Rifampicin-monoresistant Mycobacterium tuberculosis disease among children in Cape Town, South Africa.

SETTING: Tygerberg Children's Hospital (TCH) and Brooklyn Chest Hospital (BCH), South Africa. OBJECTIVES: To describe paediatric cases of rifampicin (RMP) monoresistant tuberculosis (RMR-TB) disease. DESIGN: Records of children with culture-confirmed RMR-TB between 1 March 2003 and 28 February 2009 were identified from a prospectively recorded database of drug-resistant TB at TCH and BCH. Mutation analysis was performed on available specimens. RESULTS: Eighteen children with a median age of 6.9 years (range 2 months-12.8 years) were identified. Nine (50%) were human immunodeficiency virus (HIV) infected and four (22%) were HIV-exposed but non-infected. Eleven (61%) had had previous TB treatment or prophylaxis. Nine children (50%) had cavitary disease and five children (22%) had extra-pulmonary disease. Twelve (67%) had adult TB source cases, including five (42%) adults with known RMR-TB. Primary transmission occurred among 11 children (61%) and acquisition of RMR-TB was possible in seven (39%) with prior RMP exposure. Median delay to specific RMR-TB treatment was 70 days (range 23-188). One child died from RMR-TB meningitis. Gene mutations consistent with RMR-TB were confirmed in five available samples. CONCLUSION: RMR-TB disease is increasingly encountered, particularly among HIV-infected and HIV-exposed non-infected children. Delay in commencing appropriate treatment for RMR-TB and high rates of cavitary disease could be a source of RMR-TB transmission.

Ethionamide cross- and co-resistance in children with isoniazid-resistant tuberculosis.

BACKGROUND: Ethionamide (ETH) is a structural analogue of isoniazid (INH). Both are pro-drugs requiring activation by separate and common enzyme pathways, which could lead to co- and/or cross-resistance. OBJECTIVE: To characterise paediatric INH-resistant mycobacterial isolates to investigate the presence of ETH resistance and mutations in the katG gene and the inhA promoter region. METHODS: Forty-five INH-resistant and 19 INH-susceptible Mycobacterium tuberculosis control isolates from children from the Western Cape Province, South Africa, were analysed to quantify INH minimal inhibitory concentration, test for ETH resistance and investigate mutations in the katG gene and/or inhA promoter region. RESULTS: Among 45 INH-resistant children, ETH resistance was present in 19 of 39 (49%). An inhA promoter mutation was identified in 15 (33.3%); 12/14 (86%) of these isolates were also ETH-resistant. Of the 21 isolates with a katG mutation, six (29%) were ETH-resistant. No isolate had both katG and inhA promoter mutations. Nine (20%) isolates had neither inhA promoter nor katG mutations. Of 15 isolates with inhA promoter mutation, 14 (93%) displayed low- or intermediate-level INH resistance. Among the 19 INH-susceptible isolates, ETH resistance was present in 1/18 (6%) and none showed inhA or katG gene mutations. CONCLUSION: We found a high level of cross- and co-resistance with ETH among INH-resistant M. tuberculosis isolates from children in this geographic area.

Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis.

IS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110 RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110 RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.

Spread of an emerging Mycobacterium tuberculosis drug-resistant strain in the western Cape of South Africa.

BACKGROUND: South Africa has a high burden of drug-resistant tuberculosis (TB). METHODS: Routine drug susceptibility testing was performed prospectively over a 2-year period on Mycobacterium tuberculosis isolates in two health districts of the Western Province, South Africa. A cluster of drug-resistant strains that shared a rare mutation in katG315 was found in 64 of the 450 cases identified as having been infected with drug-resistant TB. Isolates belonging to this cluster were phenotypically and genotypically characterised. Epidemiological and clinical characteristics were used to identify mechanisms leading to the acquisition and spread of this drug-resistant strain. RESULTS: An outbreak of an emerging non-Beijing drug-resistant strain infecting 64 pulmonary tuberculosis (PTB) cases was identified. This previously undetected genotype (now designated DRF150) is characterised by five IS6110 insertions, specific spoligotypes and high levels of resistance to the first-line TB medications isoniazid, streptomycin and rifampicin. In 45% of the cases it is also resistant to ethambutol and pyrazinamide. Key factors leading to the development and spread of this drug-resistant genotype were inappropriate chemotherapy, poor adherence to treatment and prolonged periods of infectiousness due to delays in susceptibility testing. CONCLUSIONS: Molecular markers allowed early identification of an emerging non-Beijing drug-resistant strain.

An outbreak of drug-resistant tuberculosis caused by a Beijing strain in the western Cape, South Africa.

