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Nucleic acid sequencing for the evaluation of bacterial species and systematics: applications for identification

Conference paper
Authors Edward R.B. Moore
Liselott A Svensson
Christel Unosson
Nahid Karami
Published in Proceedings zur VAAM-Jahrestagung 2009, March 8-11, Bochum, Germany, FGE03
Pages 49
ISSN 0947-0867
Publication year 2009
Published at Institute of Biomedicine, Department of Infectious Medicine
Pages 49
Language en
Subject categories Biological Systematics


Identification of prokaryotes in the complexity of microbial diversity is increasingly problematic for clinical diagnoses and environmental microbiology. DNA sequence-based analyses of bacteria have enabled the identification of microorganisms in the environment and are being adopted as routine in clinical analyses. DNA-based methods are suited to analyses of fastidious organisms, as well as those presenting health risks during cultivation. Comparative 16S rRNA gene sequence analyses are able to estimate phylogenetic relationships, although it is recognised that such analyses are not able to provide definitive species identifications. Among the most difficult problems for clinical diagnostics is the identification of organisms within “complexes” of closely related species, comprising pathogenic and non-pathogenic species with limited differentiating characteristics, e.g., 16S rRNA gene sequence dissimilarities among such organisms are often less than 1.0%. However, these species complexes are comprised of organisms with different pathogenic and virulence potential and it is essential to be able to obtain reliable identifications. A “polyphasic” multi-locus sequence analysis (MLSA) strategy can be established for the identification of bacteria, including “first-phase” comparisons of partial 16S rRNA gene sequences, for identification to the sub-genus level, and subsequent, “second-phase” analyses of one or more conserved house-keeping genes, for identification to the species level. However, it is recognised that house-keeping genes are not equally useful for all taxa. An average nucleotide index (ANI), based upon sequence similarities among house-keeping genes, may be applied for establishing expected gene sequence “cut-offs” that differentiate the species of a given taxon. Thus, a potential key to effective bacterial identification depends upon the selection of conserved genes with levels of resolution high enough to differentiate the most closely related species.

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