Rapid methods in bacterial DNA fingerprinting

Abstract

The characterization and comparison of isolates of bacterial species by comparing restriction enzyme digests of their chromosomal DNA (fingerprints) is highly discriminatory for different strains and allows similarities between them to be readily determined. However, the utility of the technique is dependent on the selection of appropriate restriction enzyme(s) and on the method of determining the similarities between the fingerprints generated. We report here a system which circumvents these two problems. The restriction enzyme is selected from amongst those which have a suitable frequency of restriction for given enzymegenome combinations. The frequencies of restriction enzyme recognition sites are calculated from the frequencies of di-and trinucleotides in sequenced genes from the species of interest using Markov chain analysis. Fingerprints are compared by dividing them up into sections with DNA size standards, scoring the number of bands in a few of these sections, and comparing these scores (numerical profiles) to establish similarities. In this way a single electrophoretic gel yields easily analysable data which can be compared with data from other gels. The time from the acquisition of bacterial isolates to their final characterization is much reduced in comparison to existing methods.

An analysis of the diversity ofHaemophilus parainfluenzaein the adult human respiratory tract by genomic DNA fingerprinting

“…DNA fingerprinting of non-typable H. influenzae has previously been reported as a quick, reproducible, high resolution technique for identifying a large diversity of bacterial strains [15,19] that correlates well with findings from protein and rRNA studies [23]. The analysis of fingerprints by the production of a numerical profile for each isolate was essential for the simple handling of the complex patterns produced.…”

“…Bacteriological samples were collected from each of the overwintering base members (15 [19]. Fragments were separated on 0-8 % agarose gels run at 1 v/cm for 18-48 h. BamHI, KpnI and XbaI produced discriminatory fingerprints of 10-20 well separated bands in most strains.…”

Use of ribotyping in epidemiological surveillance of nosocomial outbreaks

“…Thus, strain comparison may require several electrophoretic runs in which strains generating closely related patterns in preliminary experiments are analyzed in contiguous lanes. Systematic inclusion of DNA size standards in the analyzed samples has been proposed to improve reliability, but comparison remains difficult (49). One (135).…”

Significance of Amplified Fragment Length Polymorphism in Identification and Epidemiological Examination of Candida Species Colonization in Children Undergoing Allogeneic Stem Cell Transplantation

“…Molecular techniques, based on the demonstration of variations in the conserved DNA sequences in yeast genomes, have led to identification methods based entirely on the detection of naturally occurring DNA polymorphisms (6,17,27,32,35). These techniques have been applied in a limited manner to studies of Candida colonization in immunocompromised chil-dren (5,34).…”