Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning

BACKGROUND

Global tuberculosis (TB) drug resistance (DR) surveillance focuses on rifampicin. We examined the potential of public and surveillance Mycobacterium tuberculosis (Mtb) whole-genome sequencing (WGS) data, to generate expanded country-level resistance prevalence estimates (antibiograms) using in silico resistance prediction.

METHODS

We curated and quality-controlled Mtb WGS data. We used a validated random forest model to predict phenotypic resistance to 12 drugs and bias-corrected for model performance, outbreak sampling and rifampicin resistance oversampling. Validation leveraged a national DR survey conducted in South Africa.

RESULTS

Mtb isolates from 29 countries (n=19 149) met sequence quality criteria. Global marginal genotypic resistance among mono-resistant TB estimates overlapped with the South African DR survey, except for isoniazid, ethionamide and second-line injectables, which were underestimated (n=3134). Among multidrug resistant (MDR) TB (n=268), estimates overlapped for the fluoroquinolones but overestimated other drugs. Globally pooled mono-resistance to isoniazid was 10.9% (95% CI: 10.2-11.7%, n=14 012). Mono-levofloxacin resistance rates were highest in South Asia (Pakistan 3.4% (0.1-11%), n=111 and India 2.8% (0.08-9.4%), n=114). Given the recent interest in drugs enhancing ethionamide activity and their expected activity against isolates with resistance discordance between isoniazid and ethionamide, we measured this rate and found it to be high at 74.4% (IQR: 64.5-79.7%) of isoniazid-resistant isolates predicted to be ethionamide susceptible. The global susceptibility rate to pyrazinamide and levofloxacin among MDR was 15.1% (95% CI: 10.2-19.9%, n=3964).

CONCLUSIONS

This is the first attempt at global Mtb antibiogram estimation. DR prevalence in Mtb can be reliably estimated using public WGS and phenotypic resistance prediction for key antibiotics, but public WGS data demonstrates oversampling of isolates with higher resistance levels than MDR. Nevertheless, our results raise concerns about the empiric use of short-course fluoroquinolone regimens for drug-susceptible TB in South Asia and indicate underutilisation of ethionamide in MDR treatment.

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.

1653. Estimation of country-specific tuberculosis antibiograms using a wide and deep neural net on a large genomic dataset

Background

Improved estimates of drug resistant tuberculosis (TB) burden are needed to aid control efforts. The World Health Organization (WHO) currently reports estimates for rifampin resistance (RR) or multidrug resistance (MDR) at the national level. Resistance rates to other first-line and second-line agents, e.g. ethambutol, pyrazinamide, and aminoglycosides, are rarely available, even at the country level. Our objective was to generate country and drug specific resistance prevalence estimates (antibiograms) using in silico phenotype prediction and curated public and surveillance Mycobacterium tuberculosis (MTB) genomic data.

Methods

We curated MTB genomes either by sequencing or from published literature and excluded genomes that did not meet our quality criteria (i.e. at least 10X depth in >95% of the genome). A machine learning model previously trained to predict phenotypic resistance in MTB with high accuracy, a wide and deep neural net (WDNN), was used to predict resistance to ten drugs. We corrected for resistance oversampling in genomic data by conditioning on RR and using country specific surveillance MDR/RR rates reported by the WHO.

Results

Of the 49,851 MTB genomes curated, 33,873 isolates met quality criteria. Of these, geographic data was available for 22,838 genomes. Antibiograms were generated for nine first- and second-line drugs for 36 countries. Among countries with at least 100 isolates, a high rate of resistance to fluoroquinolones and second line injectables was seen among isolates from the Republic of Moldova (15.4% [CI = 13.7-16.7%] moxifloxacin resistant, 6.3% [CI = 5.5-6.8%] kanamycin resistant, n = 330) and Russian Federation (9.3% [CI = 9.1-9.4] moxifloxacin resistant, 5.4% [CI = 5.3-5.5%] kanamycin resistant, n = 1011) (Figure 1).

