Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Sep 26, 2019

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

• As Made-To-Order DNA Gets Cheaper, Keeping It Out Of The Wrong Hands Gets Harder
  Greenfield Boyce N. NPR, Sep 24, 2019.
• How Canadian investigators use DNA to track down contaminated food
  Burke D. CBC, Sep 21, 2019.
• Pushback on Mosquito Paper
  GenomeWeb, Sep 18, 2019.
• Bat influenza viruses possess an unexpected genetic plasticity
  Univ Freiburg, Sep 17, 2019.
• Babies Born by C-Section More Likely to Carry Opportunistic Pathogens in Gut Microbiome
  GenomeWeb, Sep 18, 2019.

EVENTS / TRAINING / WEB RESOURCES

• Biomedical Discovery through SRA and the Cloud
  (blog post) Ostell J. NLM, Sep 24, 2019.

CONCEPTS / COMMENTS

• Workflow systems turn raw data into scientific knowledge
  Perkel JM. Nature, Sep 2, 2019.
• Emerging Use of CRISPR Technology - Chasing the Elusive HIV Cure.
  June Carl H et al. The New England journal of medicine 2019 Sep (13) 1281-1283
• Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook.
  Ghansah Anita et al. Malaria journal 2019 Sep (1) 324
• The future of faecal transplants
  Giles EM, et al. Nat Rev Microbiol, Sep 18, 2019.

METHODS / TOOLS

• NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.
  Connor Ryan et al. Genes 2019 Sep (9) 
• Using Genomics to Track Global Antimicrobial Resistance.
  Hendriksen Rene S et al. Frontiers in public health 2019 242 
• SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
  Zhang Shaokang et al. Applied and environmental microbiology 2019 Sep 
• Targeted Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis cultures using Illumina MiSeq and Nanopore MinION: Comparison of analytical and diagnostic performance, turnaround time and cost
  Tafess K, bioRxiv, Sep 8, 2019.
• Improving the usability and comprehensiveness of microbial databases
  Loeffler C, et al. bioRxiv, Sep 26, 2019. 
• A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
  Almeida A, et al. bioRxiv, Sep 19, 2019.

EVOLUTION / ECOLOGY / POPULATIONS

• Presence and Diversity of Extended-Spectrum Cephalosporin Resistance Among Escherichia coli from Urban Wastewater and Feedlot Cattle, in Alberta, Canada.
  Cormier Ashley C et al. Microbial drug resistance (Larchmont, N.Y.) 2019 Sep
• Genomic characterization of novel Neisseria species.
  Diallo Kanny et al. Scientific reports 2019 Sep (1) 13742
• A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.
  Ajawatanawong Pravech et al. Scientific reports 2019 Sep (1) 13718
• Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica .
  Fong Karen et al. Viruses 2019 Sep (9)
• On the Fly: Interactions Between Birds, Mosquitoes, and Environment That Have Molded West Nile Virus Genomic Structure Over Two Decades.
  Duggal Nisha K et al. Journal of medical entomology 2019 Sep 
• Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast.
  Kaufer Alexa et al. Pathogens (Basel, Switzerland) 2019 Sep (3)
• The genetic structure of Aedes aegypti populations is driven by boat traffic in the Peruvian Amazon.
  Guagliardo Sarah Anne J et al. PLoS neglected tropical diseases 2019 Sep (9) e0007552

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Antimicrobial susceptibility and molecular characterisation using whole-genome sequencing of Clostridioides difficile collected in 82 hospitals in Japan between 2014 and 2016.
  Aoki Kotaro et al. Antimicrobial agents and chemotherapy 2019 Sep
• An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.
  Van Puyvelde Sandra et al. Nature communications 2019 Sep (1) 4280
• Tracing local and regional clusters of carbapenemase-producing Klebsiella pneumoniae ST512 with whole genome sequencing, Finland, 2013 to 2018.
  van Beek Janko et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Sep (38)
• Dynamic Emergence of Mismatch Repair Deficiency Facilitates Rapid Evolution of Ceftazidime-Avibactam Resistance in Pseudomonas aeruginosa Acute Infection.
  Khil Pavel P et al. mBio 2019 Sep (5)
• An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa.
  Huang Hao et al. Nature communications 2019 07 (1) 2931
• Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids.
  Kiu Raymond et al. Microbial genomics 2019 Sep
• A case report of HIV-1 superinfection in an HIV controller leading to loss of viremia control: a retrospective of 10 years of follow-up.
  Caetano Diogo Gama et al. BMC infectious diseases 2019 Jul (1) 588
• Comparative genomics for the elucidation of multidrug resistance (MDR) in Candida lusitaniae
  Kannan A, et al. bioRxiv, Sep 24, 2019.
• Revealing the Virulence Potential of Clinical and Environmental Aspergillus fumigatus Isolates Using Whole-Genome Sequencing.
  Puértolas-Balint Fabiola et al. Frontiers in microbiology 2019 1970

