Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 28, 2018

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. View Data Selection Criteria

Archived Editions
Search AMD Clips database
Visit AMD website

Advanced Molecular Detection Clips Content

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

NEWS

• Genetically modified bacteria enlisted in fight against disease  
  Reardon S. Nature, Jun 21, 2018.
• U.S. center will fight infections with viruses  
  Servick K. Science, Jun 22, 2018.
• The DNA Cops Who Make Sure the World’s Deadliest Viruses Aren’t Rebuilt  
  Spalding R. Bloomberg, Jun 27, 2018.
• High-Resolution Snapshot of Zika Virus Reveals Clues to Fighting It  
  Baumgartner E. New York Times, Jun 26, 2018.
• World First: Human Case of Keystone Virus Identified  
  Grens K. The Scientist, Jun 22, 2018.
• A flu drug — shown to reduce the duration of symptoms — could upend treatment in U.S.  
  Branswell H. STAT, Jun 27, 2018.
• Dual RNA Sequencing Enables Host-Pathogen Transcriptome Analysis of Uncomplicated, Severe Malaria  
  GenomeWeb, Jun 27, 2018.
• Study: Gonorrhea genes expressed differently in men and women  
  Soucheray S. CIDRAP, Jun 27, 2018.
• A Common Virus May Play Role in Alzheimer’s Disease, Study Finds  
  Belluck P. New York Times, Jun 21, 2018.
• Genetically Modified Pigs Resistant to Deadly Disease Are Now a Thing  
  Nield D. ScienceAlert, Jun 22, 2018.
• Poliovirus therapy shows early promise in patients with aggressive brain cancer but questions linger  
  Feuerstein A. STAT, Jun 26, 2018.

EVENTS / TRAINING / WEB RESOURCES

• The Fears of the Rich, The Needs of the Poor: My Years at the CDC  
  (book download) Foege WH. March 2018.
• The importance of cross-disciplinary research to combat antimicrobial resistance: introducing a new pop-up journal, X-AMR  
  (announcement)Knight G, et al. Microb Genom, Jun 22, 2018.

POLICY

• Rapid Antigen Tests for Influenza: Rationale and Significance of the FDA Reclassification.  
  Green Daniel A et al. Journal of clinical microbiology 2018 Jun
• Ethical Guidelines for Genomic Research in Africa  
  Friedrich M. JAMA 2018;319(23):2371.

CONCEPTS / COMMENTS

• Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics.  
  Rocha Eduardo P C et al. Molecular biology and evolution 2018 Jun (6) 1338-1347
• Developing Zika vaccines: the lessons for disease X.  
  Barrett Alan D T et al. Genome medicine 2018 Jun (1) 47
• Unanswered questions about the 1918 influenza pandemic: origin, pathology, and the virus itself.  
  Oxford John S et al. The Lancet. Infectious diseases 2018 Jun
• Unexpected outbreaks of arbovirus infections: lessons learned from the Pacific and tropical America.  
  Musso Didier et al. The Lancet. Infectious diseases 2018 Jun
• Exploiting Viruses to Treat Diseases  
  Longo DL, Baden LR. New Engl J Med, Jun 26, 2018.
• Yellow Fever Virus: Knowledge Gaps Impeding the Fight Against an Old Foe.  
  Douam Florian et al. Trends in microbiology 2018 Jun
• Crowdsourcing Our National Gut.  
  Grieneisen Laura E et al. mSystems (3)

METHODS / TOOLS

• Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.  
  Suchard Marc A et al. Virus evolution 2018 Jan (1) vey016
• WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.  
  Devlin Joseph C et al. BMC genomics 2018 Jun (1) 493
• Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case.  
  Tanaka Mami et al. PeerJ 2018 e5018
• Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples.  
  Schneider Uffe Vest et al. PloS one 2018 (6) e0199766
• PCR Amplification Strategies towards full-length HIV-1 Genome sequencing.  
  Liu Chao Chun et al. Current HIV research 2018 Jun
• Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture.  
  Greninger Alexander L et al. mSphere 2018 Jun (3)