Figure 1: Antibiograms created using genotypic data for isolates from Republic of Moldova (n=330, rifampin-resistance rate correction: 29%, range 26-31% among new tuberculosis cases);and Russian Federation (n=1011, rifampin-resistance rate correction 35%, range 34-35%, among new tuberculosis cases. rif: rifampin, inh: isoniazid, pza: pyrazinamide, emb: ethambutol, str: streptomycin, cap: capreomycin, amk: amikacin, kan: kanamycin, moxi: moxifloxacin

Conclusion

The estimation of antibiotic resistance prevalence in MTB for pyrazinamide, ethambutol and second-line agents can be aided by the use of in silico models of drug resistance. A high rate of resistance to second-line drugs precludes large scale roll out of short-course WHO regimens for treatment of MDR-TB for empiric use in certain countries. The use of whole genome sequencing for resistance surveillance can inform policy on optimal national regimen choice for TB treatment.

Disclosures

All Authors: No reported disclosures

Slow radiological improvement and persistent low-grade inflammation after chemotherapy in tuberculosis patients with type 2 diabetes

Background

Diabetes mellitus type 2 (DM) may impede immune responses in tuberculosis (TB) and thus contribute to enhanced disease severity. In this study, we aimed to evaluate DM-mediated alterations in clinical, radiological and immunological outcomes in TB disease.

Methods

Newly diagnosed pulmonary TB patients with or without DM (TB n = 40; TB-DM n = 40) were recruited in Dhaka, Bangladesh. Clinical symptoms, sputum smear and culture conversion as well as chest radiography were assessed. Peripheral blood and sputum samples were collected at the time of diagnosis (baseline) and after 1, 2 and 6 months of standard anti-TB treatment. Blood samples were also obtained from healthy controls (n = 20). mRNA expression of inflammatory markers in blood and sputum samples were quantified using real-time PCR.

Results

The majority of TB-DM patients had poor glycemic control (HbA1c > 8%) and displayed elevated pulmonary pathology (P = 0.039) particularly in the middle (P < 0.004) and lower lung zones (P < 0.02) throughout the treatment period. However, reduction of clinical symptoms and time to sputum smear and culture conversion did not differ between the groups. Transcripts levels of the pro-inflammatory cytokines IL-1β (P = 0.003 at month-1 and P = 0.045 at month-2) and TNF-α (P = 0.005 at month-1) and the anti-inflammatory cytokine IL-10 (P = 0.005 at month-2) were higher in peripheral blood after anti-TB treatment in TB-DM compared to TB patients. Conversely in sputum, TB-DM patients had reduced CD4 (P < 0.009 at month-1) and IL-10 (P = 0.005 at month-1 and P = 0.006 at month-2) transcripts, whereas CD8 was elevated (P = 0.016 at month-2). At 1- and 2-month post-treatment, sputum IL-10 transcripts were inversely correlated with fasting blood glucose and HbA1c levels in all patients.

Conclusion

Insufficient up-regulation of IL-10 in the lung may fuel persistent local inflammation thereby promoting lung pathology in TB-DM patients with poorly controlled DM.

Circulating strains of Mycobacterium tuberculosis: 24 loci MIRU-VNTR analysis in Bangladesh

Bangladesh is among the high burden countries for tuberculosis (TB) and multidrug resistant TB (MDR-TB). As the genetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis are responsible for regional differences in drug resistance, this cross sectional study was conducted to identify the circulating M. tuberculosis strains belonging to different lineages among pulmonary tuberculosis and, to investigate the contribution of distinct M. tuberculosis lineages to rifampicin resistant (RR) and rifampicin sensitive (RS) TB. A total of 40 RR and 20 RS isolates were enrolled in this study, all of which confirmed as M. tuberculosis by MPT 64 antigen detection. Furthermore, all isolates were genotyped by 24 loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR), thus comprising the first study to employ this approach in Bangladesh. Beijing was the predominant lineage (26.8%) followed by EAI (23.2%), Delhi/CAS (16.1%), H37Rv (8.9%), Haarlem (7.1%), LAM (5.4%), Cameroon (3.6%) and a NEW-1 (1.8%). Four (7.1%) isolates remained as unidentified. Beijing strains were the significantly predominant (36.8%; p = 0.0135) among the RR isolates in comparison with other strains whereas EAI was the predominant (38.8%) lineage among RS isolates. Also, approximately 13% RR isolates showed genotypic resistance against fluoroquinolones by LPA and, hence, classed as pre-XDR TB albeit no specific lineage was found associated with these latter strains. A low transmission rate (10.5%) and high genetic diversity was detected in this setting with all the clustered strains herein identified belonging to the Beijing lineage. This study highlights 24 loci MIRU-VNTR analysis as a powerful tool for genotyping of Mycobacterium tuberculosis in this setting as it shows a high discriminatory index (0.81).

