Genetics and pulmonary medicine. 3. Genetic susceptibility to tuberculosis in human populations

Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration

The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.

Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis

Inborn errors of IFN-γ immunity can underlie tuberculosis (TB). We report three patients from two kindreds without EBV viremia or disease but with severe TB and inherited complete ITK deficiency, a condition associated with severe EBV disease that renders immunological studies challenging. They have CD4+ αβ T lymphocytopenia with a concomitant expansion of CD4-CD8- double-negative (DN) αβ and Vδ2- γδ T lymphocytes, both displaying a unique CD38+CD45RA+T-bet+EOMES- phenotype. Itk-deficient mice recapitulated an expansion of the γδ T and DN αβ T lymphocyte populations in the thymus and spleen, respectively. Moreover, the patients' T lymphocytes secrete small amounts of IFN-γ in response to TCR crosslinking, mitogens, or forced synapse formation with autologous B lymphocytes. Finally, the patients' total lymphocytes secrete small amounts of IFN-γ, and CD4+, CD8+, DN αβ T, Vδ2+ γδ T, and MAIT cells display impaired IFN-γ production in response to BCG. Inherited ITK deficiency undermines the development and function of various IFN-γ-producing T cell subsets, thereby underlying TB.

Molecular snapshot of drug-resistant Mycobacterium tuberculosis strains from the Plateau State, Nigeria

Nigeria ranks 1^st in Africa and 6^th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2–33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2–17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.

Genetic Analysis of TB Susceptibility Variants in Ghana Reveals Candidate Protective Loci in SORBS2 and SCL11A1 Genes

Despite advancements made toward diagnostics, tuberculosis caused by Mycobacterium africanum (Maf) and Mycobacterium tuberculosis sensu stricto (Mtbss) remains a major public health issue. Human host factors are key players in tuberculosis (TB) outcomes and treatment. Research is required to probe the interplay between host and bacterial genomes. Here, we explored the association between selected human/host genomic variants and TB disease in Ghana. Paired host genotype datum and infecting bacterial isolate information were analyzed for associations using a multinomial logistic regression. Mycobacterium tuberculosis complex (MTBC) isolates were obtained from 191 TB patients and genotyped into different phylogenetic lineages by standard methods. Two hundred and thirty-five (235) nondisease participants were used as healthy controls. A selection of 29 SNPs from TB disease-associated genes with high frequency among African populations was assayed using a TaqMan® SNP Genotyping Assay and iPLEX Gold Sequenom Mass Genotyping Array. Using 26 high-quality SNPs across 326 case-control samples in an association analysis, we found a protective variant, rs955263, in the SORBS2 gene against both Maf and Mtb infections (PBH = 0.05; OR = 0.33; 95% CI = 0.32–0.34). A relatively uncommon variant, rs17235409 in the SLC11A1 gene was observed with an even stronger protective effect against Mtb infection (MAF = 0.06; PBH = 0.04; OR = 0.05; 95% CI = 0.04–0.05). These findings suggest SLC11A1 and SORBS2 as a potential protective gene of substantial interest for TB, which is an important pathogen in West Africa, and highlight the need for in-depth host-pathogen studies in West Africa.

Association of Polymorphism +874 T/A Interferon Gamma Gene with Susceptibility to Pulmonary Tuberculosis in Medan, Indonesia

BACKGROUND: Pulmonary tuberculosis (TB) is still a disease that concerns in the world due to its high incidence, especially in developing countries, including Indonesia. Polymorphism +874 T/A interferon-gamma (IFN-γ) is one of the host genetic factors that have been widely studied and has been shown to be associated with susceptibility to pulmonary TB. AIM: This study aims to determine the association polymorphism +874 T/A IFN-γ gene with susceptibility to pulmonary TB in Medan population. METHODS: A total of 82 pulmonary TB patients and 85 healthy controls were examined in this case–control study. SPSS 25 is used to process and analyze all data where the Pearson Chi-square is used to analyze the association between genotype and susceptibility to pulmonary TB. RESULTS: The polymorphism +874 T/A IFN-γ gene was not significantly associated with susceptibility to pulmonary TB in patients compared to controls (p = 0.395) and there was no association between allele frequency and susceptibility to pulmonary TB (p = 0.158). CONCLUSION: Our study suggests no association of polymorphism +874 T/A IFN-γ gene with pulmonary TB in Medan, Sumatera Utara, Indonesia.

A genetic variant in the TRAF1/C5 gene lead susceptibility to active pulmonary tuberculosis by decreased TNF-α levels

Host genetics are important to consider in the role of resistance or susceptibility for developing active pulmonary tuberculosis (TB). Several association studies have reported the role of variants in STAT4 and TRAF1/C5 as risk factors to autoimmune diseases. Nevertheless, more data is needed to elucidate the role of these gene variants in infectious disease. Our data reports for the first time, variant rs10818488 in the TRAF1/C5 gene (found 47% of the population worldwide), is associated with susceptibility (OR = 1.51) to development TB. Multivariate analysis evidenced association between rs10818488 TRAF1/C5 and risk to multibacillary TB (OR = 4.18), confers increased bacteria load in the lung, indicates a decreased ability to control pathogen levels in the lung, and spread of the pathogen to new hosts. We showed that the "loss-of-function" variant in TRAF1/C5 led to susceptibility for TB by decreased production of TNF-α. Our results suggest the role of variant TRAF1/C5 in susceptibility to TB as well as in clinical presentation of multibacillary TB.

A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort

Despite decades of research and advancements in diagnostics and treatment, tuberculosis remains a major public health concern. New computational methods are needed to interrogate the intersection of host- and bacterial genomes. Paired host genotype datum and infecting bacterial isolate information were analysed for associations using a multinomial logistic regression framework implemented in SNPTest. A cohort of 853 admixed South African participants and a Ghanaian cohort of 1359 participants were included. Two directly genotyped variants, namely rs529920 and rs41472447, were identified in the Ghanaian cohort as being statistically significantly associated with risk for infection with strains of different members of the MTBC. Thus, a multinomial logistic regression using paired host-pathogen data may prove valuable for investigating the complex relationships driving infectious disease.

