The hypotheses of this study are that reduction and rational usage of antibiotics reduces development of antibiotic resistance. In Sweden, the trends do not follow this pattern. Despite a decrease in prescriptions of antibiotics, there is an increase in the number of patients infected with Methicillin-resistant Staphylococcus Aureus (MRSA), Extended Spectrum Beta-Lactamases (ESBL) and ESBL selecting for carbapenem-resistance (ESBLCARBA). This study aims to study factors affecting antibiotic resistance management. An additional aim is to use a multidisciplinary approach for a subject that has mostly been studied with quantitative methods. First, linear regressions investigated any possible significant changes of prescription rates in outpatient care, hospital usage of antibiotic groups and antibiotic resistance. After this, nine interviews were conducted with physicians in outpatient care, hospital care and with representatives from the Swedish Strategic Programme for the Rational Use of Antimicrobial Agents and Surveillance of Resistance (Strama), a network working for Swedish prevention against antibiotics resistance. There was a significant decrease in the number of prescriptions of antibiotics in outpatient care among all Swedish counties and a small, but significant increase of antibiotics used in hospitals. The number of patients infected with multidrug resistant bacteria also show a significant increase. The interviews revealed that health care workers in all counties follow the same guidelines and try to be as specific as possible in choosing antibiotics to hit specific bacteria. The respondents suggested migration and extended travelling as explanations to the growing number of cases of multidrug resistant bacteria. Further, two major factors emerged as important for an efficient antibiotic resistance management; Education/knowledge and Discussion. The results indicate a need for further research on rational usage of antibiotics and the use of broad-spectrum antibiotics in hospital care, rather than the reduction through prescriptions. The results indicate that rational usage has a bigger impact than reduction. Using a multidisciplinary approach gave a broader perspective on the issue and future studies should see the possibilities of mixing quantitative and qualitative studies.

Biological evolution can be described as a unifying concept in biology. A thorough understanding of evolution is thus important to fully understand different areas of biology. However, learning the concepts of evolution has proven difficult, both to students and teachers. During the last decade, the notion of threshold concepts in learning has emerged. Passing the threshold or grasping the threshold concept is a transformative process, thought to be irreversible and has been described as passing a portal to new areas of understanding. Threshold concepts of importance to understanding evolution has been suggested to be time, spatial scale, complexity, randomness and probability. A hypothesis is therefore that facilitating understanding of those threshold concepts also will lead to a greater understanding of evolutionary mechanisms. Visualisations in science communication and learning has gained increased interest and animations as a form of visualisations has proven to facilitate learning in some situations. Since many (threshoid) concepts in evolution are untangible, such as deep time, small scale (micro and sub micro scale) animations could be a way to make those concepts more tangible for learners. In order to explore the potential for animations in learning evolution by making threshold concepts more tangible an interactive animation was designed and tested with upper secondary students in the course Biology 1. The subject of the animation was development of antibiotic resistance in bacteria. Learning effect was measured as differences in pre and post test scores on a selection of previously used concept questions from the literature, the concept inventory of natural selection (CINS). Open ended questions were also used as well as interview sessions, to gain more insight to the eventual effects of the animation. No statiscally significant improvement in the CINS scores could be observed in total, however improvement on a specific question category (biotic potential) could be observed. The number of misconceptions on evolution seemed unaffected after animation. Indications of conceptual conflicts could also be observed after the animation, indicating a potential for conceptual change with future revisions of the animation.

