Mathematical Modelling of Mycobacterium tuberculosis VNTR Loci Estimates a Very Slow Mutation Rate for the Repeats

Abstract

Minisatellites are highly variable tandem repeats used for over 20 years in humans for DNA fingerprinting. In prokaryotes fingerprinting techniques exploiting VNTR (variable number of tandem repeats) polymorphisms have become widely used recently in bacterial typing. However although many investigations into the mechanisms underlying minisatellite variation in humans have been performed, relatively little is known about the processes that mediate bacterial minisatellite polymorphism. An understanding of this is important since it will influence how the results from VNTR experiments are interpreted. The minisatellites of Mycobacterium tuberculosis are well characterized since they are some of the few polymorphic loci in what is otherwise a very homogeneous organism. Using VNTR results from a well-defined and characterized set of M. tuberculosis strains we show that the repeats at a locus are likely to evolve by stepwise contraction or expansion in the number of repeats. A stochastic continuous-time population mathematical model was developed to simulate the evolution of the repeats. This allowed estimation of the tendency of the repeats to increase or decrease and the rate at which they change. The majority of loci tend to lose rather than gain repeats. All of the loci mutate extremely slowly, with an average rate of 2.3 x 10(-8), which is 350 times slower than that of a set of VNTR repeats with similar diversity observed experimentally in Escherichia coli. This suggests that the VNTR profile of a strain of M. tuberculosis will be indicative of its clonal lineage and will be unlikely to vary in epidemiologically-related strains.

Insights into the Origin, Emergence, and Current Spread of a Successful Russian Clone of Mycobacterium tuberculosis

“…6B). One should note that evolution by loss rather than gain of repeats has been suggested as a major mode of evolution of the VNTR loci in M. tuberculosis, based on mathematical modeling (122). In this sense, the MST shown in Fig.…”

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster

“…A variety of genetic markers, such as IS6110 restriction fragment length polymorphism (RFLP) and variable-number tandem repeat (VNTR) typing, are currently used for DNA fingerprinting of Mycobacterium tuberculosis isolates (2,7,(12)(13)(14)23). Unfortunately, these markers do not distinguish primary and subsequent sources of infection in long-term DNA fingerprinting surveillance, as the turnover of these markers is not in range with the pace of transmission (4)(5)(6).…”

Mycobacterium bovis BCG-Russia Clinical Isolate with Noncanonical Spoligotyping Profile

“…The other characteristic signature of the BCG strain is a structure of its direct repeat (DR) (clustered regular interspaced short palindromic repeats [CRISPR]) locus that may be determined by spacer oligonucleotide typing (spoligotyping) technique. The mutation rate of spoligotypes has previously been estimated as 0.0029 to 0.0133 per strain per year (8), which is much lower than the mutation rate of polymorphic variable-number tandem repeats (VNTRs) (6,16) and multicopy IS6110-restriction fragment length polymorphism (RFLP) profiles (13). This relative stability of the DR locus explains the limited utility of spoligotyping as a standalone approach for epidemiological typing since only one spoligoprofile of a BCG strain has been described to date (www .tbovis.org).…”