Vaccination Shapes Within-Host SARS-CoV-2 Diversity of Omicron BA.2.2 Breakthrough Infection.

BACKGROUND: Low-frequency intrahost single-nucleotide variants of SARS-CoV-2 have been recognized as predictive indicators of selection. However, the impact of vaccination on the intrahost evolution of SARS-CoV-2 remains uncertain at present. METHODS: We investigated the genetic variation of SARS-CoV-2 in individuals who were unvaccinated, partially vaccinated, or fully vaccinated during Shanghai's Omicron BA.2.2 wave. We substantiated the connection between particular amino acid substitutions and immune-mediated selection through a pseudovirus neutralization assay or by cross-verification with the human leukocyte antigen-associated T-cell epitopes. RESULTS: In contrast to those with immunologic naivety or partial vaccination, participants who were fully vaccinated had intrahost variant spectra characterized by reduced diversity. Nevertheless, the distribution of mutations in the fully vaccinated group was enriched in the spike protein. The distribution of intrahost single-nucleotide variants in individuals who were immunocompetent did not demonstrate notable signs of positive selection, in contrast to the observed adaptation in 2 participants who were immunocompromised who had an extended period of viral shedding. CONCLUSIONS: In SARS-CoV-2 infections, vaccine-induced immunity was associated with decreased diversity of within-host variant spectra, with milder inflammatory pathophysiology. The enrichment of mutations in the spike protein gene indicates selection pressure exerted by vaccination on the evolution of SARS-CoV-2.

Ruthenium-catalyzed C-H functionalization of indoles and indolines with 7-azabenzonorbornadienes: access to aminodihydronaphthyl indoles and indolines.

Indoles, indolines and hydronaphthylamines are ubiquitous structural motifs in natural products, pharmaceuticals, and biologically active molecules. In this paper, we report the synthesis of aminodihydronaphthyl-substituted indoles and indolines via a Ru-catalyzed carbamoyl-directed C-H functionalization of indoles and indolines with 7-azabenzonorbornadienes. In the presence of Cu(OAc)2 and AgSbF6, [Ru(p-cymene)Cl2]2 catalyzes the reaction of 1-carbamoylindoles with 7-azabenzonorbornadienes to produce 2-(1-amino-1,2-dihydronaphthalen-2-yl)indoles. Under the same conditions, the reaction of 1-carbamoylindolines with 7-azabenzonorbornadienes affords 7-(1-amino-1,2-dihydronaphthalen-2-yl)indolines. In both cases, the reactions yield cis-configured products.

Serum lipids may causally affect the occurrence of alopecia areata: A Mendelian randomization study.

PURPOSE: The etiology of alopecia areata (AA) in relation to serum lipids remains unclear, thereby prompting our intention to do Mendelian study on this subject. DESIGN: Two-sample Mendelian randomization (MR) analysis was performed in the study. The inverse variance-weighted method was used as the primary method. METHODS: In our study, we integrated a set of 123 single-nucleotide polymorphisms (SNPs) into our analysis. These SNPs have been extensively studied and are known to exhibit associations with serum lipids. We sourced these SNPs from a variety of relevant studies and consortia that specifically focus on lipid-related research, such as the MRC Integrative Epidemiology Unit. These carefully curated SNPs were then utilized as instrumental variables in our analysis, allowing us to explore and evaluate the causal relationships between these genetic variants and serum lipids. By incorporating this comprehensive set of SNPs, we aimed to enhance the precision and robustness of our findings, shedding light on the intricate interplay between genetics and serum lipids. RESULTS: In the MR analysis, a higher total lipid concentration in large low-density lipoprotein (LDL) particles (odds ratio [OR] = 1.502; 95% confidence interval [CI] = 1.086-1.953; p = 0.006), a greater ratio of cholesteryl esters to total lipids in chylomicrons and extremely large very LDL (VLDL) particles (OR = 2.174; 95% CI = 1.300-2.500; p = 0.010), and a greater ratio of cholesterol to total lipids in chylomicrons and extremely large VLDL particles (OR = 2.363;95% CI = 1.556-4.438; p = 0.004), were genetically predicted to be causally associated with an increased risk of AA, while patients with a higher triglyceride to total lipids ratio in chylomicrons and extremely large VLDL particles had a lower risk of AA (OR = 0.481; 95% CI = 0.191-1.270; p = 0.002). CONCLUSION: This study found that serum lipids may be causally implicated in AA.

