Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Dec 20, 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
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Tracing the Bugs
  GenomeWeb, Dec 18, 2018.
• On a bat's wing and a prayer
  Sun LH. Washington Post, Dec 13, 2018.
• Up for debate — WHO guidelines on prompt release of outbreak data
  Moorthy V, et al. Nature, Dec 19, 2018.
• Cell-jacking proteins could be the key to cracking Zika and dengue
  Maxmen A. Science, Dec 13, 2018.
• Medical Detectives: The Last Hope For Families Coping With Rare Diseases
  McClurg L. NPR, Dec 17, 2018.
• Tourists may be making Antarctica’s penguins sick
  Bolevich M. Science, Dec 13, 2018.

POLICY

• Public consultation - Pathogen genetic sequence data (GSD) WHO’s draft code of conduct for open and timely sharing of pathogen genetic sequence data during outbreaks of infectious disease
  WHO, Dec 2018. (comments due Jan 28, 2019)

CONCEPTS / COMMENTS

• Applying ecological resistance and resilience to dissect bacterial antibiotic responses.
  Meredith Hannah R et al. Science advances 2018 Dec (12) eaau1873
• ‘Outbreak culture’ can derail effective responses to deadly epidemics
  Salahi L, Sabeti P. STAT, Dec 17, 2018.
• Epidemic preparedness: why is there a need to accelerate the development of diagnostics?
  Peeling Rosanna W et al. The Lancet. Infectious diseases 2018 Dec
• Understanding tuberculosis transmission might be the gamechanger we need.
  Sekkides Onisillos et al. The Lancet. Infectious diseases 2018 Dec

METHODS / TOOLS

• Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.
  Egli Adrian et al. Swiss medical weekly 2018 Dec w14693 
• Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow.
  Bal A et al. BMC infectious diseases 2018 Oct (1) 537 
• Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.
  Davis Nicole M et al. Microbiome 2018 Dec (1) 226
• Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph.
  Morisse Pierre et al. Bioinformatics (Oxford, England) 2018 Dec (24) 4213-4222
• Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.
  Eren Kemal et al. PLoS computational biology 2018 Dec (12) e1006498
• A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen.
  Catanese Helen N et al. BMC bioinformatics 2018 Dec (1) 475
• Tracking virus outbreaks in the twenty-first century.
  Grubaugh Nathan D et al. Nature microbiology 2019 Jan (1) 10-19
• Minimum Information about an Uncultivated Virus Genome (MIUViG).
  Roux Simon et al. Nature biotechnology 2018 Dec
• Harnessing alternative sources of antimicrobial resistance data to support surveillance in low-resource settings.
  Ashley Elizabeth A et al. The Journal of antimicrobial chemotherapy 2018 Dec
• Tet-Inducible Production of Infectious Zika Virus from the Full-Length cDNA Clones of African- and Asian-Lineage Strains.
  Zhang Lizhou et al. Viruses 2018 Dec (12)

EVOLUTION / ECOLOGY / POPULATIONS

• Diversified Sources for Human Infections by Salmonella enterica serovar Newport.
  Pan Hang et al. Transboundary and emerging diseases 2018 Dec
• Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States.
  Zhang Shaokang et al. Emerging infectious diseases 2019 Jan (1) 82-91
• Isolation and Full-Genome Characterization of Nipah Viruses from Bats, Bangladesh.
  Anderson Danielle E et al. Emerging infectious diseases 2019 Jan (1) 166-170
• Minimum InDel pattern analysis of the Zika virus.
  Lee Hyeji et al. BMC genomics 2018 Jul (1) 535
• Widespread circulation of West Nile virus, but not Zika virus in southern Iran.
  Ziyaeyan Mazyar et al. PLoS neglected tropical diseases 2018 Dec (12) e0007022
• Genetic variability of the Aedes aegypti (Diptera: Culicidae) mosquito in El Salvador, vector of dengue, yellow fever, chikungunya and Zika.
  Joyce Andrea L et al. Parasites & vectors 2018 Dec (1) 637

