Genomics|Update|Infectious Diseases

Genomics|Update|Infectious Diseases

Volume 33  Number 22  December 4-18, 2014

Methods

Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples
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
Jeffries MKS, et al. BMC Biotechnology 2014, 14:94.

bam.iobio: a web-based, real-time, sequence alignment file inspector
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
Thomas UG. GenomeWeb, Dec 1, 2014.

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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.

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.

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution
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.

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.

Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes 
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.

Comment:

Team sequences mosquito genomes to better understand malaria parasite transmission 
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.

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Detection & Diagnosis

Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1
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
Kipanga PN, et al. Malaria J 2014; 13:429.

Comment:

Kenyan researchers combine nested PCR, high-resolution melt to detect, type malaria
Johnson M. GenomeWeb, Dec 2, 2014.

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Epidemiology, Outbreaks, Transmission

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting
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
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
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
GenomeWeb, Nov 20, 2014.

Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak
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
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
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
Varble A, et al. Cell Host Microbe 2014; 16(5): 691–700.

Comment:

Barcoding influenza virus to decode transmission
Wu G, Webby RJ. Cell Host Microbe 2014; 16(5): 559–561.

Asymptomatic malaria infections: detectability, transmissibility and public health relevance
Bousema T, et al.  Nat Rev Microbiol 2014; 12: 833–840.

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Antimicrobials, Vaccines, Interventions

Chimpanzee adenovirus vector Ebola vaccine — preliminary report
Ledgerwood JE, et al. New Engl J Med, Nov 26, 2014.

Comment:

One step closer to an Ebola virus vaccine
Bausch DG. New Engl J Med, Nov 26, 2014.

Positive results spur race for Ebola vaccine
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.

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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.

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.

Variation at HLA-DRB1 is associated with resistance to enteric fever 
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.

Comment:

Feverish prospects for seizure genetics
Sisodiya S. Nat Genet 2014; 46: 1255–1256.

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility
Seto CT, et al. Microbiome 2014, 2:42.

Comment:

Sequencing reveals changes in gut microbiome from PPI treatment, supports link to C. diff infection
Ashford M. GenomeWeb, Dec 1, 2014.

Effect of non-tuberculous Mycobacteria on host biomarkers potentially relevant for tuberculosis management
Dhanasekaran S, et al. PLoS Negl Trop Dis 2014; 8(10): e3243.

Microbiome: The bacterial tightrope
Bourzac K. Nature  2014; 516: S14–S16.

The feline oral microbiome: a provisional 16S rRNA gene based taxonomy with full-length reference sequences
Dewhurst FE, et al. Vet Microbiol, Dec 1, 2014.

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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 virus detectives: sifting through genes in search of answers on Ebola
Kolata G. New York Times, Dec 1, 2014.

15-Minute Ebola test to undergo trials in Guinea
Bajekal N. TIME, Nov 28, 2014.

ARUP study demonstrates potential of metagenomic sequencing for respiratory virus Dx
Ashford M. GenomeWeb, Dec 3, 2014.

GenomeWeb updates on molecular diagnostics:

IDT, Ubiquitome partner to develop mobile Ebola test

Cepheid gets FDA OK to market flu/RSV MDx assay

Cepheid gets FDA clearance for Xpert norovirus assay

Hologic gets CE mark for HIV viral load assay