Dataset Information

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance.

ABSTRACT: Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.

SUBMITTER: Vasala A

PROVIDER: S-EPMC7373752 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance.

Vasala Antti A Hytönen Vesa P VP Laitinen Olli H OH

Frontiers in cellular and infection microbiology 20200715

Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard metho ...[more]

PMID: 32760676

Similar Datasets

Project description:BACKGROUND:Meningitis remains a top cause of premature death and loss of disability-adjusted life years in low-income countries. In resource-limited settings, proper laboratory diagnostics are often scarce and knowledge about national and local epidemiology is limited. Misdiagnosis, incorrect treatment and overuse of antibiotics are potential consequences, especially for viral meningitis. METHODS:A prospective study was conducted over three months in a teaching hospital in Ethiopia with limited laboratory resources. Cerebrospinal fluid (CSF) samples from patients with suspected meningitis were analysed using a multiplex PCR-based system (FilmArray, BioFire), in addition to basic routine testing with microscopy and culture. Clinical data, as well as information on treatment and outcome were collected. RESULTS:Two hundred and eighteen patients were included; 117 (54%) neonates (0-29?days), 63 (29%) paediatrics (1?month-15?years) and 38 (17%) adults (?16?years). Of 218 CSF samples, 21 (10%) were PCR positive; 4% in neonates, 14% in paediatrics and 18% in adults. Virus was detected in 57% of the PCR positive samples, bacteria in 33% and fungi in 10%. All CSF samples that were PCR positive for a bacterial agent had a white cell count ?75 cells/mm3 and/or turbid appearance. The majority (90%) of patients received more than one antibiotic for treatment of the meningitis episode. There was no difference in the mean number of different antibiotics received or in the cumulative number of days with antibiotic treatment between patients with a microorganism detected in CSF and those without. CONCLUSIONS:A rapid molecular diagnostic system was successfully implemented in an Ethiopian setting without previous experience of molecular diagnostics. Viral meningitis was diagnosed for the first time in routine clinical practice in Ethiopia, and viral agents were the most commonly detected microorganisms in CSF. This study illustrates the potential of rapid diagnostic tests for reducing antibiotic usage in suspected meningitis cases. However, the cost of consumables for the molecular diagnostic system used in this study limits its use in low-income countries.

Project description:BackgroundStool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, the culture of Mycobacterium tuberculosis (M. tuberculosis) complex strains from stool perform poorly. This limits the opportunity for phenotypic drug resistance testing with this specimen. Therefore, reliable molecular methods are urgently needed for comprehensive drug resistance testing on stool specimens.MethodsWe evaluated the performance of targeted next-generation sequencing (tNGS, Deeplex® Myc-TB) for the detection of mutations associated with M. tuberculosis complex drug resistance on DNA isolated from stool specimens provided by participants from a prospective cohort of patients treated for tuberculosis in Eswatini (n = 66; 56 with and 10 participants without M. tuberculosis complex DNA detected in stool by real-time quantitative PCR), and an independent German validation cohort of participants with culture-confirmed tuberculosis (n = 21).ResultsThe tNGS assay detected M. tuberculosis complex DNA in 38 of 56 (68%) samples; for 28 of 38 (74%) samples, a full M. tuberculosis complex drug resistance prediction report was obtained. There was a high degree of concordance with sputum phenotypic drug susceptibility results (κ = 0.82). The ability to predict resistance was concentration-dependent and successful in 7/10 (70%), 18/25 (72%), and 3/21 (14%) of samples with stool PCR concentration thresholds of > 100 femtogram per microliter (fg/μl), 1 to 100 fg/μl, and < 1 fg/μl, respectively (p = 0.0004). The German cohort confirmed these results and demonstrated a similarly high concordance between stool tNGS and sputum phenotypic drug susceptibility results (κ = 0.84).ConclusionstNGS can identify drug resistance from stool provided by tuberculosis patients. This affords the opportunity to obtain critical diagnostic information for tuberculosis patients who struggle to provide respiratory specimens.

