Genomics|Update|Infectious Diseases ► Advanced Molecular Detection in Action

Genomics|Update|Infectious Diseases

Volume 34  Number 14  April 9-16, 2015

Advanced Molecular Detection in Action

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

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

Antimicrobials, Vaccines, Interventions

Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology.
Weinert LA et al. Mol. Biol. Evol. 2015 Apr (4) 1020-8

Genetic analysis of invasive pneumococcal isolates from children in Ontario, Canada, 2007-2012.
Deng X et al. Pediatr. Infect. Dis. J. 2015 Mar 31.

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: An individual-patient- and sequence-level meta-analysis.
Rhee SY et al. PLoS Med. 2015 Apr (4) e1001810 (CDC Author)

Phase 1 trials of rVSV Ebola vaccine in Africa and Europe - preliminary report.
Agnandji ST et al. N. Engl. J. Med. 2015 Apr 1. (CDC Author)

Emergency postexposure vaccination with vesicular stomatitis virus-vectored Ebola vaccine after needlestick.
Lai L et al. JAMA 2015 Mar 24-31 (12) 1249-55 (CDC Author)

Increase of RT-related transmitted drug resistance in non-CRF01_AE among HIV type 1-infected men who have sex with men in the 7 cities of China.
Zhao B et al. J. Acquir. Immune Defic. Syndr. 2015 Mar 1. (3) 250-5

Single-dose attenuated Vesiculovax vaccines protect primates against Ebola Makona virus. 
Mire Chad E et al. Nature 2015 Apr 8.

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Detection and Diagnosis

Development and application of a gp60-based typing assay for Cryptosporidium viatorum.
Stensvold CR et al. J. Clin. Microbiol. 2015 Apr 1.

Successful combination of nucleic acid amplification test diagnostics and targeted deferred Neisseria gonorrhoeae culture.
Wind CM et al. J. Clin. Microbiol. 2015 Apr 1.

Use of whole genome phylogeny and comparisons in the development of a multiplex-PCR assay to identify sequence type 36 Vibrio parahaemolyticus.
Whistler CA et al. J. Clin. Microbiol. 2015 Apr 1.

First probable case of subcutaneous infection due to Truncatella angustata. A new fungal pathogen of man?
Jagielski T et al. J. Clin. Microbiol. 2015 Mar 25.

Evaluation of three-marker GIG-EM phylogenetic typing of Escherichia coli isolates of various genetic backgrounds.
Hamamoto K et al. J. Clin. Microbiol. 2015 Mar 25.

Multidrug resistant Candida auris misidentified as C. haemulonii: Characterization by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), DNA sequencing and its antifungal susceptibility profile variability by VITEK-2, CLSI-broth microdilution and E-test method.
Kathuria S et al. J. Clin. Microbiol. 2015 Mar 25.

Simultaneous identification of multiple ß-lactamases in Acinetobacter baumannii in relation to carbapenem and ceftazidime resistance, using liquid chromatography-tandem mass spectrometry.
Trip H et al. J. Clin. Microbiol. 2015 Mar 18.

Towards an HIV-1 cure: measuring the latent reservoir.
Bruner KM et al. Trends Microbiol. 2015 Apr (4) 192-203

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Epidemiology, Outbreaks, Transmission

Colonization with the man's Escherichia coli strain among female sex partners of men with febrile urinary tract infection.
Ulleryd P et al. J. Clin. Microbiol. 2015 Apr 1.

Transmission of Mycobacterium tuberculosis in China: A population-based molecular epidemiology study.
Yang C et al. Clin. Infect. Dis. 2015 Mar 31.

Extensive household outbreak of urinary tract infection and intestinal colonization due to extended-spectrum beta lactamase (ESBL)-producing Escherichia coli sequence type 131 (ST131).
Madigan T et al. Clin. Infect. Dis. 2015 Mar 31.

A fatal outbreak of an emerging clone of extensively drug-resistant Acinetobacter baumannii with enhanced virulence.
Jones CL et al. Clin. Infect. Dis. 2015 Mar 29.

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study.
Greninger AL et al. Lancet Infect Dis 2015 Mar 30.

Norovirus genotype profiles associated with foodborne transmission, 1999-2012.
Verhoef L et al. Emerging Infect. Dis. 2015 Apr (4) 592-9 (CDC Author)

Public health investigation of two outbreaks of Shiga toxin-producing Escherichia coli O157 associated with consumption of watercress. 
Jenkins Claire et al. Appl. Environ. Microbiol. 2015 Apr 3.

Molecular epidemiology suggests Venezuela as the origin of the dengue outbreak in Madeira, Portugal in 2012-2013. 
Franco L et al. Clin. Microbiol. Infect. 2015 Apr 2.

