scholarly journals Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Phelim Bradley ◽  
N. Claire Gordon ◽  
Timothy M. Walker ◽  
Laura Dunn ◽  
Simon Heys ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Mycobacterium Tuberculosis ◽  
Sequence Data ◽  
Error Rates ◽  
Graph Representation ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Independent Validation ◽  
Validation Set ◽  
Sensitivity Specificity

Abstract The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package (‘Mykrobe predictor’) that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.

scholarly journals Evaluation of the Abbott LCx Mycobacterium tuberculosis Assay for Direct Detection of Mycobacterium tuberculosis Complex in Human Samples

1999 ◽  
Vol 37 (1) ◽  
pp. 229-232 ◽  
Author(s):  
Maria Grazia Garrino ◽  
Youri Glupczynski ◽  
Josiane Degraux ◽  
Henri Nizet ◽  
Michel Delmée
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Direct Detection ◽  
Clinical Samples ◽  
Culture Methods ◽  
Predictive Values ◽  
Direct Microscopy ◽  
Standard Culture ◽  
Small Gain ◽  
Clinical Interest ◽  
Sensitivity Specificity

Seven hundred thirty-seven clinical samples from 460 patients were processed for direct detection of Mycobacterium tuberculosis complex by a semiautomated ligase chain reaction commercial assay, the LCx Mycobacterium tuberculosis Assay (LCx assay) from Abbott Laboratories. Results were compared to those of direct microscopy and standard microbiological culture. Of 26 patients (5.7%) with a culture positive for M. tuberculosis, 22 (84.6%) were found positive by the LCx assay. The sensitivity of the LCx assay was 98% for smear-positive samples and 27% for smear-negative samples. With an overall culture positivity rate forM. tuberculosis of 8.3% (61 of 737 samples) and after resolution of discrepant results according to clinical data, the sensitivity, specificity, and positive and negative predictive values of the LCx assay were 78, 100, 95, and 98%, respectively, compared to 85, 100, 100, and 98%, respectively, for culture and 67, 99, 87, and 97%, respectively, for acid-fast staining. In conclusion, the LCx assay proved satisfactory and appears to be an easy-to-use 1-day test which must be used with standard culture methods but can considerably reduce diagnosis time versus culture. However, its clinical interest appears to be limited in our population with low mycobacterial prevalence because of its cost considering the small gain in sensitivity versus direct microscopy.

scholarly journals Evaluation of a rapid bacteriophage-based method for the detection of Mycobacterium tuberculosis in clinical samples

2003 ◽  
Vol 52 (4) ◽  
pp. 331-335 ◽  
Author(s):  
Ayman Mohamed Marei ◽  
Eman Mohamed El-Behedy ◽  
Heba Ali Mohtady ◽  
Afify Fahmy Afify
Keyword(s):  
Developing Countries ◽  
Mycobacterium Tuberculosis ◽  
Clinical Performance ◽  
Low Cost ◽  
Urine Samples ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Microbiological Culture ◽  
Time To Diagnosis ◽  
Sensitivity Specificity

Rapid, sensitive and low-cost methods are needed urgently for the detection of Mycobacterium tuberculosis in clinical samples, especially in developing countries. To this end, the clinical performance of FASTPlaqueTBTM (a bacteriophage-based method) has been studied in parallel with microscopy, standard microbiological culture and in-house IS6110-based PCR methods. A total of 64 samples, including 42 sputum samples and 22 urine samples, were tested in this study. The sensitivity, specificity and overall accuracy values for the FASTPlaqueTB assay relative to that of culture were respectively 76.5, 95 and 90 %. The corresponding values for the in-house IS6110-based PCR assay were 88, 91 and 90 % and, for Ziehl–Neelsen staining, were 59, 95 and 85 %. FASTPlaqueTB gave better clinical performance with urine samples than with sputum samples (sensitivity, specificity and overall accuracy were 100 % with urine samples and 64, 93 and 84 % with sputum samples). The 100 % sensitivity of FASTPlaqueTB was higher than that of the corresponding values for PCR (67 %) with urine samples. In conclusion, FASTPlaqueTB proved to be sensitive, cheap relative to the PCR and rapid. It is able to detect M. tuberculosis in clinical samples within 1 day, reducing the time to diagnosis in comparison with culture.

scholarly journals Pharmacodynamic Functions of Synthetic Derivatives for Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis

2020 ◽  
Vol 11 ◽  
Author(s):  
Mojdeh Dinarvand ◽  
Malcolm P. Spain ◽  
Fatemeh Vafaee
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Activity ◽  
Mycobacterium Tuberculosis ◽  
Antimicrobial Agents ◽  
Resistant Bacteria ◽  
Synthetic Compounds ◽  
Methicillin Resistant ◽  
Chemical Structures ◽  
Time Kill

