Genomics|Update|Current ► Infectious Diseases

Genomics|Update|Current

Infectious Diseases

Methods

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
Quick J, et al. Gigascience 2014 Oct 20;3:22.

A novel microbead-based microfluidic device for rapid bacterial identification and antibiotic susceptibility testing
He J, et al. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2223-30.

Binning metagenomic contigs by coverage and composition
Alneberg J, et al. Nat Methods. 2014 Nov;11(11):1144-6.

Contaminomics: why some microbiome studies may be wrong
Yong E. Not Exactly Rocket Science (National Geographic blog), Nov 11, 2014.

DNA extraction kits contaminated
Grens K, The Scientist, Nov 12, 2014.

Investigating a mystery disease: tales from a viral detective
Lipkin WI. J Virol 2014 Nov 1;88(21):12176-12179.

Keeping it clean: Spotlight on contamination in microbiome studies, 
Walker A. BioMed Central blog, Nov 12, 2014.

Maximum likelihood inference of reticulate evolutionary histories
Yu Y, et al. PNAS, Oct 7, 2014.

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter SJ, et al. BMC Biology 2014; 12:87. 

The importance of sample archiving in microbial ecology
Cary SC, Fierer N. Nat Rev Microbiol, Nov 3, 2014.

Evolution, Ecology, Pathogenicity, Populations

Comparative population structure analysis of Campylobacter jejuni from human and poultry origin in Bangladesh
Islam Z, et al. Eur J Clin Microbiol Infect Dis 2014 Dec; 33(12):2173-81.

Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting 
Cotten M, et al. J Virol. 2014; 88(19): 11056-69.

Diversity and disease pathogenesis in Mycobacterium tuberculosis
Warner DF, et al. Trends Microbiol, Nov 10, 2014.

Global origin and transmission of hepatitis C virus NS3 Q80K polymorphism
McCloskey RM, et al. J Infect Dis, Nov 10, 2014.

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
Salipante SJ, et al. Genome Res, Nov 4, 2014.

Molecular characterization of Shiga-toxigenic Escherichia coli isolated from diverse sources from India by multi-locus variable number tandem repeat analysis (MLVA)
Kumar A, et al. Epidemiol Infect 2014; 142(12): 2572-2582.

Multilocus sequence typing of Mycoplasma bovis reveals host-specific genotypes in cattle versus bison
Register KB, et al. Vet Microbiol, Nov 11, 2014.

Rooting the phylogenetic tree of Middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat
Corman VM, et al. J Virol 2014 Oct;88(19):11297-303.

Virome analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis ticks reveals novel highly divergent vertebrate and invertebrate viruses
Tokarz R, et al. J Virol 2014 Oct;88(19):11480-92.

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes 
Staudova B, et al. PLoS Negl Trop Dis 2014; 8(11): e3261.

Detection & Diagnosis

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
McElvania TeKippe E, Burnham CA. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2163-71.

Pooled specimens for HIV RNA monitoring: cheaper, but is it reliable?
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
Memish ZA, et al. J Infect Dis. 2014 Nov 15;210(10):1590-4.

Epidemiology, Outbreaks, Transmission

Acute gastroenteritis outbreaks associated with ground-waterborne norovirus in South Korea during 2008–2012
Cho HG, et al. Epidemiol Infect 2014; 142(12): 2604-2609.

Four-month outbreak of invasive meningococcal disease caused by a rare serogroup B strain, identified through the use of molecular PorA subtyping, England, 2013
Chatt C, et al. Euro Surveill 2014;19(44):pii=20949.

Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing
Quick J, et al. BMJ Open 2014;4:e006278.

Antimicrobials, Vaccines, Interventions

Characterization of integrons and resistance genes in multidrug-resistant Salmonella enterica isolated from meat and dairy products in Egypt
Ahmed AM, et al. Int J Food Microbiol. 2014; 189: 39-44.

Characterization of the emerging clinically-relevant multidrug-resistant Salmonella enterica serotype 4,[5],12:i:- (monophasic variant of S. Typhimurium) clones
Mourao J, et al. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2249-57.

Complete sequence of a conjugative IncN plasmid harboring blaKPC-2, blaSHV-12, and qnrS1 from an Escherichia coli sequence type 648 strain
Li JJ, et al. Antimicrob. Agents Chemothe  2014; 58(11):  6974-6977.

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance 
Mark R Davies et al. Nature Genetics, November 17, 2014 

French regional surveillance program of carbapenemase-producing Gram-negative bacilli: results from a 2-year period
Pantel A, et al. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2285-92.

Genome-level determination of Plasmodium falciparum blood stage targets of malarial clinical immunity in the Peruvian Amazon
Torres KJ, et al. J Infect Dis, Nov 7, 2014.

High rates of intestinal colonisation with fluoroquinolone-resistant ESBL-harbouring Enterobacteriaceae in hospitalised patients with antibiotic-associated diarrhoea
Vervoort J, et al. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2215-21.

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals
Cavanagh JP, et al. J Antimicrob Chemother 2014 Nov;69(11):2920-7.

Host-Pathogen Interactions

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis.  
Rasmus Lykke Marvig et al. Nature Genetics, November 17, 2014

Diagnostic accuracy of IL-2 for the diagnosis of latent tuberculosis: a systematic review and meta-analysis
Mamishi S, et al. Eur J Clin Microbiol Infect Dis 2014 Dec;33(12):2111-2119.

Evaluation of neonatal Toll-like receptors 3 (c.1377C/T) and 9 (G2848A) gene polymorphisms in HBV intrauterine transmission susceptibility
Gao Y, et al. Epidemiol Infect, Nov 12, 2014.

Variation at HLA-DRB1 is associated with resistance to enteric fever
Dunstan SJ, et al. Nat Genet, Nov 10, 2014.

Comment:
Genome-wide association study links HLA allele to typhoid fever resistance
GenomeWeb, Nov 10, 2014.

Reviews, News & Commentaries

A promising strategy against HIV. Harvard researchers genetically ‘edit’ human blood stem cells, Harvard Gazette, November 2014

USAID, Broad Institute, Illumina join forces to combat Ebola, GEN News Highlights, Nov 19

HIV virulence depends on where virus inserts itself in host DNA, Science Daily, Nov 12