published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Public Health / Master / Master of Public Health

Thrombotic microangiopathy is featured by microangiopathic haemolytic anaemia, thrombocytopenia and the presence of peripheral fragmented red cells. Thrombotic thrombocytopenic purpura (TTP) is the major disease entity of concern, which is caused by a congenital or acquired deficiency of a von Willebrand factor (vWF) cleaving protease known as ADAMTS13 (A Disintegrin And Metalloprotease with Thrombospondin type 1 motif, member 13). Deficiency of this protease, leads to accumulation of uncleaved ultra-large hyperactive vWF multimers in peripheral circulation causing the extensive microvascular platelet aggregation in a TTP event. However, the differential diagnosis is sometimes difficult because symptoms and signs can be non-specific and the condition may resemble a number of disorders. Early recognition and definite diagnosis of TTP is critical to enable prompt plasma exchange therapy. Specific and sensitive ADAMTS13 assays will be potentially helpful. In this review, archive frozen plasma samples from six patients presented with prominent thrombotic microangiopathy were retrospectively analysed for ADAMTS13 by immunoassays. The relationship between ADAMTS13 antigen, activity and its autoantibodies and TTP was studied. Local reference ranges of these assays were also determined. The assay results were validated by identifying the clinically-confirmed cases of TTP, with also prospective serial measurements of ADAMTS13 in a few cases. Patients presented with acute TTP were characterized by a severely deficient ADAMTS13 antigen and activity level, as well as a positive autoantibody titre detected for its acquired immune aetiology ; while patients with non-TTP conditions only had mildly reduced ADAMTS13 antigen but variably decreased activity level and a negative autoantibody titre . A pooled analysis of patients and normal subjects also demonstrated a positive correlation between ADAMTS13 antigen and activity. / published_or_final_version / Pathology / Master / Master of Medical Sciences

Myeloproliferative neoplasms include a heterogeneous group of stem cell disorders with overproduction of myeloid cells. They have very different clinical courses and prognosis and are amenable to specific targeted therapy. A prompt and accurate diagnosis is therefore very important. Genetic characterisation plays an important role in diagnosis and classification of these disorders. BCR-ABL1fusion gene and JAK2V617F mutation are the particular major molecular markers to be detected because of availability of targeted therapy. In this study, a new molecular testing system was developed for the differential diagnosis of myeloproliferative neoplasms. A multiplex reverse-transcriptase polymerase chain reaction was developed for fast detection of JAK2 V617F mutation and BCR-ABL1fusion simultaneously. It was demonstrated to be fast and highly sensitive and specific for the mutations as validated by analysis of clinical samples. The sensitivity limit was well suited for clinical diagnosis. There was great potential saving in consumables and manpower with a much shortened turn-around-time in most cases when compared to conventional diagnostic protocol. / published_or_final_version / Pathology / Master / Master of Medical Sciences

Mycobacterium tuberculosis (MTB) is a major infective agent causing human tuberculosis (TB) in the worldwide. Although tuberculosis can be treated by a six-month course of antibiotics, the prevalence of extensively drug-resistance TB (XDR-TB) made the disease becomes a global health problem. In addition to the conventional MTB detection methods, molecular methods become significant in drug resistant MTB detection which can enhance effective drug treatment. In this study, 200 MTB respiratory specimens were collected from patients with suspected tuberculosis in Tuen Mun Hospital in Hong Kong. Based on the culture method as a gold standard for MTB detection, the presence of MTB in clinical samples was determined by IS6110single tube nested real-time PCR. In addition, by using High Resolution Melting (HRM) analysis, the presence of mutant type KatG315 gene for detecting isoniazid resistant MTB was determined. Among 66 MTB culture positive samples, 10 samples had positive acid fast bacilli (AFB) smears giving the diagnostic sensitivity 15.1%. IS6110 single tube nested PCR was amplified in 51 specimens giving 77.2% MTB detection sensitivity and 97.8% specificity. Among 51 samples positive for IS6110 PCR, 66.7% showed successful amplification in subsequent KatG-HRM assay. Two samples were confirmed to be isoniazid (INH) resistance in Public Health Laboratory Centre (PHLC). However, there was only one sample showing detectable KatG315 mutation in clinical specimen by using HRM while the other was only detected in the corresponding culture isolate. From the result of this study, single tube nested real-time PCR demonstrated MTB detection in clinical samples and INH resistant strain with KatG315mutationcan be detected by HRM analysis. Early detection of mycobacteria allow earlier treatment of the patient, thus transmission of the disease can be controlled. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

