Utility of genotyping of Mycobacterium tuberculosis in the contact investigation: A decision analysis

The problem with defining foreign birth as a risk factor in tuberculosis epidemiology studies

OBJECTIVE

To examine how stratifying persons born outside Canada according to tuberculosis (TB) incidence in their birth country and other demographic factors refines our understanding of TB epidemiology and local TB transmission.

BACKGROUND

Population-level TB surveillance programs and research studies in low incidence settings often report all persons born outside the country in which the study is conducted as "foreign-born"-a single label for a highly diverse population with variable TB risks. This may mask important TB epidemiologic trends and not accurately reflect local transmission patterns.

METHODS

We used population-level data from two large cohorts in British Columbia (BC), Canada: an immigration cohort (n = 337,492 permanent residents to BC) and a genotyping cohort (n = 2290 culture-confirmed active TB cases). We stratified active TB case counts, incidence rates, and genotypic clustering (an indicator of TB transmission) in BC by birth country TB incidence, age at immigration, and years since arrival.

RESULTS

Persons from high-incidence countries had a 12-fold higher TB incidence than those emigrating from low-incidence settings. Estimates of local transmission, as captured by genotyping, versus reactivation of latent TB infection acquired outside Canada varied when data were stratified by birthplace TB incidence, as did patient-level characteristics of individuals in each group, such as age and years between immigration and diagnosis.

CONCLUSION

Categorizing persons beyond simply "foreign-born", particularly in the context of TB epidemiologic and molecular data, is needed for a more accurate understanding of TB rates and patterns of transmission.

SOCIAL, HISTORICAL AND CULTURAL DIMENSIONS OF TUBERCULOSIS

Tuberculosis (TB) researchers and clinicians, by virtue of the social disease they study, are drawn into an engagement with ways of understanding illness that extend beyond the strictly biomedical model. Primers on social science concepts directly relevant to TB, however, are lacking. The particularities of TB disease mean that certain social science concepts are more relevant than others. Concepts such as structural violence can seem complicated and off-putting. Other concepts, such as gender, can seem so familiar that they are left relatively unexplored. An intimate familiarity with the social dimensions of disease is valuable, particularly for infectious diseases, because the social model is an important complement to the biomedical model. This review article offers an important introduction to a selection of concepts directly relevant to TB from health sociology, medical anthropology and social cognitive theory. The article has pedagogical utility and also serves as a useful refresher for those researchers already engaged in this genre of work. The conceptual tools of health sociology, medical anthropology and social cognitive theory offer insightful ways to examine the social, historical and cultural dimensions of public health. By recognizing cultural experience as a central force shaping human interactions with the world, TB researchers and clinicians develop a more nuanced consideration of how health, illness and medical treatment are understood, interpreted and confronted.

Transmission of multidrug-resistant tuberculosis in the UK: a cross-sectional molecular and epidemiological study of clustering and contact tracing

BACKGROUND

Between 2000 and 2012 the number of multidrug-resistant (MDR) tuberculosis cases in the UK increased from 28 per year to 81 per year. We investigated the proportion of MDR tuberculosis cases arising from transmission in the UK and associated risk factors.

METHOD

We identified patients with MDR tuberculosis notified in England, Wales, and Northern Ireland between Jan 1, 2004, and Dec 31, 2007, by linking national laboratory and surveillance data. Data for laboratory isolates, including drug sensitivities and 24-mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing were obtained routinely from the National Tuberculosis Reference laboratories as part of national tuberculosis surveillance. We investigated clusters of cases with indistinguishable MIRU-VNTR profiles to identify epidemiological links. We calculated transmission using the n-1 method and established associated risk factors by logistic regression. We also assessed the likelihood of transmission to additional secondary active tuberculosis cases, identified through conventional contact tracing.

