1
|
Rise in rifampicin-monoresistant tuberculosis in Western Cape, South Africa. Int J Tuberc Lung Dis 2012; 16:196-202. [PMID: 22236920 DOI: 10.5588/ijtld.11.0116] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Brewelskloof Hospital, Western Cape, South Africa. OBJECTIVES To verify the perceived increase in rifampicin monoresistant tuberculosis (RMR-TB) in the Cape Winelands-Overberg region and to identify potential risk factors. DESIGN A retrospective descriptive study of trends in RMR-TB over a 5-year period (2004-2008), followed by a case-control study of RMR and isoniazid (INH) monoresistant TB cases, diagnosed from April 2007 to March 2009, to assess for risk factors. RESULTS The total number of RMR-TB cases more than tripled, from 31 in 2004 to 98 in 2008. The calculated doubling time was 1.63 years (95%CI 1.18-2.66). For the assessment of risk factors, 95 RMR-TB cases were objectively verified on genotypic and phenotypic analysis. Of 108 specimens genotypically identified as RMR cases, 13 (12%) were misidentified, multidrug-resistant TB. On multivariate analysis, previous use of antiretroviral therapy (OR 6.4, 95%CI 1.3-31.8), alcohol use (OR 4.8, 95%CI 2.0-11.3) and age ≥ 40 years (OR 5.8, 95%CI 2.4-13.6) were significantly associated with RMR-TB. CONCLUSION RMR-TB is rapidly increasing in the study setting, particularly among patients with advanced human immunodeficiency virus (HIV) disease. Routine drug susceptibility testing should be considered in all TB-HIV co-infected patients, and absence of INH resistance should be confirmed phenotypically if genotypic RMR-TB is detected.
Collapse
|
2
|
Drug-resistant tuberculosis epidemic in the Western Cape driven by a virulent Beijing genotype strain. Int J Tuberc Lung Dis 2010; 14:119-121. [PMID: 20003705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Temporal analysis of drug-resistant tuberculosis (TB) cases in the Western Cape, South Africa, showed a 1.5-fold increase over a 2-year period, suggesting a doubling time of 8.2 years. This increase was strongly associated with multidrug resistance and the Beijing genotype. Forty-two per cent of the overall increase was due to the Beijing genotype strain R220, suggesting that this strain had evolved unique properties that allowed for both acquisition and transmission of drug resistance. To curb the drug-resistant TB epidemic in this setting, it will be essential to implement rapid diagnostics and efficient infection control measures, improve contact screening and ensure treatment adherence.
Collapse
|
3
|
The role of molecular epidemiology in low-income, high-burden countries. Int J Tuberc Lung Dis 2009; 13:419-420. [PMID: 19335944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
|
4
|
Effect of study duration on the interpretation of tuberculosis molecular epidemiology investigations. Tuberculosis (Edinb) 2009; 89:238-42. [PMID: 19249244 DOI: 10.1016/j.tube.2009.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/28/2008] [Accepted: 01/23/2009] [Indexed: 11/19/2022]
Abstract
Many molecular epidemiological investigations of M. tuberculosis are reported using data collected over relatively short timeframes. We postulated that such studies would tend to under-estimate the amount of disease in a community attributable to ongoing transmission. To test this hypothesis we used 12-year datasets of both real and simulated epidemics with the latter being based on two possible models of transmission. We analysed the effect of viewing the datasets through time windows of varying sizes on the measured degree of strain clustering as an indicator of ongoing transmission. We found that shorter windows significantly under-estimated transmission and that this effect was inversely correlated with the size of a cluster. Accordingly, we recommend that molecular epidemiological studies of M. tuberculosis, for the purposes of estimating transmission, be conducted over a minimum of 3-4 years and that the distribution of cluster size be taken into account in the interpretation of such data.
