M.Tech. (Biomedical Technology) / Drinking water in the greater Johannesburg area is produced by Rand Water and is transported to local Johannesburg Water where it is stored in reservoirs for distribution. At any point during the production, distribution and storage of the water, contamination with free-living amoebae, potentially containing amoeba resistant bacteria, may occur. Free-living amoebae are often resistant to the biocides used by water treatment industries and may thus be transmitted to public facilities, consumers’ homes and informal settlements through water distribution systems and during storage in small containers. The aim of our study was to analyse the water quality around Johannesburg with regard to free-living amoebae and amoeba resistant bacteria. A total of 182 tap and 5 storage tank water samples, collected from Hillbrow, Bertrams, Riverlea, Braamfischerville and Hospital Hill, were analysed for amoebae, indicator organisms, Legionellae, environmental mycobacteria, Shigella, Salmonella and Vibrio species using amoebal enrichment method. Direct microscopy indicated the presence of amoebae in 96.1% of samples. Acanthamoeba cysts were present in 69.0% of the samples. In 55.0% of these samples visibly active intracellular bacteria were observed within the sample suspensions. In the 46 samples analysed by polymerase chain reaction, the presence of Acanthamoeba species was confirmed in 65.2%, and the intracellular bacteria such as Legionella pneumophila and Mycobacterium avium was confirmed in 23.9% and 73.9% respectively. All samples indicated the presence of Shigella species while one sample contained Salmonella species on xylose lysine desoxycholate agar after amoebal enrichment processing. Vibrio species was not confirmed in the samples. Our results indicated a high risk of transmission of amoeba resistant bacteria through drinking water to people living in these areas.

Naegleria fowleri is a free-living amoeba found in freshwater lakes and ponds that is the causative agent of Primary Amoebic Meningoencephalitis (PAM). Matrix metalloproteinases (MMPs) have been described in protozoa, such as Plasmodium falciparum, Trypanosoma brucei, and Balamuthia mandrillaris, and have been linked to their increased motility and invasive capability by degrading components of the extracellular matrix (ECM). In addition, MMPs are often upregulated in tumorigenic cells and have been attributed as responsible for the metastasis of certain cancers. In the present study, in vitro experiments indicated that MMPs are linked functionally to the ECM degradation process. Gelatin zymography demonstrated protease activity in N. fowleri whole cell lysates, conditioned media, and media collected from in vitro invasion assays. Western immunoblotting confirmed the presence of the metalloproteinases MMP-2, -9, and -14. The highly virulent mouse-passaged amoebae expressed higher levels of MMPs than the weakly virulent axenically grown amoebae. The functional relevance of MMPs found in media in degradation of ECM components was confirmed through the use of MMP inhibitors. The collective in vitro results suggest that MMPs may play a critical role in the invasion of the CNS. Furthermore, the expression of select metalloproteinases may serve as amenable targets for therapeutic manipulation of expansive PAM.

Stenotrophomonas maltophilia is increasingly emerging as an opportunistic pathogen of global concern. Due to its inherent resistance to several classes of antibiotics including carbapenems and its ability to acquire mobile resistance elements, treatment of infections caused by S. maltophilia is a constant challenge for clinicians. Trimethoprim-sulphamethoxazole (TMP-SMX) is the generally accepted antibiotic of choice for the treatment of infections caused by this organism, but resistance to the drug is increasingly being reported; hence, the need for alternative therapeutic options. In this study, the antimicrobial susceptibility profile of 110 commensal S. maltophilia isolates obtained from Nkonkobe municipality, Eastern Cape Province, Republic of South Africa was investigated. Twenty-one antibiotics including TMP-SMX and the newer fluoroquinolones; levofloxacin, gatifloxacin and moxifloxacin were included in the antibiotic panel. About 63.4 percent of the isolates were susceptible to TMP-SMX with a resistance rate of 28.2 percent. The fluoroquinolones were more effective with susceptibilities ranging from 76 percent to 94.7 percent. Resistance to the fluoroquinolones ranged from 1.3 percent to 2.7 percent. Levofloxacin was the most effective fluoroquinolone tested. Phenotypic dectection of extended spectrum β-lactamases (ESBLs) showed double disc synergy test (DDST) positivity in 59.5 percent of the isolates. Cefepime was the most sensitive indicator cephalosporin in the DDST with 77.3 percent of suspected ESBL-producing isolates showing cefepime-clavulanic acid synergy. Isolates exhibited nine different ESBL phenotypes, however, PCR amplification of the bla genes revealed four isolates that possessed genes belonging to the CTX-M group (CTX-M-1 and CTX-M-8 groups). ESBL genes are usually carried on mobile elements such as plasmids and transposons which may also bear genes that mediate resistance to aminoglycosides, tetracyclines, TMP-SMX and fluoroquinolones. ESBL positive isolates appeared more susceptible to the fluoroquinolones compared to TMP-SMX but there was no significant relationship between ESBL production and susceptibility to these drugs (p > 0.05). The newer fluoroquinolones are a possible alternative treatment option for S. maltophilia infections in this environment but further studies and clinical investigations are needed to determine the in vivo efficacy of these drugs.