Project description:The increasing number of antibiotic resistant bacteria motivates prospective research toward discovery of new antimicrobial active substances. There are, however, controversies concerning the cost-effectiveness of such research with regards to the description of new substances with novel cellular interactions, or description of new uses of existing substances to overcome resistance. Although examination of bacteria isolated from remote locations with limited exposure to humans has revealed an absence of antibiotic resistance genes, it is accepted that these genes were both abundant and diverse in ancient living organisms, as detected in DNA recovered from Pleistocene deposits (30,000 years ago). Indeed, even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Bacteria can exhibit different strategies for resistance against antibiotics. New genetic information may lead to the modification of protein structure affecting the antibiotic carriage into the cell, enzymatic inactivation of drugs, or even modification of cellular structure interfering in the drug-bacteria interaction. There are still plenty of new genes out there in the environment that can be appropriated by putative pathogenic bacteria to resist antimicrobial agents. On the other hand, there are several natural compounds with antibiotic activity that may be used to oppose them. Antimicrobial peptides (AMPs) are molecules which are wide-spread in all forms of life, from multi-cellular organisms to bacterial cells used to interfere with microbial growth. Several AMPs have been shown to be effective against multi-drug resistant bacteria and have low propensity to resistance development, probably due to their unique mode of action, different from well-known antimicrobial drugs. These substances may interact in different ways with bacterial cell membrane, protein synthesis, protein modulation, and protein folding. The analysis of bacterial transcriptome may contribute to the understanding of microbial strategies under different environmental stresses and allows the understanding of their interaction with novel AMPs.

Project description:INTRODUCTION:This protocol will guide and explain the working process of a systematic scoping review on vulnerability assessment tools in the field of infectious disease outbreaks and antimicrobial resistance (AMR) crises. The scoping review will appraise existing tools or methodologies to identify local level vulnerabilities in the context of infectious disease outbreaks and AMR. Due to this focus on infectious threats and AMR, the review also considers articles using a 'One Health' approach to assess the vulnerability of individuals, groups and practices in human-animal-environment interactions. Given the broad nature of vulnerability, we aim to allocate studies discerning the process of identifying vulnerable or at-risk groups during a crisis, instead of studies taking vulnerability only as a starting point. Because considerable research has been conducted on vulnerability, disasters and climate change, we will also assemble tools developed from these fields. To our knowledge, this is the first planned systematic scoping review of vulnerability assessment tools for disease outbreaks and AMR, taking into account practices at the human-animal-environment interface that can lead to increased risk of exposure of individuals to infections, pathogen spillovers or epidemics. METHODS AND ANALYSIS:To develop the protocol, we used the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols checklist (PRISMA-P 2015) in compliance with the PRISMA Extension for Scoping Reviews Explanation and Elaboration. With the assistance of an experienced research librarian, we developed the search strategy, which targeted the following databases: Medline, Global Health database, Web of Science and Embase. A second strategy was developed for Epistemonikos, African Journals Online and Global Index Medicus because these databases do not provide the infrastructure for an advanced search. We consider studies published between 1978 and 2019 and include articles, book chapters, websites and grey literature from selected non-governmental organisations and non-profit organisations working in the health field. We contact them directly regarding whether they are working with or have developed a vulnerability assessment tool. To address the dynamic nature of our investigation, we develop a flow diagram which we continually update to reflect the selection process. Two reviewers (MJ and LL) independently screen the literature and resolve conflicts through discussion rounds. Data extraction will be conducted by four researchers (MJ, LL, EJ and RK) through inductive and deductive coding. Extracted data will be systematically compared and divergences highlighted. ETHICS AND DISSEMINATION:Ethical approval is not required because this study does not involve collection of primary data. The purpose of this review is to disseminate a catalogue of vulnerability assessment tools and a brief summary of key results and recommendations for SoNAR-Global partners in Bangladesh, Ukraine and Uganda. The catalogue will be made publicly available. On the basis of our results, SoNAR-Global partners will pilot one of these tools.

Dataset Information

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance.

Publications

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets