Publications by authors named "Shaheed V Omar"

34 Publications

Effectiveness and cardiac safety of bedaquiline-based therapy for drug-resistant tuberculosis: a prospective cohort study.

Clin Infect Dis 2021 Apr 21. Epub 2021 Apr 21.

Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa.

Background: Bedaquiline improves treatment outcomes in patients with rifampin-resistant TB (RR-TB) but prolongs the QT-interval and carries a black-box warning by the U.S. Food and Drug Administration. The World Health Organization recommends that all patients with RR-TB receive a regimen containing bedaquiline, yet a phase 3 clinical trial demonstrating its cardiac safety has not been published.

Methods: We conducted an observational cohort study of RR-TB patients from 3 provinces in South Africa who received regimens containing bedaquiline. We performed rigorous cardiac monitoring, including electrocardiograms (ECGs) performed in triplicate at four time points during bedaquiline therapy. Participants were followed until the end of therapy or 24 months. Outcomes included final tuberculosis treatment outcome and QT-prolongation, defined as any QTcF>500 ms or an absolute change from baseline (△ QTcF) >60 ms.

Results: We enrolled 195 eligible participants, of whom 40% had extensively drug-resistant (XDR) TB. Most participants (97%) received concurrent clofazimine. 74% of participants were cured or successfully completed treatment, and outcomes did not differ by HIV status. QTcF continued to increase throughout bedaquiline therapy, with a mean increase of 23.7 (SD 22.7) ms from baseline to month 6. Four participants experienced a QTcF>500 ms and 19 experienced a △QTcF>60 ms. Older age was independently associated with QT-prolongation. QT-prolongation was neither more common nor severe in participants receiving concurrent lopinavir-ritonavir.

Conclusions: Severe QT-prolongation was uncommon and did not require permanent discontinuation of either bedaquiline or clofazimine. Close QT-monitoring may be advisable in older patients.
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http://dx.doi.org/10.1093/cid/ciab335DOI Listing
April 2021

Whole-Genome Sequencing of a Mycobacterium tuberculosis Strain Belonging to Lineage 1 (Indo-Oceanic) and the East African Indian Spoligotype, Isolated in Jazan, Saudi Arabia.

Microbiol Resour Announc 2020 Aug 13;9(33). Epub 2020 Aug 13.

National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

We describe here the draft genome sequence of AY1MRC, a strain belonging to lineage 1 (Indo-Oceanic) and the East African Indian spoligotype, isolated from a patient with tuberculosis in Jazan, Saudi Arabia.
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http://dx.doi.org/10.1128/MRA.00717-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427191PMC
August 2020

A Multimethod, Multicountry Evaluation of Breakpoints for Bedaquiline Resistance Determination.

Antimicrob Agents Chemother 2020 08 20;64(9). Epub 2020 Aug 20.

Center for Tuberculosis and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.

Criteria defining bedaquiline resistance for tuberculosis have been proposed addressing an emerging concern. We evaluated bedaquiline phenotypic drug susceptibility testing (pDST) criteria using drug-resistant tuberculosis clinical isolates tested at five reference laboratories. Isolates were tested at the proposed bedaquiline MGIT960 and 7H11 agar proportion (AP) critical concentrations and also at higher dilutions. The epidemiological cutoff value for the broth microdilution (BMD) plates (frozen and dry) was investigated. Sanger sequencing was performed ( and genes) for any isolate testing resistant. The composite reference standard (CRS) defined susceptibility or resistance as is if all pDST methods agreed. If the pDST result was discordant, sequencing results were used for final classification. Geographically diverse and bedaquiline-unexposed isolates were tested ( = 495). The epidemiological cutoff value for BMD was confirmed to be 0.12 μg/ml. The majority of isolates were determined to be susceptible by all methods (467/495; 94.3%), and 28 were determined to be resistant by at least one method; 4 of these were determined to be resistant by all methods. Of the 28 resistant isolates, 12 harbored Rv0678 mutations exclusively. Isolates with insertions/deletions were more likely to be determined to be resistant by more than one method (5/7) compared to isolates with a single nucleotide polymorphism (1/5). Applying the CRS to 24 discordant pDST, BMD dry correctly detected most (15/24; 63%), followed by MGIT960 and BMD frozen (13/24; 61%) and lastly AP (12/24; 50%). Applying the CRS, the prevalence of bedaquiline resistance was 2.2% and ranged from 1.4 to 3.4%, depending on the method used. All methods performed well for bedaquiline susceptibility determination; however, resistance detected should be investigated by a second, alternative method.
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http://dx.doi.org/10.1128/AAC.00479-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449194PMC
August 2020

Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing.

