TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach.

MOTIVATION: The interplay between protein and nucleic acid participates in diverse biological activities. Accurately identifying the interaction between protein and nucleic acid can strengthen the understanding of protein function. However, conventional methods are too time-consuming, and computational methods are type-agnostic predictions. We proposed an ensemble predictor termed TSNAPred and first used it to identify residues that bind to A-DNA, B-DNA, ssDNA, mRNA, tRNA and rRNA. TSNAPred combines LightGBM and capsule network, both learned on the feature derived from protein sequence. TSNAPred utilizes the sliding window technique to extract long-distance dependencies between residues and a weighted ensemble strategy to enhance the prediction performance. The results show that TSNAPred can effectively identify type-specific nucleic acid binding residues in our test set. What is more, it also can discriminate DNA-binding and RNA-binding residues, which has improved 5% to 10% on the AUC value compared with other state-of-the-art methods. The dataset and code of TSNAPred are available at: https://github.com/niewenjuan-csu/TSNAPred.

Computational anti-COVID-19 drug design: progress and challenges.

Vaccines have made gratifying progress in preventing the 2019 coronavirus disease (COVID-19) pandemic. However, the emergence of variants, especially the latest delta variant, has brought considerable challenges to human health. Hence, the development of robust therapeutic approaches, such as anti-COVID-19 drug design, could aid in managing the pandemic more efficiently. Some drug design strategies have been successfully applied during the COVID-19 pandemic to create and validate related lead drugs. The computational drug design methods used for COVID-19 can be roughly divided into (i) structure-based approaches and (ii) artificial intelligence (AI)-based approaches. Structure-based approaches investigate different molecular fragments and functional groups through lead drugs and apply relevant tools to produce antiviral drugs. AI-based approaches usually use end-to-end learning to explore a larger biochemical space to design antiviral drugs. This review provides an overview of the two design strategies of anti-COVID-19 drugs, the advantages and disadvantages of these strategies and discussions of future developments.

Nanopore sequencing for smear-negative pulmonary tuberculosis-a multicentre prospective study in China.

PURPOSE: In this prospective study, the diagnosis accuracy of nanopore sequencing-based Mycobacterium tuberculosis (MTB) detection was determined through examining bronchoalveolar lavage fluid (BALF) samples from pulmonary tuberculosis (PTB) -suspected patients. Compared the diagnostic performance of nanopore sequencing, mycobacterial growth indicator tube (MGIT) culture and Xpert MTB/rifampin resistance (MTB/RIF) assays. METHODS: Specimens collected from suspected PTB cases across China from September 2021 to April 2022 were tested then assay diagnostic accuracy rates were compared. RESULTS: Among the 111 suspected PTB cases that were ultimately diagnosed as PTB, the diagnostic rate of nanopore sequencing was statistically significant different from other assays (P < 0.05). Fleiss' kappa values of 0.219 and 0.303 indicated fair consistency levels between MTB detection results obtained using nanopore sequencing versus other assays, respectively. Respective PTB diagnostic sensitivity rates of MGIT culture, Xpert MTB/RIF and nanopore sequencing of 36.11%, 40.28% and 83.33% indicated superior sensitivity of nanopore sequencing. Analysis of area under the curve (AUC), Youden's index and accuracy values and the negative predictive value (NPV) indicated superior MTB detection performance for nanopore sequencing (with Xpert MTB/RIF ranking second), while the PTB diagnostic accuracy rate of nanopore sequencing exceeded corresponding rates of the other methods. CONCLUSIONS: In comparison with MGIT culture and Xpert MTB/RIF assays, BALF's nanopore sequencing provided superior MTB detection sensitivity and thus is suitable for testing of sputum-scarce suspected PTB cases. However, negative results obtained using these assays should be confirmed based on additional evidence before ruling out a PTB diagnosis.

Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis.