FAST implementation in Bangladesh: high frequency of unsuspected tuberculosis justifies challenges of scale-up

SETTING

National Institute of Diseases of the Chest and Hospital, Dhaka; Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Dhaka; and Chittagong Chest Disease Hospital, Chittagong, Bangladesh.

OBJECTIVE

To present operational data and discuss the challenges of implementing FAST (Find cases Actively, Separate safely and Treat effectively) as a tuberculosis (TB) transmission control strategy.

DESIGN

FAST was implemented sequentially at three hospitals.

RESULTS

Using Xpert® MTB/RIF, 733/6028 (12.2%, 95%CI 11.4-13.0) patients were diagnosed with unsuspected TB. Patients with a history of TB who were admitted with other lung diseases had more than twice the odds of being diagnosed with unsuspected TB as those with no history of TB (OR 2.6, 95%CI 2.2-3.0, P < 0.001). Unsuspected multidrug-resistant TB (MDR-TB) was diagnosed in 89/1415 patients (6.3%, 95%CI 5.1-7.7). Patients with unsuspected TB had nearly five times the odds of being diagnosed with MDR-TB than those admitted with a known TB diagnosis (OR 4.9, 95%CI 3.1-7.6, P < 0.001). Implementation challenges include staff shortages, diagnostic failure, supply-chain issues and reliance on external funding.

CONCLUSION

FAST implementation revealed a high frequency of unsuspected TB in hospitalized patients in Bangladesh. Patients with a previous history of TB have an increased risk of being diagnosed with unsuspected TB. Ensuring financial resources, stakeholder engagement and laboratory capacity are important for sustainability and scalability.

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

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.

Evaluation of efficiency of nested multiplex allele-specific PCR assay for detection of multidrug resistant tuberculosis directly from sputum samples

For an effective control of tuberculosis, rapid detection of multidrug resistant tuberculosis (MDR-TB) is necessary. Therefore, we developed a modified nested multiplex allele-specific polymerase chain reaction (MAS-PCR) method that enables rapid MDR-TB detection directly from sputum samples. The efficacy of this method was evaluated using 79 sputum samples collected from suspected tuberculosis patients. The performance of nested MAS-PCR method was compared with other MDR-TB detection methods like drug susceptibility testing (DST) and DNA sequencing. As rifampicin (RIF) resistance conforms to MDR-TB in greater than 90% cases, only the presence of RIF-associated mutations in rpoB gene was determined by DNA sequencing and nested MAS-PCR to detect MDR-TB. The concordance between nested MAS-PCR and DNA sequencing results was found to be 96·3%. When compared with DST, the sensitivity and specificity of nested MAS-PCR for RIF-resistance detection were determined to be 92·9 and 100% respectively.

SIGNIFICANCE AND IMPACT OF THE STUDY

For developing- and high-TB burden countries, molecular-based tests have been recommended by the World Health Organization for rapid detection of MDR-TB. The results of this study indicate that, nested MAS-PCR assay might be a practical and relatively cost effective molecular method for rapid detection of MDR-TB from suspected sputum samples in developing countries with resource poor settings.

Anti-tuberculosis drug resistance in Bangladesh: reflections from the first nationwide survey

OBJECTIVE

To determine the prevalence of tuberculosis (TB) drug resistance in Bangladesh.

DESIGN

Weighted cluster sampling among smear-positive cases, and standard culture and drug susceptibility testing on solid medium were used.

RESULTS

Of 1480 patients enrolled during 2011, 12 falsified multidrug-resistant TB (MDR-TB) patients were excluded. Analysis included 1340 cases (90.5% of those enrolled) with valid results and known treatment antecedents. Of 1049 new cases, 12.3% (95%CI 9.3-16.1) had strains resistant to any of the first-line drugs tested, and 1.4% (95%CI 0.7-2.5) were MDR-TB. Among the 291 previously treated cases, this was respectively 43.2% (95%CI 37.1-49.5) and 28.5% (95%CI 23.5-34.1). History of previous anti-tuberculosis treatment was the only predictive factor for first-line drug resistance (OR 34.9). Among the MDR-TB patients, 19.2% (95%CI 11.3-30.5; exclusively previously treated) also showed resistance to ofloxacin. Resistance to kanamycin was not detected.

