tissues evaluated at autopsy from cART-treated patients with undetectable viral load. 
  Lamers Susanna L et al. Journal of virology 2016 Jul
• L159F and V321A Sofosbuvir-Associated Hepatitis C Virus NS5B Substitutions. 
  Svarovskaia Evguenia S et al. The Journal of infectious diseases 2016 Apr (8) 1240-7
• HIV virological failure and drug resistance in a cohort of Tanzanian HIV-infected adults. 
  Hawkins Claudia et al. The Journal of antimicrobial chemotherapy 2016 Jul (7) 1966-74 
• Multilocus sequence typing of Candida tropicalis shows clonal cluster enrichment in azole-resistant isolates from patients in shanghai, China. 
  Wang Ying et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Jul
• Genomic analysis reveals a common breakpoint in amplifications of the Plasmodium vivax multidrug resistance 1 locus in Thailand. 
  Auburn Sarah et al. The Journal of infectious diseases 2016 Jul

DETECTION / DIAGNOSIS

• Rapid molecular determination of methicillin resistance in staphylococcal bacteraemia improves early targeted antibiotic prescribing: a randomized clinical trial. 
  Emonet Stephane et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Jul
• Paired real-time PCR assays for detection of Borrelia miyamotoi in North American Ixodes scapularis and Ixodes pacificus (Acari: Ixodidae). 
  Graham Christine B et al. Ticks and tick-borne diseases 2016 Jul 
• Point-Counterpoint: A Nucleic acid amplification test for Streptococcus pyogenes should replace antigen detection and culture for the detection of bacterial pharyngitis. 
  Pritt Bobbi S et al. Journal of clinical microbiology 2016 Jul
• A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity. 
  Gong Yu-Nong et al. PloS one 2016 (3) e0151495
• Detection of Listeria monocytogenes in CSF from Three Patients with Meningoencephalitis by Next-Generation Sequencing. 
  Yao Ming et al. Journal of clinical neurology (Seoul, Korea) 2016 Jul
• Laboratory Innovation Towards Quality Program Sustainability. 
  Abimiku Alash'le et al. Current HIV/AIDS reports 2016 Aug 
• Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes. 
  Thomson Emma et al. Journal of clinical microbiology 2016 Jul
• Human Papillomavirus Genotyping Testing Practice in 2014: Results of a College of American Pathologists National Survey. 
  Zhao Chengquan et al. Archives of pathology & laboratory medicine 2016 Aug 
• Molecular and serological techniques to detect co-circulation of DENV, ZIKV and CHIKV in suspected dengue-like syndrome patients. 
  Cabral-Castro Mauro Jorge et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2016 Jul 108-111
• Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease - Florida, 2016. 
  Bingham Andrea M et al. MMWR. Morbidity and mortality weekly report 2016 (18) 475-8 
• Identification of Stachybotrys spp. by MALDI-TOF mass spectrometry. 
  Ulrich Sebastian et al. Analytical and bioanalytical chemistry 2016 Jul

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Prospective Study of Plasmodium vivax Malaria Recurrence after Radical Treatment with a Chloroquine-Primaquine Standard Regimen in Turbo, Colombia. 
  Zuluaga-Idárraga Lina et al. Antimicrobial agents and chemotherapy 2016 Aug (8) 4610-9 

HOST-MICROBE INTERACTIONS

• Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. 
  Yu Guoqin et al. Genome biology 2016 (1) 163
• The Vaginal Microbiome: Current Understanding and Future Directions. 
  Martin David H et al. The Journal of infectious diseases 2016 Aug S36-41
• Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome 
  Sze M, Schloss PD. bioRxiv, Jul 20, 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.

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.