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Series GSE19071 Query DataSets for GSE19071
Status Public on Nov 25, 2009
Title Isolation and characterization of environmental Bacillus isolates which may harbor B. anthracis virulence genes
Platform organism Bacillus anthracis
Sample organisms Bacillus cereus; Bacillus anthracis str. Sterne
Experiment type Genome variation profiling by array
Summary The goal of this project was to screen soil samples for bacteria that may harbor B. anthracis virulence-associated genes (VAGs). There is currently no information about the prevalence of these types of organisms in the environment. Due to increased environmental monitoring of select agents by programs such as BioWatch and biodetection systems in place at the United States Post Offices and Department of State locations, it has become critical that we not only better understand the natural range of B. anthracis but also how widespread B. anthracis virulence genes are in environmental communities. Naturally occurring isolates containing the B. anthracis virulence genes could generate false-positive results in tests that detect the anthrax toxins, capsule or their associated genes. Understanding the true diversity and pathogenic potential of Bacillus spp. and particularly the B. cereus group is crucial not only in terms of understanding data from environmental monitoring but also diagnosing patients with clinical presentations similar to anthrax in the future. Severe and fatal disease caused by strains similar to B. anthracis could unnecessarily initiate emergency responses if anthrax was incorrectly suspected. Conversely, these strains may be used as bioterror agents requiring science-based responses; presently our limited understanding of these organisms does not permit data-driven decision making.

We have investigated 700 aerobic sporoform soil isolates obtained from two areas in the Southwest of the US. Soil samples from the first site had been taken from public access land approximately 50 meters across from the work site of a fatal pneumonia case in a welding factory. This took place in year 2003 when B. cereus was isolated from a metal worker. The second site was targeted because of a recent case involving a deceased mule suspected to have died of a B. anthracis infection. Soil samples were initially analyzed at the CDC. Isolates were obtained by heating the soil at 65 degrees Celcius for 30 minutes followed by plating on agar media. All isolates were screened by PCR for the presence of B. anthracis genomic traits such as toxin genes (cya, lef and pag) as well as chromosomal markers. All isolates were also tested for their hemolytic activity as well as phage sensitivity.
 
Overall design Eighty-four query strains were investigated in this study, with each query strain hybridized against the reference strain, Sterne. Two dye-swap experiments were performed with seventeen strains, for a total of four hybridizations per query strain. The other strains have a single dye experiment, for a total of two hybridizations per query strain. Each 70mer oligo spotted on the B. cereus species microarray is spotted once. Positive controls on the array consist of oligos designed from the sequenced reference genome, Sterne, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.
 
Contributor(s) Papazisi L, Remortel BG, Appalla L, Onmus-Leone F, Sajadi H, Ratnayke S, Sun Q, Wan C, Podnecky N, Beesley CA, Fleischmann RD, Hoffmaster A, Peterson SN
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Submission date Nov 17, 2009
Last update date Mar 21, 2012
Contact name Chun-Hua Wan
E-mail(s) cwan@jcvi.org
Phone 301-795-7707
Organization name The J. Craig Venter Institute
Department Pathogen Functional Genomics Resources Center (PFGRC)
Lab IFX
Street address 9704 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Platforms (2)
GPL9095 JCVI PFGRC Bacillus anthracis 23K vt3a array designed primarily based on strain Sterne
GPL9098 JCVI PFGRC Bacillus anthracis 25K vt3b array designed primarily based on strain Sterne
Samples (202)
GSM470447 T3AQBC06092008A_3248_CY5_STERNE_CY3_13824589_A
GSM470488 T3AQBC06092008A_3293_CY5_STERNE_CY3_13824588_A
GSM470489 T3AQBC06092008A_3390_CY5_STERNE_CY3_13824590_A
Relations
BioProject PRJNA120475

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19071_RAW.tar 251.3 Mb (http)(custom) TAR (of MEV)
Processed data included within Sample table
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