During October 2005, four children in a school in Cape Town were identified with multidrug-resistant tuberculosis (MDR-TB). Genetic analysis confirmed that these isolates belonged to a single cluster (Beijing cluster 220) and that all harboured a -15 inhA(C-T) promoter mutation demonstrating transmission. Genetic analysis of isolates cultured from patients from the Boland-Overberg-South Cape-Karoo and Cape Town regions showed that 28% (58/209) of patients infected with a Beijing strain had the cluster 220 genotypes and that all harboured the same -15 inhA(C-T) promoter mutation. The presence of these transmissible MDR-TB strains may pose a threat to the community, and rigorous infection control measures are needed to ensure the safety of those exposed.

Ethambutol resistance testing by mutation detection.

OBJECTIVE: To identify chromosomal mutations that confer resistance to ethambutol (EMB) in Mycobacterium tuberculosis. DESIGN: Drug-resistant (n = 235) and drug-susceptible (n = 117) M. tuberculosis isolates collected from the Western Cape in South Africa were subjected to embB gene analysis and the results were compared to phenotypic EMB testing. RESULTS: Genotypic analysis identified mutations at codon 306 of the embB gene in 20% (47/235) of the resistant isolates in comparison to only 1.7% (4/235) of those that were phenotypically resistant to EMB by the agar diffusion method. No gene mutations were detected in susceptible isolates. Phenotypic retesting in BACTEC demonstrated that the 47 genotypically resistant isolates were phenotypically resistant to EMB. This implies that 91.4% (43/47) of EMB resistance had been phenotypically missed by routine laboratory procedures. EMB resistance was closely linked to multidrug resistance (MDR); 87.2% (41/47) of the EMB-resistant isolates were resistant to both isoniazid and rifampicin. A newly developed one-step amplification refractory mutation system polymerase chain reaction (ARMS-PCR) method correctly detected the EMB-resistant genotype. CONCLUSION: Implementation of more accurate diagnosis of EMB resistance may enhance patient management in South Africa, as standardised treatment of MDR-TB with second-line drugs is currently dependent on the outcome of the EMB resistance test.

Identification of MDR-TB Beijing/W and other Mycobacterium tuberculosis genotypes in Nairobi, Kenya.

SETTING: Suspected tuberculosis (TB) patients in Nairobi, Kenya. OBJECTIVE: To identify the presence of multidrug-resistant (MDR) Beijing/W type and other genotypes of Mycobacterium tuberculosis. METHODS: Thirty-three isolates resistant to one or more drugs (resistance ratio method), including 15 MDR isolates and 40 susceptible isolates selected at random, were analysed by dot-blot hybridisation for mutations associated with resistance to isoniazid, rifampicin, streptomycin and ethambutol. All strains were genotypically classified using spoligotyping. RESULTS: Of the 33 drug-resistant isolates, 21 (64%) were from males and 12 (36%) were from females. Mutations associated with resistance to isoniazid (katG 315) and rifampicin (rpoB526, 531) were confirmed in 83.3% and 100% of the isolates, respectively, and in 87% of the MDR isolates. Mutations were detected in 25% and 71.5% of the isolates resistant to streptomycin (rpsL43) and ethambutol (embB306), respectively. No mutations were detected in drug-susceptible isolates. Spoligotyping grouped the isolates into 25 groups. Ten of these groups corresponded to previously identified strain groups, including seven families in the international database. One of these families (CAS1) comprised six (40%) of the 15 MDR isolates. Another family (Beijing) had six (8.3%) isolates, of which two (33.3%) were MDR (Beijing/W). CONCLUSION: This study is the first in Kenya and the second in sub-Saharan Africa to report the presence of MDR Beijing/W type and other possible drug-resistant outbreak strains. Application of the molecular techniques and markers will allow us to monitor the spread of existing drug-resistant strains and the appearance of new ones.

IS6110-mediated deletion polymorphism in the direct repeat region of clinical isolates of Mycobacterium tuberculosis.

This study investigates the phenomenon of IS6110-mediated deletion polymorphism in the direct repeat (DR) region of the genome of Mycobacterium tuberculosis. Clinical isolates and their putative predecessors were compared using a combination of DR region restriction fragment length polymorphism, IS6110 DNA fingerprinting, spoligotyping, and DNA sequencing, which allowed the mapping of chromosome structure and deletion junctions. The data suggest that adjacently situated IS6110 elements mediate genome deletion. However, in contrast to previous reports, deletions appear to be mediated by inversely oriented IS6110 elements. This suggests that these events may occur via mechanisms other than RecA-mediated homologous recombination. The results underscore the important role of IS6110-associated deletion hypervariability in driving M. tuberculosis genome evolution.

