Obligat anaerob wachsende Bakterien sind an einer Vielzahl von Infektionen beteiligt. Dabei ist Bacteroides fragilis einer der wichtigsten opportunistischen Erreger unter den Anaerobiern. Bei Verdacht auf eine Infektion durch obligate Anaerobier muss nach Materialentnahme für die mikrobiologische Diagnostik unverzüglich eine kalkulierte Therapie eingeleitet werden. Oft ist eine chirurgische Therapie notwendig, die ebenso wie eine adäquate Antibiotikatherapie entscheidend für den Verlauf der Erkrankung ist. Wichtige Substanzen für eine Therapie bei Infektionen mit Beteiligung von B. fragilis sind Clindamycin, Imipenem, Metronidazol und Piperacillin/Tazobactam. Um Aussagen zur in vitro Wirksamkeit dieser Antibiotika gegenüber obligaten Anaerobiern treffen zu können, wurden in der vorliegenden Arbeit die Aktivitäten von verschiedenen Konzentrationen des jeweiligen Antibiotikums auf das Wachstum von sensiblen und resistenten B. fragilis Stämmen mittels Absterbekinetik untersucht. In Abhängigkeit von der zuvor ermittelten minimalen Hemmkonzentration des jeweiligen Antibiotikums wurden die Stämme in 2 Gruppen eingeteilt. Die erste Gruppe umfasst alle Stämme mit einer MHK ≤ 8 µg/ml. In der zweiten Gruppe sind die Stämme mit einer MHK > 8 µg/ml zusammengefasst. Die einzelnen Stämme wurden mit einem Vielfachen der minimalen Hemmkonzentration (MHK) beziehungsweise einem Vielfachen der im menschlichen Blutplasma maximal erreichbaren Konzentration (Cmax) des jeweiligen Antibiotikums inkubiert und die Bakterienkonzentration zu definierten Zeitpunkten ermittelt. Dadurch können sowohl die Wirksamkeit unterschiedlicher Antibiotikakonzentrationen als auch verschiedene Antibiotikaklassen miteinander verglichen und Aussagen zu Empfehlungen für kalkulierte Therapien getroffen werden.

Bacterial water pollution is a significant problem because it is associated with reduction in the ‘quality’ of water systems with a potential impact on human health. Faecal indicator bacteria (FIB) are usually used to monitor the quality of water, and to indicate the presence of pathogens in water bodies. However, enumeration alone does not enable identification of the precise origin of these pathogens. This study aimed to monitor the quality of bathing water and associated fresh water in and out of the ‘bathing season’ in the UK, and to evaluate the use of microbial source tracking (MST) such as the host-specific based polymerase chain reaction (PCR) and quantitative PCR (qPCR) to recognize human and other animal sources of faecal pollution. The culture-dependent EU method of estimating FIB in water and sediment samples was performed on beach in the South Sands, Kingsbridge estuary, Devon, UK- a previously ‘problematic’ site. FIB were present at significant levels in the sediments, especially mud, as well as fresh water from the stream and pond flowing onto South Sands beach. However, the quality of bathing water was deemed to be ‘good’ and met with the EU bathing water directive 2006. Using MST it was possible to successfully classify the nature of the source from which the bacteria came. PCR was applied to detect the Bacteroides species 16S rRNA genetic markers from human sewage and animal faeces. All water and sediment samples displayed positive results with a general Bacteroides marker indicating the presence of Bacteroides species. Host-specific PCR showed the human Bacteroides genetic marker only in the sediment of the stream. However, limitations in the ‘types’ of probes available and in the persistence of these markers were identified. Thus, novel dog-specific Bacteroides conventional PCR and qPCR primer sets were developed to amplify a section of the 16S rRNA gene unique to the Bacteroides genetic marker from domestic dog faeces, and these were successfully used to quantify those markers in water samples at a ‘dog permitted’ and ‘dog banned’ beach (Bigbury-on-Sea, Devon, UK). Generic, human and dog Bacteroides PCR primer sets were also used to evaluate the persistence of Bacteroides genetic markers in controlled microcosms of water and sediment at differing salinities (< 0.5 and 34 psu) and temperature (10 and 17 ºC). The rates of decline were found did not differ significantly over 14 and 16 days for the water and sediment microcosms, respectively. Beach sediments which were studied in this project may act as a reservoir for adhesive FIB, and this was confirmed using fluorescence in situ hybridisation (FISH). The similarity in the persistence of these Bacteroides 16S rRNA genetic markers in environmental water and sediment suggests that viable but non-culturable (VBNC) Bacteroides spp. do not persist in the natural environment for long. Therefore, 16S rRNA genetic markers can be of value as additional faecal indicators of bathing water pollution and in source tracking. Thus, in this study MST methods were successfully used and in future applications, dog-specific primer sets can be added to the suite of host-specific Bacteroides genetic markers available to identify the source(s) of problem bacteria found on failing beaches.

