Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Nov 21, 2019

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

• Mailing free home HIV tests helps detect more infections
  Tanner L. AP, Nov 18, 2019.

POLICY

• Sequence and destroy: the quest to eliminate the last stocks of deadly rinderpest virus.
  Butler Declan et al. Nature 2019 08 (7767) 18

CONCEPTS / COMMENTS

• Precision Medicine and Mysteries in Clinical Microbiology: Rationalizing Epidemiology, Genotype and Phenotype to Guide Therapeutics.
  Perez Federico et al. Antimicrobial agents and chemotherapy 2019 Nov
• Fecal Microbiota Transplantation for Dysbiosis - Predictable Risks.
  Blaser Martin J et al. The New England journal of medicine 2019 Nov (21) 2064-2066
• Biomarkers of Infection and Sepsis.
  Opal Steven M et al. Critical care clinics 2020 Jan (1) 11-22
• Biological challenges of phage therapy and proposed solutions: a literature review.
  Caflisch Katherine M et al. Expert review of anti-infective therapy 2019 Nov
• Antibiotics: past, present and future.
  Hutchings Matt et al. Current opinion in microbiology 2019 Nov 72-80

METHODS / TOOLS

• Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO.
  Wilcox Alexander H et al. Microbial genomics 2019 Nov
• Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs.
  Hopken Matthew W et al. Journal of virological methods 2019 Nov 113777
• DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples.
  Alawi Malik et al. Scientific reports 2019 Nov (1) 16841
• ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum.
  Pillonel Trestan et al. Nucleic acids research 2019 Oct
• mNGS in clinical microbiology laboratories: on the road to maturity.
  Han Dongsheng et al. Critical reviews in microbiology 2019 Nov 1-18 
• Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics.
  Hicks Allison L et al. PLoS biology 2019 Nov (11) e3000547
• Predicting the secondary structure of globular proteins using neural network models.
  Qian N et al. Journal of molecular biology 1988 Aug (4) 865-84

EVOLUTION / ECOLOGY / POPULATIONS

• Whole-genome sequencing identifies highly related Pseudomonas aeruginosa strains in multiple washbasin U-bends at several locations in one hospital: evidence for trafficking of potential pathogens via wastewater pipes.
  Moloney E M et al. The Journal of hospital infection 2019 Nov
• Presence of Legionella spp. in cooling towers: the role of microbial diversity, Pseudomonas, and continuous chlorine application.
  Paranjape Kiran et al. Water research 2019 Nov 115252
• Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens.
  Weigand Michael R et al. mSystems 2019 Nov (6) 
• Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species.
  Wassenaar Trudy M et al. MicrobiologyOpen 2019 Nov e973
• Recombination between Vaccine and Field Strains of Porcine Reproductive and Respiratory Syndrome Virus.
  Wang Anping et al. Emerging infectious diseases 2019 12 (12) 2335-2337
• Introduction of Avian Influenza A(H6N5) Virus into Asia from North America by Wild Birds.
  Jeong Sol et al. Emerging infectious diseases 2019 11 (11) 2138-2140
• Epidemiologic, Entomologic, and Virologic Factors of the 2014-15 Ross River Virus Outbreak, Queensland, Australia.
  Jansen Cassie C et al. Emerging infectious diseases 2019 12 (12) 2243-2252
• A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.
  Farrer Rhys A et al. mBio 2019 Nov (6)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus.
  Coe Kathryn A et al. PLoS pathogens 2019 Nov (11) e1007862
• Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.
  Robertson James et al. PloS one 2019 (11) e0218638
• Complex Class 1 Integron in a Clinical Escherichia coli Strain From Vietnam Carrying Both mcr-1 and bla NDM-1 .
  Le-Vo Hong-Ngoc et al. Frontiers in microbiology 2019 2472
• The Global Ascendency of OXA-48-Type Carbapenemases.
  Pitout Johann D D et al. Clinical microbiology reviews 2019 Dec (1)
• Molecular mechanism of azithromycin resistance among typhoidal Salmonella stains in Bangladesh identified through passive pediatric surveillance.
  Hooda Yogesh et al. PLoS neglected tropical diseases 2019 Nov (11) e0007868
• CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae.
  Mackow Natalie A et al. PloS one 2019 (11) e0225131
• Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016.
  French Nigel P et al. Emerging infectious diseases 2019 12 (12) 2226-2234
• Canine Distemper Virus in Asiatic Lions of Gujarat State, India.
  Mourya Devendra T et al. Emerging infectious diseases 2019 11 (11) 2128-2130

DETECTION / DIAGNOSIS

• A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification.
  Doster Enrique et al. Frontiers in microbiology 2019 2499
• Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids.
  Sydenham Thomas V et al. Microbial genomics 2019 Nov
• Hepatitis C Virus among Female Sex Workers: A Cross-Sectional Study Conducted along Rivers and Highways in the Amazon Region.
  Oliveira-Filho Aldemir B et al. Pathogens (Basel, Switzerland) 2019 Nov (4)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Genetic relationship between bacteria isolated from intraoperative air samples and surgical site infections at a major teaching hospital in Ghana.
  Stauning Marius Ahm et al. The Journal of hospital infection 2019 Nov
• Short communication: Multistate outbreak of Listeria monocytogenes infections retrospectively linked to unpasteurized milk using whole-genome sequencing.
  Nichols Megin et al. Journal of dairy science 2019 Nov  
• A multi-species cluster of GES-5 carbapenemase producing Enterobacterales linked by a geographically disseminated plasmid.
  Ellington Matthew J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov 
• Opioid Use Fueling HIV Transmission in an Urban Setting: An Outbreak of HIV Infection Among People Who Inject Drugs-Massachusetts, 2015-2018.
  Alpren Charles et al. American journal of public health 2019 Nov e1-e8  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination.
  Ryt-Hansen Pia et al. PloS one 2019 (11) e0224854 
• Novel gRNA design pipeline to develop broad-spectrum CRISPR/Cas9 gRNAs for safe targeting of the HIV-1 quasispecies in patients.
  Sullivan Neil T et al. Scientific reports 2019 Nov (1) 17088

HOST-MICROBE INTERACTIONS

• The seminal microbiome in health and disease.
  Altmäe Signe et al. Nature reviews. Urology 2019 Nov
• Gut mycobiota under scrutiny: fungal symbionts or environmental transients?
  Fiers William D et al. Current opinion in microbiology 2019 Nov 79-86
• Longitudinal multi-omics of host-microbe dynamics in prediabetes.
  Zhou Wenyu et al. Nature 2019 05 (7758) 663-671
• Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study.
  Lindfors Katri et al. Gut 2019 Nov
• Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer.
  Astudillo-de la Vega H et al. Advances in experimental medicine and biology 2019 147-156

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.