Sci Rep 2020 01 23;10(1):1013. Epub 2020 Jan 23.

National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa.

Universal drug susceptibility testing (DST) is an important requirement of the End TB Strategy. The Sensititre broth micro-dilution assay (BMD) tests multiple drugs quantitatively. We defined interpretive criteria for this assay and analysed genotypic-phenotypic relationships. 385 Mycobacterium tuberculosis clinical isolates were processed for BMD and whole genome sequencing. The epidemiological cut-off value 99% (ECV) amongst genotypically wild type (gWT) strains defined susceptibility. Minimum inhibitory concentration distributions of the resistance-associated variants (RAVs) for each drug were analysed. Susceptibility (µg/mL) criteria were determined as follows: rifampicin (≤0.125), isoniazid (≤0.25), ethambutol (≤2.0), moxifloxacin (≤0.5), levofloxacin (≤1.0), amikacin (≤2.0), kanamycin (≤8.0), capreomycin (≤4.0), clofazimine (≤0.25) and linezolid (≤2.0). Most drugs showed clear separation between gWT and RAV. Isoniazid showed a tri-modal pattern with 14/17 strains at ECV harbouring a fabG1 c. -15C > T RAV. Ethambutol RAVs at embB codons 306, 405 and 497 were responsible for resistance and showed differential distributions. Moxifloxacin RAVs (gyrA codon 90) were a dilution or two higher than the ECV while gyrB RAVs were uncommon and showed drug specific resistance propensity. Interpretive criteria established were robust facilitating progress towards universal DST and individualised precision medicine. This study demonstrates the value of quantitative DST to accurately interpret mutation data.
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http://dx.doi.org/10.1038/s41598-020-57992-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978314PMC
January 2020

Validation of Bedaquiline Phenotypic Drug Susceptibility Testing Methods and Breakpoints: a Multilaboratory, Multicountry Study.

J Clin Microbiol 2020 03 25;58(4). Epub 2020 Mar 25.

Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.

Drug-resistant tuberculosis persists as a major public health concern. Alongside efficacious treatments, validated and standardized drug susceptibility testing (DST) is required to improve patient care. This multicountry, multilaboratory external quality assessment (EQA) study aimed to validate the sensitivity, specificity, and reproducibility of provisional bedaquiline MIC breakpoints and World Health Organization interim critical concentrations (CCs) for categorizing clinical isolates as susceptible/resistant to the drug. Three methods were used: Middlebrook 7H11 agar proportion (AP) assay, broth microdilution (BMD) assay, and mycobacterial growth indicator tube (MGIT) assay. Each of the five laboratories tested the 40-isolate (20 unique isolates, duplicated) EQA panel at three time points. The study validated the sensitivity and specificity of a bedaquiline MIC susceptibility breakpoint of 0.12 μg/ml for the BMD method and WHO interim CCs of 1 μg/ml for MGIT and 0.25 μg/ml for the 7H11 AP methods. Categorical agreements between observed and expected results and sensitivities/specificities for correctly identifying an isolate as susceptible/resistant were highest at the 0.25, 0.12, and 1 μg/ml bedaquiline concentrations for the AP method, BMD (frozen or dry plates), and MGIT960, respectively. At these concentrations, the very major error rates for erroneously categorizing an isolate as susceptible when it was resistant were the lowest and within CLSI guidelines. The most highly reproducible bedaquiline DST methods were MGIT960 and BMD using dry plates. These findings validate the use of standardized DST methodologies and interpretative criteria to facilitate routine phenotypic bedaquiline DST and to monitor the emergence of bedaquiline resistance.
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http://dx.doi.org/10.1128/JCM.01677-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098739PMC
March 2020

Study of Stepwise Acquisition of and Mutations Conferring Bedaquiline Resistance.

Antimicrob Agents Chemother 2019 08 25;63(8). Epub 2019 Jul 25.

Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa

Bedaquiline resistance within may arise through efflux-based () or target-based () pathway mutations. mutant populations from each of five sequential steps in a passaging approach, using a pyrazinamide-resistant ATCC strain, were subjected to MIC determinations and whole-genome sequencing. Exposure to increasing bedaquiline concentrations resulted in increasing phenotypic resistance (up to >2 μg/ml) through MIC determination on solid medium (Middlebrook 7H10). mutations were dynamic, while mutations were fixed, once occurring. We present the following hypothesis for emergence of bedaquiline resistance: mutations may be the first transient step in low-level resistance acquisition, followed by high-level resistance due to fixed mutations.
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http://dx.doi.org/10.1128/AAC.00292-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658778PMC
August 2019

Whole genome sequencing for drug resistance determination in .