Collapse
|
5
|
Changing Mycobacterium tuberculosis population highlights clade-specific pathogenic characteristics. Tuberculosis (Edinb) 2008; 89:120-5. [PMID: 19054717 DOI: 10.1016/j.tube.2008.09.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/29/2008] [Accepted: 09/29/2008] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis strains can be classified into a number of major clades according to defined evolutionary markers. It is hypothesised that strains comprising these clades have evolved different properties which may influence a local strain population structure. To investigate this, we analysed the incidence of tuberculosis caused by the predominant clades (Beijing, Haarlem, LAM, Quebec and the Low-Copy Clade) found in a community within the Cape Town metropole in South Africa over a 12-year period. We found that while the incidence of cases infected with strains of the Haarlem, LAM, Quebec and the Low-Copy Clades remained relatively stable, that of cases of the Beijing clade increased exponentially over time, with a doubling time of 4.86 years (P=0.018). This growth was exclusively attributable to drug-susceptible strains. Although drug-resistant Beijing cases remained constant in number, non-Beijing drug-resistant cases declined over time (P=0.007). Drug-susceptible Beijing-infected cases had a greater proportion of smear-positive sputa than their non-Beijing counterparts (P=0.013) and were less likely to be successfully treated (retreatment cases) (P=0.026). Recent evidence suggests that these differences likely reflect enhanced pathogenicity rather than transmissibility. The rapid emergence of Beijing strains demonstrates adaptation to conditions within the study community and poses a grave challenge to future TB control.
Collapse
|
6
|
Evidence that the spread of Mycobacterium tuberculosis strains with the Beijing genotype is human population dependent. J Clin Microbiol 2007; 45:2263-6. [PMID: 17475755 PMCID: PMC1933015 DOI: 10.1128/jcm.02354-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes a comparative analysis of the Beijing mycobacterial interspersed repetitive unit types of Mycobacterium tuberculosis isolates from Cape Town, South Africa, and East Asia. The results show a significant association between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (P < 0.0001).
Collapse
|
7
|
A recently evolved sublineage of the Mycobacterium tuberculosis Beijing strain family is associated with an increased ability to spread and cause disease. J Clin Microbiol 2007; 45:1483-90. [PMID: 17360841 PMCID: PMC1865897 DOI: 10.1128/jcm.02191-06] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to reconstruct the evolutionary history of Beijing strains of Mycobacterium tuberculosis and to test the hypothesis that evolution has influenced the ability of the Beijing strains within the different Beijing sublineages to spread and cause disease. A PCR-based method was used to analyze the genome structure of 40 different loci in 325 Beijing isolates collected from new and retreatment tuberculosis patients from an urban setting and 270 Beijing isolates collected from high-risk tuberculosis patients from a rural setting in the Western Cape, South Africa. The resulting data were subjected to phylogenetic analysis using the neighbor joining algorithm. Phylogenetic reconstructions were highly congruent with the "gold standard" phylogenetic tree based on synonymous single-nucleotide polymorphisms, thereby allowing a prediction of the order in which the evolutionary events had occurred. A total of seven independently evolving Beijing sublineages were identified. Analysis of epidemiological data in relation to the Beijing sublineage suggested an association between recent evolutionary change and frequency of occurrence in an urban population (P<0.001) as well as in the rural population (P<0.001). This concept was further supported by an association between more recently evolved Beijing strains and an increased ability to transmit and to cause disease (odds ratio, 5.82; 95% confidence interval, 3.13 to 10.82 [P<0.001]). An association between Beijing sublineage and demographic and clinical parameters and drug resistance could not be demonstrated. From these data, we suggest that the pathogenic characteristics of Beijing strains are not conserved but rather that strains within individual lineages have evolved unique pathogenic characteristics.
Collapse
|
8
|
Predominance of a single genotype of Mycobacterium tuberculosis in regions of Southern Africa. Int J Tuberc Lung Dis 2007; 11:311-8. [PMID: 17352098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
SETTING Zimbabwe and Zambia. OBJECTIVE To determine the genetic diversity of Mycobacterium tuberculosis strains isolated from tuberculosis (TB) patients in Zimbabwe and Zambia. DESIGN M. tuberculosis isolates cultured from TB patients presenting at referral hospitals in Zimbabwe and health care clinics in Zambia were characterised by IS6110 genotyping and/or spoligotyping using internationally standardised methods. Genotypic data were compared to those from Cape Town and the SpolDB3.0 database. RESULTS A predominant group of strains could be identified among 116/246 (47.2%) Zimbabwean isolates by their characteristic IS6110-banding pattern and unique spoligotype signature, where spacers 21-24, 27-30 and 33-36 were deleted. Comparison with strains from Cape Town showed that they were closely related to a family of strains present in 2.3% of Cape Town patients. Comparison of the spoligotypes with those obtained from 114 isolates from Zambia showed that 74 (65%) of these isolates had the same spoligotype signature. Spoligotypes in the SpolDB3.0 database showed that this group of strains was rarely isolated in other parts of the world, but was commonly isolated in Southern Africa. CONCLUSION A predominant group of strains infecting approximately half of the patients in the study are major contributors to the TB epidemic in this region. We have designated this group of strains the Southern Africa 1 (SAF1) family.
