Journal articles on the topic 'Mycobacterium detection NRA'

Emergence of multidrug-resistant tuberculosis (MDR-TB) urgently demands for simple, rapid and inexpensive methods of its detection for the effective treatment of drug resistant tuberculosis, particularly in low-income countries. This prospective study was carried out at National Tuberculosis Reference Laboratory and South Asian Association of Regional Cooperation (SAARC) Tuberculosis and HIV/AIDS Centre, Thimi, Bhaktapur, Nepal, from November 2009 to May 2010 to evaluate nitrate reductase assay (NRA) efficacy for rapid determination of streptomycin, isoniazid, rifampicin and ethambutol susceptibility of Mycobacterium tuberculosis strains. A total of 113 clinical isolates of M. tuberculosis were tested for four first line antitubercular drugs by nitrate reductase assay and were compared with standard proportion method. Results were available in 7-14 days by NRA as compared to proportion method which generally takes 4-6 weeks. The sensitivity and specificity of NRA were 98.1% and 100% for isoniazid, 95.1% and 98.6% for rifampicin, 91.4% and 94.9% for streptomycin, and 78.6% and 97.9% for ethambutol respectively. Agreement between NRA and proportion method were 99.1%, 97.3%, 93.8%, 95.6% for isoniazid, rifampicin, streptomycin and ethambutol, respectively. NRA is easier, inexpensive and reliable method for susceptibility testing of Mycobacterum tuberculosis for isoniazid and rifampicin, the two most important drugs for the treatment of tuberculosis. The reduction in susceptibility testing time, and higher sensitivity and specificity of NRA method is of fundamental importance in detecting MDR-TB.
 Key words: Drug susceptibility, MDR-TB, NRA, proportion method

The global increase in tuberculosis drug resistant which is a threat to its control, require low cost method of diagnosis and detection. Available conventional and molecular methods consume time, and are expensive for countries with high disease burden. Nitrate Reductase Assay (NRA) and Microscopic Observation Drug Susceptibility (MODS) performance to directly detect tuberculosis resistance to four drugs was evaluated. The NRA (liquid and solid) and MODS performance of smear-positive sputum samples were evaluated; Sensitivities and specificities were compared with Proportion Method (PM). Sensitivity and specificity of liquid NRA (LNRA) were 90% and 98% (rifampicin), 81.8% and 100% (isoniazid), 88.9% and 98.1% (streptomycin), and 57.1% and 94.4% (ethambuthol). Also, the sensitivity and specificity for solid NRA (SNRA) were 69.2% and 98.3% (rifampicin); 100% and 100% (isoniazid); 88.9% and 95.2% (streptomycin); 70% and 80.6% (ethambuthol). Moreover, For MODS, rifampicin and isoniazid sensitivity and specificity was 100%, it was 100% and 98.1% for streptomycin, and 71.4% and 98.2% for ethambuthol. At day 14, the results available for LNRA, SNRA and MODS were 93%, 68.5% and 100% respectively. The agreement between LNRA and PM was 97% (RIF, INH and SM) and 90% (EMB). For SNRA, it was 93% (RIF), 100% (INH), 94% (SM) and 89% (EMB). While for MODS, it was 100% (RIF and INH), 98% (SM) and 95% (EMB). Direct NRA and MODS are sensitive, reliable and fast for antituberculosis drug susceptibility; they have potential to effectively and reliably detect drug resistant tuberculosis in the low resource countries.

Introduction: Emergence of multidrug-resistant tuberculosis (MDR-TB) urgently demands for simple, rapid and inexpensive methods of its detection for the effective treatment of drug resistant tuberculosis, particularly in low-income countries. Methodology: This prospective study was carried out at National Tuberculosis Reference Laboratory and South Asian Association of Regional Cooperation (SAARC) Tuberculosis and HIV/AIDS Centre, Thimi, Bhaktapur, Nepal, from November 2009 to May 2010 to evaluate nitrate reductase assay (NRA) efficacy for rapid determination of streptomycin, isoniazid, rifampicin and ethambutol susceptibility of Mycobacterium tuberculosis strains. Results: A total of 113 clinical isolates of M. tuberculosis were tested for four first line antitubercular drugs by nitrate reductase assay and were compared with standard proportion method. Results were available in 7-14 days by NRA as compared to proportion method which generally takes 4-6 weeks. The sensitivity and specificity of NRA were 98.1% and 100% for isoniazid, 95.1% and 98.6% for rifampicin, 91.4% and 94.9% for streptomycin, and 78.6% and 97.9% for ethambutol, respectively. Agreement between NRA and proportion method were 99.1%, 97.3%, 93.8%, 95.6% for isoniazid, rifampicin, streptomycin and ethambutol, respectively. Conclusion: NRA is easier, inexpensive and reliable method for susceptibility testing of Mycobacterum tuberculosis for isoniazid and rifampicin, the two most important drugs for the treatment of tuberculosis. The reduction in susceptibility testing time, and higher sensitivity and specificity of NRA method is of fundamental importance in detecting MDR-TB. SAARC Journal of Tuberculosis, Lung Diseases & HIV/AIDS; 2012; IX(2) 5-8 DOI: http://dx.doi.org/10.3126/saarctb.v9i2.7971

