Last Posted: Sep 15, 2019
Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population.
Evans Benjamin R et al. Scientific reports 2019 Sep (1) 13047
Baseline human gut microbiota profile in healthy people and standard reporting template
CH King et al, PLOS One, September 11, 2019
Scientists use gene-edited stem cells to treat HIV — with mixed success
J Lambert, Nature, September 12, 2019
A Genetic Approach to the Association Between PCSK9 and Sepsis.
Feng QiPing et al. JAMA network open 2019 Sep (9) e1911130
CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia.
Xu Lei et al. The New England journal of medicine 2019 Sep
Shotgun metagenomics: A promising new method toward diagnosing infections
S Rosen, Mayo clinic Blog, September 2019
The association of gut microbiota characteristics in Malawian infants with growth and inflammation
AW Kamng'ona et al, Scientific Reports, September 9, 2019
Outsmarting Outbreaks: Using Genomics to Track Viruses
Scripps Institute, video, September 5, 2019
Molecular imaging of bacterial infections: Overcoming the barriers to clinical translation
AA Ordonez et al, Science, September 5, 2019
Integrating a One Health approach into epidemiology to improve public policy
LH Kahn, Int J Epidemiology, August 31, 2019
The Infectious Diseases Public Health Genomics Knowledge Base (PHGKB) is an online, continuously updated, searchable database of published scientific literature, CDC resources, and other materials that address the translation of genomic discoveries into improved
Advanced Molecular Detection Clips (current edition) Published on Aug 29, 2019
Advanced Molecular Detection Clips (AMD 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.
Discovery of "hidden" outbreak hints that Zika virus can spread silently
Scripps Research, Aug 22, 2019.
A community-guided genome editing project can fight Lyme disease
Esvelt KM. STAT, Aug 22, 2019.
Gene editing to stop Lyme disease: caution is warranted
Snow A. STAT, Aug 26, 2019.
Do Fungi Play a Role in C. Diff Infection?
Walker M. MedPage Today, Aug 28, 2019.
An Ingenious Microscope Could Change How Quickly Disease Is Detected
Yong E. Atlantic, Aug 22, 2019.
CONCEPTS / COMMENTS
Genomic analysis informs malaria evolution.
Sibley Carol Hopkins et al. Science (New York, N.Y.) 2019 Aug (6455) 752-753
A roadmap for malaria research.
Winzeler Elizabeth A et al. Science (New York, N.Y.) 2019 Aug (6455) 753-754
Protozoan persister-like cells and drug treatment failure.
Barrett Michael P et al. Nature reviews. Microbiology 2019 Aug
Tiny Hidden Genes within Our Microbiome.
Mittelman Karin et al. Cell 2019 Aug (5) 1034-1035
METHODS / TOOLS
An improved nucleic acid extraction method from dried blood spots for amplification of Plasmodium falciparum kelch13 for detection of artemisinin resistance.
Zainabadi Kayvan et al. Malaria journal 2019 Jun (1) 192
Sequenceserver: a modern graphical user interface for custom BLAST databases.
Priyam Anurag et al. Molecular biology and evolution 2019 Aug
Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing.
Grützke Josephine et al. Frontiers in microbiology 2019 1805
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.
Vilne Baiba et al. Frontiers in microbiology 2019 1722
The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.
Howick Virginia M et al. Science (New York, N.Y.) 2019 Aug (6455)
EVOLUTION / ECOLOGY / POPULATIONS
Linked seasonal outbreaks of Salmonella Typhimurium among passerine birds, domestic cats and humans, Sweden, 2009 to 2016.
Söderlund Robert et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Aug (34)
Major subpopulations of Plasmodium falciparum in sub-Saharan Africa.
Amambua-Ngwa Alfred et al. Science (New York, N.Y.) 2019 Aug (6455) 813-816
Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe.
Pichler Verena et al. PLoS neglected tropical diseases 2019 Aug (8) e0007554
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Whole genome-based public health surveillance of less common STEC serovars and untypable strains identifies four novel O genotypes.
Lang Christina et al. Journal of clinical microbiology 2019 Jul
Clinical Resistome Screening of 1,110 Escherichia coli Isolates Efficiently Recovers Diagnostically Relevant Antibiotic Resistance Biomarkers and Potential Novel Resistance Mechanisms.
Volz Carsten et al. Frontiers in microbiology 2019 1671
Molecular profiling of tissue biopsies reveals unique signatures associated with streptococcal necrotizing soft tissue infections.
Thänert Robert et al. Nature communications 2019 Aug (1) 3846
Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak.
Buhl Michael et al. Frontiers in microbiology 2019 1742
Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex.
