Molecular typing based on 12 loci containing variable numbers of tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTRs) has been adopted in combination with spoligotyping as the basis for large-scale, high-throughput genotyping of Mycobacterium tuberculosis. However, even the combination of these two methods is still less discriminatory than IS6110 fingerprinting. Here, we define an optimized set of MIRU-VNTR loci with a significantly higher discriminatory power. The resolution and the stability/robustness of 29 loci were analyzed, using a total of 824 tubercle bacillus isolates, including representatives of the main lineages identified worldwide so far. Five loci were excluded for lack of robustness and/or stability in serial isolates or isolates from epidemiologically linked patients. The use of the 24 remaining loci increased the number of types by 40%-and by 23% in combination with spoligotyping-among isolates from cosmopolitan origins, compared to those obtained with the original set of 12 loci. Consequently, the clustering rate was decreased by fourfold-by threefold in combination with spoligotyping-under the same conditions. A discriminatory subset of 15 loci with the highest evolutionary rates was then defined that concentrated 96% of the total resolution obtained with the full 24-locus set. Its predictive value for evaluating M. tuberculosis transmission was found to be equal to that of IS6110 restriction fragment length polymorphism typing, as shown in a companion population-based study. This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies.The genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control by, e.g., indicating possible epidemiological links between TB patients, detecting (un)suspected outbreaks and laboratory cross-contamination, and distinguishing exogenous reinfection from endogenous reactivation in relapse cases. For these purposes, IS6110 restriction fragment length polymorphism (RFLP) typing (48) has been used as the gold standard method for more than a decade. However, this method is labor-intensive, requires weeks for culturing the isolates and subsequent DNA purification, and suffers from problems of interpretability and portability of the complex banding patterns. In addition, it provides insufficient discrimination among isolates with low (Ͻ6) IS6110 copy numbers, a problem that is only partly overcome by using PCR-based spoligotyping as a secondary method (6).Genotyping based on variable numbers of tandem repeats (VNTRs) of different classes of interspersed genetic elements named mycobacterial interspersed repetitive units (MIRUs) (12,25,32,36,40,43,44) is increasingly used to solve these problems. This method relies on PCR amplification of multiple loci using primers specific for the flanking regions of each repeat locus and on the determination of the sizes of the amplicons...

BackgroundMycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required.MethodsWe attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years.ResultsMultiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links.ConclusionsThis in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.

During TB cytokines play a role in host defence. To determine the cytokine pattern during various disease stages of TB, serum levels of IL-12, interferon-gamma (IFN-gamma), IL-4, IL-6 and IL-10 were measured in 81 patients with active TB, 15 patients during therapy and 26 patients after anti-tuberculous therapy as well as in 16 persons who had been in close contact with smear-positive TB and in 17 healthy controls. IFN-gamma was elevated during active TB when compared with healthy controls, declining during and after treatment. IL-12 (p40 and p70) serum levels were not significantly higher in patients with active TB compared with any of the other groups. IL-4 levels were low in all groups. IL-6 and IL-10 serum levels were elevated in patients with active TB and during treatment. In patients with active TB serum levels of IFN-gamma and IL-6 were higher in patients with fever, anorexia and malaise. IL-12 levels were higher in patients with a positive smear. Cytokine levels did not correlate with localization of TB (pulmonary versus extrapulmonary), or skin test positivity. Cytokines directing a Th1 response (IL-12) or a Th2 response (IL-4) were not elevated in sera of this large group of patients with pulmonary and extrapulmonary TB. In patients with active TB, cytokines that were elevated in serum were IFN-gamma, IL-6 and IL-10.

