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Title: Discrimination of bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray.

Abstract

Analysis of 16S rRNA sequences is a commonly used method for the identification and discrimination of microorganisms. However, the high similarity of 16S and 23S rRNA sequences of Bacillus cereus group organisms (up to 99-100%) and repeatedly failed attempts to develop molecular typing systems that would use DNA sequences to discriminate between species within this group have resulted in several suggestions to consider B. cereus and B. thuringiensis, or these two species together with B. anthracis, as one species. Recently, we divided the B. cereus group into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, based on 16S rRNA, 23S rRNA and gyrB gene sequences and identified subgroup-specific makers in each of these three genes. Here we for the first time demonstrated discrimination of these seven subgroups, including subgroup Anthracis, with a 3D gel element microarray of oligonucleotide probes targeting 16S and 23S rRNA markers. This is the first microarray enabled identification of B. anthracis and discrimination of these seven subgroups in pure cell cultures and in environmental samples using rRNA sequences. The microarray bearing perfect match/mismatch (p/mm) probe pairs was specific enough to discriminate single nucleotide polymorphisms (SNPs) and was ablemore » to identify targeted organisms in 5 min. We also demonstrated the ability of the microarray to determine subgroup affiliations for B. cereus group isolates without rRNA sequencing. Correlation of these seven subgroups with groupings based on multilocus sequence typing (MLST), fluorescent amplified fragment length polymorphism analysis (AFLP) and multilocus enzyme electrophoresis (MME) analysis of a wide spectrum of different genes, and the demonstration of subgroup-specific differences in toxin profiles, psychrotolerance, and the ability to harbor some plasmids, suggest that these seven subgroups are not based solely on neutral genomic polymorphisms, but instead reflect differences in both the genotypes and phenotypes of the B. cereus group organisms.« less

Authors:
; ; ; ; ; ; ; ; ; ; ;  [1]
  1. Biochip Technology Center
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
FOR; USDOD
OSTI Identifier:
1033092
Report Number(s):
ANL/BTC/JA-38847
Journal ID: ISSN 0009-2797; CBINA8; TRN: US201202%%583
DOE Contract Number:  
DE-AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Chemico-Biological Interactions
Additional Journal Information:
Journal Volume: 171; Journal Issue: 2; Journal ID: ISSN 0009-2797
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; BACILLUS; BACILLUS CEREUS; BEARINGS; CELL CULTURES; DNA; ELECTROPHORESIS; ENZYMES; GENES; MICROORGANISMS; NUCLEOTIDES; OLIGONUCLEOTIDES; PLASMIDS; PROBES; TOXINS

Citation Formats

Bavykin, S G, Mikhailovich, V M, Zakharyev, V M, Lysov, Y P, Kelly, J J, Alferov, O S, Jackman, J, Stahl, D A, Mirzabekov, A D, Gavin, I M, Kukhtin, A V, Chandler, D, Engelhardt Inst. of Molecular Biology), Northwestern Univ.), and Georgetown Univ.). Discrimination of bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray.. United States: N. p., 2008. Web. doi:10.1016/j.cbi.2007.09.002.
Bavykin, S G, Mikhailovich, V M, Zakharyev, V M, Lysov, Y P, Kelly, J J, Alferov, O S, Jackman, J, Stahl, D A, Mirzabekov, A D, Gavin, I M, Kukhtin, A V, Chandler, D, Engelhardt Inst. of Molecular Biology), Northwestern Univ.), & Georgetown Univ.). Discrimination of bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray.. United States. doi:10.1016/j.cbi.2007.09.002.
Bavykin, S G, Mikhailovich, V M, Zakharyev, V M, Lysov, Y P, Kelly, J J, Alferov, O S, Jackman, J, Stahl, D A, Mirzabekov, A D, Gavin, I M, Kukhtin, A V, Chandler, D, Engelhardt Inst. of Molecular Biology), Northwestern Univ.), and Georgetown Univ.). Wed . "Discrimination of bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray.". United States. doi:10.1016/j.cbi.2007.09.002.
@article{osti_1033092,
title = {Discrimination of bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray.},
author = {Bavykin, S G and Mikhailovich, V M and Zakharyev, V M and Lysov, Y P and Kelly, J J and Alferov, O S and Jackman, J and Stahl, D A and Mirzabekov, A D and Gavin, I M and Kukhtin, A V and Chandler, D and Engelhardt Inst. of Molecular Biology) and Northwestern Univ.) and Georgetown Univ.)},
abstractNote = {Analysis of 16S rRNA sequences is a commonly used method for the identification and discrimination of microorganisms. However, the high similarity of 16S and 23S rRNA sequences of Bacillus cereus group organisms (up to 99-100%) and repeatedly failed attempts to develop molecular typing systems that would use DNA sequences to discriminate between species within this group have resulted in several suggestions to consider B. cereus and B. thuringiensis, or these two species together with B. anthracis, as one species. Recently, we divided the B. cereus group into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, based on 16S rRNA, 23S rRNA and gyrB gene sequences and identified subgroup-specific makers in each of these three genes. Here we for the first time demonstrated discrimination of these seven subgroups, including subgroup Anthracis, with a 3D gel element microarray of oligonucleotide probes targeting 16S and 23S rRNA markers. This is the first microarray enabled identification of B. anthracis and discrimination of these seven subgroups in pure cell cultures and in environmental samples using rRNA sequences. The microarray bearing perfect match/mismatch (p/mm) probe pairs was specific enough to discriminate single nucleotide polymorphisms (SNPs) and was able to identify targeted organisms in 5 min. We also demonstrated the ability of the microarray to determine subgroup affiliations for B. cereus group isolates without rRNA sequencing. Correlation of these seven subgroups with groupings based on multilocus sequence typing (MLST), fluorescent amplified fragment length polymorphism analysis (AFLP) and multilocus enzyme electrophoresis (MME) analysis of a wide spectrum of different genes, and the demonstration of subgroup-specific differences in toxin profiles, psychrotolerance, and the ability to harbor some plasmids, suggest that these seven subgroups are not based solely on neutral genomic polymorphisms, but instead reflect differences in both the genotypes and phenotypes of the B. cereus group organisms.},
doi = {10.1016/j.cbi.2007.09.002},
journal = {Chemico-Biological Interactions},
issn = {0009-2797},
number = 2,
volume = 171,
place = {United States},
year = {2008},
month = {1}
}