Methicillin Resistant Staphylococcus Aureus (MRSA) has been receiving significant attention, highlighting an increased risk of infectious transmission associated with athletic participation. As MRSA infections are becoming increasing virulent, athletic trainers are presented with immediate prevention challenges. While recommendations have been offered by the Centers for Disease Control and Prevention outlining basic prevention procedures, adherence to proposed guidelines and actual perception of the threat still pose the greatest hurdles to eradication of MRSA. Success in control and prevention of transmission of MRSA in athletic environments can be furthered by first investigating the perceptions of the problem in one of the first line of defense for athletes—their athletic trainers. Of particular importance are the perceptions of trainers' adherence to guidelines, perceptions of protocol standards, and relative threat of MRSA in the athletic environment. This study attempts to determine these perceptions and predict how athletic trainers will receive and adhere to standardized guidelines through written policy for MRSA prevention. Results reflect an increase in the awareness of MRSA as a threat to athletics since 2004. Overall positive perception of the development of guidelines and protocols specifically targeted to prevention of MRSA transmission in the athletic environment were also defined through this study. Athletic trainers surveyed expressed strong desire for additional training in procedures specific to reducing transmission of MRSA to prevent outbreaks. / Ph. D.

Seventy-four methicillin-resistant Staphylococcus aureus (MRSA) from two Malaysian hospitals were characterised by both phenotypic and genotypic techniques. These isolates were collected over an 18 year time period in the years, 1982, 1989, 1994 and 2000. All of the Malaysian MRSA isolates were found to be multiresistant and resistant to at least five different antimicrobial agents. Over 30% of them were non-typable by the International Basic Set of bacteriophages. The majority of the typable isolates were susceptible to the group III phages, especially phage 85. The majority of the isolates carried one to six plasmids. Only two isolates were plasmid free. The plasmid profiles of these isolates, other than the 1982 isolates, were very similar to each other. Contour-clamped homogeneous electric field (CHEF) gel electrophoresis was used to examine the genetic relatedness of the isolates. Twenty-six CHEF patterns were found among the isolates. These CHEF patterns were closely related to each other. The predominant CHEF pattern A was found in the 1982, 1989 and 1994 isolates. The CHEF patterns of the year 2000 isolates were different to CHEF pattern A, but still closely related. All of the isolates were found to carry the Allotype III SCCmec and have coagulase-gene type 24. Multilocus sequence typing was preformed on the isolates with CHEF pattern A collected in different years. These isolates were found to have either sequence type 239 (ST239), or its single locus variant. The predominant Malaysian clone belongs to the pandemic clone ST239-MRSA-III that is pandemic in Asian countries. (Enright, 2003, Ko et al., 2005). / A 1.5 kb cryptic plasmid found in Malaysian isolates was indistinguishable from a cryptic plasmid found in an Australian isolate. A 3.0 kb cryptic plasmid found in Malaysian isolates was undistinguishable from a 3.0 kb plasmid found in Singaporean isolates. Class II multiresistance plasmids of 28, 30.5 and 35 kb were commonly found together in many Malaysian MRSA isolates. Both the 28 and 30.5 kb plasmids encode resistance to the heavy-metals and nucleic acid-binding (NAB) compounds. The 35 kb plasmid carries heavy-metal and NAB resistance but also encodes β-lactamase. Structurally these three plasmids are almost identical and probably have the same origin. The differences observed between these plasmids is probably due to excision or partial deletion of the β-lactamase transposon of the original plasmid. The 28 kb plasmid is identical to the 28 kb plasmid of Singaporean and some Australian isolates. A 