With the advancement of isothermal nucleic acid amplification techniques, detection of the pathogenic DNA in clinical samples at point-of-need is no longer a dream. The newly developed recombinase polymerase amplification (RPA) assay incorporated in a suitcase laboratory has shown promising diagnostic efficacy over real-time PCR in detection of leishmania DNA from clinical samples. For broader application of this point-of-need system, we undertook a current multi-country diagnostic evaluation study towards establishing this technique in different endemic settings which would be beneficial for the ongoing elimination programs for leishmaniasis. For this study purpose, clinical samples from confirmed visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL) patients were subjected to both real-time PCR and RPA assay in Bangladesh, India, and Nepal. Further skin samples from confirmed cutaneous leishmaniasis (CL) patients were also included from Sri Lanka. A total of 450 clinical samples from VL patients, 429 from PKDL patients, 47 from CL patients, and 322 from endemic healthy/healthy controls were under investigation to determine the diagnostic efficacy of RPA assay in comparison to real-time PCR. A comparative sensitivity of both methods was found where real-time PCR and RPA assay showed 96.86% (95% CI: 94.45–98.42) and 88.85% (95% CI: 85.08–91.96) sensitivity respectively in the diagnosis of VL cases. This new isothermal method also exhibited promising diagnostic sensitivity (93.50%) for PKDL cases, when a skin sample was used. Due to variation in the sequence of target amplicons, RPA assay showed comparatively lower sensitivity (55.32%) than that of real-time PCR in Sri Lanka for the diagnosis of CL cases. Except for India, the assay presented absolute specificity in the rest of the sites. Excellent concordance between the two molecular methods towards detection of leishmania DNA in clinical samples substantiates the application of RPA assay incorporated in a suitcase laboratory for point-of-need diagnosis of VL and PKDL in low resource endemic settings. However, further improvisation of the method is necessary for diagnosis of CL.

Asthma is a chronic disease affecting over 300 million people worldwide. Airway inflammation is a central feature of asthma. Quantitative sputum cytometry is the most validated method to assess this and to adjust anti-inflammatory therapy, yet it is underutilized due to rigorous processing that requires expensive specialized technicians. To address these limitations, this thesis focuses on the development of several point of need biosensors that rapidly quantify respiratory biomarkers as alternatives to traditional laboratory tests. The project began by developing a paper based sensor for detection of myeloperoxidase (MPO), a neutrophil biomarker. A test was developed using commercially available antibodies, showing direct correlation between the test line colour intensity and total neutrophils. This work was expanded to include a second protein target, eosinophil peroxidase (EPX), for identification of eosinophils. Although the test performed well using neat samples, it failed to identify EPX in clinical sputum samples. Analyzing pre-treatment methods identified that a quick immunoprecipitation technique using protein A/G beads followed by syringe filtration allowed for the device to successfully quantify EPX, eliminating the need for a centrifuge. However, the limited supply of commercial anti-EPX antibodies combined with the need for sample pre-treatment prompted investigation into alternative detection avenues. Nucleic acid aptamers were explored, with aptamer selection for EPX producing several aptamer candidates. Binding affinity and specificity tests were performed, with the T1-5 aptamer emerging. T1-5 was capable of selectively binding EPX over MPO with high affinity. This aptamer was integrated into a simple pull-down assay, capable of detecting EPX with an order of magnitude lower limit of detection than the antibody test. Overall this work has developed multiple sensors with the potential to overcome the limitations of accessibility to sputum cytometry, rapidly identify the presence and type of airway inflammation, and deliver personalized treatment strategies that not only reduce the global healthcare burden, but also greatly improve a patient’s quality of life. / Thesis / Doctor of Philosophy (PhD)

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Quantification of pathogen load, although challenging, is of paramount importance for accurate diagnosis and clinical management of a range of infectious diseases in a point-of-need testing (PONT) scenario such as in resource-limited settings. We formulated a quantification approach to test the standard-curve based absolute quantification ability of isothermal recombinase polymerase amplification (RPA) assay. As a test of principle, a 10-fold dilution series of Leishmania donovani (LD) genomic DNA prepared in nuclease-free-water (NFW), and from culture-spiked-blood (CSB) were tested, and a 15 min assay was performed. A modified algorithm was formulated to derive the detection outcome. The threshold-record times (Tr) in seconds thus obtained were plotted against the initial load of parasite genomes for log-linear regression analysis. The quantitative RPA (Q-RPA) assay was further evaluated against a LD quantitative (q)-PCR assay with DNA extracted from visceral and post-Kala-azar dermal leishmaniasis case specimens and stratified into different ranges of threshold cycle (Ct). The best-fitted regression models were found linear with mean r2/root mean square error (RMSE) values of residual points (in seconds) estimated as 0.996/8.063 and 0.992/7.46 for replicated series of NFW and CSB, respectively. In both series, the lower limit of detection reached less than 0.1 parasite genome equivalent DNA. Absolute agreement between Q-RPA and LD-qPCR was found for test positivity, and strong positive correlations were observed between the Tr and Ct values (r = 0.89; p < 0.0001) as well as between the absolute parasite loads (r = 0.87; p < 0.0001) quantified by respective assays. The findings in this very first Q-RPA assay for leishmaniasis are suggestive of its potential in monitoring LD load in clinical specimens, and the development of rapid Q-RPA assays for other infectious diseases.

