Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples

Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.

To Test or Not? Xpert MTB/RIF as an Alternative to Smear Microscopy to Guide Line Probe Assay Testing for Drug-Resistant Tuberculosis

Xpert MTB/RIF (Xpert) revolutionized tuberculosis (TB) diagnosis. Laboratory decision making on whether widely-used reflex drug susceptibility assays (MTBDRplus, first-line resistance; MTBDRsl, second-line) are conducted is based on smear status, with smear-negative specimens often excluded. We performed receiver operator characteristic (ROC) curve analyses using bacterial load information (smear microscopy grade, Xpert-generated semi-quantitation categories and minimum cycle threshold [CTmin] values) from Xpert rifampicin-resistant sputum for the prediction of downstream line probe assay results as "likely non-actionable" (no resistance or susceptible results generated). We evaluated actionable-to-non-actionable result ratios and pay-offs with missed resistance versus LPAs done universally. Smear-negatives were more likely than smear-positive specimens to generate a non-actionable MTBDRplus (23% [133/559] versus 4% [15/381]) or MTBDRsl (39% [220/559] versus 12% [47/381]) result. However, excluding smear-negatives would result in missed rapid diagnoses (e.g., only 49% [264/537] of LPA-diagnosable isoniazid resistance would be detected if smear-negatives were omitted). Testing smear-negatives with a semi-quantitation category ≥ "medium" had a high ratio of actionable-to-non-actionable results (12.8 or a 4-fold improvement versus testing all using MTBDRplus, 4.5 or 3-fold improvement for MTBDRsl), which would still capture 64% (168/264) and 77% (34/44) of LPA-detectable smear-negative resistance, respectively. Use of CTmins permitted optimization of this ratio with higher specificity for non-actionable results but decreased resistance detected. Xpert quantitative information permits identification of a smear-negative subset in whom the payoffs of the ratio of actionable-to-non-actionable LPA results with missed resistance may prove acceptable to laboratories, depending on context. Our findings permit the rational expansion of direct DST to certain smear-negative sputum specimens.

Smoked drug use in patients with TB is associated with higher bacterial burden

BACKGROUND: Smoking of illicit drugs may lead to more rapid TB disease progression or late treatment presentation, yet research on this topic is scant. We examined the association between smoked drug use and bacterial burden among patients newly initiated on drug-susceptible TB (DS-TB) therapy.METHODS: Data from 303 participants initiating DS-TB treatment in the Western Cape Province, South Africa, were analyzed. Smoked drug use was defined as self-reported or biologically verified methamphetamine, methaqualone and/or cannabis use. Proportional hazard and logistic regression models (adjusted for age, sex, HIV status and tobacco use) examined associations between smoked drug use and mycobacterial time to culture positivity (TTP), acid-fast bacilli sputum smear positivity and lung cavitation.RESULTS: People who smoked drugs (PWSD) comprised 54.8% (n = 166) of the cohort. TTP was faster for PWSD (hazard ratio 1.48, 95% CI 1.10-1.97; P = 0.008). Smear positivity was higher among PWSD (OR 2.28, 95% CI 1.22-4.34; P = 0.011). Smoked drug use (OR 1.08, 95% CI 0.62-1.87; P = 0.799) was not associated with increased cavitation.CONCLUSIONS: PWSD had a higher bacterial burden at diagnosis than those who do not smoke drugs. Screening for TB among PWSD in the community may facilitate earlier linkage to TB treatment and reduce community transmission.

Poikilocytosis of Angora goats is associated with erythrocyte density and reticulocytosis

Angora goats in South Africa experience several syndromes that result in notable morbidity and mortality in juveniles and adults, but not kids. Insight into their causes is hampered by the lack of normal reference values for this breed, and the present study therefore aimed to characterise (1) differences in the haematology of healthy kids at birth and weaning, and (2) the haematology of apparently healthy yearlings. Selected variables were measured by blood smear analysis, and complete blood counts were performed using an ADVIA 2120i. Variables at 1, 11, and 20 weeks of age were compared using the Friedman test and associations between variables of yearlings were determined by correlation analysis. In kids, red blood cell count, mean corpuscular haemoglobin concentration (MCHC), and poikilocytosis increased over time, while mean corpuscular haemoglobin (MCH) and mean corpuscular volume (MCV) decreased. Yearlings displayed a lower MCHC, and higher haemoglobin distribution width than previously reported for goats, and these were positively correlated with poikilocytosis, as were reticulocyte counts. White cell counts of yearlings exceeded normal values previously reported for goats, with some individuals displaying remarkably high mature neutrophil counts. Changes in haemoglobin variant expression or cation and water fluxes are possible explanations for the findings in kids, while in yearlings, the associations between MCHC, HDW, poikilocytosis, and reticulocytosis suggest alterations in red cell hydration in adulthood that are associated with increased red cell turnover. These findings may prove informative in the further investigation of various clinical syndromes in this population.

Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine

In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.

Management of rifampicin‐resistant TB: programme indicators and care cascade analysis in South Africa

BACKGROUND: Xpert® MTB/RIF was expected to revolutionise the management of rifampicin‐resistant TB (RR‐TB) by enabling rapid and decentralised diagnosis of rifampicin (RIF) resistance.METHODS: We performed a care cascade analysis for a cohort of RR‐TB patients managed under programmatic conditions. Cumulative incidences of time to completion of the RR‐TB care cascade steps were estimated, reasons for delay or attrition from the cascade investigated and WHO programme indicators for monitoring of RR‐TB programmes calculated.RESULTS: Of 502 patients diagnosed with RR‐TB using Xpert, 64% initiated multidrug‐resistant TB (MDR‐TB) treatment immediately, 20% after some first‐line treatment, 16% never initiated MDR‐TB treatment, mainly because of death (44%) or loss to follow‐up (26%) soon after diagnosis. A supplementary sputum sample was collected within 14 days of treatment in 58.8% of cases. Only 63% of RR‐TB cases were assessed for isoniazid resistance, and only 65% of MDR‐TB cases were evaluated for pre‐XDR‐TB (extensively drug‐resistant TB). Treatment was individualised in 57% of pre‐XDR and 68% of XDR‐TB patients. Only 8% completed the entire RR‐TB care cascade as intended.CONCLUSION: Fidelity to the RR‐TB algorithm was poor, with substantial losses at each step of the cascade, highlighting the fact that implementation of novel technologies needs to be accompanied by health system strengthening to maximise impact.

WHOLE GENOME SEQUENCING SHEDS LIGHT ON THE TRANSMISSION DYNAMICS OF A MULTIDRUG RESISTANT MYCOBACTERIUM TUBERCULOSIS OUTBREAK OVER 23 YEARS IN A HIGH INCIDENCE SETTING

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Antigen-specific interferon-gamma release is decreased following the single intradermal comparative cervical skin test in African buffaloes (Syncerus caffer)

Effective disease management of wildlife relies on the strategic application of ante-mortem diagnostic tests for early identification and removal of M. bovis-infected animals. To improve diagnostic performance, interferon-gamma release assays (IGRAs) are often used in conjunction with the tuberculin skin test (TST). Since buffaloes are major maintenance hosts of M. bovis, optimal application of bovine TB diagnostic tests are especially important. We aimed to determine whether the timing of blood collection relative to the TST has an influence on IFN-γ production and diagnostic outcome in African buffaloes. Release of IFN-γ in response to bovine purified protein derivative (PPD), avian PPD and PC-HP^® and PC-EC^® peptides was measured by Bovigam^® and an in-house IGRA in a group of Bovigam^®-positive and - negative buffaloes at the time the TST was performed and three days later. There was significantly lower IFN-γ release in response to these antigens post-TST in Bovigam^®-positive buffaloes, but no significant changes in Bovigam^®-negative buffaloes. Also, a significantly greater proportion of buffaloes were Bovigam^®-positive prior to the TST than three days later. We therefore recommend that blood samples for use in IGRAs be collected prior to or at the time the TST is performed to facilitate the correct identification of greater numbers of IGRA-positive buffaloes.

Widespread use of incorrect PCR ramp rate negatively impacts multidrug-resistant tuberculosis diagnosis (MTBDRplus)

The scale-up of rapid drug resistance testing for TB is a global priority. MTBDRplus is a WHO-endorsed multidrug-resistant (MDR)-TB PCR assay with suboptimal sensitivities and high indeterminate rates on smear-negative specimens. We hypothesised that widespread use of incorrect thermocycler ramp rate (speed of temperature change between cycles) impacts performance. A global sample of 72 laboratories was surveyed. We tested 107 sputa from Xpert MTB/RIF-positive patients and, separately, dilution series of bacilli, both at the manufacturer-recommended ramp rate (2.2 °C/s) and the most frequently reported incorrect ramp rate (4.0 °C/s). Mycobacterium tuberculosis-complex DNA (TUB-band)-detection, indeterminate results, accuracy, and inter-reader variability (dilution series only) were compared. 32 respondents did a median (IQR) of 41 (20-150) assays monthly. 78% used an incorrect ramp rate. On smear-negative sputa, 2.2 °C/s vs. 4.0 °C/s improved TUB-band positivity (42/55 vs. 32/55; p = 0.042) and indeterminate rates (1/42 vs. 5/32; p = 0.039). The actionable results (not TUB-negative or indeterminate; 41/55 vs. 28/55) hence improved by 21% (95% CI: 9-35%). Widespread use of incorrect ramp rate contributes to suboptimal MTBDRplus performance on smear-negative specimens and hence limits clinical utility. The number of diagnoses (and thus the number of smear-negative patients in whom DST is possible) will improve substantially after ramp rate correction.

Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase

Over the past six decades, there has been a decline in novel therapies to treat tuberculosis, while the causative agent of this disease has become increasingly resistant to current treatment regimens. Bacteriophages (phages) are able to kill bacterial cells and understanding this process could lead to novel insights for the treatment of mycobacterial infections. Phages inhibit bacterial gene transcription through phage-encoded proteins which bind to RNA polymerase (RNAP), thereby preventing bacterial transcription. Gp2, a T7 phage protein which binds to the beta prime (β') subunit of RNAP in Escherichia coli, has been well characterized in this regard. Here, we aimed to determine whether Gp2 is able to inhibit RNAP in Mycobacterium tuberculosis as this may provide new possibilities for inhibiting the growth of this deadly pathogen. Results from an electrophoretic mobility shift assay and in vitro transcription assay revealed that Gp2 binds to mycobacterial RNAP and inhibits transcription; however to a much lesser degree than in E. coli. To further understand the molecular basis of these results, a series of in silico techniques were used to assess the interaction between mycobacterial RNAP and Gp2, providing valuable insight into the characteristics of this protein-protein interaction.

Isolation and Potential for Transmission of Mycobacterium bovis at Human-livestock-wildlife Interface of the Serengeti Ecosystem, Northern Tanzania

Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), is a multihost pathogen of public health and veterinary importance. We characterized the M. bovis isolated at the human-livestock-wildlife interface of the Serengeti ecosystem to determine the epidemiology and risk of cross-species transmission between interacting hosts species. DNA was extracted from mycobacterial cultures obtained from sputum samples of 472 tuberculosis (TB) suspected patients and tissue samples from 606 livestock and wild animal species. M. bovis isolates were characterized using spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) on 24 loci. Only 5 M. bovis were isolated from the cultured samples. Spoligotyping results revealed that three M. bovis isolates from two buffaloes (Syncerus caffer) and 1 African civet (Civettictis civetta) belonged to SB0133 spoligotype. The two novel strains (AR1 and AR2) assigned as spoligotype SB2290 and SB2289, respectively, were identified from indigenous cattle (Bos indicus). No M. bovis was detected from patients with clinical signs consistent with TB. Of the 606 animal tissue specimens and sputa of 472 TB-suspected patients 43 (7.09%) and 12 (2.9%), respectively, yielded non-tuberculous mycobacteria (NTM), of which 20 isolates were M. intracellulare. No M. avium was identified. M. bovis isolates from wildlife had 45.2% and 96.8% spoligotype pattern agreement with AR1 and AR2 strains, respectively. This finding indicates that bTB infections in wild animals and cattle were epidemiologically related. Of the 24 MIRU-VNTR loci, QUB 11b showed the highest discrimination among the M. bovis strains. The novel strains obtained in this study have not been previously reported in the area, but no clear evidence for recent cross-species transmission of M. bovis was found between human, livestock and wild animals.

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

BACKGROUND

Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis.

METHODS

Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline.

RESULTS

Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30% to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event.

CONCLUSIONS

Our study demonstrated true levels of genetic diversity within an M. tuberculosis population and showed that genetic diversity may be re-defined when a selective pressure, such as drug exposure, is imposed on M. tuberculosis populations during the course of infection. This suggests that the genome of M. tuberculosis is more dynamic than previously thought, suggesting preparedness to respond to a changing environment.

Phage-based detection of bacterial pathogens

Bacterial pathogens cause significant morbidity and mortality annually to both humans and animals. With the rampant spread of drug resistance and the diminishing effectiveness of current antibiotics, there is a pressing need for effective diagnostics for detection of bacterial pathogens and their drug resistances. Bacteriophages offer several unique opportunities for bacterial detection. This review highlights the means by which bacteriophages have been utilized to achieve and facilitate specific bacterial detection.

Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity

The pe/ppe genes represent one of the most intriguing aspects of the Mycobacterium tuberculosis genome. These genes are especially abundant in pathogenic mycobacteria, with more than 160 members in M. tuberculosis. Despite being discovered over 15 years ago, their function remains unclear, although various lines of evidence implicate selected family members in mycobacterial virulence. In this review, we use PE/PPE phylogeny as a framework within which we examine the diversity and putative functions of these proteins. We report on the evolution and diversity of the respective gene families, as well as the implications thereof for function and host immune recognition. We summarize recent findings on pe/ppe gene regulation, also placing this in the context of PE/PPE phylogeny. We collate data from several large proteomics datasets, providing an overview of PE/PPE localization, and discuss the implications this may have for host responses. Assessment of the current knowledge of PE/PPE diversity suggests that these proteins are not variable antigens as has been so widely speculated; however, they do clearly play important roles in virulence. Viewing the growing body of pe/ppe literature through the lens of phylogeny reveals trends in features and function that may be associated with the evolution of mycobacterial pathogenicity.

Early stationary phase culture supernatant accelerates growth of sputum cultures collected after initiation of anti-tuberculosis treatment

We investigated the effect of Mycobacterium tuberculosis culture supernatant added to sputum cultures collected during the first 8 weeks of anti-tuberculosis treatment. With ongoing treatment duration, time to culture positivity decreased significantly in supernatant-enriched cultures, possibly due to stimulation of dormant or slowly metabolizing M. tuberculosis cells.

When Spectral Smearing Can Increase Speech Intelligibility

Sentences were reduced to an array of sixteen effectively rectangular bands (RBs) having center frequencies ranging from 0.25 to 8 kHz spaced at ⅓-octave intervals. Four arrays were employed, each having uniform subcritical bandwidths which ranged from 40 Hz to 5 Hz. The 40 Hz width array had intelligibility near ceiling, and the 5 Hz array about 1%. The finding of interest was that when the subcritical speech RBs were used to modulate RBs of noise having the same center frequency as the speech but having bandwidths increased to a critical (ERBn) bandwidth at each center frequency, these spectrally smeared arrays were considerably more intelligible in all but the 40 Hz (ceiling) condition. For example, when the 10 Hz bandwidth speech array having an intelligibility of 8% modulated the ERBn noise array, intelligibility increased to 48%. This six-fold increase occurred despite elimination of spectral fine structure and addition of stochastic fluctuation to speech envelope cues. (As anticipated, conventional vocoding with matching bandwidths of speech and noise reduced the 10-Hz-speech array intelligibility from 8% to 1%). These effects of smearing confirm findings by Bashford, Warren, and Lenz (2010) that optimal temporal processing requires stimulation of a critical bandwidth. [Supported by NIH].

Isolation of DNA from Mycobacterium tubercolosis

Research into and identification of Mycobacterium tuberculosis can take on a number of facets, many of which involve the use of DNA at one stage or another. The quality and quantity of DNA required will depend on the end-use requirement. For example, good yields of pure, high-molecular-weight DNA uncontaminated by DNA from other sources (i.e., homogeneous) are optimal for the generation of cosmid libraries and sequencing (1), Southern hybridization (2-6), or microarray analysis (7) for genome studies, whereas relatively crude DNA (fragmented DNA or DNA from multiple sources [i.e., heterogeneous]) may be adequate for PCR-based diagnosis (8-12) or amplification of regions of the genome for other purposes, e.g., identification of mutations conferring drug resistance (13,14).

Rise in rifampicin-monoresistant tuberculosis in Western Cape, South Africa

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.

Comparative analysis of a putative tuberculosis-susceptibility gene, MC3R, and pseudogene sequences in cattle, African buffalo, hyena, rhinoceros and other African bovids and ruminants

Studies in humans have suggested the possible involvement of melanocortin-3-receptor (MC3R) and other components of the central melanocortin system in host defense against mycobacteria. We report a genomic DNA nucleotide sequence highly homologous to human MC3R in several bovids and non-bovid African wildlife species. Nucleotide sequence analysis indicates that the orthologous genes of cattle and buffalo are highly homologous (89.4 and 90%, respectively) to the human MC3R gene. Sequence results also identified a typical non-functional, duplicated pseudogene, MC3RP, in 7 species from the family Bovidae. No pseudogene was found in animals outside Bovidae. The presence of the pseudogene in tuberculosis-susceptible species could have possible immunomodulatory effects on susceptibility to bovine tuberculosis infection, as well as a considerable influence on energy metabolism and food conversion efficiency.