Drug resistant bacteria have emerged, so robust methods are needed to evaluate combined activities of known antibiotics as well as new synthetic compounds as novel antimicrobial agents to treatment efficacy in severe bacterial infections. Marine natural products (MNPs) have become new strong leads in the drug discovery endeavor and an effective alternative to control infections. Herein, we report the bioassay guided fractionation of marine extracts from the sponges Lendenfeldia, Ircinia, and Dysidea that led us to identify novel compounds with antimicrobial properties. Chemical synthesis of predicted compounds and their analogs has confirmed that the proposed structures may encode novel chemical structures with promising antimicrobial activity against the medically important pathogens. Several of the synthetic analogs exhibited potent and broad spectrum in vitro antibacterial activity, especially against the Methicillin-resistant Staphylococcus aureus (MRSA) (MICs to 12.5 μM), Mycobacterium tuberculosis (MICs to 0.02 μM), uropathogenic Escherichia coli (MIC o 6.2 μM), and Pseudomonas aeruginosa (MIC to 3.1 μM). Checkerboard assay (CA) and time-kill studies (TKS) experiments analyzed with the a pharmacodynamic model, have potentials for in vitro evaluation of new and existing antimicrobials. In this study, CA and TKS were used to identify the potential benefits of an antibiotic combination (i.e., synthetic compounds, vancomycin, and rifampicin) for the treatment of MRSA and M. tuberculosis infections. CA experiments indicated that the association of compounds 1a and 2a with vancomycin and compound 3 with rifampicin combination have a synergistic effect against a MRSA and M. tuberculosis infections, respectively. Furthermore, the analysis of TKS uncovered bactericidal and time-dependent properties of the synthetic compounds that may be due to variations in hydrophobicity and mechanisms of action of the molecules tested. The results of cross-referencing antimicrobial activity, and toxicity, CA, and Time-Kill experiments establish that these synthetic compounds are promising potential leads, with a favorable therapeutic index for antimicrobial drug development.

scholarly journals Comparison of Enhanced Mycobacterium tuberculosisAmplified Direct Test with COBAS AMPLICOR Mycobacterium tuberculosis Assay for Direct Detection ofMycobacterium tuberculosis Complex in Respiratory and Extrapulmonary Specimens

2000 ◽  
Vol 38 (4) ◽  
pp. 1559-1562 ◽  
Author(s):  
Claudio Scarparo ◽  
Paola Piccoli ◽  
Alessandra Rigon ◽  
Giuliana Ruggiero ◽  
Mariuccia Scagnelli ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Direct Detection ◽  
Diagnostic Technique ◽  
Clinical Samples ◽  
Direct Test ◽  
Predictive Values ◽  
The Difference ◽  
Sensitivity Specificity ◽  
Detection Ofmycobacterium Tuberculosis ◽  
Respiratory Specimens

The new Roche COBAS AMPLICOR Mycobacterium tuberculosisAssay was compared to the Gen-Probe enhanced Mycobacterium tuberculosis Amplified Direct Test (AMTDII). A total of 486 specimens (296 respiratory and 190 extrapulmonary) collected from 323 patients were tested in parallel with both assays. Results were compared with those of acid-fast staining and culture, setting the combination of culture and clinical diagnosis as the “gold standard.” After resolution of discrepant results, the sensitivity, specificity, and positive and negative predictive values for AMTDII were 85.7, 100, 100, and 90.4% for respiratory specimens and 82.9, 100, 100, and 95.5% for extrapulmonary specimens, respectively. The corresponding values for AMPLICOR were 94.2, 100, 100, and 96.6% for respiratory specimens and 85, 100, 100, and 96.1% for extrapulmonary specimens, respectively. No significant differences were observed between the results of both assays or, within each one, between respiratory and extrapulmonary specimens. The difference between AMTDII and AMPLICOR sensitivities was related to the presence of inhibitory samples, which the former assay, lacking an internal amplification control (IAC), could not detect. The overall inhibition rate for the AMPLICOR assay was 3.9% (19 specimens). It is concluded that, although both amplification assays proved to be rapid and specific for the detection of M. tuberculosis complex in clinical samples, AMPLICOR, by a completely automated amplification and detection procedure, was shown to be particularly feasible for a routine laboratory setting. Finally, AMTDII is potentially an excellent diagnostic technique for both respiratory and extrapulmonary specimens, provided that an IAC is included with the assay.

scholarly journals Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe

2019 ◽  
Vol 4 ◽  
pp. 191 ◽  
Author(s):  
Martin Hunt ◽  
Phelim Bradley ◽  
Simon Grandjean Lapierre ◽  
Simon Heys ◽  
Mark Thomsit ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sequence Data ◽  
Universal Access ◽  
Independent Set ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
Error Rates ◽  
World Health ◽  
Sequencing Data ◽  
Resistance Prediction

Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations.  Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data.  We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.

scholarly journals Five Years’ Evaluation of the BD ProbeTec System for the Direct Molecular Detection of Mycobacterium tuberculosis Complex in Respiratory and Nonrespiratory Clinical Samples

