Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy
Paul Janssen,Renata Coopman,Geert Huys,Jean Swings,Marjo Bleeker,Pieter Vos,Marc Zabeau,Karel Kersters +7 more
TLDR
Comparison of the newly obtained data with results previously obtained by well-established genotypic and chemotaxonomic methods shows the superior discriminative power of AFLP towards the differentiation of highly related bacterial strains that belong to the same species or even biovar (i.e. to characterize strains at the infrasubspecific level).Abstract:
We investigated the usefulness of a novel DNA fingerprinting technique, AFLP, which is based on the selective amplification of genomic restriction fragments by PCR, to differentiate bacterial strains at the subgeneric level. In total, 147 bacterial strains were subjected to AFLP fingerprinting: 36 Xanthomonas strains, including 23 pathovars of Xanthomonas axonopodis and six pathovars of Xanthomonas vasicola, one strain of Stenotrophomonas, 90 genotypically characterized strains comprising all 14 hybridization groups currently described in the genus Aeromonas, and four strains of each of the genera Clostridium, Bacillus, Acinetobacter, Pseudomonas and Vibrio. Depending on the genus, total genomic DNA of each bacterium was digested with a particular combination of two restriction endonucleases and the resulting fragments were ligated to restriction halfsite-specific adaptors. These adaptors served as primer-binding sites allowing the fragments to be amplified by selective PCR primers that extend beyond the adaptor and restriction site sequences. Following electrophoretic separation on 5% (w/v) polyacrylamide/8.3 M urea, amplified products could be visualized by autoradiography because one of the selective primers was radioactively labelled. The resulting banding patterns, containing approximately 30-50 visualized PCR products in the size range 80-550 bp, were captured by a high-resolution densitoscanner and further processed for computer-assisted analysis to determine band-based similarity coefficients. This study reveals extensive evidence for the applicability of AFLP in bacterial taxonomy through comparison of the newly obtained data with results previously obtained by well-established genotypic and chemotaxonomic methods such as DNA-DNA hybridization and cellular fatty acid analysis. In addition, this study clearly demonstrates the superior discriminative power of AFLP towards the differentiation of highly related bacterial strains that belong to the same species or even biovar (i.e. to characterize strains at the infrasubspecific level), highlighting the potential of this novel fingerprinting method in epidemiological and evolutionary studies.read more
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Acinetobacter baumannii: Emergence of a Successful Pathogen
TL;DR: This review details the significant advances that have been made in understanding of this remarkable organism over the last 10 years, including current taxonomy and species identification, issues with susceptibility testing, mechanisms of antibiotic resistance, global epidemiology, clinical impact of infection, host-pathogen interactions, and infection control and therapeutic considerations.
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Polyphasic taxonomy, a consensus approach to bacterial systematics.
TL;DR: In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae.
Journal ArticleDOI
Biodiversity of Vibrios
TL;DR: Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing, which are probably important driving forces in the evolution and speciation of vibrios.
Journal ArticleDOI
Principles and Applications of Methods for DNA-Based Typing of Microbial Organisms
D. Michael Olive,Pamela Bean +1 more
TL;DR: Outbreaks of infectious disease often result from exposure to a common source of the etiologic agent, which is derived from a single cell whose progeny are genetically identical or closely related to the source organism.
Journal ArticleDOI
Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories
C. J. Jones,Keith J. Edwards,S. Castaglione,Mark O. Winfield,Francesco Sala,C.C.M. van de Wiel,G.M.M. Bredemeijer,Ben Vosman,Michaela C. Matthes,A. Daly,Reinhold Brettschneider,P. Bettini,Marcello Buiatti,Elena Maestri,Aliosha Malcevschi,Nelson Marmiroli,R. L. Aert,Guido Volckaert,Julia Rueda,Rosario Linacero,A. M. Vázquez,Angela Karp +21 more
TL;DR: This article describes a network experiment involving several European laboratories, in which the reproducibility of three popular molecular marker techniques was examined: random-amplified fragment length polymorphism (RAPD), amplified fragment length SNP (AFLP) and sequence-tagged microsatellites (SSR).
References
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DNA polymorphisms amplified by arbitrary primers are useful as genetic markers
TL;DR: A new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence is described, suggesting that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.
Journal ArticleDOI
AFLP: a new technique for DNA fingerprinting.
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TL;DR: The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity that allows the specific co-amplification of high numbers of restriction fragments.
Journal ArticleDOI
A procedure for the isolation of deoxyribonucleic acid from micro-organisms
TL;DR: A method has been described for the isolation of DNA from micro-organisms which yields stable, biologically active, highly polymerized preparations relatively free from protein and RNA, and Representative samples have been characterized for their thermal stability and sedimentation behaviour.
Journal ArticleDOI
Mathematical model for studying genetic variation in terms of restriction endonucleases
Masatoshi Nei,Wen-Hsiung Li +1 more
TL;DR: A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed and a measure called "nucleotide diversity" is proposed to express the degree of polymorphism in a population at the nucleotide level.