DNA fingerprinting with two probes decreases clustering of Mycobacterium tuberculosis.

Burman, William J.; Reves, Randall; Hawkes, Aaron; Rietmeijer, Cornelis A.; Yang, Zhenhua; El-Hajj, Hiyam; Bates, Joseph H.; Cave, M. Donald

doi:10.1164/ajrccm.155.3.9117000

Cited by 81 publications

(82 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The interpretation that equilibrium has not been reached is also consistent with studies using secondary genetic markers in TB. Although it has been shown that secondary markers allow IS fingerprint clusters to be further differentiated, it is also evident that the states of these markers are correlated with IS genotypes (25)(26)(27).…”

Section: Discussionmentioning

confidence: 99%

The dynamics of repeated elements: Applications to the epidemiology of tuberculosis

Tanaka¹

2000

Proceedings of the National Academy of Sciences

View full text Add to dashboard Cite

We propose a stepwise mutation model to describe the dynamics of DNA fingerprint variation in Mycobacterium tuberculosis. The genome of M. tuberculosis carries insertion sequences (IS6110) that are relatively stable over time periods of months but have an observable transposition rate over longer time scales. Variability in copy number and genomic location of (IS6110) can be harnessed to generate a DNA fingerprint for each strain, by digesting the genome with a restriction enzyme and using a portion of the element as a probe for Southern blots. The number of bands found for a given genome approximates the number of copies of IS6110 it carries. A large data set of such fingerprints from tuberculosis (TB) cases in San Francisco provides an observed distribution of IS6110 copy number. Implementation of the model through deterministic and stochastic simulation indicates some general features of IS͞TB dynamics. By comparing observations with outcomes of the model, we conclude that the IS͞TB system is very heterogeneous and far from equilibrium. We find that the transposition parameters have a much stronger effect than the epidemic parameters on copy number distribution. E fficient molecular methods have allowed the recent genetic characterization of parasitic agents. Such empirical work greatly enhances our understanding of the epidemiology of human diseases (1-4). These new data are the stimulus for the development of theoretical and quantitative understanding of how genetic variability among strains interacts with epidemic processes. The molecular epidemiology of tuberculosis (TB) has been well developed. The insertion sequence (IS) 6110 in the genome of Mycobacterium tuberculosis is stable on the short time scale of months, while transposing at an observable rate over longer time periods. By digesting the genome with the restriction enzyme PvuII and using a portion of the element as a probe for Southern blotting, strains can be distinguished by the resulting DNA fingerprints (2). The number of bands in each blot indicates the number of copies of IS in the isolated genome.The essential features of TB dynamics recently have been explored (5-7). Those studies take into account the various important aspects of the disease; for instance, a fraction of newly acquired infections progress to the disease immediately while the remainder enter a potentially long period of latent infection. Using estimates of epidemiological parameters from the empirical literature, those authors quantitatively characterize the length of epidemics and assess the efficacy of control strategies.Several theoretical studies have investigated transposon dynamics. Many of these are constructed for diploid genomes, particularly Drosophila (8-10). Sawyer and Hartl (11) and Moody (12) treat stochastic models of transposable elements in prokaryotes (IS elements), though without consideration of epidemic circumstances. Both studies allow a degree of horizontal transmission. The latter includes replicative transposition (increase by one copy) and deletio...

show abstract

Section: Discussionmentioning

confidence: 99%

The dynamics of repeated elements: Applications to the epidemiology of tuberculosis

Tanaka¹

2000

Proceedings of the National Academy of Sciences

View full text Add to dashboard Cite

show abstract

“…To facilitate visual reading of PGRS fingerprints, samples were electrophoresed together on the same gel according to the results with IS6110. As suggested by BURMAN et al [17] only fragments exceeding 1.6 kb were analysed.…”

