Advanced Molecular Detection in Action - CDC Genomics & Health Impact Update

Colorectal cancer, epigenetics, venous thrombosis & more hot topics in today's CDC Genomics & Health Impact Update

Volume 34  Number 9  March 5-19, 2015

Advanced Molecular Detection in Action

• Antimicrobials, Vaccines, Interventions
• Detection & Diagnosis
• Epidemiology, Outbreaks, Transmission
• Evolution, Ecology, Pathogenicity, Populations

• Host-Pathogen Interactions
• Methods
• Reviews, News & Commentaries

Antimicrobials, Vaccines, Interventions

Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics.
Kugelman Jeffrey R et al. MBio 2015 (1)

Reversible antibiotic tolerance induced in Staphylococcus aureus by concurrent drug exposure.
Haaber Jakob et al. MBio 2015 (1)

A novel bacterial pathogen of Biomphalaria glabrata: A potential weapon for schistosomiasis control?
Duval David et al. PLoS Negl Trop Dis 2015 Jan (2) e0003489

Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanghai, China, 2011-2013.
Zhao Sheng-Yuan et al. Infect Dis (Lond) 2015 Feb 24. 1-9

Spread of artemisinin-resistant Plasmodium falciparum in Myanmar: a cross-sectional survey of the K13 molecular marker.
Tun Kyaw M et al. Lancet Infect Dis 2015 Feb 18.

Identification and characterization of multi-drug resistant Salmonella enterica serotype Albert in the United States.
Folster Jason P et al. Antimicrob. Agents Chemother. 2015 Mar 2. (CDC Author)

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Detection and Diagnosis

Development of a novel liquid bead array human papillomavirus genotyping assay (PGMY-LX) and comparison with Linear Array for continuity in longitudinal cohort studies.
Farhat Sepideh et al. J. Clin. Microbiol. 2015 Feb 4.

Rapid and sensitive RT-QuIC detection of human Creutzfeldt-Jakob disease using cerebrospinal fluid.
Orrú Christina D et al. MBio 2015 (1)

A new real-time RT-PCR assay for detection of human enterovirus 68 (EV-D68) in respiratory samples.
Piralla Antonio et al. J. Clin. Microbiol. 2015 Feb 18.

Comparative evaluation of three commercial quantitative cytomegalovirus standards using digital and real-time PCR.
Hayden R T et al. J. Clin. Microbiol. 2015 Feb 18.

Single molecule arrays (Simoa) for the ultra-sensitive detection of the host immune response to dengue infection.
Gaylord Shonda T et al. J. Clin. Microbiol. 2015 Feb 18.

Novel recombinant multiepitope proteins for the diagnosis of asymptomatic Leishmania infantum-infected dogs.
Faria Angélica Rosa et al. PLoS Negl Trop Dis 2015 Jan (1) e3429

Evaluation of the loop mediated isothermal DNA amplification (LAMP) kit for malaria diagnosis in P. vivax endemic settings of Colombia.
Vallejo Andrés F et al. PLoS Negl Trop Dis 2015 Jan (1) e3453

Relative efficacy of nucleic acid amplification testing and serologic screening in preventing hepatitis C virus transmission risk in seven international regions.
Bruhn Roberta et al. Transfusion 2015 Feb 27.

Diagnostic accuracy of loop-mediated isothermal amplification as a near-patient test for meningococcal disease in children: an observational cohort study.
Bourke Thomas W et al. Lancet Infect Dis 2015 Feb 26.

Case-control comparison of bacterial and protozoan microorganisms associated with gastroenteritis: application of molecular detection.
van Coppenraet Lesla E S Bruijnesteijn et al. Clin. Microbiol. Infect. 2015 Feb 17.

Detection of Biomarkers of Pathogenic Naegleria fowleri Through Mass Spectrometry and Proteomics.
Moura Hercules et al. J. Eukaryot. Microbiol. 2015 Jan (1) 12-20 (CDC Author)

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Epidemiology, Outbreaks, Transmission

Enterovirus D68-associated severe pneumonia, China, 2014 
Zhang T, et al. Emerg Infect Dis, May 2015.

Outbreak of Salmonella newport infections linked to cucumbers - United States, 2014.
Angelo Kristina M et al. MMWR Morb. Mortal. Wkly. Rep. 2015 Feb 20. (6) 144-7

Molecular detection of the index case of a subclinical Salmonella Kentucky epidemic on a dairy farm.
Haley B J et al. Epidemiol. Infect. 2015 Mar (4) 682-6

The impact of clinical, demographic and risk factors on rates of HIV transmission: A population-based phylogenetic analysis in British Columbia, Canada.
Poon Art F Y et al. J. Infect. Dis. 2015 Mar 15. (6) 926-35

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Evolution, Ecology, Pathogenicity, Populations

Novel Thogotovirus species associated with febrile illness and death, United States, 2014 
Kosoy OI, et al. Emerg Infect Dis, May 2015.

Measles fusion machinery is dysregulated in neuropathogenic variants.
Jurgens Eric M et al. MBio 2015 (1)

Population structure and antimicrobial resistance of invasive serotype IV group B streptococcus, Toronto, Ontario, Canada 
Teatero S, et al. Emerg Infect Dis, Apr 2015

La Crosse virus in Aedes japonicus japonicus mosquitoes in the Appalachian region, United States
Harris MC, et al. Emerg Infect Dis, Apr 2015.