Combining Host Genetics and Functional Analysis to Depict Inflammasome Contribution in Tuberculosis Susceptibility and Outcome in Endemic Areas

The interplay between M. tuberculosis (Mtb) and humans is multifactorial. The susceptibility/resistance profile and the establishment of clinical tuberculosis (TB) still remains elusive. The gain-of-function variant rs10754558 in the NLRP3 gene (found in 30% of the world population) confers protection against the development of TB, indicating a prominent role played by NLRP3 inflammasome against Mtb. Through genotype-guided assays and various Mtb strains (BCG, H37Rv, Beijing-1471, MP287/03), we demonstrate that Mtb strains activate inflammasome according to the NLRP3/IL-1ß or NLRC4/IL18 preferential axis. NLRP3 and NLRC4 genetic variants contribute to the presentation of TB. For the first time, we have shown that loss-of-function variants in NLRC4 significantly contribute to the development of extra-pulmonary TB. The analysis of inflammasome activation in a cohort of TB patients and their “household contacts” (CNT) revealed that plasma IL-1ß/IFN-α ratio lets us distinguish patients from Mtb-exposed-but-healthy individuals from an endemic region. Moreover, NLRP3 inflammasome seemed “exhausted” in TB patients compared to CNT, indicating a more efficient activation of inflammasome in resistant individuals. These findings suggest that inflammasome genetics as well as virulence-dependent level of inflammasome activation contribute to the onset of a susceptible/resistant profile among Mtb-exposed individuals.

Current topics of molecular mycobacteriology

The 2nd St. Petersburg Symposium on Tuberculosis and Mycobacteria: Molecular Approach, was held in St. Petersburg, Russia on 5-6 December 2018. A special issue of Infection, Genetics and Evolution will publish articles based on the selected presentations. In this paper, I will discuss some of the hot topics of molecular mycobacteriology highlighted at this meeting that I had the pleasure to organize and honor to chair. The symposium addressed interrelated fundamental and applied issues of modern mycobacteriology such as molecular evolution and phylogenomics, host-microbe interactions and pathogenesis, coevolution of M. tuberculosis with humans, new genomic and postgenomic technologies. Molecular methods for TB diagnostics and drug resistance detection are supported by WHO and whole genome/next generation sequencing presents a comprehensive approach. At the same time, cost and implementation of new methods for direct analysis of clinical samples and/or in low-resource settings remain a great challenge. A due attention was also given to the medically important nontuberculous mycobacteria. Assessment of spectrum of the circulating mycobacterial species in the Russian Federation and the countries of the European Union was presented and the underlying reasons of the observed diversity were discussed. To conclude, the symposium became a multidisciplinary event that was useful to promote networking and exchange of knowledge and experience. The next (third) symposium was planned to be organized in 2021.

Fine-mapping analysis of a chromosome 2 region linked to resistance to Mycobacterium tuberculosis infection in Uganda reveals potential regulatory variants

Tuberculosis (TB) is a major public health burden worldwide, and more effective treatment is sorely needed. Consequently, uncovering causes of resistance to Mycobacterium tuberculosis (Mtb) infection is of special importance for vaccine design. Resistance to Mtb infection can be defined by a persistently negative tuberculin skin test (PTST-) despite living in close and sustained exposure to an active TB case. While susceptibility to Mtb is, in part, genetically determined, relatively little work has been done to uncover genetic factors underlying resistance to Mtb infection. We examined a region on chromosome 2q previously implicated in our genomewide linkage scan by a targeted, high-density association scan for genetic variants enhancing PTST- in two independent Ugandan TB household cohorts (n = 747 and 471). We found association with SNPs in neighboring genes ZEB2 and GTDC1 (peak meta p = 1.9 × 10^-5) supported by both samples. Bioinformatic analysis suggests these variants may affect PTST- by regulating the histone deacetylase (HDAC) pathway, supporting previous results from transcriptomic analyses. An apparent protective effect of PTST- against body-mass wasting suggests a link between resistance to Mtb infection and healthy body composition. Our results provide insight into how humans may escape latent Mtb infection despite heavy exposure.

Association of VDR gene polymorphisms and 22 bp deletions in the promoter region of TLR2Δ22 (-196-174) with increased risk of pulmonary tuberculosis: A case-control study in tea garden communities of Assam

BACKGROUND

A high number of pulmonary tuberculosis (PTB) cases have been reported from tea garden communities of Assam. Till date, no molecular epidemiological study was performed to investigate the association of candidate gene(s) with the risk PTB in this region. The present case-control study was aimed to investigate the association of vitamin D receptor (VDR) gene polymorphisms and 22 bp deletion in the promoter region of toll-like receptor 2 (TLR2) gene with the risk of PTB in tea garden communities of Assam.

METHODS

Genotyping of VDR polymorphisms and TLR2Δ22 (-196-174) gene was carried out for 169 PTB cases and 227 apparently healthy community controls using blood samples by PCR-RFLP followed by DNA sequencing. For association study, both univariate and multivariate logistic regression analyses were performed.

RESULTS

This study has shown that BsmI and FokI polymorphisms of VDR gene significantly associated with an increased risk of PTB (AOR = 3.58, 95% CI = 1.64-7.80, P < .01 for B/b genotype of BsmI and AOR = 2.44, 95% CI = 1.40-4.24, P < .01 for F/f genotype of FokI polymorphism). No significant association of TaqI and ApaI polymorphism of VDR gene was found with the risk of PTB. Moreover, this study has revealed that person carrying deletion allele in their TLR2Δ22 (-196-174) gene is significantly associated with an increased risk of PTB having b/b or F/f genotypes in BsmI or FokI polymorphisms of VDR gene.

CONCLUSION

This study has revealed that BsmI and FokI polymorphisms of VDR gene significantly associated with an increased risk of PTB.

Susceptibility to Mycobacterium ulcerans Disease (Buruli ulcer) Is Associated with IFNG and iNOS Gene Polymorphisms

Buruli ulcer (BU) is a chronic necrotizing disease of the skin and subcutaneous fat tissue. The causative agent, Mycobacterium ulcerans, produces mycolactone, a macrolide toxin, which causes apoptosis of mammalian cells. Only a small proportion of individuals exposed to M. ulcerans develop clinical disease, as surrounding macrophages may control the infection by bacterial killing at an early stage, while mycolactone concentration is still low. Otherwise, bacterial multiplication leads to in higher concentrations of mycolactone, with formation of necrotizing lesions that are no more accessible to immune cells. By typing a cohort of 96 Ghanaian BU patients and 384 endemic controls without BU, we show an association between BU and single nucleotide polymorphisms (SNPs) in iNOS (rs9282799) and IFNG (rs2069705). Both polymorphisms influence promoter activity in vitro. A previously reported SNP in SLC11A1 (NRAMP, rs17235409) tended to be associated with BU. Altogether, these data reflect the importance of IFNG signaling in early defense against M. ulcerans infection.

Genetic Susceptibility and Predictors of Paradoxical Reactions in Buruli Ulcer

Introduction

Buruli ulcer (BU) is the third most frequent mycobacterial disease in immunocompetent persons after tuberculosis and leprosy. During the last decade, eight weeks of antimicrobial treatment has become the standard of care. This treatment may be accompanied by transient clinical deterioration, known as paradoxical reaction. We investigate the incidence and the risks factors associated with paradoxical reaction in BU.

Methods

The lesion size of participants was assessed by careful palpation and recorded by serial acetate sheet tracings. For every time point, surface area was compared with the previous assessment. All patients received antimicrobial treatment for 8 weeks. Serum concentration of 25-hydroxyvitamin D, the primary indicator of vitamin D status, was determined in duplex for blood samples at baseline by a radioimmunoassay. We genotyped four polymorphisms in the SLC11A1 gene, previously associated with susceptibility to BU. For testing the association of genetic variants with paradoxical responses, we used a binary logistic regression analysis with the occurrence of a paradoxical response as the dependent variable.

Results

Paradoxical reaction occurred in 22% of the patients; the reaction was significantly associated with trunk localization (p = .039 by Χ²), larger lesions (p = .021 by Χ²) and genetic factors. The polymorphisms 3’UTR TGTG ins/ins (OR 7.19, p < .001) had a higher risk for developing paradoxical reaction compared to ins/del or del/del polymorphisms.

Conclusions

Paradoxical reactions are common in BU. They are associated with trunk localization, larger lesions and polymorphisms in the SLC11A1 gene.

Buruli ulcer is an infectious disease of skin, subcutaneous fat and sometimes bone, mainly affecting children in West Africa. It is considered as one of the Neglected Tropical Diseases but the disease occurs also in moderate climates like South East Australia and Japan where it may also affect adults. Once a patient has started antibiotic treatment, lesions may increase in size even if the antimicrobial treatment is effective; this is highly confusing for doctors and patients as they may think that treatment actually fails. The cause of Buruli ulcer is Mycobacterium ulcerans, related to other mycobacteria that cause disease in man, like leprosy and tuberculosis. Using data from two different studies in West Africa, we show that these paradoxical reactions are associated with trunk localization and that they occur more often in larger lesions. The chance to develop these reactions appeared partly inherited: carrying the homozygous ins/ins genotype of 3’UTR TGTG 285 polymorphism in the SLC11A1 gene increased the risk of paradoxical reactions. Vitamin D is important for the immune defense against infections by mycobacteria. Vitamin D blood concentrations were not associated with paradoxical reactions; patients generally did well, and we did not need corticosteroid immune suppression to overcome these reactions.

Alleles of HLA-DRB1*04 Associated with Pulmonary Tuberculosis in Amazon Brazilian Population

Immunogenetic host factors are associated with susceptibility or protection to tuberculosis (TB). Strong associations of HLA class II genes with TB are reported. We analyzed the HLA-DRB1*04 alleles to identify subtypes associated with pulmonary TB and their interaction with risk factors such as alcohol, smoking, and gender in 316 pulmonary TB patients and 306 healthy individuals from the Brazilian Amazon. The HLA-DRB1*04 was prevalent in patients with pulmonary TB (p<0.0001; OR = 2.94; 95% CI = 2.12 to 4.08). Direct nucleotide sequencing of DRB1 exon 2 identified nine subtypes of HLA-DRB1*04. The subtype HLA-DRB1*04:11:01 (p = 0.0019; OR = 2.23; 95% CI = 1.34 to 3.70) was associated with susceptibility to pulmonary TB while DRB1*04:07:01 (p<0.0001; OR = 0.02; 95% CI = 0.001 to 0.33) to protection. Notably, the interaction between alcohol and HLA-DRB1*04:11:01 increased the risk for developing pulmonary TB (p = 0.0001; OR = 51.3; 95% CI = 6.81 to 386). Multibacillary pulmonary TB, the clinical presentation of disease transmission, was strongly associated with interaction to alcohol (p = 0.0026; OR = 11.1; 95% CI = 3.99 to 30.9), HLA-DRB1*04:11:01 (p = 0.0442; OR = 2.01; 95% CI = 1.03 to 3.93) and DRB1*04:92 (p = 0.0112; OR = 8.62; 95% CI = 1.63 to 45.5). These results show that HLA-DRB1*04 are associated with pulmonary TB. Interestingly, three subtypes, DRB1*04:07:01, DRB1*04:11:01 and DRB1*04:92 of the HLA-DRB1*04 could be potential immunogenetic markers that may help to explain mechanisms involved in disease development.

