Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial pathogens.
OBJECTIVE
In a bioterrorism event a rapid tool is needed to identify relevant dangerous bacteria. The aim of the study was to assess the usefulness of partial 16S rRNA gene sequence analysis and the suitability of diverse databases for identifying dangerous bacterial pathogens.


RESULTS
For rapid identification purposes a 500-bp fragment of the 16S rRNA gene of 28 isolates comprising Bacillus anthracis, Brucella melitensis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, Yersinia pestis, and eight genus-related and unrelated control strains was amplified and sequenced. The obtained sequence data were submitted to three public and two commercial sequence databases for species identification. The most frequent reason for incorrect identification was the lack of the respective 16S rRNA gene sequences in the database.


CONCLUSIONS
Sequence analysis of a 500-bp 16S rDNA fragment allows the rapid identification of dangerous bacterial species. However, for discrimination of closely related species sequencing of the entire 16S rRNA gene, additional sequencing of the 23S rRNA gene or sequencing of the 16S-23S rRNA intergenic spacer is essential.


CONCLUSIONS
This work provides comprehensive information on the suitability of partial 16S rDNA analysis and diverse databases for rapid and accurate identification of dangerous bacterial pathogens.
Ruppitsch
W
W
Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria. werner.ruppitsch@ages.at <werner.ruppitsch@ages.at>
Stöger
A
A
Indra
A
A
Grif
K
K
Schabereiter-Gurtner
C
C
Hirschl
A
A
Allerberger
F
F
D001407:Bacillus / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D023482:Bioterrorism; D017347:Brucella melitensis / Q000235:genetics / Q000302:isolation & purification; D019117:Burkholderia / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics; D030541:Databases, Genetic; D005604:Francisella tularensis / Q000235:genetics / Q000302:isolation & purification; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D014734:Vibrio cholerae / Q000235:genetics / Q000302:isolation & purification; D015007:Yersinia / Q000235:genetics / Q000302:isolation & purification
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S