Background Tuberculosis (TB) infection is a contagious disease due to infection by Mycobacterium tuberculosis(MTB) causing global health burden. There is increasing effort to develop early case detection methods and also to address the issue of multidrug resistance TB (MDR-TB). Molecular methods have been applied to provide rapid and accurate diagnosis. In addition to commercial kits being available for the detection of MTB from clinical specimens, In-house PCR assays have also been developed for the detection of MTB, and can be adjusted according to the laboratories’ own demand. Several molecular techniques like TaqMan probes and Hybridization probes may be applied to target for markers of MTB, e.g. 16s rRNA and IS6110.Detection of the mutation genes, for example, katGfor isoniazid (INH), enables determination of susceptibility of the antibiotic more rapidly than traditional culture methods, and is especially useful due to the increasing emergence of MDR-TB. A wide range of genes have been reported to be related to the resistance of INH, katG315 mutation is the most common gene among them. Therefore, genotyping katG315 allows determination of the susceptibility of INH. Objective The first objective is to evaluate the diagnostic performance of IS6110 One-tube Nested Real-Time PCR for the detection of MTB. Clinical pulmonary specimens collected from Tuen Mun Hospital were retrieved for investigation. All the specimens have already been tested for COBAS TaqMan MTB test and culture results have been obtained for all the samples. During the first stage of the study, all the specimens were tested with IS6110 One-tube Nested Real-Time PCR. Sensitivity, specificity, positive predictive value, negative predictive value and diagnostic odds ratio were obtained from the comparison with the gold standard of MTB detection, i.e., culture. During the second stage of the study, samples were selected to undergo katG315 HybProbe Real-Time PCR assay to determine the genotype of katG. The performance of the assay was evaluated statistically. Result In the first stage of the study, 200 samples were tested with IS6110 One-tube Nested Real-Time PCR. The assay was found to have a sensitivity of 76.92%, specificity of 98.52%, positive predictive value of 96.15%, negative predictive value of 89.86% and the diagnostic odds ratio of 221.667. In the second stage of the study, 66 samples were selected and tested for katG315 HybProbe Real-Time PCR assay, 36 samples were successfully genotyped while 30 samples failed to be genotyped. The only culture proven INH resistance specimen was not amplified at first, and culture isolate was extracted for genotyping again. The repeated test confirmed the genotype of the resistance strain to be a mutant. Conclusion katG315 HybProbe Real-Time PCR assay is a valid approach for genotyping katG. However, the sensitivity and efficiency has to be improved before application for clinical use. From the statistics obtained, COBAS TaqMan PCR assay, which is routinely used in Tuen Mun Hospital, is statistically proven to have comparatively better performance than the IS6110 One-tube Nested Real-Time PCR. Improvement on the assay is required for IS6110 One-tube Nested Real-Time PCR. However, there is great potential of applying both IS6110 One-tube Nested Real-Time PCR and katG315 HybProbe Real-Time PCR assay in clinical use with the same platform available. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

Malaria is an infectious disease caused by eukaryotic protists in the genus Plasmodium. Approximately half of the world's population is at risk of malaria. The burden of Plasmodium falciparum malaria has increased in recent years due to the emergence of resistant strains, which have even been documented in regions previously reported as malaria-free. Although malaria vaccine research has been conducted and has showed recent positive results, there still remains no effective vaccine to prevent malaria in clinical practice. According to the World Health Organization, prompt confirmation of malaria infection by microscopy and/or rapid diagnostic test (RDT) is critical to control the spreading of malaria and to prevent the evolution of drug resistant Plasmodia strains. However, malaria diagnosis remains a significant challenge as many malaria endemic regions have inadequate access to microscopy, and antibody-based RDTs are restricted by their stability under tropical temperatures and by their cost. The objective of this study was to develop a new approach to malaria diagnosis using DNA aptamers to recognise proteins encoded by Plasmodium. The research is divided into two parts. Firstly, DNA aptamers against the diagnostic markers, P. falciparum histidine-rich protein 2 (HRP2) and P. falciparum lactate dehydrogenase (PfLDH), were selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Secondly, a selected PfLDH aptamer was incorporated into a gold nanoparticle detection system to develop an aptamer-nanoparticle conjugate as a new approach towards malaria diagnosis. The identified HRP2 and PfLDH aptamers were characterised by isothermal titration calorimetry (ITC) for their affinity to targets and were observed to bind with nanomolar affinity. As PfLDH aptamers were observed to have a higher affinity to their target, PfLDH, their specificities were further characterised by ITC using human lactate dehydrogenases, hLDHA1 and hLDHB. The PfLDH aptamers were shown to be highly specific to PfLDH with no observed affinity to human LDHs. After further characterisation, PfLDH aptamer 2008s was chosen for the next stage of the research to be combined with a nanoparticle as a route towards diagnostic application. In the second part of this study, PfLDH aptamer 2008s was conjugated to gold nanoparticles (AuNPs) to create aptamer-AuNP conjugates (2008s-AuNP). The aptamer-AuNP conjugates were characterised by their tolerance in different pH and salt concentration and in their sensitivity to PfLDH. This new approach of malaria diagnosis was further validated by incubating the aptamer-AuNP conjugates with various proteins and colour changes were observed specifically upon incubation with PfLDH but not with other proteins. Hence, a Plasmodium specific aptamer-AuNP conjugate to the malaria diagnostic marker, pLDH, has been developed in this research. This work lays the foundation for further development of novel rapid diagnostic tests based on nucleic acid aptamers and nanotechnology for robust and cost-effective malaria diagnosis with potential benefit not only for malaria but in a plethora of diagnostic applications. / published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

The evolution and spread of influenza virus impose great impact on the society in the past century. Humans are still facing the zoonotic threat arising from animal influenza viruses; however, the existing knowledge is not sufficient to provide an accurate prediction of the next pandemic strain. My objective is to put forward the preparedness for influenza pandemics in two ways: molecular diagnosis and cross-protective vaccine. Influenza gene reassortment can take place during co-infection and produce novel viruses. While the pig is regarded as the potential mixing vessel for influenza viruses, it is important to develop rapid diagnostic assays to identify reassortment events in swine surveillance. In this study, rapid diagnostic assays were developed for genotyping pandemic H1N1/2009 and closely related swine influenza viruses. Eight real-time SYBR green-based reverse transcription-polymerase chain reactions (RT-PCR) containing locked nuclei acid (LNA) probes differentiated segments derived from pandemic H1N1/2009, Eurasian avian-like (EA), and triple reassortant (TR) swine virus lineages. With the help of these assays, 41 swine isolates collected during January 2009 to January 2010 in an ongoing swine surveillance programme in Hong Kong were successfully genotyped. Ten of these viruses were pandemic H1N1/2009 viruses, suggesting zoonotic transmissions of the virus from humans to pigs. A novel pandemic reassortant was also discovered during the course of surveillance. This study is the first to show pandemic H1N1/2009 virus has reassorted with other endemic swine viruses in the pig population. The genotyping assays provide a rapid and high throughput screening method to select viruses of interesting segment combination for downstream sequencing analysis and characterization. They will be useful for understanding viral reassortment and complex evolutionary dynamics in routine swine surveillance activities. Current influenza vaccines are strain-specific and the production schedule shows significant delay to reach the general population. The study aims at engineering a novel live attenuated virus vaccine which offers cross-subtypic protection. The feasibility for the conserved hemagglutinin (HA) stalk domain to induce broadly neutralizing antibodies was investigated. By manipulating the segment-specific packaging sequences, a nine-segment A/Puerto Rico/8/1934 (H1N1) (PR8) influenza virus carrying the headless HA of a different subtype (A/Hong Kong/1/1968 (H3N2)) (HK68) was generated by reverse genetics. The virus showed attenuated growth in in vitro cell culture and reduced pathogenicity in mice. Although mice vaccinated with this vaccine were better protected in the challenge of HK68 virus in comparison to unvaccinated mice, there is not enough evidence to verify cross-reactive immunity conferred by the HK68 headless HA immunogen, due to the heterosubtypic response induced by live virus administration. The absence of cross-neutralizing antibodies in immune sera may be explained by sub-optimal folding of the HK68 headless HA. Further studies are needed to modify the immunogen into its native conformation and elucidate the underlying vaccine-host interactions. These two studies have resulted in a useful diagnostic tool to increase influenza surveillance capacity at the swine-human interface, and the foundation for better universal vaccine design based on the conserved HA stalk domain. / published_or_final_version / Public Health / Master / Master of Philosophy