Collapse
|
9
|
Spread of an emerging Mycobacterium tuberculosis drug-resistant strain in the western Cape of South Africa. Int J Tuberc Lung Dis 2007; 11:195-201. [PMID: 17263291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
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.
Collapse
|
10
|
Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers. J Clin Microbiol 2005; 42:5774-82. [PMID: 15583312 PMCID: PMC535222 DOI: 10.1128/jcm.42.12.5774-5782.2004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the clonal expansion of Mycobacterium tuberculosis and accurate identification of predominant evolutionary lineages in this species remain limited, especially with regard to low-IS6110-copy-number strains. In this study, 170 M. tuberculosis isolates with </=6 IS6110 insertions identified in Cape Town, South Africa, were characterized by principal genetic grouping, restriction fragment length polymorphism analysis, spoligotyping, IS6110 insertion site mapping, and variable-number tandem repeat (VNTR) typing. These analyses indicated that all but one of the isolates analyzed were members of principal genetic group 2 and of the same low-IS6110-copy-number lineage. The remaining isolate was a member of principal genetic group 1 and a different low-IS6110-copy-number lineage. Phylogenetic reconstruction suggests clonal expansion through sequential acquisition of additional IS6110 copies, expansion and contraction of VNTR sequences, and the deletion of specific direct-variable-repeat sequences. Furthermore, comparison of the genotypic data of 91 representative low-IS6110-copy-number isolates from Cape Town, other southern African regions, Europe, and the United States suggests that certain low-IS6110-copy-number strain spoligotypes and IS6110 fingerprints were acquired in the distant past. These clones have subsequently become widely disseminated and now play an important role in the global tuberculosis epidemic.
Collapse
|
11
|
Genotypic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from rural districts of the Western Cape Province of South Africa. J Clin Microbiol 2004; 42:891-4. [PMID: 14766882 PMCID: PMC344460 DOI: 10.1128/jcm.42.2.891-894.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from the Western Cape Province of South Africa showed that drug resistance is widespread and recently transmitted. Multidrug-resistant (MDR) isolates comprise 40% of this collection, and a large pool of isoniazid monoresistance may be a future source of MDR tuberculosis.
Collapse
|
12
|
Abstract
The stability of the genotypic marker IS6110, used to define the epidemiology of Mycobacterium tuberculosis, is one of the most important factors influencing the interpretation of DNA fingerprint data. We propose that evolved strains should be considered together with clustered strains to represent chains of ongoing transmission. For the present study we used a large set of fingerprint data for strains collected between 1992 and 1998 from residents of a community with a high incidence of tuberculosis in Cape Town, South Africa. Interstrain genetic distances were calculated by counting the banding pattern mismatches in the IS6110 DNA fingerprints of different isolates. These data demonstrate that the propensity to change by one or two bands is independent of the IS6110 copy number. Hence, the genetic distance between pairs of isolates can be simply expressed as the number of differences in the banding patterns. From this foundation, a data set which identifies newly evolved strains has been generated. Inclusion of these evolved strains into various molecular epidemiological calculations significantly increased the estimate of ongoing transmission in this study setting. The indication is that nearly all cases of tuberculosis in this community are due to ongoing transmission. This has important implications for tuberculosis control, as it indicates that the control measures used at present are unable to reduce the level of transmission. This technique may also be applicable to the study of low-incidence tuberculosis outbreaks as well as the analysis of epidemiological data from other disease epidemics.
Collapse
|
13
|
IS6110-mediated deletion polymorphism in the direct repeat region of clinical isolates of Mycobacterium tuberculosis. J Bacteriol 2003; 185:2856-66. [PMID: 12700265 PMCID: PMC154393 DOI: 10.1128/jb.185.9.2856-2866.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
Collapse
|
14
|
Microevolution of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J Clin Microbiol 2002; 40:4457-65. [PMID: 12454136 PMCID: PMC154636 DOI: 10.1128/jcm.40.12.4457-4465.2002] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region has been determined to be an important chromosomal domain for studying the evolution of Mycobacterium tuberculosis. Despite this, very little is known about microevolutionary events associated with clonal expansion and how such events influence the interpretation of both restriction fragment length polymorphism (RFLP) and spoligotype data. This study examined the structure of the DR region in three independently evolving lineages of M. tuberculosis with a combination of DR-RFLP, spoligotyping, and partial DNA sequencing. The results show that the duplication of direct variable repeat (DVR) sequences and single-nucleotide polymorphisms is rare; conversely, the deletion of DVR sequences and IS6110-mediated mutation is observed frequently. Deletion of either single or contiguous DVR sequences was observed. The deletion of adjacent DVR sequences occurred in a dependent manner rather than as an accumulation of independent events. Insertion of IS6110 into either the direct repeat or spacer sequences influenced the spoligotype pattern, resulting in apparent deletion of DVR sequences. Homologous recombination between adjacent IS6110 elements led to extensive deletion in the DR region, again demonstrating a dependent evolutionary mechanism. Different isolates from the same strain family and isolates from different strain families were observed to converge to the same spoligotype pattern. In conclusion, the binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of M. tuberculosis. This has important implications for molecular epidemiologic strain tracking and for the application of spoligotype data to phylogenetic analysis of M. tuberculosis isolates.
Collapse
|
15
|
Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region. Int J Tuberc Lung Dis 2002; 6:1001-11. [PMID: 12475147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
SETTING A retrospective study in an urban setting with a high tuberculosis incidence. OBJECTIVE To study the molecular epidemiology and disease dynamics of a prevalent Mycobacterium tuberculosis strain family, F29, a subset of the Beijing strains. DESIGN Multi-locus DNA fingerprinting and genomic analysis was used to characterise F29 isolates. Demographic and molecular epidemiologic data were correlated with those of other isolates from the setting. The geographic locations of five F29 strain clusters were plotted using a geographic information system (GIS) and an index for geographic distribution was calculated. Their cumulative temporal occurrence was also plotted. RESULTS The genomic similarity of F29 to the Beijing-strains was confirmed. A high degree of clustering predicted high disease transmission. Spatial distribution was mostly widespread except for one cluster. Smaller foci of transmission were observed. The temporal spread showed ongoing transmission. CONCLUSION F29 belongs to the Beijing strain group. The prevalence and high degree of strain clustering, with limited geographic clustering, indicates that F29 strains are endemic in the study community. However, recent epidemiologic events also contributed to the disease spread. The combination of molecular epidemiologic, spatial and temporal data has enhanced our understanding of the disease dynamics of Beijing strains in our study community.
Collapse
|
16
|
Abstract
The spoligotyping method has become an important tool for the tracking of Mycobacterium tuberculosis strains in different epidemiological settings. In this study, we demonstrate the ability of the spoligotyping technique to accurately determine the pathogenetic mechanism of recurrent disease. This methodology has advantages over conventional restriction fragment length polymorphism methods which may be useful in large-scale intervention studies.
Collapse
|
17
|
Calculation of the stability of the IS6110 banding pattern in patients with persistent Mycobacterium tuberculosis disease. J Clin Microbiol 2002; 40:1705-8. [PMID: 11980946 PMCID: PMC130951 DOI: 10.1128/jcm.40.5.1705-1708.2002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interpretation of molecular epidemiologic data of Mycobacterium tuberculosis infection is dependent on the understanding of the stability and evolutionary characteristics of the DNA fingerprinting marker used to classify clinical isolates. This study investigated the stability of the IS6110 banding pattern in serial tuberculosis isolates collected from patients resident in an area with a high incidence of tuberculosis. Evolutionary changes were observed in 4% of the strains, and a half-life (t(1/2)) of 8.74 years was calculated, assuming a constant rate of change over time. This rate may be composed of a high rate of change seen during the early disease phase (t(1/2) = 0.57 years) and a low rate of change seen in the late disease phase (t(1/2) = 10.69 years). The early rate probably reflects change occurring during active growth prior to therapy, while the low late rate may reflect change occurring during or after treatment. We demonstrate that the calculation of these rates is strongly influenced by the time interval between onset of disease and sputum sampling. These calculations are further complicated by partial replacement of the original strain population, resulting in the sporadic appearance of clonal variants in sputum specimens. Therefore, the true extent of genetic diversity may be underestimated within each host, thereby influencing molecular epidemiological data used to establish transmission chains.