20 kb plasmid in Indonesian isolates was found to be closely related to these three plasmids. A conjugative plasmid, pWBG707, conferring trimethoprim-resistance was found in Malaysian isolates. It did not carry either of the two staphylococcal trimethoprim-resistance genes, dfrA and dfrD. (Lyon and Skurray, 1987, Dale et al., 1995b) It either encodes a novel resistance gene or the recently discovered dfrG gene. (Sekiguchi et al., 2005) pWBG707 was also found to mobilise a small 3.0 kb kanamycin-resistance plasmid during conjugation. / The mecR1 and mecI genes regulating the transcription of the methicillin-resistance gene, mecA, were also examined in the isolates. The Malaysian isolate, WBG7422, with the predominant CHEF pattern A has a nonsense mutation in its mecI gene that disables it. However, its mecR1 gene is intact. The eastern Australia MRSA (EA MRSA), WBG525, has a CHEF pattern that is closely related to the Malaysian predominant CHEF pattern A and its mecI gene has a mutation identical to the Malaysian isolate. Unlike the Malaysian isolate however, its mecR1 gene has a 166 bp deletion. Both WBG7422 and WBG525 express Class III heterogeneous methicillin resistance. However, WBG525 has more highly resistant cell in its population than WBG7422. The loss of aminoglycoside resistance, together with c. 114 kb of chromosomal DNA, was observed in some Malaysian isolates. The deleted segment was found to carry the aacA-aphD gene that encodes a bifunctional aminoglycoside-modifying enzyme conferring resistance to many of the aminoglycosides. The Malaysian isolates were compared with MRSA from different countries. These MRSA included 18 epidemic MRSA (EMRSA) from the United Kingdom, 15 Australian nosocomial MRSA, five classical MRSA, 22 community-acquired MRSA (CMRSA) from Australia and New Zealand and 46 nosocomial MRSAs from eight Asian-Pacific countries and South Africa. These Asian-Pacific countries were Australia, PR China, Hong Kong, Indonesia, Japan, Philippines, Singapore and Taiwan. / The CHEF patterns of most of the Asian-Pacific and South African isolates were closely related to the Malaysian isolates. Isolates from Singapore, Indonesia and Philippines were found to have an identical CHEF pattern to the Malaysian CHEF patterns A5. The Asian-Pacific and South African isolates, including the Malaysian isolates, were found to be closely related to EMRSA-1, -4 and -7. These EMRSA belong to the ST239-MRSA-III clone and are coagulase-gene type 24. The isolates from Japan were the only Asian-Pacific isolates not related to the other Asian-Pacific isolates and EMRSAs. EMRSA-1 and EA MRSA have the same 166 bp deletion in their mecR1 gene. Both of these strains have closely related CHEF patterns, the same sequence type, coagulase-gene type and SCCmec. These results indicate that these two strains belongs to the same clone and confirms the international spread of this clone in the early 1980s. However, the Malaysian isolates have CHEF patterns that are more closely related to EMRSA-4 than to EMRSA-1. Similar to the Malaysian isolates EMRSA-4 has an intact mecR1 gene. The CMRSA isolates were not related to any of the nosocomial MRSA. They also have very diverse genetic backgrounds but carry less diverse SCCmec allotypes. Most of the CMRSA carry either Allotype IV or V SCCmec These results show that the spread of Malaysian MRSA is due to a single clonal expansion. Infection control measures would have to have been more efficient if this clone was to have been contained. The Malaysian epidemic clone is the Asian pandemic clone, ST239-MRSA-III. The Malaysian isolates and EMRSA-4 probably share the same ancestor. / The presence of the same MRSA strain in Malaysian hospitals and in the hospitals of neighbouring countries indicates that the inter-hospital spread of an epidemic MRSA has occurred. This observation also suggests that the infection control measures in Malaysian hospitals have not been totally effective. The ineffectiveness of infection control has left Malaysian hospitals vulnerable to the future importation of new pandemic clones and/or highly virulent or resistant clones.

