Publication Date: Jul 13, 2017
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.
Advanced Molecular Detection Clips Content
- How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA
Kupferschmidt K. Science, Jul 6, 2017.
- Panel's smallpox sample probe yields policy recommendations, lingering questions
Schnirring L. CIDRAP, Jul 10, 2017.
- Team Modifies Molecular Inversion Probes to Capture Kilobase-Sized DNA for Cloning, Sequencing
Karow J. GenomeWeb, Jun 30, 2017.
- Study Validates Single-Gene Biomarker That Discriminates Between Influenza and Bacterial Infections
GenomeWeb, Jun 28, 2017.
- Australian Researchers Employ POC RNA Testing to Address Growing Rate of HCV Infections
GenomeWeb, Jun 30, 2017.
- MinION in the Clinic
GenomeWeb, Jul 13, 2017.
- More reason to use Meningococcal B vaccine it could also cut the Clap
Petousis-Harris H. The Conversation, Jul 10, 2017.
- Microbiome Profiling: Big Business, but What About the Data?
Watson J. Medscape, Jun 26,, 2017.
- Surface of Mars Hostile to Microbes
Grant B. The Scientist, Jul 6, 2017.
- NASA-Led Team Examines Mycobiome of Environment Mimicking Space Habitats
GenomeWeb, Jul 11, 2017.
- Antimicrobial resistance in Neisseria gonorrhoeae: Global surveillance and a call for international collaborative action.
Wi Teodora et al. PLoS medicine 2017 Jul (7) e1002344
- Food and microbiota in the FDA regulatory framework.
Green Jonathan M et al. Science (New York, N.Y.) 2017 Jul (6346) 39-40
CONCEPTS / COMMENTS
- New technologies boost genome quality
Pennisi E. Science, Jul 7, 2017.
- Novel influenza A viruses and pandemic threats.
Uyeki Timothy M et al. Lancet (London, England) 2017 Jun (10085) 2172-2174
- Emerging Viral Infections in Pakistan: Issues, Concerns, and Future Prospects.
Khalil Ali Talha et al. Health security (3) 268-281
- Practices and promises of Facebook for science outreach: Becoming a "Nerd of Trust".
McClain Craig R et al. PLoS biology 2017 Jun (6) e2002020
METHODS / TOOLS
- PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.
Nadon Celine et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jun (23)
- Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny.
Tsang Alan K L et al. Scientific reports 2017 Jul (1) 4536
- Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.
Griffiths Emma et al. Frontiers in microbiology 2017 1068
- Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry Julie A et al. PLoS biology 2017 Jun (6) e2001414
- Completing bacterial genome assemblies with multiplex MinION sequencing
Wick RR, et al. bioRxiv, Jul 7, 2017.
- PHYLOSCANNER: Analysing Within- and Between-Host Pathogen Genetic Diversity to Identify Transmission, Multiple Infection, Recombination and Contamination
Wymant C, et al. bioRxiv, Jun 30, 2017.
- A Supervised Statistical Learning Approach For Accurate Legionella pneumophila Source Attribution During Outbreaks
Buultjens A, et al. bioRxiv, Jul 9, 2017.
- Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.
Artyomenko Alexander et al. Journal of computational biology : a journal of computational molecular cell biology 2017 Jun (6) 558-570
- Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing.
Haile Simon et al. BMC genomics 2017 Jul (1) 515
- QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii.
Shen Bang et al. Journal of visualized experiments : JoVE 2017 Jun (124)
EVOLUTION / ECOLOGY / POPULATIONS
- Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.
Dunne Karl A et al. Microbial genomics 2017 Mar (3) mgen000106
- Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes.
Moradigaravand Danesh et al. mBio 2017 Jul (4)
- Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics.
Rovetto Francesca et al. PloS one 2017 (7) e0180493
- The changing epidemiology of invasive Haemophilus influenzae disease: Emergence and global presence of serotype a strains that may require a new vaccine for control.
Tsang Raymond S W et al. Vaccine 2017 Jun
- Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology.
Hanke Dennis et al. Viruses 2017 Jul (7)
- Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016.
Midgley Sofie E et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jun (26)
- A detailed analysis of codon usage patterns and influencing factors in Zika virus.
Singh Niraj K et al. Archives of virology 2017 Jul (7) 1963-1973
- Viral outbreaks involve destabilized viruses: evidence from Ebola, Influenza and Zika
Aris-Brosou S, et al. bioRxiv, Jun 26, 2017.
- Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.
Rhodes Johanna et al. Genetics 2017 Jul
- Increasingly inbred and fragmented populations of Plasmodium vivax with declining transmission
Waltmann A, et al. bioRxiv, June 23, 2017.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Next-generation sequence analysis reveals methicillin-resistance transfer to a methicillin-susceptible Staphylococcus aureus (MSSA) strain that subsequently caused a methicillin-resistant Staphylococcus aureus (MRSA) outbreak: a descriptive study.
Weterings Veronica et al. Journal of clinical microbiology 2017 Jul
- Characterization of Carbapenem-Resistant Escherichia coli Isolates Through the Whole-Genome Sequencing Analysis.
Luo Yanping et al. Microbial drug resistance (Larchmont, N.Y.) 2017 Jul
- Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs.
Wang Qingjing et al. Microbiome 2017 Jul (1) 70
- Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and Shigella.
Hazen Tracy H et al. Antimicrobial agents and chemotherapy 2017 Jul
- Whole Genome Sequencing of Mycobacterium tuberculosis Isolates From Extrapulmonary Sites.
Sharma Kusum et al. Omics : a journal of integrative biology 2017 Jul (7) 413-425
- A Possible Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.
Thoendel Matthew et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Apr
- Trends and predictors of HIV-1 acquired drug resistance in Minas Gerais, Brazil: 2002-2012.
Duani Helena et al. The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases (2) 148-154
- Prion strains in mammals: Different conformations leading to disease.
Morales Rodrigo et al. PLoS pathogens 2017 Jul (7) e1006323
DETECTION / DIAGNOSIS
- Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.
Ceuppens Siele et al. International journal of food microbiology 2017 Jun 148-156
- Rapid accurate point-of-care tests combining diagnostics and antimicrobial resistance prediction for Neisseria gonorrhoeae and Mycoplasma genitalium.
Sadiq Syed Tariq et al. Sexually transmitted infections 2017 Jul
- Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria.
Kocurek Klaudia I et al. Journal of the American Society for Mass Spectrometry 2017 Jul
- Toward Rapid Sequenced-Based Detection and Characterization of Causative Agents of Bacteremia
Hewitt FC, et al. bioRxiv, Jul 12, 2017.
- Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay.
Sarpong-Duah Mabel et al. PLoS neglected tropical diseases 2017 Jul (7) e0005695
- Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon.
Alame-Emane Amel Kévin et al. Journal of clinical microbiology 2017 Jul (7) 2105-2115
- Development of a one-step multiplex PCR assay for differential detection of major Mycobacterium species.
Chae Hansong et al. Journal of clinical microbiology 2017 Jun
- Evaluation of a Probe-Based PCR-ELISA System for Simultaneous Semi Quantitative Detection and Genotyping of Human Cytomegalovirus (HCMV) Infection in Clinical Specimens.
Talkhabifard Majid et al. The open microbiology journal 2017 83-91
- Revealing enterovirus infection in chronic human disorders: An integrated diagnostic approach.
Genoni Angelo et al. Scientific reports 2017 Jul (1) 5013
- Detection of Emerging Vaccine-Related Polioviruses by Deep Sequencing.
Sahoo Malaya K et al. Journal of clinical microbiology 2017 Jul (7) 2162-2171
- Rapid Detection of Norovirus Using Paper-based Microfluidic Device
Weng X, Neethirajan S, bioRxiv, Jul 12, 2017.
- Rapid and point-of-care tests for the diagnosis of Trichomonas vaginalis in women and men.
Gaydos Charlotte A et al. Sexually transmitted infections 2017 Jul
- Rapid detection of Trypanosoma cruzi by colorimetric loop-mediated isothermal amplification (LAMP): A potential novel tool for the detection of congenital Chagas infection.
Rivero Rocío et al. Diagnostic microbiology and infectious disease 2017 Jun
- Development of loop-mediated isothermal amplification with Plasmodium falciparum unique genes for molecular diagnosis of human malaria.
Zhang Yijing et al. Pathogens and global health 2017 Jul 1-9
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014.
Schjørring Susanne et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Jun (25)
- Whole Genome Sequencing Overrules a Suspected Case of Carbapenem-Resistant Enterobacter cloacae Transmission.
