Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Feb 1, 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

• NIH’s New Rules Governing Human Research Go Into Effect  
  Daley J. The Scientist, Jan 25, 2018.
• New group aims to boost global AMR surveillance  
  Dall C. CIDRAP, Jan 30, 2018.
• How to Build a Better Flu Shot  
  Yeager A. The Scientist, Jan 29, 2018.
• CRISPR Editing of Human TRIM5 Gene has Potential to Inhibit HIV-1  
  GenomeWeb, Jan 29, 2018.
• Viruses Related to Zika May Also Harm Fetuses  
  Williams R. The Scientist, Jan 31, 2018.
• Tufts University Demonstrates Use of 3-D Paper Microfluidic, Sees Broad POC Potential  
  O'Connell L. 360dx
• Handheld device sequences human genome  
  Gallagher J. BBC News, Jan 29, 2018.
• Sepsis: the Achilles’ heel of health care  
  McDonough J. STAT, Jan 29, 2018.

CONCEPTS / COMMENTS

• Genome watch: Keeping tally in the microbiome  
  Almeida A, Shao Y. Nat Rev Microbiol, Jan 30, 2018.

METHODS / TOOLS

• Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.  
  Timme Ruth E et al. PeerJ 2017 e3893 
• Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.  
  Menegidio Fabiano B et al. Bioinformatics (Oxford, England) 2018 Feb (3) 514-515
• Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.  
  Äijö Tarmo et al. Bioinformatics (Oxford, England) 2018 Feb (3) 372-380
• Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.  
  Fuks Garold et al. Microbiome 2018 Jan (1) 17
• Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database. 
  Partridge Sally R et al. The Journal of antimicrobial chemotherapy 2018 Jan
• MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.  
  Olekhnovich Evgenii I et al. Bioinformatics (Oxford, England) 2018 Feb (3) 434-444
• Bacterial genome-wide association study: methodologies and applications.  
  Yang Chao et al. Yi chuan = Hereditas 2018 Jan (1) 57-65
• The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic  
  Boskova V, et al. Virus Evol, Jan 29, 2018.
• Evaluation of two DNA extraction methods on the detection of Strongyloides stercoralis infection.  
  Barda Beatrice et al. Journal of clinical microbiology 2018 Jan

EVOLUTION / ECOLOGY / POPULATIONS

• Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing.  
  Okada Kazuhisa et al. Scientific reports 2018 Jan (1) 1631
• Microbial hazards during harvesting and processing at an outdoor United States cannabis farm.  
  Green Brett J et al. Journal of occupational and environmental hygiene 2018 Jan 0 
• African Lineage Brucella melitensis Isolates from Omani Livestock.  
  Foster Jeffrey T et al. Frontiers in microbiology 2017 2702 
• Toward an integrative molecular approach to wildlife disease.  
  DeCandia Alexandra L et al. Conservation biology : the journal of the Society for Conservation Biology 2018 Jan
• Mycobacterium leprae genomes from naturally infected nonhuman primates.  
  Honap Tanvi P et al. PLoS neglected tropical diseases 2018 Jan (1) e0006190
• Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing.  
  Smeele Zoe E et al. Virus research 2018 Jan 91-105
• Multiplex PCR-Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats.  
  Kim Won-Keun et al. Emerging infectious diseases 2018 Feb (2) 249-257
• Rotavirus strain distribution in Ghana pre- and post- rotavirus vaccine introduction.  
  Lartey Belinda L et al. Vaccine 2018 Jan  
• Epidemiology characteristics of human coronaviruses in patients with respiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou.  
  Zhang Su-Fen et al. PloS one 2018 (1) e0191789
• Molecular epidemiology of respiratory syncytial virus.  
  Pangesti Krisna N A et al. Reviews in medical virology 2018 Jan
• Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific.  
  Waltmann Andreea et al. PLoS neglected tropical diseases 2018 Jan (1) e0006146

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Azithromycin-resistant Neisseria gonorrhoeae spreading amongst men who have sex with men (MSM) and heterosexuals in New South Wales, Australia, 2017.  
  Whiley David M et al. The Journal of antimicrobial chemotherapy 2018 Jan
• Spread of Vancomycin-Resistant Enterococcus faecium Isolates Despite Validated Infection Control Measures in an Italian Hospital: Antibiotic Resistance and Genotypic Characterization of the Endemic Strain.  
  Bressan Raffaela et al. Microbial drug resistance (Larchmont, N.Y.) 2018 Jan
• Detection and analysis of methicillin-resistant human-adapted sequence type 398 allows insight into community-associated methicillin-resistant Staphylococcus aureus evolution.  
  He Lei et al. Genome medicine 2018 Jan (1) 5
• Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae.  
  Benjak Andrej et al. Nature communications 2018 Jan (1) 352
• Comparative Whole-Genomic Analysis of an Ancient L2 Lineage Mycobacterium tuberculosis Reveals a Novel Phylogenetic Clade and Common Genetic Determinants of Hypervirulent Strains.  
  Rajwani Rahim et al. Frontiers in cellular and infection microbiology 2017 539
• An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction.  
  Xia Hongjie et al. Nature communications 2018 Jan (1) 414
• Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL), a Resistance Mechanism for Two Distinct Compound Classes.  
  Magistrado Pamela A et al. ACS infectious diseases 2016 Nov (11) 816-826
• Drug resistance in Plasmodium  
  Haldar K, et al. Nat Rev Microbiol, Jan 22, 2018.
• The emergence and spread of kelch 13 mutations associated with artemisinin resistance in Plasmodium falciparum parasites in twelve Thai provinces from 2007 - 2016.  
  Kobasa Theerayot et al. Antimicrobial agents and chemotherapy 2018 Jan 

DETECTION / DIAGNOSIS

• Use of whole genome sequencing to investigate an increase in Neisseria gonorrhoeae infection among women in urban areas of Australia.  
  Buckley Cameron et al. Scientific reports 2018 Jan (1) 1503
• Evaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany.  
  Simon Sandra et al. Food microbiology 2018 May 46-54
• Salmonella epidemiology: A whirlwind of change.  
  Besser John M et al. Food microbiology 2018 May 55-59 
• Co-circulation and simultaneous co-infection of dengue, chikungunya, and zika viruses in patients with febrile syndrome at the Colombian-Venezuelan border.  
  Carrillo-Hernández Marlen Yelitza et al. BMC infectious diseases 2018 Jan (1) 61
• High genetic variability of norovirus leads to diagnostic test challenges.  
  Zhuo Ran et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Nov 94-98
• Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence.  
  Fukutani Kiyoshi Ferreira et al. Frontiers in bioengineering and biotechnology 2017 84
• Expanding molecular diagnostics of helminthiasis: Piloting use of the GPLN platform for surveillance of soil transmitted helminthiasis and schistosomiasis in Ghana.  
  Cunningham Lucas J et al. PLoS neglected tropical diseases 2018 Jan (1) e0006129
• The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota. 
  Krehenwinkel Henrik et al. PloS one 2018 (1) e0189188

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Evaluating the use of whole-genome sequencing for outbreak investigations in the lack of closely related reference genome.  
  Abdelbary Mohamed M H et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Jan
• Characterization of an Outbreak of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit in Italy.  
  Corbella Marta et al. Microbial drug resistance (Larchmont, N.Y.) 2018 Jan
• Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014.  
  Waldram Alison et al. Food microbiology 2018 May 39-45
• Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015.  
  Kanagarajah Sanch et al. Food microbiology 2018 May 32-38
• The clinical and phylogenetic investigation for a nosocomial outbreak of respiratory syncytial virus infection in an adult hemato-oncology unit.  
  Nabeya Daijiro et al. Journal of medical virology 2017 Aug (8) 1364-1372
• Viral load and sequence analysis reveal the symptom severity, diversity and transmission clusters of rhinovirus infections.  
  Ng Kim Tien et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jan
• Investigation of an isolated case of human Crimean-Congo hemorrhagic fever in Central Uganda, 2015.  
  Balinandi Stephen et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2018 Jan  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults.  
  Kearney Mary F et al. PloS one 2018 (1) e0190438

HOST-MICROBE INTERACTIONS

• Searching for human oncoviruses: histories, challenges, and opportunities.  
  Cao Jian et al. Journal of cellular biochemistry 2018 Jan
• The Human Mucosal Mycobiome and Fungal Community Interactions.  
  Witherden Elizabeth A et al. Journal of fungi (Basel, Switzerland) 2017 Oct (4)
• Systematic investigation for underlying causes of recurrent infections in children: surveillance of primary immunodeficiency.  
  Yousefzadegan S et al. European annals of allergy and clinical immunology 2017 Nov
• Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.  
  Kirk Karina Frahm et al. Scientific reports 2018 Jan (1) 1902
• Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania.  
  Ravenhall Matt et al. PLoS genetics 2018 Jan (1) e1007172
• Bacterial pathogenesis and interleukin-17: interconnecting mechanisms of immune regulation, host genetics, and microbial virulence that influence severity of infection.  
  Chamoun Michelle N et al. Critical reviews in microbiology 2018 Jan 1-22

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.