Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa.

BACKGROUND: There is increasing evidence of a strain-related variation in the virulence in Mycobacterium tuberculosis that may afford a selective advantage to certain strains. The W-Beijing strain family is globally distributed, highly virulent in animal models, associated with human immunodeficiency virus infection and drug resistance, and may be an emerging strain family. Our goal was to determine whether W-Beijing strains are expanding in a region of South Africa where rates of tuberculosis are among the highest in the world. METHODS: We used spoligotyping and single nucleotide polymorphism analysis to genotype all strains of tuberculosis from children presenting to the major pediatric referral hospital in Cape Town, South Africa over a period of 4 years and strains present in 352 archived histological samples from over a 76-year period. RESULTS: The proportion of W-Beijing strains from children increased from 13% to 33% from 2000 to 2003 (P= .026). With regard to the histological samples, W-Beijing strains were absent in the samples from the period 1930-1965 and rare in the samples from the period 1966-1995 (2.8% of samples), but they were increasingly common in samples from the period 1996-2005 (20% of samples; P= .001). CONCLUSIONS: The rapid expansion of W-Beijing strains in a region with a very high background incidence of tuberculosis suggests that these strains have a significant selective advantage. The biological reasons for this observation remain unclear but warrant further study. The rapid spread of this virulent strain lineage is likely to present additional challenges for tuberculosis control.

Evaluation of a semi-automated reporter phage assay for susceptibility testing of Mycobacterium tuberculosis isolates in South Africa.

In a prospective study conducted by laboratory technologists in a diagnostic laboratory in Cape Town, South Africa, a semi-automated phage-based antibiotic susceptibility assay was implemented and the performance of the luciferase reporter mycobacteriophage (LRP) system for susceptibility testing of clinical Mycobacterium tuberculosis complex (MTC) isolates against rifampin and isoniazid was evaluated. Two hundred consecutive clinical MGIT cultures of MTC species were included in this study. Antibiotic susceptibility assays were set up manually for the LRP and BACTEC radiometric systems (BACTEC) and read in a plate luminometer and the BACTEC 460 instrument, respectively. Discrepant susceptibility results were resolved by the conventional agar proportion method. Of the 200 secondary cultures prepared for this study, 9 (4.5%) were lost to contamination (LRP 4, BACTEC 1, both 4). All of the remaining 191 cultures underwent susceptibility testing by both methods and the overall agreement between the LRP and BACTEC was 98.4% (rifampin 100%; isoniazid 96.9%). Of the 6 discrepant cultures tested by the agar proportion method, 2 gave results in agreement with the LRP. The sensitivity of the LRP for detection of drug-resistant isolates was 100% for both rifampin (n=9) and isoniazid (n=12). The median turnaround time for susceptibility testing was 2 days with the LRP and 9 days with BACTEC. In conclusion, the semi-automated LRP-based assay offers a rapid and practical approach for accurate susceptibility testing of M. tuberculosis cultures in diagnostic laboratories with limited financial resources, but with competent technologists.

Mycobacterium tuberculosis H37Ra and H37Rv differential growth and cytokine/chemokine induction in murine macrophages in vitro.

The role of tumor necrosis factor-alpha (TNF-alpha) in controlling growth of Mycobacterium tuberculosis in murine peritoneal macrophages infected in vitro was studied. TNF-alpha was shown to be required but not sufficient, and the amount of TNF-alpha produced by the infected cells did not correlate with the extent of growth control. In this system, TNF-alpha-dependent control of growth of the avirulent strain H37Ra was independent of inducible nitric oxide synthase (iNOS) and interferon-gamma (IFN-gamma), as shown by the infection of macrophages from selected gene-disrupted mice. TNF-alpha-mediated bacteriostasis of H37Ra in the infected macrophages was associated with increased expression of selected Th1-type cytokines and chemokines. In contrast, growth of the virulent strain H37Rv in macrophages involved upregulation by infected cells of Th2-type cytokines, including interleukin-5 (IL-5), IL-10, and IL-13. Taken together, these results suggest that the particular nature of macrophage activation and the cytokine and chemokine response to infection with different M. tuberculosis strains determine the ability of the cells to control the growth of the intracellular bacilli.

