Genomics|Update|Current ► Infectious Diseases

Genomics|Update|Current

Infectious Diseases

Methods

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Farhat MR, et al. Genome Medicine 2014, 6:101.

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
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]
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
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
Matranga CB, et al. Genome Biol 2014 Nov 18;15(11):519.

Equipment-free incubation of recombinase polymerase amplification reactions using body heat
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
Johnson M. GenomeWeb, Nov 18, 2014.

Evaluation of viral genome assembly and diversity estimation in deep metagenomes
Aguirre de Carcer D, et al. BMC Genomics 2014, 15:989.

Fast and sensitive protein alignment using DIAMOND
Buchfink B, et al. Nat Methods 2014 Nov 17.

Protein microarrays for parasite antigen discovery
Driguez P, et al. Methods Mol Biol 2015;1201:221-33.

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Inouye M, et al. Genome Medicine 2014, 6:90.

Rapid core-genome alignment and visualization for thousands of intraspecific microbial genomes
Treangen TJ, et al. Genome Medicine 2014, 15:524.

Unexpected cross-species contamination in genome sequencing projects
Merchant S, et al. PeerJ 2:e675.

Comment:
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”
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 
Valero LG, et al. Genome Biology 2014, 15:505.

Ecological succession and viability of human-associated microbiota on restroom surfaces 
Gibbons SM, et al. Appl Environ Microbiol, 14 November 2014.

Comment:
Toilet ecology
Gibbons S. microBEnet, Nov 17, 2014.

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity.
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
Konig C, et al. J Clin Microbiol 2014; 52(12): 4318-4324.

Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study
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
De Smet B, et al. J Clin Microbiol 2014 Nov 12.

Whole-genome comparison of Aspergillus fumigatus strains serially isolated from patients with aspergillosis
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
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
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
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
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
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?
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.

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.
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
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
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
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.

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.

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.

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.

Antimicrobials, Vaccines, Interventions

A CRISPR design for next-generation antimicrobials
Beisel CL, et al. Genome Biology 2014, 15:516.

Engineering the control of mosquito-borne infectious diseases
Gabrieli P, et al. Genome Biology 2014, 15:535. 

Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient
Vegard Eldholm, et al.  Genome Biology 2014, 15:490

Comment:
The road to drug resistance in Mycobacterium tuberculosis 
Koch A, Wilkinson R. Genome Biology 2014, 15:520.

Quantitative matrix-assisted laser desorption ionization–time of flight mass spectrometry for rapid resistance detection
Lange C, et al. J Clin Microbiol 2014; 52(12): 4155-4162.

Host-Pathogen Interactions

Bringing non-human primate research into the post-genomic era: how monkeys are teaching us about elite controllers of HIV/AIDS
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
Demeulemeester J, et al. Cell Host Microbe 2014; 16(5): 651–662.

Comment:
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
Hsiao A, et al. Nature 2014; 515: 423–426.

Comment:
Microbiota talks cholera out of the gut
Hay AJ, Zhu J. Cell Host Microbe 2014; 16(5): 549–550.

Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease
Garcia-Nunez M, et al. J Clin Microbiol 2014; 52(12): 4217-4223.

The conjunctival microbiome in health and trachomatous disease: a case control study
Zhou Y, et al. Genome Medicine 2014, 6:99.

Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication
Ericsen AJ, et al. Genome Biology 2014, 15:478.

Reviews, News & Commentaries

Contamination plagues some microbiome studies
Pennisi E. Science 14 November 2014: 346: 801. 

Dialogue between skin microbiota and immunity. 
Yasmine Belkaid, Julia A. Segre.  Science, November 21, 2014

Ebola trials to start in December
Hayden EC. Nature, Nov 13, 2014.

Eradicating malaria: how parasites' genetic 'barcodes' can stop the spread
Clark T, Roper C. Guardian, Nov 17, 2014.

Joint effort nabs next wave of US supercomputers
Witze A. Nature, Nov 14, 2014.

Next-gen sequencing user survey
Bird C. The Scientist, Nov 1, 2014.

Recombination: genomic mix 'n' match
Boinett CJ, Cain AK. Nat Rev Microbiol 2014; 12: 795.

Significance and integration of molecular diagnostics in the framework of veterinary practice
Aranaz A. Methods Mol Biol 2015;1247:19-30.

The importance of sample archiving in microbial ecology
Cary SC, Fierer N. Nat Rev Microbiol 2014; 12, 789–790.

When mutation counters infection: from sickle cell to Ebola
Lewis R. PLoS DNA Science Blog, Nov 14, 2014.

USAID, Broad, Illumina partner to help with Ebola genome surveillance in West Africa
GenomeWeb, Nov 19, 2014.

The skin microbiome: More than skin deep, by Bruce Agnew, NHGRI, Nov 20