Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for standardized methodology

Unit Molecular Microbiology, National Institute of Public Health and Environmental Protection, Bilthoven, The Netherlands.
Journal of Clinical Microbiology (Impact Factor: 4.23). 03/1993; 31(2):406-9.
Source: PubMed

ABSTRACT DNA fingerprinting of Mycobacterium tuberculosis has been shown to be a powerful epidemiologic tool. We propose a standardized technique which exploits variability in both the number and genomic position of IS6110 to generate strain-specific patterns. General use of this technique will permit comparison of results between different laboratories. Such comparisons will facilitate investigations into the international transmission of tuberculosis and may identify specific strains with unique properties such as high infectivity, virulence, or drug resistance.

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Available from: Jan Embden Van, Jul 08, 2015
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    • "The ability to distinguish isolates has shown that individuals can be re-infected with M. tuberculosis, and this poses clear challenges for vaccine development since even natural infection at best provides partial immunity. Furthermore, the advent of high resolution tests for genetic variation has revealed that individuals may simultaneously harbor infections with more than one distinct strain of M. tuberculosis (Warren et al., 1999; Sola et al., 2003; Kremer et al., 1999; van Embden et al., 1993; Imaeda, 1985). "
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    ABSTRACT: High resolution tests for genetic variation reveal that individuals may simultaneously host more than one distinct strain of M. tuberculosis. Previous studies find that this phenomenon, which we will refer to as "mixed infection", may affect the outcomes of treatment for infected individuals and may influence the impact of population-level interventions against tuberculosis. In areas where the incidence of TB is high, mixed infections have been found in nearly 20% of patients; these studies may underestimate the actual prevalence of mixed infection given that tests may not be sufficiently sensitive for detecting minority strains. Specific reasons for failing to detect mixed infections would include low initial numbers of minority strain cells in sputum, stochastic growth in culture and the physical division of initial samples into parts (typically only one of which is genotyped). In this paper, we develop a mathematical framework that models the study designs aimed to detect mixed infections. Using both a deterministic and a stochastic approach, we obtain posterior estimates of the prevalence of mixed infection. We find that the posterior estimate of the prevalence of mixed infection may be substantially higher than the fraction of cases in which it is detected. We characterize this bias in terms of the sensitivity of the genotyping method and the relative growth rates and initial population sizes of the different strains collected in sputum. Copyright © 2014. Published by Elsevier Ltd.
    Journal of Theoretical Biology 12/2014; 368. DOI:10.1016/j.jtbi.2014.12.009 · 2.30 Impact Factor
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    • "During the last decades, various molecular techniques of DNA fingerprinting have been used to discriminate between clinical strains of MTBC (reviewed in [12]). Restriction fragment length polymorphisms (RFLP) typing is based on differences in copy number and the differential genomic location of the insertion sequence (IS) 6110, and became the first gold standard method for genotyping MTBC [15]. This technique has been used successfully to define chains of ongoing TB transmission, discriminate relapse from re-infection, and to detect laboratory cross-contaminations [16] [17]. "
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    ABSTRACT: The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions. (C) 2014 The Authors. Published by Elsevier Ltd.
    Seminars in Immunology 10/2014; 26(6). DOI:10.1016/j.smim.2014.09.012 · 6.12 Impact Factor
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    • "The majority of the currently utilized methods of strain identification have been developed since 1990. It was at this time that progress was made towards the standardization of typing protocols in order to improve the quality of epidemiological investigations (Cousins et al., 1998b; van Embden et al., 1993). The major genotyping techniques (Fig. 1) used for strain differentiation of members of the MTBC can be classified in two categories, based either on whole or partial genome analysis (Durr et al., 2000). "
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    ABSTRACT: The primary isolation of a Mycobacterium sp. of the Mycobacterium tuberculosis complex from an infected animal provides a definitive diagnosis of tuberculosis. However, as Mycobacterium bovis and Mycobacterium caprae are difficult to isolate, particularly for animals in the early stages of disease, success is dependent on the optimal performance of all aspects of the bacteriological process, from the initial choice of tissue samples at post-mortem examination or clinical samples, to the type of media and conditions used to cultivate the microorganism. Each step has its own performance characteristics, which can contribute to sensitivity and specificity of the procedure, and may need to be optimized in order to achieve the gold standard diagnosis. Having isolated the slow-growing mycobacteria, species identification and fine resolution strain typing are keys to understanding the epidemiology of the disease and to devise strategies to limit transmission of infection. New technologies have emerged that can now even discriminate different isolates from the same animal. In this review we highlight the key factors that contribute to the accuracy of bacteriological diagnosis of M. bovis and M. caprae, and describe the development of advanced genotyping techniques that are increasingly used in diagnostic laboratories for the purpose of supporting detailed epidemiological investigations.
    Research in Veterinary Science 04/2014; DOI:10.1016/j.rvsc.2014.04.010 · 1.51 Impact Factor