Afr J Lab Med 2019 21;8(1):801. Epub 2019 Feb 21.

Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

South Africa remains challenged with a high tuberculosis burden accompanied by an increase in drug resistant cases. We assessed the use of the Illumina MiSeq, a next-generation sequencing platform for whole genome sequencing, followed by bioinformatic analysis using a commercial software package to determine resistance to selected drugs used for treatment in our setting. Whole genome sequencing shows potential as a diagnostic platform for the detection of drug resistance in with the provision of information for several drugs simultaneously.
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http://dx.doi.org/10.4102/ajlm.v8i1.801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407317PMC
February 2019

Clofazimine Exposure Selects Efflux Pump Mutants and Bedaquiline Resistance.

Antimicrob Agents Chemother 2019 03 26;63(3). Epub 2019 Feb 26.

Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

Six clofazimine-resistant spontaneous mutants obtained from a wild-type or pyrazinamide-resistant ATCC reference strain were selected to evaluate bedaquiline cross-resistance. The reverse was conducted for bedaquiline mutants. All clofazimine mutants harboring an mutation displayed phenotypic cross-resistance. We observed the same for bedaquiline mutants; however, bedaquiline mutants showed no phenotypic cross-resistance. This confirms that upfront clofazimine usage may impact subsequent bedaquiline use due to a shared efflux resistance pathway.
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http://dx.doi.org/10.1128/AAC.02141-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395909PMC
March 2019

Drug resistant tuberculosis in Africa: Current status, gaps and opportunities.

Afr J Lab Med 2018 6;7(2):781. Epub 2018 Dec 6.

Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia.

Background: The World Health Organization End TB Strategy targets for 2035 are ambitious and drug resistant tuberculosis is an important barrier, particularly in Africa, home to over a billion people.

Objective: We sought to review the current status of drug resistant tuberculosis in Africa and highlight key areas requiring improvement.

Methods: Available data from 2016 World Health Organization global tuberculosis database were extracted and analysed using descriptive statistics.

Results: The true burden of drug resistant tuberculosis on the continent is poorly described with only 51% of countries having a formal survey completed. In the absence of this data, modelled estimates were used and reported 92 629 drug resistant tuberculosis cases with 42% of these occurring in just two countries: Nigeria and South Africa. Of the cases estimated, the majority of patients (70%) were not notified, representing 'missed cases'. Mortality among patients with multi-drug resistant tuberculosis was 21%, and was 43% among those with extensively drug resistant tuberculosis. Policies on the adoption of new diagnostic tools was poor and implementation was lacking. A rifampicin result was available for less than 10% of tuberculosis cases in 23 of 47 countries. Second-line drug resistance testing was available in only 60% of countries. The introduction of the short multi-drug resistant tuberculosis regimen was a welcome development, with 40% of countries having implemented it in 2016. Bedaquiline has also been introduced in several countries.

Conclusion: Drug resistant tuberculosis is largely missed in Africa and this threatens prospects to achieve the 2035 targets. Urgent efforts are required to confirm the true burden of drug resistant tuberculosis in Africa. Adoption of new tools and drugs is essential if the 2035 targets are to be met.
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http://dx.doi.org/10.4102/ajlm.v7i2.781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295755PMC
December 2018

Diagnostic strategies for childhood tuberculosis in the context of primary care in a high burden setting: the value of alternative sampling methods.

Paediatr Int Child Health 2019 05 31;39(2):88-94. Epub 2018 Oct 31.

d Department of Epidemiology and Social Medicine , University of Antwerp , Antwerp , Belgium.