Efficacy of Artemisia afra phytotherapy in experimental tuberculosis.

Artemisia afra [Jacq] (Asteraceae) phytotherapy is widely used for its medicinal properties in traditional practices. In this study we investigated whether extracts of A. afra are capable of controlling mycobacterial replication. For Mycobacterium aurum cultured in the presence of aqueous-, methanol- and dichloromethane (DCM) extracts of A. afra we found that bacterial replication was inhibited by the dichloromethane extract only. Activity of the DCM extract was confirmed in dose-dependent studies against both M. aurum and M. tuberculosis with an IC(50) =270 microg/ml and IC(50) = 290microg/ml, respectively. Fractionation of the DCM extract and evaluation of its efficacy in vitro found that most of the antimycobacterial activity was associated with isolate fraction C8 that contained several sesquiterpene lactones, the most prominent of which are Artemin and Arsubin. Evaluation of the bactericidal efficacy in vitro showed that isolate fraction C8 reduced replication of M. aurum and M. tuberculosis in a dose-dependent manner with IC(50) =1.9 microg/ml and IC(50) = 2.0 microg/ml, respectively, and an MIC = 10 microg/ml. Further, isolate fraction C8 and the DCM extract was administered to M. tuberculosis-infected mice at a tolerated dose of 1000 microg/kg for up to 26 weeks and mycobacterial burdens compared to untreated-, INH/RIF treated- and aqueous-extract-treated animals to assess its bactericidal activity in vivo. Bacterial replication remained unaffected during treatment with either isolate fraction C8 or the DCM extract resulting in pulmonary and splenic bacilli burdens comparable to that of untreated mice. In contrast, INH/RIF treatment cleared M. tuberculosis infection after only 8 weeks to undetectable levels. Interestingly, treatment of M. tuberculosis-infected mice with aqueous extract of A. afra regulated pulmonary inflammation during early infection notwithstanding its inability to inhibit mycobacterial growth. This study clearly demonstrates that A. afra contains in vitro anti-mycobacterial activity, modulates pulmonary inflammation in early mycobacterial infection, and that the mouse experimental tuberculosis model may serve as a useful assay for evaluating the utility of phytotherapy.

Quantitative and functional differences between peripheral blood myeloid dendritic cells from patients with pleural and parenchymal lung tuberculosis.

Dendritic cells (DCs) play a pivotal role in generating protective host immunity to Mycobacterium tuberculosis. Few studies have addressed DC function in the context of active tuberculosis (TB), largely due to technical constraints in obtaining adequate numbers of DC from sick patients. We quantitated peripheral blood myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) in the whole blood of patients with active TB and show that blood from patients with pleural TB was characterized by high circulating levels of mDCs. We also developed and optimized a novel whole-blood assay to study mDC production of the Th1-promoting cytokine interleukin 12 (IL-12) and upregulation of the maturation marker CCR7 after incubation with mycobacteria. We found that pleural TB was associated with increased IL-12 production and CCR7 expression compared to lung parenchymal disease. Our findings suggest important differences in innate immunity between patients with different forms of active TB, and this may contribute to the differences in natural history observed between the two groups.

Translation enhancement by optimized downstream box sequences in Escherichia coli and Mycobacterium smegmatis.

The effect on translation of downstream box sequences optimized for binding to Mycobacterium smegmatis and Escherichia coli 16S rRNA in the absence of a Shine-Dalgarno (SD) region was investigated. The relative translational efficiency of each construct in either M. smegmatis or E. coli was determined. Eradication of the SD region in the absence of a downstream box abolished the translation activity. In contrast, optimized downstream box constructs resulted in a 13- and 18-fold increase in protein synthesis, relative to non-optimized DB controls in E. coli and M. smegmatis, respectively.