CONCLUSION

Although MDR-TB prevalence was relatively low, transmission of MDR-TB may be increasing in Bangladesh. MDR-TB with fluoroquinolone resistance is rapidly rising. Integrating the private sector should be made high priority given the excessive proportion of MDR-TB retreatment cases in large cities. TB control programmes and donors should avoid applying undue pressure towards meeting global targets, which can lead to corruption of data even in national surveys.

The Multi-Drug Resistant Tuberculosis Diagnosis and Treatment Cascade in Bangladesh

Objectives

To determine, in areas supported by BRAC, Bangladesh i) the pre-diagnosis and pre-treatment attrition among presumptive and confirmed Multi-Drug Resistant Tuberculosis (MDR-TB) patients and ii) factors associated with attrition.

Methods

This was a retrospective cohort study involving record review. Presumptive MDR-TB patients from peripheral microscopy centres serving 60% of the total population of Bangladesh were included in the study. Attrition and turnaround time for MDR-TB diagnosis by Xpert MTB/RIF and treatment initiation were calculated between July 2012 and June 2014.

Results

Of 836 presumptive MDR-TB patients referred from 398 peripheral microscopy centres, 161 MDR-TB patients were diagnosed. The number of diagnosed MDR-TB patients was less than country estimates of MDR-TB patients (2000 cases) during the study period. Among those referred, pre-diagnosis and pre-treatment attrition was 17% and 21% respectively. Median turnaround time for MDR-TB testing, result receipt and treatment initiation was four, zero and five days respectively. Farmers (RR=2.3, p=0.01) and daily wage laborers (RR=2.1, p=0.04) had twice the risk of having pre-diagnosis attrition. Poor record-keeping and unreliable upkeep of presumptive MDR-TB patient databases were identified as challenges at the peripheral microscopy centres.

Conclusion

There was a low proportion of pre-diagnosis and pre-treatment attrition in patients with presumptive and confirmed MDR-TB under programmatic conditions. However, the recording and reporting system did not detect all presumptive MDR-TB patients, highlighting the need to improve the system in order to prevent morbidity, mortality and transmission of MDR-TB in the community.

Repetitive transcranial magnetic stimulation in neuropathic pain secondary to malignancy: a randomized clinical trial

BACKGROUND

Significant analgesic effects of repetitive transcranial magnetic stimulation (rTMS) have been found in several studies of patients with chronic pain of various origins, but never for malignancy. The objective of this study was to assess the efficacy of 10 sessions of rTMS over the primary motor cortex (M1) in patients suffering from malignant neuropathic pain.

METHODS

Thirty-four patients were randomly allocated into one of two groups to receive real (20 Hz, 10 s, 10 trains with 80% intensity) or sham rTMS daily for 10 consecutive days. Patients were evaluated using a verbal descriptor scale (VDS), a visual analogue scale (VAS), Leeds assessment of neuropathic symptoms and signs (LANSS) and Hamilton rating scale for depression (HAM-D) at baseline, after the first, fifth and 10th treatment sessions, and then 15 days and 1 month after treatment.

RESULTS

There were no significant differences between real and sham groups in the duration of illness or pain rating scores at the baseline. A significant 'Time × Group' interaction was recorded indicating that real and sham rTMS had different effects on the VDS, VAS, LANSS and HAM-D scales. Post-hoc testing showed that the group of patients treated with real rTMS had greater improvement in all scales that persisted up to 15 days, but were not present 1 month later. Significant positive correlations between the percentage of pain reduction and HAM-D after the 10th session and 15 days later were recorded.

CONCLUSION

The results demonstrate that 10 rTMS sessions over the M1 can induce short-term pain relief in malignant neuropathic pain.

Molecular approaches for detection of the multi-drug resistant tuberculosis (MDR-TB) in Bangladesh

