70 research outputs found
Use of WGS in M. tuberculosis routine diagnosis
AbstractWhole Genome Sequencing (WGS) is becoming affordable with overall costs comparable to other tests currently in use to perform the diagnosis of drug resistant tuberculosis and cluster analysis. The WGS approach allows an “all-in one” approach providing results on expected sensitivity of the strains, genetic background, epidemiological data and indication of risk of laboratory cross-contamination.Although ideal, WGS from the direct diagnostic specimen is not yet standardized and up today the two most promising approaches are WGS from early positive liquid culture and targeted sequencing from diagnostic specimens using Next Generation Technology. Both have advantages and disadvantages. Sequencing from early MGIT requires positive cultures while targeted sequencing can be performed from a specimen positive for M. tuberculosis with a consistent gain in time to information. Aim of this study is to evaluate the feasibility and cost to use WGS with a centralized approach to speed up diagnosis of tuberculosis in a low incidence country.From March to September 2016 we collected and processed by WGS 89 early positive routine MGIT960 tubes. Time to diagnosis and accuracy of this technique were compared with the standard testing performed in the routine laboratory.An aliquot of 2ml of early positive MGIT was processed, starting with heat inactivation. DNA was then isolated by using the Maxwell 16 Cell DNA Purification Kit and Maxwell 16 MDx for automated extraction. Paired-end libraries of read-length 75–151bp were prepared using the Nextera XT DNA Sample Preparation kit, and sequenced on Illumina Miseq/Miniseq platform (based on the first available run). Total variant calling was performed according to the pipeline of the Phyresse web-tool.The DNA isolation step required 30′ for inactivation plus 30′ for extraction. The concentration obtained ranged from 0.1 to 1ng/μL, suitable for library preparation. Samples were sequenced with a turn around time of 24–48h. The percentage of reads mapped to H37Rv reference genome was 83% on average. Mean read coverage was 65×. Main challenge was the presence of non–mycobacterial DNA contamination in a variable amount. Lineage detection was possible for all cases, and mutations associated to drug resistance to antitubercular drugs were examined. We observed high diagnostic accuracy for species identification and detection of full drug resistance profile compared to standard DST testing performed in MGIT.Two events of recent transmissions including respectively three and two patients were identified and two laboratory cross-contamination were investigated and confirmed based on the analysis. Time to availability of report was around 72h from MGIT positivity compared to up to 6–9weeks for XDR-TB diagnosis with standard testing.In addition to speed, main advantages were the availability of a full prediction of resistance determinants for rifampicin resistant cases, the fast detection of potential cross-contaminations and clusters to guide epidemiological investigation and cross border tracing.Cost analysis showed that the cost per strain was approximately 150 Euro inclusive of staff cost, reagents and machine cost.WGS is a rapid, cost-effective technique that promises to integrate and replace the other tests in routine laboratories for an accurate diagnosis of DR-TB, although suitable nowadays for cultured samples only
Exportation of MDR TB to europe from setting with actively transmitted persistent strains in peru
We performed a cross-border molecular epidemiology analysis of multidrug-resistant tuberculosis in Peru, Spain, and Italy. This analysis revealed frequent transmission in Peru and exportation of a strain that recreated similar levels of transmission in Europe during 2007–2017. Transnational efforts are needed to control transmission of multidrug-resistant tuberculosis globally
Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing
Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.
Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.
Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.
Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.
Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation
Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples
Best approaches to drug-resistance surveillance at the country level
In 2014, the World Health Organization (WHO) recommendation to include the endorsed rapid molecular technologies (Xpert MTB/RIF, line probe assays) into surveillance systems and surveys allowed the testing of more tuberculosis (TB) patients for drug resistance at country level than ever before. The whole genome sequencing (WGS) approach is emerging as a more powerful tool for epidemiological and drug-resistant routine surveillances, promising a rapid and simultaneous screening of all the clinically-relevant mutations for the determination of resistance to the first-, second-line, and new anti-TB drugs. In addition, WGS can support the conventional contact tracing for epidemiological studies with high discriminatory power by tracking the circulating strains and their relatedness. These features make WGS, moreso than the conventional molecular tools, an ideal tool to monitor transmission and drug resistance trends in countries, providing deep and wide information in a standardized way.
WGS technologies have already been adopted in many supranational and reference laboratories at the centralized level, and several research groups are working to reduce the complexity and costs of these platforms, from sample preparation to the downstream analysis and interpretation of sequencing reads, with the final aim to expand the use of WGS to all laboratory levels. The landscape of the platforms available for next-generation sequencing (NGS) is rapidly enriching. It includes high-throughput instruments that can be used for centralized surveillance studies on a large scale, and “benchtop” sequencers that conversely can reach more peripheral settings for rapid and non-extensive surveys.
Traditionally, WGS is performed on genomic DNA samples extracted from clinical isolates to ensure the required high DNA quality and quantity for the following library preparation and sequencing reaction steps. Nevertheless, the researchers are trying to apply the WGS to early primary cultures and in particular directly to sputum samples, including specific procedures to remove non-mycobacterial genetic material and to enrich the Mycobacterium tuberculosis (MTB) genome. The targeted NGS approach that takes advantage of the amplification of selected regions of the MTB genome for genotyping and drug resistance determination could represent the most effective method to avoid the need of culturing MTB prior to sequencing, also enabling the implementation of NGS for surveillance purposes in resource-limited settings without infrastructures and equipment for growing TB cultures.