Distribution of strain families of Mycobacterium tuberculosis causing pulmonary and extrapulmonary disease in hospitalized children in Cape Town, South Africa.

We studied the association between strain family and extrapulmonary tuberculosis among 285 children presenting to a pediatric hospital. Extrapulmonary disease occurred in 56% of children without known human immunodeficiency virus infection, with meningitis accounting for 22% of the cases. Two strain families, LAM3/F11 and W-Beijing, predominated; but there was no overall association with extrapulmonary disease.

The Mycobacterium tuberculosis katG promoter region contains a novel upstream activator.

An Escherichia coli-mycobacterial shuttle vector, pJCluc, containing a luciferase reporter gene, was constructed and used to analyse the Mycobacterium tuberculosis katG promoter. A 1.9 kb region immediately upstream of katG promoted expression of the luciferase gene in E. coli and Mycobacterium smegmatis. A smaller promoter fragment (559 bp) promoted expression with equal efficiency, and was used in all further studies. Two transcription start sites were mapped by primer extension analysis to 47 and 56 bp upstream of the GTG initiation codon. Putative promoters associated with these show similarity to previously identified mycobacterial promoters. Deletions in the promoter fragment, introduced with BAL-31 nuclease and restriction endonucleases, revealed that a region between 559 and 448 bp upstream of the translation initiation codon, designated the upstream activator region (UAR), is essential for promoter activity in E. coli, and is required for optimal activity in M. smegmatis. The katG UAR was also able to increase expression from the Mycobacterium paratuberculosis P(AN) promoter 15-fold in E. coli and 12-fold in M. smegmatis. An alternative promoter is active in deletion constructs in which either the UAR or the katG promoters identified here are absent. Expression from the katG promoter peaks during late exponential phase, and declines during stationary phase. The promoter is induced by ascorbic acid, and is repressed by oxygen limitation and growth at elevated temperatures. The promoter constructs exhibited similar activities in Mycobacterium bovis BCG as they did in M. smegmatis.

Involvement of the N- and C-terminal domains of Mycobacterium tuberculosis KatG in the protection of mutant Escherichia coli against DNA-damaging agents.

The Mycobacterium tuberculosis KatG enzyme, like most hydroperoxidase I (HPI)-type catalases, consists of two related domains, each with strong similarity to the yeast cytochrome c peroxidase. The catalase-peroxidase activity is associated with the amino-terminal domain but currently no definite function has been assigned to the carboxy-terminal domain, although it may play a role in substrate binding. This paper reports another possible function of the KatG protein involving protection of the host cell against DNA-damaging agents. The M. tuberculosis katG gene, the 5' domain and the 3' domain were cloned separately, in-frame with the maltose-binding protein, into the vector pMAL-c2. These constructs were introduced into four DNA-repair mutants of Escherichia coli, DK1 (recA), AB1884 (uvrC), AB1885 (uvrB) and AB1886 (uvrA), which were then tested for their ability to survive treatment with UV light (254 nm), hydrogen peroxide (1.6 mg ml-1) and mitomycin C (6 micrograms ml-1). All three constructs conferred resistance to UV upon the recA E. coli cells, whereas resistance to mitomycin C was found in all repair mutants tested. Protection against hydrogen peroxide damage was less pronounced and predominantly found in the recA host. These results indicated that the M. tuberculosis katG gene can enhance DNA repair in E. coli, and that the 5' and 3' domains can function separately. UV sensitivity tests on Mycobacterium intracellulare and M. tuberculosis strains mutant in katG revealed that the katG gene product does not play an additive role in the survival of mycobacterial cells after exposure to short-wavelength UV irradiation, in repair-competent cells.

Mosaic plasmids and mosaic replicons: evolutionary lessons from the analysis of genetic diversity in IncFII-related replicons.