Inherited and acquired immunodeficiencies underlying tuberculosis in childhood

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb) and a few related mycobacteria, is a devastating disease, killing more than a million individuals per year worldwide. However, its pathogenesis remains largely elusive, as only a small proportion of infected individuals develop clinical disease either during primary infection or during reactivation from latency or secondary infection. Subacute, hematogenous, and extrapulmonary disease tends to be more frequent in infants, children, and teenagers than in adults. Life-threatening primary TB of childhood can result from known acquired or inherited immunodeficiencies, although the vast majority of cases remain unexplained. We review here the conditions conferring a predisposition to childhood clinical diseases caused by mycobacteria, including not only M.tb but also weakly virulent mycobacteria, such as BCG vaccines and environmental mycobacteria. Infections with weakly virulent mycobacteria are much rarer than TB, but the inherited and acquired immunodeficiencies underlying these infections are much better known. Their study has also provided genetic and immunological insights into childhood TB, as illustrated by the discovery of single-gene inborn errors of IFN-γ immunity underlying severe cases of TB. Novel findings are expected from ongoing and future human genetic studies of childhood TB in countries that combine a high proportion of consanguineous marriages, a high incidence of TB, and an excellent clinical care, such as Iran, Morocco, and Turkey.

Determinants of the Sympatric Host-Pathogen Relationship in Tuberculosis

Major contributions from pathogen genome analysis and host genetics have equated the possibility of Mycobacterium tuberculosis co-evolution with its human host leading to more stable sympatric host–pathogen relationships. However, the attribution to either sympatric or allopatric categories depends on the resolution or grain of genotypic characterization. We explored the influence on the sympatric host-pathogen relationship of clinical (HIV infection and multidrug-resistant tuberculosis [MDRTB]) and demographic (gender and age) factors in regards to the genotypic grain by using spacer oligonucleotide typing (spoligotyping) for classification of M. tuberculosis strains within the Euro-American lineage. We analyzed a total of 547 tuberculosis (TB) cases, from six year consecutive sampling in a setting with high TB-HIV coinfection (32.0%). Of these, 62.0% were caused by major circulating pathogen genotypes. The sympatric relationship was defined according to spoligotype in comparison to the international spoligotype database SpolDB4. While no significant association with Euro-American lineage was observed with any of the factors analyzed, increasing the resolution with spoligotyping evidenced a significant association of MDRTB with sympatric strains, regardless of the HIV status. Furthermore, distribution curves of the prevalence of sympatric and allopatric TB in relation to patients’ age showed an accentuation of the relevance of the age of onset in the allopatric relationship, as reflected in the trimodal distribution. On the contrary, sympatric TB was characterized by the tendency towards a typical (standard) distribution curve. Our results suggest that within the Euro-American lineage a greater degree of genotyping fine-tuning is necessary in modeling the biological processes behind the host-pathogen interplay. Furthermore, prevalence distribution of sympatric TB to age was suggestive of host genetic determinisms driven by more common variants.

Radiographic appearance of pulmonary tuberculosis: dogma disproved

OBJECTIVE

The purpose of this article is to review the origins of the classic teaching on pulmonary tuberculosis, its evolution in the modern literature, and the evidence that led to its demise.

CONCLUSION

Use of molecular epidemiologic techniques that entail DNA finger-printing has led to the discovery that the radiographic appearance of pulmonary tuberculosis does not depend on the time since infection. It has been confirmed that the upper lobe cavitary disease typical in adults is the disease of the immunocompetent host, whereas lower lung zone disease, adenopathy, and effusions, which are uncommon in adults, are the hallmarks of tuberculosis in an immunocompromised host.

Polymorphisms in HLA-DRB1 gene and the risk of tuberculosis: a meta-analysis of 31 studies

PURPOSE

The HLA-DRB1 gene polymorphisms have been implicated in susceptibility to tuberculosis (TB). However, a large number of studies have reported inconclusive results. This study was conducted to investigate the relationship of HLA-DRB1 gene polymorphisms and TB risk by a meta-analysis.

METHODS

A search was performed in Embase, PubMed, Wanfang Database, and China National Knowledge Internet (CNKI) up to Jul 30, 2014. Odds ratio (OR) and 95% confidence interval (95% CI) were used to assess the association. Statistical analyses were calculated by STATA 11.0 software.

RESULTS

All 31 articles involving 3,416 cases and 4,515 controls were identified. The pooled results indicated a significant association between HLA-DRB1*04 (OR 1.22, 95% CI 1.00-1.48, P = 0.048), *09 (OR 1.50, 95% CI 1.08-2.08, P = 0.016), *10 (OR 1.23, 95% CI 1.01-1.49, P = 0.035), *11 (OR 0.72, 95% CI 0.53-0.99, P = 0.044), *15 (OR 1.40, 95% CI 1.14-1.73, P = 0.001), and *16 (OR 1.33, 95% CI 1.08-1.63, P = 0.007) gene polymorphisms and TB risk. In addition, the results also show no significant association between HLA-DRB1*01 (P = 0.748), *03 (P = 0.947), *07 (P = 0.966), *08 (P = 0.440), *12 (P = 0.288), *13 (P = 0.241), and *14 (P = 0.551) gene polymorphisms and TB risk.

CONCLUSIONS

This study suggested that the HLA-DRB1*04, *09, *10, *15, and *16 gene polymorphisms may contribute to the risk of TB, especially in the East Asian. But the HLA-DRB1*11 gene polymorphism may be a protective factor for TB risk. Unfortunately, there is no significant association between the HLA-DRB1*01, *03, *07, *08, *12, *13, and *14 gene polymorphisms and TB risk.