Orientador: Lidiane Nunes Barbosa / Resumo: Combinações entre antimicrobianos, a exemplo de nisina (bacteriocina) e fármacos antibacterianos tradicionais, podem amenizar o problema da resistência bacteriana, pois o possível efeito sinérgico se torna estratégico, possibilitando o uso de doses menores no tratamento de doenças infecciosas com redução nos custos e na toxicidade, além de ter potencial na prevenção do surgimento das linhagens resistentes. No entanto, os mecanismos envolvidos na ação antibacteriana são importantes para pesquisas de novos fármacos. O objetivo do estudo foi investigar como a nisina, alguns fármacos antibacterianos e respectivas combinações interferem no metabolismo de Staphylococcus aureus Meticilina Resistente (MRSA) e Pseudomonas aeruginosa, através de ensaios de estresse oxidativo bacteriano, análises morfológicas por microscopia eletrônica de transmissão (MET) e análise do perfil de proteínas expressas nas bactérias quando expostas aos antimicrobianos e suas combinações em concentrações subletais. Inicialmente foram realizados ensaios visando obter os valores de concentração inibitória mínima (CIM) e concentração subletal máxima (CSM) para nisina e fármacos como tetraciclina, ciprofloxacina, vancomicina, polimixina B, oxacilina e cefalotina para ambas bactérias. Na sequencia, foram realizados ensaios para verificação de sinergismo entre nisina e antibacterianos utilizando metodologia da curva de sobrevivência, sendo escolhidas para ensaios posteriores, as combinações com demostração de sine... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Combinations of antimicrobials, such as nisin (bacteriocin) and traditional antibacterial drugs, may assuage the problem of bacterial resistance because the possible synergistic effect becomes interesting, allowing the use of smaller doses in the treatment of infectious diseases and reduction in costs and toxicity , besides having potential in the prevention of the emergence of resistant strains. However, the mechanisms involved in antibacterial action are important for research on new drugs. The aim of this study was to investigate how nisin, antibacterial drugs and their combinations interfere in the metabolism of Methicillin Resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, verified in bacterial oxidative stress assays, morphological analyzes by transmission electron microscopy (TEM) and analysis of the protein profile expressed in bacteria when exposed to antimicrobials and combinations in sublethal concentrations. Initially, assays were performed to obtain the minimum inhibitory concentration (MIC) and maximum sublethal concentration (MSC) for nisin and drugs such as tetracycline, ciprofloxacin, vancomycin, polymyxin B, oxacillin and cephalothin for both bacteria. Subsequently, assays were performed to verify the synergism between nisin and antibacterials using time kill curve methodology and the combinations with demonstration of synergism (reduction in final bacterial count above 2 logs of CFU / mL in relation to initial inoculum) were chosen for later... (Complete abstract click electronic access below) / Doutor

Made available in DSpace on 2014-06-12T16:31:41Z (GMT). No. of bitstreams: 2 arquivo6185_1.pdf: 1986687 bytes, checksum: 8a72beab280fcdc564c73079c55a4aee (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2007 / O aumento da resistência bacteriana aos antibióticos é uma ameaça à saúde da população mundial, aumentando as recorrências por doenças infecciosas, devido ao surgimento de bactérias multirresistentes que dificulta e onera o tratamento antimicrobiano. Um exemplo importante destes germes, é o S. aureus MRSA que no Brasil, como em outras partes do mundo, são os microorganismos frequentemente isolados, tendo sua maior prevalência a nível hospitalar, sendo também uma importante causa de infecções na comunidade. A ocorrência de S. aureus MRSA multirresistentes susceptíveis só a vancomicina, constitui um grave problema a resolver, ainda mais, com o surgimento recente de cepas de S. aureus com susceptibilidade intermediária e resistentes a vancomicina. Deste fato, é de fundamental importância, a pesquisa de compostos alternativos, principalmente a partir de plantas medicinais que constitui uma fonte inesgotável de novas moléculas. No presente trabalho, foram escolhidas duas plantas para estudar o perfil fitoquímico e antimicrobiano: Caesalpinia pyramidalis Tull. (Catingueira), das leguminosas e Schinopsis brasiliensis Engl. (Baraúna ou braúna), das anacardiáceas, ambas as famílias com representantes de reconhecida atividade biológica, incluída a antimicrobiana. Neste sentido foi estudada a atividade dos extratos secos (por extração hexanólica, em acetato de etila ou metanol) da folha, casca do caule, casca da raiz, flor, vagem e semente da Braúna e Catingueira inicialmente frente a padrões ATCC de bactérias Gram negativas e Gram positivas, confirmando-se uma melhor ação para Staphylococcus aureus. Na segunda etapa os ensaios foram realizados com 22 cepas de Staphylococcus aureus, 18 isolados clínicos MRSA multirresistentes