BACKGROUND: To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary tuberculosis (PTB) patients and compare the results to results obtained for MGIT and Xpert assays. METHODS: Cases with suspected PTB (n = 55) were diagnosed from January 2019 to December 2021 based on results of nanopore sequencing, MGIT culture, and Xpert MTB/RIF testing of BALF and sputum samples collected during hospitalization. Diagnostic accuracies of assays were compared. RESULTS: Ultimately, data from 29 PTB patients and 26 non-PTB cases were analyzed. PTB diagnostic sensitivities of MGIT, Xpert MTB/RIF, and nanopore sequencing assays were 48.28%, 41.38%, and 75.86%, respectively, thus demonstrating that nanopore sequencing provided greater sensitivity than was provided by MGIT culture and Xpert assays (P < 0.05). PTB diagnostic specificities of the respective assays were 65.38%, 100%, and 80.77%, which corresponded with kappa coefficient (κ) values of 0.14, 0.40, and 0.56, respectively. These results indicate that nanopore sequencing provided superior overall performance as compared to Xpert and MGIT culture assays and provided significantly greater PTB diagnostic accuracy than Xpert and sensitivity comparable to that of the MGIT culture assay. CONCLUSION: Our findings suggest that improved detection of PTB in suspected cases was achieved using nanopore sequencing-based testing of BALF or sputum samples than was achieved using Xpert and MGIT culture-based assays, and nanopore sequencing results alone cannot be used to rule out PTB.

Adjunctive interleukin-2 for the treatment of drug-susceptible tuberculosis: a randomized control trial in China.

PURPOSE: Evaluation of the efficacy and safety of IL-2 in the treatment of drug-susceptible tuberculosis. METHODS: First, the cases of diagnosed drug-susceptible tuberculosis were randomized into two groups-the control group that received the background regimen of isoniazid, rifampin, pyrazinamide, and ethambutol, and the experimental group that received the background regimen plus IL-2. The efficacy and safety evaluations were performed throughout the therapy process as well as 12 months after the treatment completion. RESULTS: A total of 1151 patients underwent the randomization, among which 539 (96.2%) of the 560 in the experimental group achieved the sputum culture conversion to negative, compared to the 551 (93.2%) of the 591 in the control group, after 2 months of treatment, with significant difference observed between the groups (P = 0.025). Cavity closure after 2 months in the IL-2 (experimental) group was 60/211 (28.4%) compared to 46/248 (18.5%) in the control group, with a significant difference between the groups (P = 0.001). After treatment completion, the proportion of favorable outcomes was 559/560 (99.8%) in the experimental group and 587/591 (99.3%) in the control group, with no significant difference between the groups. Twelve months after treatment completion, relapse occurred in 15/560 (2.6%) in the IL-2 group and 19/591 (3.2%) in the control group, with no significant difference. CONCLUSION: IL-2 may enhance culture conversion and the cavity closure rate in the early treatment phase, although the enhancement may not be significant after treatment completion.

SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost.

BACKGROUND: Identifying miRNA and disease associations helps us understand disease mechanisms of action from the molecular level. However, it is usually blind, time-consuming, and small-scale based on biological experiments. Hence, developing computational methods to predict unknown miRNA and disease associations is becoming increasingly important. RESULTS: In this work, we develop a computational framework called SMALF to predict unknown miRNA-disease associations. SMALF first utilizes a stacked autoencoder to learn miRNA latent feature and disease latent feature from the original miRNA-disease association matrix. Then, SMALF obtains the feature vector of representing miRNA-disease by integrating miRNA functional similarity, miRNA latent feature, disease semantic similarity, and disease latent feature. Finally, XGBoost is utilized to predict unknown miRNA-disease associations. We implement cross-validation experiments. Compared with other state-of-the-art methods, SAMLF achieved the best AUC value. We also construct three case studies, including hepatocellular carcinoma, colon cancer, and breast cancer. The results show that 10, 10, and 9 out of the top ten predicted miRNAs are verified in MNDR v3.0 or miRCancer, respectively. CONCLUSION: The comprehensive experimental results demonstrate that SMALF is effective in identifying unknown miRNA-disease associations.

Validation of Cycloserine Efficacy in Treatment of Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis in Beijing, China.

Cycloserine (Cs) is recommended by the World Health Organization as a second-line drug to treat multidrug-resistant tuberculosis (MDR-TB); however, its efficacy has never been sufficiently evaluated. To gain some insights into the value of cycloserine for MDR-TB treatment, in vitro bacteriostatic effect was determined and patient validations were performed prospectively. The in vitro activity of Cs against 104 wild-type Mycobacterium tuberculosis strains was determined, and serum Cs concentrations were measured for 73 MDR TB patients 2 h after administration. The treatment outcomes for 27 MDR-TB patients who had baseline isolates and were treated with Cs-containing regimens were followed up. The MICs for 90% of the recruited 104 wild-type strains were below 32 µg/ml. Eighteen out of 52 patients had peak serum concentrations (Cmax) below 20 µg/ml at the dosage of 500 mg daily, while 13 out of 21 patients had peak serum concentrations higher than 35 µg/ml at the dosage of 750 mg daily. The percentage of favorable treatment outcomes among patients with a Cmax/MIC ratio of ≥1 was statistically significantly higher than that among the group with a Cmax/MIC ratio of <1 (P = 0.022). The epidemiological cutoff value for Cs susceptibility testing was 32 µg/ml. A high percentage of patients receiving the recommended dosage of 10 mg/kg for Cs administration could not acquire desirable blood concentrations; therefore, adjusting the dosage according to drug concentration monitoring is necessary. The Cmax/MIC ratio might be a good indicator for predicting the treatment outcome for patients with MDR-TB or extensively drug-resistant TB (XDR-TB) who are being administered Cs-containing regimens.

[Detection of mutations in the gyrA and gyrB genes associated with fluoroquinolone-resistance among clinical isolates of Mycobacterium abscessus in China].

OBJECTIVE: To determine molecular mutations in gyrA and gyrB genes and their association with fluoroquinone-resistance among Mycobacterium abscessus isolates from China. METHODS: Antimicrobial susceptibility profile of Mycobacterium abscessus isolates was evaluated for resistance to levofloxacin (LFX) and moxifloxacin (MFX). The quinolone resistant determing regions (QRDR) of gyrA and gyrB genes of all the isolates was sequenced and analyzed. RESULTS: A total 70 Mycobacterium abscessus isolates were analyzed, including 45 (64%) M. abscessus subsp. abscessus and 25 (36%) M. abscessus subsp. massiliense. Analysis of antimicrobial susceptibility profile showed 97% (n=68) of isolates were resistance to LFX and 14.3% (n=10) of isolates were resistance to MFX. All the MFX-resistant strains were resistant to LFX. Cross-resistance to LFX and MFX was noted in 14.3% (n=10) of isolates. Sequencing analysis revealed that the Ser83Ala substitution in the gyrA gene and Lys447Arg and Ser464Asn substitutions in the gyrB gene were found in all the isolates from both M. abscessus subsp. abscessus and M. abscessus subsp. massiliense. No mutation was found to be associated with cross-resistance of M. abscessus to LFX and MFX in the entire gyrA and gyrB gene. CONCLUSIONS: Our data suggest that there is no clear correlation between the type of mutation in the gene gyrA and gyrB, and the MIC levels of LFX and MFX for resistant M. abscessus strains.

[The analysis of species identification and susceptibility testing of Mycobacterium abscessus].

OBJECTIVES: To evaluate the method of differentiating Mycobacterium abscessus subsp. abscessus (subsp. M. abscessus) from Mycobacterium abscessus subsp. massiliense (subsp. M. massiliense), and to investigate the activity of different antibiotics in vitro. METHODS: Sixty Mycobacterium abscessus (M. abscessus) isolates previously identified by using 16S rRNA sequence, were identified by comparative sequence analysis of rpoB and hsp65, and were divided into subsp. M. abscessus and subsp. M. massiliense. Two subspecies' resistant proportions were compared by chi-square test. Finally the relationship between clarithromycin resistance and erm(41) was analyzed. RESULTS: Of all the 60 M. abscessus isolates, 65% (39/60) belonged to subsp. M. abscessus, 35% (21/60) belonged to subsp. M. massiliense. 97% (38/39) subsp. M. abscessus and 95% (20/21) subsp. M. massiliense were susceptible to amikacin. 92% (36/39) subsp. M. abscessus and 95% (20/21) subsp. M. massiliense were susceptible to azithromycin. 74% (29/39) subsp. M. abscessus and 67% (14/21) subsp. M. massiliense were susceptible to imipenem. 46% (18/39) subsp. M. abscessus and 76% (16/21) subsp. M. massiliense were moderately susceptible to cefoxitin. 82% (32/39) subsp. M. abscessus were resistant to clarithromycin, and 95% (20/21) subsp. M. massiliense were susceptible to clarithromycin. Of all the 28 subsp. M. abscessus isolates which were sequenced suscessfully, 23 isolates were resistant to clarithromycin, and 22 isolates in them had T28 in erm(41), and the rest one had C28 in erm(41). However, all the 5 subsp. M. abscessus isolates which were susceptible to clarithromycin had C28 in erm(41). CONCLUSIONS: M. abscessus can be divided into subsp. M. abscessus and subsp. M. massiliense by using rpoB and hsp65. Amikacin, azithromycin and imipenem showed excellent inhibition activity against M. abscessus in vitro. Cefoxitin also showed a good inhibition activity. Clarithromycin had a poor inhibition activity against subsp. M. abscessus, but a good inhibition activity against subsp. M. massiliense. Erm(41) was related to clarithromycin resistance.

Non-tuberculous mycobacterial disease: progress and advances in the development of novel candidate and repurposed drugs.

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens that can infect all body tissues and organs. In particular, the lungs are the most commonly involved organ, with NTM pulmonary diseases causing serious health issues in patients with underlying lung disease. Moreover, NTM infections have been steadily increasing worldwide in recent years. NTM are also naturally resistant to many antibiotics, specifically anti-tuberculosis (anti-TB) drugs. The lack of drugs targeting NTM infections and the increasing drug resistance of NTM have further made treating these mycobacterial diseases extremely difficult. The currently recommended NTM treatments rely on the extended indications of existing drugs, which underlines the difficulties of new antibiotic discovery against NTM. Another challenge is determining which drug combinations are most effective against NTM infection. To a certain extent, anti-NTM drug development depends on using already available antibiotics and compounds. Here, we aimed to review new antibiotics or compounds with good antibacterial activity against NTM, focusing on their mechanisms of action, in vitro and in vivo antibacterial activities.

Antibacterial activity of the novel oxazolidinone contezolid (MRX-I) against Mycobacterium abscessus.

Objective: To evaluate contezolid (MRX-I) antibacterial activity against Mycobacterium abscessus in vitro and in vivo and to assess whether MRX-I treatment can prolong survival of infected zebrafish. Methods: MRX-I inhibitory activity against M. abscessus in vitro was assessed by injecting MRX-I into zebrafish infected with green fluorescent protein-labelled M. abscessus. Thereafter, infected zebrafish were treated with azithromycin (AZM), linezolid (LZD) or MRX-I then maximum tolerated concentrations (MTCs) of drugs were determined based on M. abscessus growth inhibition using one-way ANOVA. Linear trend analysis of CFU counts and fluorescence intensities (mean ± SE values) was performed to detect linear relationships between MRX-I, AZM and LZD concentrations and these parameters. Results: MRX-I anti-M. abscessus minimum inhibitory concentration (MIC) and MTC were 16 µg/mL and 15.6 µg/mL, respectively. MRX-I MTC-treated zebrafish fluorescence intensities were significantly lower than respective LZD group intensities (whole-body: 439040 ± 3647 vs. 509184 ± 23064, p < 0.01); head: 74147 ± 2175 vs. 95996 ± 8054, p < 0.05). As MRX-I concentration was increased from 0.488 µg/mL to 15.6 µg/mL, zebrafish whole-body, head and heart fluorescence intensities decreased. Statistically insignificant differences between the MRX-I MTC group survival rate (78.33%) vs. corresponding rates of the 62.5 µg/mL-treated AZM MTC group (88.33%, p > 0.05) and the 15.6 µg/mL-treated LZD MTC group (76.67%, p > 0.05) were observed. Conclusion: MRX-I effectively inhibited M. abscessus growth and prolonged zebrafish survival when administered to M. abscessus-infected zebrafish, thus demonstrating that MRX-I holds promise as a clinical treatment for human M. abscessus infections.

Clinical Utility of Contezolid-Containing Regimens in 25 Cases of Linezolid-Intolerable Tuberculosis Patients.

Objective: Linezolid is increasingly used in the treatment of multidrug-resistant (MDR) M. tuberculosis (TB) with good efficacy; however, its clinical use is limited by intolerable adverse events (AEs). This usually results in dose adjustment or even discontinuation. Contezolid is a new oxazolidinone antibiotic with in vitro antibacterial activity against MDR TB equivalent to linezolid, but its safety and efficacy in MDB TB treatment has not been established. Methods: We conducted a retrospective study on 25 TB patients who received both linezolid and contezolid in Beijing Chest Hospital from January 1, 2022, to January 31, 2023. All patients received linezolid-containing anti-TB regimen first and then switched to contezolid-containing regimens due to the intolerable linezolid-related AEs. Results: Most (68%, 17/25) of the patients were diagnosed with RR-TB or MDR-TB. A total of 30 AEs were reported in these patients. About 26.7% (8/30) of the AEs were Grade 3 (severe) in severity. After switching to contezolid-containing anti-TB regimens for at least 1 month, the linezolid-related AEs were resolved or improved in 90% of the cases. Clinical improvement was observed in all patients after treatment with contezolid-containing regimen, with negative results of sputum culture and/or smear for M. tuberculosis in 84% of the patients. Conclusion: Contezolid can be the first choice instead of linezolid to combine with other anti-TB drugs if necessary. Well-designed clinical trials are required to further confirm the safety and efficacy of contezolid in the treatment of TB patients.

Antibacterial activity of the novel compound Sudapyridine (WX-081) against Mycobacterium abscessus.

Objective: This study aimed to investigate sudapyridine (WX-081) antibacterial activity against Mycobacterium abscessus in vitro and its effect on in vivo bacterial growth and host survival using a zebrafish model of M. abscessus infection. Methods: WX-081 in vitro antibacterial activity was assessed based on growth inhibition of M. abscessus standard strain ATCC19977 and 36 clinical isolates. Maximum tolerated concentrations (MTCs) of WX-081, bedaquiline, and azithromycin and inhibition of M. abscessus growth were assessed in vivo after fluorescently labelled bacilli and drugs were injected into zebrafish. Bacterial counts were analysed using one-way ANOVA and fluorescence intensities of zebrafish tissues were analysed and expressed as the mean ± SE. Moreover, Kaplan-Meier survival analysis was conducted to assess intergroup differences in survival of M. abscessus-infected zebrafish treated with different drug concentrations using a log-rank test, with a p value <0.05 indicating a difference was statistically significant. Results: Drug sensitivity testing of M. abscessus standard strain ATCC19977 and 36 clinical isolates revealed MICs ranging from 0.12-0.96 µg/mL and MIC50 and MIC90 values of 0.48 µg/mL and 0.96 µg/mL, respectively. Fluorescence intensities of M. abscessus-infected zebrafish tissues was lower after treatment with the WX-081 MTC (62.5 µg/mL) than after treatment with the azithromycin MTC (62.5 µg/mL) and the bedaquiline MTC (15.6 µg/mL). When the concentration of WX-081 increased from 1.95µg/mL to 1/8 MTC(7.81µg/mL), the survival rate of zebrafish at 4-9 dpf decreased from 90.00% to 81.67%. Conclusion: WX-081 effectively inhibited M. abscessus growth in vitro and in vivo and prolonged survival of M. abscessus-infected zebrafish, thus indicating that WX-081 holds promise as a clinical treatment for M. abscessus infection.

Bedaquiline resistance pattern in clofazimine-resistant clinical isolates of tuberculosis patients.

OBJECTIVES: Bedaquiline (BDQ) is a potent drug for treating drug-resistant tuberculosis (TB). Here, we analysed the resistance profiles of BDQ in CFZ-resistant clinical isolates and investigated the clinical risk factors of BDQ and CFZ cross/co-resistance. METHODS: The AlarmarBlue microplate assay was performed to determine the minimum inhibitory concentration (MIC) of the CFZ-resistant Mycobacterium tuberculosis (MTB) clinical isolates to CFZ and BDQ. The clinical characteristics of the respective patients were analysed to explore the possible risk factors of BDQ resistance. The drug-resistance-associated genes including Rv0678, Rv1979c, atpE, pepQ and Rv1453 were sequenced and analysed. RESULTS: A total of 72 clinical CFZ-resistant MTB isolates were collected; among these, half were identified as BDQ-resistant. The MIC value of BDQ closely correlated with CFZ (Spearman's q = 0.766, P < 0.005). Among the isolates with a MIC of CFZ ≥4 mg/L, 92.31% (12/13) were resistant to BDQ. Pre-XDR and exposure to BDQ or CFZ are the major risk factors for concurrent BDQ resistance. Among the 36 cross/co-resistant isolates, 50% (18/36) had mutations in Rv0678, 8.3% (3/36) had mutations in Rv0678+Rv1453, 5.6% (2/36) had mutations in Rv0678+Rv1979c, 2.8% (1/36) had mutations in Rv0678+Rv1979c+Rv1453, 2.8% (1/36) had mutations in atpE+Rv0678+Rv1453, 2.8% (1/36) had mutations in Rv1979c, and 27.7% (10/36) had no variations in the target genes. CONCLUSION: Nearly half of the CFZ-resistant isolates were still sensitive to BDQ, whereas this rate dramatically decreased among patients with pre-XDR TB or those who had been exposed to BDQ or CFZ.

