Drug Susceptibility Testing Results Research Articles

Management of Polydrug-Resistant Tuberculosis

Background and Objectives: There is a lack of information regarding the effective duration of treatment necessary to prevent the development of acquired resistance when fluoroquinolones (FQ), and/or pyrazinamide (Z) resistance has occurred in patients with polydrug-resistant tuberculosis and isoniazid resistance. The management of these kinds of patients should be carried out in experienced centers according to drug susceptibility test results, clinical status of the patient and the extensity of the disease. Materials and Methods: We evaluated treatment regimens, treatment outcomes, and drug adverse effects in seven patients with polydrug-resistant tuberculosis, including those with Z and/or FQ resistance in a retrospective analysis Results: Regarding the patients with polydrug-resistant tuberculosis in addition to isoniazid (H) resistance, three had Z, two had FQ, and the remaining two had both Z and FQ resistance. In the intensive phase of the treatment, the patients were given at least four drugs according to drug susceptibility tests, and at least three drugs in the continuation phase. The duration of treatment was 9-12 months. Two of the patients were foreign nationals, and could not be followed up with due to returning to their home countries. Regarding the remaining five patients, three of them were terminated as they completed treatment, and two as cured. No recurrence was observed in the first year of the treatment. The most common, and serious drug side effect was seen for amikacin. Conclusions: In patients with polydrug-resistant TB, if Z and/or FQ resistance is detected in addition to H resistance, the treatment of these patients should be conducted on a case-by-case basis, taking into account the patient's resistance pattern, clinical condition, and disease prognosis. Close monitoring of the side effects will increase the success rate of the treatment.

Ways to improve the effectiveness of treatment of patients with destructive pulmonary tuberculosis with multiple and broad drug resistance of the pathogen

SummaryTreatment of patients with destructive forms of drug-resistant pulmonary tuberculosis remains a difficult problem. The presence of a destruction cavity in the lung reduces the effectiveness of therapy and is a negative prognostic factor. The objective of the study: to search for the optimal tactics for the treatment of destructive drug-resistant pulmonary tuberculosis and to evaluate the impact of collapsing procedures and surgical interventions on the outcome of treatment according to immediate and long-term observations. Materials and methods. The study included 398 patients with destruc-tive pulmonary tuberculosis with registered multiple (MDR-TB) in 61.3% and extensively drug-resistant (XDR-TB) in 38.7% of patients. Depending on the treat-ment tactics chosen in the clinic, 2 groups of patients were formed who received individualized chemothera-py based on the results of drug susceptibility testing of the pathogen and were comparable in other significant evaluation criteria. The main group consisted of 269 pa-tients, whose management tactics included the staged use of invasive methods of treatment, the comparison group — 129 patients who received only adequately selected anti-tuberculosis chemotherapy due to the im-possibility of using invasive methods. Staged invasive treatment included collapsotherapeutic techniques used in the absence of regression of the tuberculosis process against the background of adequately selected chemo-therapy for 1.5–2 months, and, if the previous stage was ineffective, resection surgery 4–6 months after the start of treatment in the clinic. Results: In the main group, collapse therapy procedures were performed in 179/269 (66.5%) patients, and they were successful in 106/115 (92.2%) patients with MDR-TB and in 51/64 (79.7%) pa-tients with XDR TB (p=0.44). Surgical interventions were performed in 25/269 (9.3%) patients, which were effec-tive in 20/25 (80%). Postoperative complications were registered in 4/25 (16%) patients. In general, microbiolog-ical conversion of sputum and closure of decay cavities were registered in 245/269 (91.1%) patients of the main group and in 75 out of 129 (58.6%) of the comparison group. Conclusion. Timely correction of treatment tac-tics based on the staged application of collapse therapy and surgical methods made it possible to achieve a cure in 91.1% of previously ineffectively treated patients with destructive pulmonary MDR/XDR tuberculosis.

ЭФФЕКТИВНОСТЬ ВЕРИФИКАЦИИ ТУБЕРКУЛЕЗА ОРГАНОВ ДЫХАНИЯ У БОЛЬНЫХ СО ЗЛОКАЧЕСТВЕННЫМИ НОВООБРАЗОВАНИЯМИ ВНЕЛЕГОЧНОЙ И ЛЕГОЧНОЙ ЛОКАЛИЗАЦИЙ

Aim: to analyze effectiveness of the algorithm for verification of pulmonary TB and the structure of clinical forms of pulmonary TB in patients with malignancies of extrapulmonary or pulmonary localizations. Materials and methods. A cohort retrospective study included 126 patients with malignancies and the diagnosis of active TB or residual post-TB changes or other lung diseases verified by sputum studies (stage 1), bronchoscopy (stage 2), and diagnostic surgery (stage 3).Results. The effectiveness of diagnosis verification based on three stages was 96%. The diagnosis of TB was significantly more frequent – in 40.5% (р < 0.001) than sarcoid reactions – 11.1%, metastatic tumors in the lungs – 15.1%, newly detected malignancies with comorbid TB – 6.3%, or bronchiectasis – 27% of cases. Stage 1 was effective for diagnosis verification in 30.9%, stage 2 – 61.6%, and stage 3 – 100% of cases. In 51 TB patients extrapulmonary malignancies prevailed – 84.3% vs lung cancer – 15.7% (р = 0.001); the most common were breast cancer (25.4%) and gastrointestinal cancer (15.7%). In 60.8% of cases TB was detected during complete/incomplete remission of cancer, in 21.5% – during new detection of cancer/TB comorbidity, in 17.6% – during cancer recurrence (р < 0.001). Active TB was diagnosed in 60.8%, residual post-TB changes – 39.2% of cases (р < 0.05). We established the prevalence of infiltrative pulmonary TB (25.8%) and intrathoracic lymph node TB (25.8%) vs other forms of pulmonary TB (р < 0.05). The detection of M. tuberculosis (MTB) DNA by molecular genetic methods was higher (77.4% of observations) than the detection of AFB by luminescent microscopy (58.1%) or MTB by cultural methods (38.7%) (р < 0.05). We obtained results of drug susceptibility testing in 67.9% of cases. TB was caused by drug susceptible MTB in в 68.4% and drug resistant MTB – 31.6% of cases (р < 0.05). Extensive drug resistance was determined in 15.7%, multiple drug resistance – 5.2%, and poly/monoresistance – 5.2% of cases. Conclusion. Among patients with malignancies, pulmonary TB was commonly detected during cancer remission; in two thirds of observations TB was confirmed by detection of MTB in sputum samples and bronchobiopsies, predominantly by molecular genetic methods; two thirds of cases had drug susceptible TB.

PncA Large Deletion is the Characteristic of Pyrazinamide-Resistant Mycobacterium tuberculosis belonging to the East Asian Lineage.

Pyrazinamide (PZA) is often used as an add-on agent in the treatment of multidrug-resistant tuberculosis, regardless of phenotypic drug susceptibility testing (pDST) results. However, evaluating the effectiveness of PZA is challenging because of its low pH activity, which can result in unreliable pDST results. This study aimed to investigate the genomic characteristics associated with PZA resistance that can be used to develop genotypic DST. A publicly available whole genome sequencing (WGS) dataset of 10,725 Mycobacterium tuberculosis complex genomes (3,326 phenotypically PZA-resistant and 7,399 phenotypically PZA-susceptible isolates) were analyzed. In total, 2,934 pncA non-silent mutations were identified in 2,880 isolates (26.9%). Detected mutations were found throughout the entire coding region of pncA in a scattered pattern, of which the most frequent mutation was p.Q10P (n = 278), followed by p.H57D (n = 167) and c.-11A>G (n = 122). The sensitivity and specificity of the group 1 or 2 mutations reported by the World Health Organization (WHO) mutational catalogue were 73.0% and 98.9%, respectively. We further identified 18 novel pncA mutations that were significantly associated with phenotypically PZA-resistant. In addition to these mutations, we identified 102 large deletions in the pncA gene, and all but two isolates were phenotypically resistant to PZA isolates. Notably, pncA deletions were mutually exclusive to pncA mutations, and more than half of the isolates with pncA large deletions belonged to the East Asian lineage (67.6%). The sensitivity, specificity, positive predictive value, and negative predictive value of the pooled variants (group 1 or 2 mutations, novel resistance-associated mutations, and large deletions of the pncA gene) were 79.0%, 98.9%, 97.0%, and 91.3%, respectively. The area under the curve (AUC) value for the pooled variants was significantly higher than the AUC value for the group 1 or 2 mutations (P <0.001), indicating that the pooled variants have a better discriminative ability for predicting PZA resistance. Using WGS, we found that the pncA mutations are scattered without specific mutational hotspots, and large deletions associated with PZA resistance are more common in the East Asian lineage of M. tuberculosis isolates. Our data also demonstrated the reliability of group 1 or 2 mutations presented in the WHO mutation catalogue and the need for further investigation on group 3 mutations, contributing to the evaluation of the current knowledge base on mutations associated with the PZA-resistant M. tuberculosis complex.

