Tuberculosis in HIV-infected individuals in Ho Chi Minh City, Vietnam

Early and accurate detection of TB disease in HIV-infected individuals is a critical step for a successful TB program. In Vietnam, the diagnosis of TB disease, which is based predominantly on the clinical examination, chest radiography (CXR) and acid fast bacilli (AFB) sputum smear, has shown to be of low sensitivity in immunocompromised patients. The sputum culture is not routinely performed for patients with AFB negative smears, even in HIV-infected individuals.^ In that background, we conducted this cross-sectional study to estimate the prevalence of sputum culture-confirmed pulmonary tuberculosis (PTB), smear-negative PTB, and multidrug-resistant TB (MDR-TB) in the HIV-infected population in Ho Chi Minh City (HCMC), the largest city in Vietnam where both TB and HIV are highly prevalent. We also evaluated the diagnostic performance of various algorithms based on routine available tools in Vietnam such as symptoms screening, CXR, and AFB smear. Nearly 400 subjects were consecutively recruited from HIV-infected patients seeking care at the An Hoa Clinic in District 6 of Ho Chi Minh City from August 2009 through June 2010. Participants’ demographic data, clinical status, CXR, and laboratory results were collected. A multiple logistic regression model was developed to assess the association of covariates and PTB. ^ The prevalence of smear-positive TB, smear-negative TB, resistant TB, and MDR-TB were 7%, 2%, 5%, 2.5%, and 0.3%, respectively. Adjusted odds ratios for low CD4+ cell count, positive sputum smear, and CXR to positive sputum culture were 3.17, 32.04, and 4.28, respectively. Clinical findings alone had poor sensitivity, but the combination of CD4+ cell count, sputum smear, and CXR proved to perform a more accurate diagnosis.^ This study results support the routine use of sputum culture to improve the detection of TB disease in HIV-infected individuals in Vietnam. When routine sputum culture is not available, an algorithm combining CD4+ cell count, sputum smear, and CXR is recommended for diagnosing PTB. Future studies on more affordable, rapid, and accurate tests for TB infection would also be necessary to timely provide specific treatments for patients in need, reduce mortality, and minimize TB transmission to the general population.^

Endemic tuberculosis, the homeless, and public transportation: A merging of geographical information systems surveillance and the Houston Tuberculosis Initiative Surveillance project

To reach the goals established by the Institute of Medicine (IOM) and the Centers for Disease Control's (CDC) STOP TB USA, measures must be taken to curtail a future peak in Tuberculosis (TB) incidence and speed the currently stagnant rate of TB elimination. Both efforts will require, at minimum, the consideration and understanding of the third dimension of TB transmission: the location-based spread of an airborne pathogen among persons known and unknown to each other. This consideration will require an elucidation of the areas within the U.S. that have endemic TB. The Houston Tuberculosis Initiative (HTI) was a population-based active surveillance of confirmed Houston/Harris County TB cases from 1995–2004. Strengths in this dataset include the molecular characterization of laboratory confirmed cases, the collection of geographic locations (including home addresses) frequented by cases, and the HTI time period that parallels a decline in TB incidence in the United States (U.S.). The HTI dataset was used in this secondary data analysis to implement a GIS analysis of TB cases, the locations frequented by cases, and their association with risk factors associated with TB transmission. ^ This study reports, for the first time, the incidence of TB among the homeless in Houston, Texas. The homeless are an at-risk population for TB disease, yet they are also a population whose TB incidence has been unknown and unreported due to their non-enumeration. The first section of this dissertation identifies local areas in Houston with endemic TB disease. Many Houston TB cases who reported living in these endemic areas also share the TB risk factor of current or recent homelessness. Merging the 2004–2005 Houston enumeration of the homeless with historical HTI surveillance data of TB cases in Houston enabled this first-time report of TB risk among the homeless in Houston. The homeless were more likely to be US-born, belong to a genotypic cluster, and belong to a cluster of a larger size. The calculated average incidence among homeless persons was 411/100,000, compared to 9.5/100,000 among housed. These alarming rates are not driven by a co-infection but by social determinants. The unsheltered persons were hospitalized more days and required more follow-up time by staff than those who reported a steady housing situation. The homeless are a specific example of the increased targeting of prevention dollars that could occur if TB rates were reported for specific areas with known health disparities rather than as a generalized rate normalized over a diverse population. ^ It has been estimated that 27% of Houstonians use public transportation. The city layout allows bus routes to run like veins connecting even the most diverse of populations within the metropolitan area. Secondary data analysis of frequent bus use (defined as riding a route weekly) among TB cases was assessed for its relationship with known TB risk factors. The spatial distribution of genotypic clusters associated with bus use was assessed, along with the reported routes and epidemiologic-links among cases belonging to the identified clusters. ^ TB cases who reported frequent bus use were more likely to have demographic and social risk factors associated with poverty, immune suppression and health disparities. An equal proportion of bus riders and non-bus riders were cultured for Mycobacterium tuberculosis, yet 75% of bus riders were genotypically clustered, indicating recent transmission, compared to 56% of non-bus riders (OR=2.4, 95%CI(2.0, 2.8), p<0.001). Bus riders had a mean cluster size of 50.14 vs. 28.9 (p<0.001). Second order spatial analysis of clustered fingerprint 2 (n=122), a Beijing family cluster, revealed geographic clustering among cases based on their report of bus use. Univariate and multivariate analysis of routes reported by cases belonging to these clusters found that 10 of the 14 clusters were associated with use. Individual Metro routes, including one route servicing the local hospitals, were found to be risk factors for belonging to a cluster shown to be endemic in Houston. The routes themselves geographically connect the census tracts previously identified as having endemic TB. 78% (15/23) of Houston Metro routes investigated had one or more print groups reporting frequent use for every HTI study year. We present data on three specific but clonally related print groups and show that bus-use is clustered in time by route and is the only known link between cases in one of the three prints: print 22. (Abstract shortened by UMI.)^