: Hospital studies have demonstrated the usefulness of alternative sampling strategies to expectorated sputum and new diagnostics for the diagnosis of childhood tuberculosis (TB) but there is limited evidence of how these approaches work in the primary-care setting. : To assess the feasibility and yield of a variety of sample types and diagnostic tests for childhood TB at a primary-care clinic. : A prospective cohort of children (<10 years) with signs and symptoms of TB was enrolled at a primary-care clinic in Johannesburg, South Africa. Tuberculin skin testing (TST) and chest X-ray (CXR) were performed in all. In those unable to expectorate, one induced sputum (IS), one ambulatory gastric aspirate (GA) and two nasopharyngeal aspirates (NPA) were collected. Stool was collected from all. Samples were processed for smear microscopy, liquid culture and Xpert MTB/RIF. The Determine TB LAM Ag (LAM) test was used for HIV-positive children. : From July 2013-December 2014, 119 children were enrolled, 21 (18%) of whom were HIV-positive. TST was positive in 25/105 (24%) and 70/116 (70%) had a positive CXR. Four (3%) had confirmed TB, 101 (85%) unconfirmed TB and 15 (13%) unlikely TB. Of the 469 samples collected, smear microscopy was positive in none, Xpert was positive in four (<1%) and culture was positive in two (<1%). Three of 11 (27%) HIV-positive patients were positive by LAM. Treatment was commenced in 48/119 (40%). : At primary-care, alternative sampling strategies proved feasible but resulted in a low diagnostic yield. Extensive efforts to bacteriologically diagnose children did not contribute to clinical management.
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http://dx.doi.org/10.1080/20469047.2018.1533321DOI Listing
May 2019

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

N Engl J Med 2018 10 26;379(15):1403-1415. Epub 2018 Sep 26.

Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.

Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.

Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.

Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).
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http://dx.doi.org/10.1056/NEJMoa1800474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121966PMC
October 2018

Prevalence of drug-resistant tuberculosis in South Africa - Authors' reply.

Lancet Infect Dis 2018 08;18(8):836-837

Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Johannesburg, South Africa; Department of Science, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

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http://dx.doi.org/10.1016/S1473-3099(18)30422-5DOI Listing
August 2018

Prevalence of drug-resistant tuberculosis and imputed burden in South Africa: a national and sub-national cross-sectional survey.

Lancet Infect Dis 2018 07 21;18(7):779-787. Epub 2018 Apr 21.

National Institute for Communicable Diseases, Johannesburg, South Africa; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa; Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.

Background: Globally, per-capita, South Africa reports a disproportionately high number of cases of multidrug-resistant (MDR) tuberculosis and extensively drug-resistant (XDR) tuberculosis. We sought to estimate the prevalence of resistance to tuberculosis drugs in newly diagnosed and retreated patients with tuberculosis provincially and nationally, and compared these with the 2001-02 estimates.

Methods: A cross-sectional survey was done between June 15, 2012-June 14, 2014, using population proportionate randomised cluster sampling in the nine provinces in South Africa. 343 clusters were included, ranging between 31 and 48 per province. A patient was eligible for inclusion in the survey if he or she presented as a presumptive case during the intake period at a drug resistance survey enrolling facility. Consenting participants (≥18 years old) completed a questionnaire and had a sputum sample tested for resistance to first-line and second-line drugs. Analysis was by logistic regression with robust SEs, inverse probability weighted against routine data, and estimates were derived using a random effects model.

Findings: 101 422 participants were tested in 2012-14. Nationally, the prevalence of MDR tuberculosis was 2·1% (95% CI 1·5-2·7) among new tuberculosis cases and 4·6% (3·2-6·0) among retreatment cases. The provincial point prevalence of MDR tuberculosis ranged between 1·6% (95% CI 0·9-2·9) and 5·1% (3·7-7·0). Overall, the prevalence of rifampicin-resistant tuberculosis (4·6%, 95% CI 3·5-5·7) was higher than the prevalence of MDR tuberculosis (2·8%, 2·0-3·6; p=0·01). Comparing the current survey with the previous (2001-02) survey, the overall MDR tuberculosis prevalence was 2·8% versus 2·9% and prevalance of rifampicin-resistant tuberculosis was 3·4% versus 1·8%, respectively. The prevalence of isoniazid mono-resistant tuberculosis was above 5% in all provinces. The prevalence of ethionamide and pyrazinamide resistance among MDR tuberculosis cases was 44·7% (95% CI 25·9-63·6) and 59·1% (49·0-69·1), respectively. The prevalence of XDR tuberculosis was 4·9% (95% CI 1·0-8·8). Nationally, the estimated numbers of cases of rifampicin-resistant tuberculosis, MDR tuberculosis, and isoniazid mono-resistant tuberculosis for 2014 were 13 551, 8249, and 17 970, respectively.

Interpretation: The overall prevalence of MDR tuberculosis in South Africa in 2012-14 was similar to that in 2001-02; however, prevalence of rifampicin-resistant tuberculosis almost doubled among new cases. Furthermore, the high prevalence of isoniazid mono-resistant tuberculosis, not routinely screened for, and resistance to second-line drugs has implications for empirical management.