The number of cases of Clostridium difficile infection (CDI) has been increasing globally. CDI is the main cause of nosocomial diarrhoea, which may be life-threatening in complicated cases, and also costs the health care societies millions of pounds annually. The predominant types and their resistance to antibiotics have been changing and one of the major selective pressures which causes this is antimicrobial use. Although much is known about the role of the toxins in pathogenesis of CDI, the role of immunogenic cell wall components is unclear. They may play a role in colonisation and pathology and a study of these could clarify the infection process. It is therefore important to study the immune responses against these bacterial wall components from different strains and their effects on stimulation of leukocytes to produce cytokines and chemokines. This study was divided into four parts: 1. An epidemiological study to determine frequencies of the predominant types of C. difficile, thus 140 C. difficile isolates from surgical patients and their environment during 2009 were investigated to define their PCR ribotype. This utilised capillary sequencing gel electrophoresis for their analysis. 2. The determination of antimicrobial susceptibility to six antibiotics (ampicillin, erythromycin, tetracycline, metronidazole, moxifloxacin and vancomycin) was assessed and MIC determination by agar dilutions. 3. Investigation of host immunity to molecules with conserved molecular patterns. Surface-layer proteins (SLPs), lipocarbohydrate (LC) and flagellar proteins were separated and purified from five ribotypes of C. difficile (001, 002, 027, 078 and106) predominant in Scotland. a) The immune responses to these molecules were assessed by ELISA by exposing serum of patients and healthy donors and measuring specific IgG levels. b) Innate immunity was investigated by distinguishing responses of a macrophage cell line (THP1) to the above molecules. Induction of interleukins (IL)-1β, IL-6, IL- 8, IL-10 and IL-12 interleukins and TNF-α was detected by ELISA. In this study 15 different ribotypes were identified. The most frequent were 001, 020, 106 ribotypes (52.8%, 7.4% and 5.7%), respectively, while 13 isolates could not be assigned a ribotype. However, all isolates were sensitive to vancomycin, metronidazole and moxifloxacin, but 74.28% of isolates were resistant to erythromycin. The IgG level against bacterial antigens (SLPs, LC and flagella proteins) in donors’ serum showed almost normal distribution to all antigens from the different ribotypes and the sensitivity of the assays was increased by raising the concentration of antigens. Levels to SLPs were generally the highest, but the flagellar protein exceeded the SLPs of the 027 ribotype. The donors, controls, patients and carrier sera gave similar results. The greatest induction of interleukins was obtained using 50μg of antigen with the THP-1 cells activated with 50ng of PMA. The highest induction of all antigens was for IL-10. The highest values for the control LPS was with IL-12. But the best effect for SLPs of 027 was for IL-10 (109.1ng/ml), while the weakest for TNF for SLPs of 027 (4.7ng/ml). In general the IL-1β, IL-6, IL-8 and TNF concentrations ranged from 4.7-60ng/ml for all antigens and in contrast IL-12 and IL-10 average ranged 11- 109.1ng/ml. To conclude, the prevalence of C. difficile and their antibiotic susceptibility are constantly changing. IgG antibodies to SLPs and flagellar proteins from the hypervirulent ribotype 027 were highest in the community and hospitalized individuals. The molecules of conserved molecular patterns are immunogenic with various levels of response in the monocytic THP1 cells. SLPs were best in inducing interleukins. Flagellar proteins from 027 ribotypes accompanied SLPs in IL-10 induction levels. Consequently SLPs and flagellar proteins from 027 ribotypes appeared the best immunogenic bacterial molecules.