FINDINGS

204 patients were diagnosed with MDR tuberculosis in the study period; 189 (92·6%) had an MIRU-VNTR profile. We identified 12 clusters containing 40 individuals and 149 unique strains. The proportion of cases attributable to recent transmission, on the basis of molecular data, was 15% (40 cases clustered-12 clusters/189 with a strain type). The proportion of cases attributable to recent transmission (ie, transmission within the UK) after adjustment for epidemiological links was 8·5% (22 cases with epidemiological links-six clusters/189 cases with a strain type). Being UK born (odds ratio 4·81; 95% CI 2·03-11·36, p=0·0005) and illicit drug use (4·75; 1·19-18·96, p=0·026) were significantly associated with clustering. The most common transmission setting was the household but 21 of 22 of epidemiological links were missed by conventional contact tracing. 13 secondary active tuberculosis cases identified by conventional contact tracing were mostly contacts of patients with MDR tuberculosis from countries of high tuberculosis burden. 11 (85%) of 13 shared the same country of birth as the index case, of whom ten did not share a strain type or drug resistance pattern.

INTERPRETATION

Transmission of MDR tuberculosis in the UK is low and associated with being UK born or illicit drug use. MIRU-VNTR typing with cluster investigation was more successful at identifying transmission events than conventional contact tracing. Individuals with tuberculosis who have had contact with a known MDR tuberculosis source case from a country of high tuberculosis burden should have drug-sensitivity testing on isolates to ensure appropriate treatment is given.

FUNDING

Public Health England.

Outbreak or coincidental cases of tuberculosis? Genotyping provides the clue

We illustrate how genotyping of mycobacterial strains contributed to the discovery of an undetected outbreak of tuberculosis in a hospital ward, ruling out misleading assumptions of transmission chains. Genotyping should be taken into account in routine tests for the control of tuberculosis.

Unlocking pathogen genotyping information for public health by mathematical modeling

Molecular typing and mathematical modeling have gone through rapid development in the past decade. Both offer new insights into the epidemiology of infectious diseases, thereby contributing to a better understanding of transmission dynamics. Infectious disease surveillance and control benefit from the optimum use of these techniques. In this paper, we review recent developments and propose methods to integrate pathogen ecology and molecular evolution based on their common dependence on the underlying host contact patterns.

Three-year longitudinal study of genotypes of Mycobacterium tuberculosis in a low prevalence population

OBJECTIVE

To investigate the molecular epidemiology of tuberculosis, temporal and spatial distribution of Mycobacterium tuberculosis isolates and associations between genotypes and clinical characteristics, in a low prevalence population.

METHODS

A total of 930 M. tuberculosis isolates referred to the New South Wales (NSW, Australia) Mycobacterium Reference Laboratory in 2004-2006 were characterised by mycobacterial interspersed repetitive unit (MIRU) and spacer oligonucleotide (spoligo) typing. Associations between genotypes, patient age, disease site and drug resistance were explored and the predictive power of molecular typing was analysed using Bayesian Belief Networks.

RESULTS

Among isolates from 855 NSW residents, there were 287 spoligotypes, 494 MIRU types and 643 unique spoligotype-MIRU type combinations. They formed 73 spoligotype, 104 MIRU type and 76 spoligo-MIRU clusters, most of which contained only two isolates. The majority (87.7%) of spoligotype clusters contained several MIRU profiles and 64.4% of MIRU clusters contained several spoligotypes. The three most common M. tuberculosis clades were Beijing (24.1%), East African Indian (11.8%) and Central Asian (6.5%); 6.9% and 0.7% isolates were resistant to isoniazid and rifampicin, respectively. There was no proof of association between genotype and drug resistance but isoniazid resistance increased independently over time. Given the low rates of genotype clustering, statistical analysis of genotype-phenotype associations was limited. Potential associations were not confirmed by Bayesian classifiers.

