Volume 33 Number 22 December 4-18, 2014
Methods
Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Strong MJ, et al. PLOS Pathog 2014; 10(11): e1004437.
Strong MJ, et al. PLOS Pathog 2014; 10(11): e1004437.
A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Jeffries MKS, et al. BMC Biotechnology 2014, 14:94.
Jeffries MKS, et al. BMC Biotechnology 2014, 14:94.
bam.iobio: a web-based, real-time, sequence alignment file inspector![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Miller CA, et al. Nat Methods 2014; 11: 1189.
Miller CA, et al. Nat Methods 2014; 11: 1189.
Comment:
New web-based apps from BC, U of Utah offer faster, more intuitive looks at genomic data files![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Thomas UG. GenomeWeb, Dec 1, 2014.
Thomas UG. GenomeWeb, Dec 1, 2014.
Evolution, Ecology, Pathogenicity, Populations
The presence of the pAA plasmid in the German O104:H4 Shiga toxin type 2a (Stx2a)–producing enteroaggregative Escherichia coli strain promotes the translocation of Stx2a across an epithelial cell monolayer
Boisen N, et al. J Infect Dis 2014; 210(12): 1909-1919.
Boisen N, et al. J Infect Dis 2014; 210(12): 1909-1919.
Comment:
The worst of both worlds: examining the hypervirulence of the shigatoxigenic/enteroaggregative Escherichia coli O104:H4
Steiner TS. J Infect Dis 2014; 210(12): 1860-1862.
Steiner TS. J Infect Dis 2014; 210(12): 1860-1862.
Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
von Mentzer A, et al. Nat Genet 2014; 46: 1321–1326.
von Mentzer A, et al. Nat Genet 2014; 46: 1321–1326.
Genetic diversity and evolutionary relationships among Legionella pneumophila clinical isolates, Portugal, 1987 to 2012
Chasqueira MJ, et al. Euro Surveill 2014;19(46):pii=20965.
Chasqueira MJ, et al. Euro Surveill 2014;19(46):pii=20965.
The evolutionary history and spatiotemporal dynamics of the fever, thrombocytopenia and leukocytopenia syndrome virus (FTLSV) in China
Huang X, et al. PLoS Negl Trop Dis 2014; 8(10): e3237.
Huang X, et al. PLoS Negl Trop Dis 2014; 8(10): e3237.
Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes
Neafsey DE, et al. Science, Nov 27, 2014.
Neafsey DE, et al. Science, Nov 27, 2014.
Extensive introgression in a malaria vector species complex revealed by phylogenomics
Fontaine MC, et al. Science, Nov 27, 2014.
Fontaine MC, et al. Science, Nov 27, 2014.
Comment:
Team sequences mosquito genomes to better understand malaria parasite transmission
GenomeWeb, Dec 1, 2014.
GenomeWeb, Dec 1, 2014.
Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates
Ocholla H, et al. J Infect Dis 2014; 210(12): 1991-2000.
Ocholla H, et al. J Infect Dis 2014; 210(12): 1991-2000.
Detection & Diagnosis
Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Singleton J, et al. PLoS ONE 9(11): e113693.
Singleton J, et al. PLoS ONE 9(11): e113693.
High-resolution melting analysis reveals low Plasmodium parasitaemia infections among microscopically negative febrile patients in western Kenya![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Kipanga PN, et al. Malaria J 2014; 13:429.
Comment:Kipanga PN, et al. Malaria J 2014; 13:429.
Kenyan researchers combine nested PCR, high-resolution melt to detect, type malaria![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Johnson M. GenomeWeb, Dec 2, 2014.
Johnson M. GenomeWeb, Dec 2, 2014.
Epidemiology, Outbreaks, Transmission
Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Tong S, et al. Genome Res. 2014. Dec 9
Tong S, et al. Genome Res. 2014. Dec 9
Team uses sequencing to track MRSA in resource-limited center with high transmission rates,
Genome Web, Dec 9 [by free subscription]
Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Knetsch CW, et al. Euro Surveill. 2014;19(45):pii=20954.
Knetsch CW, et al. Euro Surveill. 2014;19(45):pii=20954.
Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistantAcinetobacter baumannii in Birmingham, England![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Halachev MR, et al. Genome Med 2014, 6:70.
Halachev MR, et al. Genome Med 2014, 6:70.
Comment:
Study details the impact of WGS in resolving a three-year outbreak of opportunistic pathogen![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
GenomeWeb, Nov 20, 2014.
GenomeWeb, Nov 20, 2014.
Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
McAdam P, et al. Genome Biology 2014, 15:504.
McAdam P, et al. Genome Biology 2014, 15:504.
Presence of human non-polio enterovirus and parechovirus genotypes in an Amsterdam hospital in 2007 to 2011 compared to national and international published surveillance data: a comprehensive review![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Janes VA, et al. Euro Surveill 2014;19(46):pii=20964.
Janes VA, et al. Euro Surveill 2014;19(46):pii=20964.
Multilocus Sequence Typing (MLST) and whole-genome MLST of Campylobacter jejuni isolates from human infections in three districts during a seasonal peak in Finland![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Kovanen SM, et al. J Clin Microbiol 2014; 52(12): 4147-4154.
Kovanen SM, et al. J Clin Microbiol 2014; 52(12): 4147-4154.
Influenza A virus transmission bottlenecks are defined by infection route and recipient host![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Varble A, et al. Cell Host Microbe 2014; 16(5): 691–700.
Varble A, et al. Cell Host Microbe 2014; 16(5): 691–700.
Comment:
Barcoding influenza virus to decode transmission![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Wu G, Webby RJ. Cell Host Microbe 2014; 16(5): 559–561.
Wu G, Webby RJ. Cell Host Microbe 2014; 16(5): 559–561.
Asymptomatic malaria infections: detectability, transmissibility and public health relevance![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Bousema T, et al. Nat Rev Microbiol 2014; 12: 833–840.
Bousema T, et al. Nat Rev Microbiol 2014; 12: 833–840.
Antimicrobials, Vaccines, Interventions
Chimpanzee adenovirus vector Ebola vaccine — preliminary report![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Ledgerwood JE, et al. New Engl J Med, Nov 26, 2014.
Ledgerwood JE, et al. New Engl J Med, Nov 26, 2014.
Comment:
One step closer to an Ebola virus vaccine![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Bausch DG. New Engl J Med, Nov 26, 2014.
Bausch DG. New Engl J Med, Nov 26, 2014.
Positive results spur race for Ebola vaccine![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Callaway E. Nature, Dec 2, 2014.
Callaway E. Nature, Dec 2, 2014.
Deep-sequencing analysis of the gene encoding the hepatitis C virus nonstructural 3–4a protease confirms a low prevalence of telaprevir-resistant variants at baseline and the end of the REALIZE Study
Diernyck I, et al. J Infect Dis 2014; 210(12): 1871-1880.
Diernyck I, et al. J Infect Dis 2014; 210(12): 1871-1880.
Host-Pathogen Interactions
Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence
Payne R, et al. Proc Natl Acad Sci U S A. 2014 Dec 1.
Payne R, et al. Proc Natl Acad Sci U S A. 2014 Dec 1.
Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection
Le Clerc S, et al. J Infect Dis 2014; 210(12): 1946-1950.
Le Clerc S, et al. J Infect Dis 2014; 210(12): 1946-1950.
Variation at HLA-DRB1 is associated with resistance to enteric fever
Dunstan SJ, et al. Nat Genet 2014; 46: 1333–1336.
Dunstan SJ, et al. Nat Genet 2014; 46: 1333–1336.
Common variants associated with general and MMR vaccine–related febrile seizures
Feenstra B, et al. Nat Genet 2014; 46: 1274–1282.
Feenstra B, et al. Nat Genet 2014; 46: 1274–1282.
Comment:
Feverish prospects for seizure genetics![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Sisodiya S. Nat Genet 2014; 46: 1255–1256.
Sisodiya S. Nat Genet 2014; 46: 1255–1256.
Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Seto CT, et al. Microbiome 2014, 2:42.
Seto CT, et al. Microbiome 2014, 2:42.
Comment:
Sequencing reveals changes in gut microbiome from PPI treatment, supports link to C. diff infection![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Ashford M. GenomeWeb, Dec 1, 2014.
Ashford M. GenomeWeb, Dec 1, 2014.
Effect of non-tuberculous Mycobacteria on host biomarkers potentially relevant for tuberculosis management![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Dhanasekaran S, et al. PLoS Negl Trop Dis 2014; 8(10): e3243.
Dhanasekaran S, et al. PLoS Negl Trop Dis 2014; 8(10): e3243.
Microbiome: The bacterial tightrope![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Bourzac K. Nature 2014; 516: S14–S16.
Bourzac K. Nature 2014; 516: S14–S16.
The feline oral microbiome: a provisional 16S rRNA gene based taxonomy with full-length reference sequences![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Dewhurst FE, et al. Vet Microbiol, Dec 1, 2014.
Dewhurst FE, et al. Vet Microbiol, Dec 1, 2014.
Reviews, News & Commentaries
Microbiology: Ditch the term pathogen,
by Arturo Casadevall & Liise-anne Pirofski, Nature News, Dec 10
Top 10 innovations 2014
The Scientist, Dec 1, 2014.
The Scientist, Dec 1, 2014.
The virus detectives: sifting through genes in search of answers on Ebola![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Kolata G. New York Times, Dec 1, 2014.
Kolata G. New York Times, Dec 1, 2014.
15-Minute Ebola test to undergo trials in Guinea![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Bajekal N. TIME, Nov 28, 2014.
Bajekal N. TIME, Nov 28, 2014.
ARUP study demonstrates potential of metagenomic sequencing for respiratory virus Dx![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_vtDSGMI-yEezW7P4xVGYYkjlbjLLdcDfSqDf3al8Q8qcsxBiogiQj8SslVDfzwez2cIM6UbpbkGJDzq1MNEd92BUmj0NVtjfabKOQqWNS3ENvRw7ClRekD=s0-d)
Ashford M. GenomeWeb, Dec 3, 2014.
Ashford M. GenomeWeb, Dec 3, 2014.
GenomeWeb updates on molecular diagnostics:
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