Volume 35 Number 2 July 9-16, 2015
Antimicrobials/ Vaccines/ Interventions
Suppression of a field population of Aedes aegypti in Brazil by sustained release of transgenic male mosquitoes.
Carvalho DO et al. PLoS Negl Trop Dis 2015 Jul (7) e0003864
Carvalho DO et al. PLoS Negl Trop Dis 2015 Jul (7) e0003864
An epitope-substituted DNA vaccine improves safety and immunogenicity against dengue virus type 2.
Tang Chung-Tao et al. PLoS Negl Trop Dis 2015 Jul (7) e0003903
Tang Chung-Tao et al. PLoS Negl Trop Dis 2015 Jul (7) e0003903
Characterization of three porcine reproductive and respiratory syndrome virus isolates from a single swine farm bearing strong homology to a vaccine strain
Jiang Y, et al. Vet Microbiol, Jul 2, 2015.
Jiang Y, et al. Vet Microbiol, Jul 2, 2015.
Detection/ Diagnosis
Development of a biosensor-based rapid urine test for detection of urogenital schistosomiasis.
Mach KE et al. PLoS Negl Trop Dis 2015 Jul (7) e0003845
Mach KE et al. PLoS Negl Trop Dis 2015 Jul (7) e0003845
Failure of PCR to detect Treponema pallidum ssp. pertenue DNA in blood in latent yaws.
Marks M et al. PLoS Negl Trop Dis 2015 Jun (6) e0003905
Marks M et al. PLoS Negl Trop Dis 2015 Jun (6) e0003905
Urine nested polymerase chain reaction in neonatal septicemia.
Das B K et al. J. Trop. Pediatr. 2015 Jun 30.
Das B K et al. J. Trop. Pediatr. 2015 Jun 30.
Canonical single nucleotide polymorphisms (SNPs) for high-resolution subtyping of Shiga-toxin producing Escherichia coli (STEC) O157:H7.
Griffing SM et al. PLoS ONE 2015 (7) e0131967 (CDC Author)
Griffing SM et al. PLoS ONE 2015 (7) e0131967 (CDC Author)
Development and evaluation of three real-time PCR assays for genotyping and source tracking Cryptosporidium in water.
Li Na et al. Appl. Environ. Microbiol. 2015 Jun 19.
Li Na et al. Appl. Environ. Microbiol. 2015 Jun 19.
Development of loop-mediated isothermal amplification to detect Streptococcus suis and its application to retail pork meat in Japan.
Arai S et al. Int. J. Food Microbiol. 2015 Sep 2. 35-42
Arai S et al. Int. J. Food Microbiol. 2015 Sep 2. 35-42
Defining and evaluating a core genome MLST scheme for whole genome sequence-based typing of Listeria monocytogenes.
Ruppitsch W et al. J. Clin. Microbiol. 2015 Jul 1.
Ruppitsch W et al. J. Clin. Microbiol. 2015 Jul 1.
Epidemiology/ Outbreaks/ Transmission
Outbreak of Salmonella enterica serovar Typhimurium phage type DT41 in Danish poultry production.
Löfström C et al. Vet. Microbiol. 2015 Jul 9. (1-2) 167-72
Löfström C et al. Vet. Microbiol. 2015 Jul 9. (1-2) 167-72
Whole-genome sequencing of measles virus genotypes H1 and D8 during outbreaks of infection following the 2010 olympic winter games reveals viral transmission routes
Gardy JL, et al. J Infect Dis, Jul 6, 2015.
Gardy JL, et al. J Infect Dis, Jul 6, 2015.
Phylogenetic analysis of highly pathogenic avian influenza A(H5N8) virus outbreak strains provides evidence for four separate introductions and one between-poultry farm transmission in the Netherlands, November 2014
Bouwstra RJ, et al. Euro Surveill 2015;20(26):pii=21174.
Bouwstra RJ, et al. Euro Surveill 2015;20(26):pii=21174.
Separate norovirus outbreaks linked to one source of imported frozen raspberries by molecular analysis, Denmark, 2010-2011.
Müller L et al. Epidemiol. Infect. 2015 Aug (11) 2299-307
Müller L et al. Epidemiol. Infect. 2015 Aug (11) 2299-307
A familial cluster of human brucellosis attributable to contact with imported infected goats in Shuyang, Jiangsu Province, China, 2013.
Tan Z et al. Am. J. Trop. Med. Hyg. 2015 Jul 6.
Tan Z et al. Am. J. Trop. Med. Hyg. 2015 Jul 6.
Tracking nosocomial Klebsiella pneumoniae infections and outbreaks by whole genome analysis: small-scale Italian scenario within a single hospital.
Onori R et al. J. Clin. Microbiol. 2015 Jul 1.
Onori R et al. J. Clin. Microbiol. 2015 Jul 1.
Evolution/ Ecology/ Populations
Genetic characterisation of Porcine circovirus type 2 (PCV2) strains from feral pigs in the Brazilian Pantanal: An opportunity to reconstruct the history of PCV2 evolution.
