Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.

BACKGROUND: Mycobacterium 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. METHODS: We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. RESULTS: Multiple 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. CONCLUSIONS: This 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.

Role of the QuantiFERON(R)-TB Gold In-Tube assay in screening new immigrants for tuberculosis infection.

This study aimed to estimate the risk of progression to active tuberculosis (TB) within 2 yrs after entry in newly arriving immigrants who were screened with the QuantiFERON®-TB Gold In-Tube assay (QFT-GIT; Cellestis, Carnegie, Australia). In a case-base design, we determined the prevalence QFT-GIT-positive subjects among a representative sample of immigrants aged ≥ 18 yrs who arrived between April 2009 and March 2011 (the base cohort). Active TB patients (cases) within 2 yrs post-arrival in 2005, 2006 or 2007 were extracted from the Netherlands Tuberculosis Register. The risk of progression to active TB was estimated using Bayesian analyses to adjust for the sensitivity of QFT-GIT. Among the base cohort, 20% of 1,468 immigrants were QFT-GIT positive. Stratified by TB incidence in the person's country of origin as low (<100 cases per 100,000 population), intermediate (100-199 cases per 100,000) or high (≥ 200 cases per 100,000), the risk of progression to active TB per 100,000 arriving immigrants if QFT-GIT positive (95% credibility interval) was 456 (95% CI 307-589), 590 (397-762) and 386 (259-499), respectively, compared with 18 (0-46), 38 (0-97) and 28 (0-71) if QFT-GIT negative. Screening newly arriving immigrants with QFT-GIT contributes to detecting those at high risk of subsequent TB reactivation within 2 yrs after entry, which offers opportunities for prevention by targeted interventions.

Mycobacterial factors relevant for transmission of tuberculosis.

BACKGROUND: Tuberculosis (TB) transmission is associated with patient-related risk factors. However, DNA fingerprint analysis has provided anecdotal evidence suggesting a role for bacteriological factors. METHODS: To examine the importance of the bacteriological component in TB transmission, we investigated the number of tuberculin skin test-positive (TST induration, ≥ 10 mm) contacts and secondary cases observed in contact investigations around TB cases in relation to the size of the genotype cluster the patient belonged to at the time of diagnosis. We also compared the number of TST-positive contacts and secondary cases of patients with drug-resistant and drug-susceptible TB. RESULTS: Larger clusters were independently associated with an increased number of positive contacts. The mean number of positive contacts ranged from 3.8 for clusters of 2 cases, to 4.7 for clusters of 3-10 cases, to 6.0 for cases in clusters of >10 cases (mean increase in number of positive contacts for every extra case in the cluster, 0.21; 95% confidence interval, 0.09-0.26). The mean number of positive contacts was significantly lower among index cases with isoniazid-monoresistant TB (1.6) than among index cases with pan-susceptible TB (4.6; relative number, 0.45; 95% confidence interval, 0.22-0.92). CONCLUSION: These results suggest that spread of tuberculosis also depends on bacteriological factors.

Tuberculosis outbreaks predicted by characteristics of first patients in a DNA fingerprint cluster.

RATIONALE: Some clusters of patients who have Mycobacterium tuberculosis isolates with identical DNA fingerprint patterns grow faster than others. It is unclear what predictors determine cluster growth. OBJECTIVES: To assess whether the development of a tuberculosis (TB) outbreak can be predicted by the characteristics of its first two patients. METHODS: Demographic and clinical data of all culture-confirmed patients with TB in the Netherlands from 1993 through 2004 were combined with DNA fingerprint data. Clusters were restricted to cluster episodes of 2 years to only detect newly arising clusters. Characteristics of the first two patients were compared between small (2-4 cases) and large (5 or more cases) cluster episodes. MEASUREMENTS AND MAIN RESULTS: Of 5,454 clustered cases, 1,756 (32%) were part of a cluster episode of 2 years. Of 622 cluster episodes, 54 (9%) were large and 568 (91%) were small episodes. Independent predictors for large cluster episodes were as follows: less than 3 months' time between the diagnosis of the first two patients, one or both patients were young (<35 yr), both patients lived in an urban area, and both patients came from sub-Saharan Africa. CONCLUSIONS: In the Netherlands, patients in new cluster episodes should be screened for these risk factors. When the risk pattern applies, targeted interventions (e.g., intensified contact investigation) should be considered to prevent further cluster expansion.