Mo2 N-ZrO2 Heterostructure Engineering in Freestanding Carbon Nanofibers for Upgrading Cycling Stability and Energy Efficiency of Li-CO2 Batteries.

Li-CO2 batteries have attracted considerable attention for their advantages of CO2 fixation and high energy density. However, the sluggish dynamics of CO2 reduction/evolution reactions restrict the practical application of Li-CO2 batteries. Herein, a dual-functional Mo2 N-ZrO2 heterostructure engineering in conductive freestanding carbon nanofibers (Mo2 N-ZrO2 @NCNF) is reported. The integration of Mo2 N-ZrO2 heterostructure in porous carbons provides the opportunity to simultaneously accelerate electron transport, boost CO2 conversion, and stabilize intermediate discharge product Li2 C2 O4 . Benefiting from the synchronous advantages, the Mo2 N-ZrO2 @NCNF catalyst endows the Li-CO2 batteries with excellent cycle stability, good rate capability, and high energy efficiency even under high current densities. The designed cathodes exhibit an ultrahigh energy efficiency of 89.8% and a low charging voltage below 3.3 V with a potential gap of 0.32 V. Remarkably, stable operation over 400 cycles can be achieved even at high current densities of 50 µA cm-2 . This work provides valuable guidance for developing multifunctional heterostructured catalysts to upgrade longevity and energy efficiency of Li-CO2 batteries.

Rapid Detection of Extensive Drug Resistance by Xpert MTB/XDR Optimizes Therapeutic Decision-Making in Rifampin-Resistant Tuberculosis Patients.

The Xpert MTB/XDR assay met the critical need for etiologic diagnosis of tuberculosis and rifampin resistance in previous studies. However, its benefits in tailoring the treatment regimen and improving the outcome for patients with rifampin-resistant tuberculosis (RR-TB) require further investigation. In this study, the Xpert MTB/XDR assay was used to determine the resistance profile of second-line drugs for RR-TB patients in two registered multicenter clinical trials, TB-TRUST (NCT03867136) and TB-TRUST-plus (NCT04717908), with the aim of testing the efficacy of all-oral shorter regimens in RR-TB patients in China. Patients would receive the fluoroquinolone-based all-oral shorter regimen, the injectable-containing regimen, or the bedaquiline-based regimen depending on fluoroquinolone susceptibility by using Xpert MTB/XDR. Among the 497 patients performed with Xpert MTB/XDR, 128 (25.8%) had infections resistant to fluoroquinolones and/or second-line injectable drugs (SLIDs). A total of 371 participants were recruited for the trials, and whole-genome sequencing (WGS) was performed on all corresponding culture-positive baseline strains. Taking the WGS results as the standard, the accuracy of the Xpert MTB/XDR assay in terms of resistance detection was 95.2% to 99.0% for all drugs. A total of 33 cases had inconsistent results, 9 of which were due to resistance heterogeneity. Most of the patients (241/281, 85.8%) had sputum culture conversion at 2 months. In conclusion, the Xpert MTB/XDR assay has the potential to serve as a quick reflex test in patients with RR-TB, as detected via Xpert MTB/RIF, to provide a reliable drug susceptibility profile of the infecting Mycobacterium tuberculosis strain and to initiate optimized treatment promptly.

Totally-green cellulosic fiber with prominent sustained antibacterial and antiviral properties for potential use in spunlaced non-woven fabric production.

The worldwide spread of COVID-19 has put a higher requirement for personal medical protective clothing, developing protective clothing with sustained antibacterial and antiviral performance is the priority for safe and sustaining application. For this purpose, we develop a novel cellulose based material with sustained antibacterial and antiviral properties. In the proposed method, the chitosan oligosaccharide (COS) was subjected to a guanylation reaction with dicyandiamide in the presence of Scandium (III) triflate; because of the relatively lower molecular weight and water solubility of the COS, GCOS (guanylated chitosan oligosaccharide) with high substitution degree (DS) could be successfully synthetized without acid application. In this instance, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the GCOS were only 1/8 and 1/4 of that of COS. The introduction of GCOS onto the fiber endowed the fiber with extremely high antibacterial and antiviral performance, showing 100% bacteriostatic rate against Staphylococcus aureus and Escherichia coli and 99.48% virus load reduction of bacteriophage MS2. More importantly, the GCOS modified cellulosic fibers (GCOS-CFs) exhibit excellent sustained antibacterial and antiviral properties; namely, 30 washing cycles had negligible effect on the bacteriostatic rate (100%) and inhibition rate of bacteriophage MS2 (99.0%). Moreover, the paper prepared from the GCOS-CFs still exhibited prominent antibacterial and antiviral activity; inferring that the sheeting forming, press, and drying process have almost no effect on the antibacterial and antiviral performances. The insensitive of antibacterial and antiviral activity to water washing (spunlace) and heat (drying) make the GCOS-CFs a potential material applicable in the spunlaced non-woven fabric production.

In vitro assessment of 17 antimicrobial agents against clinical Mycobacterium avium complex isolates.

BACKGROUND: Recently, Mycobacterium avium complex (MAC) infections have been increasing, especially in immunocompromised and older adults. The rapid increase has triggered a global health concern due to limited therapeutic strategies and adverse effects caused by long-term medication. To provide more evidence for the treatment of MAC, we studied the in vitro inhibitory activities of 17 antimicrobial agents against clinical MAC isolates. RESULTS: A total of 111 clinical MAC isolates were enrolled in the study and they were identified as M. intracellulare, M. avium, M. marseillense, M. colombiense, M. yongonense, and two isolates could not be identified at the species level. MAC strains had relatively low (0-21.6%) resistance to clarithromycin, amikacin, bedaquiline, rifabutin, streptomycin, and clofazimine, and the resistant rates to isoniazid, rifampin, linezolid, doxycycline, and ethionamide were very high (72.1-100%). In addition, M. avium had a significantly higher resistance rate than that of M. intracellulare for ethambutol (92.3% vs 40.7%, P < 0.001), amikacin (15.4% vs 1.2%, P = 0.049), and cycloserine (69.2% vs 25.9%, P = 0.004). CONCLUSIONS: Our results supported the current usage of macrolides, rifabutin, and aminoglycosides in the regimens for MAC infection, and also demonstrated the low resistance rate against new drugs, such as clofazimine, tedizolid, and bedaquiline, suggesting the possible implementation of these drugs in MAC treatment.

Safety and efficacy of pegylated recombinant human granulocyte colony-stimulating factor during concurrent chemoradiotherapy for small-cell lung cancer: a retrospective, cohort-controlled trial.

OBJECTIVE: To investigate pegylated recombinant human granulocyte colony-stimulating factor (PEG-rhG-CSF) safety and efficacy in preventing hematological toxicity during concurrent chemoradiotherapy (CCRT) for small-cell lung cancer (SCLC). METHODS: We retrospectively assessed 80 SCLC patients treated with CCRT from January 2013 to December 2018 who received PEG-rhG-CSF within 48 hours after the end of chemotherapy, defined as prophylactic use, as the experimental group. An additional 80 patients who were not treated with PEG-rhG-CSF were matched 1:1 by the propensity score matching method and served as the control group. The main observations were differences in hematological toxicity, neutrophil changes, febrile neutropenia (FN) incidence and adverse reactions. Progression-free survival (PFS) and overall survival (OS) were analyzed with regular assessment and follow-up. RESULTS: The leukocyte, neutrophil, erythrocyte, and platelet counts and hemoglobin level decreased after CCRT, but the experimental group had slightly higher leukocyte and neutrophil counts than the control group (P < 0.05). The incidences of grade III-IV leukopenia (18.75% vs. 61.25%) and neutropenia (23.75% vs. 67.5%) in the experimental group were significantly lower than those in the control group (P < 0.05). The absolute neutrophil count was 4.17 ± 0.79 (× 109/L) on day 1 and peaked 6.81 ± 2.37 (× 109/L) on day 10 in the experimental group; the value in the control group was 2.81 ± 0.86 (× 109/L) on day 1. It decreased significantly and reached the minimum 0.91 ± 0.53 (× 109/L) on day 10 (P < 0.05). The experimental group had a lower FN incidence than the control group (P < 0.05). There was also no significant acute esophagitis or pulmonary toxicity. The treatment had no significant effect on PFS (11.4 months vs. 8.7 months, P = 0.958) or OS (23.9 months vs. 17.3 months, P = 0.325) over an 18.6-month median follow-up time. CONCLUSION: PEG-rhG-CSF has good efficacy and safety in preventing hematological toxicity in SCLC patients during CCRT and has no significant effects on PFS or OS.

Recent Advances in 2D Group VB Transition Metal Chalcogenides.

2D materials have received considerable research interest owing to their abundant material systems and remarkable properties. Among them, 2D group VB transition metal chalcogenides (GVTMCs) stand out as emerging 2D metallic materials and significantly broaden the research scope of 2D materials. 2D GVTMCs have great advantages in electrical transport, 2D magnetism, charge density wave, sensing, catalysis, and charge storage, making them attractive in the fields of functional devices and energy chemistry. In this review, the recent progress of 2D GVTMCs is summarized systematically from fundamental properties, growth methodologies to potential applications. The challenges and prospects are also discussed for future research in this field.

Gene expression pattern analysis using dual-color RT-MLPA and integrative genome-wide association studies of eQTL for tuberculosis suscepitibility.

BACKGROUND: When infected with Mycobacterium tuberculosis, only a small proportion of the population will develop active TB, and the role of host genetic factors in different TB infection status was not fully understood. METHODS: Forty-three patients with active tuberculosis and 49 with latent tuberculosis were enrolled in the prospective cohort. Expressing levels of 27 candidate mRNAs, which were previously demonstrated to differentially expressed in latent and active TB, were measured by dual color reverse transcription multiplex ligation dependent probe amplification assay (dcRT-MLPA). Using expression levels of these mRNAs as quantitative traits, associations between expression abundance and genome-wild single nucleotide polymorphisms (SNPs) were calculated. Finally, identified candidate SNPs were further assessed for their associations with TB infection status in a validation cohort with 313 Chinese Han cases. RESULTS: We identified 9 differentially expressed mRNAs including il7r, il4, il8, tnfrsf1b, pgm5, ccl19, il2ra, marco and fpr1 in the prospective cohort. Through expression quantitative trait loci mapping, we screened out 8 SNPs associated with these mRNAs. Then, CG genotype of the SNP rs62292160 was finally verified to be significantly associated with higher transcription levels of IL4 in LTBI than in TB patients. CONCLUSION: We reported that the SNP rs62292160 in Chinese Han population may link to higher expression of il4 in latent tuberculosis. Our findings provided a new genetic variation locus for further exploration of the mechanisms of TB and a possible target for TB genetic susceptibility studies, which might aid the clinical decision to precision treatment of TB.

Refining MDR-TB treatment regimens for ultra short therapy (TB-TRUST): study protocol for a randomized controlled trial.

BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) are unsatisfied to treat, pressing more effective and innovative treatment regimens. New efficient regimens for MDR-TB have obtained high treatment success rates. However, those regimens without drug susceptibility testing (DST) are also likely to contribute to the emergence of resistance. Precision treatments guided by DST might optimize the patients' treatment outcome individually and minimize resistance amplification. METHODS: TB-TRUST is a phase III, multicenter, open-label, randomized controlled clinical trial of non-inferiority comparing the treatment success rate between the World Health Organization (WHO) shorter regimen and the refined ultra-short regimen for fluoroquinolones and second-line injectable drugs susceptible rifampicin-resistant TB. The control arm uses the WHO injectable-containing shorter regimen for 36-44 weeks depending on time of sputum smear conversion. The investigational arm uses a refined ultra-short regimen guided by molecular DST to pyrazinamide via whole-genome sequencing (WGS) to optimize the treatment of pyrazinamide-susceptible patients with levofloxacin, linezolid, cycloserine and pyrazinamide for 24-32 weeks and pyrazinamide-resistant with levofloxacin, linezolid, cycloserine and clofazimine for 36-44 weeks. The primary outcome is the treatment success rate without relapse at 84 weeks after treatment initiation. Secondary outcomes include the time of sputum culture conversion and occurrence of adverse events. Assuming α = 0.025 level of significance (one-sided test), a power of 80%, a < 10% difference in treatment success rate between control arm and investigational (80% vs. 82%), and a 5% lost follow-up rate, the number of participants per arm to show non-inferiority was calculated as 177(354 in total). DISCUSSION: Rapid molecular testing distinguishes patients who are eligible for shorter regimen with fluoroquinolone and the WGS-guided results shorten the treatment to 6 months for pyrazinamide susceptible patients. It's foreseeable that not only novel developed medicines, but also traditional powerful medicines with the susceptibility confirmed by DST are the key factors to ensure the effect of anti-MDR-TB drugs. As a DST-guided precision treatment, TB-TRUST are expected to optimize therapy outcome in more patients who cannot afford the expensive new medicines and minimize and even avoid resistance amplification with the rational use of anti-TB drugs. TRAIL REGISTRATION: ClinicalTrial.gov, NCT03867136 . Registered on March 7, 2019.

Comparative Proteomic Profiling of Methicillin-Susceptible and Resistant Staphylococcus aureus.

Staphylococcus aureus is a highly successful human pathogen responsible for a wide range of infections. This study provides insights into the virulence, pathogenicity, and antimicrobial resistance determinants of methicillin-susceptible and methicillin-resistant S. aureus (MSSA; MRSA) recovered from non-healthcare environments. Three environmental MSSA and three environmental MRSA are selected for proteomic profiling using isobaric tag for relative and absolute quantitation tandem mass spectrometry (iTRAQ MS/MS). Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway annotation are applied to interpret the functions of the proteins detected. 792 proteins are identified in MSSA and MRSA. Comparative analysis of MRSA and MSSA reveals that 8 of out 792 proteins are upregulated and 156 are downregulated. Proteins that have differences in abundance are predominantly involved in catalytic and binding activity. Among 164 differently abundant proteins, 29 are involved in pathogenesis, antimicrobial resistance, stress response, mismatch repair, and cell wall synthesis. Twenty-two proteins associated with pathogenicity including SPA, SBI, CLFA, and DLT are upregulated in MRSA. Moreover, the upregulated pathogenic protein ENTC2 in MSSA is determined to be a super antigen, potentially capable of triggering toxic shock syndrome in the host. Enhanced pathogenicity, antimicrobial resistance, and stress response are observed in MRSA compared to MSSA.

Early Transition Metal Catalysis for Olefin-Polar Monomer Copolymerization.

Introducing polar functional groups into widely used polyolefins can enhance polymer surface, rheological, mixing, and other properties, potentially upgrading polyolefins for advanced, value-added applications. The metal catalyst-mediated copolymerization of non-polar olefins with polar comonomers represents the seemingly most straightforward, atom- and energy-efficient approach for synthesizing polar functionalized polyolefins. However, electrophilic early transition metal (groups 3 and 4)-catalyzed processes which have achieved remarkable success in conventional olefin polymerizations, encounter severe limitations here, largely associated with the Lewis basicity of the polar co-monomers. In recent years, however, new catalytic systems have been developed and successful strategies have emerged. In this Minireview, we summarize the recent progress in early transition metal polymerization catalyst development, categorized by the catalytic metal complex and polar comonomer identity. Furthermore, we discuss advances in the mechanistic understanding of these polymerizations, focusing on critical challenges and strategies that mitigate them.

Polar Isotactic and Syndiotactic Polypropylenes by Organozirconium-Catalyzed Masking-Reagent-Free Propylene and Amino-Olefin Copolymerization.

Polar functionalized isotactic and syndiotactic polypropylenes (PPs) are synthesized by direct, masking-reagent-free propylene and amino-olefin (AO, CH2 =CH(CH2 )x Nn Pr2 , x=2, 3, 6) copolymerizations using the activated precatalysts rac-[Me2 Si(indenyl)2 ]ZrMe2 and [Me2 C(Cp)(fluorenyl)]ZrMe2 , respectively. Polymerization activities at 25 °C are as high as 4208 and 535 kg/(mol h atm) with AO incorporation up to 4.0 mol % and 1.6 mol %, respectively. Remarkably, introducing the amino-olefin comonomers significantly enhances stereoselection for both isotactic (mmmm: 59.5 %→91.0 %) and syndiotactic (rrrr: 66.3 %→81.3 %) products.

Unexpected Precatalyst σ-Ligand Effects in Phenoxyimine Zr-Catalyzed Ethylene/1-Octene Copolymerizations.

Recent decades have witnessed intense research efforts aimed at developing new homogeneous olefin polymerization catalysts, with a primary focus on metal-Cl or metal-hydrocarbyl precursors. Curiously, metal-NR2 precursors have received far less attention. In this contribution, the Zr-amido complex FI2ZrX2 (FI = 2,4-di- tert-butyl-6-((isobutylimino)methyl)phenolate, X = NMe2) is found to exhibit high ethylene polymerization activity and relatively high 1-octene coenchainment selectivity (up to 7.2 mol%) after sequential activation with trimethylaluminum, then Ph3C+B(C6F5)4-. In sharp contrast, catalysts with traditional hydrocarbyl ligands such as benzyl and methyl give low 1-octene incorporation (0-1.0 mol%). This unexpected selectivity persists under scaled/industrial operating conditions and was previously inaccessible with traditional metal-Cl or -hydrocarbyl precursors. NMR, X-ray diffraction, and catalytic control experiments indicate that in this case an FI ligand is abstracted from FI2Zr(NMe2)2 by trimethylaluminum in the activation process to yield a catalytically active cationic mono-FIZr species. Heretofore this process was believed to serve only as a major catalyst deactivation pathway to be avoided. This work demonstrates the importance of investigating diverse precatalyst monodentate σ-ligands in developing new catalyst systems, especially for group 4 olefin polymerization catalysts.

Significant Polar Comonomer Enchainment in Zirconium-Catalyzed, Masking Reagent-Free, Ethylene Copolymerizations.

In principal, the direct copolymerization of ethylene with polar comonomers should be the most efficient means to introduce functional groups into conventional polyolefins but remains a formidable challenge. Despite the tremendous advances in group 4-centered catalysis for olefin polymerization, successful examples of ethylene + polar monomer copolymerization are rare, especially without Lewis acidic masking reagents. Here we report that certain group 4 catalysts are very effective for ethylene + CH2 =CH(CH2 )n NR2 copolymerizations with activities up to 3400 Kg copolymer mol-1 -Zr h-1 atm-1 , and with comonomer enchainment up to 5.5 mol % in the absence of masking reagents. Group 4 catalyst-amino-olefin structure-activity-selectivity relationships reflect the preference of olefin activation over free amine coordination, which is supported by mechanistic experiments and DFT analysis. These results illuminate poorly understood facets of d0 metal-catalyzed polar olefin monomer copolymerization processes.

Identification of Novel Mutations in LprG (rv1411c), rv0521, rv3630, rv0010c, ppsC, and cyp128 Associated with Pyrazinoic Acid/Pyrazinamide Resistance in Mycobacterium tuberculosis.

Despite progress, the mechanisms of action and resistance of pyrazinamide (PZA) are not well understood. We characterized 109 mutants resistant to pyrazinoic acid (POA), the active form of PZA, and found that while most (n = 101 [93%]) mutants had panD mutations and 4 (4%) had clpC1 mutations (S91G), new mutations in lprG (rv1411c) and rv0521 (n = 4 [4%]), rv3630, rv0010c, ppsC, and cyp128 (cytochrome P450 128) were identified, shedding new light on the mechanisms of action and resistance of PZA in M. tuberculosis.

