224 research outputs found
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Molecular diagnostics for drug-resistant tuberculosis: Can genetic tests replace conventional diagnostics as predictors of drug resistance and clinical outcome?
No full textBackground: Rapid molecular diagnostics, with their ability to quickly identify genetic mutations associated with drug resistance, have great potential to curb the spread of drug-resistant tuberculosis (DR-TB). Unfortunately, the technical and diagnostic performance of these technologies has yet to be thoroughly evaluated in diverse clinical environments, and the reliability and clinical relevance of the tuberculosis (TB) resistance mutations identified by these assays has not been well characterized.Methods: These analyses use data from a multisite, observational cohort study conducted by the Global Consortium for Drug Resistant TB Diagnostics (GCDD). Chapter 2 assesses the diagnostic performance of a pyrosequencing assay in this study and applies logistic regression to identify the variables associated with poor assay technical performance. Chapter 3 presents the frequency and distribution of all TB resistance mutations identified between clinical sites. Chapter 4 applies multivariate logistic regression to determine the associations between TB resistance mutations and patient mortality for the GCDD study cohort. Results: Chapter 2 found pyrosequencing assay performance to be high, overall, though sensitivity fluctuated between sites. Smear negativity, culture negativity, site (Moldova), and sequencing of the rpoB, gyrA, and rrs genes were associated with poor assay technical performance. Chapter 3 found inclusion of the ahpC and eis promoter gene regions to be critical for optimal test sensitivity for isoniazid resistance detection in South Africa and kanamycin resistance detection in Moldova. Chapter 4 found that the detection of a mutation associated with high-level fluoroquinolone or kanamycin resistance was significantly associated with higher odds of patient mortality by 52 weeks.Conclusions: A DR-TB diagnostic demonstrated excellent specificity in a large, multisite study, though performance was influenced by regional genetics and technical errors. Findings of the high prevalence of low-global frequency TB resistance mutations in specific sites emphasizes that these mutations may be important resistance markers in certain regions. The observation that patients with high-level gyrA and rrs resistance mutations had higher mortality odds provides strong evidence that certain high-level resistance mutations are clinically relevant. Together, these findings underscore the potential for molecular diagnostics to replace conventional growth-based diagnostics as predictors of phenotypic drug resistance and clinical outcome
Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples
No full textTargeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were resequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics, and variant calling were computed using an in-house pipeline and compared to the reference MiniSeq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depths of coverage were 4,151× and 4,177× on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug-resistant markers, including full gene deletions. In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases
Emerg Infect Dis
No full textThe epidemiology of tuberculosis (TB) in the United States is changing as the incidence of disease becomes more concentrated in foreign-born persons. Mycobacterium bovis appears to be contributing substantially to the TB incidence in some binational communities with ties to Mexico. We conducted a retrospective analysis of TB case surveillance data from the San Diego, California, region from 1994 through 2005 to estimate incidence trends, identify correlates of M. bovis disease, and evaluate risk factors for deaths during treatment. M. bovis accounted for 45% (62/138) of all culture-positive TB cases in children (<15 years of age) and 6% (203/3,153) of adult cases. M. bovis incidence increased significantly (p = 0.002) while M. tuberculosis incidence declined (p<0.001). Almost all M. bovis cases from 2001 through 2005 were in persons of Hispanic ethnicity. Persons with M. bovis were 2.55x (p = 0.01) as likely to die during treatment than those with M. tuberculosis
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Cigarette smoking and Mycobacterium tuberculosis infection among persons who inject drugs in Tijuana, Mexico