Within the last decade antibiotic resistant bacteria have become a major public health concern. A possible major contribution to this problem is thought to be the overuse of antibiotics in food animals. An estimated 70% of antibiotics dispensed yearly throughout the United States are distributed to the livestock industry as growth promoters, prophylactic, and therapeutic treatments, according to the Center for Disease Control and FDA. When food animals are exposed to low doses of antibiotics frequently over a long period of time the bacteria are able to develop resistance to antibiotics. Livestock harbor foodborne pathogens that are generally commensal bacteria in the animals themselves but can cause illness to the people exposed. The problem occurs when treatment becomes difficult, there is some speculation that livestock animals are a main contributor to the increase in antibiotic resistant foodborne pathogens. Salmonella spp. and Staphylococcus aureus are pathogens that can be isolated from livestock and cause serious illness in humans. Objectives of this study include isolating S. aureus and Salmonella from samples collected from food animals, investigating the prevalence of antibiotic resistance in the confirmed S. aureus and Salmonella isolates from animals raised in various areas of Southern New Mexico and Arizona. In this study, samples were collected from various food animals post-harvest at a USDA inspected, non-commercial animal harvest facility in Arizona, and evaluated for the presence of S. aureus and Salmonella. Samples were collected from 129 animals of the following types: Bovine (cow), Caprine (goat), Ovine (sheep), and Porcine (pig). S. aureus and Salmonella were isolated from three different types of samples per animal including hide samples, sub iliac and mesenteric lymph nodes, and nasal swabs. Each sample was cultured separately in enrichment media followed by selective/differential media. Once the pathogen was confirmed via 16s rRNA PCR for S. aureus, invA3 PCR for Salmonella, gel electrophoresis, DNA Sequencing, and other biochemical tests, an antibiotic susceptibility test was performed to check the resistance characteristics of each isolate. The pathogen was exposed to eight different antibiotics- Ampicillin, Cefoxitin, Chloramphenicol, Ciprofloxacin, Erythromycin, Streptomycin, Sulfamethoxazole/Trimethoprim, and Tetracycline; commonly used among animals and humans via the disc diffusion assay. A total of 59 and 60 of 369 samples were confirmed positive for S. aureus and Salmonella, respectively. The animal type that harbored the most Salmonella overall were Bovine/cattle and the sample type that harbored the most Salmonella overall were lymph nodes. The animal type that harbored the most S. aureus overall were porcine/pigs and the sample type that harbored the most S. aureus overall were lymph nodes. 18 out of 129 livestock animals sampled in this study were found to carry both Salmonella and S. aureus and were isolated from: 6-Porcine, 5-Bovine, 5-Caprine, and 2-Ovine. The overall antibiotic resistance prevalence in S. aureus and Salmonella were 22.88% and 32.71%, respectively. Antibiotic resistance patterns were seen in both S. aureus and Salmonella isolated from all different livestock and sample types. Of these S. aureus isolates 43 showed resistance to at least one type of antibiotic, and the most resistance was seen to Ampicillin. 53 Salmonella isolates showed resistance to at least one type of antibiotic, and the most resistance was seen to Erythromycin. The implications of this study indicate that there are antibiotic resistant Staphylococcus aureus and Salmonella found in various food animals and sample types. Most of these Salmonella and S. aureus isolates were resistant to more than one antibiotic. Appropriate control measures are needed to mitigate the problem of antibiotic resistant bacteria among food animals. These control measures could also reduce the spread of resistance from one bacterium to another and possibly lessen the antibiotic resistance problem and infections.

Master of Science / Department of Grain Science and Industry / Bhadriraju Subramanyam / Hulya Dogan / Stored-product insects and stored products from feed mills and swine farms contain antibiotic and potentially virulent Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, Enterococcus gallinarum, and Enterococcus hirae. Stored-product insects can serve as potential vectors of these enterococci which possess antibiotic resistance genes that can be spread by horizontal transfer to more serious human pathogens. In the present study, the species and concentration of enterococci from adults and larvae of key stored-product insects and insect diets and their antibiotic resistance profile were characterized. Adults of five species out of the 15 stored-product insects were tested positive for enterococci, and these included Callosobruchus maculatus (F.), Sitophilus granarius (L.), Stegobium paniceum (L.), Lasioderma serricorne (F.), and Sitophilus zeamais Motschulsky. Three enterococcal species (E. casseliflavus, E. faecalis, and E. faecium) were found in 53 to 97% of the 30 adults screened for each insect species, and the enterococcal concentrations ranged from 1.4 x 10³ to 3.1 x 10⁶ CFU/adult. About 10 to 100% of the mature larvae of the respective five insect species had these three enterococcal species with concentrations ranging from 0.3 x 10¹ to 1.4 x 10⁵ CFU/larvae. Only three of the eight insect diets screened had the same three enterococci species in addition to E. gallinarum and E. hirae at concentrations of 0.2 x 10¹ to 5.9 x 10³ CFU/g. The greatest enterococcal concentration was found in C. maculatus adults but not in their larvae or diet (cowpeas). In C. maculatus during a nine-day period after adult eclosion, the enterococcal concentrations increased exponentially from 0.6 x 10¹ to a maximum of 4.1 x 10⁷ CFU/adult. Enterococci were detected in the fecal material of C. maculatus during a four-day period with a maximum concentration of 3.3 x 10³ CFU/adult on the fourth day. A total of 298 enterococcal isolates from adults, larvae, and diets were represented by E. faecalis (51.7% of the total), E. faecium (19.1%), E. casseliflavus (18.8%), E. gallinarum (5.7%), and E. hirae (4.7%). Enterococci were phenotypically resistant to quinupristin (51.3% of the total), erythromycin (38.9%), tetracycline (30.1%), enrofloxacin (29.2%), doxycycline (11.5%), and tigecycline (2.7%). All isolates were susceptible to ampicillin and vancomycin.

