Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Apr 4, 2019

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

• Genetic sleuthing reveals rapid evolution of MDR Klebsiella outbreak
  Dall C. CIDRAP, Apr 3, 2019.
• Virus tricks the immune system into ignoring bacterial infections
  Reardon S. Nature, Mar 28, 2019.
• Phase I Trial for 'Universal' Flu Vax To Begin
  Walker M. MedPage Today, Apr 3, 2019.
• Cannabis Testing Labs Adopt Molecular Methods as Throughput, Sample Diversity Skyrocket
  Johnson M. GenomeWeb, Mar 22, 2019.
• OMICS International Fined Over $50 Million for “Deceptive Practices”
  Hou CY. The Scientist, Apr 4, 2019.
• FDA developing new rules for artificial intelligence in medicine 
  Ross C. STAT, Apr 2, 2019.

EVENTS / TRAINING / WEB RESOURCES

• Welcome to the Antimicrobial Resistance Call for Papers!
  (announcement) PLoS cross-journal call for papers. Submissions due June 28, 2019.
• Women-led Biodata Science Hackathon May 8-10, 2019
  (announcement) NCBI, Apr 2, 2019. Applications due Apr 22, 2019.
• Scientific Writing Seminar
  (training) CDC Library, Apr 11, 2019, 1:00-2:00 pm. Bldg 19, Conf Rm 139. Join via Skype: (404) 553-8912 Conference ID: 7729017

CONCEPTS / COMMENTS

• Legionella transmission through cooling towers: towards better control and research of a neglected pathogen.
  Paschke Anne et al. The Lancet. Respiratory medicine 2019 Mar
• Acute Flaccid Myelitis: Something Old and Something New
  Morens DM, et al. mBio, Apr 2, 2019.
• "Integration of viral sequences into eukaryotic host genomes: legacy of ancient infections".
  Tomonaga Keizo et al. Virus research 2019 03 1
• Microbiome-MX 2018: Microbiota and Microbiome opportunities in Mexico, a megadiverse country.
  Cornejo-Granados Fernanda et al. Research in microbiology 2019 Mar
• In praise of preprints.
  Fry Norman K et al. Microbial genomics 2019 Apr

METHODS / TOOLS

• Illumina sequencing of clinical samples for virus detection in a public health laboratory.
  Huang Bixing et al. Scientific reports 2019 Apr (1) 5409 
• The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
  Gweon HS, et al. bioRxiv, Mar 31, 2019.
• Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants.
  Banin Andrew N et al. Viruses 2019 Apr (4)
• rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.
  Wailan Alexander M et al. Microbial genomics 2019 Mar
• PlotsOfData-A web app for visualizing data together with their summaries.
  Postma Marten et al. PLoS biology 2019 Mar (3) e3000202
• Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.
  Campbell Finlay et al. PLoS computational biology 2019 Mar (3) e1006930

EVOLUTION / ECOLOGY / POPULATIONS

• Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains.
  van Dorp Lucy et al. Microbial genomics 2019 Apr
• Did new transmission cycles in anthropogenic, dense, host populations encourage the emergence and speciation of pathogenic Bordetella?
  Dewan Kalyan K et al. PLoS pathogens 2019 03 (3) e1007600
• Phylodynamic and Evolutionary analysis of Rotavirus G12 in Africa
  Motayo BO, et al. bioRxiv, Mar 28, 2019.
• Extracellular vesicles: vehicles of en bloc viral transmission.
  Altan-Bonnet Nihal et al. Virus research 2019 Mar
• A novel Babesia sp. associated with clinical signs of babesiosis in domestic cats in South Africa.
  Bosman Anna-Mari et al. Parasites & vectors 2019 Mar (1) 138

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017.
  González-Escalona Narjol et al. PloS one 2019 (4) e0214620
• Listeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential.
  Smith Alva et al. International journal of food microbiology 2019 Mar 23-32
• Emergence of Neisseria gonorrhoeae Strains Harboring a Novel Combination of Azithromycin-Attenuating Mutations.
  Pham Cau D et al. Antimicrobial agents and chemotherapy 2019 Apr (4)  
• In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance.
  Dengler Haunreiter Vanina et al. Nature communications 2019 03 (1) 1149
• Comparison of HSV-1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection.
  Bowen Christopher D et al. Journal of virology 2019 Feb
• Effect of Plasmodium falciparum sulfadoxine-pyrimethamine resistance on the effectiveness of intermittent preventive therapy for malaria in pregnancy in Africa: a systematic review and meta-analysis.
  van Eijk Anna Maria et al. The Lancet. Infectious diseases 2019 Mar  

DETECTION / DIAGNOSIS

• Machine Learning-Assisted Digital PCR and Melt Enables Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test
  Athamanolap P, et al. bioRxiv, Mar 24, 2019.
• Multistate Survey of American Dog Ticks (Dermacentor variabilis) for Rickettsia Species.
  Hecht Joy A et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2019 Apr  
• Surveillance to Track Progress Toward Polio Eradication — Worldwide, 2017–2018
  Patel JC, et al. MMWR, Apr 5, 2019.  
• Mitigating Pandemic Risk with Influenza A Virus Field Surveillance at a Swine-Human Interface
  Rambo-Martin BL, et al. bioRxiv, Mar 21, 2019.  
• Prion protein quantification in human cerebrospinal fluid as a tool for prion disease drug development.
  Vallabh Sonia M et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Apr
• DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species.
  M Hernández-Triana Luis et al. ZooKeys 2019 57-76

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Outbreak of Methicillin-resistant Staphylococcus aureus in a Hospital Center for Children's and Women's Health in a Swedish County.
  Gideskog Maria et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2019 Apr (4) 181-186
• Clonal expansion of community-associated meticillin-resistant Staphylococcus aureus (MRSA) in people who inject drugs (PWID): prevalence, risk factors and molecular epidemiology, Bristol, United Kingdom, 2012 to 2017.
  Packer Simon et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Mar (13)
• Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019.
  Jones Gabrielle et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Mar (13) 
• Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis.
  Guthrie Jennifer L et al. PloS one 2019 (4) e0214870 
• 2017 Outbreak of Ebola Virus Disease in Northern Democratic Republic of Congo.
  Nsio Justus et al. The Journal of infectious diseases 2019 Apr
• Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
  Ratmann Oliver et al. Nature communications 2019 03 (1) 1411

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.
  Magaret Craig A et al. PLoS computational biology 2019 Apr (4) e1006952

HOST-MICROBE INTERACTIONS

• Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases.
  Sanna Serena et al. Nature genetics 2019 Apr (4) 600-605
• The human microbiota is associated with cardiometabolic risk across the epidemiologic transition
  Fei N, et al. bioRxiv, Apr 1, 2019.
• Identification and evaluation of the microbiome in the female and male reproductive tracts.
  Koedooder Rivka et al. Human reproduction update 2019 Feb
• Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
  Wirbel Jakob et al. Nature medicine 2019 Apr

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.