К ВОПРОСУ О СОКРАЩЕНИИ ДЛИТЕЛЬНОСТИ ЛЕЧЕНИЯ ТУБЕРКУЛЕЗА ОРГАНОВ ДЫХАНИЯ У ПОДРОСТКОВ ПРИ ПОЛУЧЕНИИ ТЕСТА ЛЕКАРСТВЕННОЙ ЧУВСТВИТЕЛЬНОСТИ НА ЭТАПЕ ХИМИОТЕРАПИИ

We carried out a cohort retrospective study to justify the possibilities to continue the main TB treatment course in adolescents with determined drug susceptibility during treatment (without return to treatment commencement) in order to reduce the total duration of treatment. Out of 123 patients who completed treatment in 2019–2022 we selected 31 patients with drug susceptibility test (DST) results obtained by only cultural studies using BACTEC MGIT 960 after 1.5-2 months of treatment. We established that DST results obtained using BACTEC MGIT 960 during treatment would determine further treatment tactics. We compared two groups of patients. Group 1 included 17 patients susceptible to at least 3 TB drugs and positive clinical and X-ray dynamics; their treatment regimens were corrected without return to the intensive phase. Group 2 included 14 patients susceptible to 1-2 TB drugs of the administered regimen without positive clinical and X-ray dynamics; after treatment correction they received the intensive phase of treatment again. The comparison of the main chemotherapy course duration showed that the patients of group 2 received treatment for a significantly longer period of time as compared to the patients of group 1 (the Mann–Whitney U test – 30.5, the critical value 67; р &lt; 0.05).

Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs.

Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.

Mycobacterium tuberculosis Genotypes and Drug Susceptibility Test Results from Timor-Leste: A Pilot Study.

Tuberculosis (TB) is prevalent and a major public health problem in Timor-Leste. The government of Timor-Leste is prioritising the surveillance of TB and drug-susceptibility testing (DST) to understand the burden of TB and TB drug resistance in the country. Moreover, little is known about the origin of Mycobacterium tuberculosis (MTB) in Timor-Leste. This study reports MTB DST and sequencing for Timor-Leste. A pilot study was carried out in which a convenience sample of TB isolates from mucopurulent sputum collected from presumptive TB patients in the capital Dili between July and December 2016 was tested for phenotypic and genotypic evidence of drug resistance. Standard MTB culture was performed at the Timor-Leste National Health Laboratory (NHL). The MTB isolates were sent to the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Australia for DST and sequencing. Overall, 36 MTB isolates were detected at the NHL; 20 isolates were recovered during sub-culturing at VIDRL. All 20 isolates were susceptible to rifampicin, isoniazid, pyrazinamide, and ethambutol, with no genotypic markers of resistance identified. On sequencing, lineage 4 was the most common. The results of this study provide a small snapshot of MTB diversity and resistance in an under-sampled region with very high TB incidence. Future investment in whole-genome sequencing capacity in Timor-Leste will make it possible to undertake further, more representative analyses that may be used to evaluate transmission dynamics and epidemiology of genotypic markers of resistance.

Effect of sputum quality and role of Xpert® MTB/ RIF assay for detection of smear-negative pulmonary tuberculosis in same-day diagnosis strategy in Addis Ababa, Ethiopia.