Enzyme-linked immunosorbent assays using immune complexes for the diagnosis of tuberculosis.

The serodiagnosis of tuberculosis has long been the subject of investigation, but we still lack a test with widespread clinical utility. The poor sensitivity and specificity of commercial assays precludes their use as the sole means of diagnosis. All of these assays use mycobacterial antigens adsorbed onto a surface. Little attention has been paid to changes in antigen conformation that may occur as a result of passive coating of these antigens to solid supports like polystyrene. Such changes may cause technical artifacts resulting in false-positive (FP) and false-negative (FN) reactions. We have developed two different enzyme-linked immunosorbent assay (ELISA) systems, in which human serum antibodies and target antigens of Mycobacterium tuberculosis are able to associate and dissociate freely in solution to form immune complexes. In one ELISA, rabbit antibodies against M. tuberculosis, passively coated in the ELISA wells, capture the immune complexes (ICs). In the other ELISA, the ICs are detected by these same rabbit antibodies but are first captured by passively coated goat anti-rabbit IgG. We have compared these two ELISA systems with an ELISA using M. tuberculosis antigens passively adsorbed to the solid polystyrene surface of the plate. We studied sera from 81 patients with tuberculosis and 47 healthy subjects. The differences between tuberculosis (TB) patients and healthy subjects were statistically significant in all three of our ELISA systems. However, the ELISA systems using soluble M. tuberculosis antigens distinguished better between TB patients and healthy subjects than the ELISA using surface-adsorbed M. tuberculosis antigens. We suggest that in the latter ELISA, passive adsorption of the target antigens induces conformational change, generating altered epitopes that are recognized by antibodies present in the serum from even healthy people. These altered conformational epitopes are recognized by antibodies that were originally evoked by antigens other than M. tuberculosis, known as heterophile antigens.

Mycobacterium tuberculosis, Beijing genotype strains not associated with radiological presentation of pulmonary tuberculosis.

Mycobacterium tuberculosis strains of the Beijing genotype have been involved in various outbreaks of multidrug-resistant tuberculosis. Some studies suggest that the infection with the Beijing genotype is associated with a different host immune response. Since this might also lead to a different chest X-ray (CXR) presentation, we compared CXRs of patients with pulmonary tuberculosis, 33 of whom were infected with the Beijing genotype and 76 with other genotypes. No significant differences were detected. We conclude that the Beijing genotype is not associated with a different CXR presentation.

Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis.

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.

Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis.

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.

Clustered tuberculosis cases: do they represent recent transmission and can they be detected earlier?

Clustered tuberculosis cases with Mycobacterium tuberculosis isolates showing identical restriction fragment length polymorphism patterns are assumed to be the result of disease transmission. In a prospective, population-based study in the province of North Holland, The Netherlands, we combined molecular methods with highly detailed epidemiologic information to determine why many clustered cases are not detected at an early stage. Of 481 patients, 138 (29%) fell into 43 clusters, suggesting recent transmission in 20%. Of 155 patients in clusters occurring within 2 years before or after the diagnosis of the disease, 21 (14%) had no epidemiologic links with other patients. Independent predictors of the absence of such links were female sex and Turkish, Moroccan, or other African ethnicity. Of 47 patients with a clear epidemiologic link, 37 (24% of 155) were identified early, e.g., by contact tracing, and 10 (6%) were missed. In 85 (55%) patients, an epidemiologic link was likely but undetected when using conventional contact tracing. Compared with clearly linked patients, only male sex was independently associated with presence in this last group. Our results indicate that 86% of clustered study patients had epidemiologic links and that opportunities for earlier identification using conventional tuberculosis control strategies are limited.

Nosocomial Mycobacterium bovis-bacille Calmette-Guérin infections due to contamination of chemotherapeutics: case finding and route of transmission.

We studied nosocomial infections due to Mycobacterium bovis bacille Calmette-Guérin (BCG) Onco-TICE bacteria, transmitted by contamination of medication prepared in BCG Onco-TICE-contaminated hoods in the pharmacy, in 5 immunocompromised patients at 3 hospitals. The BCG strains cultured from the patients had the same DNA profile as the BCG Onco-TICE strain used for bladder instillation. To prevent these infections, a change from open to closed preparation was made; strictly separated preparation in time of BCG Onco-TICE instillation and chemotherapy was enforced, the biological safety cabinet was disinfected between preparations, and gloves were changed between preparations.