The repair of DNA double-strand breaks (DSBs) is required for the survival of all organisms. In bacteria, DNA DSBs can occur during normal housekeeping processes such as DNA replication or by exogenous damage due to chemicals or radiation. DSBs will compromise the integrity of the genome if left un-repaired, and can be fatal to an organism. Repair of DSBs by homologous recombination (HR) replicates missing chromosomal regions before joining of the separated DNA ends. In Escherichia coli the HR repair steps are; pre-synapsis, synapsis and post-synapsis. In the pre-synaptic stage a DSB is processed into a 3′ single-strand overhang, the substrate required for strand invasion in the synapsis stage and the eventual repair of the DSB. At present there are three identified pre-synapsis systems involved in recombination in bacteria; represented by the AdnAB, AddAB and the RecBCD protein complexes. Each system functions in a similar manner but differ in the physical composition of the machinery. This project investigated the pre-synaptic system of Bacteroides fragilis NCTC9343. Genes encoding putative pre-synapsis proteins were initially identified through analysis of the NCTC9343 genome. The function of these proteins was investigated in vivo by rescue of a repair-deficient strain of E. coli. This demonstrated that Bacteroides fragilis encodes a two component system, where both genes products are required to work in concert for pre-synaptic processing of DSBs. The identified genes were BF2192 and BF2191, and have been renamed addA and addB, respectively. To further examine the role of the AddAB proteins in DSB repair, a Bacteroides fragilis strain with a deletion of addAB was constructed and shown to be extremely sensitive to DNA damaging agents. The AddAB complex was purified and found to be an ATP-dependant helicase and exonuclease that acted on double-stranded DNA ends. In conclusion, this project has identified the proteins involved in pre-synaptic processing of DSBs in B. fragilis NCTC9343, consisting of AddAB homologues, and shown their protective role in repair of DNA damage.