No full textIncludes bibliographical references (pages 92-93)Background: Cigarette smoking is thought to be a major driver of the global tuberculosis epidemic. However, limited evidence exists to support a causal relationship between smoking and Mycobacterium tuberculosis (Mtb) infection. Cigarette smoking and Mtb infection are highly prevalent among persons who inject drugs, and smoking cessation interventions might help reduce tuberculosis risk in this population. Objectives: This dissertation research sought to expand the current knowledge of the relationship between cigarette smoking and Mtb infection and to describe patterns of cigarette smoking and quit attempts among persons who inject drugs. Methods: Data from longitudinal studies of persons who inject drugs in Tijuana, Mexico, were used to conduct the following studies: 1) a longitudinal analysis of the association between self-reported number of cigarettes smoked per day and incident Mtb infection; 2) a cross-sectional study to describe the association between salivary cotinine levels and Mtb infection; and 3) a cross-sectional study to describe cigarette smoking patterns and quit attempts that lasted ???1 day during the past six months. QuantiFERON-TB Gold In-Tube (QFT) was used to determine Mtb infection. Results: For Study 1, Poisson regression analysis of 129 participants who were QFT negative at baseline found no evidence of an association between self-reported number of cigarettes smoked per day and QFT conversion after controlling for age, gender, education, and alcohol. For 208 participants in Study 2, using multivariable logbinomial regression models adjusted for sex and education, cotinine levels were not associated with QFT positivity when included as smoking categories, but were independently associated with QFT positivity when included as an ordinal variable (prevalence ratio = 1.09 per +1 cotinine level; 95% confidence interval = 1.01 ??? 1.17). Study 3 found that 124 (20.6%) of the 601 current cigarette smokers had made a recent quit attempt. Conclusion: A dose-response relationship was observed between smoking intensity and Mtb infection when cigarette smoke exposure was measured using salivary cotinine but not when using self-report. One out of five participants reported recently making attempts to quit smoking. Cigarette smoking cessation interventions should be implemented for persons who inject drugs and other populations at high risk for tuberculosi
Target product profile for a diagnostic assay to differentiate between bacterial and non-bacterial infections and reduce antimicrobial overuse in resource-limited settings: an expert consensus
No full textAcute fever is one of the most common presenting symptoms globally. In order to reduce the empiric use of antimicrobial drugs and improve outcomes, it is essential to improve diagnostic capabilities. In the absence of microbiology facilities in low-income settings, an assay to distinguish bacterial from non-bacterial causes would be a critical first step. To ensure that patient and market needs are met, the requirements of such a test should be specified in a target product profile (TPP). To identify minimal/optimal characteristics for a bacterial vs. non-bacterial fever test, experts from academia and international organizations with expertise in infectious diseases, diagnostic test development, laboratory medicine, global health, and health economics were convened. Proposed TPPs were reviewed by this working group, and consensus characteristics were defined. The working group defined non-severely ill, non-malaria infected children as the target population for the desired assay. To provide access to the most patients, the test should be deployable to community health centers and informal health settings, and staff should require 90% and >80% for sensitivity and specificity, respectively. Other key characteristics, to account for the challenging environment at which the test is targeted, included: i) time-to-result <10 min (but maximally <2 hrs); ii) storage conditions at 0-40°C, ≤90% non-condensing humidity with a minimal shelf life of 12 months; iii) operational conditions of 5-40°C, ≤90% non-condensing humidity; and iv) minimal sample collection needs (50-100μL, capillary blood). This expert approach to define assay requirements for a bacterial vs. non-bacterial assay should guide product development, and enable targeted and timely efforts by industry partners and academic institutions
Host Biomarkers for Distinguishing Bacterial from Non-Bacterial Causes of Acute Febrile Illness: A Comprehensive Review.