Thesis advisor: Jianmin Gao / With the rapid evolution of antibiotic resistance, the need for more effective antibiotics is imminent. Bacterial membranes are an appealing target due to their accessibility and relatively conserved structures. Membrane targeting antibiotics, especially cationic antimicrobial peptides (CAMPs) such as host defense peptides, have been increasingly explored as novel antibiotics and tunable innate antimicrobials. The latter could be achieved by treatment with an antibiotic adjuvant: a compound that would increase the potency of host CAMPs without killing the bacteria on its own. Boosting the host’s own immune system with an adjuvant is beneficial over using antibiotics and would theoretically avoid triggering bacterial resistance. One mechanism of bacterial resistance is increasing the cationic charge of the membrane. As CAMPs are electrostatically attracted to anionic bacterial membranes, making the membrane more cationic decreases that attraction, rendering CAMPs less effective. To target this resistance mechanism chemically, two antibiotic adjuvant strategies were explored as co-treatments with various CAMPs: membrane targeting peptides used to bind and block surface amines, and small molecules used to either acetylate surface amines or convert a cationic membrane phospholipid to an anionic phospholipid. Co-treatment of the Staphylococcus aureus (S. aureus) membrane targeting peptide KAM-CT and various CAMPs increased S. aureus susceptibility to those CAMPs. Bacterial surface acetylation using sulfo-NHS-acetate followed by CAMP treatment caused up to 10 times increased CAMP potency. Hydrazine and hydroxylamine were shown to cleave the lysine moiety from the lysyl-phosphatidylglycerol (Lys-PG) phospholipid to generate phosphatidylglycerol (PG) in liposome models. S. aureus was treated with a hydroxylamine-CAMP conjugate, but it showed decreased antibiotic activity compared to the CAMP alone. To better understand what was happening in the bacteria, a novel Lys-PG quantification protocol was created by fluorophore labeling Lys-PG and quantifying the labeled Lys-PG via normal phase high-performance liquid chromatography (NP-HPLC). Cyclic peptides, such as KAM-CT, represent complex yet synthetically attainable moieties that could be used as novel antibiotics adjuvants. Expanding the repertoire of reversible covalent chemistries, especially those applied to peptide cyclization, is desirable due to the high potency and selectivity of such interactions. Herein, we also describe a novel reversible covalent chemistry between 2-formylphenylboronic acid (FPBA) and 2,3-diaminopropionic acid (Dap): the imidazolidino boronate (IzB) conjugate. It was found to be potent (Kd = 100 μM) and quickly reversible (t1 = ~6 sec) under physiological conditions. IzB formation was successfully employed as a peptide cyclization strategy as there was little interference from biologically relevant small molecules, except cysteine. Cysteine interference was utilized to create “smart” peptides that can linearize upon increasing cysteine concentrations via thiazolidino boronate (TzB) formation with the FPBA moiety in the peptide. Such “smart” peptides could be used as pH-responsive peptides or cysteine sensors able to report on the cysteine concentration in complex media. / Thesis (MS) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis advisor: Roche P. John / The growing threat of antibiotic resistance makes it extremely important that citizens be informed about the risks posed by antibiotic-resistant bacteria, and measures with which they can reduce these risks. The print media are major sources of such information for members of the public. In the present study, articles from major newspapers in the United States and Canada appearing between 1998 and 2002 were surveyed to determine the extent to which mention was made of antibiotic resistance and the risks associated with antibiotic resistance, the contextual precision with which this information was communicated, and the extent to which information was presented about causes, and risk-reduction measures, associated with antibiotic resistance. The majority of articles surveyed mentioned antibiotic resistance, but most failed to mention associated risks (i.e., the risk of illness and/or the risk of mortality). Articles that did report risks, did so only at a low level of contextual precision. A relatively low percentage of articles mentioned causes of antibiotic resistance, and even fewer mentioned risk reduction measures. These findings suggest that the print media could improve the efficacy with which they inform the public about issues associated with antibiotic resistance. / Thesis (BS) — Boston College, 2003. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Biology. / Discipline: College Honors Program.