Franzo G et al. Vet. Microbiol. 2015 Jul 9. (1-2) 158-62
Franzo G et al. Vet. Microbiol. 2015 Jul 9. (1-2) 158-62
Plasmodium vivax diversity and population structure across four continents.
Koepfli C et al. PLoS Negl Trop Dis 2015 Jun (6) e0003872
Koepfli C et al. PLoS Negl Trop Dis 2015 Jun (6) e0003872
Comparison of the oral microbiomes of canines and their owners using next-generation sequencing.
Oh C et al. PLoS ONE 2015 (7) e0131468
Oh C et al. PLoS ONE 2015 (7) e0131468
Recombinant transfer in the basic genome of Escherichia coli
Dixit PD, et al. Proc Natl Acad Sci, Jul 7, 2015.
Dixit PD, et al. Proc Natl Acad Sci, Jul 7, 2015.
Global circulation patterns of seasonal influenza viruses vary with antigenic drift
Bedford T, et al. Nature, Jul 9, 2015. (CDC Author)
Bedford T, et al. Nature, Jul 9, 2015. (CDC Author)
Genetic analyses of GII.17 norovirus strains in diarrheal disease outbreaks from December 2014 to March 2015 in Japan reveal a novel polymerase sequence and amino acid substitutions in the capsid region
Matsushima Y, et al. Euro Surveill 2015;20(26):pii=21173.
Matsushima Y, et al. Euro Surveill 2015;20(26):pii=21173.
Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.
Deng X et al. Emerging Infect. Dis. 2014 Sep (9) 1481-9
Deng X et al. Emerging Infect. Dis. 2014 Sep (9) 1481-9
Molecular epidemiology of novel pathogen "Brachyspira hampsonii" reveals relationships between diverse genetic groups, regions, host species and other pathogenic and commensal Brachyspira.
Mirajkar NS et al. J. Clin. Microbiol. 2015 Jul 1.
Mirajkar NS et al. J. Clin. Microbiol. 2015 Jul 1.
Host-Microbe Interactions
Mitochondrial DNA haplogroups and neurocognitive impairment during HIV infection.
Hulgan T et al. Clin. Infect. Dis. 2015 Jun 30.
Hulgan T et al. Clin. Infect. Dis. 2015 Jun 30.
Limits and patterns of cytomegalovirus genomic diversity in humans
Kowalik T, et al. Proc Nat Acad Sci, Jul 6, 2015.
Kowalik T, et al. Proc Nat Acad Sci, Jul 6, 2015.
Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children.
Kay GL et al. PLoS Negl Trop Dis 2015 Jun (6) e0003861
Kay GL et al. PLoS Negl Trop Dis 2015 Jun (6) e0003861
A retrospective metagenomics approach to studying blastocystis.
Andersen Lee O'Brien et al. FEMS Microbiol. Ecol. 2015 Jun 29.
Andersen Lee O'Brien et al. FEMS Microbiol. Ecol. 2015 Jun 29.
Human prion protein sequence elements impede cross-species chronic wasting disease transmission.
Kurt TD et al. J. Clin. Invest. 2015 Apr (4) 1485-96
Kurt TD et al. J. Clin. Invest. 2015 Apr (4) 1485-96
Methods/Tools
MLgsc: A Maximum-likelihood general sequence classifier.
Junier T et al. PLoS ONE 2015 (7) e0129384
Junier T et al. PLoS ONE 2015 (7) e0129384
Use of alignment-free phylogenetics for rapid genome sequence-based typing of Helicobacter pylori virulence markers and antibiotic susceptibility.
van Vliet AH et al. J. Clin. Microbiol. 2015 Jul 1.
van Vliet AH et al. J. Clin. Microbiol. 2015 Jul 1.
Comparing K-mer based methods for improved classification of 16S sequences.
Vinje H et al. BMC Bioinformatics 2015 205
Vinje H et al. BMC Bioinformatics 2015 205
BioMaS: a modular pipeline for bioinformatic analysis of metagenomic AmpliconS.
Fosso B et al. BMC Bioinformatics 2015 203
Fosso B et al. BMC Bioinformatics 2015 203
IVA: accurate de novo assembly of RNA virus genomes.
Hunt M et al. Bioinformatics 2015 Feb 28.
Hunt M et al. Bioinformatics 2015 Feb 28.
EpIC: a rational pipeline for epitope immunogenicity characterization.
Marciniuk K et al. Bioinformatics 2015 Mar 6.
Marciniuk K et al. Bioinformatics 2015 Mar 6.
nextflu: real-time tracking of seasonal influenza virus evolution in humans.
Neher RA et al. Bioinformatics 2015 Jun 26.
Neher RA et al. Bioinformatics 2015 Jun 26.
Pathogenicity / Antimicrobial Resistance
Genomic context of azole resistance mutations in Aspergillus fumigatus determined using whole-genome sequencing.
