Volume 34 Number 22 June 4-11, 2015
Antimicrobials, Vaccines, Interventions
Transcriptome profiling and genetic study reveal amplified carboxylesterase genes implicated in temephos resistance, in the Asian tiger mosquito Aedes albopictus.
Grigoraki L et al. PLoS Negl Trop Dis 2015 May (5) e0003771
Grigoraki L et al. PLoS Negl Trop Dis 2015 May (5) e0003771
Mechanisms of methicillin resistance in Staphylococcus aureus.
Peacock SJ et al. Annu. Rev. Biochem. 2015 Jun 2. 577-601
Peacock SJ et al. Annu. Rev. Biochem. 2015 Jun 2. 577-601
Unprecedented silver-resistance in clinically isolated Enterobacteriaceae: Major implications for burn and wound management.
Finley PJ et al. Antimicrob. Agents Chemother. 2015 May 26.
Finley PJ et al. Antimicrob. Agents Chemother. 2015 May 26.
Detection and Diagnosis
Testing pooled sputum with Xpert MTB/RIF for the diagnosis of pulmonary tuberculosis to increase affordability in low income countries
Abdurrahman ST, et al. J Clin Microbiol, May 27, 2015.
Abdurrahman ST, et al. J Clin Microbiol, May 27, 2015.
International external quality assessment study for molecular detection of Lassa virus.
Nikisins S et al. PLoS Negl Trop Dis 2015 May (5) e0003793
Nikisins S et al. PLoS Negl Trop Dis 2015 May (5) e0003793
The use of biomarkers and molecular methods for the earlier diagnosis of invasive aspergillosis in immunocompromised patients.
Ambasta A et al. Med. Mycol. 2015 May 30.
Ambasta A et al. Med. Mycol. 2015 May 30.
Diagnosis of toxoplasmosis and typing of Toxoplasma gondii.
Liu Q et al. Parasit Vectors 2015 292
Liu Q et al. Parasit Vectors 2015 292
Emerging techniques for pathogen discovery in endophthalmitis.
Hong BK et al. Curr Opin Ophthalmol 2015 May (3) 221-5
Hong BK et al. Curr Opin Ophthalmol 2015 May (3) 221-5
Epidemiology, Outbreaks, Transmission
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.
Quick J et al. Genome Biol. 2015 May 30. (1) 114
Quick J et al. Genome Biol. 2015 May 30. (1) 114
A clonal outbreak of tuberculosis in a homeless population in the interior of British Columbia, Canada, 2008-2015.
Cheng JM et al. Epidemiol. Infect. 2015 May 28. 1-7
Cheng JM et al. Epidemiol. Infect. 2015 May 28. 1-7
Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions.
Hué S et al. AIDS 2014 Aug 24. (13) 1967-75
Hué S et al. AIDS 2014 Aug 24. (13) 1967-75
Pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in Seri Kembangan, Malaysia, and their correlation with grades of food premises.
Abdul-Mutalib Noor-Azira et al. Int. J. Food Microbiol. 2015 May 4. 57-65
Abdul-Mutalib Noor-Azira et al. Int. J. Food Microbiol. 2015 May 4. 57-65
Evolution, Ecology, Pathogenicity, Populations
Draft genome sequence of 24570, the type strain of Shigella flexneri.
Baker KS et al. Genome Announc 2015 (3)
Baker KS et al. Genome Announc 2015 (3)
Defining core genome of Salmonella enterica serovar typhimurium for genomic surveillance and epidemiological typing.
Fu S et al. J. Clin. Microbiol. 2015 May 27.
Fu S et al. J. Clin. Microbiol. 2015 May 27.
Genetic characterization of peste des petits ruminants virus, Turkey, 2009-2013.
Sevik M et al. Res. Vet. Sci. 2015 May 21.
Sevik M et al. Res. Vet. Sci. 2015 May 21.
The avian-origin PB1 gene segment facilitated replication and transmissibility of the H3N2/1968 pandemic influenza virus.