Analysis of the lung transcriptome in Mycobacterium tuberculosis-infected mice reveals major differences in immune response pathways between TB-susceptible and resistant hosts

Using whole genome microarrays, we compared changes in gene expression patterns in the lungs of TB-resistant A/Sn and TB-susceptible I/St mice at day 14 following infection with Mycobacterium tuberculosis H37Rv. Analyses of differentially expressed genes for representation of gene ontology terms and activation of regulatory pathways revealed interstrain differences in antigen presentation, NK, T and B cell activation pathways. In general, resistant A/Sn mice exhibited a more complex pattern and stronger activation of host defense pathways compared to the TB-susceptible I/St mouse strain. In addition, in I/St mice elevated activation of genes involved in neutrophil response was observed and confirmed by quantitative RT-PCR and histopathology. Furthermore, a specific post infection upregulation of cysteine protease inhibitors was found in susceptible I/St mice.

Cellular hyperproliferation and cancer as evolutionary variables

Technological advances in biology have begun to dramatically change the way we think about evolution, development, health and disease. The ability to sequence the genomes of many individuals within a population, and across multiple species, has opened the door to the possibility of answering some long-standing and perplexing questions about our own genetic heritage. One such question revolves around the nature of cellular hyperproliferation. This cellular behavior is used to effect wound healing in most animals, as well as, in some animals, the regeneration of lost body parts. Yet at the same time, cellular hyperproliferation is the fundamental pathological condition responsible for cancers in humans. Here, I will discuss why microevolution, macroevolution and developmental biology all have to be taken into consideration when interpreting studies of both normal and malignant hyperproliferation. I will also illustrate how a synthesis of evolutionary sciences and developmental biology through the study of diverse model organisms can inform our understanding of both health and disease.

C-type lectins with a sweet spot for Mycobacterium tuberculosis

The pattern of receptors sensing pathogens onto host cells is a key factor that can determine the outcome of the infection. This is particularly true when such receptors belong to the family of pattern recognition receptors involved in immunity. Mycobacterium tuberculosis, the etiologic agent of tuberculosis interacts with a wide range of pattern-recognition receptors present on phagocytes and belonging to the Toll-like, Nod-like, scavenger and C-type lectin receptor families. A complex scenario where those receptors can establish cross-talks in recognizing pathogens or microbial determinants including mycobacterial components in different spatial and temporal context starts to emerge as a key event in the outcome of the immune response, and thus, the control of the infection. In this review, we will focus our attention on the family of calcium-dependent carbohydrate receptors, the C-type lectin receptors, that is of growing importance in the context of microbial infections. Members of this family appear to be key innate immune receptors of mycobacteria, capable of cross-talk with other pattern recognition receptors to induce or modulate the inflammatory context upon mycobacterial infection.

The effect of mannose binding lectin gene polymorphisms on susceptibility to tuberculosis in different ethnic groups

In order to investigate the role of MBL gene polymorphisms in susceptibility to tuberculosis (TB) we genotyped 487 TB cases and 232 controls. Among African-American individuals, the frequency of B allele was lower among controls than cases (p < 0.01), but we found no differences between cases and controls of white and Hispanic ethnicity.

Effect of matrix metalloproteinase-9 -1562C/T gene polymorphism on manifestations of pulmonary tuberculosis

Increased levels of matrix metalloproteinase-9 (MMP-9) in patients with tuberculous meningitis, tuberculous pleuritis, and advanced pulmonary tuberculosis (TB) suggest a pivotal role for MMP-9 in the development of pulmonary TB and its clinical manifestations. The present study was performed to evaluate the role of the -1562C/T single nucleotide polymorphism (SNP) in the promoter region of the human MMP-9 gene in development of pulmonary TB and its radiographic characteristics. A case-control study was performed with a study population of 205 patients with pulmonary TB and 223 healthy controls. Differences were explored in the allele and genotype distributions of the -1562C/T polymorphism between patients with pulmonary TB and healthy controls, between patients with single- and multi-lobe involvement, and between patients with and without cavities. The -1562C/C genotype was more common in patients with multi-lobe involvement than in those with single-lobe involvement (81.8 vs. 67.6%, P=0.03). However, there were no significant differences in the distribution between patients with pulmonary TB and healthy controls (P=0.40) or between patients with and without cavities (P=0.18). These results suggest that the -1562C/C genotype is associated with the intrapulmonary spread of TB rather than its development.

Mycobacterium tuberculosis co-existence with humans: making an imprint on the macrophage P2X(7) receptor gene?

The development of tuberculosis (TB) infection in humans depends on the mycobacterial strain and the human host, and is multigenically controlled in both. ATP ligation of P2X(7) receptors expressed on human macrophages infected with mycobacteria induces cell death and subsequent loss of intracellular bacterial viability. This study analysed the allelic distribution of two single-nucleotide polymorphisms (SNPs) in the P2RX7 gene in the Slavic population of the St Petersburg area of Russia. Analysis of the -762 C/T P2RX7 promoter SNP revealed no significant association between pulmonary TB patients and control subjects (3x2 chi(2)=3.2, 1 d.f., P=0.2). The -762C allele was highly and almost equally represented in both groups in this study (68.2 % in patients and 69.3 % in controls). This result differs strikingly from a Gambian study where this allele was found in only 7 and 12 % of pulmonary TB patients and controls, respectively [Li, C. M., Campbell, S. J., Kumararatne, D. S., Bellamy, R., Ruwende, C., McAdam, K. P. W. J., Hill, A. V. S. & Lammas, D. A. (2002). J Infect Dis 186, 1458-1462]. In contrast, the frequency of the C allele at position 1513 in exon 13, resulting in a loss of P2X(7) function, was significantly higher among pulmonary TB patients in this study (P=0.02). Thus, analysis of the P2X(7) receptor gene in the Russian Slavic population showed that the 1513C allele, acting dominantly, is a possible risk factor for clinical TB, whereas the -762 P2RX7 polymorphism did not appear to be associated with human susceptibility to TB.

Heredity versus environment in tuberculosis in twins: the 1950s United Kingdom Prophit Survey Simonds and Comstock revisited

RATIONALE

In his 1978 article on tuberculosis (TB) in twins, Comstock concluded that the 2.5-fold higher concordance rate for TB among monozygotic versus dizygotic twins in the Prophit survey of the 1950s implicated inherited susceptibility as a major risk factor for TB in humans. His analysis did not take into account strong imbalance of variables within subgroups, underestimating possible confounding effects of environmental factors.

OBJECTIVES

To reconsider the role of environmental versus hereditary factors in determining the concordance rate of TB among twin pairs.

METHODS

Reanalysis of the Prophit Survey.

MEASUREMENTS AND MAIN RESULTS

A known Mycobacterium tuberculosis-positive or M. tuberculosis-negative sputum in the index TB case markedly influenced the odds ratio (OR) of concordance in the twin pairs. In 87 pairs with co-twins exposed to a sputum-negative index case, monozygotic and dizygotic twins did not differ in concordance for TB (OR, 1.1; 95% confidence interval [95% CI], 0.4-2.8). A higher concordance rate for TB among monozygotic versus dizygotic twins was confined to 106 pairs with the co-twins exposed to a sputum-positive index case (OR, 3.4; 95% CI, 1.6-7.2), and was highest in adolescent twins living together. ORs of TB concordance were proportional to intensity of exposure (sputum smear positivity, physical proximity between twin pairs, contagiousness of disease, and living together) rather than to zygosity.

CONCLUSIONS

In the Prophit survey of susceptibility to TB among twins, environmental factors (i.e., intensity of exposure to tubercle bacilli) outweigh the importance of hereditary factors. Environmental factors and the context of transmission should be given more emphasis when studying interindividual and population differences in susceptibility to infectious diseases such as TB.

Allelic variation in BTNL2 and susceptibility to tuberculosis in a South African population

Tuberculosis and sarcoidosis show phenotypic features of granulomatous disease. The bacterium Mycobacterium tuberculosis can induce the expression of the sarcoidosis susceptibility gene BTNL2 in monocyte-derived macrophages. BTNL2 was therefore investigated as a candidate gene for tuberculosis in a case-control association study in the South African Coloured population. We sequenced the coding regions of BTNL2 to detect known and novel polymorphisms and genotyped 18 SNPs in 432 pulmonary tuberculosis cases and 482 controls. We did not find a significant association between the truncating rs2076530 SNP, previously associated with sarcoidosis, and tuberculosis. No association was found between any of the other SNPs studied and disease and none of the estimated haplotypes showed any association with TB. Comparative analyses with the South African data from this study and published data on German and American populations revealed that, for a segment of BTNL2, the admixed, but not stratified, South African population resembles the African-Americans more than white populations.

An ecological study of tuberculosis transmission in California

OBJECTIVES

We evaluated the association between ecological factors and rates of tuberculosis within California, using pediatric tuberculosis as an indicator of new transmission.

METHODS

Ecological variables such as racial/ethnic distribution, immigration level, education, employment, poverty, and crowding were obtained from the United States Census for each census tract in California. These data were incorporated into a negative binomial regression model with the rate of pediatric tuberculosis disease in each census tract as an outcome variable. Disease rates were obtained by geocoding reported cases. Subsections of the state (San Francisco and Los Angeles) were examined independently.

RESULTS

Census tracts with lower median incomes, more racial/ethnic minorities, and more immigrants had higher rates of pediatric tuberculosis. Other frequently cited risk factors such as overcrowding and unemployment were not associated with increased disease after adjusting for other measures. Risks were comparable across regions, but subtle differences were noted.

CONCLUSIONS

The techniques used in this work provide a way to examine a disease within its social context. The results confirmed that tuberculosis in California continues to be a disease of poverty and racial/ethnic minorities.

Analysis of cellular phenotypes that mediate genetic resistance to tuberculosis using a radiation bone marrow chimera approach

Adoptive transfer of bone marrow cells from tuberculosis-resistant (I/St x A/Sn)F(1) donor mice into lethally irradiated susceptible I/St recipients changed their phenotype following infection with virulent Mycobacterium tuberculosis. Compared to I/St-->I/St control animals, F(1)-->I/St chimeras demonstrated (i) prolonged survival time, (ii) increased antimycobacterial function of lung macrophages, (iii) elevated gamma interferon production by lung cells, and (iv) decreased infiltration of the lungs with CD4(+) and CD8(+) T cells and Ly-6G(+) neutrophils.

Association of HLA-DR and HLA-DQ Genes With Susceptibility to Pulmonary Tuberculosis in Koreans: Preliminary Evidence of Associations With Drug Resistance, Disease Severity, and Disease Recurrence

Only 10% of persons infected with Mycobacterium tuberculosis develop clinical tuberculosis (TB), indicating the existence of host genetic factors regulating disease expression. We investigated the association of human leukocyte antigen (HLA) class II genes with the susceptibility to pulmonary TB in Koreans, with special emphasis on their association with drug resistance, disease severity, and disease recurrence. Human leukocyte antigens (HLA)-DRB1 and -DQB1 gene polymorphisms were analyzed in 160 Korean patients with pulmonary TB and 200 ethnically matched healthy controls. HLA-DRB1*0803 (25.0% vs. 14.5% in controls, OR = 1.97, p = 0.012, corrected p (p(c)) > 0.05) and DQB1*0601 (27.5% vs. 15.5% in controls, OR = 2.07, p = 0.005, p(c) > 0.05) were weakly associated with general susceptibility to TB. DRB1*0803 was significantly associated with drug resistance (30.9% vs. 14.5%, OR = 2.63, p(c) = 0.047) and more advanced lung lesion (29.8% vs. 14.5%, OR = 2.50, p(c) = 0.022). DRB1*0803 showed the strongest association with disease recurrence, especially after curative treatment for the earlier infection (47.4% vs. 14.5%, OR = 5.31, p(c) = 0.00009). DQB1*0601, which is strongly linked to DRB1*0803 in this population showed similar changes in the patients as those of DRB1*0803. It is suggested that DRB1*0803 and DQB1*0601 alleles are associated with disease progression of TB in Koreans, exerting influence on the development of drug resistance, severe disease, and recurrent disease.

