Feasibility analysis of a bacterial isolation technology.

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dc.contributor.advisorNieuwoudt, MJen_ZA
dc.contributor.advisorHoffmann, JEen_ZA
dc.contributor.advisorGrobbelaar, Men_ZA
dc.contributor.authorWessels, FJen_ZA
dc.contributor.otherStellenbosch University. Faculty of Engineering. Dept. of Mechanical and Mechatronic Engineering.en_ZA
dc.date.accessioned2024-02-26T12:42:02Zen_ZA
dc.date.accessioned2024-04-26T19:39:17Zen_ZA
dc.date.available2024-02-26T12:42:02Zen_ZA
dc.date.available2024-04-26T19:39:17Zen_ZA
dc.date.issued2024-02en_ZA
dc.descriptionThesis (MEng)--Stellenbosch University, 2024.en_ZA
dc.description.abstractENGLISH ABSTRACT: Currently it is highly challenging to use whole genome sequencing on expectorated sputum samples for the detection and analysis of Mycobacterium tuberculosis. This is due, in large part, to the lack of a suitable sample preparation process that can take expectorated sputum as input and output highly purified Mycobacterium tuberculosis genomic material. This thesis proposes a new strategy for combining existing methods in the literature into such a sputum sample preparation process. To initiate this new strategy, the project selects and tests the feasibility of a cell isolation technology for the final stage in the sample preparation process. Through a comparison of candidate cell isolation technologies in terms of the stakeholder requirements for the sample preparation process, the deterministic lateral displacement method was identified as the most promising technology for the application. More specifically, the approach involved employing two sequential deterministic lateral displacement arrays that use cylindrical and I-shaped obstacles to evaluate the Mycobacterium tuberculosis rod-shaped cells based on their diameter and length, respectively. This would, in theory, allow the Mycobacterium tuberculosis rods to be separated from a first group of cells that are larger than the diameter of the rods and a second group of cells that are smaller than the length of the rods. Then, if the lower limit of the first group of cells overlapped with the upper limit of the second group of cells, only purified Mycobacterium tuberculosis cells would remain at the end of the two arrays. To investigate the feasibility of using this method for the final stage in the sample preparation process, Computational Fluid Dynamics flow simulations were used to design a 2000:1 scale model of the proposed geometry. The experiments on this upscaled model provided an enhanced perspective of the problem on two fronts, which should be of value to future work on this topic. Firstly, the upscaled experiments generated high resolution footage of the particle behaviour, which is difficult to do at the microscale. This footage allowed for the identification and analysis of behavioural patterns in the model Mycobacterium tuberculosis cells. Most notably, this showed that motion occurs predominantly in the xy-plane, that rotating rocking motion punctuated by periodic flipping dominates the contactless flow, and that various particle-to-obstacle interactions occur in a rigid hierarchy. Secondly, the upscaled device allowed for a detailed quantification of the flow field, which is next to impossible at the microscale. These flow measurements show that the I-shaped obstacles pose a 38.6% higher fluidic resistance than the cylindrical obstacles at a column slant angle of 1.59°. These upscaled results provide an ideal foundation for future numerical investigations, as they provide both high-quality qualitative data of the particle behaviour and high-quality quantitative data of the flow field. This data may be used as validation benchmarks for future simulations that continue the investigation started here.en_ZA
dc.description.abstractAFRIKAANS OPSOMMING: Tans is dit uiters uitdagend om 'n volle-genoomvolgordebepaling op sputum ekspektorant monsters te gebruik vir die diagnose en ontleding van Mycobacterium tuberculosis. Hierdie stand van sake word grootliks toegeskryf aan die gebrek van 'n geskikte monstervoorbereidingsproses wat sputum ekspektorant kan verwerk om gesuiwerde Mycobacterium tuberculosis genomiese materiaal te produseer. In hierdie tesis word ‘n nuwe strategie voorgestel om bestaande metodes uit die literatuur te kombineer om 'n toepaslike sputum-voorbereidingsproses te ontwikkel. Om hierdie voorgestelde strategie te bewerkstellig, kies en toets die projek die lewensvatbaarheid van 'n sel-isolasietegnologie vir die finale fase van die monstervoorbereidingsproses. Deur verskillende sel-isolasie tegnologieë teen mekaar op te weeg, in terme van die vereistes van die belanghebbendes in die monstervoorbereidingsproses, is daar bepaal dat die deterministiese laterale verplasingsmetode die mees belowende metode vir die toepassing is. Meerspesifiek is daar besluit om twee deterministiese laterale verplasingsmatrikse in serie te koppel, wat onderskeidelik Silindriese en I-vormige pilare gebruik om die stafievormige Mycobacterium tuberculosis selle op hul diameter en lengte te evalueer. Teoreties sou hierdie benadering dit moontlik maak om die Mycobacterium tuberculosis stafies van ʼn eerste groep selle te skei wat groter as hul diameter is en van ʼn tweede groep wat kleiner as hul lengte is. Dan, indien die laerlimiet van die eerste groep selle en die hoërlimiet van die tweede groep selle oorvleuel, sal slegs die gesuiwerde Mycobacterium tuberculosis selle aan die einde van die twee matrikse oorbly. Om die lewensvatbaarheid van hierdie metode vir die finale fase in die monstervoorbereidingsproses te ondersoek, is Rekenaarvloeidinamika-simulasies gebruik om 'n 2000:1 skaalmodel van die voorgestelde geometrie te ontwerp. Die eksperimente op hierdie opgeskaalde model het 'n verskerpde perspektief van die probleem op twee fronte gebied, wat van waarde kan wees vir toekomstige werk in hierdie veld. Eerstens het die opgeskaleerde eksperimente hoë resolusie beeldmateriaal van die partikelgedrag gegenereer, wat moeilik is om op die mikroskaal te verkry. Hierdie beeldmateriaal het die identifisering en ontleding van gedragspatrone in die model Mycobacterium tuberculosis selle moontlik gemaak. Dit het veral getoon dat beweging hoofsaaklik in die xy-vlak plaasvind, dat 'n roterende wiegbeweging onderbreek deur periodieke omkantelings die dominante gedrag in die kontaklose vloei is, en dat verskeie partikel-tot-pilaar-interaksies in 'n rigiede hiërargie plaasvind. Tweedens het die opgeskaalde toestel 'n gedetailleerde kwantifisering van die vloeiveld moontlik gemaak, wat byna onmoontlik is op die mikroskaal. Hierdie vloeimetings het getoon dat die I-vormige pilare 'n 38.6% hoër vloeiweerstand as die silindriese pilare bied by ʼn kolom hoek van 1.59°. Die opgeskaalde resultate bied 'n ideale fondasie waarop toekomstige numeriese ondersoeke kan bou, aangesien dit beide hoë-gehalte kwalitatiewe data van die partikelgedrag en hoë-gehalte kwantitatiewe data van die vloeiveld bied. Hierdie data bied 'n maatstaf waarteen toekomstige simulasies gevalideer kan word en bevorder dus so die voorsetting van die ondersoek.af_ZA
dc.description.versionMastersen_ZA
dc.format.extentxx, 89, A1-A40 pages : illustrationsen_ZA
dc.identifier.urihttps://scholar.sun.ac.za/handle/10019.1/130494en_ZA
dc.language.isoen_ZAen_ZA
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshSeparation (Technology)en_ZA
dc.subject.lcshCell separationen_ZA
dc.subject.lcshMycobacterium tuberculosisen_ZA
dc.subject.lcshSample preparation (Chemistry)en_ZA
dc.subject.lcshUCTDen_ZA
dc.titleFeasibility analysis of a bacterial isolation technology.en_ZA
dc.typeUCTDen_ZA
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