The nitrate reductase assay (NRA) was used as an alternative method for detection of resistance to the first-line antituberculous drugs isoniazid, rifampicin, ethambutol and streptomycin. A total of 320 strains of Mycobacterium tuberculosis were studied and the results compared with the proportion method (PM) on Löwenstein–Jensen medium. The mean time to obtain results was 10 days and the overall agreement between the NRA and PM was 98.8 %. The NRA was easy to perform and represents a useful tool for rapid and accurate determination of drug-resistant M. tuberculosis strains in low-resource countries.

<strong>Aims: </strong>To evaluate nitrate reductase assay for detection of multi-drug resistant <em>Mycobacterium tuberculosis</em> among patients at National Tuberculosis Reference Laboratory Zaria Nigeria. <strong>Study Design:</strong> Hospital based cross sectional study <strong>Place and Duration of Study:</strong> National Tuberculosis Reference Laboratory Zaria Nigeria from December 2015 to June 2016. <strong>Methodology:</strong> A total of 437 re-treatment patients’ samples were screened for Acid Fast Bacilli (AFB), 72 were smear positive. Out of 72 smears positive, 62 were culture positive, using Lowenstein Jensen medium, 57 were found to be <em>Mycobacterium tuberculosis</em> complex (MTBC) using immunochromatographic test. In this study the susceptibility of 57 MTBC isolates to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and Ethambutol (EMB) was determined by Lowenstein Jensen proportion method (LJPM) and Nitrate Reductase Assay (NRA) <strong>Results:</strong> The sensitivity and specificity of NRA compared to that of LJPM were observed to be 98% and 89%, 98% and 92%, 64% and 80%, 68% and 77% for RIF, INH, STR, and EMB respectively. Positive predictive values were 91%, 93%, 87% and 83% for RIF, INH, STR and EMB respectively. Negative predictive values were 80%, 92%, 67% and 90% for RIF, INH, STR and EMB respectively .Overall, the sensitivity, specificity ,positive predictive value and negative predictive value of NRA in detecting MDR-TB were 90%,82%,85%and 73% respectively. Good agreement was found in all the tests with κ values of 0.63, 0.61, 0.61 and 0.62 for RIF, INH, EMB and MDR-TB respectively only STR shows moderate agreements with k value of 0.59. <strong>Conclusion:</strong> In the emergence of MDR-TB, the NRA may be of great importance due to its higher sensitivity and specificity for the rapid detection of rifampicin and isoniazid resistance, the two most important drugs for tuberculosis treatment. On the basis of our findings, NRA has the potential to be a useful tool for accurate detection of MDR-TB in the study area.

Conventional culture and drug susceptibility testing (DST) methods for Mycobacterium tuberculosis are laborious and time consuming. For this reason alternative rapid culture and DST techniques are urgently needed to shorten the time for drug-resistance detection. A total of 222 smear-positive sputum samples were evaluated by the direct nitrate reductase assay (D-NRA) on Lowenstein–Jensen medium, for the rapid and simultaneous detection of resistance to isoniazid, rifampicin, kanamycin and ofloxacin. p-Nitrobenzoic acid was also included for identification of the M. tuberculosis complex. Results were compared with the BACTEC MGIT 960 as gold standard. The general performance of the D-NRA was very good, reaching a global value of 97 %. D-NRA had a turn-around time of 16.9 days to obtain results while that of the indirect MGIT 960 system was 29 days. D-NRA is a low-cost technology, easy to set up in clinical laboratories and suitable to be used for DST of M. tuberculosis in all smear-positive samples.