Detection of Mycobacterium tuberculosis infection in dogs in a high-risk setting

Dogs infected with Mycobacterium tuberculosis can develop clinical tuberculosis (TB) but there are currently no validated immunological assays for diagnosing this infection in this species. Using a post mortem survey we investigated the prevalence of non-clinical M. tuberculosis infection and clinical TB disease in a high-risk population of dogs and developed and utilised a novel interferon-gamma release assay to determine the risk of transmission of M. tuberculosis from TB patients to contact dogs. The prevalence of clinical TB in dogs from a high-risk setting was 1% (95% CI: 0-5%) while the prevalence of immunological sensitization to M. tuberculosis antigens in dogs living in contact with sputum smear-positive TB patients was 50%. The IGRA proved a useful test of M. tuberculosis infection in dogs and the high levels of transmission of this pathogen from humans to companion dogs should be considered when assessing the zoonotic risks associated with such animals.

inhA promoter mutations: a gateway to extensively drug-resistant tuberculosis in South Africa?

SETTING

Western Cape and Eastern Cape Provinces, South Africa.

OBJECTIVE

To assess the potential association between the evolution of extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis and mutations in the inhA promoter or the katG gene.

DESIGN

Analysis of the frequency distribution of isoniazid (INH) resistance conferring mutations in a population sample of drug-resistant isolates of M. tuberculosis.

RESULTS

In the Western Cape and Eastern Cape Provinces, the percentage of isolates exhibiting inhA promoter mutations increased significantly from respectively 48.4% and 62.4% in multidrug-resistant tuberculosis (MDR-TB) isolates to 85.5% and 91.9% in XDR isolates. Data from the Western Cape revealed that significantly more XDR-TB isolates showed mutations in the inhA promoter than in katG (85.5% vs. 60.9%, P < 0.01), while the respective proportions were equal for INH-resistant non-MDR-TB isolates (∼30%).

CONCLUSIONS

inhA promoter mutations are strongly associated with XDR-TB in South Africa. We suggest that this is due to the dual resistance to ethionamide and (low-dose) INH conferred by inhA promoter mutations. The use of molecular probe assays such as the GenoType® MTBDRplus assay, which allows the detection of inhA promoter mutations, could enable treatment regimens to be adjusted depending on the pharmacogenetic properties of the mutations detected.

The use of light-emitting diode fluorescence to diagnose mycobacterial lymphadenitis in fine-needle aspirates from children

BACKGROUND

Fine-needle aspiration biopsy (FNAB) is a simple, safe and effective method for investigating suspected mycobacterial lymphadenitis in children. Fluorescence microscopy can provide rapid mycobacterial confirmation. Light-emitting diodes (LEDs) provide a cheap and robust excitation light source, making fluorescence microscopy feasible in resource-limited settings.

OBJECTIVE

To compare the diagnostic performance of LED fluorescence microscopy on Papanicolaou (PAP) stained smears with the conventional mercury vapour lamp (MVL).

METHODS

FNAB smears routinely collected from palpable lymph nodes in children with suspected mycobacterial disease were PAP-stained and evaluated by two independent microscopists using different excitatory light sources (MVL and LED). Mycobacterial culture results provided the reference standard. A manually rechargeable battery-powered LED power source was evaluated in a random subset.

RESULTS

We evaluated 182 FNAB smears from 121 children (median age 31 months, interquartile range 10-67). Mycobacterial cultures were positive in 84 of 121 (69%) children. The mean sensitivity with LED (mains-powered), LED (rechargeable battery-powered) and MVL was respectively 48.2%, 50.0% and 51.8% (specificity 78.4%, 86.7% and 78.4%). Inter-observer variation was similar for LED and MVL (κ = 0.5).

CONCLUSION

LED fluorescence microscopy provides a reliable alternative to conventional methods and has many favourable attributes that would facilitate improved, decentralised diagnostic services.

Use of fluoroquinolone antibiotics leads to tuberculosis treatment delay in a South African gold mining community

BACKGROUND

Empiric use of fluoroquinolone (FQ) antibiotics could delay tuberculosis (TB) treatment and lead to FQ-resistant TB.

METHODS

We examined the impact of FQ use on TB outcomes, including smear status, treatment delay and FQ resistance, through a retrospective cohort study of 440 FQ-exposed and 511 non-exposed patients in a gold mining community in South Africa. We considered both recent (≤ 100 days before sputum collection) and distant exposure (≤ 1 year). We examined 201 and 180 isolates from FQ-exposed and non-exposed individuals for the presence of gyrA mutations.