identificados como Clones Epidêmicos, 2 isolados S. aureus MSSA e 2 cepas padrões ATCC. Dos resultados obtidos para as plantas em estudo, a Schinopsis brasiliensis apresentou melhor atividade sobre as cepas de S. aureus, inclusive os clones epidêmicos mais resistentes. Os extratos secos de extração metanólica foram mais ativos com dados de CMI para a flor e raiz de Braúna de 125 μg.mL-1 quanto que pela técnica de poços foram obtidos para uma das cepas de Staphylococcus aureus MRSA multirresistente (CEB) halos da ordem de 20 mm. Os extratos secos de extração por acetato de etila mostraram-se menor ação, o que pode ser atribuído à uma difusão diminuída no agar. Nos testes, os antibióticos usados como padrão foram tetraciclina e oxacilina na determinação das CMI e tetraciclina na técnica de poços, confirmando a oxacilina o caráter MRSA ou MSSA das cepas e a tetraciclina seu perfil de resistência. Os dois diluentes utilizados DMSO à 50% e Tween 80 à 4% não apresentaram nenhuma inibição. Concluindo, considera-se que as plantas em estudo e particularmente a Schinopsis brasiliensis apresentou uma atividade promissora sobre as cepas de S. aureus MRSA inclusive os clones multirresistentes, considerando-se que em parte esta atividade é justificada pela presença de flavonóides e, especialmente, ácidos fenólicos que foram detectados experimentalmente por bioautografia confirmando dados da literatura e por screening fitoquímico

Methicillin-resistenta Staphylococcus aureus (MRSA) som bär på genen mecA, har förekommit och spridit sig över hela världen, främst i sjukhusmiljö, och orsakat utbrott av vårdrelaterade (så kallade nosokomiala) infektioner. Dessa infektioner kan inte behandlas med stafylokock-penicilliner och MRSA-bakterierna är ofta resistenta även mot flera andra grupper av antibiotika vilket medför att infektionerna ofta är påtagligt svårbehandlade. Under senare år har emellertid allt fler fall beskrivits av samhällsförvärvad MRSA infektion, det vill säga uppträdande av MRSA hos personer som tidigare ej har haft kontakt med sjukhusvård eller behandlats med antibiotika. Det har länge varit oklart om de samhällsförvärvade MRSA [community-acquired (CA-MRSA)] representerar spridning av bakterier från sjukhusmiljön ut till samhället eller om dessa MRSA är spontant uppträdande. Många av dessa stammar har dessutom visat sig bära på sjukdomsrelaterade gener som vanligen inte återfinns hos S. aureus, t.ex. Panton Valentine leukocidin (PVL) som associeras med hudinfektioner och allvarlig lunginflammation med hög dödlighet hos unga och annars friska individer. Denna avhandling beskriver den molekylära epidemiologin hos MRSA med fokus på samhällsförvärvade MRSA som utgjorde mer än hälften av samtliga fall av MRSA i Örebro län och som dessutom ofta producerade PVL toxinet, vars funktion vidare analyserades i detalj. Undersökning av ursprung och släktskap hos samtliga MRSA som isolerats i Örebro län, samt karaktärisering av det genetiskt element som kallas staphylococcal cassette chromosome mec (SCCmec) vilket innehåller genen mecA och ibland även andra resistensgener, visade att CA-MRSA inte är relaterade till de nosokomiala MRSA, och att dessa har uppstått oberoende av varandra. Flertalet MRSA visade sig dessutom bära på SCCmec, och resistensmekanismer, som tidigare inte beskrivits. Troligen har dessa MRSA uppstått genom ett genetiskt utbyte av SCCmec mellan methicillin-resistenta koagulas-negativa stafylokocker (MR-KNS), som utgör huvudparten av normalfloran på huden, och methicillin-känsliga S. aureus som därvid erhåller genen mecA och resistensmekanismer mot samtliga stafylokockantibiotika. I den här avhandlingen framläggs bevis för att ett sådant genetiskt utbyte har skett på Barnkliniken på Universitetssjukhuset i Örebro i slutet på 1990-talet, vilket resulterade i uppkomsten av en ny klon av MRSA som därefter orsakade ett allvarligt utbrott. Kartläggning av DNA-sekvensen hos flertalet unika SCCmec från svenska MRSA gav dessutom en bättre förståelse för hur resistens uppkommer och sprider sig, samt mekanismerna bakom detta. Dessa nya kunskaper kan bidra till en förbättrad diagnostik av MRSA. Detta är framför allt av stor betydelse eftersom nya effektiva kloner av MRSA verkar kunna uppstå ute i samhället med potential att orsaka svårbehandlade infektioner men även att sprida sig bland den friska befolkningen. / Material and methods - During a period of 14 years, around 2000 patients with head injuries were admitted to the emergency ward at Lindesberg County Hospital and Örebro Medical Centre Hospital. Six hundred subjects suffered from skull fracture and/or brain contusion and diagnosis was established using a computed tomography scan (CT). The degree of initial brain injury was estimated using the Swedish Reaction Level Scale (RLS). Sixty-six subjects were investigated with pure tone audiometry in close proximity to the trauma, and this gave an opportunity to study the issue of progress. The investigation took place two to 14 years after trauma, and the results were compared to matched control groups. A battery of different audiological methods was used to investigate peripheral and central auditory function, and a specially designed acoustic environmental room was also utilized. Cognition was investigated using a computer-based test-battery, text information process system (TIPS). Self-assessed hearing, cognition and quality of life were explored using different questionnaires. Results - A high percentage of peripheral and central auditory impairments and also cognitive shortcomings were demonstrated. Progress of SNHL was a common finding, and fracture, high age at trauma and large initial hearing loss predicted progress. Antibody-mediated autoimmunity as a mechanism behind posttraumatic progress of SNHL or clear evidence for sympathetic cochleolabyrinthitis could not be demonstrated. Binaural auditory deficits could be demonstrated when tested in a realistic acoustic environment. Tinnitus, vertigo and memory shortcomings proved to be common sequelae, even in a long-term perspectiveCognitive shortcomings were found in several of these well-rehabilitated subjects.On a group level, there was a good correlation between self-assessments and audiometric results, even if some individuals had a tendency to over- or underestimate their abilities. Conclusion - Auditory and cognitive long-term sequelae of CHI are a common finding even in well-rehabilitated and socially well-functioning subjects, as are vertigo and tinnitus. Vertigo and tinnitus are also common sequelae after CHI, therefore a basic audiovestibular investigation after CHI is recommended, at least in selected cases.Early awareness of the risk for hearing and cognitive sequelae after CHI could lead to measurements taken to prevent tension-related symptoms.Early detection of HI offers an opportunity to try immunosuppressive treatment in cases with a large initial SNHL.

>Magister Scientiae - MSc / The aim of this study was to compare the trough plasma levels of Aspen-Vancomycin® (AV); and Sandoz-Vancocin CP® (SV) in premature infants with suspected Methicillin Resistant Staphylococcus aureus (MRSA) infection. The study was designed as a prospective, double blind, randomised trial involving male and female premature infants admitted in the Neonatal Intensive care Unit (NICU) at Netcare Blaauwberg and N1-city Hospitals for treatment of suspected MRSA-infection between April 2012 and June 2013. The inclusion criteria were: 29-35 weeks postmenstrual age (PMA), informed and written consent from parents of each premature infant enrolled in the study. Blood samples (0.3-0.4ml) were collected for renal function test and vancomycin trough levels determination. Blood samples for vancomycin trough level assay were collected thirty minutes prior to the administration of the third dose of vancomycin. Statistical analysis was performed and estimation was made giving an indication of how many infants will be needed to make the study statistically significant. Wilcoxon Two-Sample test was performed to determine the p-values and Spearman correlation coefficients were used to determine the correlation between trough levels and variables. P-values < 0.05 were considered significant. A total of 19 premature infants met with study criteria, 10 (5 females and 5 males) received AV and 9 (6 females and 3 males) receive d SV. There was no statistical significant difference between the demographic (GA, BW, PMA, PNA, weight at trial entry, height at trial entry) and biological (albumin, serum creatinine concentration and glomerular filtration rate) parameters of the premature infants in the AV and SV group. There were no statistical significant difference between trough level 1 of AV and SV, although trough level 1 had a lower trend in the SV group (p=0.118). No AV trough level 1 was below the minimum effective concentration (<5μg/ml). It was found that 30% of AV trough level 1 was within the therapeutic range (5-10μg/ml) and 70% of AV trough level 1, were above minimum toxic concentration (>10mg/l). It was found that 22.2% of SV trough level 1 was below minimum effective concentration, 44.4% of SV trough level 1 was within therapeutic range and 33.3% of trough level 1 was above minimum toxic concentration. No correlation was found between trough level 1 and the demographic and biological parameters of the premature infants in the AV group. SV had a positive correlation with GA, BBW, PMA and a negative correlation with PNA

