Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Mar 28, 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
• Host-Microbe Interactions

NEWS

• Antibiotic Resistance in European Wastewater Microbes Coincides with Regional Clinical Resistance
  GenomeWeb, Mar 27, 2019.
• How a Nigerian genome team contained a Lassa fever outbreak with international partners
  Zarley BD. Quartz, Mar 27, 2019.
• Proteomic Test to Diagnose, Differentiate Zika, Dengue Developed by A*STAR Team
  360dx, Mar 20, 2019.
• Allele Shows Pyrethroid Resistance’s Spread in African Mosquitos
  Wilke C. The Scientist, Mar 22, 2019.
• Spontaneous Preterm Birth Clues Identified in Cervicovaginal Microbiome
  GenomeWeb, Mar 22, 2019.
• New Human Genome Reference Projects Combine Long Nanopore Reads, Other Data Types
  Karow J. GenomeWeb, Mar 26, 2019.

EVENTS / TRAINING / WEB RESOURCES

• NCBI Computational Virology Workshop at LSU New Orleans!
  (announcement) NCBI, Mar 27, 2019. Application deadline Apr 5, 2019.
• Innovative teaching in the digital age goes viral.
  Gomez-Lucia Esperanza et al. Nature microbiology 2019 Apr (4) 562-564

CONCEPTS / COMMENTS

• Evolving resistance to pathogens
  Miller IF, Metcalf JE. Science, Mar 22, 2019.
• Artificial intelligence can improve decision-making in infection management
  Rawson TM, et al. Nat Comm, Mar 25, 2019.
• A powerful, non-invasive test to rule out infection.
  O'Grady Justin et al. Nature microbiology 2019 Apr (4) 554-555
• Talking about a microbiome revolution.
  Cryan John F et al. Nature microbiology 2019 Apr (4) 552-553
• The use of genomic DNA sequences as type material for valid publication of bacterial species names will have severe implications for clinical microbiology and related disciplines
  Bisgaard M, et al. Diagn Microbiol Infect Dis, Mar 22, 2019.

METHODS / TOOLS

• Methodology for whole genome sequencing of MRSA in a routine hospital microbiology laboratory.
  Raven Kathy E et al. Journal of clinical microbiology 2019 Mar 
• Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.
  Clarke Erik L et al. Microbiome 2019 Mar (1) 46
• High-throughput screening of bacterial pathogens in clinical specimens using 16S rDNA qPCR and fragment analysis.
  Wagner K et al. Diagnostic microbiology and infectious disease 2019 Apr (4) 287-292
• Visual tools to assess the plausibility of algorithm-identified infectious disease clusters: an application to mumps data from the Netherlands dating from January 2009 to June 2016.
  Soetens Loes et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Mar (12)
• Transmission trees on a known pathogen phylogeny: enumeration and sampling.
  Hall Matthew et al. Molecular biology and evolution 2019 Mar
• Cluster-transition determining sites underlying the antigenic evolution of seasonal influenza viruses.
  Quan Lijun et al. Molecular biology and evolution 2019 Mar

EVOLUTION / ECOLOGY / POPULATIONS

• Klebsiella quasipneumoniae provides a window into carbapenemase gene transfer, plasmid rearrangements and patient interactions with the hospital environment.
  Mathers Amy J et al. Antimicrobial agents and chemotherapy 2019 Mar
• Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns.
  Fogelson Susan B et al. PloS one 2019 (3) e0214274
• Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010-2018.
  Arana Ainara et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Mar
• Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1.
  Forth Jan H et al. Emerging infectious diseases 2019 Jun (6)
• Sequential Emergence and Wide Spread of Neutralization Escape Middle East Respiratory Syndrome Coronavirus Mutants, South Korea, 2015.
  Kim Yeon-Sook et al. Emerging infectious diseases 2019 Jun (6)
• G1P[8] Rotavirus in children with severe diarrhea in the post-vaccine introduction era in Brazil: Evidence of reassortments and structural modifications of the antigenic VP7 and VP4 regions.
  Santos F S et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Apr 255-266 
• Expansion of urban cutaneous leishmaniasis into rural areas of southeastern Iran: Clinical, epidemiological and phylogenetic profiles explored using 7SL high resolution melting-PCR analysis.
  Razavinasab Seyed Zia et al. Transboundary and emerging diseases 2019 Mar
• Mosquito microevolution drives Plasmodium falciparum dynamics.
  Gildenhard Markus et al. Nature microbiology 2019 Mar 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.
  Gouliouris Theodore et al. Genome research 2019 Mar
• Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States.
  Mendes Rodrigo E et al. Open forum infectious diseases 2019 Mar (Suppl 1) S69-S78
• Characterization of novel Mycobacterium tuberculosis pncA gene mutations in clinical isolates from the Ukraine.
  Daum L T et al. Diagnostic microbiology and infectious disease 2019 Apr (4) 334-338
• Study of the underlying mechanisms and consequences of pathogenicity differences between two in vitro selected G1-H9N2 clones originating from a single isolate.
  Nguyen Giang Thu et al. Veterinary research 2019 Mar (1) 18
• Efficacy and safety of artemether-lumefantrine for the treatment of uncomplicated malaria and prevalence of Pfk13 and Pfmdr1 polymorphisms after a decade of using artemisinin-based combination therapy in mainland Tanzania.
  Ishengoma Deus S et al. Malaria journal 2019 Mar (1) 88  
• A cytochrome P450 allele confers pyrethroid resistance on a major African malaria vector, reducing insecticide-treated bednet efficacy.
  Weedall Gareth D et al. Science translational medicine 2019 Mar (484)