INTRODUCTION: The most common method for detection of drug-resistant-Tuberculosis (DR-TB) in resource-limited settings (RLSs) is indirect susceptibility testing on Lowenstein-Jensen (LJ) medium with results available only after 2-3 months. Rapid detection of drug resistance by direct Nitatre Reductase Assay (NRA) expedites Tuberculosis patient management. The objective of the study is to access the feasibility and performance of Direct NRA for detection of DR-TB in National Tuberculosis Center under the National Tuberculosis Control Programme (NTP). MATERIALS AND METHODS: Out of 416 previously treated and new pulmonary TB suspect cases; a total of 117 (28.1%) smear-positive sputa with a positivity score of 1+ or more were used in the study. The NRA results were compared with the gold standard LJ proportion method for 110 (94%) specimens while 7 were either contaminated or culture negative. RESULTS: In comparison with LJ proportion method, the respective sensitivities, specificities, NPV, PPV and kappa agreement were 97.2% (95% CI, 86-100), 95.9%(95% CI, 89-99), 92.1% (95% CI, 78-99) 98.6% (95% CI, 92-100), and 0.92 for INH, 100% (95%CI, 90-100), 98.7% (95% CI, 93- 100), 97.1% (95% CI, 85-100), 100% (95% CI, 95- 100) and 0.98 for RFM, 97.1% (95% CI, 85-100) ,96.1% (95%, 89-99), 91.7% (95% CI, 78-98), 98.7% ((95% CI, 93-100) and 0.92 for SM and 100% (95% CI, 88-100), 97.7% (95% CI, 91-100), 93.3% (95% CI, 78-99), 100% (95% CI, 95- 100)and 0.93 for EMB. CONCLUSIONS: The results obtained by direct NRA demonstrated excellent concordance for all drugs. Direct NRA is an assay which detects DR-TB directly from sputum rapidly and has the potential to become an alternative to existing methods particularly in resource-poor settings.DOI: http://dx.doi.org/10.3126/ijim.v2i2.8319 Int J Infect Microbiol 2013;2(2):34-39

Conventional methods based on measurement of growth in culture media containing antibiotics are available for detection of drug resistance in Mycobacterium Tuberculosis requiring several weeks for results. Newer methods like BACTEC are costly. Hence a simple and rapid alternative method of Nitrate Reductase Assay (NRA) was used in this study to detect resistance to Isoniazid (INH) and Rifampicin (RIF). Sputum samples were collected from patients attending DOTS centre at NKPSIMS from July 2012 to May 2013. Smear AFB Positive samples were only included. After decontamination, 112 sputum were inoculated on plain LJ and 3 Middle Brook 7H9 media (One Plain MB with KNO3, one with KNO3 and INH, one with KNO3 and RIF). Nitrate reduction was tested on Days 7, 10, 14 and 18 of incubation. Control strain H37Rv was used as positive control for nitrate reduction. Eleven samples were contaminated. NRA was performed on 101 samples. Fourteen were resistant to INH, whereas 6 were resistant to RIF and INH. Maximum (46) samples were nitrate positive on day 14. Twenty Eight and 22 samples were positive on day 10 and day 18 respectively. Positivity was seen as early as 7th day in only 5 samples. The present study concludes that this test, being easy, rapid, simple and time saving, can be applied directly on sputum positive patients without waiting for the culture. Thus, NRA can be used as rapid detection test for MDRTB cases in low resource settings.

Introduction: The present study aimed to evaluate a rapid and inexpensive colorimetric nitrate reductase assay (NRA) performed directly on sputum specimens for detection of drug resistance in Mycobacterium tuberculosis (MTB). Methodology: A total of 55 sputum samples were decontaminated and processed by modified Petroff's method. A part of the resulting suspension was used to perform direct NRA (DNRA) and direct proportion method (DPM) analysis. Of the 55 samples, 45 could be used to compare the two methods. Indirect drug sensitivity testing (DST) was also done for 14 MTB strains. Results: Excellent agreement was found between DNRA and DPM testing with κ values of 1, 0.91, 0.91, and 1 for RIF, INH, STR and EMB respectively. The sensitivities and specificities of DNRA compared to that of DPM were observed to be 100 and 100%, 100 and 93%, 95 and 96%, 100 and 100 % for RIF, INH, STR, and EMB respectively. Comparing the results of DNRA, DPM and indirect NRA with those of the gold standard indirect PM for 14 MTB strains showed that sensitivities, specificities and percent agreements were 100, 100 and 100% for all four tested drugs. Results for most of the specimens (55.6%) were available in 21 days with DNRA. Conclusions: We have saved valuable time by omitting the pre-isolation step and conclude that DNRA is a rapid, accurate and inexpensive method for direct DST of MTB and may become an appropriate alternative method for the resource limited settings.

Abstract Objective.—To assess the clinical utility of the commercial nucleic acid amplification (NAA) tests (ie, Amplified Mycobacterium Tuberculosis Direct Test, Gen-Probe, Inc and AMPLICOR Mycobacterium tuberculosis Test, Roche Molecular Systems, Inc) for direct detection of Mycobacterium tuberculosis complex. Data Sources.—Review of the English-language literature. Conclusions.—The performance of both NAA tests is excellent (sensitivity, ≥95%; specificity, 100%) when testing respiratory specimens that are smear-positive for acid-fast bacilli (AFB). Only the Gen-Probe assay is approved for testing respiratory specimens regardless of the AFB smear result. Data from 3 studies showed that the sensitivity of the Mycobacterium Tuberculosis Direct Test in smear-negative patients ranged from 83% to 85%, and that the specificity was 99%. Both NAA tests have been used to test nonrespiratory specimens; in some studies, the performance was comparable to the performance obtained for respiratory specimens, whereas in others, it was lower. The NAA tests also appear to be reliable tools for rapid detection of M tuberculosis complex in positive broth cultures of all specimen types (except blood). The impact of the NAA tests on patient outcome varies based on the result of the AFB smear. In smear-positive patients, public health and hospital infection-control resources are predominantly affected. The potential for influencing patient outcome is much greater when the AFB smear is negative. In smear-negative patients, the NAA test could provide more rapid diagnosis of tuberculosis and subsequent initiation of therapy; eliminate the need for invasive diagnostic procedures, which are both costly and pose an added risk to the patient; and allow earlier discharge of hospitalized patients. Prospective studies concerning the cost-effectiveness of the NAA tests are needed.

Abstract Nucleic acid amplification (NAA) tests for direct detection of Mycobacterium tuberculosis complex in respiratory specimens have the potential to provide a more rapid diagnosis of pulmonary tuberculosis (TB) than is currently possible by conventional stain, culture, and identification tests. Currently, 2 NAA tests—enhanced Amplified Mycobacterium Tuberculosis Direct (MTD) Test (Gen-Probe, Inc) and Amplicor Mycobacterium tuberculosis Test (Roche Molecular Systems, Inc)—have been approved by the Food and Drug Administration for testing respiratory specimens that are smear positive for acid-fast bacilli (AFB). This restriction to AFB smear–positive specimens was based on data from the initial clinical trials conducted to evaluate these products that showed low sensitivity (ie, 48%–53%) and less-than-optimal specificity (ie, 96%–99%) in AFB smear–negative specimens. Data from the clinical trial for the enhanced MTD test and from 2 subsequent studies, however, suggest that this version of the MTD test is a reliable tool for rapid diagnosis of pulmonary TB, regardless of the AFB smear result. Both NAA tests have been evaluated for diagnosis of extrapulmonary TB, and results were comparable to the results of tests performed with respiratory specimens. The NAA tests also appear to be reliable for rapid identification of M tuberculosis complex in positive broth cultures of all specimen types except blood. The impact of the NAA tests on patient outcome varies based on the AFB smear result. With smear-positive results, public health and hospital infection control resources are predominantly affected. With smear-negative results, however, the potential for affecting patient outcome is much greater. In patients with smear-negative results, the NAA test can result in earlier diagnosis of TB and subsequent initiation of therapy. Use of these tests also may eliminate the need for invasive diagnostic procedures, which are costly and pose an added risk to the patient, and they may allow earlier discharge of hospitalized patients.

Objective: We investigated data from US public health laboratories funded through the Centers for Disease Control and Prevention’s Tuberculosis Elimination and Laboratory Cooperative Agreement to document trends and challenges in meeting national objectives in tuberculosis (TB) laboratory diagnoses. Methods: We examined data on workload and turnaround time from public health laboratories’ progress reports during 2009-2013. We reviewed methodologies, laboratory roles, and progress toward rapid detection of Mycobacterium tuberculosis complex through nucleic acid amplification (NAA) testing. We compared selected data with TB surveillance reports to estimate public health laboratories’ contribution to national diagnostic services. Results: During the study period, culture and drug susceptibility tests decreased, but NAA testing increased. Public health laboratories achieved turnaround time benchmarks for drug susceptibility tests at lower levels than for acid-fast bacilli smear and identification from culture. NAA positivity in laboratories among surveillance-reported culture-positive TB cases increased from 26.6% (2355 of 8876) in 2009 to 40.0% (2948 of 7358) in 2013. Public health laboratories provided an estimated 50.9% (4285 of 8413 in 2010) to 57.2% (4210 of 7358 in 2013) of culture testing and 88.3% (6822 of 7727 in 2011) to 94.4% (6845 of 7250 in 2012) of drug susceptibility tests for all US TB cases. Conclusions: Public health laboratories contribute substantially to TB diagnoses in the United States. Although testing volumes mostly decreased, the increase in NAA testing indicates continued progress in rapid M tuberculosis complex detection.