EVOLUTION / ECOLOGY / POPULATIONS

• Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.  
  Smet Annemieke et al. The ISME journal 2018 Jun
• Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.  
  Domman Daryl et al. Nature genetics 2018 Jun
• Multi locus sequence typing of Burkholderia pseudomallei isolates from India unveils molecular diversity and confers regional association in Southeast Asia.  
  Balaji Veeraraghavan et al. PLoS neglected tropical diseases 2018 Jun (6) e0006558
• Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential.  
  Gemmell Matthew R et al. Emerging microbes & infections 2018 Jun (1) 116
• Geography but not alternative host species explain the spread of raccoon rabies virus in Vermont.  
  Nadin-Davis S A et al. Epidemiology and infection 2018 Jun 1-10
• Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species.  
  Lee Kuo-Ming et al. Emerging microbes & infections 2018 Jun (1) 111
• Identification and characterization of novel mosquito-borne (Kammavanpettai virus) and tick-borne (Wad Medani) reoviruses isolated in India.  
  Yadav Pragya D et al. The Journal of general virology 2018 Jun 
• Avian influenza surveillance in domestic waterfowl and environment of live bird markets in Bangladesh, 2007-2012.  
  Khan Salah Uddin et al. Scientific reports 2018 Jun (1) 9396 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Droplet Digital PCR detection of Helicobacter pylori clarithromycin resistance reveals frequent heteroresistance.  
  Sun Lu et al. Journal of clinical microbiology 2018 Jun
• Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections.  
  Goswami Cosmika et al. Microbial genomics 2018 Jun
• Linking minimum inhibitory concentrations to whole genome sequence-predicted drug resistance in Mycobacterium tuberculosis strains from Romania.  
  Ruesen Carolien et al. Scientific reports 2018 Jun (1) 9676
• Prevalence of pretreatment HIV drug resistance in Cameroon following a nationally representative WHO survey.  
  Tchouwa Gaëlle F et al. The Journal of antimicrobial chemotherapy 2018 Jun  

DETECTION / DIAGNOSIS

• Multiplex PCR analysis for the rapid detection of Klebsiella pneumoniae carbapenem-resistant (ST258, 11) and hypervirulent (ST23, 65, 86, 375) strains.  
  Yu Fangyou et al. Journal of clinical microbiology 2018 Jun
• Accuracy of different bioinformatics methods in detecting antibiotic resistance and virulence factors from Staphylococcus aureus whole genome sequences.  
  Mason Amy et al. Journal of clinical microbiology 2018 Jun
• Identification of Nocardia Species from Clinical Isolates Using Maldi-Tof Mass Spectrometry.  
  Marín Mercedes et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Jun
• Evaluation of Sepsis Flow Chip for identification of Gram-negative bacilli and detection of antimicrobial resistance genes directly from positive blood cultures.  
  Rodríguez-Lucas Carlos et al. Diagnostic microbiology and infectious disease 2018 Jul (3) 205-209
• High-resolution melting PCR analysis for rapid genotyping of Burkholderia mallei.  
  Girault G et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 May 1-4
• Evaluation of a new T2 Magnetic Resonance assay for rapid detection of emergent fungal pathogen Candida auris on clinical skin swab samples.  
  Sexton D Joseph et al. Mycoses 2018 Jun 
• The First Case of Trypanosoma cruzi-Associated Retinitis in an Immunocompromised Host Diagnosed With Pan-Organism Polymerase Chain Reaction.  
  Conrady Christopher D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jun (1) 141-143
• The host response as a tool for infectious disease diagnosis and management.  
  Lydon Emily C et al. Expert review of molecular diagnostics 2018 Jun

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Core Genome Multi Locus Sequence Typing and Single Nucleotide Polymorphism Analyses in the Epidemiology of Brucella melitensis Infections.  
  Janowicz Anna et al. Journal of clinical microbiology 2018 Jun
• Population structure of OXA-48-producing Klebsiella pneumoniae ST405 isolates during a hospital outbreak characterized by genomic typing.  
  López-Camacho Elena et al. Journal of global antimicrobial resistance 2018 Jun
• A clone of the emergent Streptococcus pyogenes emm89 clade responsible for a large outbreak in a post-surgery oncology unit in France.  
  Plainvert Céline et al. Medical microbiology and immunology 2018 Jun
• National outbreak of Salmonella Give linked to a local food manufacturer in Malta, October 2016.  
  Donachie A et al. Epidemiology and infection 2018 Jun 1-8 
• Fatal Sepsis Associated with Bacterial Contamination of Platelets — Utah and California, August 2017
  Horth RZ, et al. MMMWR, Jun 29, 2018.  
• Spillover of a hepatitis A outbreak among men who have sex with men (MSM) to the general population, the Netherlands, 2017.  
  Friesema Ingrid Hm et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Jun (23)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Strategic Response to an Outbreak of Circulating Vaccine-Derived Poliovirus Type 2 - Syria, 2017-2018.  
  Mbaeyi Chukwuma et al. MMWR. Morbidity and mortality weekly report 2018 Jun (24) 690-694  

HOST-MICROBE INTERACTIONS

• Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study.  
  Berkhout Daniel J C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jun
• The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis.  
  Wandro Stephen et al. mSphere 2018 Jun (3)
• Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women  
  Nudel K, et al. mSphere, Jun 27, 2018.
• Importance of case age in the purported association between phylogenetics and hemolytic uremic syndrome in Escherichia coli O157:H7 infections.  
  Tarr G A M et al. Epidemiology and infection 2018 Jun 1-6
• A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.  
  Singhania Akul et al. Nature communications 2018 Jun (1) 2308
• Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria  
  Lee HJ, et al. Sci Transl Med, Jun 27, 2018.
• E. coli and colorectal cancer: a complex relationship that deserves a critical mindset.  
  Wassenaar Trudy M et al. Critical reviews in microbiology 2018 Jun 1-14

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB