Stefan Niemann

Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains

The human immunity-related GTPase M (IRGM) has been shown to be critically involved in regulating autophagy as a means of disposing cytosolic cellular structures and of reducing the growth of intracellular pathogens in vitro. This includes Mycobacterium tuberculosis, which is in agreement with findings indicating that M. tuberculosis translocates from the phagolysosome into the cytosol of infected cells, where it becomes exposed to autophagy. To test whether IRGM plays a role in human infection, we studied IRGM gene variants in 2010 patients with pulmonary tuberculosis (TB) and 2346 unaffected controls. Mycobacterial clades were classified by spoligotyping, IS6110 fingerprinting and genotyping of the pks1/15 deletion. The IRGM genotype -261TT was negatively associated with TB caused by M. tuberculosis (OR 0.66, CI 0.52-0.84, P(nominal) 0.0009, P(corrected) 0.0045) and not with TB caused by M. africanum or M. bovis (OR 0.95, CI 0.70-1.30. P 0.8). Further stratification for mycobacterial clades revealed that the protective effect applied only to M. tuberculosis strains with a damaged pks1/15 gene which is characteristic for the Euro-American (EUAM) subgroup of M. tuberculosis (OR 0.63, CI 0.49-0.81, P(nominal) 0.0004, P(corrected) 0.0019). Our results, including those of luciferase reporter gene assays with the IRGM variants -261C and -261T, suggest a role for IRGM and autophagy in protection of humans against natural infection with M. tuberculosis EUAM clades. Moreover, they support in vitro findings indicating that TB lineages capable of producing a distinct mycobacterial phenolic glycolipid that occurs exclusively in strains with an intact pks1/15 gene inhibit innate immune responses in which IRGM contributes to the control of autophagy. Finally, they raise the possibility that the increased frequency of the IRGM -261TT genotype may have contributed to the establishment of M. africanum as a pathogen in the West African population.

Molecular Characterization of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis Strains Isolated in Poland

A total of 105 rifampin (RMP)- and/or isoniazid (INH)-resistant strains of Mycobacterium tuberculosis isolated from different parts of Poland in 2000 were screened for mutations associated with resistance to these drugs by two molecular methods, namely sequence analysis and real-time PCR technology. Three loci associated with drug resistance were selected for characterization: they were rpoB (RMP), katG, and the regulatory region of inhA (INH). Nineteen different mutations were identified in 64 RMP-resistant strains, and five new alleles were described. The most common point mutations were in codons 531 (41%), 516 (16%), and 526 (9%) of the rpoB gene. Mutations were not found in two (3%) of the isolates. In the case of resistance to INH, six different mutations in the katG gene of 83 resistant strains were detected. Fifty-seven (69%) isolates exhibited nucleotide substitutions at codon 315. One strain harbored a mutation affecting codon 279 (Gly279Thr). Twelve of 26 INH-resistant strains with the wild-type codon 315 (14.5% of all strains tested) had the mutation -15C-->T in the regulatory region of inhA. A full correlation between the DNA sequence analysis and real-time PCR data was obtained. We conclude that the real-time PCR method is fast and reliable for the detection of RMP and INH resistance-associated mutations in M. tuberculosis clinical isolates.ABSTRACT Molecular characterization of the drug resistance of Mycobacterium tuberculosis strains with different origins can generate information that is useful for developing molecular methods. These methods are widely applicable for rapid detection of drug resistance. A total of 166 rifampin (RIF)- and/or isoniazid (INH)-resistant strains of M. tuberculosis have been isolated from different parts of Vietnam; they were screened for mutations associated with resistance to these drugs by sequence analysis investigating genetic mutations associated with RIF and INH resistance. Seventeen different mutations were identified in 74 RIF-resistant strains, 56 of which (approximately 76%) had mutations in the so-called 81-bp “hot-spot” region of the rpoB gene. The most common point mutations were in codons 531 (37.8%), 526 (23%), and 516 (9.46%) of the rpoB gene. Mutations were not found in three strains (4.05%). In the case of INH resistance, five different mutations in the katG genes of 82 resistant strains were detected, among which the nucleotide substitution at codon 315 (76.83%) is the most common mutation. This study provided the first molecular characterization of INH and RIF resistance of M. tuberculosis strains from Vietnam, and detection of the katG and rpoB mutations of the INH and RIF-resistant strains should be useful for rapid detection of the INH- and RIF-resistant strains by molecular tests.

