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This thesis describes dip tank field trials and laboratory investigations on the acaricide Amitraz. Amitraz is a triazapenta- diene compound which is relatively unstable in fouled dip washes. The field trials were conducted on the farm Sea View according to the "Total Replacement Method" and on the farm Sea Ways according to the "Lime Stabilization Method" of dipping. The results of these trials showed that Amitraz was stable in clean dip washes, and under conditions of high pH resulting from the addition of slaked lime to the dip wash. Using mixed bacterial populations optimum conditions for degradation of Amitraz in the laboratory were determined. Bacterial cultures degraded Amitraz most efficiently in media supplemented with yeast extract or with a high content of sterile cattle faeces. Amitraz concentrations were determined by gas chromatography. A culture. efficient at degrading Amitraz was enriched from a dip tank sludge inoculum. From this culture ten bacterial isolates were identified; nine of these were of the genus Pseudomonas and one was an Achromobacter sp. Experiments with both mixed and pure cultures demonstrated that bacterial degradation of Amitraz was by the process of co-metabolism. The existence of four degradation products was shown using thin layer chromatography. Tentative identification of two of the products was made.

Bacterial populations proliferating in a pilot scale biological nutrient removal system (BNR) were studied. The objective of the research was to develop media and methods to identify bacterial populations in BNR systems. Samples were obtained from the last aerobic zone of a University of Cape Town (UCT)-type system. The most probable numbers (MPN) of bacteria in the samples were analyzed in liquid media containing volatile fatty acids as sole sources of carbon. Samples were also transferred to denitrification medium, and MPN's of denitrifiers were recorded. The growth in liquid medium was plated on solid medium. Gram-negative cultures were isolated and identified. The phosphorus-removal capacity of five isolates also was studied. The results indicated that several different genera of bacteria are involved in the removal of phosphorus in an operating BNR system. Four major groups of phosphorus storing bacteria, Aeromonas/Vibrio, coliforms, Pseudomonas spp and Acinetobacter spp, were recovered. The identification of cultures on denitrification medium also recovered Pseudomonas, Aeromonas, coliforms and Acinetobacter, indicating the overlap in the function of these genera. The phosphorus accumulations in three of the tested cultures showed accumulations in excess of 10 percent. The MPN's of bacteria in acetate and propionate media obtained using samples from the pilot scale BNR system and a full scale activated sludge system were statistically analyzed. The analyses showed significant differences between MPN in acetate and propionate medium using samples from the BNR system, whereas there were no significant differences in samples from the conventional activated sludge plant. The possibility of the application of these data in process control and modeling is proposed. / Ph. D.

A mechanistic model was developed, which described the growth of a bacterial colony on an agar medium. Diffusion of substrate (nutrients/oxygen) through the colony are considered. Rate of substrate use by the organisms is assumed to follow Michaelis-Menton kinetics for substrate concentrations between prescribed limits. Above and below the prescribed concentration limits, the substrate use rate is assumed constant and zero, respectively. Supply of substrate to the colony was assumed to be non-limiting. Under these conditions, the model predicted that diffusion of substrate through the colony will eventually control colony growth. It also described a slower eponential growth rate of the colony when the organisms utilized an alternate substrate for one that became deficient throughout a portion of the colony, and a constant linear growth rate when an alternate substrate was not utilized. Consistent with published literature, a mathematical description of substrate supply through the agar indicated that, under normal conditions, glucose supply through the agar to the colony would not be expected to limit colony growth before oxygen diffusion through the colony limited growth.

Quality control procedures during food processing may involve either lengthy enrichment steps, precluding enumeration of bacteria in contaminated food, or direct inoculation of food samples onto appropriate selective media for subsequent enumeration. However, sublethally injured bacteria often fail to grow on selective media, enabling them to evade detection and intervention measures and ultimately threaten the health of consumers. This study compares traditional selective and nonselective agar-based overlays versus two commercial systems (Petrifilm and Easygel) for recovery of injured Escherichia coli B-41560, originally an isolate from ground beef. Bacteria were propagated in tryptic soy broth (TSB), ground beef, or infant milk formula (IMF) to a density of 106-108 CFU/mL, and stressed for six minutes either in lactic acid (pH of 4.5) or heat-shocked for 3 min. at 60°C. Samples were pour- plated in basal layers of either tryptic soy agar (TSA), Sorbitol MacConkey (SMAC), or Violet Red Bile (VRB) agar and resuscitated for 4h prior to addition of agar overlays. Other stressed bacteria were plated directly onto the commercial media Petrifilm and Easygel. Our results indicate that the use of selective and nonselective agar overlays for sensitive recovery and accurate enumeration of E. coli B-41560 is dependent on the stress treatment and food system. These data underscore the need to implement food safety measures that address sublethally- injured bacteria such as E. coli O157:H7, without the use of enrichment steps, in order to avoid underestimation of true densities for target pathogens. / Department of Biology

Azotobacter and various fungi were grown together in nitrogen-free media. Maximal fungal growth in the medium used was possible only at the expense of Azotobacter cells and growth was always accompanied by acid production. When the medium reached a pH of 2, the bacterial cells were aggregated on fungal hyphae and the culture fluid appeared to be free of Azotobacter. Aspergillus niger grew well at the expense of viable bacteria and other fungi grew well on heat-killed cells of A. vinelandii. Members of the genus Hormodendrum, although not causing significant decrease in pH, were also able to clear turbid cultures of Azotobacter. However, clearing, which involved the attachment of bacteria to fungal hyphae, was dependent on acid production by the fungi. Bacterial aggregation was followed by hyphal attachment, bacterial inactivation, and finally, bacterial cell lysis.

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.

Access to abstract permanently restricted to Ball State community only / Access to thesis permanently restricted to Ball State community only / Department of Biology