Interferon-gamma release assays for latent tuberculosis infection in child and young adult candidates or recipients of tumor necrosis factor inhibitor therapy

Background. Inhibition of tumor necrosis factor (TNF) is associated with progression of latent tuberculosis infection (LTBI) to active disease. LTBI screening prior to starting TNF inhibitor therapy is recommended. Blood tests, collectively known as interferon-gamma release assays (IGRAs), offer a means other than the tuberculin skin test (TST) of screening for LTBI. However, in the setting of immune compromise, anergy may limit the clinical utility of IGRAs. ^ Methods. A cross-sectional study was conducted in children and young adults ≤ 21 years of age who were cared for at Texas Children's Hospital in Houston, TX, during 2011 and who were candidates for, or were receiving, tumor necrosis factor (TNF)-inhibitor therapy. All subjects answered a risk factor questionnaire and were tested for LTBI by two commercially available IGRAs (QuantiFERON-Gold In-Tube assay and the T-SPOT.TB assay), along with the TST. T-cell phenotypes were evaluated through flow cytometry, both at baseline and after antigen stimulation. ^ Results. Twenty-eight subjects were enrolled. All were TST negative and none were IGRA positive. Results were negative for the 27 subjects who were tested with QuantiFERON-Gold In-Tube. However, 26% of subjects demonstrated anergy in the T-SPOT.T. Patients with T-SPOT. TB anergy had lower quantitative IFN-γ responses to mitogen in the QFT assay—the mean IFN-γ level to mitogen in patients without T-SPOT.TB anergy was 9.84 IU/ml compared to 6.91 IU/ml in patients with T-SPOT.TB anergy (P = 0.046). Age and use of TNF inhibitors, corticosteroids, or methotrexate use were not significantly associated with T-SPOT.TB anergy. Antigen stimulation revealed depressed expression of intracellular IFN-γ in subjects with T-SPOT. TB anergy. ^ Conclusions. The frequency of anergy in this population is higher than would be expected from studies in adults. There appears to be inappropriate IFN-γ responses to antigen in subjects with T-SPOT. TB anergy. This immune defect was detected by the T-SPOT. TB assay but not by the QuantiFERON-Gold In-Tube assay. Further data are needed to clarify the utility of IGRAs in this population.^