No full textIn resource limited settings acute febrile illnesses are often treated empirically due to a lack of reliable, rapid point-of-care diagnostics. This contributes to the indiscriminate use of antimicrobial drugs and poor treatment outcomes. The aim of this comprehensive review was to summarize the diagnostic performance of host biomarkers capable of differentiating bacterial from non-bacterial infections to guide the use of antibiotics.Online databases of published literature were searched from January 2010 through April 2015. English language studies that evaluated the performance of one or more host biomarker in differentiating bacterial from non-bacterial infection in patients were included. Key information extracted included author information, study methods, population, pathogens, clinical information, and biomarker performance data. Study quality was assessed using a combination of validated criteria from the QUADAS and Lijmer checklists. Biomarkers were categorized as hematologic factors, inflammatory molecules, cytokines, cell surface or metabolic markers, other host biomarkers, host transcripts, clinical biometrics, and combinations of markers.Of the 193 citations identified, 59 studies that evaluated over 112 host biomarkers were selected. Most studies involved patient populations from high-income countries, while 19% involved populations from low- and middle-income countries. The most frequently evaluated host biomarkers were C-reactive protein (61%), white blood cell count (44%) and procalcitonin (34%). Study quality scores ranged from 23.1% to 92.3%. There were 9 high performance host biomarkers or combinations, with sensitivity and specificity of ≥85% or either sensitivity or specificity was reported to be 100%. Five host biomarkers were considered weak markers as they lacked statistically significant performance in discriminating between bacterial and non-bacterial infections.This manuscript provides a summary of host biomarkers to differentiate bacterial from non-bacterial infections in patients with acute febrile illness. Findings provide a basis for prioritizing efforts for further research, assay development and eventual commercialization of rapid point-of-care tests to guide use of antimicrobials. This review also highlights gaps in current knowledge that should be addressed to further improve management of febrile patients
A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis
No full textMiotto, Paolo. et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J 2017; 50: 1701354.
[https://doi.org/10.1183/13993003.01354-2017]. 13 páginas, 2 figuras, 4 tablas.A clear understanding of the genetic basis of antibiotic resistance in Mycobacterium tuberculosis is required to accelerate the development of rapid drug susceptibility testing methods based on genetic sequence.Raw genotype-phenotype correlation data were extracted as part of a comprehensive systematic review to develop a standardised analytical approach for interpreting resistance associated mutations for rifampicin, isoniazid, ofloxacin/levofloxacin, moxifloxacin, amikacin, kanamycin, capreomycin, streptomycin, ethionamide/prothionamide and pyrazinamide. Mutation frequencies in resistant and susceptible isolates were calculated, together with novel statistical measures to classify mutations as high, moderate, minimal or indeterminate confidence for predicting resistance.We identified 286 confidence-graded mutations associated with resistance. Compared to phenotypic methods, sensitivity (95% CI) for rifampicin was 90.3% (89.6-90.9%), while for isoniazid it was 78.2% (77.4-79.0%) and their specificities were 96.3% (95.7-96.8%) and 94.4% (93.1-95.5%), respectively. For second-line drugs, sensitivity varied from 67.4% (64.1-70.6%) for capreomycin to 88.2% (85.1-90.9%) for moxifloxacin, with specificity ranging from 90.0% (87.1-92.5%) for moxifloxacin to 99.5% (99.0-99.8%) for amikacin.This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug-resistant phenotypes. These data have implications for the clinical interpretation of molecular diagnostics and next-generation sequencing as well as efficient individualised therapy for patients with drug-resistant tuberculosis.This study was supported by tEhe Bill and Melinda Gates Foundation under grant agreement FIND OPP1115209 to address how to score mutations in the ReSeqTB data sharing platform initiative. The funder of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. K. Dheda is