RESULTS

Patients recently exposed to ≥ 5 days of FQ were less likely to be smear-positive (OR 0.27, 95%CI 0.11-0.63), with an increased time to treatment (time ratio 2.02, 95%CI 1.19-3.44). The strength of association decreased when we considered distant exposure. Adjusting for smear status nullified the effect of FQ exposure on treatment delay. We detected a gyrA mutation in one isolate (0.5%) taken from an individual exposed to FQ for 8 days.

CONCLUSION

FQ exposure is associated with treatment delay, mediated by negative smear status. Short exposures to FQ do not routinely lead to resistance encoded by gyrA mutations. We recommend prudent use of FQ in settings with a high burden of human immunodeficiency virus and TB.

Mycobacterial genotype is associated with disease phenotype in children

OBJECTIVE

To investigate the association between mycobacterial genotype and disease phenotype in children.

METHODS

We describe hospitalised children diagnosed with culture-confirmed tuberculosis (TB) in South Africa, a high TB burden setting. Disease phenotype was classified as intrathoracic or extrathoracic based on mycobacterial culture site. Mycobacterial genotyping was completed using spoligotyping.

RESULTS

We analysed 421 isolates from 392 children (median age 2 years, range 0.1-12). Intrathoracic disease was present in 294 (75%) children and extrathoracic disease in 98 (25%). The Beijing genotype was the most prevalent (32.9%), followed by the Latin American Mediterranean (LAM, 28.8%), and S genotypes (6.4%). Age was significantly associated with genotype. Children with the Beijing (OR = 2.36, 95%CI 1.21- 4.60) and S genotypes (OR = 3.47, 95%CI 1.26-9.56) were more likely to have extrathoracic disease compared to children infected with the LAM genotype, in analyses adjusted for age and drug resistance.

CONCLUSIONS

TB genotype and disease phenotype in children were associated. Beijing and S genotypes were more frequently cultured from extrathoracic cultures, indicating potential improved ability to disseminate. Strain-related phenotypes could explain different disease spectra in geographic settings where certain strains are successful. Studies of mycobacterial human interaction should consider host immune responses, clinical and epidemiological factors.

Drug-resistant tuberculosis epidemic in the Western Cape driven by a virulent Beijing genotype strain

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.

Mycobacterial transport medium for routine culture of fine needle aspiration biopsies

Fine needle aspiration biopsy (FNAB) offers a simple outpatient technique for specimen collection in child tuberculosis suspects with peripheral lymphadenopathy. To perform FNAB with mycobacterial culture on an outpatient basis requires use of a sterile transport medium to facilitate bedside inoculation, maintain organism viability and reduce contamination risk en route to the laboratory. The mycobacterial yield and time to positive culture following bedside inoculation into standard mycobacterial growth indicator tubes were compared with initial inoculation into an inexpensive "in-house" liquid growth medium. Of 150 FNAB performed, 57 (38%) cultured Mycobacterium tuberculosis complex. There was one case each with non-tuberculous mycobacteria and Mycobacterium bovis BCG; the remaining 55 being M tuberculosis. Results were concordant in 142 (94.7%) bedside and laboratory inoculation pairs. There was no significant difference in time to positive culture between bedside and laboratory inoculation (16.2 days (SD 0.87) vs 17.1 days (SD 0.85)). Provision of inexpensive specimen transport bottles and practical tuition in FNAB should improve cost-effective diagnosis of tuberculosis at the primary healthcare level.

Fine needle aspiration biopsy: an undervalued diagnostic modality in paediatric mycobacterial disease

Mycobacterial disease, and particularly tuberculosis (TB), is an escalating problem in developing countries, fuelled by the parallel human immunodeficiency virus (HIV) pandemic. In TB endemic countries children carry a very high burden of disease, which may be unrecognised due to the difficulty in making a diagnosis based on clinical, radiological or laboratory methods. One of the main hurdles is the difficulty of obtaining adequate specimens for bacteriological confirmation of disease in children. TB lymphadenitis is the most common extra-pulmonary manifestation of TB, and up to 22% of children with persistent cervical lymphadenopathy and no local cause may have tuberculous adenitis. Fine needle aspiration biopsy (FNAB), a simple and safe out-patient procedure that can be performed by nurses in resource-limited settings, and that provides material for direct microscopy as well as culture and susceptibility testing, provides an excellent opportunity to obtain bacteriological confirmation. However, it remains a greatly underutilised specimen collection modality. This review provides a comprehensive overview of the difficulties faced in the diagnosis of paediatric TB in resource-limited settings, and suggests ways to utilise FNAB as a practical modality for the rapid and effective diagnosis of mycobacterial disease in the significant subset of patients who present with peripheral lymphadenopathy. It also provides detail on how best to perform the technique, and suggests ways of making it more widely available in resource-limited settings, which carry the brunt of the paediatric TB disease burden.

