E-TABM-148 - Comparative genomic hybridization of seven strains of the human pathogenic acetic acid bacterium Granulibacter bethesdensis

Status
Released on 23 November 2007, last updated on 2 May 2014
Organism
Granulibacter bethesdensis
Samples (7)
Array (1)
Protocols (3)
Description
Chronic granulomatous disease (CGD) is a rare genetic defect in neutrophil superoxide formation in which patients develop recurrent life-threatening infections with Staphylococcus aureus, Serratia marcescens, Burkholderia cepacia, Nocardia and Aspergillus species. We recently described a novel member of the Acetobacteraceae, Granulibacter bethesdensis, in several CGD patients who presented with fever and lymphadenitis. In order to more fully understand the infectivity of this novel human pathogen we sequenced the genome of Granulibacter bethesdensis to its entirety and identified a single, circular chromosome consisting of 2,708,355 base pairs with a G+C content of 59.07%. We identified 2,437 predicted protein-encoding open reading frames (ORFS) of which, 75.17% have a biological functional annotation. Comparison of G. bethesdensis to another member of the Acetobacteraceae, Gluconobacter oxydans, indicates functional conservation between the two genomes, but also the presence of ORFS unique to G. bethesdensis consistent with virulence, adherence, DNA uptake and methanol utilization. In addition, comparative genome analysis of G. bethesdensis to known CGD pathogens demonstrated broad conservation of putative virulence factors. Finally, G. bethesdensis isolate DNAs were hybridized to a high density custom array, towards characterizing plasticity zones, which occur in regions with genes related to DNA uptake systems, transcriptional regulators and those of unknown function. Together these results provide insight into a novel human pathogen, which is geographically dispersed, is undergoing gain or loss of important DNA elements and which infects patients with CGD.
Experiment types
comparative genomic hybridization by array, comparative genome hybridization
Contact
Dan Sturdevant
Citation
Genome Sequence Analysis of a Novel Human Pathogenic Acetic Acid Bacterium Granulibacter bethesdensis. David E. Greenberg; Stephen F. Porcella; Adrian M. Zelazny; Frida Stock; Kimmo Virtaneva; Dan Sturdevant; John Kupko; Kent Barbian; Amenah Babar; David W. Dorward; Patrick R. Murray;Steven M. Holland. Proc Natl Acad Sci U S A 
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-TABM-148.idf.txt
Sample and data relationshipE-TABM-148.sdrf.txt
Raw data (1)E-TABM-148.raw.1.zip
Processed data (1)E-TABM-148.processed.1.zip
Array designA-AFFY-74.adf.txt
R ExpressionSetE-TABM-148.eSet.r
Links