The present study demonstrates that blue grouse on Vancouver Island are infected with two species of Haemoproteus, probably two species of Leucocytozoon and a species of Trypanosoma. Haemoproteus dendragapi n.sp. is described from the Nanaimo Lakes Area. The growth rate of H. canachites gametocytes is much more rapid than that described by Fallis in Ontario. The very young tissue stages of H. canachites are described from lung preparations of grouse chicks. The life cycle of Leucocytozoon bonasae has been completed by using a new vector, Cnephia minus. As reported by Fallis in Ontario, Simulium aureum has been found to be a vector of L. bonasae on Vancouver Island. This study has verified Woodcock's often ignored hypothesis that the morphology of the gametocyte-host cell complex changes with age of infection. A probable new species of Leucocytozoon is described from the Campbell River Area. In-vitro culture of the trypanosome from grouse blood has been carried out. A yearling blue grouse has been successfully infected by inoculation of metacyclic trypansomes from the culture. / Science, Faculty of / Zoology, Department of / Graduate

Manganese-deficient Streptococcus sanguinis mutants exhibit a dramatic decrease in virulence for infective endocarditis and in aerobic growth in manganese-limited media. Loss of activity of a manganese-dependent, oxygen-dependent ribonucleotide reductase (RNR) could explain the decrease in virulence. When the genes encoding this RNR are deleted, there is no growth of the mutant in aerobic broth culture or in an animal model. Testing the contribution of the aerobic RNR to the phenotype of a manganese transporter mutant, a heterologous class II RNR from Lactobacillus leichmannii called NrdJ that requires B12 rather than manganese as a cofactor was previously introduced into an RNR mutant of S. sanguinis. Aerobic growth was only partially restored. Currently, we sought to improve NrdJ-dependent growth by (i) amending the medium to increase cellular levels of B12; (ii) characterizing a spontaneous mutant of the NrdJ-complemented strain with improved aerobic growth; and (iii) altering this strain through further genetic manipulation.