Diagnostic strategies and outcomes on three New Zealand deer farms with severe outbreaks of bovine tuberculosis

SETTING

Three commercial deer herds, each containing more than 500 deer, experienced outbreaks of tuberculosis (TB) ranging from a 6% prevalence to disease levels >50%. Intensive diagnostic testing was carried out over short time intervals after the initial diagnosis of TB.

OBJECTIVE

To eradicate M. bovis infection from herds of farmed red deer (Cervus elaphus) in New Zealand, which had significant outbreaks of tuberculosis (>5%), using complementary diagnostic tests and elective slaughter of all test positive animals.

DESIGN

Whole herd mid cervical skin tests (MCT) were used as the primary test and a comparative cervical test (CCT) as an ancillary test. In an attempt to enhance TB eradication, ancillary blood tests comprising; lymphocyte transformation tests (LT) and enzyme-linked immunosorbent assays (ELISA) were used in parallel with MCT, or as serial tests, to complement skin testing.

RESULTS

One deer herd (N), which had an acute outbreak (6%) of TB in adult stock, responded quickly to testing and the disease was eradicated within 12 months. A second more chronically infected herd (B), with low prevalence (2%) of TB initially in pregnant hinds which were retained over the breeding cycle, developed widespread uncontrollable spread of infection, that could not be contained by exhaustive testing. The final herd (S), which had an acute outbreak of TB at a prevalence >90% in young fawns, responded well to testing and became TB-free within 1 year.

CONCLUSIONS

TB can be eradicated from infected farmed deer herds, using currently available TB tests, irrespective of disease prevalence. The caveat is that disease must be diagnosed early in the acute phase of infection. Undiagnosed infection over winter in breeding hinds in one herd produced a refractory infection in adult males and females and uncontrollable spread to newborn fawns. Disease could not be eradicated using comprehensive diagnostic schedules. A widespread but controllable outbreak of acute TB in another herd, appeared to have caused sufficient selective pressure on adult stock that genetically resistant adults were selected within a very short time frame (<1 year).

Different innate ability of I/St and A/Sn mice to combat virulent Mycobacterium tuberculosis: phenotypes expressed in lung and extrapulmonary macrophages

Mice of the I/St and A/Sn inbred strains display a severe and moderate course, respectively, of disease caused by Mycobacterium tuberculosis. Earlier, we showed that the response to mycobacterial antigens in I/St mice compared to that in A/Sn mice is shifted toward Th2-like reactivity and a higher proliferative activity and turnover of T cells. However, the physiologic basis for different expressions of tuberculosis severity in these mice remains largely unknown. Here, we extend our previous observations with evidence that I/St interstitial lung macrophages are defective in the ability to inhibit mycobacterial growth and to survive following in vitro infection with M. tuberculosis H37Rv. A unique feature of this phenotype is its exclusive expression in freshly isolated lung macrophages. The defect is not displayed in ex vivo macrophages obtained from the peritoneal cavity nor in macrophages developed in vitro from progenitors extracted from various organs, including the lung itself. In addition, we show that, in sharp contrast to peritoneal macrophages, the mycobactericidal capacity of lung macrophages is not elevated in the presence of exogenous gamma interferon. Our data suggest that the in vivo differentiation in a particular anatomical microenvironment determines the pattern of macrophage-mycobacterium interaction. Thus, caution should be exercised when conclusions based upon the results obtained in a particular in vitro system are generalized to the functions of all phagocytes during M. tuberculosis infection.

Historical intensity of natural selection for resistance to tuberculosis

Infections have long been thought to exert natural selection on humans. Infectious disease resistance is frequently invoked as a mechanism shaping human genetic diversity, but such hypotheses have rarely been quantitatively evaluated with direct measures of disease-related mortality. Enhancement of genetically determined resistance to tuberculosis by natural selection has been proposed as a factor explaining the decline of tuberculosis in Europe and North America in the period 1830-1950 (before the advent of antimicrobial chemotherapy) and the apparently reduced susceptibility of Europeans and their descendants to tuberculosis infection and/or disease. We used Swedish vital statistics from 1891 to 1900 to estimate that individuals who escaped mortality from pulmonary tuberculosis (PTB) during the European tuberculosis epidemic would have enjoyed a fitness advantage of 7-15% per generation compared to individuals who were susceptible to PTB mortality; individuals with 50% protection would have had a selection coefficient of 4-7%/generation. Selection during the peak of the European TB epidemic could have substantially reduced the frequency of already rare alleles conferring increased susceptibility to PTB mortality, but only if the phenotypic effects of these alleles were very large. However, if resistant alleles were rare at the beginning of this period, 300 years would not have been long enough for such selection to increase their frequency to epidemiologically significant levels. Reductions in the frequency of rare susceptibility alleles could have played at most a small part in the decline of the epidemic in the century preceding 1950. Natural selection by PTB deaths during the European TB epidemic alone cannot account for the presently low level of TB disease observed among Europeans and their descendants just prior to the appearance of antibiotic treatment.

Complex disease and the new clinical sciences

Medical research today is dominated by a genocentric point of view. At the same time, clinical discovery and patient-oriented research have become less common. Here, I suggest that these developments are interdependent, each representing the flip side of an inaccurate view of how clinical advance occurs.