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Burdens of Invasive Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus Disease, Minnesota, USA.
  Koeck Mackenzie et al. Emerging infectious diseases 2019 Jan (1) 171-174
• Emerging Multidrug-Resistant Hybrid Pathotype Shiga Toxin-Producing Escherichia coli O80 and Related Strains of Clonal Complex 165, Europe.
  Cointe Aurélie et al. Emerging infectious diseases 2018 Dec (12) 2262-2269
• Parechovirus A3 (PeV-A3)-associated myalgia/myositis occurs irrespective of its genetic cluster: a longitudinal molecular epidemiology of PeV-A3 in Yamagata, Japan between 2003 and 2016.
  Mizuta Katsumi et al. Journal of medical microbiology 2018 Dec
• Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.
  Muñoz José F et al. Nature communications 2018 12 (1) 5346

DETECTION / DIAGNOSIS

• Detection of Pediatric Bacterial Meningitis Pathogens from Cerebrospinal Fluid by Next-Generation Sequencing Technology.
  Guo Ling-Yun et al. The Journal of infection 2018 Dec
• Routine use of MALDI-TOF MS for anaerobic bacterial identification in clinical microbiology.
  Shannon Samantha et al. Anaerobe 2018 Dec 191-196 
• Culture-free genotyping of Neisseria gonorrhoeae revealed distinct strains at different anatomical sites in a quarter of patients, the Netherlands, 2012 to 2016.
  van der Veer Brian Mjw et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Dec (50)
• rpoB Targeted Loop-Mediated Isothermal Amplification (LAMP) Assay for Consensus Detection of Mycobacteria Associated With Pulmonary Infections.
  Grandjean Lapierre Simon et al. Frontiers in medicine 2018 332
• Utility of whole genome sequencing for multidrug resistant Mycobacterium tuberculosis isolates in a reference TB laboratory in New Zealand.
  Basu Indira et al. The New Zealand medical journal 2018 Dec (1487) 15-22 
• A point-of-care diagnostic for differentiating Ebola from endemic febrile diseases.
  Sebba David et al. Science translational medicine 2018 Dec (471)
• Inaccurate Multilocus Sequence Typing of Acinetobacter baumannii.
  Castillo-Ramírez Santiago et al. Emerging infectious diseases 2019 Jan (1) 186-187
• Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples.
  Kafetzopoulou Liana E et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Dec (50)
• Molecular detection of dengue virus in patients suspected of Ebola virus disease in Ghana.
  Bonney Joseph Humphrey Kofi et al. PloS one 2018 (12) e0208907
• Novel Orthobunyavirus Identified in the Cerebrospinal Fluid of a Ugandan Child With Severe Encephalopathy.
  Edridge Arthur W D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jan (1) 139-142
• Keystone Virus Isolated From a Florida Teenager With Rash and Subjective Fever: Another Endemic Arbovirus in the Southeastern United States?
  Lednicky John A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jan (1) 143-145

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Epidemiological investigation of an Acinetobacter baumannii outbreak using Core Genome Multilocus Sequence Typing.
  Venditti Carolina et al. Journal of global antimicrobial resistance 2018 Dec 
• Overestimation of an outbreak of Enterobacter cloacae in a neonatal intensive care unit in Germany, 2015.
  Steffen Gyde et al. The Pediatric infectious disease journal 2018 Dec
• A community outbreak of Legionnaires' disease in Geneva, Switzerland, June to September 2017.
  Zanella Marie-Céline et al. Swiss medical weekly 2018 Nov w14687
• Orogenital Transmission of Neisseria meningitidis Causing Acute Urethritis in Men Who Have Sex with Men.
  Jannic Arnaud et al. Emerging infectious diseases 2019 Jan (1) 175-176
• Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.
  Rasmussen David A et al. Virus evolution 2018 Jul (2) vey037

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Open-source discovery of chemical leads for next-generation chemoprotective antimalarials.
  Antonova-Koch Yevgeniya et al. Science (New York, N.Y.) 2018 12 (6419)

HOST-MICROBE INTERACTIONS

• Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.
  Kintses Bálint et al. Nature microbiology 2018 Dec
• Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.
  Vatanen Tommi et al. Nature microbiology 2018 Dec
• Insights into immunity from clinical and basic science studies of DOCK8 immunodeficiency syndrome.
  Su Helen C et al. Immunological reviews 2019 Jan (1) 9-19
• Human papillomavirus and the landscape of secondary genetic alterations in oral cancers.
  Gillison Maura L et al. Genome research 2018 Dec

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