1. Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization
- Author
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Pedro Eduardo Almeida da Silva, Hanny Willems, Tom Venken, Stefan Niemann, An Jacobs, Hillary N. Wood, Kyle H. Rohde, Ana Júlia Reis, Jef Hooyberghs, and Susanne Homolka
- Subjects
0301 basic medicine ,Bacterial Diseases ,Microarrays ,Extensively Drug-Resistant Tuberculosis ,Gene Identification and Analysis ,Antitubercular Agents ,Artificial Gene Amplification and Extension ,Drug resistance ,Polymerase Chain Reaction ,law.invention ,FLUOROQUINOLONE ,law ,Medicine and Health Sciences ,Multiplex ,Polymerase chain reaction ,education.field_of_study ,Multidisciplinary ,biology ,Hybridization probe ,Nucleic Acid Hybridization ,Multidisciplinary Sciences ,Actinobacteria ,Infectious Diseases ,Bioassays and Physiological Analysis ,Science & Technology - Other Topics ,Medicine ,MYCOBACTERIUM-TUBERCULOSIS ,DNA microarray ,HETERORESISTANCE ,Research Article ,DNA, Bacterial ,Science ,030106 microbiology ,Population ,Molecular Probe Techniques ,Computational biology ,Microbial Sensitivity Tests ,DIAGNOSIS ,Research and Analysis Methods ,Microbiology ,Polymorphism, Single Nucleotide ,Mycobacterium tuberculosis ,Molecular Genetics ,03 medical and health sciences ,Microbial Control ,Multiplex polymerase chain reaction ,Genetics ,Tuberculosis ,Humans ,education ,Molecular Biology Techniques ,RIFAMPIN RESISTANCE ,Mutation Detection ,Molecular Biology ,Pharmacology ,Science & Technology ,Bacteria ,Organisms ,RAPID DETECTION ,Biology and Life Sciences ,biology.organism_classification ,Tropical Diseases ,EVOLUTION ,Probe Hybridization ,030104 developmental biology ,Antimicrobial Resistance ,Multiplex Polymerase Chain Reaction - Abstract
In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (
- Published
- 2019