Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 17, 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
• 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

• Multi-Omics Approach Uncovers Prognostic Biomarkers for Bloodstream Infections  
  Gilmore J. GenomeWeb, May 11, 2018.
• UCSF Team Illustrates How Metagenomic Sequencing Can Diagnose Complicated Cases of Meningitis  
  Heger M. GenomeWeb, Apr 17, 2018.
• $1 Smartphone-Based Test for Infectious Diseases Being Developed  
  O'Connor L. 360dx, May 10, 2018.
• Molecular typing gives more precise picture of gonorrhea in Europe  
  Dall C. CIDRAP, May 16, 2018.
• Experimental vaccine to be used against Ebola outbreak in the DRC  
  Branswell H. STAT, May 13, 2018.
• American Gut Project Reports Microbiome Results for 11K Participants  
  GenomeWeb, May 15, 2018.
• Citizen Science Microbiome Project Publishes Results  
  Frontline Genomics, May 16, 2018.
• As D.I.Y. Gene Editing Gains Popularity, ‘Someone Is Going to Get Hurt’  
  Baumgaertner E. New York Times, May 14, 2018.

EVENTS / TRAINING / WEB RESOURCES

• A Next-Generation Sequencing Primer-How Does It Work and What Can It Do?  
  Alekseyev Yuriy O et al. Academic pathology 2374289518766521

CONCEPTS / COMMENTS

• Juggling resistance mutations  
  Rutledge GG, Amato R. Nat Rev Microbiol 2018; 16:32.
• Fasting the microbiome to treat diabetes  
  Cohen LJ. Sci Transl Med, May 16, 2018.

METHODS / TOOLS

• Piercing the dark matter: bioinformatics of long-range sequencing and mapping.  
  Sedlazeck Fritz J et al. Nature reviews. Genetics 2018 Mar
• SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control.  
  Al-Ghalith Gabriel A et al. mSystems (3)
• A large-scale analysis of bioinformatics code on GitHub  
  Russell P, et al. bioRxiv, May 18, 2018.
• Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data  
  Ravishankar S, et al. bioRxiv, May 16, 2018. 
• Generation and comparative genomics of synthetic dengue viruses.  
  Goz Eli et al. BMC bioinformatics 2018 May (Suppl 6) 140
• Estimating epidemic incidence and prevalence from genomic data  
  Vaughn TG, et al. bioRxiv, May 3, 2018.
• American Gut: an Open Platform for Citizen Science Microbiome Research  
  McDonald D, et al. mSystems, May 15, 2018.

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. 
  Baker Kate S et al. Scientific reports 2018 May (1) 7389
• High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing.  
  Patel Pooja N et al. Genome announcements 2018 May (19) 
• Sequencing and phylogenetic characterization of Brucella canis isolates, Ohio, 2016.  
  Wang L et al. Transboundary and emerging diseases 2018 May
• Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.  
  Schuenemann Verena J et al. PLoS pathogens 2018 May (5) e1006997
• Genetic diversity of human sapovirus across the Americas.  
  Diez-Valcarce Marta et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2018 May 65-72
• Genome Sequences of Akhmeta Virus, an Early Divergent Old World Orthopoxvirus.  
  Gao Jinxin et al. Viruses 2018 05 (5) 
• NS1 codon usage adaptation to humans in pandemic Zika virus.  
  Freire Caio César de Melo et al. Memorias do Instituto Oswaldo Cruz 2018 May (5) e170385
• A new "American" subgroup of African-lineage Chikungunya virus detected in and isolated from mosquitoes collected in Haiti, 2016.  
  White Sarah Keller et al. PloS one 2018 (5) e0196857
• Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation.  
  Wang Daxi et al. Advances in parasitology 2018 155-208

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.  
  Wheeler Nicole E et al. PLoS genetics 2018 May (5) e1007333
• Clonal expansion of environmentally-adapted Escherichia coli contributes to propagation of antibiotic resistance genes in beef cattle feedlots.  
  Tymensen Lisa et al. The Science of the total environment 2018 May 657-664
• Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis. 
  Ahlstrom Christina A et al. Scientific reports 2018 May (1) 7361
• Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey  
  Harris SR, et al. Lancet Infect Dis, May 15, 2018.
• Limited influence of hospital wastewater on the microbiome and resistome of wastewater in a community sewerage system.  
  Buelow Elena et al. FEMS microbiology ecology 2018 May
• Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia.  
  Uyaguari-Díaz Miguel I et al. Frontiers in microbiology 2018 852
• Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates.  
  Pan Fen et al. Infection and drug resistance 2018 659-670
• Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.  
  Zhou Xinrui et al. BMC genomics 2018 May (Suppl 2) 88