Novel Mutations Associated with Clofazimine Resistance in Mycobacterium abscessus.

Mycobacterium abscessus is a major nontuberculous mycobacterial (NTM) pathogen and is responsible for about 80% of all pulmonary infections caused by rapidly growing mycobacteria. Clofazimine is an effective drug active against M. abscessus, but the mechanism of resistance to clofazimine in M. abscessus is unknown. To investigate the molecular basis of clofazimine resistance in M. abscessus, we isolated 29 M. abscessus mutants resistant to clofazimine and subjected them to whole-genome sequencing to identify possible mutations associated with clofazimine resistance. We found that mutations in the MAB_2299c gene (which encodes a possible transcriptional regulatory protein), MAB_1483, and MAB_0540 are most commonly associated with clofazimine resistance. In addition, mutations in MAB_0416c, MAB_4099c, MAB_2613, MAB_0409, and MAB_1426 were also associated with clofazimine resistance but less frequently. Two identical mutations which are likely to be polymorphisms unrelated to clofazimine resistance were found in MAB_4605c and MAB_4323 in 13 mutants. We conclude that mutations in MAB_2299c, MAB_1483, and MAB_0540 are the major mechanisms of clofazimine resistance in M. abscessus Future studies are needed to address the role of the identified mutations in clofazimine resistance in M. abscessus Our findings have implications for understanding mechanisms of resistance to clofazimine and for rapid detection of clofazimine resistance in this organism.

Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis.

OBJECTIVES: d-Cycloserine is an important second-line drug used to treat MDR- and XDR-TB. However, the mechanisms of resistance to d-cycloserine are not well understood. Here we investigated the molecular basis of d-cycloserine resistance using in vitro-isolated resistant mutants. METHODS: Mycobacterium tuberculosis H37Rv was subjected to mutant selection on 7H11 agar plates containing varying concentrations of d-cycloserine. A total of 18 d-cycloserine-resistant mutants were isolated and subjected to WGS. The identified mutations associated with d-cycloserine resistance were confirmed by PCR and Sanger sequencing. RESULTS: We identified mutations in 16 genes that are associated with d-cycloserine resistance. Interestingly, we found mutations only in alr (rv3423c) encoding alanine racemase, but not in other known d-cycloserine resistance-associated genes such as ddl, cycA or ald. Instead, we identified 13 new genes [rv0059, betP (rv0917), rv0221, rv1403c, rv1683, rv1726, gabD2 (rv1731), rv2749, sugI (rv3331), hisC2 (rv3772), the 5' intergenic region of rv3345c and rv1435c, and the 3' region of rv0759c] that had solo mutations associated with d-cycloserine resistance. Our findings indicate that the mechanisms of d-cycloserine resistance are more complex than previously thought and involve genes participating in different cellular functions such as lipid metabolism, methyltransferase, the stress response and transport systems. CONCLUSIONS: New mutations in diverse genes associated with d-cycloserine resistance have been identified that shed new light on the mechanisms of action and resistance of d-cycloserine. Future studies are needed to verify these findings in clinical strains so that molecular detection of d-cycloserine resistance for improved treatment of MDR-TB can be developed.

Targeted Metagenome Based Analyses Show Gut Microbial Diversity of Inflammatory Bowel Disease patients.

Inflammatory bowel disease (IBD) is a multifactorial disease including both genetic and environmental factors. We compared the diversity of intestinal microbesamong a cohort of IBD patients to study the microbial ecological effects on IBD. Fecal samples from patients were sequenced with next generation sequence technology at 16S rDNA region. With statistical tools, microbial community was investigated at different level. The gut microbial diversity of Crohn's disease (CD) patients and colonic polyp (CP) patients significantly different from each other. However, the character of ulcerative colitis (UC) patients has of both CD and CP features. The microbial community from IBD patients can be very different (CD patient) or somewhat similar (UC patients) to non-IBD patients. Microbial diversity can be an important etiological factor for IBD clinical phenotype.