La pathogénicité des bactéries a toujours été attribuée à des facteurs de virulence et les bactéries pathogènes sont considérées comme étant mieux armées, comparé à des bactéries ne provoquant pas de maladies. Selon les premières études génomiques, le fait de supprimer un certain nombre de gènes des bactéries pathogènes, limiterait leur capacité à infecter leurs hôtes. Au contraire, des études de génomique comparatives récentes, démontrent que la spécialisation des bactéries dans les cellules eucaryotes est associée à une perte de gènes massive, en particulier pour les endosymbiontes allopatriques qui sont isolés depuis longtemps dans une niche intracellulaire. En effet, les bactéries sympatriques, extracellulaires, ont souvent des génomes plus grands et présentent une résistance et une plasticité plus importante. Ces bactéries constituent, de fait, plutôt des complexes d’espèces que de vraies espèces. Certaines bactéries spécialistes, comme les bactéries pathogènes, arrivent à s’échapper de ces complexes et à coloniser une niche, bénéficiant alors d’un nom d’espèce. Leur spécialisation leur permet de devenir allopatriques et leurs pertes de gènes favorisent une évolution réductive. Ces observations nous ont conduits à réaliser une étude afin de quantifier le taux de perte de gènes lors de l’évolution de ces bactéries extracellulaires vers celle de bactéries spécialistes intracellulaires. Notre objectif était de vérifier que ce qui caractérise l’évolution des bactéries intracellulaires est bien la réduction génomique, en prenant en compte tous les événements possibles de gains de gènes. Par ailleurs, dans une étude neutre comparant les 12 espèces pandémiques les plus dangereuses pour l’homme avec les espèces non-épidémiques les plus proches, nous avons voulu identifier des spécificités génomiques associées à la capacité virulente de bactéries pathogènes et démontrer que, à part les toxines et les modules toxine-antitoxine, ce qui caractérise ces espèces ce ne sont pas les facteurs de virulence, mais la perte des gènes de régulation. Au final, les bactéries pathogènes ont un répertoire virulent dans lequel les gènes absents sont aussi importants que les gènes présents. / The virulence of pathogenic bacteria has been attributed to virulence factors and pathogenic bacteria are considered to have more genes compared to bacteria that do not cause disease. According to the first genomic studies, removing a certain number of genes from pathogenic bacteria impairs their capacity to infect hosts. However, more recent studies have demonstrated that the specialization of bacteria in eukaryotic cells is associated with massive gene loss, especially for allopatric endosymbionts that have been isolated for a long time in an intracellular niche. Indeed, bacteria living in sympatry often have bigger genomes and exhibit greater resistance and plasticity and constitute species complexes rather than true species. Specialists, including specific pathogenic bacteria, escape these bacterial complexes and colonize a niche; thereby gaining a species name. Their specialization allows them to adopt allopatric lifestyle and experience reductive genome evolution. These observations led us to design a study to quantify the rate of gene losses during the evolution of free-living bacteria to intracellular specialists. Our objective was to verify that what characterizes the evolution of intracellular bacteria is genomic reduction, taking under consideration all possible gene gain events. Furthermore, in another neutral study comparing the 12 most dangerous pandemic bacteria to Humans to their closest non-epidemic species, we wished to identify any genomic specificities associated to the virulent capacity of pathogenic bacteria and demonstrate that, besides toxins and surprisingly, toxin-antitoxin modules, pathogenic bacteria are not characterized by more virulence factors, but rather by a loss of regulatory genes. Finally, virulent bacteria exhibit a genomic repertoire in which absent genes are as important as present ones.

La qualité de l'eau est une préoccupation majeure pour la santé publique et la préservation de l'environnement. Nous proposons d’utiliser les phages comme des biosenseurs pour détecter les pathogènes humains ou animaux présents dans les eaux de surface, un outil nommé Phagosensor.La mise au point d’un phagosensor prototype a permis d’optimiser la détection des bactéries par cytométrie en flux. Les résultats montrent que cet outil est extrêmement rapide, sensible, et très spécifique. L’outil phagosensor permet de détecter des bactéries cibles présentes dans un environnement complexe tel que l’eau de mer.Le prototype fonctionnel a servi de base à la construction de phagosensors spécifiques de bactéries pathogènes. Les résultats montrent que la stratégie développée à partir du prototype peut être rapidement transposée à la détection de pathogènes tel que Salmonella. Le séquençage de novo et l’annotation des génomes de trois phages isolés de l’environnement permettront la construction de nouveaux phagosensors spécifiques de souches d’E. coli pathogènes.Cette stratégie a été adaptée à la détection d’un signal luminescent post-infection en utilisant les phages recombinants portant l’opéron luxCDABE. Les bactéries infectées sont rapidement détectables.L’ensemble de ces résultats démontre que la stratégie développée est applicable à la construction de phagosensor sur demande pour une détection rapide, sensible et spécifique des bactéries d’intérêt que ce soit en fluorescence ou en luminescence. La détection dans l’eau de mer suggère, qu’à terme, des outils pourront être conçus pour la détection de bactéries pathogènes dans d’autres matrices telles que le sang ou les aliments. / Water quality is a major concern for public health and natural environment preservation. We propose to use phages to develop biosensor tools able to detect human and animal pathogens present in water. The construction of a phagosensor prototype using an optimized genetic engineering strategy, infection and detection conditions, allowed the specific detection of bacteria. The results show that detection is fast, specific and highly sensitive. Moreover, the phagosensor tool detects target bacteria in a complex environment such as seawater. Phagosensors specific of pathogenic bacteria were constructed following the strategy developed for the prototype. Results show that the strategy we designed can be successfully transposed to detect pathogens such as Salmonella. De novo sequencing and genomes annotation of three phages isolated from the environment were carried out to develop phagosensors that are specific of pathogenic E. coli. This technology was then adapted to detect a luminescent signal arising post-infection using genetically modified phages carrying the entire luxCDABE operon. The bacteria infected with the lux recombinant phages were rapidly detected by luminescence emission. Together, these results demonstrate that our technology can be applied to construct various phagosensors adapted to the detection of different bacterial species of interest and using at least two output signals. These tools allow a rapid, specific and highly sensitive detection that are close to the European guideline. Efficient bacterial detection in seawater suggests that phagosensors could be developed to detect pathogenic bacteria in other matrices such as blood or food.