DETECTION / DIAGNOSIS

• From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics.
  Dulanto Chiang Augusto et al. The Journal of infectious diseases 2019 Sep
• Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing.
  Shevchenko Sofiya G et al. Applied and environmental microbiology 2019 Sep
• Multistate population and whole genome sequence based strain surveillance of invasive pneumococci recovered in the United States during 2017.
  Varghese Jasmine et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Sep  
• Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing.
  Gargis Amy S et al. Scientific reports 2019 Sep (1) 13501 
• A qPCR assay for Bordetella pertussis cells that enumerates both live and dead bacteria.
  Ramkissoon S, et al. bioRxiv, Sep 25, 2019.
• Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing
  Crawford E, et al. bioRxiv, Sep 16, 2019.
• Development and evaluation of LAMP-coupled lateral flow device for the detection of MAP in livestock at point of care resource-limited areas.
  Punati Rudrama Devi et al. Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2019 Sep
• RNA-based high-risk HPV genotyping and identification of high-risk HPV transcriptional activity in cervical tissues.
  van den Heuvel Corina N A M et al. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2019 Sep
• DisCVR: Rapid viral diagnosis from high-throughput sequencing data.
  Maabar Maha et al. Virus evolution 2019 Jul (2) vez033
• Prevalence of HIV-1 drug resistance amongst newly diagnosed HIV-infected infants age 4-8 weeks, enrolled in three nationally representative PMTCT effectiveness surveys, South Africa: 2010, 2011-12 and 2012-13.
  Hunt Gillian M et al. BMC infectious diseases 2019 Sep (Suppl 1) 787
• Genomes of intracellular Leishmania parasites directly sequenced from patients
  Domagalska MA, et al. bioRxiv, Sep 26, 2019.
• Rare mutations in Pfmdr1 gene of Plasmodium falciparum detected in clinical isolates from patients treated with anti-malarial drug in Nigeria.
  Idowu Abel O et al. Malaria journal 2019 Sep (1) 319
• A high throughput multi-locus insecticide resistance marker panel for tracking resistance emergence and spread in Anopheles gambiae.
  Lucas Eric R et al. Scientific reports 2019 Sep (1) 13335

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A recurrent and transesophageal echocardiography-associated outbreak of extended-spectrum β-lactamase-producing Enterobacter cloacae complex in cardiac surgery patients.
  Van Maerken Tom et al. Antimicrobial resistance and infection control 2019 152
• Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).
  Blackburn Ruth M et al. Influenza and other respiratory viruses 2019 Sep

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Tuberculosis drug discovery in the CRISPR era.
  Rock Jeremy et al. PLoS pathogens 2019 Sep (9) e1007975
• A histone methyltransferase inhibitor can reverse epigenetically acquired drug resistance in the malaria parasite Plasmodium falciparum
  Chan A, et al. bioRxiv, Sep 19, 2019.

HOST-MICROBE INTERACTIONS

• Microbiomes as sources of emergent host phenotypes
  Lynch JB, Hsiao EY. Science, Sep 27, 2019.
• Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth.
  Shao Yan et al. Nature 2019 Sep
• Formula alters preterm infant gut microbiota and increases its antibiotic resistance load
  Parnanen K, et al. bioRxiv, Sep 25, 2019.
• Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe.
  Flygel Trym T et al. The Journal of infectious diseases 2019 Sep
• Evidence that vertical transmission of the vaginal microbiota can persist into adolescence
  Bassis CM, et al. bioRxiv, Sep 16, 2019.
• The Intestinal Microbiota Contributes to the Control of Highly Pathogenic H5N9 Influenza Virus Replication in Ducks
  Figueroa T, et al. bioRxiv, Sep 24, 2019.
• Structural changes in the gut microbiome of short-term and long-term medical workers compared to normal controls
  Zheng N, et al. bioRxiv, Sep 15, 2019.
• Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.
  Ravi Anuradha et al. Microbial genomics 2019 Sep
• A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens.
  Li Xinghua et al. Genetics, selection, evolution : GSE 2019 Sep (1) 51
• Identification and characterization of SEC24D as a susceptibility gene for hepatitis B virus infection.
  Jiang Xianzhong et al. Scientific reports 2019 Sep (1) 13425

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.