The rapid emergence of multidrug resistant bacterial strains represents a major global healthcare issue. Amongst five known classes of membrane transporters, which play a huge role in multidrug efflux, primary-active ATP-binding cassette (ABC) transporters are ATP powered whilst secondary-active transporters utilize electrochemical ion gradients to drive substrate transport. Mechanistic insights into transport by these proteins can help with the design and development of novel therapeutic agents against multidrug resistance, and can increase our understanding of the physiological functions of these transporters. Although available crystal structures illustrate a common alternate access model for transport by ABC transporters, the mechanisms by which metabolic energy is coupled to the transport cycle is still elusive. This thesis presents a series of functional studies using whole cells as well as artificial phospholipid membranes to study the energetics of transport, and the influence of membrane phospholipids on substrate transport by the homodimeric Escherichia coli lipid A/multidrug ABC exporter MsbA. Current alternating access models for ABC exporters involve cycling between conformations with inward- and outward-facing substrate-binding sites in membrane domains (MDs) in response to engagement and hydrolysis of ATP at the nucleotide-binding domains (NBDs). Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. In this thesis, analogous substrate transport reactions are also studied for two other ABC exporters, the MsbA homologue LmrA and the human multidrug transporter ABCG2. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. It also raises questions about the role of NBDs in the transport process. Comparisons of drug transport and resistance in cells expressing MsbA-MD (truncated MsbA lacking the NBD) and full length MsbA (MsbA-WT) demonstrate increased transport efficiency of MsbA-WT compared to MsbA-MD. In addition, growth studies using E. coli WD2 cells, which are conditionally defective in MsbA’s essential activity in lipid A transport, show that lipid A transport can be restored by the expression of MsbA-WT but not MsbA-MD or ATP-hydrolysis impaired Walker A mutant (MsbA- ΔK382). Lastly, we also present biochemical experiments with proteoliposomes with a defined phospholipid composition, which suggest that cardiolipin is essential for the transport activity of MsbA. These techniques open the way to further explore lipid-proteins interactions and examine the physiological role(s) of MsbA. In conclusion, this thesis produces new insights in the mechanisms of transport and energy coupling in ABC exporters.

Rhodococcus equi is a soil-dwelling facultative intracellular pathogen that can infect many mammals, including humans. R. equi is most well known for its ability to cause severe pyogranulomatous disease in foals, primarily involving the lungs although other body systems may also be affected. The disease is endemic on many horse-breeding farms worldwide and poses a severe threat to the horse breeding industry because there is no vaccine available. Current prophylaxis is based on systematic preventative treatments with macrolides combined with rifampicin, which are also used to treat clinical cases of the disease in foals. In this thesis I have used a combination of wet laboratory and bioinformatic approaches to identify the molecular basis of emerging combined resistance to macrolides and rifampicin in R. equi foal isolates from the USA. The genomes of a selection of resistant and susceptible strains from across the USA were sequenced and assembled. Resistance genes were systematically searched by reciprocal best-match BLASTP comparisons to known antibiotic resistance determinants. This led to the discovery of a novel erythromycin ribosomal methylase (erm) gene, erm(46), in all resistant strains. Complementation analysis in a susceptible R. equi strain showed that erm(46) was sufficient to confer resistance to all macrolides, lincosamides, and streptogramin B. The erm(46) gene is carried by an integrative conjugative element (ICE) which is transferable between R. equi strains. The ICE is formed by two distinct parts, a class I integron associated with an IS6100 sequence and the erm(46) determinant carried by a sub-element which contains putative actinobacterial conjugative translocase apparatus and a transposase/integrase. All resistant strains also carry the same non synonymous point mutation in rpoB conferring rifampicin resistance. Thus, these strains are carrying double resistance to the most commonly used antibiotics to treat R. equi worldwide. Phylogenetic