Human infection with a zoonotic orthopoxvirus in the country of Georgia. 
Vora Neil M et al. N. Engl. J. Med. 2015 Mar 26. (13) 1223-30

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Evolution, Ecology, Pathogenicity, Populations

Whole genome comparisons suggest random distribution of Mycobacterium ulcerans genotypes in a buruli ulcer endemic region of Ghana.
Ablordey AS et al. PLoS Negl Trop Dis 2015 Mar (3) e0003681

Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15
Arafa AS, et al. Eurosurveillance, Apr 2, 2015.

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
Kay GL, et al. Nat Commun Apr 7, 2015; 6:6717.

Selection and spread of artemisinin-resistant alleles in Thailand prior to the global artemisinin resistance containment campaign.
Talundzic E et al. PLoS Pathog. 2015 Apr (4) e1004789 (CDC Author)

Molecular diversity of Bacillus anthracis in the Netherlands: investigating the relationship to the worldwide population using whole-genome SNP discovery. 
Derzelle Sylviane et al. Infect. Genet. Evol. 2015 Apr 2.

Global migration of influenza A viruses in swine. 
Nelson Martha I et al. Nat Commun 2015 6696

Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. 
Bose Michael E et al. PLoS ONE 2015 (3) e0120098

Insights into the environmental reservoir of pathogenic Vibrio parahaemolyticus using comparative genomics. 
Hazen Tracy H et al. Front Microbiol 2015 204

Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences. 
Hoenen T et al. Science 2015 Apr 3. (6230) 117-9

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Host-Pathogen Interactions

Predicting vaccine responsiveness.
Boyd SD et al. Cell Host Microbe 2015 Mar 11. (3) 301-307

The changing face of asthma and its relation with microbes.
Earl CS et al. Trends Microbiol. 2015 Mar 31.

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.
Kim HB et al. Vet. Microbiol. 2015 Mar 23.

Telomere length as an indicator of the robustness of B- and T-cell response to influenza in older adults.
Najarro K et al. J. Infect. Dis. 2015 Mar 31. (CDC Author)

Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. 
Lin Shih-Wen et al. Obesity (Silver Spring) 2015 Apr (4) 862-9

Cancer and the microbiota. 
Garrett Wendy S et al. Science 2015 Apr 3. (6230) 80-6 

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Methods

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
Combs PA et al. PeerJ 2015 e869

Bacterial rose garden for metagenomic SNP-based phylogeny visualization.
Alexeev D et al. BioData Min 2015 10 

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Policy

NIH makes initial revisions to guidelines for genomic data analysis in the cloud
GenomeWeb, Apr 3, 2015.

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Reviews, News and Commentaries

Clinical end users embrace PCR MDx panels as debate continues on size, cost, utility
Johnson M. GenomeWeb, Apr 3, 2015.

Bruker receives FDA clearance for expanded MALDI Biotyper system
GenomeWeb, Apr 3, 2015.

Genome compiler inks collaboration with addgene to integrate plasmid data into software
GenomeWeb, Apr 3, 2015.

NIAID-led Partnership Seeks to Establish Bioinformatics Centers in Africa 
Thomas UG. GenomeWeb, Apr 3, 2015.

Just hit 'print': Office inkjet printer could produce simple tool to identify infectious disease, food contaminants
Science Daily, Apr 7, 2015.

Metagenomic analysis finds ancient TB victims harbored multiple bacterial strains
GenomeWeb, Apr 7, 2015.

Mobidiag C. difficile test receives CE mark
GenomeWeb, Apr 8, 2015.

African hub set up to boost research autonomy 
Nordling L. Nature, Apr 8, 2015.

Biomeme Eyes DIY Market for Mini PCR Cycler; Currently Working with Military, Research Testers 
Ashford M. GenomeWeb, Apr 7, 2015.

2 New Ebola Vaccines Pass Important Early Test, Researchers Say 
Grady D. New York Times, Apr 8, 2015.

Interest grows in vaccines to fight foodborne illness 
Deng B. Nature, Apr 7, 2015.

Point-counterpoint: Large multiplex PCR panels should be first line tests for detection of respiratory and intestinal pathogens.
Schreckenberger P et al. J. Clin. Microbiol. 2015 Mar 11.

Genotyping of Mycobacterium tuberculosis in China and missing links in the chain of ongoing transmission of tuberculosis.
Arend SM et al. Clin. Infect. Dis. 2015 Mar 31.

Food industry's current and future role in preventing microbial foodborne illness within the United States.
Doyle MP et al. Clin. Infect. Dis. 2015 Mar 30.

Can sequence data predict enterovirus D68 infection outcome?
Norder H et al. Lancet Infect Dis 2015 Mar 30.

Core services: Reward bioinformaticians 
Chang J. Nature, Apr 8, 2015.

Epigenetics and animal virus infections. 
Galvan Silvia C et al. Front Genet 2015 48