Tuberculosis in Texas correctional facilities between 2005--2009

It has been well documented that inmates incarcerated in prisons and correctional facilities exhibit higher incidence and prevalence of mycobacterium tuberculosis (TB) disease than the general population. This has public health implications because correctional systems may serve as reservoirs for TB disease that can lead to TB outbreaks in the facilities or can be spread to the general public once inmates are released. Although Texas has one of the largest correctional systems in both the US and the world, little is known about TB prevalence and incidence among Texas inmates. The purpose of this study was to elucidate the relationship between TB incidence and incarceration in Texas correctional facilities and investigate differences in various demographic factors. ^ The study used the national TB database from the US Centers for Disease Control and Prevention (CDC) to calculate and compare the overall incidences of TB disease among correctional facility inmates and similar non-inmates in Texas during 2005–2009. Data were also stratified by age, gender, race/ethnicity, birth status, and HIV status and compared between inmates and non-inmates using chi-squared analysis and relative risks with 95% confidence intervals to assess any significant differences. ^ Results suggest that the overall TB incidence among Texas correctional facility inmates per year (88.6 per 100,000) was significantly higher than that of Texas non-inmates (6.3 per 100,000); a 14 fold difference. Relative risk analyses by gender, race/ethnicity, and those with HIV infection found that the TB incidences for all these demographics were significantly and consistently higher in inmates compared to non-inmates. In particular, Hispanic inmates were more likely to develop TB than their non-inmate counterparts by a relative risk of 23.9 (95% CI 19.4–29.4). Likewise, both male and female inmates were more likely to develop TB than non-inmates (RR = 10.2, 95% CI 8.5–12.2; RR = 20.8, 95% CI 12.2–25.3, respectively), although female inmates unconventionally exhibited a higher TB incidence and relative risk than males inmates, which has not been shown. Among those with HIV infections, correctional facility inmates were 2.6 times were likely to develop TB disease than non-inmates (95% CI 1.5–4.4). ^ Inmates in Texas correctional facilities have a higher incidence of TB than non-inmates. Part of this higher risk may be because a large proportion of inmates come from populations already at high risks for TB, such as foreign born immigrants, those infected with HIV, and low SES groups such as many racial/ethnic minorities. Thus, these results may be used as a basis for more controlled and detailed research in the area, and to further characterize incarceration as a risk factor for TB incidence. They may also bring much needed attention about this health disparity to public health officials, legislators, and health administrators to expand and improve TB control in Texas correctional facilities, particularly among inmates released to the community, and reduce the risk of TB transmission to the general population.^

Economic evaluation of latent tuberculosis infection screening among health care workers in Houston

Since interferon-gamma release assays (IGRAs) were introduced in the 2000's, tuberculin skin testing (TST) and IGRAs have been used in various latent tuberculosis infection (LTBI) screening settings. IGRAs are laboratory-based tests and are considered not to be affected by previous Bacille de Calmette et Guérin (BCG) vaccination; however, they are more costly when compared directly with TST, which does not require specimen processing in a laboratory. This study aimed to examine TST and two types of IGRAs, QuantiFERON-TB Gold in Tube (QFT-GIT) and T-SPOT. TB (TSPOT), from an economic viewpoint. Firstly, a systematic literature review was conducted to identify cost related analyses of LTBI screening. Secondly, specific cost information detailing each test's items and labor was collected from an LTBI screening program of health care workers in Houston, and the cost of each test was computed. Thirdly, using the computed cost estimate of each test, cost-effectiveness analyses were conducted to compare TST and IGRAs.^ A literature search showed that a limited number of studies have been conducted, but the IGRA's economic advantages were common among studies. Cost analyses showed that IGRAs were much more costly than TST. The results were consistent with previous studies. In cost-effectiveness analyses, where test cost and consequential TB-related cost were considered, IGRAs showed variable advantages over TST depending on the targeted population. When only non BCG-vaccinated people were considered, TST was the least costly option among the three tests. On the other hand, when only BCG-vaccinated people were considered, IGRAs were less costly options. These results were mostly consistent even with varying assumption parameters.^ IGRAs can be more costly than TST, but their economic disadvantages are alleviated when the target population was BCG-vaccinated. Based on current knowledge, IGRAs may be recommended in a population where the BCG history is mixed. Additional studies are needed to better understand IGRA's reliability among low-incidence and low-risk populations in which background TB prevalence is low.^