ALOX5 variants associated with susceptibility to human pulmonary tuberculosis

The 5-lipoxygenase (ALOX5)-derived lipid mediators leukotrienes and lipoxins have regulatory functions in inflammation by modulating activities of immune cells and cytokine production. Recently, it was shown in ALOX5-/- mice that host control of Mycobacterium tuberculosis is regulated by 5-lipoxygenase (5-LO). ALOX5 polymorphisms were genotyped in 1916 sputum-positive patients with pulmonary tuberculosis (TB) from Ghana and in 2269 exposed, apparently healthy controls. Polymorphisms of a variable number of tandem repeats (VNTR) of the ALOX5 promoter and of the exonic non-synonymous variant g.760G>A were analysed by fragment length determination and fluorescence resonance energy transfer, respectively, and DNA sequencing. Mycobacterial lineages of >1400 isolates were differentiated biochemically and genetically. Carriers of one variant (n repeats not equal 5) and one wild-type VNTR allele (n = 5) or of the exonic allele g.760A had a higher risk of TB [P(corrected) = 0.026, odds ratio (OR) 1.19 (95% CI 1.04-1.37) and P(corrected) = 0.026, OR 1.21 (95% CI 1.04-1.41), respectively]. The association of the exonic variant was stronger in infections caused by the mycobacterial lineage M. africanum West-African 2 [P(corrected) = 0.024, OR 1.70; (95% CI 1.2-2.6)]. Determination of haplotypes revealed the strongest associaton with TB for the non-5/760A haplotype compared with the non-5/760G haplotype (P = 0.003, OR 1.50). Our observation of an association of ALOX5 variants with susceptibility to TB contributes evidence of the importance of 5-LO products to the regulation of immune responses to M. tuberculosis.

Mycobacterium africanum Subtype II Is Associated with Two Distinct Genotypes and Is a Major Cause of Human Tuberculosis in Kampala, Uganda

ABSTRACT The population structure of 234 Mycobacterium tuberculosis complex strains obtained during 1995 and 1997 from tuberculosis patients living in Kampala, Uganda (East Africa), was analyzed by routine laboratory procedures, spoligotyping, and IS6110 restriction fragment length polymorphism (RFLP) typing. According to biochemical test results, 157 isolates (67%) were classified as M. africanum subtype II (resistant to thiophen-2-carboxylic acid hydrazide), 76 isolates (32%) were classified as M. tuberculosis, and 1 isolate was classified as classical M. bovis. Spoligotyping did not lead to clear differentiation of M. tuberculosis and M. africanum, but all M. africanum subtype II isolates lacked spacers 33 to 36, differentiating them from M. africanum subtype I. Moreover, spoligotyping was not sufficient for differentiation of isolates on the strain level, since 193 (82%) were grouped into clusters. In contrast, in the IS6110-based dendrogram, M. africanum strains were clustered into two closely related strain families (Uganda I and II) and clearly separated from the M. tuberculosis isolates. A further characteristic of both M. africanum subtype II families was the absence of spoligotype spacer 40. All strains of family I also lacked spacer 43. The clustering rate obtained by the combination of spoligotyping and RFLP IS6110 analysis was similar for M. africanum and M. tuberculosis, as 46% and 49% of the respective isolates were grouped into clusters. The results presented demonstrate that M. africanum subtype II isolates from Kampala, Uganda, belong to two closely related genotypes, which may represent unique phylogenetic branches within the M. tuberculosis complex. We conclude that M. africanum subtype II is the main cause of human tuberculosis in Kampala, Uganda.