Abdolrasouli A et al. MBio 2015 (3)
Abdolrasouli A et al. MBio 2015 (3)
Examination of the enterotoxigenic Escherichia coli population structure during human infection.
Sahl JW et al. MBio 2015 (3)
Sahl JW et al. MBio 2015 (3)
Sequence-specific fidelity alterations associated with West Nile virus attenuation in mosquitoes.
Van Slyke GA et al. PLoS Pathog. 2015 Jun (6) e1005009
Van Slyke GA et al. PLoS Pathog. 2015 Jun (6) e1005009
Emergence of serotype IV group B Streptococcus adult invasive disease in Manitoba and Saskatchewan, Canada, is driven by clonal sequence type 459 strains.
Teatero S et al. J. Clin. Microbiol. 2015 Jul 1.
Teatero S et al. J. Clin. Microbiol. 2015 Jul 1.
Haemophilus ducreyi cutaneous ulcer strains are nearly identical to class I genital ulcer strains.
Gangaiah D et al. PLoS Negl Trop Dis 2015 Jul (7) e0003918 (CDC Author)
Gangaiah D et al. PLoS Negl Trop Dis 2015 Jul (7) e0003918 (CDC Author)
Comparative genome analysis of Wolbachia strain wAu.
Sutton ER et al. BMC Genomics 2014 928
Sutton ER et al. BMC Genomics 2014 928
Policy
Pathogen genomics into practice
Luheshi L, et al. PHG Foundation (UK), Jul 9, 2015.
Luheshi L, et al. PHG Foundation (UK), Jul 9, 2015.
Reviews/ News/ Commentaries
Ceres Eyes $5M funding round to broadly commercialize Lyme disease Dx
Bonislawski A. GenomeWeb, Jul 6, 2015.
Bonislawski A. GenomeWeb, Jul 6, 2015.
Field evaluation of rapid Ebola immunoassay reveals limitations of PCR-based testing
Rizk C. GenomeWeb, Jul 1, 2015.
Rizk C. GenomeWeb, Jul 1, 2015.
FDA OKs herpes blood test
Grens K. The Scientist, Jul 6, 2015.
Grens K. The Scientist, Jul 6, 2015.
Genome researchers raise alarm over big data
Hayden EC. Nature, Jul 7, 2015.
Hayden EC. Nature, Jul 7, 2015.
DNA Genotek's Gut Microbiome Kit gets CE-IVD Mark
GenomeWeb, Jul 7, 2015.
GenomeWeb, Jul 7, 2015.
Following feasibility study, UK registry plans to implement PacBio for HLA typing by year's end
Karow J. GenomeWeb, Jul 6, 2015.
Karow J. GenomeWeb, Jul 6, 2015.
New standard seeks to alleviate challenges of sharing bioinformatics tools and workflows
Thomas UG. GenomeWeb, Jul 1, 2015.
Thomas UG. GenomeWeb, Jul 1, 2015.
Getting to the root of epidemic spread with phylodynamic analysis of genomic data.
du Plessis Louis et al. Trends Microbiol. 2015 Jul (7) 383-6
du Plessis Louis et al. Trends Microbiol. 2015 Jul (7) 383-6
Has the airway microbiome been overlooked in respiratory disease?
Salami Olawale et al. Genome Med 2015 (1) 62
Salami Olawale et al. Genome Med 2015 (1) 62
Narcolepsy link to pandemic flu vaccine becomes clearer
Vogel G. Science, Jul 3, 2015.
Vogel G. Science, Jul 3, 2015.
Mosquitoes reset malaria parasites.
Spence Philip J et al. PLoS Pathog. 2015 Jul (7) e1004987
Spence Philip J et al. PLoS Pathog. 2015 Jul (7) e1004987
Microbiome privacy risk.
Callaway E et al. Nature 2015 May 14. (7551) 136
Callaway E et al. Nature 2015 May 14. (7551) 136
Schistosomiasis reaches Europe.
Boissier J et al. Lancet Infect Dis 2015 Jul (7) 757-8
Boissier J et al. Lancet Infect Dis 2015 Jul (7) 757-8
What was old is new again: using the host response to diagnose infectious disease.
Ko ER et al. Expert Rev. Mol. Diagn. 2015 Jul 4. 1-16
Ko ER et al. Expert Rev. Mol. Diagn. 2015 Jul 4. 1-16
Big data: Astronomical or genomical?
Stephens ZD et al. PLoS Biol. 2015 Jul (7) e1002195
Stephens ZD et al. PLoS Biol. 2015 Jul (7) e1002195
Data analysis: Create a cloud commons
Stein LD, et al. Nature, Jul 8, 2015.
Stein LD, et al. Nature, Jul 8, 2015.
Tools for drools: A general guide to collecting and processing saliva
Chi KR. The Scientist, Jul 1, 2015.
Chi KR. The Scientist, Jul 1, 2015.
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