INDUCTION OF STRONGER AND LONG LASTING VACCINE IMMUNITY TO TUBERCULOSIS

Tuberculosis is a major cause of death due to an infection in mankind. BCG vaccine protects against childhood tuberculosis although, it fails to protect against adult tuberculosis. BCG vaccine localizes to immature phagosomes of macrophages, and avoids lysosomal fusion, which decreases peptide antigen production. Peptides are essential for macrophage-mediated priming of CD4 and CD8 T cells respectively through MHC-II and MHC-I pathways. Furthermore, BCG reduces the expression of MHC-II in macrophages of mice after infection, through Toll-like receptor-1/2 (TLR-1/2) mediated signaling. In my first aim, I hypothesized that BCG-induced reduction of MHC-II levels in macrophages can decrease CD4 T cell function, while activation of other surface Toll-like receptors (TLR) can enhance CD4 T cell function. An in vitro antigen presentation model was used where, TLR activated macrophages presented an epitope of Ag85B, a major immunogen of BCG to CD4 T cells, and T cell derived IL-2 was quantitated as a measure of antigen presentation. Macrophages with BCG were poor presenters of Ag85B while, TLR-7/9/5/4 and 1/2 activation led to an enhanced antigen presentation. Furthermore, TLR-7/9 activation was found to down-regulate the degradation of MHC-II through ubiquitin ligase MARCH1, and also stimulate MHC-II expression through activation of AP-1 and CREB transcription elements via p38 and ERK1/2 MAP kinases. I conclude from Aim-I studies that TLR-7/9 ligands can be used as more effective ‘adjuvants’ for BCG vaccine. In Aim-II, I evaluated the poor CD8 T cell function in BCG vaccinated mice thought to be due to a decreased leak of antigens into cytosol from immature phagosomes, which reduces the MHC-I mediated activation of CD8 T cells. I hypothesized that rapamycin co-treatment could boost CD8 T cell function since it was known to sort BCG vaccine into lysosomes increasing peptide generation, and it also enhanced the longevity of CD8 T cells. Since CD8 T cell function is a dynamic event better measurable in vivo, mice were given BCG vaccine with or without rapamycin injections and challenged with virulent Mycobacterium tuberculosis. Organs were analysed for tetramer or surface marker stained CD8 T cells using flow cytometry, and bacterial counts of organisms for evaluation of BCG-induced protection. Co-administration of rapamycin with BCG significantly increased the numbers of CD8 T cells in mice which developed into both short living effector- SLEC type of CD8 T cells, and memory precursor effector-MPEC type of longer-living CD8 T cells. Increased levels of tetramer specific-CD8 T cells correlated with a better protection against tuberculosis in rapamycin-BCG group compared to BCG vaccinated mice. When rapamycin-BCG mice were rested and re-challenged with M.tuberculosis, MPECs underwent stronger recall expansion and protected better against re-infection than mice vaccinated with BCG alone. Since BCG induced immunity wanes with time in humans, we made two novel observations in this study that adjuvant activation of BCG vaccine and rapamycin co-treatment both lead to a stronger and longer vaccine-mediated immunity to tuberculosis.

Correlation of tuberculosis and human immunodeficiency virus in Harris County, Texas from 2009 through 2010 using Geographic Information Systems

A population based ecological study was conducted to identify areas with a high number of TB and HIV new diagnoses in Harris County, Texas from 2009 through 2010 by applying Geographic Information Systems to determine whether distinguished spatial patterns exist at the census tract level through the use of exploratory mapping. As of 2010, Texas has the fourth highest occurrence of new diagnoses of HIV/AIDS and TB.[31] The Texas Department of State Health Services (DSHS) has identified HIV infected persons as a high risk population for TB in Harris County.[29] In order to explore this relationship further, GIS was utilized to identify spatial trends. ^ The specific aims were to map TB and HIV new diagnoses rates and spatially identify hotspots and high value clusters at the census tract level. The potential association between HIV and TB was analyzed using spatial autocorrelation and linear regression analysis. The spatial statistics used were ArcGIS 9.3 Hotspot Analysis and Cluster and Outlier Analysis. Spatial autocorrelation was determined through Global Moran's I and linear regression analysis. ^ Hotspots and clusters of TB and HIV are located within the same spatial areas of Harris County. The areas with high value clusters and hotspots for each infection are located within the central downtown area of the city of Houston. There is an additional hotspot area of TB located directly north of I-10 and a hotspot area of HIV northeast of Interstate 610. ^ The Moran's I Index of 0.17 (Z score = 3.6 standard deviations, p-value = 0.01) suggests that TB is statistically clustered with a less than 1% chance that this pattern is due to random chance. However, there were a high number of features with no neighbors which may invalidate the statistical properties of the test. Linear regression analysis indicated that HIV new diagnoses rates (β=−0.006, SE=0.147, p=0.970) and census tracts (β=0.000, SE=0.000, p=0.866) were not significant predictors of TB new diagnoses rates. ^ Mapping products indicate that census tracts with overlapping hotspots and high value clusters of TB and HIV should be a targeted focus for prevention efforts, most particularly within central Harris County. While the statistical association was not confirmed, evidence suggests that there is a relationship between HIV and TB within this two year period.^

