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

Genomics|Update|Infectious Diseases

Volume 35  Number 8  August 20- September 3, 2015

Advanced Molecular Detection in Action

• News/ Reviews/ Commentaries
• Methods/ Tools
• Evolution/ Ecology/ Populations
• Pathogenicity / Antimicrobial Resistance

• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Host-Microbe Interactions

News/ Reviews/ Commentaries

Lassa virus sequence gives insight into viral origins, evolution
GenomeWeb, Aug 13, 2015.

Beacon project cracks the door for genomic data sharing
Krol A. Bio-IT World, Aug 14, 2015.

NIH to award up to $12M to fund DNA, RNA sequencing research
GenomeWeb, Aug 17, 2015.

Mayo team turns to NGS method to understand role of HPV in cancer
Heger M. GenomeWeb, Aug 18, 2015.

MIT team develops multiplexed POC immunoassay for infectious disease testing
Bonislawski A. GenomeWeb, Aug 18, 2015.

Paper-based test can quickly diagnose Ebola in remote areas
Phys.Org, Aug 18, 2015.

Synthetic DNA-based MERS vaccine shows promise
Azvolinsky A. The Scientist, Aug 19, 2015.

Are human intestinal eukaryotes beneficial or commensals?
Lukes J et al. PLoS Pathog. 2015 Aug (8) e1005039

Diagnostics and discovery in viral central nervous system infections.
Lipkin WI et al. Brain Pathol. 2015 Sep (5) 600-4

Population genetics, evolutionary genomics, and genome-wide studies of malaria: A view across the international centers of excellence for malaria research.
Carlton JM et al. Am. J. Trop. Med. Hyg. 2015 Aug 10.

Clinical value of whole-genome sequencing of Mycobacterium tuberculosis.
Takiff HE et al. Lancet Infect Dis 2015 Aug 12.

Editorial commentary: The irreversibility of HIV drug resistance.
Kouyos RD et al. Clin. Infect. Dis. 2015 Sep 1. (5) 837-9

Effect of culture-independent diagnostic tests on future emerging infections program surveillance
Langley G, et al. Emerg Infect Dis, Sep 2015.

The many considerations of "one health" genomics
Rands C. PHG Foundation, Aug 18, 2015.

Host biology in light of the microbiome: Ten principles of holobionts and hologenomes.
Bordenstein SR et al. PLoS Biol. 2015 Aug (8) e1002226

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Methods/Tools

New routes to phylogeography: A Bayesian structured coalescent approximation.
De Maio N et al. PLoS Genet. 2015 Aug (8) e1005421

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.
Lai B et al. BMC Bioinformatics 2015 244

Syndromic surveillance of infectious diseases meets molecular epidemiology in a workflow and phylogeographic application.
Janies D et al. Stud Health Technol Inform 2015 766-70

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.
Bratcher HB et al. BMC Genomics 2014 1138

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering.
Verbist B et al. BMC Bioinformatics 2015 59

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
Kalkatawi M et al. BMC Genomics 2015 (1) 616

Rapid and easy In silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data.
Joensen KG et al. J. Clin. Microbiol. 2015 Aug (8) 2410-26

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Evolution/ Ecology/ Populations

Whole genomic constellation of the first human G8 rotavirus strain detected in Japan.
Agbemabiese CA et al. Infect. Genet. Evol. 2015 Aug 11.

Clinical sequencing uncovers origins and evolution of Lassa virus.
Andersen KG et al. Cell 2015 Aug 13. (4) 738-50

Comparative genome analysis of Mycoplasma pneumoniae.
Xiao L et al. BMC Genomics 2015 (1) 610

Intraspecies genomic diversity and long-term persistence of Bifidobacterium longum.
Chaplin AV et al. PLoS ONE 2015 (8) e0135658

Detection of diverse novel bat astrovirus sequences in the Czech Republic.
Dufkova L et al. Vector Borne Zoonotic Dis. 2015 Aug (8) 518-21

Microevolution of anthrax from a young ancestor (M.A.Y.A.) suggests a soil-borne life cycle of Bacillus anthracis.
Braun P et al. PLoS ONE 2015 (8) e0135346

Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis.
Xu Y et al. Sci Rep 2015 12888

Detection and circulation of Hepatits b virus immune escape mutants among asymptomatic community dwellers in Ibadan, Southwestern Nigeria.
Cephas FTO et al. Int. J. Infect. Dis. 2015 Aug 14

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Pathogenicity / Antimicrobial Resistance

Global gene expression profiling through the complete life cycle of Trypanosoma vivax.
Jackson AP et al. PLoS Negl Trop Dis 2015 Aug (8) e0003975

Dominance of international 'high-risk clones' among metallo-beta-lactamase-producing Pseudomonas aeruginosa in the UK.
Wright LL et al. J. Antimicrob. Chemother. 2015 Jan (1) 103-10

Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt.
Pelleau S et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Aug 10. 

