Bacteriology Commons^™

Turbidimetric Bioassays: A Solution To Antimicrobial Activity Detection In Asymptomatic Bacteriuria Isolates Against Uropathogenic Escherichia Coli, Ciara Kenneally, Craig P. Murphy, Roy D. Sleator, Eamonn P. Culligan

Department of Biological Sciences Publications

Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and …

Bactericidal Effects Of Chlorine And Bacteriophages On Mycobacteria In Conventionally Treated Water., Max Kevane-Campbell

ORBioM (Open Research BioSciences Meeting)

Introduction

Mycobacteria are members of the order Actinomycetales and the only genus in the family Mycobacteriaceae. The distinguishing characteristics that are found in mycobacteria include acid-fastness and the presence of mycolic acids. Mycobacteria can be commonly classified as non-spore-forming, aerobic, slender rod-shaped, and are slow-growers. Natural reservoirs that mycobacteria can be found in are aquatic and terrestrial environments. Recent studies have shown that mycobacteria that can cause skin lesions, immune and/or pulmonary dysfunctions and chronic diseases, i.e., Mycobacterium avium subsp. Paratuberculosis, M. kansasii, and M. xenopi, can be isolated from common household tap water. Tap water can originate from …

Mycobacteriophage: A Demonstration Of The Reduction Of M. Smegmatis In Various Matrices., Laura O'Connell

ORBioM (Open Research BioSciences Meeting)

Background

Mycobacterial disease is a major cause of fatality worldwide, with approximately 1.5 million deaths for every 10 million infections. These infections are difficult to treat due to the intrinsic resistance of its mycolic acid rich cell wall to many antibiotics. There is potential for mycobacteriophage (MP) to be used therapeutically for multidrug- and extensively-drug resistant infections. Mycobacterium smegmatis mc² 155 is a useful substitute for slow-growing pathogenic mycobacteria, as it propagates quickly under lab conditions. This feature of M. smegmatis increases the pace of analysis, by ensuring the quick isolation and characterisation of MP and acting as a …

Effect Of Sub-Inhibitory Concentrations Of Nitrofurantoin, Ciprofloxacin And Trimethoprim On In-Vitro Biofilm Formation In Uropathogenic Escherichia Coli, Shane Whelan

ORBioM (Open Research BioSciences Meeting)

The purpose of the current study was to determine the effect of sublethal concentrations of nitrofurantoin, ciprofloxacin and trimethoprim on biofilm formation in 57 uropathogenic Escherichia coli strains (UPEC).

The MIC of nitrofurantoin, ciprofloxacin and trimethoprim was determined for 57 UPEC isolates. Biofilm formation for each isolate with and without sub-lethal concentrations of each antibiotic was then quantified, and the statistical significance of changes in biofilm formation was ascertained by way of a Dunnett's test.

The effects of sub-MIC antibiotics on biofilm formation of UPEC were variable. A total of 22.8% of strains were induced to form biofilm by nitrofurantoin, …

Investigation Of The Urobiome For The Production Of Novel Antimicrobials Against Uropathogenic E. Coli (Upec), Jennifer Jones

ORBioM (Open Research BioSciences Meeting)

BACKGROUND: Urinary tract infections (UTIs) are one of the most common bacterial infections globally with antibiotic treatment becoming increasingly less effective. The urobiome remains a relatively understudied niche as a source of potentially novel antimicrobials (e.g., bacteriocins). Improvements to bacterial culturing and sequencing techniques have highlighted the potentially rich source of alternative treatments and control strategies to target uropathogenic E. coli (UPEC).

MATERIALS AND METHODS: (a) BAGEL 4 was used for bioinformatic screening of the genomes of urobiome isolates to identify bacteriocin gene clusters (BGC).

(b) Expanded quantitative urine culture (EQUC) was used to culture mid-stream urine samples to isolate …

An Investigation Into The Prevalence Of Vancomycin-Resistant Enterococci Within An Irish Hospital, Dylan Casey

International Undergraduate Journal of Health Sciences

Vancomycin-resistant enterococci (VRE) are well-recognised nosocomial pathogens that pose a significant threat to public health. Associated with poorer clinical outcomes than their vancomycin-sensitive counterparts, the prevalence of VRE in Ireland has increased in recent times, with the European Antimicrobial Resistance Surveillance Network reporting that out of 29 countries, Ireland demonstrated the highest rates of vancomycin resistance among invasive Enterococcus faecium isolates between 2011 and 2014 (2011; 34.9%, 2012; 44.0%, 2013; 42.7%, 2014; 45.1%). Herein, we investigate VRE prevalence in the Mercy University Hospital (MUH) – an acute care hospital in southern Ireland. A total of 21 first-time VRE infections were …

A Rapid Viability And Drug‑Susceptibility Assay Utilizing Mycobacteriophage As An Indicator Of Drug Susceptibilities Of Anti‑Tb Drugs Against Mycobacterium Smegmatis Mc2 155, Gillian Catherine Crowley, Jim O'Mahony, Aidan Coffey, Riona G. Sayers, Paul D. Cotter

Department of Biological Sciences Publications

Background: A rapid in-house TM4 mycobacteriophage-based assay, to identify multidrug resistance against various anti-tuberculosis drugs, using the fast-growing Mycobacterium smegmatis mc² 155 in a microtiter plate format was evaluated, based on phage viability assays. Methods: A variety of parameters were optimized before the study including the minimum incubation time for the drugs, phage and M. smegmatis mc² 155 to be in contact. An increase in phage numbers over 2 h was indicative that M. smegmatis mc² 155 is resistant to the drugs under investigation, however when phage numbers remained static, M. smegmatis mc² 155 found to …

Inhibition Of Listeria Monocytogenes By Human Gut Bacteria, Patrycja Sylvia Olesky

Masters

Listeria monocytogenes is a foodborne pathogen, which continues to be problematic to the food industry due to its ability survive within food products and persist within food processing environments. The growing trend towards natural food preservatives and antimicrobial agents increases the need for the development of novel, natural anti-Listeria agents. Evidence presented in the literature suggests that the human gut microbiota is a reservoir of novel antimicrobial agents. It was therefore hypothesized that novel anti-Listeria agents are produced by human gut-derived bacteria. The objective of this study was to isolate and characterize gut bacteria with anti-Listeria monocytogenes activity. A total …

A Diagnostic And Control Programme For Johne’S Disease On Irish Dairy Farms, Aideen Kennedy

Theses

Johne’s disease (JD) is an enteritis of ruminants with potential zoonotic implications. JD diagnosis and control present difficulties given JDs prolonged subclinical nature. In order to improve JD control in Ireland, PhD aims included conducting a national survey documenting high-risk husbandry practices employed on Irish farms, thereby targeting areas for improved management. Furthermore as JD has been associated with on-farm economic losses internationally, this research programme aimed to analyse production losses associated with testing JD ELISA positive on Irish dairy farms. A longitudinal study was also conducted to assess if successful JD control can be achieved using gold-standard protocols. Due …

Mycobacterium Species Identification In An Acute Hospital: Towards Rapid Identification, And Improved Epidemiology, Using Novel Mass Spectrometry Analysis, James Anthony O'Connor

Theses

Mycobacteria are a heterogeneous group of bacteria that cause a wide spectrum of disease, including Tuberculosis (TB), the single biggest killer worldwide. The genus also incorporates over 170 nontuberculosis (NTM) species, many of which are opportunistic pathogens. The aim of this project was to ascertain the burden of mycobacterial disease in the region and to determine the efficacy of Matrix-Assisted Laser Desorption/Ionisation time-of-flight (MALDI-tof) mass spectrometry (MS) for novel uses as a rapid identification method for clinical mycobacteria and as a typing tool for Mycobacterium tuberculosis complex isolates. A five-year retrospective epidemiological study of the region was conducted, the first …

Metabolic Characteristics Of Macrophage Activation With Phenotype Microarrays, Tanya Kathryn D'Souza

Theses

Inflammation is a natural protective response and is characterised by the activation of numerous immune cells, including macrophages which can release a variety of inflammatory mediators. Macrophages play a flexible role in the initiation and effector phases of the immune response and change their behaviour to respond to environmental stimuli. The main objectives in this study were to create and characterise different macrophage behaviours and employ a novel metabolic characterisation platform the Phenotype Microarray^TM to attribute additional characteristics to the currently well recognised phenotypes. Five activated macrophage states were demonstrated and characterised. Unactivated macrophages (MO) demonstrated undetectable levels of …

Comparative Genomic Analysis Of Two Serotype 1/2b Listeria Monocytogenes Isolates From Analogous Environmental Niches Demonstrates The Influence Of Hypervariable Hotspots In Defining Pathogenesis, Aidan Casey, Kieran Jordan, Aidan Coffey, Edward M. Fox, Olivia Mcauliffe

Department of Biological Sciences Publications

The vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but …

Analysis Of Johne's Disease Elisa Status And Associated Performance Parameters In Irish Dairy Cows, A. E. Kennedy, N. Byrne, A. B. Garcia, Jim O'Mahony, R. G. Sayers

Department of Biological Sciences Publications

Background

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.

Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Functional Screening Of The Cronobacter Sakazakii Baa-894 Genome Reveals A Role For Prop (Esa_02131) In Carnitine Uptake, Audrey Feeney, Roy D. Sleator

Department of Biological Sciences Publications

Cronobacter sakazakii is a neonatal pathogen responsible for up to 80% of fatalities in infected infants. Low birth weight infants and neonates infected with C. sakazakii suffer necrotizing enterocolitis, bacteraemia and meningitis. The mode of transmission most often associated with infection is powdered infant formula (PIF) which, with an aw of ∼0.2, is too low to allow most microorganisms to persist. Survival of C. sakazakii in environments subject to extreme hyperosmotic stress has previously been attributed to the uptake of compatible solutes including proline and betaine. Herein, we report the construction and screening of a C. sakazakii genome bank and …

Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator

Department of Biological Sciences Publications

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …

Transcriptome Analysis Of Listeria Monocytogenes Exposed To Biocide Stress Reveals A Multi-System Response Involving Cell Wall Synthesis, Sugar Uptake, And Motility, Aidan Casey, Edward M. Fox, Stephan Schmitz-Esser, Aidan Coffey, Olivia Mcauliffe, Kieran Jordan

Department of Biological Sciences Publications

Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing …

Phages Of Non-Diary Lactococci: Isolation And Characterization Of Phi L47, A Phage Infecting The Grass Isolate Lactococcus Lactis Ssp Cremoris Dpc6860, Daniel Cavanagh, Caitríona M. Guinane, Horst Neve, Aidan Coffey, R. Paul Ross, Gerald F. Fitzgerald, Olivia Mcauliffe

Department of Biological Sciences Publications

Lactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron …

Antifungal Activity Of Lactobacillus Against Microsporum Canis, Microsporum Gypseum And Epidermophyton Floccosum, Jiahui Guo, Brid Brosnan, Ambrose Furey, Elke K. Arendt, Padraigin Murphy

Department of Biological Sciences Publications

A total of 220 lactic acid bacteria isolates were screened for antifungal activity using Aspergillus fumigatus and Aspergillus niger as the target strains. Four Lactobacillus strains exhibited strong inhibitory activity on agar surfaces. All four were also identified as having strong inhibitory activity against the human pathogenic fungi Microsporum canis, Microsporum gypseum and Epidermophyton floccosum. One of the four lactobacilli, namely Lb. reuteri ee1p exhibited the most inhibition against dermatophytes. Cell-free culture supernatants of Lb. reuteri ee1p and of the non-antifungal Lb. reuteri M13 were freeze-dried and used to access and compare antifungal activity in agar plate assays …

Emerging Dynamics Of Human Campylobacteriosis In Southern Ireland, Susan Bullman, Daniel Corcoran, James O'Leary, Derry O'Hare, Brigid Lucey, Roy D. Sleator

Department of Biological Sciences Publications

Infections with Campylobacter spp. pose a significant health burden worldwide. The significance of Campylobacter jejuni/Campylobacter coli infection is well appreciated but the contribution of non-C. jejuni/C. coli spp. to human gastroenteritis is largely unknown. In this study, we employed a two-tiered molecular study on 7194 patient faecal samples received by the Microbiology Department in Cork University Hospital during 2009. The first step, using EntericBio® (Serosep), a multiplex PCR system, detected Campylobacter to the genus level. The second step, utilizing Campylobacter species-specific PCR identified to the species level. A total of 340 samples were confirmed as Campylobacter genus positive, 329 of …

Characterisation Of Bacterial Extracellular Polysaccharides (Eps) And Other Complex Carbohydrates With Prebiotic Potential, Padraigin Murphy

Theses

Prebiotics are selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health’ It is not the prebiotic by itself but rather the changes induced in microflora composition that is responsible for its effects. Several sources of prebiotic were used in this study, namely extracellular polysaccharides (EPS) originating from Lactic Acid Bacteria (LAB), barley, oat. Laminaria digitata. Laminaria hyperborea and Saccharomyces cerevisiae. EPS-producing LAB were isolated from a wide variety of environmental and gastrointestinal niches. The strains were typed and classified according to their EPS-producing ability …

Campylobacter Ureolyticus: An Emerging Gastrointestinal Pathogen?, Susan Bullman, Daniel Corcoran, James O'Leary, Brigid Lucey, Deirdre Byrne, Roy D. Sleator

Department of Biological Sciences Publications

A total of 7194 faecal samples collected over a 1-year period from patients presenting with diarrhoea were screened for Campylobacter spp. using EntericBios, a multiplex-PCR system. Of 349 Campylobacter-positive samples, 23.8% were shown to be Campylobacter ureolyticus, using a combination of 16S rRNA gene analysis and highly specific primers targeting the HSP60 gene of this organism. This is, to the best of our knowledge, the first report of C. ureolyticus in the faeces of patients presenting with gastroenteritis and may suggest a role for this organism as an emerging enteric pathogen.