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IS6110 fingerprinting of Mycobacterium tuberculosis is the standard identification method in studies on transmission of tuberculosis. However, intensive epidemiological investigation may fail to confirm transmission links between patients clustered by IS6110-restriction fragment length polymorphism (RFLP) typing. We applied typing based on variable numbers of tandem repeats (VNTRs) of mycobacterial interspersed repetitive units (MIRUs) to isolates from 125 patients in 42 IS6110 clusters, for which thorough epidemiological data were available, to investigate the potential of this method in distinguishing epidemiologically linked from nonlinked patients. Of seven IS6110 clusters without epidemiological links, five were split by MIRU-VNTR typing, while nearly all IS6110 clusters with proven or likely links displayed conserved MIRU-VNTR types. These results provide molecular evidence that not all clusters determined on the basis of multibanded IS6110 RFLP patterns necessarily reflect transmission of tuberculosis. They support the use of MIRU-VNTR typing as a more reliable and faster method for transmission analysis.IS6110 restriction fragment length polymorphism (RFLP) typing of Mycobacterium tuberculosis has been used extensively in studies on tuberculosis transmission and is one of the most widely applied and standardized molecular typing methods (1,6,10,31,34,35). M. tuberculosis isolates from epidemiologically linked patients generally show identical IS6110 RFLP patterns, thus comprising transmission clusters. Consequently, the finding that a substantial proportion of tuberculosis cases in industrialized countries is clustered by DNA fingerprinting is interpreted as a reflection of a high rate of recent transmission (2,5,8,14,22,27,28,32,39). However, IS6110-based RFLP fingerprints are not always reliable indicators of epidemiological linkage between tuberculosis patients (7, 33). Even the most meticulous analysis of all available data on possible contacts between clustered patients does not reveal epidemiological links in all cases (33). Furthermore, because in many settings tuberculosis often results from casual contacts, the majority of the links can be identified only after combining the genotyping of the M. tuberculosis isolates with intensive epidemiologic investigation. In addition, opportunities for early and thus more-efficient prevention and intervention are limited by the fact IS6110 RFLP typing is labor intensive and requires weeks for culturing M. tuberculosis.Typing methods based on mycobacterial interspersed repetitive unit (MIRU)-VNTR analysis offer a potential solution to the drawbacks faced using IS6110 RFLP typing. MIRU-VNTR analysis determines the number of tandem repeats at multiple independent loci (12, 29). This PCR-based method is highly reproducible and much faster than IS6110-RFLP typing and displays a discriminatory power close to that of IS6110-RFLP, especially in low-incidence areas (9,15,18,23,25,30). Previous studies have demonstrated the ability of MIRU-VNTR typing to split certai...

Serum concentrations of tumor necrosis factor-alpha (TNF), interleukin (IL)-1beta, and their circulating inhibitors soluble TNF receptor type I (sTNFRI), type II (sTNFRII), IL-1 receptor antagonist (IL-1ra), and soluble IL-1 receptor type II (sIL-1RII) were measured for 123 patients with tuberculosis (TB) in various stages of disease, in persons who had been in close contact with patients with contagious pulmonary TB, and in healthy controls. Levels of sTNFRI, sTNFRII, and IL-1ra, but not of sIL-1RII, were elevated in patients with active TB compared with contacts and controls and declined during treatment. The concentrations of these mediators did not differ between patients with pulmonary and extrapulmonary TB. The levels of sTNFRI and IL-1ra were higher in patients with fever and anorexia. Neither TNF nor IL-beta was detectable. We conclude that serum concentrations of sTNFRs I and II and IL-1ra may serve as markers of disease activity of TB. Sequential measurements of these cytokine inhibitors may be useful in the monitoring of antituberculous therapy.

We conducted a retrospective, population-based study with use of restriction fragment length polymorphism (RFLP) analysis to determine the incidence of and risk factors for clustering of Mycobacterium tuberculosis isolates, indicative of recently transmitted infection, among patients with culture-proven tuberculosis diagnosed between 1 July 1992 and 1 January 1995 in Amsterdam. We found that 214 (47%) of 459 patients were in 53 clusters, probably because of recent transmission of M. tuberculosis among 161 (35%) of these patients. Conventional contact tracing resulted in identification of 5.6% of the 161 patients. Clustering was more frequent among Dutch patients (59.3%) than among foreign ethnic patients (42.1%) (P = .002). The independent risk factor for clustering among Dutch patients was younger age; the independent risk factors among foreign ethnic patients were hard-drug use; alcohol abuse; and country of origin (Surinam or the Netherlands Antilles). These findings suggest the shortcomings of the usual tuberculosis control policies in Amsterdam. We identified several risk factors for clustering, which may guide adjustment of tuberculosis control and contact tracing strategies.

In low-incidence countries in the European Union (EU), tuberculosis (TB) is concentrated in big cities, especially among certain urban high-risk groups including immigrants from TB high-incidence countries, homeless people, and those with a history of drug and alcohol misuse. Elimination of TB in European big cities requires control measures focused on multiple layers of the urban population. The particular complexities of major EU metropolises, for example high population density and social structure, create specific opportunities for transmission, but also enable targeted TB control interventions, not efficient in the general population, to be effective or cost effective. Lessons can be learnt from across the EU and this consensus statement on TB control in big cities and urban risk groups was prepared by a working group representing various EU big cities, brought together on the initiative of the European Centre for Disease Prevention and Control. The consensus statement describes general and specific social, educational, operational, organisational, legal and monitoring TB control interventions in EU big cities, as well as providing recommendations for big city TB control, based upon a conceptual TB transmission and control model.