Comparative genomic analysis of meningitis and bacteremia causing pneumococci identifies a common core genome.
Kulohoma BW et al. Infect. Immun. 2015 Aug 10. 

Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain- and sequence type-specific adaptation.
Bruchmann S et al. Environ. Microbiol. 2015 Aug 11.

Molecular detection and characterization of Mycoplasma pneumoniae among patients hospitalized with community-acquired pneumonia in the United States.
Diaz MH et al. Open Forum Infect Dis 2015 Sep (3) ofv106 (CDC Author)

Unravelling genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing.
Faucon F et al. Genome Res. 2015 Jul 23.

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Detection/ Diagnosis

Polymerase chain reaction, pyrosequencing, and culture of infected and uninfected site skin biopsy specimens cannot identify etiology of cellulitis.
Crisp JG et al. Clin. Infect. Dis. 2015 Aug 3.

Randomized controlled clinical trial evaluating multiplex polymerase chain reaction for pathogen identification and therapy adaptation in critical care patients with pulmonary or abdominal sepsis.
Tafelski S et al. J. Int. Med. Res. 2015 Jun (3) 364-77

Rapid and fully automated bacterial pathogen detection on a centrifugal-microfluidic LabDisk using highly sensitive nested PCR with integrated sample preparation.
Czilwik G et al. Lab Chip 2015 Aug 3.

Comparison between conventional culture and NAATs for the microbiological diagnosis in gonococcal infection
Serra-Pladevall J, et al. Diagn Microbiol Infect Dis, Aug 8, 2015.

Real-time PCR assays for genotyping of Cryptococcus gattii in North America.
Kelley EJ et al. BMC Microbiol. 2014 125

16S rRNA gene sequence-based identification of bacteria in automatically incubated blood culture materials from tropical sub-Saharan Africa.
Frickmann H et al. PLoS ONE 2015 (8) e0135923

Analytical performance of the automated multianalyte point-of-care mariPOC® for the detection of respiratory viruses.
Sanbonmatsu-Gámez S et al. Diagn. Microbiol. Infect. Dis. 2015 Jul 18.

Development and evaluation of MALDI-TOF MS-based serotyping for Streptococcus pneumoniae.
Nakano S et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Aug 19.

New real time PCR assays for detection of inducible and acquired clarithromycin resistance in mycobacterium abscessus group.
Shallom SJ et al. J. Clin. Microbiol. 2015 Aug 12.

Identification of Nocardia species by matrix-assisted laser desorption/ionization - time of flight mass spectrometry.
Khot PD et al. J. Clin. Microbiol. 2015 Aug 12.

HIV drug resistance testing by high-multiplex "wide" sequencing on the Illumina MiSeq.
Lapointe H et al. Antimicrob. Agents Chemother. 2015 Aug 17.

Diversity and antibiotic resistance profiles of Pseudomonads from a hospital wastewater treatment plant.
Santoro DO et al. J. Appl. Microbiol. 2015 Aug 18.

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Epidemiology/ Outbreaks/ Transmission

Characterization of foodborne outbreaks of salmonella enterica serovar enteritidis with whole-genome sequencing SNP-based analysis for surveillance and outbreak detection.
Taylor AJ et al. J. Clin. Microbiol. 2015 Aug 12.

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance.
Nordahl PT et al. Sci Rep 2015 11444

Whole-genome comparison uncovers genomic mutations between group B streptococci sampled from infected newborns and their mothers.
Almeida A et al. J. Bacteriol. 2015 Aug 17.

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Host-Microbe Interactions

Gut microbiota modulate the immune effect against hepatitis B virus infection.
Xu D et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Aug 14.

Temporal and spatial variation of the human microbiota during pregnancy
DiGiulio DB, et al. Proc Nat Acad Sci, Aug 17, 2015.

Investigation of the association between the fecal microbiota and breast cancer in postmenopausal women: a population-based case-control pilot study.
Goedert JJ et al. J. Natl. Cancer Inst. 2015 Aug (8) 

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.
Castro-Nallar E et al. BMC Med Genomics 2015 50