Im urbanen Abwasser findet sich eine Vielzahl pathogener Mikroorganismen, welche ein Risiko für Tier, Mensch und Umwelt darstellen. Um die Integration dieser und vieler weiterer Schadstoffe in den öffentlichen Wasserkreislauf zu verhindern, ist deren Eliminierung durch Klärwerke und die Überwachung dieser Abläufe von besonderer Relevanz. Obwohl die Präsenz mikrobiologischer Parameter dabei bisher lediglich akzessorisch betrachtet wird, sollten besonders Zoonosen im Abwasser aufgrund ihrer hohen Gesundheitsgefahr für Tiere und Menschen Beachtung in den vorgeschriebenen Kontrollen finden. Hierfür eignen sich besonders molekularbiologische Methoden, wie beispielsweise die zeiteffiziente real-time PCR, welche eine hohe Sensitivität und Spezifität garantiert. Eine Grundvoraussetzung für diesen DNA-basierten Pathogennachweis ist eine schnelle und effiziente Nukleinsäuren-Extraktion am Point-of-Need. Viele existierende Extraktionsverfahren werden diesem Anspruch jedoch aufgrund zeitintensiver und komplexer Protokolle nicht gerecht. Ziel dieser Studie war es, eine Extraktionsmethode für mikrobielle DNA aus Abwasser zu entwickeln, mit welcher Pathogene mittels molekularer Detektionsmethoden wie beispielsweise real-time PCR nachgewiesen werden können. Die Extraktion der DNA des grampositiven Bakteriums S. aureus, des gramnegativen Bakteriums E. coli und des Parasiten C. parvum basierte auf einer „Reverse Purification“. Um einen effizienten Zellaufschluss und DNA-Nachweis zu garantieren, wurde das Verfahren um a) mechanische (Bead Beating), b) chemische (alkalische Inkubation bei Raumtemperatur oder 95 °C) und/oder c) enzymatische (Proteinase K) Vorbehandlungen ergänzt. Das Bead Beating-Protokoll wurde anschließend durch die Variation der Kugelgrößen und den Einsatz von Vortexer oder Hulamixer anstelle eines komplexen Bead Beaters adaptiert. Mithilfe einer Verdünnungsreihe der Pathogene in experimentell kontaminiertem Abwasser wurde das Detektionslimit bestimmt und bei 95 %-iger Wahrscheinlichkeit durch das Wilrich&Wilrich Modell kalkuliert. Zusätzlich dazu wurden die Nukleinsäurekonzentrationen der einzelnen Protokolle mittels NanodropTM (Spektralphotometer) und QubitTM (Fluorometer) gemessen. Die Resultate wurden denen einer Silica-Säulen-basierten Referenzmethode gegenübergestellt. Die effizienteste Methode zum Zellaufschluss der Bakterien steigerte die Extraktionseffizienz gegenüber der Referenzmethode um das Vierfache und beinhaltete eine Kombination aus Bead Beating (mit 0,1mm Glaskugeln und einem Vortexer) und Proteinase K bei 60°C für 10 Minuten. Im Fall von C. parvum erwies sich Proteinase K als effektivste Vorbehandlung (siebenfacher Anstieg der Extraktionsmenge). Basierend auf der etablierten Extraktionsmethode wurde bis zu 0,74 Zellen pro Reaktion von S. aureus, 9,94 Zellen von E. coli und 13,55 Oozysten von C. parvum in experimentell kontaminiertem Abwasser extrahiert und detektiert. Zwischen den detektierten Nukleinsäurekonzentrationen und den ermittelten Extraktionseffizienzen in der real-time PCR wurde keine Korrelation festgestellt. Zur Extraktion mikrobieller DNA aus Abwasser wurde eine Methode für grampositive Bakterien (S. aureus), gramnegative Bakterien (E. coli) und Protozoen (C. parvum) entwickelt, welche eine schnelle und sensitive Erregerdetektion mittels real-time PCR garantiert. Diese Vorteile ermöglichen ein mobil einsetzbares Abwassermonitoring am Point-of-Need.:1 EINLEITUNG 2 LITERATURÜBERSICHT 2.1 Mikrobielle Risiken im Abwasser 2.1.1 Staphylococcus aureus 2.1.2 Escherichia coli 2.1.3 Cryptosporidium parvum 2.2 Ablauf der Abwasseraufbereitung in Deutschland 2.3 Abwassermonitoring 2.3.1 Aktuelle Gesetzeslage und Empfehlungen 2.3.2 Zusätzliche Einsatzmöglichkeiten 2.4 Nachweismethoden im Abwasser: der Vergleich zwischen Kultur und real-time PCR 2.5 Extraktionsverfahren mikrobieller DNA 2.5.1 Konventionelle Extraktionsverfahren 2.5.2 Festphasen-Nukleinsäurenextraktion 3 PUBLIKATION 3.1 Stellungnahme zum Eigenanteil der Publikation 3.2 Publikation 4 DISKUSSION UND SCHLUSSFOLGERUNG 5 ZUSAMMENFASSUNG 6 SUMMARY 7 REFERENZEN 8 ABBILDUNGSVERZEICHNIS 9 TABELLENVERZEICHNIS 10 ANHANG 11 DANKSAGUNG