Effect of study duration on the interpretation of tuberculosis molecular epidemiology investigations

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.

Changing Mycobacterium tuberculosis population highlights clade-specific pathogenic characteristics

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.

Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Sri Lanka

The strain diversity of 100 Mycobacterium tuberculosis isolates collected over a period of 18 months from tuberculosis (TB) cases in Sri Lanka was studied by spoligotyping. When compared to the international spoligotyping database, 43 spoligotype patterns were identified, of which 20 were previously described. The majority of isolates (72.45%) were clustered into major genetic group 1, and the most common spoligotype pattern belonged to the Beijing (ST1) strain family. All the Beijing strain isolates belonged to more recently evolved sublineages of M. tuberculosis. The characterization of Sri Lankan M. tuberculosis isolates by spoligotyping shows a heterogeneous pattern. The physical separation from the main Indian peninsula may be responsible for the different patterns observed between the two countries. An in-depth field study is needed to understand the spread and the true epidemiology of this infection.

Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa

SETTING

The epidemiology of extensively drug-resistant tuberculosis (XDR-TB), an emerging threat to TB control, is not well understood.

OBJECTIVE

To gain insight into the genotypic population structure of XDR Mycobacterium tuberculosis strains in South Africa using a molecular approach and thereby determine whether XDR-TB is mainly acquired or transmitted.

DESIGN

Sputum isolates from patients with multidrug-resistant tuberculosis (MDR-TB) were submitted to the National Referral Laboratory for second-line drug susceptibility testing. The XDR-TB isolates were spoligotyped and these data were compared to the geographic origin of the isolate.

RESULTS

Of the 699 MDR-TB isolates submitted for testing between June 2005 and December 2006, 101 (17%) patients had a culture that was resistant to either ofloxacin or kanamycin, and 41 (6%) were resistant to both drugs (XDR-TB). Spoligotyping of the XDR-TB isolates identified 17 genotypes. As a result of the high genotypic diversity and geographical distribution, we estimate that between 63% and 75% of cases developed XDR-TB through acquisition.

CONCLUSION

Acquisition of extensive drug resistance appears to be the primary mechanism driving the XDR-TB epidemic in South Africa. This urgent TB control issue has to be addressed to prevent the spread of this potentially incurable disease.

Evidence that the spread of Mycobacterium tuberculosis strains with the Beijing genotype is human population dependent

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).

A recently evolved sublineage of the Mycobacterium tuberculosis Beijing strain family is associated with an increased ability to spread and cause disease

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.

Predominance of a single genotype of Mycobacterium tuberculosis in regions of Southern Africa

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.

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.

Spoligotype signatures in the Mycobacterium tuberculosis complex

Evolution of the direct repeat region in Mycobacterium tuberculosis has created unique spoligotype signatures specifically associated with IS6110-defined strain families. Spoligotyping signatures may enable the analysis of the strain population structure in different settings and will enable the rapid identification of strain families that acquire drug resistance or escape protective immunity in drug and vaccine trials.

Frequency and implications of pyrazinamide resistance in managing previously treated tuberculosis patients

OBJECTIVE

To determine the extent of pyrazinamide (PZA) resistance in isolates from previously treated patients from the Western Cape, South Africa.

DESIGN

Drug-resistant isolates, isolates resistant to one or more drugs other than PZA (PZA resistance is not routinely determined) (n = 127), and drug-susceptible (n = 47) clinical isolates of Mycobacterium tuberculosis from previously treated patients from the Western Cape were phenotypically (BACTEC MGIT 960) and genotypically (pncA gene sequencing) analysed for PZA resistance.

RESULTS

MGIT analysis found that 68 of the 127 drug-resistant isolates were PZA-resistant. Nearly all (63/68) PZA-resistant isolates had diverse nucleotide changes scattered throughout the pncA gene, and five PZA-resistant isolates had no pncA mutations. Of the 47 phenotypically susceptible isolates, 46 were susceptible to PZA, while one isolate was PZA-monoresistant (OR = 53.0, 95% CI = 7.1-396.5). A pncA polymorphism (Thr114Met) that did not confer PZA resistance was also identified. PZA resistance was strongly associated with multidrug-resistant tuberculosis (MDR-TB).