DETECTION / DIAGNOSIS

• Molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) on New Zealand dairy farms: application of a culture-independent assay and whole genome sequencing.  
  Browne A Springer et al. Applied and environmental microbiology 2018 May
• Molecular test for chlamydia and gonorrhoea used at point of care in remote primary healthcare settings: a diagnostic test evaluation.  
  Causer Louise M et al. Sexually transmitted infections 2018 May 
• Efficient detection of symptomatic and asymptomatic patient samples for Babesia microti and Borrelia burgdorferi infection by multiplex qPCR.  
  Primus Shekerah et al. PloS one 2018 (5) e0196748
• Biodiversity of Environmental Leptospira : Improving Identification and Revisiting the Diagnosis.  
  Thibeaux Roman et al. Frontiers in microbiology 2018 816
• Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing.  
  Telele Nigus Fikrie et al. Scientific reports 2018 May (1) 7556 
• Circulating Salivary miRNA hsa-miR-221 as Clinically Validated Diagnostic Marker for Hand, Foot, and Mouth Disease in Pediatric Patients.  
  Min Nyo et al. EBioMedicine 2018 May
• Multi-site evaluation of the LN34 pan-lyssavirus real-time RT-PCR assay for post-mortem rabies diagnostics.  
  Gigante Crystal M et al. PloS one 2018 (5) e0197074 
• Simultaneous co-detection of wild-type and vaccine strain measles virus using the BD MAX system.  
  Thapa Kiran et al. Pathology 2018 May 
• Detection of nineteen enteric viruses in raw sewage in Japan.  
  Thongprachum Aksara et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 May
• Generation of a novel next-generation sequencing-based method for the isolation of new human papillomavirus types.  
  Brancaccio Rosario N et al. Virology 2018 May 1-10
• Five-year National Surveillance of Invasive Candidiasis: Species Distribution and Azole Susceptibility from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) Study.  
  Xiao Meng et al. Journal of clinical microbiology 2018 May
• Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.  
  Wilson Michael R et al. JAMA neurology 2018 Apr

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Notes from the Field: Investigation of an Outbreak of Salmonella Paratyphi B Variant L(+) tartrate + (Java) Associated with Ball Python Exposure — United States, 2017
  Krishnasamy V, et al. MMWR, May 19, 2018. 
• Genotyping and Whole Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005-2014.  
  Guthrie Jennifer L et al. The Journal of infectious diseases 2018 May
• Towards the elimination of paediatric tuberculosis in high-income, immigrant-receiving countries: a 25-year conventional and molecular epidemiological case study.  
  Dhawan Vivek et al. ERJ open research 2018 Apr (2)
• The use of whole-genome sequencing in cluster investigation of an MDR-TB outbreak.  
  Lalor Maeve K et al. The European respiratory journal 2018 May
• Large Outbreak of Hepatitis C Virus Associated With Drug Diversion by a Healthcare Technician.  
  Alroy-Preis Sharon et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 May 
• Molecular typing and whole genome next generation sequencing of human adenovirus 8 strains recovered from four 2012 outbreaks of keratoconjunctivitis in New York State.  
  Lamson Daryl M et al. Journal of medical virology 2018 May

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Microbial taxonomic and metabolic alterations during faecal microbiota transplantation to treat Clostridium difficile infection.  
  Kellingray Lee et al. The Journal of infection 2018 May

HOST-MICROBE INTERACTIONS

• Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies.  
  Mboowa Gerald et al. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale 2018 1875217
• Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes.  
  DiNardo Andrew R et al. Journal of immunology (Baltimore, Md. : 1950) 2018 May
• Impact of HLA-DRB1 allele polymorphisms on control of HIV infection in a Peruvian MSM cohort.  
  Oriol-Tordera B et al. HLA 2017 Oct (4) 234-237
• Epigenome-wide study for the offspring exposed to maternal HBV infection during pregnancy, a pilot study.  
  Cheng Qijun et al. Gene 2018 Jun 76-85
• Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.  
  Olde Loohuis Loes M et al. Translational psychiatry 2018 May (1) 96
• The fallopian tube microbiome: implications for reproductive health.  
  Pelzer Elise S et al. Oncotarget 2018 Apr (30) 21541-21551

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.