analysis based on the core genome demonstrated that all resistant strains are clonal. This indicates that although conjugal acquisition of the erm(46) conjugative element may occur at a high frequency, the need for the concurrent presence of a second rpoB mutation for survival in the macrolide and rifampicin dominated farm environment has effectively selected for the spread of a single clone. In the second section of this work, we sequenced a further 20 R. equi genomes from difference sources (equine, porcine, bovine, human), including representatives of each of the seven major genogroups previously defined in our laboratory based on pulsed field gel electrophoresis. I have used the newly acquired genetic information to study the genome of R. equi and analyse its diversity within and outwith its species group. This enabled us to explore the pan genome and define that R. equi is a genetically well-defined bacterial species. Our results provide definitive evidence that resolves the current dispute over R. equi classification, specifically they do not support the recent proposal (based on classical polyphasic bacterial taxonomical methods) that R. equi should be transferred to a new genus. Our core-genome phylogenomic analyses unambiguously show that the genus Rhodocococcus is monophyletic and that R. equi forms a clade together with the most recently described related environmental species R. defluvii that radiates from within the genus. Together with other shared biological and genetic characteristics, namely the unique niche-adaptive mechanism based on evolutionarily related extrachromosomal replicons, R. equi should be conseidered a bona fide member of the genus Rhodococcus. We also confirm that Rhodococcus spp. and Nocardia spp. are sufficiently distinct to warrant them belonging to different genera. In conclusion, this work used whole genome sequencing to characterize the molecular basis underlying the emergence and clonal spread of multi-resistant R. equi in horse breeding farms in the USA. This work also highlights the limitations of classical taxonomical approaches in bacterial systematics, and illustrates the importance of incorporating modern phylogenomic approaches to understand the evolutionary relationships between bacterial strains and their accurate taxonomic position.

TB remains a major health issue worldwide causing around 1.5 deaths each year. The recent phase III clinical trials of shortened TB treatment failed to show superiority compared to the current regimen and this mainly because of relapse. Relapse is thought to be caused by dormant bacteria. Dormancy in Mycobacterium species has been shown to be associated with the accumulation of intracellular lipids, defining two phenotypes: the lipid rich (LR) cells (associated with dormancy) and the lipid poor (LP) cells (non-dormant). LR cells were shown to have a higher phenotypic antibiotic resistance compared to LP cells. Studying these two phenotypes is therefore central in tuberculosis research to understand better the disease and also potentially start to reveal the bacteriology of relapse. We investigated the power of Raman spectroscopy, a label-free and non-destructive technique, to discriminate LR and LP bacteria both in-vitro and ex-vivo. This represents the first Raman spectroscopy study that tries to discriminate the phenotypes of M. tuberculosis and investigate them directly at the site of the disease. Using total lipid extract of M. tuberculosis, we showed the location of the main lipid bands in the Raman spectrum. The two major lipid peaks were located around 1300 cm⁻¹ and 1450 cm⁻¹. Raman spectroscopy can discriminate LR and LP cells with high sensitivity and specificity. The main differences between the two groups are located in the two major Raman lipid peaks, the lipid band A (1300 cm⁻¹) and lipid band B (1440 to 1450 cm⁻¹). The two phenotypes were successfully discriminated in TB infected guinea pig lung tissue sections also from in-vitro culture using wavelength modulated Raman (WMR) spectroscopy combined with fluorescence imaging. We developed a protocol to perform both Raman spectroscopy and immunohistochemistry on the same tissue sample. We studied the evolution of LR and LP proportion in mycobacterial population as the growth conditions changed and showed that LR cells could rapidly convert to LP cells as they face favourable growth conditions. The results presented in this thesis showed that LR M. tuberculosis cells could be predominant at the site of infection. This would suggest that drug sensitivity testing should be performed on culture presenting both LR and LP cells in high proportion.