Funding: President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention under the terms of 1U19GH000571.
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http://dx.doi.org/10.1016/S1473-3099(18)30222-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800151PMC
July 2018

Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study.

Lancet Infect Dis 2018 06 21;18(6):675-683. Epub 2018 Mar 21.

Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany.

Background: In many countries, regular monitoring of the emergence of resistance to anti-tuberculosis drugs is hampered by the limitations of phenotypic testing for drug susceptibility. We therefore evaluated the use of genetic sequencing for surveillance of drug resistance in tuberculosis.

Methods: Population-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing.

Findings: Isolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87-94) for rpoB (rifampicin resistance), 86% (74-93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39-68) for pncA (pyrazinamide resistance), 85% (77-91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81-92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing.

Interpretation: Genetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation.

Funding: Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.
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http://dx.doi.org/10.1016/S1473-3099(18)30073-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5968368PMC
June 2018

Whole-Genome Sequence of a Isolate from a Pediatric Patient in South Africa.

Genome Announc 2018 Jan 18;6(3). Epub 2018 Jan 18.

Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa

We describe here the draft genome sequence of a isolate from a pediatric patient in Western Cape, South Africa. To our knowledge, this is the second reported genome of this rapidly growing nontuberculous mycobacterial species.
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http://dx.doi.org/10.1128/genomeA.01478-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773733PMC
January 2018

Defining Bedaquiline Susceptibility, Resistance, Cross-Resistance and Associated Genetic Determinants: A Retrospective Cohort Study.

EBioMedicine 2018 Feb 9;28:136-142. Epub 2018 Jan 9.

National Department of Health, Tuberculosis Control and Management Cluster, Pretoria, South Africa.

Background: Bedaquiline (BDQ) is a novel agent approved for use in combination treatment of multi-drug resistant tuberculosis (MDR-TB). We sought to determine BDQ epidemiological cut-off values (ECVs), define and assess interpretive criteria against putative resistance associated variants (RAVs), microbiological outcomes and cross resistance with clofazimine (CFZ).

Methods: A retrospective cohort study was conducted. Minimal inhibitory concentrations (MIC) to BDQ were determined using 7H9 broth microdilution (BMD) and MGIT960. RAVs were genetically characterised using whole genome sequencing. BDQ ECVs were determined using ECOFFinder and compared with 6-month culture conversion status and CFZ MICs.

Findings: A total of 391 isolates were analysed. Susceptible and intermediate categories were determined to have MICs of ≤0.125μg/ml and 0.25μg/ml using BMD and ≤1μg/ml and 2μg/ml using MGIT960 respectively. Microbiological failures occurred among BDQ exposed patients with a non-susceptible BDQ MIC, an Rv0678 mutation and ≤2 active drug classes. The Rv0678 RAVs were not the dominant mechanism of CFZ resistance and cross resistance was limited to isolates with an Rv0678 mutation.

Interpretation: Criteria for BDQ susceptibility are defined and will facilitate improved early detection of resistance. Cross- resistance between BDQ and CFZ is an emerging concern but in this study was primarily among those with an Rv0678 mutation.
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http://dx.doi.org/10.1016/j.ebiom.2018.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5835552PMC
February 2018

Draft Genome Sequence of Isolated from an HIV-Positive Patient in South Africa.

Genome Announc 2017 Aug 3;5(31). Epub 2017 Aug 3.

Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

Here, we report a draft genome sequence of obtained from a sputum sample of a South African HIV-infected patient with suspected pulmonary tuberculosis. The genome described here comprises 6,931,852 bp, revealing 66.2% G+C content, 6,808 coding sequences, and 81 RNA genes.
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http://dx.doi.org/10.1128/genomeA.00759-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543650PMC
August 2017

Some Synonymous and Nonsynonymous Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR Assays.

Antimicrob Agents Chemother 2017 04 24;61(4). Epub 2017 Mar 24.

Department of Medicine, University of Cambridge, Cambridge, United Kingdom

In this study, using the Hain GenoType MTBDR assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in in result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
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http://dx.doi.org/10.1128/AAC.02169-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5365657PMC
April 2017

Transmission of Extensively Drug-Resistant Tuberculosis in South Africa.