Chiner-Oms Á et al. Science advances 2019 Jun (6) eaaw3307
Molecular and Clinical Comparison of Enterovirus D68 Outbreaks among Hospitalized Children, Ohio, USA, 2014 and 2018.
Wang Huanyu et al. Emerging infectious diseases 2019 Nov (11)
SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection.
Lui Wing-Yu et al. Emerging microbes & infections 2019 (1) 662-674
DETECTION / DIAGNOSIS
Increased Clinical Specificity with Ultrasensitive Detection of Clostridioides difficile Toxins: Reduction of Overdiagnosis Compared to Nucleic Acid Amplification Tests.
Sandlund Johanna et al. Journal of clinical microbiology 2019 Aug
Improved species level clinical identification of Enterobacteriaceae through broad range dnaJ PCR and sequencing.
McLean Kathryn et al. Journal of clinical microbiology 2019 Aug
Opportunities revealed for antimicrobial stewardship and clinical practice with implementation of a rapid respiratory multiplex assay.
Weiss Zoe et al. Journal of clinical microbiology 2019 Aug
Phylogenetic Analysis of Multi-Drug Resistant Klebsiella pneumoniae Strains From Duodenoscope Biofilm: Microbiological Surveillance and Reprocessing Improvements for Infection Prevention.
Ciccozzi Massimo et al. Frontiers in public health 2019 219
Ultrasensitive Detection of Clostridioides difficile Toxins in Stool Using Single Molecule Counting Technology: Comparison with CCCNA Free Toxin Detection.
Hansen Glen et al. Journal of clinical microbiology 2019 Aug
Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region.
Kosecka-Strojek Maja et al. Frontiers in cellular and infection microbiology 2019 278
Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray.
Filippone Claudia et al. Scientific reports 2019 Aug (1) 12404
A high-throughput and multiplex microsphere immunoassay based on non-structural protein 1 can discriminate three flavivirus infections.
Tyson Jasmine et al. PLoS neglected tropical diseases 2019 Aug (8) e0007649
Cryptosporidium Genotyping for Epidemiology Tracking.
Roellig Dawn M et al. Methods in molecular biology (Clifton, N.J.) 2020 103-116
Epidemiological and molecular investigation of resurgent cutaneous leishmaniasis in Sudan.
Collis Sarah et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Aug
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Outbreaks of Salmonella illness associated with frozen raw breaded chicken products in Canada, 2015-2019.
Morton V K et al. Epidemiology and infection 2019 Aug e254
A cluster of melioidosis infections in hatchling saltwater crocodiles ( Crocodylus porosus ) resolved using genome-wide comparison of a common north Australian strain of Burkholderia pseudomallei .
Rachlin Audrey et al. Microbial genomics 2019 Aug
Multidrug-Resistant Salmonella I 4,,12:i:- and Salmonella Infantis Infections Linked to Whole Roasted Pigs from a Single Slaughter and Processing Facility.
Kawakami Vance et al. Journal of food protection 2019 Sep (9) 1615-1624
Tracking Carbapenem-Producing Klebsiella pneumoniae Outbreak in an Intensive Care Unit by Whole Genome Sequencing.
Chen Chen et al. Frontiers in cellular and infection microbiology 2019 281
Increasing incubation periods during a prolonged monophasic Salmonella Typhimurium outbreak with environmental contamination of a commercial kitchen at Oslo Airport, Norway, 2017.
Siira Lotta et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Aug (34)
Whole Genome Sequencing to Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission Within and Between Regional Long-Term Acute Care Hospitals.
Han Jennifer H et al. Antimicrobial agents and chemotherapy 2019 Aug
Genotyping Approach for Potential Common Source of Enterocytozoon bieneusi Infection in Hematology Unit.
Desoubeaux Guillaume et al. Emerging infectious diseases 2019 Sep (9) 1625-1631
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.
Grubaugh Nathan D et al. Cell 2019 Aug (5) 1057-1071.e11
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Development of a multiple-antigen protein fusion vaccine candidate that confers protection against Bacillus anthracis and Yersinia pestis.
Gallagher Theresa B et al. PLoS neglected tropical diseases 2019 Aug (8) e0007644
Comparative genomic analysis between newly sequenced Brucella abortus vaccine strain A19 and another Brucella abortus vaccine S19.
Wang Shuyi et al. Genomics 2019 Aug
First report case with negative genetic study (array CGH, exome sequencing) in patients with vertical transmission of Zika virus infection and associated brain abnormalities.
Candelo Estephania et al. The application of clinical genetics 2019 141-150
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.
Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update 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 update, 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.