CONCLUSION

An alarmingly high proportion of South African drug-resistant M. tuberculosis isolates are PZA-resistant, indicating that PZA should not be relied upon in managing patients with MDR-TB in the Western Cape. A method for the rapid detection of PZA resistance would be beneficial in managing patients with suspected drug resistance.

Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference

Differentiation of members of the Mycobacterium tuberculosis complex by conventional mycobacteriological methods is time consuming, making surveillance of species-specific disease difficult. A two-step, multiplex polymerase chain reaction (PCR) method based on genomic regions of difference (RD1, RD1(mic), RD2(seal), RD4, RD9 and RD12) was developed for the differentiation of M. canettii, M. tuberculosis, M. africanum, M. microti, M. pinnipedii, M. caprae, M. bovis and M. bovis BCG. The size of the respective multiplex PCR amplification products corresponded to the presence of the different M. tuberculosis complex members. This method allows for rapid differentiation, making it suitable for routine laboratories and surveillance purposes.

Bacille Calmette-Guérin vaccine-induced disease in HIV-infected and HIV-uninfected children

BACKGROUND

Bacille Calmette-Guérin (BCG)--a live, attenuated vaccine--is routinely given to neonates in settings where tuberculosis is endemic, irrespective of human immunodeficiency virus (HIV) exposure. HIV-infected infants and other immunodeficient infants are at risk of BCG-related complications. We report the presentation, treatment, and mortality of children who develop BCG disease, with emphasis on HIV-infected children. In addition, we present a revised classification of BCG disease in children and propose standard diagnostic and management guidelines.

METHODS

This retrospective, hospital-based study was conducted in the Western Cape Province, South Africa. Mycobacterium tuberculosis complex isolates recovered from children aged <13 years during the period of August 2002 through January 2005 were speciated by polymerase chain reaction to confirm Mycobacterium bovis BCG. Clinical data were collected through medical file review. BCG disease was classified according to standard and revised disease classifications. Mortality was assessed at the end of the study period.

RESULTS

BCG disease was diagnosed in 25 children; 22 (88%) had local disease, and 8 (32%) had distant or disseminated disease; 5 children (20%) had both local and distant or disseminated disease. Seventeen children were HIV infected; 2 children had other immunodeficiencies. All 8 children with distant or disseminated disease were immunodeficient; 6 were HIV infected. The mortality rate was 75% for children with distant or disseminated disease.

CONCLUSIONS

BCG vaccination poses a risk to infants perinatally infected with HIV and to other primary immunodeficient children. The proposed pediatric BCG disease classification reflects clinically relevant disease categories in HIV-infected children. The suggested diagnostic and treatment guidelines should improve existing case management and surveillance. Prospective evaluation of management strategies for BCG disease in HIV-infected and HIV-uninfected children is essential.

The burden of childhood tuberculosis: a public health perspective

The burden of childhood tuberculosis (TB) reflects recent transmission within a community and the level of TB control achieved within the adult (maintenance host) population. Children contribute little to the maintenance of the TB epidemic, but they may suffer severe TB-related morbidity and mortality. This review describes the main determinants of the burden of childhood TB within a particular community. Basic infectious disease principles identify the community, and not the individual, as the central entity that sustains an epidemic. The prevalence of TB is determined by the community's exposure to Mycobacterium tuberculosis, and their vulnerability to developing disease following exposure. The main variables that influence both exposure and vulnerability are discussed. Multiple variables are linked to poverty, and it is their cumulative effect, rather than the exact degree of poverty, that seems most important. Diligent contact tracing and the use of preventive chemotherapy will reduce the TB-related suffering of children. The burden of childhood TB, however, is a reflection of our ability to control the epidemic; this remains the ultimate challenge. Current efforts to control the TB epidemic aim to reduce transmission by treating sputum smear-positive adults, while very little emphasis is placed on reducing the vulnerability of high-burden communities. Successful control of the epidemic is the most effective way to reduce the burden of childhood TB, but this will require a holistic approach that acknowledges the importance of sustainable poverty alleviation.

Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers

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.

IS6110-mediated deletion polymorphism in isogenic strains of Mycobacterium tuberculosis

Previous studies have described IS6110-mediated polymorphism as an important driving force in Mycobacterium tuberculosis genome evolution and have provided indirect evidence for IS6110-driven deletion events. This study provides the first description of an IS6110-mediated deletion event in truly isogenic strains. We also provide further support for the hypothesis that the region from Rv1754 to Rv1765 is a hot spot for IS6110 insertion and deletion events.

Genotypic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from rural districts of the Western Cape Province of South Africa

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.

Use of genetic distance as a measure of ongoing transmission of Mycobacterium tuberculosis

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.