Collapse
|
18
|
Evolution of the IS6110-based restriction fragment length polymorphism pattern during the transmission of Mycobacterium tuberculosis. J Clin Microbiol 2002; 40:1277-82. [PMID: 11923345 PMCID: PMC140391 DOI: 10.1128/jcm.40.4.1277-1282.2002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interpretation of the molecular epidemiological data of Mycobacterium tuberculosis is dependent on the validity of the assumptions that have been made. It is assumed that the IS6110 banding pattern is sufficiently stable to define epidemiological events representing ongoing transmission. However, molecular epidemiological data also support the observation that the IS6110 banding pattern may change over time. Factors affecting this rate may include the nature and duration of disease in a host and the opportunity to experience different host environments during the transmission cycle. To estimate the rate of IS6110 change occurring during the process of transmission, M. tuberculosis isolates from epidemiologically linked patients were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis. The identification of IS6110 banding pattern changes during ongoing transmission suggested that a rate could be estimated. IS6110 change was significantly associated with strains with >5 IS6110 elements (P = 0.013) and was not observed in low-copy-number isolates. The minimum rate of appearance of variant strains was calculated to be 0.14 variant cases per source-case per year. This data suggest that clustering of isolates based on identical RFLP patterns is expected to underestimate transmission in patients infected with high-copy-number isolates. A model based on the rate of appearance of both variant and invariant strains demonstrates that the genotypically defined population structure may change by 18.6% during the study period of approximately 6.5 years. The implications for the use of RFLP data for epidemiologic study are discussed.
Collapse
|
19
|
Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion. Tuberculosis (Edinb) 2001; 81:291-302. [PMID: 11584597 DOI: 10.1054/tube.2001.0300] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
SETTING M. tuberculosis isolates were collected from patients attending health clinics in a high incidence urban community and in a low incidence rural setting in South Africa. OBJECTIVE To reconstruct the evolutionary history of a group of closely related M. tuberculosis isolates using IS6110, DRr and MTB484(1) restriction fragment length polymorphism (RFLP) data. DESIGN Mycobacterium tuberculosis isolates containing an average of ten IS6110 elements, with a similarity index of > or = 65% were genotypically classified by DNA fingerprinting using the IS6110 derived probes IS-3' and IS-5', as well as the DRr and MTB484(1) probes, in combination with PvuII or Hinfl endonuclease digestion. These RFLP data were subjected to phylogenetic analysis using both genetic distance and parsimony algorithms. RESULTS Phylogenetic analysis predicted the existence of two independently evolving lineages, possibly evolving from a common ancestral strain. The topology of the phylogenetic tree was supported by comprehensive bootstrapping and the specific partitioning of DNA methylation phenotypes. The observed difference in the branch lengths of the two lineages may suggest differential evolutionary rates. Isolates collected from different geographical regions demonstrate independent evolution, suggesting that it is highly unlikely that strains have been recently transmitted between the two regions. The number of evolutionary events identified in this strain family differs significantly from that of previously characterized strain families, implying that evolutionary rate may be strain family dependent. CONCLUSION Based on this analysis we propose that the algorithm used to calculate recent epidemiological events should be revised to incorporate the evolutionary characteristics of individual strain families, thereby enhancing the accuracy of molecular epidemiological calculations.