supported by the South African MRC and the EDCTP. I. Comas is supported by the Ministerio de Economía y Competitividad (Spanish Government) research grant SAF2016–77346-R and the European Research Council (ERC) (638553-TB-ACCELERATE). L. Chindelevitch is supported by a Sloan Fellowship. S. Niemann is supported by grants of the German Center for Infection Research. Funding information for this article has been deposited with the Crossref Funder Registry.Peer reviewe
Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment
No full text[No Abstract Available]Unitaid [2019-32-FIND MDR]; BMGF [OPP1105925]; German Federal Ministry of Education and Research through KfW; Dutch Ministry of Foreign Affairs; Australian Department of Foreign Affairs and Trade; MinCiencias, Colombia [221389622138966621666216 CT-783-2018]; Sante Publique France; Janssen; National Services Scotland; Spanish Science Ministry [PID2019-104477RB-I00]; ERC [CoG 101001038]; Swiss National Science Foundation [320030_153442, 189498]; US National Institutes of Health; National Institute of Allergy and Infectious Diseases; Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Cancer Institute; National Institute of Mental Health; National Institute on Drug Abuse; National Heart, Lung, and Blood Institute; National Institute on Alcohol Abuse and Alcoholism; National Institute of Diabetes and Digestive and Kidney Diseases; Fogarty International Center; NIH NIAID [R01AI155765, R01 AI137080, U01 AI150508]; DAINA grant from the National Science Centre, Poland [2017/27/L/NZ6/03279]; US National Institutes of Health [NO1-AI95383, NO1-AI-70022]; Innosuisse [36198.1 IP-LS]; Federal Government of Germany; Royal Society of Tropical Medicine and Hygiene; National Institute for Health Research Cambridge Biomedical Research Centre; Fundacao para a Ciencia e a Tecnologia, Portugal [PTDC/BIA-MIC/30692/2017, UID/Multi/04413/2020, DL57/CEECIND/0256/2017]; German Center for Infection Research, Excellenz Cluster Precision Medicine in Chronic Inflammation, Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG) [EXC 2167]; Belgian Directorate General for Development; FIND; NIH NIAD [P30 AI036214, R21 AI135756]; Swedish Heart and Lung Foundation; Swedish Research Council; Centers for Disease Control and Prevention; South African Medical Research Council; Wellcome Trust [FC0010218, 203135]; Francis Crick Institute - Cancer Research UK [FC0010218]; UKRI [FC0010218]; National Library of Medicine: Asia-Pacific [U01AI069907]; National Library of Medicine: CCASAnet [U01AI069923]; National Library of Medicine: Central Africa [U01AI096299]; National Library of Medicine: East Africa [U01AI069911]; National Library of Medicine: NA-ACCORD [U01AI069918]; National Library of Medicine: Southern Africa [U01AI069924]; National Library of Medicine: West Africa [U01AI069919]As current or former employees or consultants for FIND, the work of R.B. Baldan, I. Comas, C.M. Denkinger, D.L. Dolinger, S.B. Georghiou, C.U. Koser and T.C. Rodwell on the systematic reviews, including this viewpoint, was supported by Unitaid (grant 2019-32-FIND MDR), BMGF (grant OPP1105925), the German Federal Ministry of Education and Research through KfW, the Dutch Ministry of Foreign Affairs, the Australian Department of Foreign Affairs and Trade, and UK aid from the British people. N. Alvarez and J. Robledo are funded by MinCiencias, Colombia (number 221389622138966621666216 CT-783-2018). A. Aubry and N. Veziris work at the Centre National de Reference des Mycobacteries, which receives an annual grant from Sante Publique France and have received research grants from Janssen for studies on bedaquiline. P. Claxton and I.F. Laurenson are funded through National Services Scotland. I. Comas was supported by PID2019-104477RB-I00 from the Spanish Science Ministry and by ERC (CoG 101001038). M. Egger is supported by the Swiss National Science Foundation (grant number 320030_153442 and 189498) and the US National Institutes of Health, National Institute of Allergy and Infectious Diseases, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Cancer Institute, the National Institute of Mental Health, the National Institute on Drug Abuse, the National Heart, Lung, and Blood Institute, the National Institute on Alcohol Abuse and Alcoholism, the National Institute of Diabetes and Digestive and Kidney Diseases, the Fogarty International Center, and the National Library of Medicine: Asia-Pacific, U01AI069907; CCASAnet, U01AI069923; Central Africa, U01AI096299; East Africa, U01AI069911; NA-ACCORD, U01AI069918; Southern Africa, U01AI069924; West Africa, U01AI069919. M.R. Farhat is supported by NIH NIAID R01AI155765. S.K. Heysell was funded by NIH NIAID grants R01 AI137080 and U01 AI150508. T. Jagielski was supported by a DAINA grant (number 2017/27/L/NZ6/03279) from