Public Health Genomics Knowledge Base (v1.0)
Advanced Molecular Detection Clips
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.
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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
Antimicrobials / Vaccines / Interventions
Host-Microbe Interactions
NEWS
A trail of microbes
Kupferschmidt K. Science, Mar 11, 2016.
Spoiler alert
Yan W. The Scientist, Mar 1, 2016.
Deadly disease outbreak in Wisconsin baffles public health officials
Landman K. STAT, Mar 14, 2016.
Study Finds Surprising Benefit of Viral DNA: Fighting Other Viruses
Zimmer C. New York Times, Mar 3, 2016.
Genome of Virulent Fungus Missing Parts of RNAi Pathways Present in Related Species
GenomeWeb, Mar 4, 2016.
Microsoft Research scientist David Heckerman on how we could attack HIV like spam
Kim M. Washington Post, Mar 4, 2016.
The red-hot debate about transmissible Alzheimer's
Abbott A. Nature, Mar 16, 2016.
FDA Seeks Info on Houston Hospitals' Molecular Zika Virus Assay
GenomeWeb, Mar 15, 2016.
Researchers Demonstrate New PCR-Based Method More Sensitive Than ELISA in Detecting Antibodies
Johnson M. GenomeWeb, Mar 9, 2016.
Rapid, Inexpensive 'Lab-on-a-Drone' PCR Enabled With Convective Flow Thermal Cycling
Johnson M. GenomeWeb, Mar 8, 2016.
ASU Team's Immunosignature Profiles Indicate Technique's Suitability for Longitudinal Testing
Bonislawski A. GenomeWeb, Mar 3, 2016.
Clinical NGS Test Developers Discuss Sample Prep Challenges of Assay Validation
Heger M. GenomeWeb, Mar 9, 2016.
FDA Clears Cepheid Xpert Carba-R Test on GeneXpert System
GenomeWeb, Mar 9, 2016.
EVENTS / TRAINING / WEB RESOURCES
Search for WGS Sequences using Stand-alone BLAST!
(announcement) NCBI News, Mar 7, 2016.
CONCEPTS / COMMENTS
The ethics of sustainable genomic research in Africa.
Parker Michael et al. Genome biology 2016 (1) 44
Considerations in centralizing whole genome sequencing for microbiology in a public health setting.
Arnold Cath et al. Expert review of molecular diagnostics 2016 Mar
Divorcing Strain Classification from Species Names.
Baltrus David A et al. Trends in microbiology 2016 Mar
MICROBIOLOGY. The invisible dimension of fungal diversity.
Hibbett David et al. Science (New York, N.Y.) 2016 Mar (6278) 1150-1
Maintaining a safe blood supply in an era of emerging pathogens.
Marks Peter W et al. The Journal of infectious diseases 2016 Mar
Back to the future: Rethinking global control of tuberculosis.
Bloom Barry R et al. Science translational medicine 2016 Mar (329) 329ps7
The Emerging Zika Virus Epidemic in the Americas: Research Priorities.
Lazear Helen M et al. JAMA 2016 Mar
Partnerships, Not Parachutists, for Zika Research.
Heymann David L et al. The New England journal of medicine 2016 Mar
Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally.
Zumla Alimuddin et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016 Mar
METHODS / TOOLS
PEPR: pipelines for evaluating prokaryotic references.
Olson Nathan D et al. Analytical and bioanalytical chemistry 2016 Mar
MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.
Lugli Gabriele Andrea et al. FEMS microbiology letters 2016 Mar
Data in support of proteomic analysis of pneumococcal pediatric clinical isolates to construct a protein array.
Olaya-Abril Alfonso et al. Data in brief 2016 Mar 917-22
EVOLUTION / ECOLOGY / POPULATIONS
Genomic Analysis of Companion Rabbit Staphylococcus aureus.
Holmes Mark A et al. PloS one 2016 (3) e0151458
First report of the emerging zoonotic agent Wohlfahrtiimonas chitiniclastica isolated from a retail frozen chicken in Rio de Janeiro, Brazil.
Matos Jorge et al. Antonie van Leeuwenhoek 2016 Mar
Distribution and relationships of antimicrobial resistance determinants among extended-spectrum cephalosporin or carbapenem-resistant Escherichia coli isolated from rivers and sewage treatment plants in India.
Akiba Masato et al. Antimicrobial agents and chemotherapy 2016 Mar
Genomic diversity of necrotic enteritis associated strains of Clostridium perfringens: A review.
Lacey Jake A et al. Avian pathology : journal of the W.V.P.A 2016 Mar 1-17
Genomic epidemiology and molecular resistance mechanisms of azithromycin resistant Neisseria gonorrhoeae in Canada from 1997 to 2014.
Demczuk Walter et al. Journal of clinical microbiology 2016 Mar
Draft Genome Sequences of Strains Representing Each of the Elizabethkingia Genomospecies Previously Determined by DNA-DNA Hybridization.
Nicholson Ainsley C et al. Genome announcements 2016 (2)
Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989-2013.
du Plessis Mignon et al. Journal of clinical microbiology 2016 Mar
Bordetella pertussis epidemiology and evolution in the light of pertussis resurgence.
Sealey Katie L et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb 136-143
Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States.
Engelthaler David M et al. Emerging infectious diseases 2016 Apr (4) 734-738
Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.
Petrovska Liljana et al. Emerging infectious diseases 2016 Apr (4) 617-624
Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India.
Afreen Nazia et al. PLoS neglected tropical diseases 2016 Mar (3) e0004511
Molecular characterization of a novel reassortant H1N2 influenza virus containing genes from the 2009 pandemic human H1N1 virus in swine from eastern China.
Peng Xiuming et al. Virus genes 2016 Mar
Global genomic epidemiology of Salmonella Typhimurium DT104.
Leekitcharoenphon Pimlapas et al. Applied and environmental microbiology 2016 Mar
Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008.
Choi Seon Young et al. mBio 2016 (2)
Whole genome sequencing reveals genetic heterogeneity of G3P[8] rotaviruses circulating in Italy.
Medici Maria Cristina et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar
A Mycobacterial Perspective on Tuberculosis in West Africa: Significant Geographical Variation of M. africanum and Other M. tuberculosis Complex Lineages.
Gehre Florian et al. PLoS neglected tropical diseases 2016 Mar (3) e0004408
Molecular analysis and MIRU-VNTR typing of Mycobacterium avium subsp. avium, 'hominissuis' and silvaticum strains of veterinary origin.
Rónai Zsuzsanna et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar
Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses.
Ramey Andrew M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar 176-185
Limited evidence of intercontinental dispersal of avian paramyxovirus serotype 4 by migratory birds.
Reeves Andrew B et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb 104-108
Molecular characterization of new emerging GII.17 norovirus strains from South China.
Xue Liang et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb 1-7
Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.
Gachara George et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb 98-103
Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans.
Dinis Jorge M et al. Journal of virology 2016 (7) 3355-65
Genomic Sequence of the First Porcine Rotavirus Group H Strain in the United States.
Hull Jennifer J et al. Genome announcements 2016 (2)
Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic
Zhu Z, et al. Emerg Microbes Infect, Mar 16, 2016.
Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015.
Lamers Mart M et al. Emerging infectious diseases 2016 Apr (4) 716-719
Characterizing the genetic diversity of the monkey malaria parasite Plasmodium cynomolgi.
Sutton Patrick L et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Mar
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
First Report of cfr-Encoding Plasmids in the Pandemic Sequence Type (ST) 22 Methicillin-Resistant Staphylococcus aureus Staphylococcal Cassette Chromosome mec Type-IV Clone.
Shore Anna C et al. Antimicrobial agents and chemotherapy 2016 Mar
Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples.
Fernández-Natal I et al. New microbes and new infections 2016 Mar 116-21
Presence of plasmid-mediated quinolone resistance determinants and mutations in gyrase and topoisomerase in Salmonella enterica isolates with resistance and reduced susceptibility to ciprofloxacin.
Casas Monique Ribeiro Tiba et al. Diagnostic microbiology and infectious disease 2016 Jan
Hepatitis C virus quasispecies and pseudotype analysis from acute infection to chronicity in HIV-1 co-infected individuals.
Ferns R Bridget et al. Virology 2016 Mar 213-224
Phylogenetic evidence for intratypic recombinant events in a novel human adenovirus C that causes severe acute respiratory infection in children.
Wang Yanqun et al. Scientific reports 2016 23014
Prevalence and dynamics of the K65R drug resistance mutation in HIV-1-infected infants exposed to maternal therapy with lamivudine, zidovudine and either nevirapine or nelfinavir in breast milk.
Inzaule Seth C et al. The Journal of antimicrobial chemotherapy 2016 Mar
Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification.
Riemenschneider Mona et al. BioData mining 2016 10
Genomic epidemiology of artemisinin resistant malaria.
et al. eLife 2016
DETECTION / DIAGNOSIS
Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing.
Graham R M A et al. Sexually transmitted infections 2016 Mar
Capsular typing method for Streptococcus agalactiae using whole genome sequence data.
Sheppard Anna E et al. Journal of clinical microbiology 2016 Mar
Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia.
Ruppé Etienne et al. Future microbiology 2016 Mar
Ultrafast, sensitive and large-volume on-chip real-time PCR for the molecular diagnosis of bacterial and viral infections.
Houssin Timothée et al. Lab on a chip 2016 Mar
Genotyping of Nocardia farcinica with multilocus sequence typing.
Du P et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Mar
Evaluation of efficiency of nested MAS-PCR assay for detection of Multidrug Resistant Tuberculosis (MDR-TB) directly from sputum samples.
Mistri Somen Kumar et al. Letters in applied microbiology 2016 Mar
Severe sensitivity loss in an influenza A molecular assay due to antigenic drift variants during the 2014/15 influenza season.
Overmeire Yarah et al. Diagnostic microbiology and infectious disease 2016 Mar
Molecular diagnosis of Puumala virus-caused hemorrhagic fever with renal syndrome.
Lagerqvist Nina et al. Journal of clinical microbiology 2016 Mar
Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach.
Decuypere Saskia et al. PLoS neglected tropical diseases 2016 Mar (3) e0004480
Use of Malachite Green-Loop Mediated Isothermal Amplification for Detection of Plasmodium spp. Parasites.
Lucchi Naomi W et al. PloS one 2016 (3) e0151437
Still Searching for a Suitable Molecular Test to Detect Hidden Plasmodium Infection: A Proposal for Blood Donor Screening in Brazil.
Lima Giselle Fernandes Maciel de Castro et al. PloS one 2016 (3) e0150391
Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing.
Logue Kyle et al. PLoS neglected tropical diseases 2016 Mar (3) e0004512
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Outbreak Caused by blaOXA-72-Producing Acinetobacter baumannii ST417 Detected in Clinical and Environmental Isolates.
Tamayo-Legorreta Elsa et al. Microbial drug resistance (Larchmont, N.Y.) 2016 Mar (2) 129-33
Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.
Burall Laurel S et al. PloS one 2016 (3) e0150797
Whole-Genome Sequencing for the Investigation of a Hospital Outbreak of MRSA in China.
Kong Zhenzhen et al. PloS one 2016 (3) e0149844
Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.
Outhred Alexander C et al. PloS one 2016 (3) e0150550
OXA-48 Producing Klebsiella pneumoniae in a Household Contact of a Previously Infected Patient: Person-to-Person Transmission or Coincidental Community Acquisition?
Yusuf Erlangga et al. Microbial drug resistance (Larchmont, N.Y.) 2016 Mar (2) 134-6
Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States
Engelthaler DM, et al. Emerg Infect Dis, Apr 2016.
Possible Airborne Person-to-Person Transmission of Mycobacterium bovis - Nebraska 2014-2015.
Buss Bryan F et al. MMWR. Morbidity and mortality weekly report 2016 (8) 197-201
The need to implement effective new entrant tuberculosis screening in children: evidence from school 'outbreak'.
Williams Bhanu et al. Journal of public health (Oxford, England) 2016 Mar
Nosocomial Co-Transmission of Avian Influenza A(H7N9) and A(H1N1)pdm09 Viruses between 2 Patients with Hematologic Disorders.
Chen Huazhong et al. Emerging infectious diseases 2016 Apr (4) 598-607
Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR.
Bonsall David et al. Emerging infectious diseases 2016 Apr (4) 671-678
Severe Infections with Human Adenovirus 7d in 2 Adults in Family, Illinois, USA, 2014.
Kajon Adriana E et al. Emerging infectious diseases 2016 Apr (4) 730-733
Molecular characterization of human Cryptosporidium spp. isolates after an unusual increase in late summer 2012.
Roelfsema Jeroen H et al. Parasites & vectors 2016 (1) 138
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