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

Genomics|Update|Infectious Diseases

Volume 34  Number 16  April 23-30, 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

Rapid emergence of highly pathogenic avian influenza subtypes from a subtype H5N1 hemagglutinin variant 
de Vries E, et al. Emerg Infect Dis, May 2015.

Prediction of virological response by pretreatment hepatitis B virus reverse transcriptase quasispecies heterogeneity: the advantage of using next generation sequencing.
Han Y et al. Clin. Microbiol. Infect. 2015 Apr 13.

Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing 
Williams OM, et al. Emerg Infect Dis, Jun 2015.

Mass screening and treatment on the basis of results of a Plasmodium falciparum-specific rapid diagnostic test did not reduce malaria incidence in Zanzibar.
Cook J et al. J. Infect. Dis. 2015 May 1. (9) 1476-83

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Detection and Diagnosis

Evaluation of fingerstick cryptococcal antigen lateral flow assay in HIV-infected persons: a diagnostic accuracy study.
Williams D et al. Clin. Infect. Dis. 2015 Apr 1. 

Comparison of double locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations
Cholley P, et al. Diagn Microbiol Infect Dis, Apr 16, 2015.

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis.
Flight WG et al. J. Clin. Microbiol. 2015 Apr 15.

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Epidemiology, Outbreaks, Transmission

Whole genome sequencing for national surveillance of Shiga toxin producing Escherichia coli O157.
Dallman TJ et al. Clin. Infect. Dis. 2015 Apr 17.

Molecular epidemiology of Plasmodium falciparum malaria outbreak, Tumbes, Peru, 2010-2012.
Baldeviano GC et al. Emerging Infect. Dis. 2015 May (5)

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Evolution, Ecology, Pathogenicity, Populations

Comparative sequence analyses of La Crosse virus strain isolated from patient with fatal encephalitis, Tennessee, USA 
Lambert AJ, et al. Emerg Infect Dis, May 2015. (CDC Author)

Full-genome sequence of influenza A(H5N8) virus in poultry linked to sequences of strains from Asia, the Netherlands, 2014 
Bouwstra R, et al. Emerg Infect Dis, May 2015.

Genetic characterization of highly pathogenic avian influenza (H5N8) virus from domestic ducks, England, November 2014 
Hanna A, et al. Emerg Infect Dis, May 2015.

Influenza A(H5N8) virus similar to strain in Korea causing highly pathogenic avian influenza in Germany 
Harder T, et al. Emerg Infect Dis, May 2015.

KPC and NDM-1 genes in related Enterobacteriaceae strains and plasmids from Pakistan and the United States 
Pesesky MW, et al. Emerg Infect Dis, Jun 2015.

Emerging OP354-like P[8] rotaviruses have rapidly dispersed from Asia to other continents.
Zeller M et al. Mol. Biol. Evol. 2015 Apr 8.

The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.
Baker KS et al. Lancet 2014 Nov 8. (9955) 1691-7

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.
Mikalsen T et al. BMC Genomics 2015 Apr 10. (1) 282

A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia.
Ogedengbe ME et al. Int. J. Parasitol. 2015 May (6) 361-5 (CDC Author)

The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution.
Cwiklinski K et al. Genome Biol. 2015 (1) 71

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Host-Pathogen Interactions

Functional dynamics of the gut microbiome in elderly people during probiotic consumption.
Eloe-Fadrosh EA et al. MBio 2015 (2)

The microbiome of uncontacted Amerindians
Clemente JC, et al. Science Advances, Apr 17, 2015.

The gut microbiome in cardio-metabolic health.
Hansen TH et al. Genome Med 2015 (1) 33

Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.
Yano JM et al. Cell 2015 Apr 9. (2) 264-76

Integrating host gene expression and the microbiome to explore disease pathogenesis.
Byrd AL et al. Genome Biol. 2015 (1) 70

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.
Leone V et al. Cell Host Microbe 2015 Apr 14.