Probiotic Therapy - Recruiting Old Friends To Fight New Foes, Roy D. Sleator

Department of Biological Sciences Publications

Against a backdrop of increasing antibiotic resistance, and the emergence of new and evolving pathogens, clinicians are increasingly forced to consider alternative therapies - probiotics are one such alternative.

The Detection And Analysis Of Selected Pathogens In The Water Supply Of Dairy Cohort Herds., Niall Drummond

Theses

The issue of food safety is a growing concern to Irish agriculture and to the food industry. In the last twenty years, many novel pathogens, which can cause concern to the food industry, have been identified. Organisms such as Verocytotoxigenic Escherichia coli (VTEC) cause hemorrhagic colitis and Haemolytic Uremic Syndrome (HUS), which is the major cause of acute renal failure in children in many countries, and it’s presence in food is a cause of growing concern. Other pathogens causing concern are those implicated as causative agents of Acute Gastroenteritis (AGE) and these can be bacterial, viral and parasitic organisms.

Consumption …

Mupirocin Resistance In Staphylococci: An Investigation Of Current Status And Potential Alternative Therapies, Susan O'Shea

Theses

Mupirocin is a topical antibiotic used in hospital infection control practices to control transmission of staphylococci, in particular MRSA, which has become a major problem in Irish hospitals and has a significant impact on patient morbidity and mortality. Overreliance on mupirocin to eradicate MRSA carriage and to prevent infection has led to mupirocin resistance among staphylococcal species. Two distinct types of resistance have developed within strains: low'-level mupirocin resistance (LMR) and high-level mupirocin resistance (HMR).

The aim of this study was to assess the prevalence and types of mupirocin resistance in a large population of clinical staphylococcal isolates including Methicillin …

Clostridium Difficile: Comparative Evaluation Of Two Detection Techniques And Characterisation Of Clinical Isolates., Rebecca Dennehy

Theses

Clostridium difficile is one of the most common causes of antibiotic associated diarrhoea. The presence of C difficile in stool samples may be detected by a variety of means including enzyme immunoassays and culture. Enzyme immunoassays detect the presence of the toxins produced by the organism, toxin A and/or toxin B, but are known to lack sensitivity. The aim of this study was to compare the commercial ELISA assay currently used for the detection of C difficile toxins in Waterford Regional Hospital to culture for the organism to selective media. To compare the sensitivity of the two methods serial dilutions …

Evaluation Of Four Novel Broad-Host-Range Antimicrobial Agents., Jiahui Guo

Theses

The overall objective of this thesis was to evaluate the antimicrobial effects of four novel broad-host-range antimicrobial agents. The first was a milk-derived lipoprotein developed by Westgate Biologicals with the support of Enterprise Ireland. This lipoprotein which was designated LactiSAL, was evaluated against a wide range of bacterial species associated with humans. Essentially, the LactiSAL was incorporated at a variety of concentrations into agar media, which were appropriate for cultivation of the different genera. Agars were examined for colony formation, after which it was possible to quantify the minimal inhibitory concentration for each genus. Subsequently, LactiSAL was incorporated at levels …

Development Of A Genomic Approach For The Study Of A Coryneform Bacterial Collection., Carole Feurer

Theses

In the last few years, genomics has profoundly changed research in the biological sciences and in particular in microbiology. Recent studies have demonstrated that comparative genomics is a powerful approach contributing to a deeper understanding of the evolution of microorganisms. Bacterial collections are important resources of microorganisms, however, the potential that genomics has to offer remains to be realised as it is still virtually absent in any study involving strain collections. This feature thus framed the experimental objectives for this study, whose aim was to define the most comprehensive way to apply genomic based methods (high throughput sequencing and bioinformatics) …

Integronlike Structures In Campylobacter Spp. Of Human And Animal Origin, Brigid Lucey, D. Crowley, P. Moloney, B. Cryan, M. Daly, F. O'Halloran, E. J. Threlfall, S. Fanning

Department of Biological Sciences Publications

Resistance to antimicrobial agents used to treat severe Campylobacter spp. gastroenteritis is increasing worldwide. We assessed the antimicrobial resistance patterns of Campylobacter spp. isolates of human and animal origin. More than half (n = 32) were resistant to sulphonamide, a feature known to be associated with the presence of integrons. Analysis of these integrons will further our understanding of Campylobacter spp. epidemiology.