The prompt diagnosis of smear-negative cases is a prerequisite to controlling tuberculosis (TB). Several new laboratory approaches, including nucleic acid amplification (NAA), are being evaluated in various disease settings to meet this challenge. However, NAA needs simplification before it is widely accepted. Furthermore, a supporting smear result improves confidence in and reliability of PCR. In this context, an asymmetric devR PCR assay using two molecular beacon probes for visual or fluorimetric end-point detection of Mycobacterium tuberculosis was developed. The assays reproducibly detected 25 fg M. tuberculosis DNA versus 100 fg by conventional gel electrophoresis (henceforth referred to as gel assay). The devR and IS6110 PCR assays were blindly evaluated on sputum specimens obtained from a directly observed-treatment short-course centre. Universal sample processing (USP) smear microscopy and culture were used as a supportive test and the ‘gold’ standard, respectively. Among the 148 specimens analysed, 120 were M. tuberculosis culture-positive. Amongst the 122 direct smear-negative samples, 96 were culture-positive, of which 61 were detected by USP smear microscopy. All 35 USP smear-negative samples were positive by three or more PCR methods. devR PCR had a sensitivity of 92.5 % in the fluorimetric assay versus 86.7 % by visual inspection and 90.8 % by the gel method. IS6110 PCR performed at almost equivalent levels. devR visual and fluorimetric assays considered together yielded an increased sensitivity of 95 % without compromising on a specificity of 92.9 %. The results suggest that the USP smear test is useful for diagnosing direct smear-negative TB and judiciously restricting PCR testing to only smear-negative samples. When used together, these tests can provide rapid diagnosis of smear-negative TB in a cost-effective manner.

The routine conventional phenotypic bacteriological tests available for pulmonary tuberculosis (PTB) diagnosis, such as microscopy by Ziehl Neelsen staining, and Lowenstein Jensen method of solid culture, requires a long time for revealing positivity, resulting in a delayed diagnosis. After Mycobacterium tuberculosis (MTB) genome was discovered, nucleic acid amplification techniques were developed with more rapid detection and identification of rifampicin resistance in respiratory and extra-pulmonary specimens. GeneXpert is a DNA-polymerase chain reaction technique based on NAA, which allows an accurate genotypic method for a quick diagnosis of PTB diagnosis. The aim of the study was to assess retrospectively the yield of genotypic assay GeneXpert in revealing multidrug resistant TB compare to phenotypic confirmation by solid culture. 512 patients with positive and negative smears of suspected PTB were investigated by conventional phenotypic assays. PTB diagnosis assessed by positive genotypic assay and confirmed by phenotypic conventional solid culture method was 78.12%. The yield of GeneXpert in revealing rifampicin resistance was high (n=79/512; 15.43%) with 12.5% additional resistance against isoniazid revealed by positive solid cultures and drug susceptibility test. GeneXpert assay is a very useful method for rapid detection of MTB and drug resistance, which facilitates timely diagnosis and appropriate management of pulmonary tuberculosis.

A number of nucleic acid amplification assays (NAAs) have been employed to detect tubercle bacilli in clinical specimens for tuberculosis (TB) diagnosis. Among these, loop-mediated isothermal amplification (LAMP) is an NAA possessing superior isothermal reaction characteristics. In the present study, a set of six specific primers targeting the Mycobacterium tuberculosis 16S rRNA gene with high sensitivity was selected and a LAMP system (MTB-LAMP) was developed. Using this system, a total of 200 sputum samples from Nepalese patients were investigated. The sensitivity of MTB-LAMP in culture-positive samples was 100 % (96/96), and the specificity in culture-negative samples was 94.2 % (98/104, 95 % confidence interval 90.5–97.9 %). The positive and negative predictive values of MTB-LAMP were 94.1 and 100 %, respectively. These results indicate that this MTB-LAMP method may prove to be a powerful tool for the early diagnosis of TB.