BackgroundThere is limited information on the performance of the Xpert® MTB/RIF test for diagnosis of smear-negative pulmonary tuberculosis (SNPT) and rifampicin resistance (RR) in the same-day diagnosis approach. The effects of sputum quality and other factors affecting the Xpert performance are also under-investigated.ObjectiveThis study aimed to determine the performance of the Xpert® MTB/RIF test for detection of SNPT and RR in the same-day diagnosis strategy and the effect of sputum quality and other factors on its performance.MethodsA cross-sectional study was conducted from August 2017 to January 2018 across 16 health facilities in Addis Ababa, Ethiopia. Two spot sputum samples were collected from 418 presumptive SNPT patients, tested with Xpert® MTB/RIF, then compared to tuberculosis culture. Additionally, culture isolates were tested for RR by BACTEC MGIT™ 960 drug susceptibility testing (DST) and MTBDRplus version 2.ResultsThe Xpert® MTB/RIF test detected 24 (5.7%) SNPT cases, with a sensitivity of 92.3% (75.9% – 97.9%) and specificity of 99.2% (97.8% – 99.7%) compared with tuberculosis culture. Xpert® MTB/RIF also detected three (11.58%) RR strains with 100.0% concordance with BACTEC MGIT™ 960 DST and MTBDRplus results. Three blood-stained SNPT samples were positive by Xpert (30.0%), which was 6.9 times higher compared to salivary sputum (odds ratio: 6.9, 95% confidence interval: 1.36–34.96, p = 0.020).ConclusionThe performance of the Xpert® MTB/RIF to detect SNPT and RR in same-day diagnosis is high. However, SNPT positivity varies among sputum qualities, and good sample collection is necessary for better test performance.

Problems of anti-tuberculosis therapy in patients on hemodialysis

The objective: to determine possibility of prescribing and safety of various anti-tuberculosis drugs and their combinations as part of a therapeutic or preventive course of anti-tuberculosis therapy (ATBT) in patients with end-stage chronic kidney disease (CKD) receiving hemodialysis replacement therapy in the settings with high prevalence of drug resistant strains of Mycobacterium tuberculosis.Subjects and Methods. 42 patients receiving hemodialysis replacement therapy were followed-up by Central Tuberculosis Research Institute: of them, 31 (73.8%) had active tuberculosis and 11 (26.2%) had residual post-tuberculous changes in the respiratory organs. During the follow-up, the nature and severity of adverse reactions to anti-tuberculosis drugs were assessed.Results. In the patients with end-stage CKD suffering from respiratory tuberculosis, drug resistant strains prevailed – 68.2%. Some of adverse events developed when taking anti-tuberculosis drugs were as follows: deterioration of uremia in 20.5% of cases, cardiovascular complications – in 17.9%, and neurotoxic reactions – in 15.4%. Progression of uremia occurred more often in the followed-up patients taking anti-tuberculosis drugs versus hepatotoxic reactions (p = 0.02). When treating tuberculosis patients with end-stage CKD, isoniazid was discontinued due to adverse events in 12.8% of cases and pyrazinamide in 12.8% of cases, other drugs were discontinued less frequently. Compilation of individual regimens of anti-tuberculosis drugs with the consideration of drug susceptibility testing results, contraindications, and concomitant diseases made it possible to provide an adequate anti-tuberculosis therapy for patients with end-stage CKD with tuberculosis infection in 92.9% of cases for a period of more than 6 months.

Prevalence and transmission of pyrazinamide-resistant Mycobacterium tuberculosis in Hunan Province,China

Objective: To provide a scientific reference for the prevention and treatment of pyrazinamide-resistant tuberculosis (PZA-R TB), we analyzed the prevalence and risk factors of pyrazinamide-resistant tuberculosis in Hunan province and described the genotyping and clustering characteristics of the pyrazinamide-resistant Mycobacterium tuberculosis (PZA-R MTB) isolates. Methods: The drug susceptibility test results of first-line anti-tuberculosis drugs including isoniazid (INH), rifampicin (RFP), streptomycin (SM), ethambutol (EMB) and pyrazinamide (PZA), and the characteristics of patients were collected from 3 862 tuberculosis patients in Hunan Chest Hospital (Institute of Tuberculosis Control and Prevention) from January 2016 to December 2018. The prevalence of PZA-R TB was calculated and risk factors were analyzed by univariate and multivariable logistic regression analysis. Two hundred and twelve Mycobacterium tuberculosis isolates selected from June 2017 to June 2018 were genotyped using the 24-loci MIRU-VNTR system. The genetic difference value (h), and the Hunter-Gaston index (HGI) were used to evaluate the resolution and variation for the 24 loci. MIRU-VNTR results were analyzed using BioNumerics 5.0 software to conduct cluster analysis. Clustered isolates were further analyzed by pncA gene sequencing. Results: The rate of PZA-R TB among tuberculosis patients and MDR patients was 14.7%(566/3 862) and 60.5%(511/844), respectively. Multivariable logistic regression analysis showed that patients who were INH mono-resistance and MDR had a higher risk of developing PZA resistance, compared with TB patients who were pan-sensitive to anti-TB drugs (INH, RFP, SM, and EMB). The adjusted OR value (95%CI) was 13.08(5.67-30.18), 298.41(164.88-540.08), respectively, and P values were all less than 0.01. Clustering analysis showed that 65 strains formed 19 clusters, the clustering rate was 30.7%(65/212). Of 19 clusters, eight clusters had at least two isolates with identical pncA mutation types within each cluster. In eight clusters, cluster 4, 6, 16 had four, three, and two patients who lived in the same county, respectively, thus providing probable epidemiological links for the recent transmission of PZA-R Mycobacterium tuberculosis. At least 47.6%(101/212) of PZA drug-resistant TB patients were suggestive of primary drug resistance caused by transmission. Conclusions: The prevalence of PZA-R TB was severe in Hunan province. PZA susceptibility testing should be performed for isolates resistant to any first-line anti-tuberculosis drugs, especially for MDR-MTB isolates. Nearly half of tuberculosis patients were suggestive of primary drug resistance caused by transmission. The prevention and treatment strategy of PZA-R TB should focus on the standardized treatment and management of patients as well as control of the source of infection.

Impact of alcohol drinking and tobacco smoking on the drug-resistance of newly diagnosed tuberculosis: a retrospective cohort study in Shandong, China, during 2004–2020

ObjectivesTo investigate the independent and collective impact of alcohol drinking and tobacco smoking on the drug-resistance of newly diagnosed tuberculosis (TB).DesignThis was a retrospective cohort study.SettingShandong, China.ParticipantsPatients with newly diagnosed...

Continuous surveillance of drug-resistant TB burden in Rwanda: a retrospective cross-sectional study.

Since the roll-out of the Xpert MTB/RIF assay, continuous surveillance can provide an estimate of rifampicin-resistant TB (RR-TB) prevalence, provided high drug susceptibility testing (DST) coverage is achieved. We use national data from Rwanda to describe rifampicin DST coverage, estimate the prevalence of RR-TB and assess its predictors. Routinely collected DST data were entered into an electronic TB case-based surveillance system. DST coverage was calculated among all bacteriologically confirmed pulmonary TB patients notified from 1 July 2019 to 30 June 2020 in Rwanda. The prevalence of RR-TB was estimated among those with DST results. Univariable and multivariable analysis was performed to explore predictors for RR TB. Among 4066 patients with bacteriologically confirmed pulmonary TB, rifampicin DST coverage was 95.6% (4066/4251). RR-TB was diagnosed in 73 patients. The prevalence of RR-TB was 1.4% (53/3659; 95% CI 1.09 to 1.89%) and 4.9% (20/406; 95% CI 3.03 to 7.51%) in new and previously treated TB cases, respectively. Predictors of RR-TB were: (1) living in Kigali City (adjusted OR [aOR] 1.65, 95% CI 1.03 to 2.65); (2) previous TB treatment (aOR 3.64, 95% CI 2.14 to 6.19); and (3) close contact with a known RR-TB patient (aOR 11.37, 95% CI 4.19 to 30.82). High rifampicin DST coverage for routine reporting allowed Rwanda to estimate the RR-TB prevalence among new and previously treated patients.

Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Isolates Using Whole-Genome Sequencing in Tianjin, China.

ObjectiveTuberculosis (TB) caused by Mycobacterium tuberculosis remains a global concern. This study aimed to determine the molecular characteristics of fluoroquinolone-resistant and multidrug-resistant M. tuberculosis strains using whole-genome sequencing to predict drug resistance in M. tuberculosis in Tianjin, China, which has not been established previously.MethodsTwenty-one fluoroquinolone-resistant and multidrug-resistant M. tuberculosis strains were isolated from sputum samples. Phenotypic drug resistance against 12 anti-tuberculosis drugs was determined using drug susceptibility testing. Whole-genome sequencing was performed to predict drug resistance in M. tuberculosis based on genome regions associated with drug resistance. The sensitivity of whole-genome sequencing for predicting drug resistance was calculated based on phenotypic drug susceptibility testing information.ResultsAmong the 21 isolates, mutations in 15 genome regions associated with drug resistance, including rpoB for rifampicin; katG and inhA promoter for isoniazid; gyrA and gyrB for ofloxacin and moxifloxacin; rpsL for streptomycin; rrs for streptomycin, amikacin, kanamycin and capreomycin; pncA and panD for pyrazinamide; embB, embC-embA, aftA, and ubiA for ethambutol; ethA for protionamide; and folC for para-aminosalicylic acid, were detected. Compared with traditional drug susceptibility testing results, the sensitivities for whole-genome sequencing of rifampin, isoniazid, ofloxacin, moxifloxacin, streptomycin, ethambutol, pyrazinamide, kanamycin, and amikacin resistance were 100%, 90.48%, 95.24%, 92.86%, 95.27%, 85.71%, 66.67%, 50%, and 50%, respectively. The sensitivities for whole-genome sequencing of capreomycin, protionamide, and para-aminosalicylic acid were not calculated because only one isolate showed phenotypic drug resistance. Mutations determined in drug susceptibility-associated genes can explain phenotypic drug resistance in most isolates. Notably, these mutations were absent in certain drug-resistant isolates, indicating other drug resistance mechanisms.ConclusionWhole-genome sequencing represents an effective diagnostic tool for fluoroquinolone-resistant and multidrug-resistant TB though it has some obstacles. Whole-genome sequencing should be used to predict drug resistance prior to performing traditional phenotypic drug susceptibility testing in Tianjin, China.

Empiric Addition of Quinolones to First-Line Tuberculosis Treatment Is Associated With Increased Odds of XDR-TB

BackgroundMultidrug-resistant tuberculosis (MDR-TB) represents a significant clinical and public health challenge worldwide. Out of concern for possible resistance, some providers prescribe first- and second-line tuberculosis treatment together before completing drug susceptibility testing (DST), which may increase emergent resistance.MethodsMDR-TB patients at an Indian referral center were enrolled in an observational cohort. Participants with drug susceptibility test (DST) results were categorized as prescribed fluoroquinolones, streptomycin, both, or neither with first-line treatment before DST. Odds of additional resistance to fluoroquinolones and aminoglycosides (XDR-TB) were calculated in association with empiric combined first- and second-line treatment before DST.ResultsOf 494 participants, 130 (26.3%) received a fluoroquinolone or streptomycin with first-line drugs before DST. Odds of XDR-TB were associated with fluoroquinolone prescription before DST [odds ratio (OR): 2.19, 95% confidence interval (CI): 1.26–3.76). The association with XDR-TB persisted in multivariable analysis (adjusted OR: 2.43, 95% CI: 1.19-4.91). Combined empiric first- and second-line treatment before DST was not associated with eventual outcomes.ConclusionMany participants received empiric combined first- and second-line drugs before DST, which was associated with XDR-TB. To minimize emerging resistance, treatment-associated side effects, and provide the best possible care, this approach should be discouraged in favor of early DST and DST-guided TB treatment.

SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission.

Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have appeared, until now no website integrates drug-resistance prediction with strain genetic relationships and species identification of nontuberculous mycobacteria (NTM). We have established a free, function-rich, user-friendly online platform for MTB WGS data analysis (SAM-TB, http://samtb.szmbzx.com) that integrates drug-resistance prediction for 17 antituberculosis drugs, detection of variants, analysis of genetic relationships and NTM species identification. The accuracy of SAM-TB in predicting drug-resistance was assessed using 3177 sequenced clinical isolates with results of phenotypic drug-susceptibility tests (pDST). Compared to pDST, the sensitivity of SAM-TB for detecting multidrug-resistant tuberculosis was 93.9% [95% confidence interval (CI) 92.6–95.1%] with specificity of 96.2% (95% CI 95.2–97.1%). SAM-TB also analyzes the genetic relationships between multiple strains by reconstructing phylogenetic trees and calculating pairwise single nucleotide polymorphism (SNP) distances to identify genomic clusters. The incorporated mlstverse software identifies NTM species with an accuracy of 98.2% and Kraken2 software can detect mixed MTB and NTM samples. SAM-TB also has the capacity to share both sequence data and analysis between users. SAM-TB is a multifunctional integrated website that uses WGS raw data to accurately predict antituberculosis drug-resistance profiles, analyze genetic relationships between multiple strains and identify NTM species and mixed samples containing both NTM and MTB. SAM-TB is a useful tool for guiding both treatment and epidemiological investigation.

Factors Associated with Treatment Outcome in Patients with Nontuberculous Mycobacterial Pulmonary Disease: A Large Population-Based Retrospective Cohort Study in Shanghai.

Infectious diseases caused by nontuberculous mycobacteria (NTM) are increasingly common. This retrospective cohort study examined factors associated with outcomes in patients from Shanghai who had NTM pulmonary disease (NTMPD) from January 2014 to December 2018. The causative bacterial species, drug susceptibility test results, treatment outcomes, sputum culture conversion rate, and risk factors associated with treatment failure were determined. The most common species were Mycobacterium avium complex (MAC) (50%), M. abscessus (28%), and M. kansasii (15%). Over five years, the proportions of M. kansasii and M. abscessus increased, and that of MAC decreased. The treatment success rate was significantly greater for patients infected with M. kansasii (89.9%) than MAC (65.0%, p < 0.001) and M. abscessus (36.1%, p < 0.001). Multivariate analysis indicated the risk factors for treatment failure were pathogenic NTM species (M. abscessus: aOR = 9.355, p < 0.001; MAC: aOR = 2.970, p < 0.001), elevated ESR (>60 mm/h: aOR = 2.658, p < 0.001), receipt of retreatment (aOR = 2.074, p < 0.001), and being middle-aged or elderly (>60 years-old: aOR = 1.739, p = 0.021; 45–60 years-old: aOR = 1.661, p = 0.034). The main bacterial species responsible for NTMPD were MAC, M. abscessus, and M. kansasii. Patients who were infected by M. abscessus or MAC, with elevated ESR, received retreatment, and were middle-aged or elderly had an increased risk of treatment failure.

Pattern of resistance to second line anti-tuberculosis drugs and associated risk factors among multidrug-resistant patients of pulmonary tuberculosis from Agra region of Uttar Pradesh, North India

Present study was aimed to determine the status of second-line anti-TB drug resistance and risk factorsfor extensively drug-resistance (XDR)-tuberculosis among multi-drug resistant (MDR)-tuberculosis patients from Agra region of Uttar Pradesh, North India.A total of 279 MDR-Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients of Agra region of Uttar Pradesh were analyzed for the resistance to second-line anti-TB drugs (SLDs). The demographic, behavioral, clinical and social information was compared with the results of drug susceptibility testing and analyzed statistically. Out of 279 MDR-isolates, 195 (69.89%) isolates were found resistant to at least one of the SLDs. The rates of general resistance to each of the drugs were as follows: kanamycin (42.29%), amikacin (17.92%), levofloxacin (40.14%) and ofloxacin (51.97%). Among the MDR-TB isolates, 53.76, 43.01 and 26.88% isolates were resistant to fluoroquinolone, second line injectable drugs and XDR, respectively. Among the demographic/ clinical variables, occupation, gender and number of family members were associated with the development of XDR-TB in MDR-TB patients of Agra region of Uttar Pradesh(P value: &lt;0.05).Present study has provided baseline information about the risk factors associated with SLDs resistance and XDRamong MDR-TB patients which can be useful to strengthen the implementation of targeted interventions in order to minimize the cases of drug resistance tuberculosis in Uttar Pradesh, North India.