Molecular analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with persistent disease in the Khartoum region of Sudan.

SETTING: Patients with positive smears for acid-fast bacilli were enrolled at tuberculosis (TB) clinics in the Khartoum region of Sudan. OBJECTIVE: To identify the presence of drug resistant genotypes in M. tuberculosis isolates which are difficult to treat. METHODS: Genus specific PCR-SSCP was performed to confirm the presence of M. tuberculosis in clinical isolates. Genotypic drug resistance testing was performed by mutation analysis and spoligotyping was used to monitor transmission and to identify epidemic strains. RESULTS: Fifty (48%) of the original 105 samples were classified as M. tuberculosis. Four (4%) of the samples were typed as mycobacteria other than TB, while the remaining (n =50) samples were refractory to further molecular analysis. The fifty amplifiable M. tuberculosis samples were used for subsequent mutation analysis and typing. Mutations were identified in the genes conferring resistance to INH (kat G, 12%), RIF (rpoB, 8%), SM (r psL and rrs, 30%) and EMB (embB, 4%). Two of the samples (4%) had mutations in genes associated to both INH and RIF and can be classified as MDR-TB. Thirty-three percent (13/39) of the persistant tuberculosis cases (5/18 treatment failure; 5/14 relapse; 3/7 defaulter) had mutations accounting for drug resistance. A total of 27 different spoligotypes were identified from 49/50 samples. Twenty-nine (59%) of the isolates were grouped into one of seven clusters, while 20 (41%) showed unique patterns. One patient was infected with M. bovis. CONCLUSION: This is the first molecular approach to characterize clinical isolates of M. tuberculosis from Sudan. The results show that drug resistance is indeed a serious problem and it may compliment the efforts of the National Tuberculosis Programme to improve strategies to control this disease.

Sequence polymorphism in the rrs gene of Mycobacterium tuberculosis is deeply rooted within an evolutionary clade and is not associated with streptomycin resistance.

A mutation (C-to-T transition) at position 491 of the rrs gene was identified in a Mycobacterium tuberculosis strain family (n = 208 isolates) that was predominant in a suburb of Cape Town, South Africa. This nucleotide change is not involved in streptomycin resistance, and we suggest caution in assuming that all mutations in genes targeted by antituberculosis drugs confer drug resistance.

Analysis for a limited number of gene codons can predict drug resistance of Mycobacterium tuberculosis in a high-incidence community.

Correct and rapid diagnosis is essential in the management of multidrug-resistant tuberculosis (MDR-TB). In this population-based study of 61 patients with drug-resistant tuberculosis, we evaluated the frequency of mutations and compared the performance of genotypic (mutation analysis by dot blot hybridization) and phenotypic (indirect proportion method) drug resistance tests. Three selected codons (rpoB531, rpoB526, and katG315) allowed identification of 90% of MDR-TB cases. Ninety percent of rifampin, streptomycin, and ethambutol resistance and 75% of isoniazid resistance were detected by screening for six codons: rpoB531, rpoB526, rrs-513, rpsL43, embB306, and katG315. The performance (reproducibility, sensitivity, and specificity) of the genotypic method was superior to that of the routine phenotypic method, with the exception of sensitivity for isoniazid resistance. A commercialized molecular genetic test for a limited number of target loci might be a good alternative for a drug resistance screening test in the context of an MDR "DOTS-plus" strategy.

Detection of mutations in drug resistance genes of Mycobacterium tuberculosis by a dot-blot hybridization strategy.

SETTING: Mycobacterium tuberculosis isolates from patients in communities endemic for tuberculosis in South Africa. OBJECTIVE: To develop a reliable PCR-based dot-blot hybridization strategy to detect mutations conferring drug resistance. DESIGN: Different loci in six genes associated with drug resistance to isoniazid, rifampacin, streptomycin and ethambutol were selected to develop the PCR-based dot-blot hybridization strategy. RESULTS: Primers and probes to detect mutations at codons 315, 463 (katG) 269 (kasA), 531, 526 (rpoB) 43 (rpsL), 513 (rrs) and 306 (embB) were designed and used to develop a PCR-based dot-blot hybridization strategy. The dot-blot hybridization strategy with wild-type probes can efficiently be used to detect drug resistant mutations since these do not hybridize to mutant loci. Stripped blots and mutant probes can be used to identify the precise mutation. The embB gene (ethambutol resistance) was used to show how the dot-blot strategy can assist with the prediction of drug resistance more accurately. The method is rapid, reproducible, not technically demanding and samples can be done in batches. Additional loci can easily be incorporated. CONCLUSIONS: A PCR-based dot-blot hybridization strategy is described which can accurately identify drug resistant strains and the method is useful for patients at risk and in areas endemic for tuberculosis.