N Engl J Med 2017 01;376(3):243-253

From the Emory University Rollins School of Public Health and School of Medicine (N.S.S., S.C.A., S.A., A.C., N.R.G.) and the Centers for Disease Control and Prevention (N.S.S.) - both in Atlanta; Albert Einstein College of Medicine and Montefiore Medical Center (N.S.S., J.C.M.B., N.R.G.), Columbia University Mailman School of Public Health (B.M., T.S.B.), and the American Museum of Natural History (A.N.) - all in New York; the National Institute for Communicable Diseases, Johannesburg (N.I., H.M., S.V.O.), University of KwaZulu-Natal and National Health Laboratory Service, Durban (P. Moodley, K.M., T.M., P. Mpangase), and the South African Medical Research Council, Cape Town (N.M., T.K.) - all in South Africa; and the Public Health Research Institute, New Jersey Medical School-Rutgers University, Newark (E.S., B.K.).

Background: Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions.

Methods: We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014. Interviews and medical-record reviews were used to elicit information on the participants' history of tuberculosis and HIV infection, hospitalizations, and social networks. Mycobacterium tuberculosis isolates underwent insertion sequence (IS)6110 restriction-fragment-length polymorphism analysis, targeted gene sequencing, and whole-genome sequencing. We used clinical and genotypic case definitions to calculate the proportion of cases of XDR tuberculosis that were due to inadequate treatment of multidrug-resistant (MDR) tuberculosis (i.e., acquired resistance) versus those that were due to transmission (i.e., transmitted resistance). We used social-network analysis to identify community and hospital locations of transmission.

Results: Of the 404 participants, 311 (77%) had HIV infection; the median CD4+ count was 340 cells per cubic millimeter (interquartile range, 117 to 431). A total of 280 participants (69%) had never received treatment for MDR tuberculosis. Genotypic analysis in 386 participants revealed that 323 (84%) belonged to 1 of 31 clusters. Clusters ranged from 2 to 14 participants, except for 1 large cluster of 212 participants (55%) with a LAM4/KZN strain. Person-to-person or hospital-based epidemiologic links were identified in 123 of 404 participants (30%).

Conclusions: The majority of cases of XDR tuberculosis in KwaZulu-Natal, South Africa, an area with a high tuberculosis burden, were probably due to transmission rather than to inadequate treatment of MDR tuberculosis. These data suggest that control of the epidemic of drug-resistant tuberculosis requires an increased focus on interrupting transmission. (Funded by the National Institute of Allergy and Infectious Diseases and others.).
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http://dx.doi.org/10.1056/NEJMoa1604544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330208PMC
January 2017

Correlation of Mutations with Minimal Inhibitory Concentration of Rifampin and Rifabutin in in an HIV/AIDS Endemic Setting, South Africa.

Front Microbiol 2016 5;7:1947. Epub 2016 Dec 5.

Centre for Tuberculosis, National Institute for Communicable DiseasesSandringham, South Africa; Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoria, South Africa.

Treatment of tuberculosis (TB) and HIV co-infections is often complicated by drug-to-drug interactions between anti-mycobacterial and anti-retroviral agents. Rifabutin (RFB) is an alternative to rifampin (RIF) for TB regimens and is recommended for HIV patients concurrently receiving protease inhibitors because of reduced induction of CYP3A4. This study sought to determine the proportion of RFB susceptible isolates among RIF-resistant strains in a high HIV prevalence setting in South Africa. In addition, the study explored the association between mutations and minimum inhibitory concentrations (MIC) of RIF and RFB. A total of 189 multidrug resistant (MDR) isolates from the Centre for Tuberculosis repository were analyzed. The MICs were determined using a MYCOTB Sensititre plate method and the gene was sequenced. Of the 189 MDR isolates, 138 (73%) showed resistance to both RIF and RFB, while 51 (27%) isolates were resistant to RIF but retained susceptibility to RFB. The S531L was the most frequent point mutation in 105/189 (56%) isolates, followed by H526Y in 27/189 (14%) isolates. Resistance to both RIF and RFB was found predominantly in association with mutations S531L (91/105, 87%), H526Y (20/27, 74%), and H526D (15/19, 79%), while D516V (15/17, 88%), and L533P (3/4, 75%) were found in RIF-resistant, RFB-susceptible isolates. This study has shown that up to 27% of MDR-TB patients in South Africa may benefit from a treatment regimen that includes RFB.
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http://dx.doi.org/10.3389/fmicb.2016.01947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5136537PMC
December 2016

Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.

J Clin Microbiol 2016 10 3;54(10):2547-52. Epub 2016 Aug 3.

Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa.

The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035400PMC
http://dx.doi.org/10.1128/JCM.00408-16DOI Listing
October 2016

Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project.

Lancet Infect Dis 2016 10 7;16(10):1185-1192. Epub 2016 Jul 7.