CONCLUSIONS

Spoligo and MIRU typing demonstrated low levels of M. tuberculosis clustering in NSW; temporal and spatial changes in M. tuberculosis genotypes reflected migration patterns to Australia. No analytically significant associations between M. tuberculosis genotypes and clinical phenotypes were detected.

Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex

Spacer oligonucleotide typing, or spoligotyping, is a rapid, polymerase chain reaction (PCR)-based method for genotyping strains of the Mycobacterium tuberculosis complex (MTB). Spoligotyping data can be represented in absolute terms (digitally), and the results can be readily shared among laboratories, thereby enabling the creation of large international databases. Since the spoligotype assay was standardized more than 10 yr ago, tens of thousands of isolates have been analyzed, giving a global picture of MTB strain diversity. The method is highly reproducible and has been developed into a high-throughput assay for large molecular epidemiology projects. In the United States, spoligotyping is employed on nearly all newly identified culture-positive cases of tuberculosis as part of a national genotyping program. The strengths of this method include its low cost, its digital data results, the good correlation of its results with other genetics markers, its fair level of overall differentiation of strains, its high-throughput capacity, and its ability to provide species information. However, the method's weaknesses include the inability of spoligotyping to differentiate well within large strain families such as the Beijing family, the potential for convergent evolution of patterns, the limited success in improving the assay through expansion, and the difficulty in obtaining the specialized membranes and instrumentation.

Factors associated with differences between conventional contact tracing and molecular epidemiology in study of tuberculosis transmission and analysis in the city of Barcelona, Spain

The aim of this study was to analyze the factors associated with conventional contact tracing (CCT) and molecular epidemiology (ME) methods in assessing tuberculosis (TB) transmission, comparing the populations studied and the epidemiological links established by both methods. Data were obtained from TB case and CCT registries, and ME was performed using IS6110-based restriction fragment length polymorphism (RFLP) analysis and mycobacterial interspersed repetitive unit 12 (MIRU12) typing as a secondary typing method. During two years (2003 and 2004), 892 cases of TB were reported, of which 687 (77%) were confirmed by culture. RFLP analysis was performed with 463 (67.4%) of the 687 isolated strains, and MIRU12 types in 75 strains were evaluated; 280 strains (60.5%) had a unique RFLP pattern, and 183 (39.5%) shared patterns, grouping into 65 clusters. CCT of 613 (68.7%) of 892 cases detected 44 clusters involving 101 patients. The results of both CCT and ME methods yielded 96 clusters involving 255 patients. The household link was the one most frequently identified by CCT (corresponding to 80.7% of the cases clustered by this method), whereas nonhousehold and unknown links were associated with 94.1% of the strains clustered by ME. When both methods were used in 351 cases (39.3%), they showed the same results in 214 cases (61%). Of the remainder, 106 (30.2%) were clustered only by ME, 19 (5.5%) were clustered only by CCT, and 12 (3.4%) were clustered by both methods but into different clusters. Patients with factors potentially associated with social problems were less frequently studied by CCT (P = 0.002), whereas patients of <15 years of age, most with negative cultures, were less frequently studied by ME (P = 0.005). Significant differences in the populations studied by ME versus CCT were observed, possibly explaining the scarce correlation found between the results of these methods. Moreover, ME allowed the detection of nonhousehold contact relationships, whereas CCT was more useful for tracing transmission chains involving patients of <15 years of age. In conclusion, the two methods are complementary, suggesting the need to improve the methodology of contact study protocols.

Pathogen profiling for disease management and surveillance

The usefulness of rapid pathogen genotyping is widely recognized, but its effective interpretation and application requires integration into clinical and public health decision-making. How can pathogen genotyping data best be translated to inform disease management and surveillance? Pathogen profiling integrates microbial genomics data into communicable disease control by consolidating phenotypic identity-based methods with DNA microarrays, proteomics, metabolomics and sequence-based typing. Sharing data on pathogen profiles should facilitate our understanding of transmission patterns and the dynamics of epidemics.