Classical sequencing and NGS approaches have been successfully used in a recent study conducted in five countries with high burden of TB and multidrug resistant tuberculosis (MDR-TB) and aimed at investigating levels of resistance to pyrazinamide among patients with TB by pncA sequencing [doi: 10.1016/S1473-3099(16)30190-6]. This work innovatively demonstrated that the establishment of strong links between national (peripheral and reference laboratories) and supranational laboratories, with the former possibly processing indirect or direct samples and generating sequencing data, and the latter supporting them for bioinformatics analysis and data interpretation, will soon make WGS and targeted NGS the preferred tools to conduct public health surveillances in TB field, thus helping the strategies adopted by TB control programs at local and national levels
Absence of antibodies to tissue-type plasminogen activator in patients with previous deep vein thrombosis
Antibodies to tissue-type plasminogen activator in plasma from patients with primary antiphospholipid syndrome
A reduction in fibrinolysis has been described in association with thrombosis in the primary antiphospholipid syndrome (PAPS). In this study, we measured anti-tissue-type plasminogen activator (t-PA) antibodies and anti-fibrin-bound t-PA antibodies as possible causes of hypofibrinolysis in 39 patients with PAPS. We also evaluated the differences in anti t-PA antibodies between patients without previous thrombosis (20 patients) and patients with previous episodes of thrombosis (19 patients: deep vein thrombosis in nine, ischaemic stroke in six, arterial leg thrombosis in one, hepatic vein thrombosis in one, thrombophlebitis in one and cerebral venous thrombosis in one). Anti-t-PA antibodies were measured by an enzyme-linked immunosorbent assay (ELISA), and anti-t-PA fibrin-bound antibodies were measured by a solid-phase fibrin immunoassay (SOFIA) in 39 patients with PAPS and in 39 controls matched for gender and age. High levels of IgG anti-t-PA were found in three out of 39 patients with PAPS, and all three patients had a history of thrombosis; four other patients, one of whom had a history of thrombotic events, had high titres of antibodies directed against fibrin-bound t-PA. In addition, patients with ischaemic stroke had significantly higher levels of IgG anti-t-PA than patients without thrombosis (P = 0.029). In conclusion, our data showed that, in patients with PAPS, the highest levels of anti-t-PA antibodies were present in subjects with previous thrombotic events. The discrepancy in the results obtained with two methods of detection of anti-t-PA antibodies, ELISA and SOFIA, indicates a different interaction of the antibodies with the t-PA molecules, which are directly bound to polystyrene plates in ELISA and bound to fibrin as a bridging molecule in SOFI
Antibodies to tissue-type plasminogen activator (tPA) in patients with antiphospholipid syndrome : evidence of interaction between the antibodies and the catalytic domain of tPA in 2 patients
The causes of thrombosis and pregnancy loss in anti phospholipid syndrome (APS) are still unknown, although several hypotheses have been proposed and hypofibrinolysis has been implicated. Anti-tissue-type plasminogen activator (tPA) antibodies may induce fibrinolytic defects and preliminary data indicate an association with thrombosis in APS. We measured plasma anti-tPA antibody levels in 91 consecutive patients with APS, 91 healthy controls, 40 patients with antiphospholipid antibodies without APS symptoms, and 23 patients with systemic lupus erythematosus (SLE) without antiphospholipid antibodies and APS symptoms. Patients with APS had anti-tPA antibody levels higher than controls (P = .0001), patients with SLE (P = .0001), and asymptomatic antiphospholipid patients (P = .05). A subgroup of 53 patients had plasma levels of tPA antigen higher (P = .0001) and tPA activity lower (P = .05) than controls, with an inverse correlation (r = -0.454; P = .003) between anti-tPA antibody levels and tPA activity and no correlation with tPA antigen. The 2 patients with the highest antibody levels had tPA activity below the normal range. Their antibodies were, respectively, IgG1 and IgG3; both recognized human tPA, recombinant tPA, and the catalytic domain of tPA, but not beta(2)-glycoprotein 1, prothrombin, or plasminogen. Our data indicate that anti-tPA antibodies specifically interacting with the catalytic domain of tPA can be found in patients with APS, representing a possible cause of hypofibrinolysis
Quinine treatment in severe Plasmodium falciparum malaria in children: a holter monitoring
Aim. Malaria has elevated incidence and mortality rate especially in African children. Standard treatment in severe Plasmodium falciparum malaria is parenteral quinine in most rural hospitals of developing countries, but little is known about the toxicity of quinine in children. Quinine has potential heart toxicity due to prolongation of the QT that could lead to the onset of dangerous ventricular arrhythmias. The aim of our work is the evaluation of cardiac toxicity of i.v. quinine in children affected by severe Plasmodium falciparum malaria. Methods. Ten children admitted to Mugana hospital (North Tanzania) affected by severe malaria, were treated with a loading dose of 20 mg/kg salt of quinine followed by 10 mg/kg every 8 hours. Holter monitoring was performed for the first 24 hours of treatment with special attention to ventricular and supraventricular arrhythmias, QT prolongation and RR variability. Results. No patient died, and treatment was well tolerated. Heart rate means ranged between 100 and 156 bpm in the population studied, with single values from 56 to 186 bpm. Minimal not significant supraventricular and ventricular arrhythmias were recorded, with no more than 6 isolated supraventricular extrasystoles and 6 supraventricular pairs of extrasystoles, and no more than 15 isolated ventricular extrasystoles. No major, life threatening ventricular arrhythmias were observed. RR analysis did not show significant fluctuations. Conclusion. These data suggest that in the pediatric African population affected by severe Plasmodium falciparum malaria quinine infusion seems to be well tolerated
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