the National Science Centre, Poland. J.L. Johnson was supported by contracts NO1-AI95383 and NO1-AI-70022 of the US National Institutes of Health. P.M. Keller was supported by Innosuisse 36198.1 IP-LS. C.U. Koser is a research associate at Wolfson College and visiting scientist at the Department of Genetics, University of Cambridge. The Federal Government of Germany supported C.U. Koser as part of his work for the European Laboratory Initiative, WHO Regional Office for Europe. C.U. Koser was further supported by the Royal Society of Tropical Medicine and Hygiene and the National Institute for Health Research Cambridge Biomedical Research Centre and received an observership by the European Society of Clinical Microbiology and Infectious Diseases to the EUCAST Development Laboratory for Bacteria (Vaxjo, Sweden), hosted by Gunnar Kahlmeter and Erika Matuschek. D. Machado and M. Viveiros are funded in part by Fundacao para a Ciencia e a Tecnologia, Portugal (PTDC/BIA-MIC/30692/2017, UID/Multi/04413/2020 and DL57/CEECIND/0256/2017). S. Niemann is supported by the German Center for Infection Research, Excellenz Cluster Precision Medicine in Chronic Inflammation EXC 2167, Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG). S.V. Omar has received funding to prepare and provide training for Janssen Pharmaceutica activities. L. Rigouts is supported by the Belgian Directorate General for Development. T.C. Rodwell was additionally funded in part by FIND and NIH NIAD, grants: P30 AI036214 and R21 AI135756. T.; Schon is funded by the Swedish Heart and Lung Foundation and the Swedish Research Council. T.R. Sterling has received funding from the US National Institutes of Health and the Centers for Disease Control and Prevention. G. Theron and R. Warren are supported by baseline funding from the South African Medical Research Council. R.J. Wilkinson receives funding from the Wellcome Trust (203135) and from the Francis Crick Institute, which is supported by Cancer Research UK (FC0010218), UKRI (FC0010218) and the Wellcome Trust (FC0010218). The views expressed here are those of the authors and do not necessarily correspond to those of their respective employers
Emerg Infect Dis
No full textTo detect early cases of pandemic (H1N1) 2009 infection, in 2009 we surveyed 303 persons from marginalized populations of drug users, sex workers, and homeless persons in Tijuana, Mexico. Six confirmed cases of pandemic (H1N1) 2009 were detected, and the use of rapid, mobile influenza testing was demonstrated
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The use of vocal coordination in male African elephant group departures: evidence of active leadership and consensus
No full textGroup-living animals engage in coordinated vocalizations to depart from a location as a group, and often, to come to a consensus about the direction of movement. Here, we document for the first time, the use of coordinated vocalizations, the "let's go" rumble, in wild male African elephant group departures from a waterhole. We recorded vocalizations and collected behavioral data as known individuals engaged in these vocal bouts during June-July field seasons in 2005, 2007, 2011, and 2017 at Mushara waterhole within Etosha National Park, Namibia. During departure events, we documented which individuals were involved in the calls, the signature structure of each individual's calls, as well as the ordering of callers, the social status of the callers, and those who initiated departure. The "let's go" rumble was previously described in tight-knit family groups to keep the family together during coordinated departures. Male elephants are described as living in loose social groups, making this finding particularly striking. We found that this vocal coordination occurs in groups of closely associated, highly bonded individuals and rarely occurs between looser associates. The three individuals most likely to initiate the "let's go" rumble bouts were all highly socially integrated, and one of these individuals was also the most dominant overall. This finding suggests that more socially integrated individuals might be more likely to initiate, or lead, a close group of associates in the context of leaving the waterhole, just as a high-ranking female would do in a family group. The fact that many individuals were involved in the vocal bouts, and that departure periods could be shorter, longer, or the same amount of time as pre-departure periods, all suggest that there is consensus with regard to the act of leaving, even though the event was triggered by a lead individual
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