Susceptibility to development of Mycobacterium ulcerans disease: review of possible risk factors

Mycobacterium ulcerans disease, also known as Buruli ulcer (BU), is a disease of subcutaneous fat tissue. BU is prevalent in riverine and swamp areas of the tropical zone in Africa, Asia and South America, and a few scattered foci in Australia. The mode of transmission of M. ulcerans has not been fully elucidated, but inoculation into the subcutaneous tissues probably occurs through penetrating skin trauma. BU has not been linked with HIV infection. Antimycobacterial drug treatment is ineffective, and treatment is surgical. Patients eventually develop scars and contractures, with resulting disabilities, and the disease imposes a large burden on affected populations. The incidence of BU has dramatically increased in West African countries over the last decade. There is an urgent need for research into host and environmental risk factors for BU in order to develop effective strategies to combat this disease. We review possible genetic host susceptibility factors for BU that are relevant in other mycobacterial diseases: natural resistance-associated macrophage protein-1 (NRAMP-1), HLA-DR, vitamin D3 receptor, mannose binding protein, interferon-gamma (IFN-gamma) receptor, tumour necrosis factor alpha (TNF-alpha), interleukin (IL)-1 alpha, 1 beta and their receptor antagonists; and IL-12. Schistosoma haematobium infection is highly endemic in many BU foci in West Africa, with a striking increase in transmission after river dams were constructed. This observation, and the observations from interaction of schistosomiasis and tuberculosis, have fueled our hypothesis that schistosomiasis is a risk factor for BU by driving the host immune response towards a predominantly Th-2 pattern, away from a Th-1 preponderant protection against mycobacterial infection. If the latter hypothesis is confirmed, enhanced schistosomiasis control should impact on BU.

Challenges in prevention, diagnosis and therapy of emerging fungal diseases. Aspergillosis: A case study

Diseases caused by pathogenic filamentous fungi, are an emerging threat to public health in the wake of increasing incidence of HIV and tuberculosis. At this point, discovery and development of fungal therapeutics and diagnostics are serious challenges for biomedical researchers. Recent technological advances in genomics and proteomics offer great scope for development of preventive and therapeutic measures for fungal diseases.Aspergillus, one of the medically important filamentous pathogenic fungi causes a wide spectrum of clinical disorders ranging from allergic aspergillosis to systemic invasive aspergillosis. Increase in incidence of drug resistance and the cytotoxic effects are two serious limitations of the antifungal drugs presently in use. This is primarily due to lack of understanding of biological mechanisms operative in these fungi. Today, it is possible to understand the biological mechanisms of the fungus for its colonisation, survival and invasion of the host. Future developments based on such leads can result in development of precise and specific diagnostic, therapeutic and preventive measures for a wide clinical spectrum of fungal diseases.

HIV/AIDS among African Americans: progress or progression?

OBJECTIVES

To review data on the extent of HIV infection and associated risk behaviors, the occurrence of AIDS, and HIV-related mortality in African Americans and to suggest what can be done to reduce HIV exposure and infection in this population.

DESIGN/METHODS

Review of epidemiologic, published, multisite data on HIV infection in, and related behaviors of, African Americans.

RESULTS

On every epidemiologic measure in common use, African Americans, compared with the four other federally recognized racial/ethnic groups, have the most severe epidemic. The trend data show continuing growth in the African American epidemic despite the availability of effective behavioral interventions and biomedical treatments. Few published intervention studies with African American populations have been adequately evaluated; nor have they focused proportionately on men who have sex with men, a group in the African American community with continuing high rates of infection.

CONCLUSIONS

Rates of HIV transmission and disease among African Americans are high, disproportionate, and are not declining as significantly in response to effective interventions as they are among whites. Attention is urgently needed to increase our understanding of risk behaviors, social networks, and specific factors in the African American community that can be altered to reduce HIV infection. Macroenvironmental factors--poverty, social class, racism--need to be studied to suggest possible intervention components to reduce rates of HIV transmission and to increase the use of therapies that are more effectively slowing disease progression and lowering death rates among whites.

Analysis of HLA antigens in Mycobacterium avium-intracellulare pulmonary infection

Mycobacterium avium-intracellulare (MAI) pulmonary infection may occur in subjects with no preexisting lung disease and no known immunodeficiency, showing radiologically nodular bronchiectasis. There have remained some unresolved problems in the pathogenesis of the disorder, including the predominance in elderly women and the presence of not deteriorated or deteriorated disease. In the present study, we examined whether immunogenetic susceptibility is present in the disorder. We evaluated 64 cases of MAI disease and analyzed their short-term natural history by assessing symptoms, sputum bacteriology, and chest computed tomographic findings. The frequencies of human leukocyte antigen (HLA) alleles in patients were compared with those in 100 healthy Japanese control subjects. We assayed the HLA-A, -B, -C, -DR, and -DQ antigens serologically. Among 64 patients, 37 (35 females) did not show deterioration, whereas 27 (24 females) showed deterioration after an interval of 30 +/- 15 mo. There was no significant frequency of HLA-B and -C alleles in either group. In 37 not deteriorated patients, DR-6 was positive in 14 (37.8%) patients but in only 16 (16%) control subjects (p = 0.0061, odds ratio [OR] = 3.20). DQ-4 was positive in 10 (27.0%) patients but in only 10 (10%) control subjects (p = 0. 0122, OR = 3.33). In 27 deteriorated patients, HLA-A26 was positive in 14 (51.9%) patients but in only 21 (21.0%) control subjects (p = 0.0015, OR = 4.05). MAI pulmonary infection with nodular bronchiectasis shows two types of outcome, deteriorated and not deteriorated. The subjects with A-26 antigen might indicate the deterioration of MAI infection.