No associations of human pulmonary tuberculosis with Sp110 variants

Background: After a recent report on the role of the Ipr1 gene in mediating innate immunity in a mouse model of Mycobacterium tuberculosis infection, the human Ipr1 homologue, Sp110, was considered a promising candidate for an association study in human tuberculosis. Methods: In a sample of >1000 sputum positive, HIV negative West African patients with pulmonary tuberculosis and >1000 exposed, apparently healthy controls, we have genotyped 21 Sp110 gene variants that were either available from public databases, including HapMap data, or identified by DNA re-sequencing. Results: No significant differences in the frequencies of any of the 21 variants were observed between patients and controls. This applied also for HapMap tagging variants and the corresponding haplotypes, when including sliding window analyses with three adjacent variants, and when stratifying controls for positivity and negativity according to the results of intradermal tuberculin (purified protein derivative, PPD) skin tests. DNA re-sequencing revealed 13 novel Sp110 variants in the 5′-UTR, exons, and adjacent intronic regions. Conclusions: Based on the results obtained in this case-control study, the hypothesis that Sp110 variants and haplotypes might be associated with distinct phenotypes of human M tuberculosis infection is doubtful.

The Species Mycobacterium africanum in the Light of New Molecular Markers

ABSTRACT The findings of recent studies addressing the molecular characteristics of Mycobacterium tuberculosis complex isolates have initiated a discussion on the classification of M. africanum, especially of those isolates originating from East Africa (cluster F, subtype II) and displaying phenotypic and biochemical characteristics more similar to those of M. tuberculosis. To further address this question, we analyzed a representative collection of 63 M. tuberculosis complex strains comprising 30 M. africanum subtype I strains, 20 M. africanum subtype II strains, 10 randomly chosen M. tuberculosis isolates, and type strains of M. tuberculosis, M. bovis, and M. africanum for the following biochemical and molecular characteristics: single-nucleotide polymorphisms (SNPs) in gyrB and narGHJI and the presence or absence of RD1, RD9, and RD12. For all molecular markers analyzed, subtype II strains were identical to the M. tuberculosis strains tested. In contrast, the subtype I strains as well as the M. africanum type strain showed unique combinations of SNPs in gyrB and genomic deletions (the absence of RD9 and the presence of RD12), which proves their independence from M. tuberculosis and M. bovis. Accordingly, all subtype I strains displayed main biochemical characteristics included in the original species description of M. africanum. We conclude that the isolates from West Africa were proved to be M. africanum with respect to the phenotypic and genetic markers analyzed, while the isolates from East Africa must be regarded as phenotypic variants of M. tuberculosis (genotype Uganda). We propose the addition of the molecular characteristics defined here to the species description of M. africanum, which will allow clearer species differentiation in the future.

Variant G57E of Mannose Binding Lectin Associated with Protection against Tuberculosis Caused by Mycobacterium africanum but not by M. tuberculosis

Structural variants of the Mannose Binding Lectin (MBL) cause quantitative and qualitative functional deficiencies, which are associated with various patterns of susceptibility to infectious diseases and other disorders. We determined genetic MBL variants in 2010 Ghanaian patients with pulmonary tuberculosis (TB) and 2346 controls and characterized the mycobacterial isolates of the patients. Assuming a recessive mode of inheritance, we found a protective association between TB and the MBL2 G57E variant (odds ratio 0.60, confidence interval 0.4–0.9, P 0.008) and the corresponding LYQC haplotype (P corrected 0.007) which applied, however, only to TB caused by M. africanum but not to TB caused by M. tuberculosis. In vitro, M. africanum isolates bound recombinant human MBL more efficiently than did isolates of M. tuberculosis. We conclude that MBL binding may facilitate the uptake of M. africanum by macrophages, thereby promoting infection and that selection by TB may have favoured the spread of functional MBL deficiencies in regions endemic for M. africanum.

IL10 haplotype associated with tuberculin skin test response but not with pulmonary TB.

