Infectious Diseases
Methods
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Farhat MR, et al. Genome Medicine 2014, 6:101.
Farhat MR, et al. Genome Medicine 2014, 6:101.
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Hong LZ, et al. Genome Biology 2014, 15:517.
Hong LZ, et al. Genome Biology 2014, 15:517.
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
[PDF 432.40 KB]![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Timothy D Read and Ruth C Massey Genome Medicine 2014, 6:109
Timothy D Read and Ruth C Massey Genome Medicine 2014, 6:109
Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Olsen RJ, et al. J Clin Microbiol 2014; 52(12): 4210-4216.
Olsen RJ, et al. J Clin Microbiol 2014; 52(12): 4210-4216.
Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Matranga CB, et al. Genome Biol 2014 Nov 18;15(11):519.
Matranga CB, et al. Genome Biol 2014 Nov 18;15(11):519.
Equipment-free incubation of recombinase polymerase amplification reactions using body heat![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Crannell ZA, et al. PLoS ONE 9(11): e112146.
Crannell ZA, et al. PLoS ONE 9(11): e112146.
Comment:
Rice U team shows feasibility of body heat-activated isothermal amplification for low-resource MDx![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Johnson M. GenomeWeb, Nov 18, 2014.
Rice U team shows feasibility of body heat-activated isothermal amplification for low-resource MDx
Johnson M. GenomeWeb, Nov 18, 2014.
Evaluation of viral genome assembly and diversity estimation in deep metagenomes![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Aguirre de Carcer D, et al. BMC Genomics 2014, 15:989.
Aguirre de Carcer D, et al. BMC Genomics 2014, 15:989.
Fast and sensitive protein alignment using DIAMOND![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Buchfink B, et al. Nat Methods 2014 Nov 17.
Buchfink B, et al. Nat Methods 2014 Nov 17.
Protein microarrays for parasite antigen discovery![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Driguez P, et al. Methods Mol Biol 2015;1201:221-33.
Driguez P, et al. Methods Mol Biol 2015;1201:221-33.
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Inouye M, et al. Genome Medicine 2014, 6:90.
Inouye M, et al. Genome Medicine 2014, 6:90.
Rapid core-genome alignment and visualization for thousands of intraspecific microbial genomes![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Treangen TJ, et al. Genome Medicine 2014, 15:524.
Treangen TJ, et al. Genome Medicine 2014, 15:524.
Unexpected cross-species contamination in genome sequencing projects![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Merchant S, et al. PeerJ 2:e675.
Merchant S, et al. PeerJ 2:e675.
Comment:
Researchers find sequences from contaminants within genomes housed in public databases![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
GenomeWeb, Nov 20, 2014.
Researchers find sequences from contaminants within genomes housed in public databases
GenomeWeb, Nov 20, 2014.
Evolution, Ecology, Pathogenicity, Populations
16S rRNA gene sequencing, multilocus sequence analysis, and mass spectrometry identification of the proposed new species “Clostridium neonatale”![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Bouvet P, et al. J Clin Microbiol 2014; 52(12): 4129-4136.
Bouvet P, et al. J Clin Microbiol 2014; 52(12): 4129-4136.
Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease ![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Valero LG, et al. Genome Biology 2014, 15:505.
Valero LG, et al. Genome Biology 2014, 15:505.
Ecological succession and viability of human-associated microbiota on restroom surfaces ![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Gibbons SM, et al. Appl Environ Microbiol, 14 November 2014.
Gibbons SM, et al. Appl Environ Microbiol, 14 November 2014.
Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity.![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Stuart D Dowall et al. Genome Biology, November 22, 2014
Stuart D Dowall et al. Genome Biology, November 22, 2014
Multilocus sequence typing of Corynebacterium ulcerans provides evidence for zoonotic transmission and for increased prevalence of certain sequence types among toxigenic strains![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Konig C, et al. J Clin Microbiol 2014; 52(12): 4318-4324.
Konig C, et al. J Clin Microbiol 2014; 52(12): 4318-4324.
Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Zhou Y, et al. J Clin Microbiol 2014; 52(12): 4260-4266.
Zhou Y, et al. J Clin Microbiol 2014; 52(12): 4260-4266.
Whole genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
De Smet B, et al. J Clin Microbiol 2014 Nov 12.
De Smet B, et al. J Clin Microbiol 2014 Nov 12.
Whole-genome comparison of Aspergillus fumigatus strains serially isolated from patients with aspergillosis![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Hagiwara D, et al. J Clin Microbiol 2014; 52(12): 4202-4209.
Hagiwara D, et al. J Clin Microbiol 2014; 52(12): 4202-4209.
Detection & Diagnosis
Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Bartels MD, et al. J Clin Microbiol 2014; 52(12): 4305-4308.
Bartels MD, et al. J Clin Microbiol 2014; 52(12): 4305-4308.
Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Ip M, et al. J Clin Microbiol 2014; 52(12): 4244-4252.
Ip M, et al. J Clin Microbiol 2014; 52(12): 4244-4252.
Evaluation of the Bruker Biotyper and VITEK MS MALDI-TOF MS systems for the identification of unusual and/or difficult-to-identify microorganisms isolated from clinical specimens![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
McElvania TeKippe E, Burnham CA. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2163-71.
McElvania TeKippe E, Burnham CA. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2163-71.
Genomic load from sputum samples and nasopharyngeal swabs for diagnosis of pneumococcal pneumonia in HIV-infected adults![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Albrich WC, et al. J Clin Microbiol 2014; 52(12): 4224-4229.
Albrich WC, et al. J Clin Microbiol 2014; 52(12): 4224-4229.
Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires reevaluation of current diagnostics![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
van der Graaf-van Bloois L, et al. J Clin Microbiol 2014; 52(12): 4183-4188.
van der Graaf-van Bloois L, et al. J Clin Microbiol 2014; 52(12): 4183-4188.
Pooled specimens for HIV RNA monitoring: cheaper, but is it reliable?![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
El Bouzidi K, et al. Clin Infect Dis 2014; 59 (9): 1346-1347.
El Bouzidi K, et al. Clin Infect Dis 2014; 59 (9): 1346-1347.
Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Memish ZA, et al. J Infect Dis. 2014 Nov 15;210(10):1590-4.
Memish ZA, et al. J Infect Dis. 2014 Nov 15;210(10):1590-4.
The Enigma ML FluAB-RSV assay: a fully automated molecular test for the rapid detection of influenza A, B and respiratory syncytial viruses in respiratory specimens.![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Goldenberg SD1, Edgeworth JD. Expert Rev Mol Diagn 2014 Nov 17:1-10.
Goldenberg SD1, Edgeworth JD. Expert Rev Mol Diagn 2014 Nov 17:1-10.
Epidemiology, Outbreaks, Transmission
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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Bousema T, et al. Nat Rev Microbiol 2014; 12: 833–840.
Bousema T, et al. Nat Rev Microbiol 2014; 12: 833–840.
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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
McAdam P, et al. Genome Biology 2014, 15:504.
McAdam P, et al. Genome Biology 2014, 15:504.
Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
GenomeWeb, Nov 20, 2014.
Study details the impact of WGS in resolving a three-year outbreak of opportunistic pathogen
GenomeWeb, Nov 20, 2014.
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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Wu G, Webby RJ. Cell Host Microbe 2014; 16(5): 559–561.
Barcoding influenza virus to decode transmission
Wu G, Webby RJ. Cell Host Microbe 2014; 16(5): 559–561.
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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=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.
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_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Knetsch CW, et al. Euro Surveill. 2014;19(45):pii=20954.
Knetsch CW, et al. Euro Surveill. 2014;19(45):pii=20954.
Antimicrobials, Vaccines, Interventions
A CRISPR design for next-generation antimicrobials![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Beisel CL, et al. Genome Biology 2014, 15:516.
Beisel CL, et al. Genome Biology 2014, 15:516.
Engineering the control of mosquito-borne infectious diseases![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Gabrieli P, et al. Genome Biology 2014, 15:535.