Feline coronavirus (FCoV) is endemic in cat populations worldwide. Persistently, subclinically infected cats play a significant role in spreading the infection. Testing fecal samples of cats may facilitate efforts to decrease the viral burden within a population. Real-time RT-PCR is highly sensitive and specific for the detection of FCoV but must be performed in a fully equipped laboratory. A simple and accurate assay is needed to identify FCoV at the point-of-need. The aim of this study was to develop a rapid FCoV detection assay based on isothermal amplification technology, i.e., reverse transcription-recombinase polymerase amplification (RT-RPA). Primers were designed to target the highly conserved 3′ untranslated region of the 7b gene. Running on a constant temperature of 42 °C, reverse transcription as well as DNA amplification and detection was achieved in a maximum of 15 min. A probit analysis revealed a detection limit of 58.5 RNA copies/reaction. For cross-detection, nucleic acids from 19 viruses were tested. Both RT-RPA and real-time RT-PCR showed cross-detection with canine coronavirus and transmissible gastroenteritis virus, but not with other pathogens. To evaluate clinical performance, RNA was extracted from 39 fecal samples from cats. All samples were tested simultaneously with real-time RT-PCR resulting in a RT-RPA sensitivity and specificity of 90.9% and 100%, respectively. RT-RPA can be considered a promising simple method for rapid detection of FCoV.

To detect Post-kala-azar leishmaniasis (PKDL) cases, several molecular methods with promising diagnostic efficacy have been developed that involve complicated and expensive DNA extraction methods, thus limiting their application in resource-poor settings. As an alternative, we evaluated two rapid DNA extraction methods and determined their impact on the detection of the parasite DNA using our newly developed recombinase polymerase amplification (RPA) assay. Skin samples were collected from suspected PKDL cases following their diagnosis through national guidelines. The extracted DNA from three skin biopsy samples using three different extraction methods was subjected to RPA and qPCR. The qPCR and RPA assays exhibited highest sensitivities when reference DNA extraction method using Qiagen (Q) kit was followed. In contrast, the sensitivity of the RPA assay dropped to 76.7% and 63.3%, respectively, when the boil & spin (B&S) and SpeedXtract (SE) rapid extraction methods were performed. Despite this compromised sensitivity, the B&S-RPA technique yielded an excellent agreement with both Q-qPCR (k = 0.828) and Q-RPA (k = 0.831) techniques. As expected, the reference DNA extraction method was found to be superior in terms of diagnostic efficacy. Finally, to apply the rapid DNA extraction methods in resource-constrained settings, further methodological refinement is warranted to improve DNA yield and purity through rigorous experiments.

<p dir="ltr">The necessity for on-farm, point-of-need (PON) nucleic acid amplification tests (NAATs) arises from the prolonged turnaround times and high costs associated with traditional laboratory equipment. This thesis aims to address these challenges by developing devices and a user-interface application designed for the efficient, accurate, and rapid detection of <i>Bacteroidales</i> as an indicator of fecal contamination on fresh produce farms.</p><p dir="ltr">In pursuit of this, I collaborated with lab members to engineer a Field-Applicable Rapid Microbial Loop-mediated isothermal Amplification Platform, FARM-LAMP. This device is portable (164 x 135 x 193 mm), energy-efficient (operating under 20 W), achieves the target 65°C with ± 0.2°C fluctuations, and is compatible with paper-based biosensors for loop-mediated isothermal amplification (LAMP). Subsequently, I led the fabrication of the microfluidic Field-Applicable Sampling Tool, FAST, designed to deliver high-throughput (10 samples per device), equal flow-splitting of fluids to paper-based biosensors, eliminating the need for a laboratory or extensive training. FARM-LAMP achieved 100% concordance with standard lab-based tests when deployed on a commercial lettuce farm and FAST achieved an average accuracy of 89% in equal flow-splitting and 70% in volume hydration.</p><p dir="ltr">A crucial aspect of device development is ensuring that results are easily interpretable by users. To this end, I developed a Python-based image analysis codebase to quantify sample positivity for fecal contamination, ranging from 0% (no contamination) to nearly 100% (definite contamination) and the concentration of field samples. It utilizes calculus-based mathematics, such as first and second derivative analysis, and incorporates image analysis techniques, including hue, saturation, and value (HSV) binning to a sigmoid function, along with contrast limited adaptive histogram equalization (CLAHE). Additionally, I developed a preliminary graphical user interface in Python that defines a prediction model for the concentration of <i>Bacteroidales</i> based on local weather patterns.</p><p dir="ltr">This thesis encompasses hardware development for on-field quantification and the creation of a preliminary user-interface application to assess fecal contamination risk on fresh produce farms. Integrating these devices with a user-interface application allows for rapid interpretation of results on-farm, aiding in the effective development of strategies to ensure safety in fresh produce operations.</p>