Wendel I et al. J. Virol. 2015 Apr (8) 4170-9
Wendel I et al. J. Virol. 2015 Apr (8) 4170-9
Co-prevalance of PMQR and 16S rRNA methylase genes in clinical Escherichia coli isolates with high diversity of CTX-M from diseased farmed pigeons.
Yang L et al. Vet. Microbiol. 2015 May 18.
Yang L et al. Vet. Microbiol. 2015 May 18.
Positive selection drives preferred segment combinations during influenza virus reassortment.
Zeldovich KB et al. Mol. Biol. Evol. 2015 Jun (6) 1519-32
Zeldovich KB et al. Mol. Biol. Evol. 2015 Jun (6) 1519-32
Epidemic clones, oceanic Gene pools, and eco-LD in the free living marine pathogen vibrio parahaemolyticus.
Cui Y et al. Mol. Biol. Evol. 2015 Jun (6) 1396-410
Cui Y et al. Mol. Biol. Evol. 2015 Jun (6) 1396-410
Host-Microbe Interactions
Signature patterns of MHC diversity in three Gombe communities of wild chimpanzees reflect fitness in reproduction and immune defense against SIVcpz.
Wroblewski EE et al. PLoS Biol. 2015 May (5) e1002144
Wroblewski EE et al. PLoS Biol. 2015 May (5) e1002144
Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota.
Liu J et al. Clin. Microbiol. Infect. 2015 May 27.
Liu J et al. Clin. Microbiol. Infect. 2015 May 27.
Fighting fire with fire: endogenous retrovirus envelopes as restriction factors.
Malfavon-Borja R et al. J. Virol. 2015 Apr (8) 4047-50
Malfavon-Borja R et al. J. Virol. 2015 Apr (8) 4047-50
Methods
Inferring horizontal gene transfer.
Ravenhall M et al. PLoS Comput. Biol. 2015 May (5) e1004095
Ravenhall M et al. PLoS Comput. Biol. 2015 May (5) e1004095
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.
Coll F et al. Genome Med 2015 (1) 51
Coll F et al. Genome Med 2015 (1) 51
Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples.
Rosseel T et al. J. Virol. Methods 2015 May 26.
Rosseel T et al. J. Virol. Methods 2015 May 26.
Building a pan-genome reference for a population.
Nguyen N et al. J. Comput. Biol. 2015 May (5) 387-401
Nguyen N et al. J. Comput. Biol. 2015 May (5) 387-401
Development of a nucleic acid extraction procedure for simultaneous recovery of DNA and RNA from diverse microbes in water.
Hill VR et al. Pathogens 2015 (2) 335-54 (CDC Author)
Hill VR et al. Pathogens 2015 (2) 335-54 (CDC Author)
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
Berlin K et al. Nat. Biotechnol. 2015 May 25.
Berlin K et al. Nat. Biotechnol. 2015 May 25.
Evolution of tRNA repertoires in Bacillus inferred with OrthoAlign.
Tremblay-Savard O et al. Mol. Biol. Evol. 2015 Jun (6) 1643-56
Tremblay-Savard O et al. Mol. Biol. Evol. 2015 Jun (6) 1643-56
Phylodynamic inference with kernel ABC and its application to HIV epidemiology.
Poon Art FY et al. Mol. Biol. Evol. 2015 May 25.
Poon Art FY et al. Mol. Biol. Evol. 2015 May 25.
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Benavente ED et al. BMC Bioinformatics 2015 155
Benavente ED et al. BMC Bioinformatics 2015 155
MANTIS: an R package that simulates multilocus models of pathogen evolution.
Lourenço J et al. BMC Bioinformatics 2015 176
Lourenço J et al. BMC Bioinformatics 2015 176
Reviews, News and Commentaries
Smartphone app to aid personalised treatment of deadly disease
Bazeley R. PHG Foundation, May 11, 2015.
Bazeley R. PHG Foundation, May 11, 2015.
TGAC to use $230K grant to develop bioinformatics tools for research, clinical use
Thomas UG. GenomeWeb, May 28, 2015.[by free subscription only]
Thomas UG. GenomeWeb, May 28, 2015.[by free subscription only]
The Federal Government is unprepared for a large-scale animal disease outbreak
Katz E. Gov Exec, May 28, 2015.
Katz E. Gov Exec, May 28, 2015.
Alternate pathways yield new antibiotics
Keener AB. The Scientist, May 29, 2015.
Keener AB. The Scientist, May 29, 2015.
MERS-CoV in Korea, China
Vence T. The Scientist, June 1, 2015.
Vence T. The Scientist, June 1, 2015.
Contact lenses can change the ocular microbiome
Keener AB. The Scientist, June 1, 2015.
Keener AB. The Scientist, June 1, 2015.
Liberia's LIBR genome center monitors Ebola outbreak, emerging pathogens
Heger M. GenomeWeb, May 29, 2015.
Heger M. GenomeWeb, May 29, 2015.
AITbiotech lands CE-IVD mark for Dengue test kit
GenomeWeb, May 29, 2015.
GenomeWeb, May 29, 2015.
Researchers argue for standard format to cite lab resources
Chawla DS. Nature, May 29, 2015
Chawla DS. Nature, May 29, 2015
Mobidiag lands CE-IVD mark for gastric pathogen detection and drug resistance test
GenomeWeb, Jun 3, 2015.
GenomeWeb, Jun 3, 2015.
Pooling sputum leads to 30 percent cost savings for Xpert TB testing
Johnson M. GenomeWeb, Jun 3, 2015.
Johnson M. GenomeWeb, Jun 3, 2015.
Scientists release Ebola sequencing data to global research community online
University of Cambridge, Jun 3, 2015.
University of Cambridge, Jun 3, 2015.
Nanopore sequencer enables rapid analysis of Ebola outbreak in West Africa
Karow J. GenomeWeb, Jun 3, 2015.
Karow J. GenomeWeb, Jun 3, 2015.
FDA clears Roche HSV 1 and 2 Test
GenomeWeb, Jun 4, 2015.
GenomeWeb, Jun 4, 2015.
TB-Profiler uses whole genome data to better predict resistance to therapeutics
Thomas UG. GenomeWeb, Jun 4, 2015..[by free subscription only]
Thomas UG. GenomeWeb, Jun 4, 2015..[by free subscription only]
DARPA announces winners for most accurate forecasts of infectious mosquito-spread virus
Sarkar D. FierceHomelandSecurity, May 27, 2015.
Sarkar D. FierceHomelandSecurity, May 27, 2015.
kallisto paper summary: near-optimal RNA-seq quantification
(blog) Next Gen Seek, May 31, 2015.
(blog) Next Gen Seek, May 31, 2015.
Use of the microbiome in the practice of epidemiology: a primer on -omic technologies.
Foxman Betsy et al. Am. J. Epidemiol. 2015 May 29.
Foxman Betsy et al. Am. J. Epidemiol. 2015 May 29.
Chimps, humans, and the hominid struggle against viruses.
Roberts Roland G et al. PLoS Biol. 2015 May (5) e1002145
Roberts Roland G et al. PLoS Biol. 2015 May (5) e1002145
Ebola in antiquity?
Kazanjian P. Clin Infect Dis, Jun 1, 2015.
Kazanjian P. Clin Infect Dis, Jun 1, 2015.
Immuno-based detection of Shiga toxin-producing pathogenic Escherichia coli in food - A review on current approaches and potential strategies for optimization.
Baker CA et al. Crit. Rev. Microbiol. 2015 May 27. 1-20
Baker CA et al. Crit. Rev. Microbiol. 2015 May 27. 1-20
Elucidating microbial codes to distinguish individuals.
Byrd AL et al. Proc. Natl. Acad. Sci. U.S.A. 2015 May 26.
Byrd AL et al. Proc. Natl. Acad. Sci. U.S.A. 2015 May 26.
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