Sphingolipids (SLs) are complex lipid-derived structures that are essential components of cell membranes in eukaryotes and some bacteria. SLs and their complex derivatives ceramides are known to be involved in multiple processes such as the formation of lipid rafts, cell signalling and membrane trafficking. The first step of SL biosynthesis is universal to all sphingolipid-producing organisms from bacteria to humans and is catalysed by the enzyme serine palmitoyltransferase (SPT). SPT is a member of the alpha-oxoamine synthase (AOS) family of pyridoxal- 5'-phosphate-dependent enzymes. All AOS family enzymes retain a high degree of structural homology and catalyse the decarboxylative Claisen-like condensation of amino acids with thioester substrates. The SPT enzyme catalyses the formation of the universal SL precursor, 3-ketodihydrosphingosine (KDS), by condensation of L-serine and coenzyme A-derived palmitic acid. Being the key controller in SL biosynthesis, SPT plays a big role in regulating natural and pathological processes. A lot of research interest has been recently generated by SLs isolated from bacterial members of the human microbiome and their roles in human health. Increasing evidence suggests that some of these SLs possess immunoregulatory effects and can have a direct impact on the immunity of the host. Bacteroides fragilis is a commensal gut-dwelling bacterium that belongs to a few human microbionts known to produce unique iso-branched sphingolipids (isoSLs); these have been shown to influence the human iNKT cell count. The production of SLs in B.fragilis is completely regulated by a gene product BF2461. In this work, BF2461 was expressed and purified; using a combination of UV-vis spectrometry, enzymatic assays, mass spectrometry and protein X-ray crystallography, it has been confirmed to be an SPT. The substrate specificity of the BfSPT has been assessed with a range of different chain-length substrates, including less common 15 and 17-carbon chain length coenzyme A substrates. The enzyme can produce different types of SL precursors with a preference for the 16-carbon chain substrate palmitoyl- CoA. However, at high levels of PCoA, a substrate inhibition is observed that might point to a natural control mechanism employed by the bacterium in favour of producing iso-branched SLs (isoSLs). The structure of BfSPT has been elucidated in a complex with its amino acid substrate L-serine. Search and analysis of putative SPTs from other microbiome-associated bacteria that produce isoSLs show that they share high similarity with an average amino acid conservation of 74%, suggesting they might be adapted to a particular type of substrate. In this respect, BfSPT might be the first isoSL-producing SPT to be structurally characterised, and the first one to have a direct impact on human health. Further structural data were obtained on protein complexes with L-cycloserine and L-penicillamine, some common inhibitors of the PLP-dependent enzymes. The structure obtained in the presence of L-penicillamine provides the first direct structural evidence of the inhibitory mechanism by a thiazolidine complex formation in the active site of a PLP-dependent enzyme. These findings shed light on certain aspects of the reaction and inhibition mechanisms of BfSPT as well as opening new prospects into researching this interesting target and its impact on the human microbiome.

As of 2010, there are approximately twenty one surface water locations classified as impaired for Escherichia coli (E. coli) contamination in the State of Arizona. Of note is the San Francisco River (SFR) which is currently listed on the US EPA 303d list of impaired waters due to E. coli bacteria present at higher concentrations than the US EPA standards for partial- and full-body contact. In 2010-2011 surface water samples were collected at sites within the impaired region to monitor E. coli and areas known for heavy recreational uses. Of 70 samples collected over 1 year, 81% were positive for universal Bacteroides marker (Allbac). Of the 57 Allbac-positive samples, 68% show contributions of the human-specific marker and 60% were positive for bovine-specific marker. While 28% of the total samples assayed showed elevated levels of E. coli (>235 MPN/100mL), there were minimal significant correlations between Bacteroides and generic E. coli across all samples. While this information is significant, past research has suggested that successfully distinguishing the sources of fecal contamination will not alone reduce or eliminate disease associated with contaminated water unless these investigations are coupled with public outreach and education. With this in mind a survey was developed to gather information about water quality perceptions, water use, peoples' attitudes, knowledge, and behaviors related to the water resources in Clifton, AZ. Survey questions consisted of multiple choice and Likert scales questions and were provided in both English and Spanish and were conducted during the summer of 2012 and winter of 2013. A total of 150 surveys were deployed with 38 surveys completed for a response rate of 25%. Our study findings indicate mixed attitudes on water quality with 80% reporting the SFR has poor water quality for drinking and 39% agree the SFR has poor water quality for swimming. Yet, 84% consider the river safe enough for picnics and activities near the water. Also, it was interesting to note participants' opinions regarding consequences of poor water quality with 66% of respondents indicating that they are concerned with poor water quality and their health. Clifton is a very tight knit community so it was not unexpected that the majority of the respondents (61%) get water quality information by having conversations with other people and 68% from newspapers, factsheets and brochures. Based on the survey responses, our team worked to develop two peer reviewed Extension publications entitled; Microbial Source Tracking: Watershed Characterization and Source Identification (Arizona Cooperative Extension, #AZ1547) and Water Quality, E. coli, and Your Health (#AZ1624). Publications have been developed in both English and Spanish and will be part of future outreach to this and other Arizona communities. It is our goal that these survey findings can be used to better tailor outputs appropriate for the targeted audience, namely the local Hispanic population. These results are important because they add to understanding perceptions of water quality and health risks in this rural community; and can lend towards enhanced outreach practices in other similar communities.