The principal obstacles in the treatment of tuberculosis (TB) are delayed and inaccurate diagnosis which often leads to the onset of the drug resistant TB cases. To avail the appropriate treatment of the patients and to hinder the transmission of drug-resistant TB, accurate and rapid detection of resistant isolates is critical. Present study was designed to demonstrate the efficacy of molecular techniques inclusive of line probe assay (LPA) and GeneXpert MTB/RIF methods for the detection of multi-drug resistant (MDR) TB. Sputum samples from 300 different categories of treated and new TB cases were tested for the detection of possible mutation in the resistance specific genes (rpoB, inhA and katG) through Genotype MTBDRplus assay or LPA and GeneXpert MTB/RIF tests. Culture based conventional drug susceptibility test (DST) was also carried out to measure the efficacy of the molecular methods employed. Among 300 samples, 191 (63.7%) and 193 (64.3%) cases were found to be resistant against rifampicin in LPA and GeneXpert methods, respectively; while 189 (63%) cases of rifampicin resistance were detected by conventional DST methods. On the other hand, 196 (65.3%) and 191 (63.7%) isolates showed isoniazid resistance as detected by LPA and conventional drug susceptibility test (DST), respectively. Among the drug resistant isolates (collectively 198 in LPA and 193 in conventional DST), 189 (95.6%) and 187 (96.9%) were considered to be MDR as examined by LPA and conventional DST, respectively. Category-II and -IV patients encountered higher frequency of drug resistance compared to those from category-I and new cases. Considering the higher sensitivity, specificity and accuracy along with the required time to results significantly shorter, our study supports the adoption of LPA and GeneXpert assay as efficient tools in detecting drug resistant TB in Bangladesh.

Slide drug susceptibility test for the detection of multidrug-resistant tuberculosis in Bangladesh

The present study attempted to comparatively assess and establish a suitable detection method of multidrug-resistant tuberculosis (MDR-TB) from previously treated TB cases in Bangladesh. Of 130 Zeihl-Neelsen smear-positive fresh sputum specimens, 112 samples were found to contain viable bacilli as visualized under the light-emitting diode fluorescence microscope after fluorescein di-acetate staining, and 109 positive cases were detected through Löwenstein-Jensen culture. The samples were further tested to survey the drug resistance both by slide drug susceptibility test (DST) and by conventional DST: 94 MDR-TB cases were detected within 10 days through the slide DST, whereas 82 cases were observed through the conventional DST, requiring about 3 months. Because the rapidity, sensitivity and accuracy of the slide DST method were found to be comparatively satisfactory when compared to the conventional DST method; we recommend the slide DST method as the standard diagnostic tool in perspective of Bangladesh for the detection of MDR-TB.

Comparisons among the diagnostic methods used for the detection of extra-pulmonary tuberculosis in Bangladesh

The present study was an attempt to establish a suitable method for the effective diagnosis of extra-pulmonary tuberculosis in Bangladesh. In this regard, detection of Mycobacterium tuberculosis from 390 different extra-pulmonary specimens was performed by Bright-Field microscopy, light-emitting diode fluorescence microscopy and Lowenstein-Jensen culture methods, followed by an extensive comparison among these methods. M. tuberculosis was detected in 53 cases through the conventional Lowenstein-Jensen culture method; 49 cases were detected under Bright-Field microscope, whereas the light-emitting diode fluorescence microscopy detected 64 cases. Out of 53 culture-positive isolates, 12 were found to be multi-drug resistant. Light-emitting diode fluorescence microscopy was found to be more sensitive and effective than both the Bright-Field microscopy and the Lowenstein-Jensen culture methods. Incidentally, light-emitting diode fluorescence microscopy appeared imperative to detecting the multi-drug resistant tuberculosis.

Risk Factors of Neonatal Mortality in Bangladesh

Introduction: To address United Nations Millennium Develop­ment Goal 4 (MDG 4) on reducing childhood mortality by three-quarter by 2015, there is a need for better population-based data on the rates and causes of neonatal death. This study aims to identify the risk factors of neonatal mortality in Bangladesh.Methods: The study used data from the nationally representative 2007 Bangladesh Demographic and Health Survey. The survey gathered information regarding socioeconomic, demographic, environmental and maternal and child health care of 10,996 ever married women and 6,058 children. Both bivariate and multivariate statistical analyses were used to assess the relationship between neonatal mortality and contextual factors.Results: The prevalence of neonatal mortality was 37/1,000. The statistical analyses yielded quantitatively important and reliable estimates of neonatal death. The multivariate logistic regression analysis yielded significantly increased risk of neonatal mortality for children with mother who had no formal education, the Muslims, whose mother were adolescents age 15-19, first ranked birth and twin babies.       Conclusion: Emphasis should be given to improve female education in Bangladesh for a better chance of satisfying important factors that can improve infant survival: the quality of infant feeding, general care, household sanitation, and adequate use of preventive and curative health services.Key words: Maternal and child health; Female education; MDG 4; Neonatal mortalityDOI: http://dx.doi.org/10.3126/jnps.v32i1.4845  J. Nepal Paediatr. Soc. Vol.32(1) 2012 37-46