Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Feb 8, 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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Snooping around in hospital pipes, scientists find DNA that fuels the spread of superbugs  
  Healy MA. Los Angeles Times, Feb 6, 2018.
• If you drink untreated water — and you shouldn’t — this is what you’re drinking  
  Branswell H. STAT, Feb 7, 2018.
• FDA cites progress, hurdles in antibiotic development  
  Dall C. CIDRAP, Feb 6, 2018.
• Medicines from engineered bacteria offer promise — and pitfalls  
  Smith D. STAT, Feb 6, 2018.
• Is It Influenza or Adenovirus?  
  Kelly JC. Medscape, Feb 2, 2018.
• Zika studies highlight brain damage, possible genetic link  
  Schnirring L. CIDRAP, Feb 5, 2018.
• Biohacker Injects DIY Herpes Vaccine on Facebook Live  
  Williams S. The Scientist, Feb 5, 2018.
• Parasite Genome Analysis Points to Rapid Rise of Antimalarial Drug Resistance in Cambodia  
  GenomeWeb, Feb 2, 2018.
• Paper DNA Detection Device Enables Diagnosis of Helminth Infections  
  Johnson M. GenomeWeb, Feb 5, 2018.
• Gut Microbes Combine to Cause Colon Cancer, Study Suggests  
  Kolata G. New York Times, Feb 1, 2018.

CONCEPTS / COMMENTS

• The Utility of Multiplex Molecular Tests for Enteric Pathogens: a Micro-Comic Strip  
  McAdam AJ, Burnham CD. J Clin Microbiol 2018;56(2):e01916-17
• Big data needs a hardware revolution  
  (editorial) Nature, Feb 6, 2018.

METHODS / TOOLS

• An optimized DNA extraction method for molecular identification of coccidian species.  
  Tang Xiaoli et al. Parasitology research 2018 Feb
• A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.  
  Collins Caitlin et al. PLoS computational biology 2018 Feb (2) e1005958
• Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:.  
  Saltykova Assia et al. PloS one 2018 (2) e0192504
• The development and application of bioinformatics core competencies to improve bioinformatics training and education.  
  Mulder Nicola et al. PLoS computational biology 2018 Feb (2) e1005772

EVOLUTION / ECOLOGY / POPULATIONS

• Circulation of canine parvovirus among dogs living in human-wildlife interface in the Atlantic forest biome, Brazil.  
  Vieira Flávia V et al. Heliyon 2017 Dec (12) e00491
• A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.  
  Yebra Gonzalo et al. PloS one 2018 (2) e0192081
• Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors.  
  Whitmer Shannon L M et al. Cell reports 2018 Jan (5) 1159-1168 
• Genetic characterization and diversity of circulating influenza A/H1N1pdm09 viruses isolated in Jeddah, Saudi Arabia between 2014 and 2015.  
  Hashem Anwar M et al. Archives of virology 2018 Feb
• Molecular surveillance of norovirus, 2005-16: an epidemiological analysis of data collected from the NoroNet network.  
  van Beek Janko et al. The Lancet. Infectious diseases 2018 Jan
• Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens.  
  Ismail Ashrafali M et al. Emerging microbes & infections 2018 Feb (1) 10
• Molecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus.  
  Jamal Syed M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Feb
• The persistence and oscillations of submicroscopic Plasmodium falciparum and Plasmodium vivax infections over time in Vietnam: an open cohort study.  
  Nguyen Thuy-Nhien et al. The Lancet. Infectious diseases 2018 Feb

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Identification of novel variants of the colistin resistance gene mcr-3 in Aeromonas spp. from the national resistance monitoring programme GERM-Vet and from diagnostic submissions.  
  Eichhorn Inga et al. The Journal of antimicrobial chemotherapy 2018 Jan
• Genetically distinct lineages of Salmonella Typhimurium ST313 and ST19 are present in Brazil.  
  Panzenhagen Pedro Henrique N et al. International journal of medical microbiology : IJMM 2018 Jan
• Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance  
  Weingarten RA, et al. mBio, Feb 6, 2018.
• Phenotypic heterogeneity: a bacterial virulence strategy.  
  W A Weigel et al. Microbes and infection 2018 Jan
• Whole genome typing of the recently emerged Canadian serogroup W Neisseria meningitidis Sequence Type-11 clonal complex isolates associated with invasive meningococcal disease.  
  Tsang Raymond S W et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2018 Feb
• Whole genome sequencing enabled the detection of a colistin-resistant hypermutating citrobacter werkmanii strain harbouring a novel metallo-beta-lactamase VIM-48.  
  Peter S et al. International journal of antimicrobial agents 2018 Feb
• Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis.  
  Mortimer Tatum D et al. mSystems (1)
• Could omics unlock the secret of surviving tuberculous meningitis?  
  Dunstan Sarah J et al. The Lancet. Infectious diseases 2018 Feb
• Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study.  
  Amato Roberto et al. The Lancet. Infectious diseases 2018 Feb