Abstract Background Nucleic acid amplification (NAA) tests rapidly detect Mycobacterium tuberculosis complex directly from clinical specimens, providing valuable results for those evaluated for tuberculosis. Methods We analyzed characteristics of cases with NAA testing performed, compared cases with positive and negative NAA test results, and calculated turnaround time and time-to-treatment for all verified cases reported to the National Tuberculosis Surveillance System in the United States during 2011–2017. Results Among 67,082 verified tuberculosis cases with NAA testing information, 30,820 (45.9%) were reported as not having a NAA test performed; the proportion without NAA testing declined annually, from 60.5% in 2011 to 33.6% in 2017. Of 67,082 verified cases, 27,912 (41.6%) had positive, 8,215 (12.2%) had negative, and 135 (0.2%) had indeterminate NAA test results. Among the 33,937 cases with an acid-fast-bacilli–smear-positive result, 70.9% (24,093) had a NAA test performed; 38.0% (11,490) of the 30,244 with an acid-fast-bacilli–smear-negative result had a NAA test performed. Although sputum was the most common specimen type tested, 79.8% (7,023 of 8,804) of non-sputum specimen types had a positive NAA test result. Overall, 63.7% of cases with laboratory testing had NAA test results reported &amp;lt;6 days following specimen collection; for 13,891 cases not yet on treatment, median time-to-treatment after the laboratory report date was 2 days. Conclusions Our analyses demonstrate increased NAA test utilization between 2011 and 2017. However, a large proportion of cases did not have a NAA test performed, reflecting challenges in broader uptake, suggesting an opportunity to expand use of this diagnostic methodology.

Abstract This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently &amp;gt;1.1 million bacterial isolates, more recently including Streptococcus spp. and Mycobacterium tuberculosis, in addition to Salmonella,Escherichia/Shigella,Clostridioides,Vibrio,Helicobacter,YersiniaandMoraxella. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualizing bacterial genomic population structures, based on pre-computed hierarchical clusters. Access to data and analysis tools is provided through an enhanced graphical user interface and a new application programming interface (RESTful API). EnteroBase is now being developed and operated by an international consortium, to accelerate the development of the platform and ensure the longevity of the resources built. EnteroBase can be accessed at https://enterobase.warwick.ac.uk as well as https://enterobase.dsmz.de.

Abstract Lesions and stable secondary structures in mRNA severely impact the translation efficiency, causing ribosome stalling and collisions. Prokaryotic ribosomal proteins Rps3, Rps4 and Rps5, located in the mRNA entry tunnel, form the mRNA helicase center and unwind stable mRNA secondary structures during translation. However, the mechanism underlying the detection of lesions on translating mRNA is unclear. We used Cryo-EM, biochemical assays, and knockdown experiments to investigate the apurinic/apyrimidinic (AP) endoribonuclease activity of bacterial ribosomes on AP-site containing mRNA. Our biochemical assays show that Rps3, specifically the 130RR131 motif, is important for recognizing and performing the AP-endoribonuclease activity. Furthermore, structural analysis revealed cleaved mRNA product in the 30S ribosome entry tunnel. Additionally, knockdown studies in Mycobacterium tuberculosis confirmed the protective role of Rps3 against oxidative and UV stress. Overall, our results show that prokaryotic Rps3 recognizes and processes AP-sites on mRNA via a novel mechanism that is distinct from eukaryotes.

Abstract The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

Tuberculose é uma doença infecciosa causada pelo Mycobacterium tuberculosis que continua sendo uma das principais causas de morte por doença infecciosa. Este estudo teve como objetivo a identificação de potenciais inibidores da pantotenato sintetase, enzima essencial para a bactéria, através de triagem virtual hierárquica. Modelos baseados na forma e volume moleculares foram construídos e validados para filtrar um banco de dados com estruturas químicas produtos naturais. As moléculas selecionadas foram acopladas na estrutura do alvo molecular, obtido junto ao Protein Data Bank sob o código 3IUB com o programa FRED. O composto ZINC000012489800 foi a mais bem ranqueada. As interações intermoleculares mostraram interações hidrofóbicas, ligações de hidrogênio (aceptoras e doadoras) e iônicas, entre o composto identificado e aminoácidos importantes para o reconhecimento molecular já descritas na literatura. 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