Bureau for Global Health, US Agency for International Development, Washington, DC, USA.

Background: Pyrazinamide and fluoroquinolones are essential antituberculosis drugs in new rifampicin-sparing regimens. However, little information about the extent of resistance to these drugs at the population level is available.

Methods: In a molecular epidemiology analysis, we used population-based surveys from Azerbaijan, Bangladesh, Belarus, Pakistan, and South Africa to investigate resistance to pyrazinamide and fluoroquinolones among patients with tuberculosis. Resistance to pyrazinamide was assessed by gene sequencing with the detection of resistance-conferring mutations in the pncA gene, and susceptibility testing to fluoroquinolones was conducted using the MGIT system.

Findings: Pyrazinamide resistance was assessed in 4972 patients. Levels of resistance varied substantially in the surveyed settings (3·0-42·1%). In all settings, pyrazinamide resistance was significantly associated with rifampicin resistance. Among 5015 patients who underwent susceptibility testing to fluoroquinolones, proportions of resistance ranged from 1·0-16·6% for ofloxacin, to 0·5-12·4% for levofloxacin, and 0·9-14·6% for moxifloxacin when tested at 0·5 μg/mL. High levels of ofloxacin resistance were detected in Pakistan. Resistance to moxifloxacin and gatifloxacin when tested at 2 μg/mL was low in all countries.

Interpretation: Although pyrazinamide resistance was significantly associated with rifampicin resistance, this drug may still be effective in 19-63% of patients with rifampicin-resistant tuberculosis. Even though the high level of resistance to ofloxacin found in Pakistan is worrisome because it might be the expression of extensive and unregulated use of fluoroquinolones in some parts of Asia, the negligible levels of resistance to fourth-generation fluoroquinolones documented in all survey sites is an encouraging finding. Rational use of this class of antibiotics should therefore be ensured to preserve its effectiveness.

Funding: Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.
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http://dx.doi.org/10.1016/S1473-3099(16)30190-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030278PMC
October 2016

Field evaluation of a novel preservation medium to transport sputum specimens for molecular detection of Mycobacterium tuberculosis in a rural African setting.

Trop Med Int Health 2016 06 16;21(6):776-82. Epub 2016 May 16.

Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.

Objectives: To assess the performance of an innovative method of transporting sputum to centralised facilities for molecular detection of Mycobacterium tuberculosis: using a swab to inoculate sputum in a transport medium, PrimeStore(®) Molecular Transport Medium (PS-MTM).

Methods: Two sputum specimens were obtained from suspected patients with tuberculosis (TB) at rural healthcare facilities in South Africa. A swab was taken from each specimen and placed into PS-MTM, prior to it being processed by either liquid culture or Xpert MTB/RIF assay (Xpert).

Results: A total of 141 patients (including 47 with laboratory-confirmed TB) were included in this analysis. M. tuberculosis was detected at 29% by culture and 29% by Xpert, whereas 31% tested positive by IS6110 real-time PCR of PS-MTM from the culture and 36% from the Xpert-paired specimen. Concordance between the method under evaluation with culture was 82% (McNemar, P = 0.55) and 84% (McNemar, P = 0.05) for Xpert. Stratified by culture result, the detection rate by IS6110 real-time PCR of PS-MTM was similar to Xpert for patients with positive culture (P = 0.32), but significantly higher if culture was negative (P = 0.008).

Conclusions: These results suggest that swab collection of sputum into PS-MTM for transport is a promising method for diagnosis of TB in rural healthcare settings, thereby potentially improving the options available for molecular diagnosis of TB in countries incapable of applying decentralised high-tech molecular testing.
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http://dx.doi.org/10.1111/tmi.12701DOI Listing
June 2016

A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings.

PLoS One 2016 11;11(1):e0146106. Epub 2016 Jan 11.

Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa.

Background: In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR.

Methods: A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods.

Results: Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases.

Conclusion: We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146106PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713439PMC
July 2016

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

Nat Commun 2015 Dec 21;6:10063. Epub 2015 Dec 21.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package ('Mykrobe predictor') that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.
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http://dx.doi.org/10.1038/ncomms10063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703848PMC
December 2015

Laboratory evaluation of a specimen transport medium for downstream molecular processing of sputum samples to detect Mycobacterium tuberculosis.

J Microbiol Methods 2015 Oct 14;117:57-63. Epub 2015 Jul 14.

Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.