This study was conducted from March 3, through June 2, 1951, in order to determine to what extent pathogenic bacteria were entering the Trinity River between East Fort Worth, Texas and South Dallas, Texas, from municipal sewage disposal plants.

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen. Several antibiotic resistant strains of P. aeruginosa are commonly found as secondary infection in immune-compromised patients leaving significant mortality and healthcare cost. Pseudomonas aeruginosa successfully avoids the process of phagocytosis, the first line of host defense, by secreting several toxic effectors. Effectors produced from P. aeruginosa Type III secretion system are critical molecules required to disrupt mammalian cell signaling and holds particular interest to the scientists studying host-pathogen interaction. Exoenzyme S (ExoS) is a bi-functional Type III effector that ADP-ribosylates several intracellular Ras (Rat sarcoma) and Rab (Response to abscisic acid) small GTPases in targeted host cells. The Rab5 protein acts as a rate limiting protein during phagocytosis by switching from a GDP- bound inactive form to a GTP-bound active form. Activation and inactivation of Rab5 protein is regulated by several Rab5-GAPs (GTPase Activating Proteins) and Rab5-GEFs (Rab5-Guanine nucleotide Exchange Factors). Some pathogenic bacteria have shown affinity for Rab proteins during infection and make their way inside the cell. This dissertation demonstrated that Rab5 plays a critical role during early steps of P. aeruginosa invasion in J774-Eclone macrophages. It was found that live, but not heat inactivated, P. aeruginosa inhibited phagocytosis that occurred in conjunction with down-regulation of Rab5 activity. Inactivation of Rab5 was dependent on ExoS ADP-ribosyltransferase activity, and more than one arginine sites in Rab5 are possible targets for ADP-ribosylation modification. However, the expression of Rin1, but not other Rab5GEFs (Rabex-5 and Rap6) reversed this down-regulation of Rab5 in vivo. Further studies revealed that the C-terminus of Rin1 carrying Rin1:Vps9 and Rin1:RA domains are required for optimal Rab5 activation in conjunction with active Ras. These observations demonstrate a novel mechanism of Rab5 targeting to phagosome via Rin1 during the phagocytosis of P. aeruginosa. The second part of this dissertation investigated antimicrobial activities of Dehydroleucodine (DhL), a secondary metabolite from Artemisia douglasiana, against P. aeruginosa growth and virulence. Populations of several P. aeruginosa strains were completely susceptible to DhL at a concentration between 0.48~0.96 mg/ml and treatment at a threshold concentration (0.12 mg/ml) inhibited growth and many virulent activities without damaging the integrity of the cell suggesting anti-Pseudomonas activity of DhL.

A leptospirose é uma zoonose causada por bactérias patogênicas do gênero Leptospira. Apesar de sua importância, a patogênese e virulência permanecem não elucidadas. As leptospiras não apresentam proteases conhecidas de degradação de matriz extracelular, atividade crucial para a penetração e disseminação nos hospedeiros. Assim, foi proposta a investigação da interação de leptospiras com plasminogênio/plasmina e as implicações para a infecção. As leptospiras capturam plasminogênio na superfície, e este é convertido à plasmina por ativadores do hospedeiro. A plasmina associada propicia degradação de componentes de matriz extracelular, habilidade de penetração e evasão imune. Adicionalmente, as leptospiras estimulam a expressão de ativadores de plasminogênio e metaloproteases de matriz. Os resultados contribuem para o conhecimento do processo infeccioso das leptospiras, descrevendo um novo mecanismo de patogenicidade. / Leptospirosis is a zoonosis caused by pathogenic bacteria from genus Leptospira. Despite its importance, the pathogenicity and virulence remain to be elucidated. The leptospires do not present known proteases able to degrade extracellular matrix, an activity essential for the penetration and dissemination within the hosts. Therefore, we proposed the investigation of the leptospiral interaction with plasminogen/plasmin and its implications for infection. Leptospires capture plasminogen on the surface, which is converted to plasmin by hosts activators. Surface-bound plasmin confers extracellular matrix components degradation, penetration ability and immune evasion. Additionally, leptospires stimulate plasminogen activators and matrix metaloproteases expressions. The results constitute one possible mechanism that contributes to the invasion process and the rapid dissemination of Leptospira.