Linezolid Pharmacokinetics/Pharmacodynamics-Based Optimal Dosing for Multidrug-Resistant Tuberculosis.

OBJECTIVES: Linezolid can significantly impact drug-resistant tuberculosis (DR-TB) patient outcomes. However, the long-term use of this drug for TB treatment has been limited by adverse reactions and uncertainty regarding optimal dosage regimens for balancing drug efficacy and safety across different populations. This study attempted to find the optimal dosing regimen of linezolid in different populations. METHODS: A total of 355 blood samples were collected from 126 DR-TB patients. Population pharmacokinetic analysis (using a one-compartment model) and dose simulations were conducted using NONMEM and R software. The ratio between the area under the free drug plasma concentration-time curve to the MIC (fAUC/MIC) of > 119 and trough concentration (Cmin) ≤ 2 mg/L served as efficacy and safety targets, respectively, toward the formulation of optimal dosage regimens based on a ≥ 90% cumulative fraction of response. RESULTS: Body weight and blood urea nitrogen levels were the most significant covariates of apparent volume, while creatinine clearance and haemoglobin level significantly influenced apparent clearance. The probability of target attainment for different dosage regimens was evaluated via Monte Carlo simulation. For subjects with MICs of 0.125, 0.25 and 0.5 mg/L, specific total daily doses of ≥ 300 mg, ≥ 450 mg and ≥ 900 mg were required to reach the target, respectively. Subjects with body weight ≤ 70 kg and MIC ≥ 1 mg/L received a total 1200 mg daily dose to reach the probability of target attainment target. Notably, single dosing was safer than multiple dosing at the same daily dose. The optimal dosage regimens for subjects with body weight < 50 kg and ≥ 50 kg were 450 mg/d and 600 mg/d (once daily), respectively. CONCLUSION: Optimal dosage regimens for patients weighing < 50 kg and ≥ 50 kg were 450 mg/d and 600 mg/d, respectively. A single dose was safer than multiple doses.

Value of serum cytokine biomarkers TNF-α, IL-4, sIL-2R and IFN-γ for use in monitoring bacterial load and anti-tuberculosis treatment progress.

Tuberculosis (TB) patient serum cytokine levels may be predictive of anti-tuberculosis treatment progress. Here, serum levels of cytokines TNF-α, IL-4, sIL-2R and IFN-γ were measured then correlated to clinical TB manifestations, bacterial burden, chest imaging findings and clinical course. Study subjects included 67 newly diagnosed pulmonary TB (PTB) patients with active disease admitted to Beijing Chest Hospital for anti-TB chemotherapeutic treatment. Blood was drawn at 0 months (pre-treatment), 1-2 months (at any time between 1 and 2 month) and after 6 months completion of treatment and serum TNF-α, IL-4, sIL-2R and IFN-γ levels were measured in duplicate using enzyme-linked immunosorbent assays (ELISAs). Correlation analysis was conducted to evaluate sensitivity and specificity of cytokine levels as predictors of disease activity and treatment progress. The results indicated that the pre-treatment serum TNF-α level of the smear-negative group was lower than that of the smear 1+ group, while serum TNF-α after 6 months completion of treatment and IFN-γ levels at 1-2 months and after 6 months completion of treatment were significantly lower, respectively, than at 0 months (before treatment) (P < 0.05). Using a cut-off value of 845 pg/ml, serum TNF-α level was predictive of treatment progress, with a sensitivity of 51%, specificity of 60% and AUC of 0.594 (P = 0.013). Meanwhile, using a cut-off value of 393 pg/ml, serum IFN-γ provided superior monitoring efficacy, with a sensitivity of 60%, specificity of 64% and AUC of 0.651 (P = 0.017). In conclusion, both serum TNF-α and IFN-γ levels might be useful biomarkers for monitoring treatment progress.

Nosocomial tuberculosis transmission from 2006 to 2018 in Beijing Chest Hospital, China.

INTRODUCTION: Strong evidence is lacking to support effectiveness of currently implemented tuberculosis infection prevention control (TB-IPC) measures for preventing nosocomial tuberculosis (TB) transmission. This 13-year analysis is the longest follow-up investigation to date to identify risk factors underlying nosocomial TB transmission. METHODS: We monitored all staff of Beijing Chest Hospital each year from 2006 to 2018. Age, gender, duration, department, education, income, respirator, ultraviolet, and ventilation were chosen as variables. Univariate cox regression, correlation analysis, and multivariate cox regression were analyzed sequentially. RESULTS: Using multivariable cox regression analysis, variables of income, ultraviolet germicidal irradiation (UVGI), natural ventilation and mechanical ventilation conferred significant protective effects, with odds ratios of 0.499, 0.058, 0.003, and 0.015, respectively (P < 0.05). Medical N95 respirator conferred an excellent protective effect, with an associated TB infection rate of 0%. Notably, inadequately maintained mechanical ventilation systems were less protective than natural ventilation systems. CONCLUSION: UVGI, adequate ventilation, and use of medical N95 respirator may be risk factors of nosocomial TB transmission.

Species Identification and Clarithromycin Susceptibility Testing of 278 Clinical Nontuberculosis Mycobacteria Isolates.

Purpose of this paper is to analyze different species' proportion of nontuberculosis mycobacteria (NTM) and susceptibility to clarithromycin of different species. 278 clinical NTM isolates were identified into species by using 16S rRNA, rpoB and hsp65. Then clarithromycin susceptibility testing against different species was done separately, using microplate Alamar Blue assay. Finally, resistance isolates' erm(41) of M. abscessus were sequenced in order to analyze mechanisms for clarithromycin resistant. In this test, 131 isolates (47%) belonged to M. avium complex (MAC), and 70 isolates (25%) belonged to M. abscessus. Nearly all the M. abscessus subsp. abscessus resistant to clarithromycin had T28 in erm(41). However, all the M. abscessus subsp. abscessus susceptible to clarithromycin had C28 in erm(41). In this study, we find that MAC was the most common pathogens of NTM, and the second one was M. abscessus. However, M. chelonei, M. fuerth, and M. gordon were rare. Clarithromycin had a good inhibition activity against all the NTM species except M. abscessus subsp. abscessus. The erm(41) genotype is of high relevance to clarithromycin resistance.

Relative bioavailability of rifampicin in four Chinese fixed-dose combinations compared with rifampicin in free combinations.

BACKGROUND: Decreases in the bioavailability of rifampicin (RFP) can lead to the development of drug resistance and treatment failure. Therefore, we investigated the relative bioavailability of RFP from one four-drug fixed-dose combination (FDC; formulation A) and three two-drug FDCs (formulations B, C, and D) used in China, compared with RFP in free combinations of these drugs (reference), in healthy volunteers. METHODS: Eighteen and twenty healthy Chinese male volunteers participated in two open-label, randomized two-period crossover (formulations A and C) or one three-period crossover (formulations B and D) study, respectively. The washout period between treatments was 7 days. Bioequivalence was assessed based on 90% confidence intervals, according to two one-sided t-tests. All analyses were done with DAS 3.1.5 (Mathematical Pharmacology Professional Committee of China, Shanghai, China). RESULTS: Mean pharmacokinetic parameter values of RFP obtained for formulations A, B, C, and D products were 11.42 ± 3.41 µg/ml, 7.86 ± 5.78 µg/ml, 13.05 ± 6.80 µg/ml, and 16.18 ± 3.87 µg/ml, respectively, for peak plasma concentration (C max ), 91.43 ± 30.82 µg·h-1·ml-1 , 55.49 ± 37.58 µg·h-1·ml-1 , 96.50 ± 47.24 µg·h-1·ml-1 , 101.47 ± 33.07 µg·h-1·ml-1 , respectively, for area under the concentration-time curve (AUC 0-24 h ). CONCLUSIONS: Although the concentrations of RFP for formulations A, C, and D were within the reported acceptable therapeutic range, only formulation A was bioequivalent to the reference product. The three two-drug FDCs (formulations B, C and D) displayed inferior RFP bioavailability compared with the reference (Chinese Clinical Trials registration number: ChiCTR-TTRCC-12002451).