Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium that is also a major opportunistic human pathogen in nosocomial infections and cystic fibrosis chronic lung infections. These P. aeruginosa infections can be extremely difficult to treat due to the high intrinsic antibiotic resistance and broad repertoire of virulence factors, both of which are highly regulated. It was demonstrated here that the psrA gene, encoding a transcriptional regulator, was up-regulated in response to sub-inhibitory concentrations of antimicrobial peptides. Compared to wild-type and the complemented mutant, a P. aeruginosa PAO1 psrA::Tn5 mutant displayed intrinsic super-susceptibility to polymyxin B, a last resort antimicrobial used against multi-drug resistant infections, and indolicidin, a bovine neutrophil antimicrobial peptide; this super-susceptibility phenotype correlated with increased outer membrane permeability. The psrA mutant was also defective in simple biofilm formation, rapid attachment, and normal swarming motility, phenotypes that could be complemented by the cloned psrA gene. The role of PsrA in global gene regulation was studied by comparing the psrA mutant to wild-type by microarray analysis, demonstrating that 178 genes were up or down-regulated by greater than 2-fold (P ≤0.05). Dysregulated genes included those encoding known PsrA targets, the type III secretion apparatus and effectors, adhesion and motility genes and a variety of metabolic, energy metabolism and outer membrane permeability genes. This indicates that PsrA is a central regulator of antimicrobial peptide resistance and virulence. P. aeruginosa containing a mutation in the PhoQ sensor kinase-encoding gene was highly attenuated for persistence in a rat chronic lung infection model. In addition, the polymyxin B hyper-resistant phoQ mutant displayed reduced type IV pili-dependent twitching motility and was less cytotoxic towards human bronchial epithelial cells, indicating that the virulence defect observed could be due at least in part to these phenotypes. Using microarrays it was further demonstrated that PhoQ regulates a large number of genes that are PhoP-independent and that the phoQ mutation leads to up-regulation of PhoP- and PmrA regulated genes as well as other genes consistent with its virulence phenotypes.

Bacterial isolates from animals, foods and clinical samples with resistances to one or more antibiotics are being found frequently each year. Selective pressure exerted by antibiotic growth promoters in food animals has been considered a main cause for the development of antibiotic resistance and antibiotic use has been strongly criticized as a serious public health threat. The gastrointestinal tract of animals not only serves as a reservoir of zoonotic agents but also as a spot for exchange of genetic information between pathogenic and commensal bacteria. Humans get infections from resistant bacteria either through the food chain, contaminated water or by direct contact with animals. In this situation much of the concern has been directed against the use of antibiotic growth promoters in animals. The removal of synthetic antibiotics from animal diets created other problems such as a decline in animal welfare and an increase in the use of therapeutic antibiotics. So there is a need for new alternatives to antimicrobial drugs to overcome resistance development and related problems. Plants and plant-derived compounds have long been considered to posess antimicrobial activity since they were frequently used in ancient medicine as natural remedies to treat human infections. Identifying new sources of natural antimicrobials and inhibitors of resistance development will yield novel therapeutic drugs and extend the useful life of existing antibiotics. In the present work, individual and combined effects of five essential oils (eugenol, thymol, carvacrol, cinnamaldehyde, allyl isothiocyanate (AIT)) and a formaldehyde-based feed additive, Termin 8, with antibiotics against 4 antibiotic resistant bacteria with known determinants for resistance were tested using broth microdilution and the checker board assay. The bacteria showed considerable susceptibility towards these antimicrobials and a significant reduction in the minimum inhibitory concentrations (MICs) of antibiotics was noted when paired combinations of antibiotic and antimicrobial were used. The synergistic interaction was further confirmed by the extent of decrease in logarithmic count or viable population (Log DP). Although most of the combinations were synergistic by fractional inhibitory concentration (FIC) values, fewer combinations showed synergistic interaction when Log DP was considered. Gram-positive bacteria were more sensitive to the antimicrobials than Gram-negative bacteria. In combination studies, carvacrol was more effective and showed synergistic interaction with at least three antibiotics. When used alone, AIT was more effective and the concentration needed to exhibit antimicrobial action was much lower when compared to other compounds. An in vitro study was conducted to assess the antibacterial effects of Termin 8 and thymol in chicken caecal digesta and poultry feed samples by using a thin agar layer (TAL) method. Concentrations greater than the MIC of both the compounds was required to exert antimicrobial activity in the feed and digesta samples. The natural antimicrobials and Termin 8 had significant inhibitory effects on the drug resistant bacteria and synergistically enhanced the efficacy of antibiotics when used in combination. Further studies are needed to test their effectiveness in animal models.

Introduction: Streptococcus pneumoniae is the main bacterial cause of pneumonia, bacteremia and meningitis. Incidence rates have decreased since the initiation of pneumococcal vaccines, but antibiotic resistant strains continue to emerge and place a heavy burden on healthcare systems to treat such serious resistant infections. This study looks at risk factors that increase a patients probability of contracting a drug resistant strain of S. pneumo. Methods: Confirmed cases of S. pneumo were acquired through the Active Bacterial Core Surveillance program from 2009-2012 for the state of Georgia. Cumulative incidence rates, odds ratios and Pearson’s chi square were calculated to test for trends. Multi-logistic regression model was designed to control for covariates. Antibiotic Susceptibility results were analyzed by resistant profiles through WHONET. Results: Cumulative incidence rates have decreased significantly, however antibiotic resistant and multidrug resistant strains have increased. Incidence rates for children less than five and adults over 65 have decreased, however, the burden of disease remains in young to middle adults. Antibiotic resistant strains have shifted from penicillin to erythromycin and cefotaxime. Discussion: Interventions need to be targeted towards young to middle aged adults. Antibiotic stewardship programs should seek uniform guidelines to battle the increasing emergence of multidrug resistant strains.

Environmental pathogens, such as Escherichia coli and Streptococcus uberis, are currently the major cause of mastitis within dairy herds. This leads to severe financial losses, lower production rates and deterioration of the general health of the herd. E. coli mastitis is becoming a major threat to high milk-producing dairy herds. This is because of its increasing resistance to antibiotics, rendering antibiotic treatment regimes against E. coli infections mostly ineffective. The aim of this study was to develop a method to select mastitis causing E. coli isolates for the formulation of effective herd specific vaccines. Two methods, namely a genotyping method (Random Amplification of Polymorphic DNA; RAPD) and an antibiogram based method, were used. A dairy farm milking approximately 1000 Holstein cows in the Darling area, Western Cape Province, was selected for this study. The study was conducted over a period of 48 months and mastitis samples were analysed for mastitis pathogens. Antibiogram testing (disk diffusion method) and an in-house developed RAPD analysis method were used to analyse the E. coli isolates. A total of 921 milk samples were analysed from which 181 E. coli isolates were recovered. The number of all other common mastitis pathogens combined was 99 isolates (Streptococcus uberis 18, Streptococcus dysgalactiae 46, Streptococcus agalactiae 1, Staphylococcus epidermidis 21, Arcanobacterium pyogenes 13). All E. coli isolates, except for one, were resistant to at least three antibiotics. Antibiotic variance profiles were also highly erratic. The RAPD analysis revealed high levels of polymorphisms and clear epidemiological trends were observed over time. No similarities in the variance profiles between the antibiotic variance data and phylogenetic data were observed. Formalin inactivated autogenous vaccines were produced containing E. coli isolated from the herd. The vaccines were formulated using the RAPD or antibiogram data of the E. coli isolates. A total of 5 vaccines were formulated using RAPD data (Rvaccines) and one vaccine was formulated using antibiotic variance data (A-vaccine). The RAPD formulated vaccines were more effective than the antibiotic variance formulated vaccine. After each R-vaccination, the number of E. coli mastitis cases declined within the herd. The A-vaccinations seemed to have had no effect, which lead to a rise in E. coli mastitis cases. RAPD analysis on new emerging isolates was able to detect genetic variation from vaccine strains, which in turn facilitated the formulation of new updated vaccines with higher effectiveness than the previous vaccine. Mastitis data prior to and after the vaccination period revealed significant higher incidences of mastitis in the herd than during the vaccination period. This study demonstrated that sufficient sampling practices coupled with a reliable genotyping method, resulted in the formulation of updatable vaccines which were highly effective in controlling E. coli mastitis within the herd. / Thesis (M Environmental Sciences)--North-West University, Potchefstroom Campus, 2012

Bacterial isolates from animals, foods and clinical samples with resistances to one or more antibiotics are being found frequently each year. Selective pressure exerted by antibiotic growth promoters in food animals has been considered a main cause for the development of antibiotic resistance and antibiotic use has been strongly criticized as a serious public health threat. The gastrointestinal tract of animals not only serves as a reservoir of zoonotic agents but also as a spot for exchange of genetic information between pathogenic and commensal bacteria. Humans get infections from resistant bacteria either through the food chain, contaminated water or by direct contact with animals. In this situation much of the concern has been directed against the use of antibiotic growth promoters in animals. The removal of synthetic antibiotics from animal diets created other problems such as a decline in animal welfare and an increase in the use of therapeutic antibiotics. So there is a need for new alternatives to antimicrobial drugs to overcome resistance development and related problems. Plants and plant-derived compounds have long been considered to posess antimicrobial activity since they were frequently used in ancient medicine as natural remedies to treat human infections. Identifying new sources of natural antimicrobials and inhibitors of resistance development will yield novel therapeutic drugs and extend the useful life of existing antibiotics. In the present work, individual and combined effects of five essential oils (eugenol, thymol, carvacrol, cinnamaldehyde, allyl isothiocyanate (AIT)) and a formaldehyde-based feed additive, Termin 8, with antibiotics against 4 antibiotic resistant bacteria with known determinants for resistance were tested using broth microdilution and the checker board assay. The bacteria showed considerable susceptibility towards these antimicrobials and a significant reduction in the minimum inhibitory concentrations (MICs) of antibiotics was noted when paired combinations of antibiotic and antimicrobial were used. The synergistic interaction was further confirmed by the extent of decrease in logarithmic count or viable population (Log DP). Although most of the combinations were synergistic by fractional inhibitory concentration (FIC) values, fewer combinations showed synergistic interaction when Log DP was considered. Gram-positive bacteria were more sensitive to the antimicrobials than Gram-negative bacteria. In combination studies, carvacrol was more effective and showed synergistic interaction with at least three antibiotics. When used alone, AIT was more effective and the concentration needed to exhibit antimicrobial action was much lower when compared to other compounds. An in vitro study was conducted to assess the antibacterial effects of Termin 8 and thymol in chicken caecal digesta and poultry feed samples by using a thin agar layer (TAL) method. Concentrations greater than the MIC of both the compounds was required to exert antimicrobial activity in the feed and digesta samples. The natural antimicrobials and Termin 8 had significant inhibitory effects on the drug resistant bacteria and synergistically enhanced the efficacy of antibiotics when used in combination. Further studies are needed to test their effectiveness in animal models.

Coincident with human activity in recent decades, human-associated microorganisms have arrived to the Antarctic region, possibly linked to increasing presence of scientific bases and ship-borne tourists. In the Arctic, humans have been present for a very long time, and the few parts of the Arctic without human activities is decreasing with time. The studies in this thesis investigate the occurrence of different pathogens in Antarctic and Arctic wildlife, especially in birds. The first study shows the existence of Enteropatogenic Escherichia coli (EPEC) in Antarctic fur seals. The EPEC isolates were so called atypical EPECs, carrying the eae gene but lacking the bfp gene. This is the first record of a diarrheogenic E. coli in wild animals in the Antarctic. The second study displays that spreading of antibiotic resistance mechanisms appears to be much more efficient than previously was known. Enterococcus faecium isolated from Alaskan birds showed high resistance to vancomycin and teicoplanin, but also to ampicillin and ciprofloxacin. These isolates also carried vanA genes and the virulent esp gene, which places the isolates in the clinical clone CC17 and indicates the isolates had a human origin. Bacteria from birds that reside in the Bering Strait region in the third study, demonstrates that only six of 145 E. coli from 532 birds had reduced antibiotic susceptibility. Despite this, selective screen on E. coli showed only four ESBL-producing isolates. The four E. coli isolates carried CTX-M genes. One isolate belonged to the E. coli O25b - ST131 genotype, which is a successful clone with a global spread. In the fourth study, 123 seawater samples and 400 fresh penguin feces were analyzed. From these, 71 E. coli strains were isolated and only one E. coli from penguins was resistant to one antibiotic (cloramfenicol), whereas in E. coli from seawater, resistance against ampicillin, tetracycline, streptomycin and trim-sulfa were detected. E. coli carrying ESBL type CTX -M genes were also detected and Multilocus Sequencing Typing (MLST) showed six different sequence types (ST) previously reported in humans: ST131, ST227, ST401, ST410, ST685 and ST937. In the short time interval between the second study (2005) and the third study (2010) in relation to the fifth study (2012) we found a dramatic increase in antibiotic-resistant genes in the Arctic region. Enterococci, E. coli, and Kl. pneumoniae carried antibiotic resistance genes to an extent and variety not previously reported. E. coli from Arctic birds showed resistant to 1, 2, 3, 4, and 5 different antibiotics. Resistant gene type vanA was confirmed in enterococci and ESBL genes type TEM, SHV and CTX-M in E. coli and Kl. pneumoniae was detected. Multilocus Sequencing typing (MLST), indicating that both E. coli and Kl. pneumoniae carrying ESBL markers that connects them to the humans. In summary, the combined studies strengthen that bacteria that cause infections in humans could spread to relatively pristine environments. We concluded that human and associated antibiotic-resistant bacteria has reached a global level, then we showed that ESBL- carrying bacteria circulating nowadays also in the last ESBL-free continent, Antarctica.

Antibiotics are an important method for protecting human health. Unfortunately, the development of antibiotic resistance has decreased the effectiveness of antibiotics in treating disease and preventing deaths associated with bacterial infection. The objective of this dissertation research was to gain a better understanding of anthropogenic influences on occurrence of tetracycline resistance and use of traditional disinfection methods for the reduction of tetracycline resistant bacteria and genes. Culture based and molecular methods were used to evaluate the occurrence of tetracycline resistance in a rapidly urbanizing watershed, identify the dominant resistant organisms and resistance genes in the watershed, and evaluate the use of UV and chlorine to reduce the concentration of resistant bacteria and resistance genes. Results from this research showed that tetracycline resistance was prevalent and is maintained in this study area. Several bacterial species (Aeromonas, Acinetobacter, Chryseobacterium, E. coli, Pseudomonas, and Serratia) made up the resistant population. The results also indicated that tet(W) was the major resistance gene in this watershed and that a majority of the resistant bacteria were capable of transferring their resistance. Landuse did not cause a difference in occurrence of resistant bacteria or resistance genes which suggests that a rapidly urbanizing watershed could experience resistance. It was also identified that environmental media (sediment and water) influence the occurrence and prevalence of resistant bacteria and resistance genes. The results indicate that streambed sediment may act as a reservoir for resistance and resistance might be transported in the water. Finally, the results showed that neither UV nor chlorine disinfection were effective in reducing tet(W) concentrations though the results varied greatly among species. Results from this research indicate that preventing the occurrence and distribution of resistance gene in the environment is difficult, and resistance will most likely be maintained. Therefore, in order to prevent the spread of antibiotic resistance, it will be important to prevent antibiotic resistance from becoming established in the environment. This can be done by educating the public about the importance of misusing and mismanaging antibiotics. Additionally, classifying antibiotics for either human or veterinary use may help slow the development of resistance. This should prevent clinically important antibiotics from being used in sub-therapeutic doses, which could decrease the selective pressure in the environment. Also clinically relevant bacteria can be prevented from interacting with resistant bacteria in the environment by disinfecting human waste.

Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium that is also a major opportunistic human pathogen in nosocomial infections and cystic fibrosis chronic lung infections. These P. aeruginosa infections can be extremely difficult to treat due to the high intrinsic antibiotic resistance and broad repertoire of virulence factors, both of which are highly regulated. It was demonstrated here that the psrA gene, encoding a transcriptional regulator, was up-regulated in response to sub-inhibitory concentrations of antimicrobial peptides. Compared to wild-type and the complemented mutant, a P. aeruginosa PAO1 psrA::Tn5 mutant displayed intrinsic super-susceptibility to polymyxin B, a last resort antimicrobial used against multi-drug resistant infections, and indolicidin, a bovine neutrophil antimicrobial peptide; this super-susceptibility phenotype correlated with increased outer membrane permeability. The psrA mutant was also defective in simple biofilm formation, rapid attachment, and normal swarming motility, phenotypes that could be complemented by the cloned psrA gene. The role of PsrA in global gene regulation was studied by comparing the psrA mutant to wild-type by microarray analysis, demonstrating that 178 genes were up or down-regulated by greater than 2-fold (P ≤0.05). Dysregulated genes included those encoding known PsrA targets, the type III secretion apparatus and effectors, adhesion and motility genes and a variety of metabolic, energy metabolism and outer membrane permeability genes. This indicates that PsrA is a central regulator of antimicrobial peptide resistance and virulence. P. aeruginosa containing a mutation in the PhoQ sensor kinase-encoding gene was highly attenuated for persistence in a rat chronic lung infection model. In addition, the polymyxin B hyper-resistant phoQ mutant displayed reduced type IV pili-dependent twitching motility and was less cytotoxic towards human bronchial epithelial cells, indicating that the virulence defect observed could be due at least in part to these phenotypes. Using microarrays it was further demonstrated that PhoQ regulates a large number of genes that are PhoP-independent and that the phoQ mutation leads to up-regulation of PhoP- and PmrA regulated genes as well as other genes consistent with its virulence phenotypes.

Foodborne diseases caused by non-typhoidal Salmonella represent an important public health problem worldwide (Zhao et al., 2003). The transmission of Salmonella between animals and humans has been well established in epidemiological studies. In the case of complicated illness caused by Salmonella where antibiotics need to be administered, treatment can be compromised if the infecting organism is resistant to the prescribed antimicrobial agent. This study and earlier studies have shown that many Salmonella carry temperate bacteriophages as lysogens. Many of these bacteriophages are capable of mediating generalised transduction (Schicklmaier and Schmieger, 1995; Schicklmaier et al., 1998; Mmolawa et al., 2002). Schmieger and Schicklmaier (1999) demonstrated that bacteriophages ES18 and PDT17 are capable of transduction of antibiotic resistance genes from DT104. Phage-mediated transduction of antibiotic resistance genes has been largely neglected in the study of genetic transfer of antibiotic resistance in bacteria. This study investigates whether bacteriophages exist in antibiotic resistant Salmonella isolates. Such temperate phages in antibiotic resistant isolates could play a significant role in the transfer of resistance to other species of enteric bacteria, such as E. coli. Molecular epidemiology studies of antibiotic resistance genes were undertaken with Salmonella isolates from chicken, pig and human sources that were subjected to PCR for ampicillin (blaTEM-1), tetracycline (tetA, tetB) and streptomycin (aadA1, aadA2, strA, strB) resistance genes as well as Class 1 integrons. The blaTEM-1 gene was widely detected in isolates from pigs and chickens but rarely detected in human isolates. The tetB gene was more commonly found in pig isolates, while the tetA gene was associated with tetracycline resistance in chicken isolates. The strA and strB genes were responsible for streptomycin resistance in the S. Typhimurium isolates while the aadA1 gene was commonly detected in S. Kiambu and S. Virchow isolates. The aadA2 gene was associated with streptomycin resistance in the S. Ohio isolates from pigs. Class 1 integrons were widely distributed across serovars tested from chicken, pig and human sources. Temperate bacteriophages were induced using mitomycin C from antibiotic resistant Salmonella. These phages were able to infect antibiotic-sensitive Salmonella isolates from humans. Bacteriophages induced from one S. Sofia isolate also plaqued on Shigella flexneri. Bacteriophages induced from one S.Kiambu isolate and S. Typhimurium DB21 with an inserted Tn10 transposon (S. Typhimurium DB21 Tn10) were capable of transducing ampicillin and tetracycline resistance, respectively into S. Enteritidis PT1 isolates by in vitro methods. The molecular basis for resistance was established in subsequent PCR for antibiotic resistance genes in donor and recipient strains. This finding, in particular in the wild-type S. Kiambu strain, indicates that Salmonella from a natural source are able to infect and transfer antibiotic resistance by generalised transduction in controlled laboratory experiments. This current study has investigated the transfer of tetracycline and ampicillin resistance from a wild-type Salmonella strain and a laboratory strain of Salmonella to wild-type Salmonella bacteria as it occurs within the normal flora of the chicken gastrointestinal tract. It was demonstrated that the genetic transfer of tetracycline and ampicillin resistance genes as well as Class 1 integrons can occur within the chicken gastrointestinal tract. Transfer of tetracycline and ampicillin resistance could be demonstrated both in vitro and by using bacteriophage lysates obtained from in vivo studies in transduction experiments. It was clearly shown that bacteriophage isolated from chicken faeces and caeca could infect antibiotic sensitive recipient Salmonella. Interaction between phages of the administered Salmonella strains may be occuring with phages of bacteria in the normal flora allowing previously inactive phage in the indigenous flora to plaque on indicator strains. Additionally, strong evidence was presented to suggest that the environment of the chicken gastrointestinal tract could mediate phage type conversion in recipient and transductant strains. Phage typing of these recipient and transductant strains demonstrated a trend for recipient strains to become more resistant to phages in the S. Enteritidis typing panel. This led to weakened phage reactions such RDNC (reaction does not conform) and untypable. The acquisition of phages may be a way for Salmonella to enhance competitive fitness and generate new strains in order to evolve and diversify. Or the acquisition of plasmids either by transduction or conjugation may also mediate phage type conversion. MLVA typing was performed on selected recipient, donor and transductant strains. The changes to tandem repeat loci in Salmonella isolates that have passed through a chicken gastrointestinal tract have not been described before. The changes to fragment length suggest that the bacterial chromosome is undergoing rearrangement; this may be attributed to a number of factors including acquisition of phages, prophage integration into tRNA sites, slipped-strand mispairing or the adaption to changing environment, in this case the chicken gastrointestinal tract. This study has provided molecular epidemiological data on the antibiotic resistance genes and integrons present in Australian Salmonella isolates from human and animal sources. Information on the role of bacteriophages in the transfer of antibiotic resistance genes in vitro and in a chicken gastrointestinal tract has also been established. / Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2010

With the spread of antibiotic resistance, alternative treatment methods for bacterial pathogens are needed. Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that is a common cause of healthcare associated infections and is listed as a critical priority for research and development of treatments by the Centers for Disease Control and Prevention. P. aeruginosa poses an increased risk to patients within the surgical or intensive care unit, patients with indwelling catheters, cystic fibrosis, and burn wound victims. With a paucity of antibiotics in the pipeline for Gram negative bacteria, phage therapy has reemerged as a potential treatment option. Bacteriophages were first discovered in 1917 by Felix d’Herelle, but by the end of World War II, they were all but forgotten in favor of antibiotics. Eastern European countries and the former Soviet Union continued to develop phage therapy since its discovery, but studies were not on par with today’s standards. Recently the idea of phage therapy has reemerged in the Western world due to antibiotic resistance. In vitro and in vivo studies have shown that bacteriophages are easily isolated from the environment, with P. aeruginosa specific phages commonly found in hospital waste water and in sewage. Phage therapy has shown to be very effective at treating planktonic and biofilm forms of antibiotic resistant P. aeruginosa in vitro and in vivo. In humans, clinical trials are limited but phage therapy has successfully treated chronic otitis infections caused by P. aeruginosa and other studies have demonstrated the safety of phage therapy, reporting mild, if any, adverse effects. Bacteriophages may also synergize with several antibiotics, suggesting it may be beneficial to use them in conjunction to treat difficult or chronic infections. Additionally, P. aeruginosa bacteriophages may be beneficial in prophylactic treatment as well. When phages were combined with chlorine, a significant decrease in P. aeruginosa counts in chronic biofilms was observed, while also reducing its ability to form new biofilms. Similar results were noted when phages were applied to the lumen of catheters. These early results are promising for the future, but there are many steps that must be taken before starting new clinical trials and the widespread use of phage therapy begins.