Background: Modern molecular-based approaches for the detection of Mycobacterium tuberculosis in sputum samples promise quicker and more accurate detection of cases. However, processing sputum samples at central diagnostic facilities provides a diagnostic approach, but requires a safe and efficient system that is not affected by transport delays and ambient temperature to be feasible. We evaluated the technical properties of PrimeStore®-Molecular Transport Medium (PS-MTM) for its ability to inactivate mycobacteria, ensuring stability of DNA over time at ambient temperatures and to assess the compatibility of the transport medium with DNA extraction systems.

Methods: Assessment of the transport medium for application of sputum samples processed for the detection of M. tuberculosis included the inactivation of M. tuberculosis in spiked sputum samples, compatibility of the medium with three commercial nucleic extraction systems and stability of DNA in the medium at ambient temperature over 28 days. We further performed a clinical laboratory evaluation on 256 sputum specimens sent for tuberculosis investigation.

Results: Complete inactivation of M. tuberculosis occurred within 30 min of exposure at a ratio of 1:3 for sputum to PS-MTM. Sputum specimen in PS-MTM showed very good compatibility with automated bead-based extraction systems, producing high DNA output (estimated lower limits of detection: ~170 CFU/ml). Furthermore, PS-MTM samples remained stable over 28 days at ambient temperature displaying no significant change over time in Ct-values (<5% on a mean starting value of 22.47). Of the 256 clinical sputum specimens, 10.2% were culture positive and 11.0% were positive by real-time PCR of PS-MTM samples.

Conclusions: Collecting and transporting sputum from TB suspects in PS-MTM offer safe transport at ambient temperature, DNA stability for extended periods without cooling and specimens directly suitable for molecular testing. This novel approach may support introduction and further scale-up of molecular diagnostics for TB in resource-limited settings.
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http://dx.doi.org/10.1016/j.mimet.2015.07.010DOI Listing
October 2015

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

Lancet Infect Dis 2015 Oct 23;15(10):1193-1202. Epub 2015 Jun 23.

Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.

Background: Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis.

Methods: Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identified from the drug-resistance scientific literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance.

Findings: We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7-93·7) and 98·4% specificity (98·1-98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identified among mutations under selection pressure in non-candidate genes.

Interpretation: A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workflows, phasing out phenotypic drug-susceptibility testing while reporting drug resistance early.

Funding: Wellcome Trust, National Institute of Health Research, Medical Research Council, and the European Union.
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http://dx.doi.org/10.1016/S1473-3099(15)00062-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579482PMC
October 2015

Performance of a Novel Algorithm Using Automated Digital Microscopy for Diagnosing Tuberculosis.

Am J Respir Crit Care Med 2015 Jun;191(12):1443-9

3 London School of Hygiene and Tropical Medicine, London, United Kingdom.

Rationale: TBDx automated microscopy is a novel technology that processes digital microscopic images to identify acid-fast bacilli (AFB). Use of TBDx as part of a diagnostic algorithm could improve the diagnosis of tuberculosis (TB), but its performance characteristics have not yet been formally tested.

Objectives: To evaluate the performance of the TBDx automated microscopy system in algorithms for diagnosis of TB.

Methods: Prospective samples from patients with presumed TB were processed in parallel with conventional smear microscopy, TBDx microscopy, and liquid culture. All TBDx-positive specimens were also tested with the Xpert MTB/RIF (GXP) assay. We evaluated the sensitivity and specificity of two algorithms-(1) TBDx-GXP (TBDx with positive specimens tested by Xpert MTB/RIF) and (2) TBDx alone-against the gold standard liquid media culture.

Measurements And Main Results: Of 1,210 samples, 1,009 were eligible for evaluation, of which 109 were culture positive for Mycobacterium tuberculosis. The TBDx system identified 70 specimens (68 culture positive) as having 10 or more putative AFB (high positive) and 207 (19 culture positive) as having 1-9 putative AFB (low positive). An algorithm in which "low-positive" results on TBDx were confirmed by GXP had 78% sensitivity (85 of 109) and 99.8% specificity (889 of 900), requiring 21% (207 of 1,009) specimens to be processed by GXP. As a stand-alone test, a "high-positive" result on TBDx had 62% sensitivity and 99.7% specificity.

Conclusions: TBDx used in diagnostic algorithms with GXP provided reasonable sensitivity and high specificity for active TB while dramatically reducing the number GXP tests performed. As a stand-alone microscopy system, its performance was equivalent to that of a highly experienced TB microscopist.
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http://dx.doi.org/10.1164/rccm.201502-0390OCDOI Listing
June 2015