Comparison of Different Methods for Drug Susceptibility Testing of Mycobacterium tuberculosis to Rifampicin

The objective: to compare results of drug susceptibility testing to rifampicin by molecular genetic methods and phenotypic tests of Mycobacterium tuberculosis isolates obtained from clinical specimens of tuberculosis patients.Subjects and Methods. 915 samples of M. tuberculosis DNA and 426 cultures were used in this study. Genotypic tests (TB-TEST (BIOCIP-IMB, Russia), GenoType MTBDRplusV2) and phenotypic technologies (absolute concentration method, Bactec MGIT 960 system, Sensititre Myco TB kit) were used.Results. A high percentage (98.7%; CI 97.7-99.7%) of confirmation of the results of the molecular genetic test (TB-TEST) by the phenotypic test (absolute concentration method) was demonstrated. In some cases, the Bactec MGIT 960 system as well as the absolute concentration method were shown to produce false negative results of rifampicin resistance in some cases.

Clinical Characteristics and Antimicrobial Susceptibility of Mycobacterium intracellulare and Mycobacterium abscessus Pulmonary Diseases: A Retrospective Study.

The incidence of nontuberculous mycobacteria (NTM) diseases is increasing every year. The present study was performed to investigate the clinical characteristics, CT findings, and drug susceptibility test (DST) results of patients diagnosed with M. intracellulare or M. abscessus nontuberculous mycobacterial pulmonary disease (NTMPD). This retrospective study included patients diagnosed with NTMPD due to M. intracellulare or M. abscessus for the first time at Anhui Chest Hospital between 01/2019 and 12/2021. The patients were grouped as M. intracellulare-NTMPD group or M. abscessus-NTMPD group. Clinical features, imaging data and DST data, were collected. Patients with M. intracellulare infection had a higher rate of acid-fast smears (66.1% vs. 45.2%, P=0.032) and a higher rate of cavitation based on pulmonary imaging (49.6% vs. 19.4%, P=0.002) than patients with M. abscessus infection, but both groups had negative TB-RNA and GeneXpert results, with no other characteristics significant differences. The results of DST showed that M. intracellulare had high susceptibility rate to moxifloxacin (95.9%), amikacin (90.1%), clarithromycin (91.7%), and rifabutin (90.1%). M. abscessus had the highest susceptibility rate to amikacin (71.0%) and clarithromycin (71.0%). The clinical features of M. intracellulare pneumopathy and M. abscessus pneumopathy are highly similar. It may be easily misdiagnosed, and therefore, early strain identification is necessary. M. intracellulare has a high susceptibility rate to moxifloxacin, amikacin, clarithromycin, and rifabutin, while M. abscessus has the highest susceptibility rate to amikacin and clarithromycin. This study provides an important clinical basis for improving the management of NTMPD.

Clinical Impact of the Line Probe Assay and Xpert® MTB/RIF Assay in the Presumptive Diagnosis of Drug-Resistant Tuberculosis in Brazil: A Pragmatic Clinical Trial.

ABSTRACTBackground: Rapid molecular methods such as the line probe assay (LPA) and Xpert® MTB/RIF assay (Xpert) have been recommended by the World Health Organization for drug-resistant tuberculosis (DR-TB) diagnosis. We conducted an interventional trial in DR-TB reference centers in Brazil to evaluate the impact of the use of LPA and Xpert. Methods: Patients with DR-TB were eligible if their drug susceptibility testing results were available to the treating physician at the time of consultation. The standard reference MGITTM 960 was compared with Xpert (arm 1) and LPA (arm 2). Effectiveness was considered as the start of the appropriate TB regimen that matched drug susceptibility testing (DST) and the proportions of culture conversion and favorable treatment outcomes after 6 months. Results: A higher rate of empirical treatment was observed with MGIT alone than with the Xpert assay (97.0% vs. 45.0%) and LPA (98.2% vs. 67.5%). Patients started appropriate TB treatment more quickly than those in the MGIT group (median 15.0 vs. 40.5 days; p<0.01) in arm 1. Compared to the MGIT group, culture conversion after 6 months was higher for Xpert in arm 1 (90.9% vs. 79.3%, p=0.39) and LPA in arm 2 (80.0% vs. 83.0%, p=0.81). Conclusions: In the Xpert arm, there was a significant reduction in days to the start of appropriate anti-TB treatment and a trend towards greater culture conversion in the sixth month.