Human complement component C3 -binding proteins of Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis, is a facultative intracellular pathogen that uses the host mononuclear phagocyte as a niche for survival and replication during infection. Complement component C3 has previously been shown to enhance the binding of M. tuberculosis to mononuclear phagocytes. Using a C3 ligand affinity blot protocol, we identified a 30 kDa C3-binding protein in M. tuberculosis as heparin-binding hemagglutinin (HbhA). HbhA was found to be a hydrophobic protein that localized to the cell membrane/cell wall fraction of M. tuberculosis, and this protein has previously been shown by others to be located on the surface of M. tuberculosis. The C3-binding activity of HbhA was localized to the C-terminus of the protein, which consists of lysine-alanine repeats. Full-length recombinant HbhA coated onto latex beads was shown to mediate the adherence of the beads to murine macrophage-like cells in both a C3-dependent and a C3-independent manner. An in-frame 576 by deletion in the hbhA gene was created in a virulent strain of M. tuberculosis using a PCR technique known as gene splicing by overlap extension (SOEing). Using the ΔhbhA mutant, HbhA was found not to be necessary for growth of M. tuberculosis in laboratory media or in macrophage-like cells, nor is HbhA required for adherence of M. tuberculosis to macrophage-like cells. HbhA is, however, required for infectivity of M. tuberculosis in mice. Mice infected with the ΔhbhA mutant show decreased growth in the lungs, liver, and spleen compared to mice infected with the wild-type strain. Using the ΔhbhA mutant strain, we were able to purify and identify a second 30-kDa C3-binding protein, HupB. These data demonstrate that HbhA is required for the in vivo but not the in vitro survival of M. tuberculosis and that HbhA is not necessary for the adherence of M. tuberculosis to the macrophage-like cells used in these studies. The expression of two proteins that bind human C3 may aid in the efficient binding of M. tuberculosis to complement receptors for uptake into mononuclear cells, or may influence other aspects of the host-parasite interaction. ^

Who Develops Innovations in Medicine for the Poor? Trends in Patent Applications Related to Medicines for HIV/AIDS, Tuberculosis, Malaria and Neglected Diseases

Who invents medicines for the poor of the world? This question becomes very important where the WTO allows low income countries to be unbound by the TRIPS agreement. This agreement concerns medicines for infectious diseases such as HIV/AIDS, tuberculosis and malaria. These diseases cause serious damage to low income countries. Under these circumstances, some scholars wonder if anyone will continue innovative activities related to treating these diseases. This paper sought to answer this question by collecting and analyzing patent data of medicines and vaccines for diseases using the database of the Japan Patent Office. Results indicate that private firms have led in innovation not only for global diseases such as HIV/AIDS but also diseases such as malaria that are spreading exclusively in low income countries. Innovation for the three infectious diseases is diverse among firms, and frequent patent applications by high-performing pharmaceutical firms appear prominent even after R&D expenditure, economies of scale, and economies of scope are taken into account.

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory.

La Evolucion historica del concepto sobre la tuberculosis pulmonar

Separata de t.2, n.3. de Clinica Hispanica

Desarrollo de un sistema de digitalización y análisis de imágenes de microscopía para el diagnóstico de tuberculosis mediante inteligencia colectiva y gamificación

En este Trabajo de Fin de Grado se diseña, implementa y evalúa un sistema se digitalización de muestras de esputo basado en telefonía móvil e integrable con TuberSpot. Además, se proponen técnicas de procesamiento de imagen para el control de calidad del análisis y se implementa un mecanismo para evaluar la eficiencia de la inteligencia colectiva y la gamificación en este contexto. El sistema de adquisición propuesto utiliza smartphones, adaptadores móvil-microscopio y una aplicación Android. El protocolo de adquisición se ha diseñado conforme a un estudio realizado con personal médico cualificado. El control de calidad se basa en la inserción de bacilos simulados en las imágenes. Para la evaluación de eficiencia de TuberSpot se crea, en colaboración con médicos especialistas, un repositorio de imágenes en las que posición y número de bacilos quedan registrados.

Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization

Tuberculosis is a chronic infectious disease that is transmitted by cough-propelled droplets that carry the etiologic bacterium, Mycobacterium tuberculosis. Although currently available drugs kill most isolates of M. tuberculosis, strains resistant to each of these have emerged, and multiply resistant strains are increasingly widespread. The growing problem of drug resistance combined with a global incidence of seven million new cases per year underscore the urgent need for new antituberculosis therapies. The recent publication of the complete sequence of the M. tuberculosis genome has made possible, for the first time, a comprehensive genomic approach to the biology of this organism and to the drug discovery process. We used a DNA microarray containing 97% of the ORFs predicted from this sequence to monitor changes in M. tuberculosis gene expression in response to the antituberculous drug isoniazid. Here we show that isoniazid induced several genes that encode proteins physiologically relevant to the drug’s mode of action, including an operonic cluster of five genes encoding type II fatty acid synthase enzymes and fbpC, which encodes trehalose dimycolyl transferase. Other genes, not apparently within directly affected biosynthetic pathways, also were induced. These genes, efpA, fadE23, fadE24, and ahpC, likely mediate processes that are linked to the toxic consequences of the drug. Insights gained from this approach may define new drug targets and suggest new methods for identifying compounds that inhibit those targets.

Attenuation of virulence in Mycobacterium tuberculosis expressing a constitutively active iron repressor

Iron is an essential nutrient for the survival of most organisms and has played a central role in the virulence of many infectious disease pathogens. Mycobacterial IdeR is an iron-dependent repressor that shows 80% identity in the functional domains with its corynebacterial homologue, DtxR (diphtheria toxin repressor). We have transformed Mycobacterium tuberculosis with a vector expressing an iron-independent, positive dominant, corynebacterial dtxR hyperrepressor, DtxR(E175K). Western blots of whole-cell lysates of M. tuberculosis expressing the dtxR(E175K) gene revealed the stable expression of the mutant protein in mycobacteria. BALB/c mice were infected by tail vein injection with 2 × 105 organisms of wild type or M. tuberculosis transformed with the dtxR mutant. At 16 weeks, there was a 1.2 log reduction in bacterial survivors in both spleen (P = 0.0002) and lungs (P = 0.006) with M. tuberculosis DtxR(E175K). A phenotypic difference in colonial morphology between the two strains also was noted. A computerized search of the M. tuberculosis genome for the palindromic consensus sequence to which DtxR and IdeR bind revealed six putative “iron boxes” within 200 bp of an ORF. Using a gel-shift assay we showed that purified DtxR binds to the operator region of five of these boxes. Attenuation of M. tuberculosis can be achieved by the insertion of a plasmid containing a constitutively active, iron-insensitive repressor, DtxR(E175K), which is a homologue of IdeR. Our results strongly suggest that IdeR controls genes essential for virulence in M. tuberculosis.

Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination

One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally discovered a striking reduction of silent nucleotide substitutions compared with other human bacterial pathogens. The lack of neutral mutations in structural genes indicates that M. tuberculosis is evolutionarily young and has recently spread globally. Species diversity is largely caused by rapidly evolving insertion sequences, which means that mobile element movement is a fundamental process generating genomic variation in this pathogen. Three genetic groups of M. tuberculosis were identified based on two polymorphisms that occur at high frequency in the genes encoding catalase-peroxidase and the A subunit of gyrase. Group 1 organisms are evolutionarily old and allied with M. bovis, the cause of bovine tuberculosis. A subset of several distinct insertion sequence IS6110 subtypes of this genetic group have IS6110 integrated at the identical chromosomal insertion site, located between dnaA and dnaN in the region containing the origin of replication. Remarkably, study of ≈6,000 isolates from patients in Houston and the New York City area discovered that 47 of 48 relatively large case clusters were caused by genotypic group 1 and 2 but not group 3 organisms. The observation that the newly emergent group 3 organisms are associated with sporadic rather than clustered cases suggests that the pathogen is evolving toward a state of reduced transmissability or virulence.