Serial high-resolution analysis of blood virome and host cytokines expression profile of a patient with fatal H7N9 infection by massively parallel RNA sequencing.
Hu Y et al. Clin. Microbiol. Infect. 2015 Apr 13.

Inter-individual differences in the gene content of human gut bacterial species.
Zhu A et al. Genome Biol. 2015 Apr 21. (1) 82

Hepatitis C virus reinfection and spontaneous clearance of reinfection - the InC3 study.
Sacks-Davis R et al. J. Infect. Dis. 2015 Apr 15.

Disseminated Ureaplasma infection as a cause of fatal hyperammonemia in humans 
Bharat A, et al. Sci Transl Med 2015; 7:284re3.

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Methods

Shared resources, shared costs-leveraging biocuration resources.
Orchard S et al. Database (Oxford) 2015

HLAreporter: a tool for HLA typing from NGS data
Huang Y, et al. Genome Med 2015; 7:25.

Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.
Visser MD et al. PLoS Comput. Biol. 2015 Mar (3) e1004140

3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics.
Weighill DA et al. PLoS Comput. Biol. 2015 Mar (3) e1004079

Quality control of microbiota metagenomics by k-mer analysis.
Plaza OF et al. BMC Genomics 2015 (1) 183

Temporal and technical variability of human gut metagenomes.
Voigt AY et al. Genome Biol. 2015 Apr 8. (1) 73

Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics 
Hou HW, et al. Lab Chip, Apr 17, 2015.

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Reviews, News and Commentaries

MALDI Facing competition in clinical microbiology space from alternative mass spec methods
Bonislawski A. GenomeWeb, Apr 17, 2015.

Curetis second-gen pneumonia test gets CE mark, set to launch later this month
Macron D. GenomeWeb, Apr 17, 2015.

Could viral infections instigate juvenile ALS?
Dance A. Alzforum, Apr 16, 2015.

New genetic mutation could signal start of malaria drug resistance in Africa
EurekAlert! Apr 17, 2015.

Virus hiding in our genome protects early human embryos
Coghlan A. New Scientist, Apr 20, 2015.

Twins experiment reveals genetic link with mosquito bites
Univ of Florida, Apr 22, 2015.

Great basin gets FDA OK for Strep B test
GenomeWeb, Apr 22, 2015.

Scientists to share real-time genetic data on MERS, Ebola 
Voice of America, Apr 21, 2015.

Survey finds high interest in long-range genome data, nanopore tech while Illumina rules NGS market
Karow J. GenomeWeb, Apr 21, 2015.

JCVI bacterial sequencing interrogates bleeding edge of antibiotic resistance genes
Han AP. GenomeWeb, Apr 22, 2015.

Team tracks airborne microbes using household dust samples collected by US volunteers
GenomeWeb, Apr 21, 2015.

Combating the next lethal epidemic
Hotez PJ. Science, Apr 17, 2015.

The infallible microbial identification test: does it exist?
van Belkum A et al. J. Clin. Microbiol. 2015 May (5) 1786

Reply to "the infallible microbial identification test: does it exist?".
Alby K et al. J. Clin. Microbiol. 2015 May (5) 1787

Old war, new battle, new fighters!
Sousa S et al. J. Infect. Dis. 2015 May 1. (9) 1361-3

Bugs full of viruses.
Gall A et al. Nat. Rev. Microbiol. 2015 May (5) 253

Tackling antibiotic resistance: the environmental framework.
Berendonk TU et al. Nat. Rev. Microbiol. 2015 May (5) 310-7

Whole-genome sequencing in outbreak analysis.
Gilchrist CA et al. Clin. Microbiol. Rev. 2015 Jul (3) 541-563

There's more to come from Moore
Nature, Apr 17, 2015.

The cost of sequencing is still going down 
(blog) opinionomics, Mar 23, 2015.

Highway to health
(Editorial) Nature, Apr 23, 2015.

The safety of the blood supply - time to raise the bar.
Snyder Edward L et al. N. Engl. J. Med. 2015 Apr 22.