The field of molecular fecal source tracking in the water environment has developed rapidly since the first PCR assays for general and host-­‐specific Bacteroides 16s rRNA markers were published. Numerous host-­‐specific molecular markers and PCR assays have been developed, adding greater specificity, sensitivity and quantitative methods to the array of options. The public demand for readying methods for transfer to the commercial lab, so that they may be used to generate data for public utilities, citizen action groups and regulatory agencies, has fueled the development of an entire new research community. These methods, however plentiful, have not found community agreement and there is no consensus concerning the appropriate implementation of molecular fecal source tracking in the field. Some issues plaguing the implementation include imperfect marker specificity, environmental variability, DNA extraction variability, PCR inhibition and high cost of molecular analysis. This thesis presents an approach for locating hot spots of human fecal pollution in an urban watershed by using published methodologies for the collection of molecular fecal source tracking data along with a tiered watershed screening tool for cost reduction and two data normalization techniques which ameliorate several known sources of error and strengthen the efficacy of watershed application.

The City of Georgetown, Kentucky relies on a vast karst spring network as a drinking water source. This karst feature has several inputs from sinkholes and streams in the Cane Run Watershed: a watershed associated with a variety of land uses in the recharge area. The recharge area encompasses the area from North Lexington to Georgetown and is composed of urban, suburban, agricultural and industrial usage. A serious water quality issue exists with respect to the impact of fecal contamination within the spring recharge area. Identification of fecal contamination is quantified by microbial indicators adapted from surface water applications: fecal load (E. coli), fecal source (two human-host specific Bacteroides DNA markers) and fecal age (AC/TC ratio). These three criteria are used in a categorical Microbial Source Tracking (MST) model to assign a Sanitary Category Value (SCV) between 0 and 3 for each sample location. Low SCVs (1.5) are associated with high values of fecal load, low fecal age and detectable concentration of human-specific markers. SCV measured during dry weather conditions are indicative of potentially leaking human sewers. Due to retention and conservation of fecal load (E. coli) and age (AC/TC) microbial indicators in the karstic environment, ambiguous SCV model results cannot pinpoint, with statistical confidence, fecal sources in a karstic environment. Human-host specific genetic markers (HF183 and HuBac) were also detected at all sample sites above limits of detection, indicating steady inflow of fecal material during all sample events. By adding a flow multiplier and expressing HF183 and HuBac values as a load, it was strongly indicated that a human fecal source was entering the groundwater conduit and impacting Royal Spring independent from other upstream fecal sources. Interpretation of these trends, while strongly indicated, cannot be supported with statistical evidence.

Campylobacter jejuni is a major cause of bacterial gastroenteritis in the developed world; however, many aspects of its biology remain poorly understood, including its colonization of the mucus layer lining the gastrointestinal tract. In this study, we utilized microarray transposon tracking to compile a list of 195 genes essential for the growth of C. jejuni in vitro under microaerophilic conditions. Then we characterized C. jejuni growing in an extracted intestinal mucus medium. We found that C. jejuni will grow efficiently in a medium comprised of either chick and piglet intestinal mucus, and that these media have a dramatic impact on its transcriptome. Within the genes identified as differentially expressed during growth in a mucus medium, we identified a single operon, (cj0481-cj0490), which we have subsequently characterized as being responsible for both the uptake and metabolism of L-fucose. This represents the first observation of carbohydrate metabolism by the otherwise asaccharolytic C. jejuni. We further found that the inability to utilize L-fucose puts C. jejuni at a competitive disadvantage when colonizing the piglet intestine, but not the chick cecum. Finally, we examined C. jejuni’s ability to utilize mucins as a carbon source while growing within the mucus layer. We found that despite mucins being a major source of L-fucose and amino acids within the intestine, C. jejuni has a minimal ability to degrade and utilize mucins on its own. However, close proximity to mucolytic bacteria within the microbiota of the intestine, allows for increased C. jejuni growth. Together, this paints the picture of an organism that is well adapted to survival within the mucus lining of the intestine and establishing itself as part of the intestinal microbiota.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 5 uppsatser.