Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 3, 2019

Advanced Molecular Detection Clips Content

• News
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Q&A: BARDA Director Rick Bright Discusses New Programs, Focus on Diagnostics
  Johnson M. GenomeWeb, Sep 30, 2019.
• Plague Genomes Reveal How Pandemic Spread in 14th, 18th Centuries
  GenomeWeb, Oct 2, 2019.
• Bacteria are likely hiding in your household washing machine
  LaMotte S. CNN, Sep 28, 2019.
• A germ from a dog's mouth led to amputation. Researchers blamed a gene change
  AP, Los Angeles Times, Sep 26, 2019.
• With C. Auris Proliferating, NYSDOH Wadsworth Center to Fund Device Development for POC Tests
  Johnson M. 360dx, Sep 25, 2019.
• Tsunamis linked to spread of deadly fungal disease
  McGrath M. BBC News, Oct 2, 2019.
• Emerging parasitic disease mimics the symptoms of visceral leishmaniasis in people
  (news release) NIAID via EurekAlert, Oct 1, 2019.
• Error in Study Linking HIV Resistance Gene to Increased Mortality
  Makowski E. The Scientist, Sep 30, 2019.

CONCEPTS / COMMENTS

• Technology to advance infectious disease forecasting for outbreak management.
  George Dylan B et al. Nature communications 2019 Sep (1) 3932 
• Data standards may be wonky, but they will transform health care
  Mandl KD, Kohane IS. STAT, Oct 3, 2019.
• On the Emergence of Cryptococcus gattii in the Pacific Northwest: Ballast Tanks, Tsunamis, and Black Swans.
  Engelthaler David M et al. mBio 2019 Oct (5)
• ANTIBIOTIC RESISTANT BACTERIA IN WILDLIFE: PERSPECTIVES ON TRENDS, ACQUISITION AND DISSEMINATION, DATA GAPS, AND FUTURE DIRECTIONS.
  Ramey Andrew M et al. Journal of wildlife diseases 2019 Sep
• How to meet your 'silent partner': tips for approaching editors at conferences.
  Yao Yixin et al. Genome biology 2019 Sep (1) 200
• Novelist Cormac McCarthy's tips on how to write a great science paper
  Savage V, Yeh P. Nature, Sep 26, 2019.

METHODS / TOOLS

• Evolution of biosequence search algorithms: a brief survey.
  Kucherov Gregory et al. Bioinformatics (Oxford, England) 2019 Oct (19) 3547-3552
• Bit-parallel sequence-to-graph alignment.
  Rautiainen Mikko et al. Bioinformatics (Oxford, England) 2019 Oct (19) 3599-3607
• Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections.
  Huang Weihua et al. Microorganisms 2019 Sep (10)
• Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.
  Ali Raja Hashim et al. Molecular biology and evolution 2019 Oct (10) 2340-2351
• SHERLOCK: nucleic acid detection with CRISPR nucleases.
  Kellner Max J et al. Nature protocols 2019 Oct (10) 2986-3012
• Targeted isolation and cultivation of uncultivated bacteria by reverse genomics.
  Cross Karissa L et al. Nature biotechnology 2019 Sep
• Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci.
  Janes Victoria A et al. Antimicrobial resistance and infection control 2019 153
• Incorporating Statistical Test and Machine Intelligence Into Strain Typing of Staphylococcus haemolyticus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.
  Chung Chia-Ru et al. Frontiers in microbiology 2019 2120
• Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2.
  Hamidian Mohammad et al. Microbial genomics 2019 Sep
• Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies.
  Jones Rhys et al. Tuberculosis (Edinburgh, Scotland) 2019 Sep 101865
• A Fully Integrated Real-Time Detection, Diagnosis, and Control of Community Diarrheal Disease Clusters and Outbreaks (the INTEGRATE Project): Protocol for an Enhanced Surveillance System.
  McIntyre Kirsty Marie et al. JMIR research protocols 2019 Sep (9) e13941
• Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing
  Doyle SR, et al. Front Genet, Sep 20, 2019. 

EVOLUTION / ECOLOGY / POPULATIONS

• Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes
  Spyrou MA, et al. Nat Commun, Oct 2, 2019.
• Genetic diversity of respiratory enteroviruses and rhinoviruses in febrile adults, Singapore, 2007-2013.
  Linster Martin et al. Influenza and other respiratory viruses 2019 Sep
• Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted?
  Coleman Kristen K et al. The Journal of infectious diseases 2019 Sep
• Isolation and characterization of Akhmeta virus from wild caught rodents ( Apodemus spp.) in Georgia.
  Doty Jeffrey B et al. Journal of virology 2019 Sep 
• Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation.
  Hill Sarah C et al. The Lancet. Infectious diseases 2019 Oct (10) 1138-1147
• A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.
  Skittrall Jordan P et al. PLoS computational biology 2019 Sep (9) e1007345
• Ecological indicators of mammal exposure to Ebolavirus.
  Schmidt John Paul et al. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2019 Sep (1782) 20180337

