Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Feb 15, 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

Archived Editions
Search AMD Clips database
Visit AMD website

Advanced Molecular Detection Clips Content

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

NEWS

• Safety blunders expose lab staff to potentially lethal diseases in UK  
  Sample I. The Guardian, Feb 9, 2018.
• Public Health Experts Look Ahead to Better Flu Control-—Improved vaccines, more research to chose the right strains needed  
  Walker M. MedPage Today, Feb 13, 2018.
• Can gene therapy be harnessed to fight the AIDS virus?  
  Marchione M. ABC News, Feb 13, 2018.
• Dengue Disease Risk Linked to Gene Variants Among World Populations  
  GenomeWeb, Feb 15, 2018.
• The Importance of Infants’ Exposure to Micro-Organisms  
  Brody JE. New York Times, Feb 5, 2018.
• Genome Editing Reaching Farm Animals, Though Regulatory Uncertainty Looms  
  Anderson A. GenomeWeb, Feb 9, 2018.

METHODS / TOOLS

• Nanopore sequencing and assembly of a human genome with ultra-long reads.  
  Jain Miten et al. Nature biotechnology 2018 Jan
• Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6  
  Gootenberg JS, et al. Science, Feb 15, 2018.
• Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231.  
  Baptista Rodrigo P et al. Microbial genomics 2018 Feb
• A next-generation sequencing and bioinformatics protocol for Malaria drug Resistance marker Surveillance (MaRS).  
  Talundzic Eldin et al. Antimicrobial agents and chemotherapy 2018 Feb 
• HIITE: HIV-1 Incidence and Infection Time Estimator.  
  Park Sung Yong et al. Bioinformatics (Oxford, England) 2018 Feb
• Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): Study protocol of a prospective, observational, noninterventional, multicenter, clinical trial.  
  Brenner Thorsten et al. Medicine 2018 Feb (6) e9868

EVOLUTION / ECOLOGY / POPULATIONS

• Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.  
  Kozak-Muiznieks Natalia A et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Feb 
• Shigella phages isolated during a dysentery outbreak reveal uncommon structures and broad species diversity.  
  Doore Sarah M et al. Journal of virology 2018 Feb
• Comparative genomics shows Mycobacterium ulcerans migration and expansion has preceded the rise of Buruli ulcer in south-eastern Australia.  
  Buultjens Andrew H et al. Applied and environmental microbiology 2018 Feb
• Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease.  
  Versteeg Bart et al. BMC genomics 2018 Feb (1) 130
• In-depth genome analyses of viruses from vaccine-derived rabies cases and corresponding live-attenuated oral rabies vaccines.  
  Pfaff Florian et al. Vaccine 2018 Feb
• Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks.  
  Bryant N A et al. Transboundary and emerging diseases 2018 Feb
• Near-Complete Genome Sequences of Several New Norovirus Genogroup II Genotypes.  
  Chhabra Preeti et al. Genome announcements 2018 Feb (6)
• Whole-Genome Sequence of Human Rhinovirus C47, Isolated from an Adult Respiratory Illness Outbreak in Butte County, California, 2017.  
  Pan Chao-Yang et al. Genome announcements 2018 Feb (5) 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Neisseria gonorrhoeae host adaptation and pathogenesis.  
  Quillin Sarah Jane et al. Nature reviews. Microbiology 2018 Feb
• High genetic plasticity in multidrug resistant ST3-IncHI2 plasmids revealed by sequence comparison and phylogenetic analysis.  
  Fang Liang-Xing et al. Antimicrobial agents and chemotherapy 2018 Feb
• Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.  
  Weingarten Rebecca A et al. mBio 2018 Feb (1)
• Submicroscopic placental infection by non-falciparum Plasmodium spp.  
  Doritchamou Justin Y A et al. PLoS neglected tropical diseases 2018 Feb (2) e0006279
• The impact of insecticide applications on the dynamics of resistance: The case of four Aedes aegypti populations from different Brazilian regions.  
  Garcia Gabriela de Azambuja et al. PLoS neglected tropical diseases 2018 Feb (2) e0006227 
• Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae.  
  Weetman David et al. Scientific reports 2018 Feb (1) 2920 

DETECTION / DIAGNOSIS

• Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli.  
  Camprubí-Font Carla et al. Scientific reports 2018 Feb (1) 2695
• Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Meditated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens.  
  Higgins Owen et al. International journal of molecular sciences 2018 Feb (2)
• Multiplex PCR for detection of plasmid-mediated colistin resistance determinants,  
  Rebelo Ana Rita et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Feb (6)
• Oxford Screening CSF and Respiratory samples ('OSCAR'): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing.  
  Sharp Colin et al. BMC research notes 2018 Feb (1) 120
• A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system.  
  Oba Mami et al. Biochemical and biophysical research communications 2018 01 (2) 1871-1877
• Highlights from the 2016 HIV diagnostics conference: The new landscape of HIV testing in laboratories, public health programs and clinical practice. 
  Wesolowski Laura G et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Jun 63-68 
• Increased species-assignment of filamentous fungi using MALDI-TOF MS coupled with a simplified sample processing and an in-house library.  
  Zvezdanova M E et al. Medical mycology 2018 Feb
• Development of a lateral flow recombinase polymerase assay for the diagnosis of Schistosoma mansoni infections.  
  Poulton Kate et al. Analytical biochemistry 2018 Feb 65-71
• A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination.  
  Ankarklev Johan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Feb
• Identification and Preliminary Evaluation of a Novel Recombinant Protein for Serodiagnosis of Strongyloidiasis.  
  Arifin Norsyahida et al. The American journal of tropical medicine and hygiene 2018 Feb
• Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection-A systematic review and meta-analysis.  
  Buonfrate Dora et al. PLoS neglected tropical diseases 2018 Feb (2) e0006229

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• When are pathogen genome sequences informative of transmission events?  
  Campbell F, et al. PLoS Pathogens, Feb 8, 2018.
• Temporal associations between national outbreaks of meningococcal serogroup W and C disease in the Netherlands and England: an observational cohort study.  
  Knol Mirjam J et al. The Lancet. Public health 2017 Oct (10) e473-e482
• Emergence and control of linezolid-resistant Staphylococcus epidermidis in an ICU of a German hospital.  
  Weßels Christina et al. The Journal of antimicrobial chemotherapy 2018 Feb
• The role of extended and whole genome sequencing for tracking transmission of measles and rubella viruses: report from the Global Measles and Rubella Laboratory Network meeting, 2017.  
  et al. Releve epidemiologique hebdomadaire 2018 Feb (6) 55-9 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation.  
  Anderson Christopher S et al. BMC bioinformatics 2018 Feb (1) 51

HOST-MICROBE INTERACTIONS

• How the microbiome challenges our concept of self.  
  Rees Tobias et al. PLoS biology 2018 Feb (2) e2005358
• Our Gut Microbiome: The Evolving Inner Self.  
  Kundu Parag et al. Cell 2017 Dec (7) 1481-1493
• Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome  
  Oliveira M, et al. PLoS Negl Trop Dis, Feb 15, 2018.
• Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia.  
  Clarke Geraldine M et al. eLife 2017 01
• Human Papillomavirus DNA methylation as a biomarker for cervical precancer: Consistency across 12 genotypes and potential impact on management of HPV-positive women.  
  Clarke Megan A et al. Clinical cancer research : an official journal of the American Association for Cancer Research 2018 Feb

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.