Section: Comparison Of Rflp Patternsmentioning

confidence: 99%

“…Even though these large urban areas have a high proportion of patients infected with human immunodeficiency virus (HIV), who are known to be more susceptible to in-fections and at greater risk of latent TB infection rapidly progressing to active disease, these figures greatly exceed general assumptions regarding transmission (~10%; [10]). Both studies concentrating on these big cities are based on the assumptions that deoxyribonucleic acid (DNA) fingerprinting using the IS6110 sequence as a probe provides ac-curate typing of M. tuberculosis isolates and, furthermore, that the identification of cluster strains necessarily implies recent transmission.Most recent concepts of molecular epidemiology utilizing additional genetic markers, such as the polymorphic GC-rich repetitive sequence (PGRS; [11,12]) and/or the 36 base pair (bp) direct repeat (DR; [13,14]) have, however, demonstrated that DNA fingerprinting with the IS-6110 technique was not always sufficient, particularly, in those cases where isolates have fewer than six copies of IS6110 [15][16][17]. Use of supplementary fingerprinting techniques markedly decreased clustering and, thus, put the transmission links suggested by molecular biology more in line with epidemiological data.…”

mentioning

confidence: 99%

“…Most recent concepts of molecular epidemiology utilizing additional genetic markers, such as the polymorphic GC-rich repetitive sequence (PGRS; [11,12]) and/or the 36 base pair (bp) direct repeat (DR; [13,14]) have, however, demonstrated that DNA fingerprinting with the IS-6110 technique was not always sufficient, particularly, in those cases where isolates have fewer than six copies of IS6110 [15][16][17]. Use of supplementary fingerprinting techniques markedly decreased clustering and, thus, put the transmission links suggested by molecular biology more in line with epidemiological data.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Transmission of tuberculosis in the metropolitan area of Zurich: a 3 year survey based on DNA fingerprinting

Pfyffer¹,

Strässle²,

Rose³

et al. 1998

Eur Respir J

View full text Add to dashboard Cite

Restriction fragment length polymorphism (RFLP) analysis of Mycobacterium tuberculosis based on the insertion sequence IS6110 has recently been standardized and become an important molecular tool in answering questions such as: 1) transmission of the disease in community [1,2] and international settings [3] as well as via the nosocomial route [4,5]; 2) reactivation versus reinfection of tuberculosis (TB) [6]; and 3) cross contamination of cultures in the laboratory [7].Large population-based studies undertaken in New York [8] and San Francisco [9] utilizing IS6110-based RFLP analyses have revealed clusters, which inferred that recen-tly transmitted TB encompassed 30-40% of TB cases. Even though these large urban areas have a high proportion of patients infected with human immunodeficiency virus (HIV), who are known to be more susceptible to in-fections and at greater risk of latent TB infection rapidly progressing to active disease, these figures greatly exceed general assumptions regarding transmission (~10%; [10]). Both studies concentrating on these big cities are based on the assumptions that deoxyribonucleic acid (DNA) fingerprinting using the IS6110 sequence as a probe provides ac-curate typing of M. tuberculosis isolates and, furthermore, that the identification of cluster strains necessarily implies recent transmission.Most recent concepts of molecular epidemiology utilizing additional genetic markers, such as the polymorphic GC-rich repetitive sequence (PGRS; [11,12]) and/or the 36 base pair (bp) direct repeat (DR; [13,14]) have, however, demonstrated that DNA fingerprinting with the IS-6110 technique was not always sufficient, particularly, in those cases where isolates have fewer than six copies of IS6110 [15][16][17]. Use of supplementary fingerprinting techniques markedly decreased clustering and, thus, put the transmission links suggested by molecular biology more in line with epidemiological data.In the present study RFLP patterns of M. tuberculosis strains isolated from TB patients of the metropolitan area of Zurich (population 1.2 million; area: 1,729 km 2 ) over a period of 3 yrs were analysed to determine the frequency of recent transmission, which eventually reflects the effectiveness of current measures of TB control, i.e., on case finding and management, contact tracing and preventive therapy strategies. Methods Patient populationThe study cohort included 444 patients of the Canton of Zurich, all being treated for TB between 1991 and 1993 (278 males, 166 females; 216 Swiss-born (48.6%), 228 foreign-born (51.4%)). Restriction fragment length polymorphism (RFLP) analysis was performed by using IS6110 and the polymorphic GC-rich sequence (PGRS) as genetic markers. Transmission of tuberculosis in the metropolitan area ofNinety nine isolates shared by 77 patients (21.3%) were associated with 28 IS6110-defined clusters. However, secondary typing of low copy number isolates decreased the number of clusters to 25, encompassing 81 isolates from 63 (17.5%) patients. By deoxyribonucleic acid (DNA) fin...