DETECTION / DIAGNOSIS

• Use of a multiplex DNA extraction PCR in the identification of pathogens in travelers' diarrhea.  
  Connor Bradley A et al. Journal of travel medicine 2018 Jan (1) 
• Molecular typing of Legionella pneumophila isolates from environmental water samples and clinical samples using a five-gene sequence typing and standard Sequence-Based Typing.  
  Zhan Xiao-Yong et al. PloS one 2018 (2) e0190986
• Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg.  
  Usongo Valentine et al. PloS one 2018 (2) e0192233
• Simultaneous immunodetection of anthrax, plague and tularemia from blood cultures utilizing multiplexed suspension arrays.  
  Mechaly Adva et al. Journal of clinical microbiology 2018 Jan
• Impact of Cerebrospinal Fluid Multiplex Assay on Diagnosis and Outcomes of Central Nervous System Infections in Children: A Before and After Cohort Study.  
  O'Brien Matthew P et al. The Pediatric infectious disease journal 2018 Feb 
• Clostridium sphenoides Chronic Osteomyelitis Diagnosed Via Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry, Conflicting With 16S rRNA Sequencing but Confirmed by Whole Genome Sequencing.  
  Perkins Matthew J et al. Military medicine 2017 Jan (1) e1669-e1672
• Recommendations for enterovirus diagnostics and characterisation within and beyond Europe.  
  Harvala Heli et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2018 Feb 11-17 
• Sequencing of hepatitis C virus for detection of resistance to direct-acting antiviral therapy: A systematic review.  
  Bartlett Sofia R et al. Hepatology communications 2017 Jul (5) 379-390
• Diagnostic Testing for Zika Virus: A Post-Outbreak Update.  
  Theel Elitza S et al. Journal of clinical microbiology 2018 Jan
• ViroFind: A novel target-enrichment deep-sequencing platform reveals a complex JC virus population in the brain of PML patients.  
  Chalkias Spyros et al. PloS one 2018 (1) e0186945
• First detection of Cryptosporidium DNA in blood and cerebrospinal fluid of HIV-infected patients.  
  Velásquez Jorge Néstor et al. Parasitology research 2018 Feb
• Breathprinting Reveals Malaria-Associated Biomarkers and Mosquito Attractants.  
  Schaber Chad L et al. The Journal of infectious diseases 2018 Feb
• Converging Human and Malaria Vector Diagnostics with Data Management towards an Integrated Holistic One Health Approach.  
  Mitsakakis Konstantinos et al. International journal of environmental research and public health 2018 Feb (2)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018  
  Skowronski DM, et al. Eurosurveillance, Feb 5, 2018. 

HOST-MICROBE INTERACTIONS

• Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors.  
  Dada Nsa et al. Scientific reports 2018 Feb (1) 2084 
• Carriage of Cronobacter sakazakii in the very preterm infant gut.  
  Chandrasekaran Sukantha et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jan
• Intestinal microbiota development and gestational age in preterm neonates.  
  Korpela Katri et al. Scientific reports 2018 Feb (1) 2453
• The Role of Gut Microbiome and Associated Metabolome in the Regulation of Neuroinflammation in Multiple Sclerosis and Its Implications in Attenuating Chronic Inflammation in Other Inflammatory and Autoimmune Disorders.  
  Dopkins Nicholas et al. Immunology 2018 Feb
• Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations.  
  Mayhew David et al. Thorax 2018 Jan
• Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study.  
  Jia Peilin et al. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2017 Jun (4) 413-426

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