2015 ◽  
Vol 64 (4) ◽  
pp. 391-394 ◽  
Author(s):  
Can Bicmen ◽  
Onur Karaman ◽  
Ayriz T. Gunduz ◽  
Onur F. Erer ◽  
Meral Coskun ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Early Diagnosis ◽  
Molecular Detection ◽  
Mycobacterium Tuberculosis Complex ◽  
Clinical Samples ◽  
Tuberculosis Complex ◽  
Predictive Values ◽  
Smear Negative ◽  
Sensitivity Specificity ◽  
Culture Negative

In this study, Mycobacterium tuberculosis complex was detected by BD ProbeTec ET system in 4716 respiratory and 167 nonrespiratory samples [mostly (98%) smear negative]. Sensitivity, specificity, positive and negative predictive values were 81.8%, 98.3, 85.1 and 97.9 for respiratory and 100%, 96.2, 64.7 and 100, for nonrespiratory samples, respectively. Among 149 (3.1%) ProbeTec DTB positive and culture negative samples, 72 (65 respiratory and seven nonrespiratory) (48.3%) were recovered from the patients who were evaluated as having TB infection. The system has been found as useful in early diagnosis of tuberculosis infection in association with the clinical, radiological and histopathological findings.

scholarly journals Occurrence of bacteria with a dangerous extent of antibiotic resistance in poultry in the Central Region of Moravia

2018 ◽  
Vol 87 (2) ◽  
pp. 165-172 ◽  
Author(s):  
Jan Bardoň ◽  
Patrik Mlynárčik ◽  
Petra Procházková ◽  
Magdaléna Röderová ◽  
Kristýna Mezerová ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Broad Spectrum ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Methicillin Resistant ◽  
Beta Lactamases ◽  
E Coli ◽  
Human Food Chain ◽  
Extended Spectrum Beta Lactamases ◽  
Phenotypic Tests

The study aimed to determine the occurrence ofEnterobacteriaceaeproducing broad-spectrum beta-lactamases, vancomycin-resistant enterococci (VRE) and methicillin-resistantStaphylococcus aureusstrains in poultry in Moravia, Czech Republic, including phenotypic and genotypic analyses of the extent of resistance. Using chromogenic screening media, a total of 240 clinical samples collected from poultry and the poultry farm environment were processed. Phenotypic tests identified 23 isolates of broad-spectrum beta-lactamase-producingEscherichia coliand one VRE isolate (Enterococcus faeciumwith VanA resistance). Methicillin-resistantStaphylococcus aureusstrains were not detected. Among the isolates producing broad-spectrum beta-lactamases, 17 produced extended-spectrum beta-lactamases, most frequently CTX-M; the remaining 6 isolates were CIT-type AmpC enzymes. No carbapenemase-producing strains were detected. Pulsed-field gel electrophoresis showed that 21E. colistrains (91%) were genetically unrelated isolates. Increasing resistance of bacteria to antibiotic agents poses a serious issue for both human and veterinary medicine globally. For humans, a potential source of resistant bacteria may be animals or their products entering the human food chain, for example poultry. The presented study extends existing knowledge about the occurrence of resistant bacteria in poultry in Moravia and describes the phenotype and genotype of their resistance to antibiotics.

scholarly journals Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adriana Maria Sanabria ◽  
Jessin Janice ◽  
Erik Hjerde ◽  
Gunnar Skov Simonsen ◽  
Anne-Merethe Hanssen
Keyword(s):  
Staphylococcus Aureus ◽  
Blood Culture ◽  
Virulence Genes ◽  
Sequence Data ◽  
Joint Infection ◽  
Clinical Samples ◽  
Virulence Determinants ◽  
Periprosthetic Tissue ◽  
Shotgun Metagenomics ◽  
Genome Coverage

AbstractShotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.

scholarly journals Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

2015 ◽  
Author(s):  
Phelim Bradley ◽  
N Claire Gordon ◽  
Timothy M Walker ◽  
Laura Dunn ◽  
Simon Heys ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Single Molecule ◽  
Sequence Data ◽  
Error Rates ◽  
De Bruijn Graph ◽  
Phenotypic Resistance ◽  
Genetic Mechanisms ◽  
Phenotypic Methods ◽  
Sensitivity Specificity ◽  
Scale Control

Rapid and accurate detection of antibiotic resistance in pathogens is an urgent need, affecting both patient care and population-scale control. Microbial genome sequencing promises much, but many barriers exist to its routine deployment. Here, we address these challenges, using a de Bruijn graph comparison of clinical isolate and curated knowledge-base to identify species and predict resistance profile, including minor populations. This is implemented in a package, Mykrobe predictor, for S. aureus and M. tuberculosis, running in under three minutes on a laptop from raw data. For S. aureus, we train and validate in 495/471 samples respectively, finding error rates comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.3%/99.5% across 12 drugs. For M. tuberculosis, we identify species and predict resistance with specificity of 98.5% (training/validating on 1920/1609 samples). Sensitivity of 82.6% is limited by current understanding of genetic mechanisms. We also show that analysis of minor populations increases power to detect phenotypic resistance in second-line drugs without appreciable loss of specificity. Finally, we demonstrate feasibility of an emerging single-molecule sequencing technique.

Sign in / Sign up

Export Citation Format

Share Document