show abstract

“…In contrast, in the study of BURMAN et al [32] (in Denver, USA) 40 of the 51 patients (78%) with clustered isolates had definite or possible epidemiological links identified through contact tracing.…”

mentioning

confidence: 76%

Utility of molecular epidemiology of tuberculosis

Soolingen¹

1998

Eur Respir J

View full text Add to dashboard Cite

Just 10 yrs ago it was still generally accepted that bacteria of the Mycobacterium tuberculosis complex were so highly conserved, that phage typing, which could distinguish about 20 different phage types, was all one needed to study the epidemiology of tuberculosis [1][2][3][4]. From the late 1980s, repetitive deoxyribonucleic acid (DNA) sequences have been described, which are associated with different levels of genetic polymorphism [5][6][7][8][9][10][11][12][13][14][15][16][17]. In 1990, the highly similar insertion sequences IS986 and IS6110 were found in the genome of M. tuberculosis [10,13,14] and, when these elements were applied in restriction fragment length polymorphism (RFLP) typing, they provided an unprecedented degree of discrimination between M. tuberculosis complex isolates. When IS986-based RFLP typing was used in 1990 to confirm for the first time a suspected outbreak of tuberculosis in the Netherlands [8], interest in the molecular epidemiology of tuberculosis was awakened.RFLP typing seemed ideal for studying small-scale transmission of M. tuberculosis, such as outbreaks in institutions, hospitals or among families [16,[18][19][20][21][22]. Within a remarkably short period of time the utility of fingerprinting for managing outbreaks was established. The RFLP typing technique was optimized and standardized to enable computer-assisted analysis of DNA fingerprints [23,24]. This facilitated large-scale epidemiological studies. However, the utility and reliability of large-scale, or even routine, application of DNA fingerprinting in tuberculosis control is still debatable and hinges on whether clustering of DNA fingerprints among patients' isolates does truly reflect transmission of M. tuberculosis. VAN DEUTEKOM et al. [29] (in Amsterdam, the Netherlands) found that only 5-10% of the links indicated by DNA fingerprinting, were also found by conventional contact tracing. Furthermore, in the molecular epidemiological study in Bern, Switzerland, conducted by GENEWEIN et al. [30] cases in totally different social groups were in the same DNA fingerprint clusters.To examine the utility of DNA fingerprinting in more detail, BRADEN et al. [31] chose another approach in the rural area of Arkansas, USA. In this study, extensive interviews with patients identified epidemiological connections for only 33 out of 78 (42%) of the clustered patients. It is unclear whether the conclusions from this study can be generalized to other (e.g. urban) populations, as it was conducted in a rural area in which a large proportion of individuals were elderly.In contrast, in the study of BURMAN et al. [32] (in Denver, USA) 40 of the 51 patients (78%) with clustered isolates had definite or possible epidemiological links identified through contact tracing.In the molecular epidemiological study in the metropolitan area of Zürich, Switzerland, presented by PFYFFER et al. [33] in this issue of the Journal, a very small percentage (20%) of cases were clustered. This reflects that in an area where tuberculosis control is orga...

show abstract

DNA fingerprinting with two probes decreases clustering of Mycobacterium tuberculosis.

Cited by 81 publications

References 21 publications

The dynamics of repeated elements: Applications to the epidemiology of tuberculosis

The dynamics of repeated elements: Applications to the epidemiology of tuberculosis

Transmission of tuberculosis in the metropolitan area of Zurich: a 3 year survey based on DNA fingerprinting

Utility of molecular epidemiology of tuberculosis

Contact Info

Product

Resources

About