Evidence from genetic association and twin studies indicates that susceptibility to tuberculosis (TB) is under genetic control. One gene implicated in susceptibility to TB is that encoding interleukin-10 (IL10). In a group of 2010 Ghanaian patients with pulmonary TB and 2346 healthy controls exposed to Mycobacterium tuberculosis, among them 129 individuals lacking a tuberculin skin test (PPD) response, we genotyped four IL10 promoter variants at positions −2849 , −1082 , −819 , and −592 and reconstructed the haplotypes. The IL10 low-producer haplotype −2849A/−1082A/−819C/−592C, compared to the high-producer haplotype −2849G/−1082G/−819C/−592C, occurred less frequent among PPD-negative controls than among cases (OR 2.15, CI 1.3–3.6) and PPD-positive controls (OR 2.09, CI 1.2–3.5). Lower IL-10 plasma levels in homozygous −2849A/−1082A/−819C/−592C carriers, compared to homozygous −2849G/−1082G/−819C/−592C carriers, were confirmed by a IL-10 ELISA (pu200a=u200a0.016). Although we did not observe differences between the TB patients and all controls, our results provide evidence that a group of individuals exposed to M. tuberculosis transmission is genetically distinct from healthy PPD positives and TB cases. In these PPD-negative individuals, higher IL-10 production appears to reflect IL-10-dependent suppression of adaptive immune responses and sustained long-term specific anergy.

Pulmonary tuberculosis: Virulence of Mycobacterium africanum and relevance in HIV co-infection

Although Mycobacterium africanum is being isolated in a significant proportion of cases of pulmonary tuberculosis in West Africa, its pathogenic potential remains a matter of discussion. Recent reports leave the question of whether M. africanum causes more severe pathology than M. tuberculosis or resembles opportunistic pathogens and might gain importance in the course of the HIV pandemic. Patients with pulmonary tuberculosis associated with M. africanum (n=556) and M. tuberculosis (n=1350) were studied in Ghana, West Africa, and compared regarding self-reported signs and symptoms, chest radiography, HIV status, mycobacterial drug resistance and mycobacterial clustering as determined by spoligotyping and IS6110 fingerprints. The rate of M. africanum infections was similar in HIV-positive (27%) and HIV-negative (30%) patients. M. africanum clustered less than M. tuberculosis (21% vs 79%; OR, 0.38; 95% CI, 0.3-0.5; p<0.001) corresponding to its lower prevalence (29% vs 70%). Clinically and radiographically, no significant differences were found except that M. africanum caused lower-lobe disease less frequently than M. tuberculosis (OR, 0.39; 95% CI, 0.2-0.7; Pc=0.01), whereby this association applied to HIV-negative patients only. No difference in virulence, as assessed by the severity of radiological presentation, was found when the two M. africanum subtypes West African 1 and West African 2 were compared. In the population studied, M. africanum closely resembled M. tuberculosis in pathology and cannot be considered an opportunistic pathogen.

Mycobacterium tuberculosis Drug Resistance, Ghana

To the Editor: The directly observed treatment strategy (DOTS) for tuberculosis (TB) treatment has been implemented in Ghana since 1994. Before then, TB was treated without adherence to any concerted guidelines. The 2003 report of the Ghanaian National Tuberculosis Programme (NTP) stated a TB incidence of 281/100,000 (1). NTP ensures treatment of all patients with an 8-month course of streptomycin, isoniazid, rifampin, and pyrazinamide (for 2 months), followed by thiacetazone and isoniazid (6 months). The cure rate for 2003 was >50% (1), and >75% is anticipated for 2005. n nTo determine the extent of drug resistance and to make suggestions for future Ghanaian NTP strategies, we assessed resistance against anti-TB drugs used in Ghana. A total of 2,064 patients with new cases of pulmonary TB were recruited at Korle Bu Teaching Hospital, Accra; Komfo Anokye Teaching Hospital, Kumasi; 15 periurban hospitals; and hospitals in the Ashanti, Eastern, and Central Regions of Ghana. These patients were consecutively enrolled in a cross-sectional study from September 2001 to December 2004. On all patients’ clinical examinations, chest radiographs, sputum smears for staining of acid-fast bacteria, HIV testing, and culturing of Mycobacterium tuberculosis complex strains were performed. Samples were taken only after informed consent was given. The study was approved by the appropriate ethics committees. n nA total of 2,064 Mycobacterium isolates were cultured at the Kumasi Centre for Collaborative Research. After decontamination of sputum samples (N-acetyl-L-cysteine/NaOH) and centrifugation, sediments were transferred onto Lowenstein-Jensen (LJ) media, incubated (37°C), and read weekly for 10 weeks for mycobacterial growth. Subsequently, cultures were sent to the German National Reference Centre for Mycobacteria in Borstel, Germany, a reference laboratory of the World Health Organization, for drug sensitivity testing (DST; proportion method on LJ media). Sensitivity to isoniazid, rifampin, pyrazinamide, ethambutol, and streptomycin was determined for 2,064 isolates and to thiacetazone for 1,288 isolates. For ambiguous results and DST of thiacetazone, the modified proportion method (Bactec 460TB; Becton Dickinson, Cockeysville, MD, USA) was performed. Data were analyzed with EpiInfo (Centers for Disease Control and Prevention, Atlanta, GA, USA) and Fourth Dimension (ACI Group, San Jose, CA, USA) software programs. n nOf the isolates, 32.8% were from female patients, and 67.8% were from male patients. The mean age of participants (33 years, range 10–60) did not differ by sex. HIV prevalence was 14.3% (males, n = 179, females, n = 117). n nA total of 1,578 (76.5%) isolates were susceptible to all drugs tested, whereas 304 (14.7%) were monodrug resistant, and 177 (8.7%) were multi- or polydrug resistant to combinations (multidrug resistance meant resistance to at least isoniazid and rifampin (2.2%); polydrug resistance meant resistance to several drugs, excluding combined resistance to isoniazid and rifampin (6.5%). The overall prevalence of any drug resistance was 23.5% (486 isolates) (Table). No differences were observed between HIV-negative and HIV-positive patients. The highest level of resistance was against streptomycin, followed by isoniazid. Resistance to rifampin, pyrazinamide, and thiacetazone was lower. Monoresistance to ethambutol was not observed; resistance to ethambutol combined with other drugs occurred in 0.9% of isolates. n n n nTable n nResistance to first-line antituberculosis drugs, Ghana* n n n nIn all, 6.5% of isolates were polydrug resistant and virtually always included resistance to isoniazid. Among isolates with double- and triple drug resistance, combinations of resistance to isoniazid and streptomycin and to isoniazid-thiacetazone-streptomycin occurred most frequently. Other combinations were relatively rare. n nIn 1989, an initial drug resistance rate of 54.5% in pulmonary TB was observed in Ghana (2); 27% were resistant to isoniazid, 23% to streptomycin, 29% to thiacetazone, 16% to streptomycin-isoniazid, and 5% to thiacetazone-streptomycin-isoniazid. A later study reported a high prevalence of primary drug resistance to isoniazid (23%), while sensitivity to rifampicin, pyrazinamide, ethambutol, streptomycin, and ciprofloxacin was maintained (3). However, the number of isolates tested was fewer in both studies (n = 99 and 25, respectively) than in ours. This report supplements data from patients in Ghana whose conditions were newly diagnosed as HIV-negative and HIV-positive. Samples were collected in 2 large regions of Ghana, the Greater Accra and the Ashanti Regions, and were supplemented by samples from additional regions. Thus, these results are likely representative of the entire country. n nThe overall primary drug resistance rate of 23.5% in Ghanaian TB patients ranks Ghana among those African countries with a high prevalence of drug-resistant TB. The high degree of mono-, multi- and polyresistance to streptomycin may be the result of selective pressure exerted by treatment of other infections with streptomycin and to incomplete treatment courses. Drug resistance to streptomycin and isoniazid are of concern, since these drugs are core components of the NTP. The relative ineffectiveness of streptomycin and the low level of resistance to ethambutol justify the most recent replacement of streptomycin by ethambutol by the Ghanaian NTP. n nLow rates of initial drug resistance have been reported in countries in which the DOTS strategy has been successfully implemented. Adequate use of standardized treatment regimens under DOTS will limit further emergence of drug resistance but not substantially reduce the current degree of resistance (4). Although the levels of drug resistance in Africa are lower than in several other countries (5), measures to provide controlled application of second-line drugs, supervision of drug distribution and compliance, enforcement of DOTS protocols, and sustained training of all personnel involved in TB management are crucial.