Genome and MIC stability in Mycobacterium tuberculosis and indications for continuation of use of isoniazid in multidrug-resistant tuberculosis.

Mycobacterium tuberculosis strains resistant to two or more of the first line antituberculosis drugs (MDR) are a serious threat to successful tuberculosis control programmes. For this retrospective study, 85 follow-up drug resistant isolates from 23 patients residing in a community with a high incidence of tuberculosis were collected and the level of in-vitro resistance to antibiotics determined quantitatively. PCR-SSCP and sequencing techniques were used to screen for gene mutations associated with resistance in 31 follow-up samples from a smaller group of eight patients. DNA fingerprint analysis was done on sequential isolates to confirm identity. Although treatment had a profound effect on changes in drug resistance patterns, the MIC for a particular agent remained constant in follow-up isolates. DNA fingerprinting and mutational analysis (14 different loci) showed that the genome of MDR strains of M. tuberculosis is relatively stable during the course of therapy. The rpoB gene was the most frequently mutated structural gene involved in drug resistance and a novel C to T mutation upstream of open reading frame (ORF)1 of the inhA operon was detected. No evidence was found of the presence of strain W (New York) in this group of MDR strains. The results stress the importance of confirming individuality of strains for the accurate calculation of frequencies of particular mutations associated with drug resistance, particularly in a high incidence area. Approximately one-half (47.8%) of the patients had isolates resistant to concentrations just above the critical concentration for isoniazid (MICs of 0.2-5 mg/L). Therefore, these patients and their contacts who develop primary drug-resistant tuberculosis may respond to higher dosages of treatment which could have a considerable impact on the cost and the ease of management of resistant tuberculosis.

Strain-specific variation in the dnaJ gene of mycobacteria.

The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique was evaluated for species identification among mycobacteria by analysis of the dnaJ gene. Nine clinical isolates of Mycobacterium tuberculosis with different fingerprint patterns all gave the same distinct SSCP banding pattern and could be distinguished from other mycobacteria, such as M. avium. In contrast, considerable strain-specific dnaJ gene variations were observed amongst 42 clinical isolates of M. avium and 13 other atypical mycobacterial strains. Only 62% of the M. avium isolates hybridised to an M. avium-specific probe and only 14% could be identified correctly as M. avium by both probe and restriction fragment length polymorphism analysis. This finding was supported by direct sequence analysis. Variations were also observed in M. gordonae and M. scrofulaceum isolates. Computerised analysis of M. avium samples broadly identified three clusters. Results suggest that although the SSCP procedure may be useful for distinguishing M. tuberculosis from other mycobacteria, this technique applied to the dnaJ gene may not be suitable for strain identification. The results stress the importance of testing a large collection of clinical isolates before new molecular procedures are introduced into routine laboratories.

Polymerase chain reaction in the diagnosis of tuberculous meningitis.

43 cerebrospinal fluid (CSF) specimens obtained from 20 children with tuberculous meningitis (TBM) at varying times during the first month of treatment were examined by polymerase chain reaction (PCR) for the presence of M. tuberculosis DNA. Overall 27 CSF specimens (63%) from 16 patients (80%) gave > or = 1 positive results and positive results were obtained from CSF specimens throughout the first 4 weeks of therapy. Nine CSF specimens (21%) gave a doubtful result (only 1 of duplicate determinations positive) and 7 (16%) a negative result. CSF from patients with suspected TBM should be submitted for PCR evaluation and positive results may be obtained up to at least 4 weeks after the start of treatment.

No evidence for point mutations in codons 12, 13, and 61 of the ras gene in a high-incidence area for esophageal and gastric cancers.

The molecular mechanisms underlying the induction of esophageal and gastric cancer are not yet understood. It is possible that different etiological factors from geographically distinct areas play a role in the onset of these cancers. Twenty-seven primary esophageal and 11 gastric cancers originating from the high-incidence areas of South Africa were analyzed for the presence of ras protooncogene mutations. We found no evidence for mutations in codons 12, 13, or 61 or the H-ras, K-ras, and N-ras genes in these primary cancers. Our results indicate that etiological factors such as fungal contamination of basic foodstuffs in a high-incidence area for these cancers do not play a role in the activation of ras genes and that mutations in these genes are not directly involved in the development of primary esophageal and gastric cancers in the South African population.