The alpha replicons of the multi-replicon plasmids pGSH500 and pLV1402 have been characterized by DNA sequence analysis. Analysis of the DNA sequence of a 3672 bp HIN:dIII fragment from pFDT100, which contains the pGSH500 alpha replicon, revealed similarity to a number of replicons belonging to, or related to, those of the IncFII family. The replicon region contains copA, tapA, repA and oriR, and replication initiation and termination sites are related to those from the IncFII replicon of R1. A copB gene was found to lie upstream of the HIN:dIII site in the parental plasmid pGSH500. Downstream of oriR, a 707 bp region shows 72.6% identity to a region of the Escherichia coli chromosome at 43.3', suggesting this region of pGSH500 may have been incorporated into the plasmid during a past chromosomal recombination event. Oligonucleotide primers homologous to consensus regions in the copB and repA genes, and the oriR regions from a number of IncFII-related replicons were used to amplify replication regions from pLV1402. Analysis of the amplified regions has shown the presence of copB, copA, tapA and repA genes. Phylogenetic analysis of Rep protein sequences from the RepFIIA family of antisense-control-regulated replicons revealed the presence of three distinct subgroups of Rep proteins. Comparative analysis of DNA and protein sequences from members of the RepFIIA family provides evidence supporting the roles of both non-selective divergence in co-integrate (multi-replicon) plasmids and Chi-mediated-recombination in replicon evolution, and in particular, that such processes may have been widespread in the evolution of the RepFIIA family.

Genetic polymorphism in Mycobacterium tuberculosis isolates from patients with chronic multidrug-resistant tuberculosis.

Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem because treatment is complicated, cure rates are well below those for drug-susceptible tuberculosis (TB), and patients may remain infectious for months or years, despite receiving the best available therapy. To gain a better understanding of MDR-TB, we characterized serial isolates recovered from 13 human immunodeficiency virus-negative patients with MDR-TB, by use of IS6110 restriction fragment-length polymorphism analysis, spacer oligonucleotide genotyping (i.e., "spoligotyping"), and sequencing of rpoB, katG, mabA-inhA (including promoter), pncA, embB, rpsL, rrs, and gyrA. For all 13 patients, chronic MDR-TB was caused by a single strain of Mycobacterium tuberculosis; 8 (62%) of the 13 strains identified as the cause of MDR-TB belonged to the W-Beijing family. The sputum-derived isolates of 4 (31%) of the 13 patients had acquired additional drug-resistance mutations during the study. In these 4 patients, heterogeneous populations of bacilli with different resistance mutations, as well as mixtures of drug-susceptible and drug-resistant genotypes, were observed. This genetic heterogeneity may require treatment targeted at both drug-resistant and drug-susceptible phenotypes.

Mycobacterium tuberculosis growth at the cavity surface: a microenvironment with failed immunity.

Protective immunity against pulmonary tuberculosis (TB) is characterized by the formation in the lungs of granulomas consisting of macrophages and activated T cells producing tumor necrosis factor alpha and gamma interferon, both required for the activation of the phagocytes. In 90% of immunocompetent humans, this response controls the infection. To understand why immunity fails in the other 10%, we studied the lungs of six patients who underwent surgery for incurable TB. Histologic examination of different lung lesions revealed heterogeneous morphology and distribution of acid-fast bacilli; only at the surface of cavities, i.e., in granulomas with a patent connection to the airways, were there numerous bacilli. The mutation profile of the isolates suggested that a single founder strain of Mycobacterium tuberculosis may undergo genetic changes during treatment, leading to acquisition of additional drug resistance independently in discrete physical locales. Additional drug resistance was preferentially observed at the cavity surface. Cytokine gene expression revealed that failure to control the bacilli was not associated with a generalized suppression of cellular immunity, since cytokine mRNA was up regulated in all lesions tested. Rather, a selective absence of CD4(+) and CD8(+) T cells was noted at the luminal surface of the cavity, preventing direct T-cell-macrophage interactions at this site, probably allowing luminal phagocytes to remain permissive for bacillary growth. In contrast, in the perinecrotic zone of the granulomas, the two cell types colocalized and bacillary numbers were substantially lower, suggesting that in this microenvironment an efficient bacteriostatic or bactericidal phagocyte population was generated.