DETECTION / DIAGNOSIS

• Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping.
  Talamantes-Becerra Berenice et al. Journal of microbiological methods 2019 Mar 11-19
• Different Resolution Power of Multilocus Variable-Number Tandem Repeat Analysis and Whole-Genome Sequencing in the Characterization of S. 1,4,[5],12:i:- Isolates.
  Petrin Sara et al. Foodborne pathogens and disease 2019 Mar
• Clinical utility of pan-microbial PCR assays in the routine diagnosis of infectious diseases.
  Khoury Nardeen et al. Diagnostic microbiology and infectious disease 2019 Mar (3) 232-237 
• Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease.
  Tembo John et al. Expert review of molecular diagnostics 2019 Mar
• GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics.
  Pezzi L et al. Antiviral research 2019 Mar
• Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection.
  Li Tengguo et al. BMC genomics 2019 Mar (1) 231 
• Molecular Strategies to Diagnose Mucormycosis.
  Millon Laurence et al. Journal of fungi (Basel, Switzerland) 2019 Mar (1)
• Field evaluation of malaria malachite green loop-mediated isothermal amplification in health posts in Roraima state, Brazil.
  Kudyba Heather M et al. Malaria journal 2019 Mar (1) 98
• Development of a SNP barcode to genotype Babesia microti infections.
  Baniecki Mary Lynn et al. PLoS neglected tropical diseases 2019 Mar (3) e0007194

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Next-generation sequencing based hospital outbreak investigation yields insight into Klebsiella aerogenes population structure and determinants of carbapenem resistance and pathogenicity.
  Malek Adel et al. Antimicrobial agents and chemotherapy 2019 Mar
• An unusual case of Erysipelothrix rhusiopathiae prosthetic joint infection from the Canadian Arctic: whole genome sequencing unable to identify a zoonotic source.
  Groeschel Michael et al. BMC infectious diseases 2019 Mar (1) 282
• Transmission patterns of HIV-1 non-R5 strains in Poland.
  Smolen-Dzirba Joanna et al. Scientific reports 2019 Mar (1) 4970
• Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions.
  Kostaki Evangelia-Georgia et al. Frontiers in microbiology 2019 370
• Notes from the Field: HIV Diagnoses Among Persons Who Inject Drugs - Northeastern Massachusetts, 2015-2018.
  Cranston Kevin et al. MMWR. Morbidity and mortality weekly report 2019 Mar (10) 253-254  

HOST-MICROBE INTERACTIONS

• Transmission of human-associated microbiota along family and social networks.
  Brito Ilana L et al. Nature microbiology 2019 Mar
• Structural variation in the gut microbiome associates with host health
  Zheevi D, et al. Nature, March 27, 2019.
• Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response.
  Montoya Dennis J et al. Cell reports 2019 Mar (13) 3574-3585.e3
• Potential immune escape mutations under inferred selection pressure in HIV-1 strains circulating in Medellín, Colombia.
  Arcia David et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Apr 267-278
• Association between IL1 gene polymorphism and human African trypanosomiasis in populations of sleeping sickness foci of southern Cameroon.
  Ofon Elvis et al. PLoS neglected tropical diseases 2019 Mar (3) e0007283

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.