Chen Mark et al. Journal of clinical microbiology 2017 Jun
- Multistate Outbreak of Salmonella Anatum Infections Linked to Imported Hot Peppers - United States, May-July 2016.
Hassan Rashida et al. MMWR. Morbidity and mortality weekly report 2017 Jun (25) 663-667
- Notes from the Field: An Outbreak of Shiga Toxin-Producing Escherichia coli O121 Infections Associated with Flour - Canada, 2016-2017.
Morton Vanessa et al. MMWR. Morbidity and mortality weekly report 2017 Jul (26) 705-706
- Population Dynamics of Staphylococcus aureus in Cystic Fibrosis Patients To Determine Transmission Events by Use of Whole-Genome Sequencing.
Ankrum Andrea et al. Journal of clinical microbiology 2017 Jul (7) 2143-2152
- Genome Sequencing Links Persistent Outbreak Of Legionellosis In Sydney To An Emerging Clone Of Legionella pneumophila ST211
Timms VJ, et al. bioRxiv, Jun 1, 2017.
- Genomic epidemiology of a major Mycobacterium tuberculosis outbreak: Retrospective cohort study in a low incidence setting using sparse time-series sampling.
Folkvardsen Dorte Bek et al. The Journal of infectious diseases 2017 Jun
- Use of whole-genome sequencing and evaluation of the apparent sensitivity and specificity of antemortem tuberculosis tests in the investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd.
Bruning-Fann Colleen S et al. Journal of the American Veterinary Medical Association 2017 Jul (2) 206-216
- Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Arias Armando et al. Virus evolution 2016 Jan (1) vew016
- Prevalence of drug resistance among HIV-1 treatment-naive patients in Greece during 2003-2015: Transmitted drug resistance is due to onward transmissions.
Paraskevis D et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jul
- Identification of major routes of HIV transmission throughout Mesoamerica.
Chaillon Antoine et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Jun 98-107
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- 10-valent pneumococcal conjugate vaccine (PCV10) decreases metabolic activity but not nasopharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae.
Andrade Dafne C et al. Vaccine 2017 Jun
- Changes in genetically drifted H3N2 influenza A viruses and vaccine effectiveness in adults 65 years and older during the 2016/17 season in Denmark.
Trebbien Ramona et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Jun 1-7
- Immunization with HIV-1 envelope T20-encoding DNA vaccines elicits cross-clade neutralizing antibody responses.
Stenler S et al. Human vaccines & immunotherapeutics 2017 Jul 0
- Nano-therapeutics: A revolution in infection control in post antibiotic era.
Zaidi Sahar et al. Nanomedicine : nanotechnology, biology, and medicine 2017 Jun
- Hospital association of the gut microbiota mobilome in preterm infants.
Ravi Anuradha et al. Pediatric research 2017 Jun
- Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants.
Zwittink Romy D et al. Molecular & cellular proteomics : MCP 2017 Jul
- Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes.
Doyle Ronan M et al. PloS one 2017 (7) e0180167
- IL-10 gene polymorphism c.-592C>A increases HPV infection susceptibility and influences IL-10 levels in HPV infected women.
Berti Fernanda Costa Brandão et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep 128-134
- Mycoplasma hominis and Mycoplasma genitalium in the Vaginal Microbiota and Persistent High-Risk Human Papillomavirus Infection.
Adebamowo Sally N et al. Frontiers in public health 2017 140
- The microbiota and autoimmunity: Their role in thyroid autoimmune diseases.
Köhling Hedda L et al. Clinical immunology (Orlando, Fla.) 2017 Jul
- Role of IL28B genotype in the liver stiffness increase in untreated patients with chronic hepatitis C.
Boglione Lucio et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Sep 195-198
- In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis.
Thorell Kaisa et al. Infection and immunity 2017 Jul
- Molecular characterization of occult hepatitis B virus infection in patients with end-stage liver disease in Colombia.
Rendon Julio Cesar et al. PloS one 2017 (7) e0180447
- RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with disease progression in dengue patients.
Banerjee Arup et al. Translational research : the journal of laboratory and clinical medicine 2017 Jun
- Polymorphisms in the vitamin D receptor gene are associated with reduced rate of sputum culture conversion in multidrug-resistant tuberculosis patients in South Africa.
Magee Matthew J et al. PloS one 2017 (7) e0180916
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.
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