Tuberculosis (TB), a severe disease caused by Mycobacteria tuberculosis (MTb), remains a globally severe health problem. In modern days, emergence of drug resistant TB is a new threat to public health since it can lead to treatment failure, increased transmission of TB to other hosts and further development of drug resistant complications. The traditional diagnostic method for TB by Acid Fast Bacilli (AFB) smear and Löwenstein–Jensen medium (LJ) culture are poor in sensitivity and time consuming respectively. There is a need for rapid diagnosis and identification of MTb. Nucleic acid amplification like PCR and real-time PCR are options for rapid diagnosis. However, such techniques require sophisticated technique and complex equipment. The high cost would constitute a barrier for countries with a high demand but only limited resources. Loop-mediated isothermal amplification (LAMP) assay is a novel technique, proven by many studies as to its high sensitivity and highly specificity to MTb. Most importantly, LAMP assay is economical and affordable by developing countries. The first objective of this study was to evaluate the analytical sensitivity and specificity of LAMP assay. The specificity of LAMP assay was determined by performing LAMP assay on 19 clinical isolates, which had already been identified previously. The clinical isolates included 14 mycobacteria tuberculosis complex (MTb), and five mycobacteria other than tuberculosis (MOTT) strains that were positive for AFB smear and LJ culture but negative for IS6110 single-tube nested real time PCR. The specificity was 100%. The analytical sensitivity as well as the limit of detection (LOD) were determined by testing on a duplicate set of serial DNA dilution, where each duplicate consisted of dilution of 100,000, 10,000, 1000, 300, 100, 10 and 1 colony forming unit/milliliter (CFU/ml). The LOD of LAMP assay was about 3 CFU per reaction. The second objective of this study evaluated the diagnostic performance of LAMP assay against AFB culture and IS6110 single tube nested real time PCR for identification of MTb in 200 respiratory specimens from 123 patients. All the specimens have already been tested for IS6110 single tube nested real time PCR, and culture results and AFB smears results have been obtained for all the specimens. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of three diagnostic methods (AFB smear microscopy, LAMP assay amplification and IS6110 single-tube nested real time PCR) were calculated with 95% confidence interval using LJ culture as gold standard. The LAMP assay had a sensitivity of 80%, specificity of 92.6%, PPV of 60% and NPV of 97.1%. However, MTb might fail to grow on the LJ culture medium for various reasons, for instance, MTb might already be dead after antibiotic treatment of the patient, or there might be poor laboratory practices during the processing of the specimens. Since the LJ culture method could produce false negatives in the situations described above, an alternative to the LJ culture method, ‘Hybrid Method’ was used as the gold standard. Under this method, a specimen was regarded as positive if the LJ culture result was positive. On the other hand, if a specimen generated a negative result using the LJ culture method, the results from the LAMP assay and IS6110 nested real time PCR would be considered, i.e., if both the LAMP assay and IS6110 nested real time PCR gave positive results while the results of LJ culture were negative, the specimen was referred to be positive in this case. In other words, a specimen would be regarded as negative if and only if the LJ culture result was negative and at least one of the LAMP assay or IS6110 was negative at the same time. Along the same line, the sensitivity, specificity, PPV and NPV of the three diagnostic methods (AFB smear microscopy, LAMP assay amplification and IS6110 single-tube nested real time PCR) were calculated with 95% confidence interval against the Hybrid Method. After resolution, the LAMP assay had a sensitivity of 87.0%, specificity of 100%, PPV of 100% and NPV of 97.1%. Our results showed that the LAMP assay has a great potential to be a new TB diagnostic test, especially in developing countries, with its lot of advantages like ease of use, cheap and fast. The LAMP assay in the study showed a high specificity, however, the sensitivity has to be improved before application in clinical use. For comparison of clinical performance, IS6110 single tube nested real time PCR had a higher sensitivity than that of LAMP assay (100% vs 80% using culture as gold standard; 100% vs 87% using ‘Hybrid Method’ as gold standard). However, LAMP assay had a higher specificity than that of IS6110 single tube nested real time PCR (92.6% vs 90.7% using culture as gold standard; 100% vs 98% using ‘Hybrid Method’ as gold standard). LAMP had been proven to be a potential and powerful tool in clinical diagnosis of MTb. Further improvement on its sensitivity is required to enable its extensive use in the clinic in the future. / published_or_final_version / Medical Sciences / Master / Master of Medical Sciences