Gabrieli P, et al. Genome Biology 2014, 15:535.
Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Vegard Eldholm, et al. Genome Biology 2014, 15:490
Vegard Eldholm, et al. Genome Biology 2014, 15:490
Comment:
The road to drug resistance in Mycobacterium tuberculosis![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Koch A, Wilkinson R. Genome Biology 2014, 15:520.
The road to drug resistance in Mycobacterium tuberculosis
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Host-Pathogen Interactions
Bringing non-human primate research into the post-genomic era: how monkeys are teaching us about elite controllers of HIV/AIDS![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Vallender EJ. Genome Biology 2014, 15:507.
Vallender EJ. Genome Biology 2014, 15:507.
HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
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Comment:
HIV virulence depends on where virus inserts itself in host DNA![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Leuven KU. Science Daily, Nov 12, 2014.
HIV virulence depends on where virus inserts itself in host DNA
Leuven KU. Science Daily, Nov 12, 2014.
Members of the human gut microbiota involved in recovery from Vibrio cholerae infection![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Hsiao A, et al. Nature 2014; 515: 423–426.
Hsiao A, et al. Nature 2014; 515: 423–426.
Comment:
Microbiota talks cholera out of the gut![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Hay AJ, Zhu J. Cell Host Microbe 2014; 16(5): 549–550.
Microbiota talks cholera out of the gut
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Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
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The conjunctival microbiome in health and trachomatous disease: a case control study![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
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Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
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Reviews, News & Commentaries
Contamination plagues some microbiome studies![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Pennisi E. Science 14 November 2014: 346: 801.
Pennisi E. Science 14 November 2014: 346: 801.
Dialogue between skin microbiota and immunity.
Yasmine Belkaid, Julia A. Segre. Science, November 21, 2014
Yasmine Belkaid, Julia A. Segre. Science, November 21, 2014
Ebola trials to start in December![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Hayden EC. Nature, Nov 13, 2014.
Hayden EC. Nature, Nov 13, 2014.
Eradicating malaria: how parasites' genetic 'barcodes' can stop the spread![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Clark T, Roper C. Guardian, Nov 17, 2014.
Clark T, Roper C. Guardian, Nov 17, 2014.
Joint effort nabs next wave of US supercomputers![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Witze A. Nature, Nov 14, 2014.
Witze A. Nature, Nov 14, 2014.
Next-gen sequencing user survey![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Bird C. The Scientist, Nov 1, 2014.
Bird C. The Scientist, Nov 1, 2014.
Recombination: genomic mix 'n' match![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Boinett CJ, Cain AK. Nat Rev Microbiol 2014; 12: 795.
Boinett CJ, Cain AK. Nat Rev Microbiol 2014; 12: 795.
Significance and integration of molecular diagnostics in the framework of veterinary practice![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Aranaz A. Methods Mol Biol 2015;1247:19-30.
Aranaz A. Methods Mol Biol 2015;1247:19-30.
The importance of sample archiving in microbial ecology![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Cary SC, Fierer N. Nat Rev Microbiol 2014; 12, 789–790.
Cary SC, Fierer N. Nat Rev Microbiol 2014; 12, 789–790.
When mutation counters infection: from sickle cell to Ebola![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
Lewis R. PLoS DNA Science Blog, Nov 14, 2014.
Lewis R. PLoS DNA Science Blog, Nov 14, 2014.
USAID, Broad, Illumina partner to help with Ebola genome surveillance in West Africa![External Web Site Icon External Web Site Icon](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_tDi6j3k1p9CW3fwK58dJOPh4DhoUIQdEpD6QLKRpbGfeyOoCdYuNJ4Q3hIkmLykwG84cPR6CyxqinRxLL1zVRDPslVF8hxbk6iIx_2XaNoKxQ_Hl9wC8zI=s0-d)
GenomeWeb, Nov 19, 2014.
GenomeWeb, Nov 19, 2014.
The skin microbiome: More than skin deep,
by Bruce Agnew, NHGRI, Nov 20
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