Collapse
|
20
|
Disruption of coding regions by IS6110 insertion in Mycobacterium tuberculosis. TUBERCLE AND LUNG DISEASE : THE OFFICIAL JOURNAL OF THE INTERNATIONAL UNION AGAINST TUBERCULOSIS AND LUNG DISEASE 2000; 79:349-59. [PMID: 10694979 DOI: 10.1054/tuld.1999.0218] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
SETTING The insertion sequence IS6110 is widely used as a DNA fingerprinting probe for the classification of Mycobacterium tuberculosis strains. This study has focused on the characterization of regions disrupted by insertion of the IS6110 element. OBJECTIVE To characterize IS6110 insertion loci in clinical isolates of M. tuberculosis, in terms of their genomic location and genetic identity, to ascertain whether IS6110 transposition could be a mechanism driving phenotypic change. DESIGN Thirty-three IS6110 insertion loci were cloned from 8 clinical isolates of M. tuberculosis. Clones representing DR locus insertions were identified by hybridization (n = 4), and all other clones were characterized by DNA sequencing (n = 29). The sequence data was analyzed in conjunction with that of 43 other insertion loci identified in published literature and DNA sequence databases. RESULTS The 76 sequences analyzed represented 66 unique insertion loci (including 9 unique insertions into the ipl locus). When mapped to the H37Rv genome, the majority of unique insertion loci demonstrated disruption of coding regions by IS6110 (n = 42; including the ipl insertions), while the remainder either occurred within intergenic regions (n = 17), or could not be mapped to the H37Rv genome sequence (n = 7). Mapping of the insertion loci reveals distribution throughout the chromosome, with isolated preferential insertion loci. CONCLUSIONS This study has demonstrated the occurrence of 66 unique IS6110 insertion loci dispersed throughout the M. tuberculosis genome, with an unexpectedly high incidence of IS6110 insertions occurring within coding regions. However, the IS6110-mediated coding region disruptions identified here may only have limited impact on phenotype, as most of the coding regions disrupted are members of multiple gene families. Disruption of individual members of a family of genes may have no effect on phenotype or could have a minor or major impact, depending on the specificity and activity of the encoded protein.
Collapse
|
21
|
Detection of mutations in drug resistance genes of Mycobacterium tuberculosis by a dot-blot hybridization strategy. TUBERCLE AND LUNG DISEASE : THE OFFICIAL JOURNAL OF THE INTERNATIONAL UNION AGAINST TUBERCULOSIS AND LUNG DISEASE 2000; 79:343-8. [PMID: 10694978 DOI: 10.1054/tuld.1999.0222] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
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.
Collapse
|
22
|
Activation of the subthalamic nucleus and pedunculopontine tegmentum: does it affect dopamine levels in the substantia nigra, nucleus accumbens and striatum? NEURODEGENERATION : A JOURNAL FOR NEURODEGENERATIVE DISORDERS, NEUROPROTECTION, AND NEUROREGENERATION 1995; 4:139-45. [PMID: 7583677 DOI: 10.1006/neur.1995.0017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Parkinson's disease is a neurodegenerative disorder, of which the most prominent morphological feature is the progressive loss of dopaminergic nigrostriatal neurons. Increased glutamatergic transmission in the basal ganglia has been implicated in the pathophysiology of Parkinson's disease (PD). This study investigated whether death of substantia nigra (SN) dopaminergic neurons could be caused by the hyperactivity of afferent pathways resulting in the release of a toxic dose of excitatory amino acids in the SN. Twice-daily unilateral stimulation of the subthalamic nucleus (STN) for 21 days, using two different pulse frequencies and current strengths, significantly increased amphetamine-induced rotation, whereas sham stimulated rats showed significantly reduced rotation. Striatal and SN dopamine (DA) levels were unaffected when compared to naïve and sham stimulated rats. However, levels of the DA metabolite, homovanillic acid (HVA), were significantly higher in the ipsilateral anterior striata of rats that had been stimulated at high frequency (100 Hz) and low current (100 microA) as compared to sham treated animals. Stimulation of the pedunculopontine tegmentum (PPT), using a single kainic acid injection, did not affect DA concentration in the ipsilateral striatum and nucleus accumbens when compared to sham-treated rats. DA levels in the contralateral striatum and nucleus accumbens of lesioned rats were significantly higher than ipsilateral levels. DOPAC/DA ratios were lower in the contralateral striatum and nucleus accumbens, suggesting decreased DA turnover. Glutamic acid decarboxylase activity was significantly higher in the ipsilateral than the contralateral SN. The physical manifestations of PD require a large reduction in caudate and putamen DA levels and no such depletion was measured in this study.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
|