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Risk Factors for Long-Term Vancomycin-Resistant Enterococci Persistence-A Prospective Longitudinal Study.
  Correa-Martinez Carlos L et al. Microorganisms 2019 Sep (10)
• Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems.
  Rovira Pablo et al. Frontiers in microbiology 2019 1980
• Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.
  Arimizu Yoko et al. Genome research 2019 Sep (9) 1495-1505
• Campylobacter species prevalence, characterisation of antimicrobial resistance and analysis of whole-genome sequence of isolates from livestock and humans, Latvia, 2008 to 2016.
  Meistere Irena et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Aug (31)
• Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.
  Golumbeanu Monica et al. Cell reports 2018 04 (4) 942-950
• Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019.
  Takashita Emi et al. Emerging infectious diseases 2019 Nov (11)
• High frequency of drug resistance mutations in the HBV genome in ART-experienced HIV-coinfected patients in southwestern Nigeria.
  Akanbi Olusola Anuoluwapo et al. Antiviral therapy 2019 Sep
• Is the Bombali virus pathogenic in humans?
  Martell Henry J et al. Bioinformatics (Oxford, England) 2019 Oct (19) 3553-3558

DETECTION / DIAGNOSIS

• Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing.
  Crawford Emily et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Sep
• Identification of Gram negative non-fermentative bacteria: How hard can it be?
  Whistler Toni et al. PLoS neglected tropical diseases 2019 Sep (9) e0007729 
• Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data
  Deelder W, et al. Front Genet, Sep 26, 2019.
• One-step pentaplex real-time polymerase chain reaction assay for detection of zika, dengue, chikungunya, West nile viruses and a human housekeeping gene.
  Mishra Nischay et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 Sep 44-50
• Rapid diagnosis of invasive candidiasis: ready for prime-time?
  Clancy Cornelius J et al. Current opinion in infectious diseases 2019 Sep 
• The Diagnosis of Fungal Neglected Tropical Diseases (Fungal NTDs) and the Role of Investigation and Laboratory Tests: An Expert Consensus Report.
  Hay Roderick et al. Tropical medicine and infectious disease 2019 Sep (4) 
• Discrimination of Aspergillus flavus from Aspergillus oryzae by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass-spectrometry.
  Hedayati Mohammad T et al. Mycoses 2019 Sep
• Non-Leishmania Parasite in Fatal Visceral Leishmaniasis-like Disease, Brazil
  Marayuma SR, et al. Emerg Infect Dis, 25(11) Nov 2019.
• A Case for Using Genomics and a Bioinformatics Pipeline to Develop Sensitive and Species-Specific PCR-Based Diagnostics for Soil-Transmitted Helminths
  Grant JR, et al. Front Genet, Sep 23, 2019. 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• The washing machine as a reservoir for transmission of extended spectrum beta-lactamase (CTX-M-15)-producing Klebsiella oxytoca ST201 in newborns.
  Schmithausen Ricarda M et al. Applied and environmental microbiology 2019 Sep 
• Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden.
  Sacchini Lorena et al. Microorganisms 2019 Sep (10)
• An outbreak of multiple genotypes of Listeria monocytogenes in New Zealand linked to contaminated ready-to-eat meats - a retrospective analysis using whole genome sequencing.
  Rivas Lucia et al. Letters in applied microbiology 2019 Sep
• Notes from the Field: Multistate Outbreak of Salmonella Agbeni Associated with Consumption of Raw Cake Mix - Five States, 2018.
  Ladd-Wilson Stephen G et al. MMWR. Morbidity and mortality weekly report 2019 Aug (34) 751-752  
• Multistate outbreaks of Salmonella infections linked to imported Maradol papayas - United States, December 2016-September 2017.
  Hassan R et al. Epidemiology and infection 2019 Sep e265  
• Listeriosis outbreak likely due to contaminated liver pâté consumed in a tavern, Austria, December 2018.
  Cabal Adriana et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Sep (39)
• New HIV-1 circulating recombinant form 94: from phylogenetic detection of a large transmission cluster to prevention in the age of geosocial-networking apps in France, 2013 to 2017.
  Wirden Marc et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Sep (39)
• Low prevalence of transmitted HIV-1 drug resistance detected by a dried blood spot (DBS)-based next-generation sequencing (NGS) method in newly diagnosed individuals in Cameroon in the years 2015-16.
  Mbunkah Herbert A et al. The Journal of antimicrobial chemotherapy 2018 07 (7) 1917-1929
• High prevalence of norovirus GII.P16/GII.2 and chicken anemia virus in two acute gastroenteritis outbreaks in Huzhou, China.
  Li Y et al. Acta virologica 2019 (3) 328-332
• Rapid Identification and Investigation of an HIV Risk Network Among People Who Inject Drugs -Miami, FL, 2018.
  Tookes Hansel et al. AIDS and behavior 2019 Sep  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection.
  Kaczorowska Joanna et al. Viruses 2019 Sep (10)

HOST-MICROBE INTERACTIONS

• The Need to Focus on Therapy Instead of Associations.
  Reid Gregor et al. Frontiers in cellular and infection microbiology 2019 327
• Regional Diversity of the Gastrointestinal Microbiome.
  Martinez-Guryn Kristina et al. Cell host & microbe 2019 09 (3) 314-324

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.