Thesis (MSc (Biomedical Technology))--Cape Peninsula University of Technology, 2017. / Background: It is well established that Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogenic organism that has been frequently identified as the cause of nosocomial and community acquired infections. Furthermore, studies have shown that over the last few decades strains of the genus Klebsiella have systematically developed resistance to numerous antibiotics. Aims and Methods: The primary aim of this study was to investigate the prevalence of K. pneumoniae in nosocomial and community isolates in the Western Cape province of South Africa. Various identification techniques such as the polymerase chain reaction (PCR) using the API 20 E, the VITEK®2 system, primers specific for the 16S-23S rDNA ITS region and the Matrix-assisted laser desorption/ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) were compared for the identification of this pathogen. The VITEK 2 system was used to detect antibiotic resistant profiles of the K. pneumoniae isolates and to identify the extended spectrum beta-lactamase (ESBL) phenotypic among these isolates. The PCR was used to detect Beta-lactam genes viz. CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively in both the genome and plasmid DNA of K. pneumoniae using gene specific primers. Results: In total 57 agar plate bacterial cultures or glycerol stock bacterial cultures were obtained during 2011. Of the 57 isolates, the API 20 E test identified 47 (82.5%) of the isolates (n = 57) as K. pneumoniae while 10 isolates (17.5%) were identified as Raoultella species. The VITEK 2 method and PCR identified all 57 isolates as K. pneumoniae (100%). Of the isolates, 82.5% (47/57) were positively identified as Klebsiella species, 14% (8/57) were identified as Klebsiella variicola and 3.5% (2/57) were shown as no reliable identification (NRI) when using the MALDI-TOF MS. Examination of the 57 isolates using primers specific for the CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively showed the following: PCR amplicons for the TEM gene were produced successfully for 46 (81%) of the 57 isolates included in this project, while 11 (19%) of the samples did not yield any TEM amplicons; PCR amplicons for the blaSHV gene were obtained successfully for 56 (98%) of the 57 DNA samples, while 1 sample (2%) did not yield any SHV amplicons; and PCR amplicons for the blaCTX-M gene were produced successfully by 89% (n = 51) of the DNA samples included in this project, while 11% (n = 6) did not yield any CTX-M amplicon. Extended-spectrum beta-lactamase phenotypes had been confirmed in 84% (n = 48) K. pneumoniae isolates while nine isolates were found to be non-ESBL. Resistance rates for these 48 isolates were high and showed resistance patterns of: Amoxicillin/Ampicillin, Amoxycillin/Clavulanate, Ceftriaxone/Cefotaxime, Cefuroxime/Cefprozil and Ceftazidime (100%, n = 48); Piperacillin/Tazobactam and Cefoxitin (98%, 47/48); Cefepime (96%, 46/48); Aztreonam (94%; 45/48); Tobramycin (81%, 39/48); Gentamycin and Ciprofloxacin (77%, 37/48); Trimethoprim/Sulfamethoxazole (67%, 32/48); and Tigecycline (25% 12/48). Conclusion: For the analysis by all four methods employed, a total agreement of 68.4% was obtained, indicating the positive identification of K. pneumoniae in 39 of the 57 samples analysed. An average agreement of 28.1% was then obtained for the comparison of results generated for three of the methods utilised, while a 3.5% average agreement was obtained for at least two methods. Furthermore, all four methods agreed that 82.5% of the isolates were Klebsiella species while three methods agreed that 17.5% of the isolates were Klebsiella species. Based on the results obtained in the current study, PCR and VITEK 2 were the methods of choice for the identification of K. pneumoniae. The current study also showed, that ESBL-K. pneumoniae strains are present in the Western Cape province, South Africa; with high resistance profiles to numerous antibiotics including the Cephalosporins.

Colletotrichum species are considered one of the most economically important plant pathogens. They cause many losses in tropical, subtropical and temperate regions affecting a wide range of plant species. In tropical and subtropical regions C. gloeosporioides and C. acutatum are associated with significant losses on pre and post-harvest anthracnoses. There are still many features to understand about Colletotrichum biology and its systematics. The accurate identification of species involved with each anthracnose is of high relevance to establish management strategies to control the disease. Although the great advances on Colletotrichum systematics, species complex such as C. gloeosporioides and C. acutatum are used in a broad sense in Brazil. These complexes were recently investigated and showed to be highly genetic and geographic variable. In this study multigene analysis were carried out based on ITS, GAPDH, CHS-1, TUB2 and CAL or HIS3 partial sequences for strains of C. gloesporioides and C. acutatum complexes collected from fruit crops in Brazil. Strains from different countries and exepitypes and others sequences available on GenBank from the species accepted on both complexes were added on dataset. Six strains from C. gloeosporiodes complex and five for C. acutatum were selected based on multigene phylogeny to investigate the pathogenicity through inoculations on detached fruit. The multigene phylogenies showed the occurrence of species in Brazil related to those complexes with a high genetic variability among them. The phylogeny of Brazilian strains belonging to the C. gloeosporioides complex showed that C. siamense represents the most genetically and host-specific variable clade. In contrast, C. asianum clade grouped only strains isolated from mango. The strains from this clade used on pathogenic test were not able to infect avocado and one of the strains caused symptoms only on mango. All strains from Brazil grouped in one subclade within the C. fructicola clade and seem to represent a genetically distinct group. C. theobromicola is first reported causing anthracnose on acerola fruit. Three new species (C. polyphialidicum, C. paranaense and C. pruni) belonging to the C. acutatum complex were recognized and their morphologic descriptions were provided. The pathogenic test for the strains in the C. acutatum complex showed their cross infection ability, but in some cases the larger lesions were produced on the original host. Most brazilian strains from C. acutatum complex grouped in one subclade within the C. nymphaeae clade and seem to be genetically distinct. / Fungos do gênero Colletotrichum são considerados um dos mais importantes economicamente na Fitopatologia. Espécies desse gênero são encontradas amplamente disseminadas e estão associadas a diversas espécies de plantas hospedeiras. Em regiões tropicais e subtropicais, espécies dos complexos C. gloeosporioides e C. acutatum são a principal causa das antracnoses em pré e póscolheita de frutos e consequentemente causam significantivas perdas. Ainda há muitos aspectos a serem compreendidos sobre o gênero Colletotrichum, como a biologia e a sistemática. A acurada identificação das espécies associadas a antracnoses é de suma importância para o estabelecimento de estratégias de controle. No entanto, apesar dos grandes avanços na sistemática desse gênero, complexos de espécies como aquelas citadas acima são tratados de modo genérico no Brasil. Estes complexos de espécies foram recentemente estudados e considerados geneticamente e geograficamente variáveis. Neste sentido, o presente trabalho teve como objetivo caracterizar isolados de Colletotrichum spp. associados a diferentes frutos e regiões do Brasil por meio de análise filogenética. Para análise multilocus, foram utilizadas sequências parciais dos genes ITS, GAPDH, CHS-1, TUB2 and CAL ou HIS3. Sequências de espécies-tipos disponíveis no GenBank e de isolados de diferentes países foram adicionadas ao conjunto de dados. Com base nos resultados obtidos por meio de filogenia multilocus, seis isolados do complexo C. gloeosporiodes e cinco do complexo C. acutatum foram escolhidos para testes de patogenicidade cruzada. A espécie C. siamense, pertencente ao complexo C. gloeosporioides, foi a mais variável geneticamente e quanto ao hospedeiro de origem. Diferentemente, apenas isolados obtidos de manga se agruparam no clado C. asianum. Isolados agrupados neste clado não infectaram abacate e um dos isolados (CPC 20969) causou sintomas apenas em manga. No clado C. fructicola, isolados coletados no Brasil se agruparam em um subclado e parecem representar um grupo geneticamente distinto. A espécie C. theobromicola é relatada pela primeira vez em acerola. Foram identificadas três novas espécies, C. polyphialidicum, C. paranaense e C. pruni, pertencentes ao complexo C. acutatum. Isolados brasileiros agrupados no clado C. nymphaeae parecem representar um grupo geneticamente distinto, todos se agruparam em um subclado. Isolados do complexo C. acutatum utilizados no teste de patogenicidade provocaram sintomas nos hospedeiros testados, porém, em algumas inoculações, as lesões foram maiores no hospedeiro de origem.

The anti-pneumococcal function of native C-reactive protein (CRP) involves its binding to phosphocholine molecules present on Streptococcus pneumoniae and subsequent activation of the complement system. However, when pneumococci recruit complement inhibitory protein factor H on their surface, they escape complement attack. Non-native forms of CRP have been shown to bind immobilized factor H. Accordingly, we hypothesized that modified CRP would bind to factor H on pneumococci, masking its complement inhibitory activity, allowing native CRP to exert its anti-pneumococcal function. As reported previously, native CRP protected mice from lethal pneumococcal infection when injected 30 minutes before infection but not when injected 24 hours after infection. However, a combination of native and mutant CRP was found to protect mice even when administered 24 hours after infection. Therefore, it is concluded that while native CRP is protective only against early-stage infection, a combination of native and mutant CRP offers protection against late-stage infection.

The obligate intracellular bacterium, Chlamydia trachomatis, and Herpes Simplex Virus Type-2 (HSV-2) are the leading sexually transmitted pathogens in the world. These infections are usually asymptomatic and clinically mild, but complications can be severe. Reports of dual detection of Chlamydia and HSV within the genital tracts of humans led our laboratory to develop an in vitro Chlamydia/HSV co-infection model. Little is known regarding the specific pathogenesis of Chlamydia and HSV co-infections, but HSV-super-infection of Chlamydia-infected cells caused the chlamydiae to deviate from their normal developmental cycle into a non-replicative state termed persistence, or the chlamydial stress response. Interactions between HSV envelope protein, gD with host cell junction protein, nectin-1, were enough to stimulate the departure from normal chlamydial development. Additional data also suggested that there might be differences between single infection and co-infection outcomes in vivo. Thus, two diverging hypotheses were investigated here: i) that host nectin-1 is required for normal chlamydial development; and ii) that pathogen shedding and/or disease progression in Chlamydia and HSV-2 co-infected animals will differ from that observed in singly-infected animals. Chlamydial infection of nectin-1 knockdown cell lines revealed no inhibition of chlamydial entry, but significant reductions in inclusion size and production of infectious chlamydiae. Additionally, nectin-1 knockout mice shed fewer Chlamydia compared to wild type mice. In other studies, we developed a novel in vivo Chlamydia and HSV-2 intravaginal super-infection model in BALB/c mice. Infection with Chlamydia muridarum, followed up to 9 days later by HSV-2 super-infection, both reduced HSV shedding and protected mice from HSV-induced fatal neurologic disease compared to HSV singly-infected animals. Protection is lost when: i) infected animals are no longer shedding C. muridarum; ii) when mice are inoculated with UV-inactivated C. muridarum; or iii) when viable chlamydiae are eliminated from the genital tract using antibiotics prior to HSV-2 super-infection. Altogether, we have determined that host nectin-1 is required for chlamydial development both in vitro and in vivo, and that chlamydial pre-infection protects mice from subsequent HSV infection. We predict that these observations may lead to novel approaches to prevent human infection by these two common sexually transmitted pathogens.

Objective: One of the main theoretical proposals of Intensive Short-term Dynamic Psychotherapy (ISTDP; Davanloo, 1990) is that experiencing of previously unconscious guilt over aggressive impulses associated with attachment trauma leads to increase in self-compassion. The present study aimed to test this assumption. Method: Videotaped sessions from five therapies from a randomized controlled trial of 20-sessions of time-limited ISTDP for treatment-refractory depression were rated with the Achievement of Therapeutic Objectives Scale (ATOS; McCullough, Larsen, Schanche, Andrews& Kuhn, 2003b). Degree of patient guilt arousal and self-compassion were rated on all available sessions. Data were analyzed using a replicated single-subject time-series approach. Results: Guilt arousal was not shown to positively predict self-compassion for any of the five patients. For one patient guilt arousal negatively predicted self-compassion two sessions ahead in time. Conclusion: The current study yields no support that the experience of guilt over aggressive feelings and impulses leads to increases in self-compassion. On the contrary, the finding that guilt negatively predicted self-compassion for one patient must be considered as an indication that this treatment process might negatively impact self-compassion for some patients in some contexts. However, there are several methodological limitations to the current study in the light of which the results should be regarded as tentative.

Growing resistance of bacteria towards antibiotics resulted in extensive research effort for development and application of new materials and techniques. Due to their unique properties, graphene quantum dots (GQDs) have attracted much attention and are a promising material with potential applications in many fields. One use of GQDs is as a photodynamic therapy agent that generates singlet oxygen. In this work, GQDs synthesized by focusing nanosecond laser pulses into a mixture of benzene and nickel(II) oxide were combined with methylene blue (MB) to eradicate Gram-negative Escherichia coli and Gram-positive Micrococcus luteus. Theoretical calculation of pressure evolution was calculated using the standard finite difference method. Detailed characterizations were performed with transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier-transform infrared (FTIR), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Furthermore, singlet oxygen generation from MB-GQD mixture was investigated by measuring the rate of 9,10-anthracenediyl-bis(methylene) dimalonic acid photobleaching at 400 nm. Combining MB with GQDs caused enhanced singlet oxygen generation, leading to improved bacterial deactivation rate. The (3-(4,5-dimethylthiazol-2- yl)-2,5-diphenyltetrazolium bromide) (MTT) assay was used to determine if GQDs in dark conditions caused human cellular side-effects and affected cancer and noncancer cellular viability. We found that even high concentrations of GQDs do not alter viability under dark conditions. These results suggest that the MB-GQD combination is a promising photodynamic therapy agent that may be useful when antibiotics resistance is present.

Lyme disease (LD) is the most prevalent vector borne disease is North America with 300,000-600,000 human cases each year. Preventative strategies for LD in humans are poorly developed and largely inadequate. While preventive vaccines for LD are widely used in veterinary medicine, there are no vaccines available for use in humans. The goal of this study was to develop a human vaccine that can elicit antibody responses that kill spirochetes in both the tick and mammalian environments. The approach applied in this study centered on the development of chimeric epitope proteins, referred to as chimeritopes. Chimeritopes consist of a series of epitopes derived from one or more proteins or protein variants. Three chimeritope proteins designated as Chv1, Chv2 and Chv3 were designed. These proteins harbor the same set of 18 linear epitopes derived from 9 different OspC type proteins. They differ in epitope arrangement or by the presence or absence of linkers between specific protein segments. The immunogenicity of each protein was assessed in multiple animal models including mice, rats, and purpose bred beagles. Immunoblot, ELISA, and IFA analyses using sera from immunized animals demonstrated that the Chv proteins elicit IgG responses that recognize a diverse array of OspC type proteins. Anti-Chv and anti-OspA antisera displayed complement dependent bactericidal activity. To assess protective efficacy, purpose bred beagles were immunized with each vaccine formulation and then challenged by infestation with infected ticks. Efficacy was assessed by monitoring seroconversion, cultivation of tissue biopsies, clinical presentation and histopathological analysis of joints and tissues. All dogs vaccinated with the Chv2-OspA combination were fully protected. All dogs in this group were seronegative for LD, biopsy culture negative and did not develop LD associated symptoms including lameness or lesions in tissues or joints. In light of market concerns centered on the use of full length OspA in a human vaccine, epitope mapping was performed to identify a linear epitope that could be employed in development of a possible OspC-OspA chimeritope. A linear epitope, designated as OspA221-240was identified. Antisera to KLH-OspA221-240displayed potent and broad bactericidal activity. Interestingly, the OspA221-240epitope has homology to residues 244 to 263 of OspB suggesting that OspB may also be a potential candidate for inclusion in a human vaccine. This study establishes proof of principle for the use of OspC chimeritopes in LD subunit vaccines and highlights the need to employ a multi-valent, multi-antigen vaccine approach in development of a human LD vaccine.

Thesis (Ph.D. (Biochemistry)) --University of Limpopo, 2009 / Refer to document / National Research Foundation (NRF) and University of Limpopo

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Abstract not available