Genomic and epidemiological characteristics provide new insights into the phylogeographical and spatiotemporal spread of porcine epidemic diarrhea virus in Asia.
Sun Min et al. J. Clin. Microbiol. 2015 Feb 18.

The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families
Schwarz EM, et al. Nat Genet, Mar 2, 2015.

Novel eurasian highly pathogenic influenza A H5 viruses in wild birds, Washington, USA, 2014 
Ip HS, et al. Emerg Infect Dis, May 2015.

Nhumirim virus, a novel flavivirus isolated from mosquitoes from the Pantanal, Brazil.
Pauvolid-Corrêa Alex et al. Arch. Virol. 2015 Jan (1) 21-7 (CDC Author)

Phenotypic and phylogenetic analysis of Vibrio parahaemolyticus isolates recovered from diarrhea cases in Guangdong Province, China.
Li Baisheng et al. Int. J. Food Microbiol. 2015 Jan 19. 13-17

Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa.
Nyaga Martin M et al. Infect. Genet. Evol. 2015 Feb 17. (CDC Author)

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Host-Pathogen Interactions

Application of a neutral community model to assess structuring of the human lung microbiome.
Venkataraman Arvind et al. MBio 2015 (1)

Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity.
Dogra Shaillay et al. MBio 2015 (1)

Genetic variants associated with susceptibility of Ashkenazi Jews to West Nile virus infection.
Danial-Farran N et al. Epidemiol. Infect. 2015 Mar (4) 857-63

Disease-specific alterations in the enteric virome in inflammatory bowel disease.
Norman Jason M et al. Cell 2015 Jan 29. (3) 447-60

Polymorphisms in HLA-DPB1 are associated with differences in rubella virus-specific humoral immunity after vaccination.
Lambert Nathaniel D et al. J. Infect. Dis. 2015 Mar 15. (6) 898-905

Resistance to hepatitis C virus: potential genetic and immunological determinants.
Mina Michael M et al. Lancet Infect Dis 2015 Feb 18.

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Methods

A complete bacterial genome assembled de novo using only nanopore sequencing data
Loman NJ, et al. bioRxiv

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.
Zhou Jizhong et al. MBio 2015 (1)

A reference bacterial genome dataset generated on the MinION? portable single-molecule nanopore sequencer.
Quick Joshua et al. Gigascience 2014 Oct 20;3:22. (CDC Author)

RELAX: Detecting relaxed selection in a phylogenetic framework.
Wertheim Joel O et al. Mol. Biol. Evol. 2015 Mar (3) 820-32

Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing.
Chen Yuan et al. Fungal Genet. Biol. 2015 Feb 64-71

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Policy

Use and misuse of material transfer agreements: lessons in proportionality from research, repositories, and litigation.
Bubela Tania et al. PLoS Biol. 2015 Feb (2) e1002060

Data sharing: Make outbreak research open access.
Yozwiak Nathan L et al. Nature 2015 Feb 26. (7540) 477-9 (CDC Author)

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Reviews, News and Commentaries

CDC researchers use sequencing, phylogenetics to identify novel virus
GenomeWeb, Feb 23, 2015.

UCSF developing NGS-based infectious disease Dx; tests metagenomic sequencing on minIon
Heger M. GenomeWeb, Feb 20, 2015.

Study describes Luminex assay as replacement for linear array HPV testing in longitudinal studies
Ashford M. GenomeWeb, Feb 20, 2015.

Abbott pathogen detection platform compares well to PCR-based gold standards for influenza A/B
Johnson M. GenomeWeb, Feb 20, 2015.

As new botulism threat implodes, more questions
Enserink M. Science 27 February 2015: 347:934-935.

Germany's GNA biosolutions developing ultrafast 'Laser PCR' Ebola test, pathogen testing platform
Johnson M. , Genome Web, Feb 26, 2015.

The world should learn from the Ebola crisis to combat MERS in Saudi Arabia
Washington Post (editorial). Feb 26, 2015.

BioFire Diagnostics receives FDA clearance for FilmArray 2.0 system
GenomeWeb, Feb 26, 2015.

Roche obtains CE Mark for Cobas HBV viral load test
GenomeWeb, Mar 2, 2015.

Alere gets CE Mark for Alere q HIV-1/2 detect assay
GenomeWeb, Mar 2, 2015.

Seegene receives Canadian approval for Allplex respiratory MDx test
GenomeWeb, Mar 2, 2015.

On botulinum neurotoxin variability.
Montecucco Cesare et al. MBio 2015 (1)

Molecular testing for viral and bacterial enteric pathogens: gold standard for viruses, but don't let culture go just yet?
Bloomfield Maxim G et al. Pathology 2015 Feb 25.

Rapid identification of pathogens using molecular techniques.
Sloots Theo P et al. Pathology 2015 Feb 24.

Horizontal gene transfer in human pathogens.
Juhas Mario et al. Crit. Rev. Microbiol. 2015 Feb (1) 101-8

Understanding Drivers of Phylogenetic Clustering in Molecular Epidemiological Studies of HIV.
Frost Simon D W et al. J. Infect. Dis. 2015 Mar 15. (6) 856-8

Artemisinin resistance: the more we know, the more complicated it appears.
Hopkins Sibley Carol et al. J. Infect. Dis. 2015 Mar 1. (5) 667-9

Illuminating meningococcal diagnosis with LAMP.
Bahr Nathan C et al. Lancet Infect Dis 2015 Feb 26.

Towards real-time monitoring of artemisinin resistance.
Menard Didier et al. Lancet Infect Dis 2015 Feb 18.