Depuis quelques années et dans plusieurs pays, un nouveau type de Staphylococcus aureus résistant à la méthicilline (SARM), le séquence type (ST) 398, a été fréquemment retrouvé chez les porcs et chez les fermiers en contact avec ces porcs. Au Canada, très peu d’informations sont disponibles concernant le SARM d’origine porcine. Une première étude dans notre laboratoire a permis de récolter 107 isolats de SARM provenant de deux abattoirs porcins du Québec. Le présent travail vise à caractériser les gènes de virulence et de résistance aux antibiotiques de ces SARM, d’étudier leur formation de biofilm en relation avec la spécificité du groupe agr et de vérifier la localisation plasmidique et la transférabilité de ces gènes à des souches de SARM d’origine humaine. Plusieurs souches ont démontré différents patrons phénotypiques de résistance aux antibiotiques. Vingt-quatre souches représentatives de ces isolats ont été soumises à une caractérisation plus approfondie par une étude génotypique en utilisant une biopuce à ADN et un grand nombre de gènes de virulence a été détecté codant pour des entérotoxines staphylococcales, des leucocidines, des hémolysines, des auréolysines, des facteurs d’immunoévasion, des superantigènes, des facteurs d’adhésion et des facteurs impliqués dans la formation de biofilm. Des gènes de résistance envers les aminoglycosides, les macrolides, les lincosamides, les tétracyclines et les biocides ont été également détectés par biopuce et leur localisation plasmidique a par la suite été déterminée. La transférabilité de ces gènes de souches porcines à des souches de SARM d’origine humaine a été démontrée par conjugaison bactérienne; ainsi le transfert horizontal de certains gènes de résistance aux antibiotiques et de virulence a été observé. Ces travaux de recherche apportent une meilleure connaissance de la résistance aux antibiotiques et de la virulence des SARM d’origine porcine et de leur potentiel de contribution à l’émergence de certaines résistances et facteurs de virulence chez le SARM d’origine humaine. / In recent years and in several countries, a new type of methicillin-resistant Staphylococcus aureus (MRSA), the sequence type (ST) 398, has been frequently found in pigs and in farmers in contact with these pigs. In Canada, little information is available concerning MRSA from pigs. A previous study in our laboratory identified 107 MRSA isolates from two pig slaughterhouses in Quebec. This study was conducted to determine antimicrobial resistance and virulence genes of MRSA from abattoir pig, to study their biofilm formation in relation with agr specificity groups and to evaluate horizontal transfer of genes to a MRSA of human clinical origin. Different phenotypic patterns of antimicrobial resistance were observed in these MRSA and a representative subset of these isolates was selected for further characterization. Twenty-four porcine MRSA were characterized by a DNA microarray, the StaphyType of CLONDIAG. Our results demonstrated that the MRSA strains from the abattoirs contain several antimicrobial resistance genes responsible for macrolide and tetracycline resistance and virulence genes encoding staphylococcal enterotoxins, hemolysins, leukocidins, aureolysin, superantigens, immunoevasion, adhesion, and biofilm development. This study presents the first evidence that horizontal transfer of some of these genes can occur between MRSA of porcine and human origin. We also report for the first time biofilm formation in Livestock Associated-MRSA of porcine origin associated with agr group II. It is possible that biofilm formation favors colonization, persistence as well as zoonotic potential. This research provides a better understanding of antimicrobial resistance and virulence of MRSA from pigs and their potential contribution to the emergence of some resistance and virulence factors in MRSA of human origin.

Antibiotic resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE), are an increasing burden on healthcare systems. Hospital acquired infections with these organisms leads to higher morbidity and mortality compared with the sensitive strains of the same species and both VRE and MRSA are on the rise worldwide including in Australian hospitals. Emerging community infectious diseases are also having an impact on hospitals. The Severe Acute Respiratory Syndrome virus (SARS Co-V) was noted for its propensity to spread throughout hospitals, and was contained largely through social distancing interventions including hospital isolation. A detailed understanding of the transmission of these and other emerging pathogens is crucial for their containment. The statistical inference and mathematical models used in this thesis aim to improve understanding of pathogen transmission by estimating the transmission rates of contagions and predicting the impact of interventions. Datasets used for these studies come from the Princess Alexandra Hospital in Brisbane, Australia and Shanxi province, mainland China. Epidemiological data on infection outbreaks are challenging to analyse due to the censored nature of infection transmission events. Most datasets record the time on symptom onset, but the transmission time is not observable. There are many ways of managing censored data, in this study we use Bayesian inference, with transmission times incorporated into the augmented dataset as latent variables. Hospital infection surveillance data is often much less detailed that data collected for epidemiological studies, often consisting of serial incidence or prevalence of patient colonisation with a resistant pathogen without individual patient event histories. Despite the lack of detailed data, transmission characteristics can be inferred from such a dataset using structured HiddenMarkovModels (HMMs). Each new transmission in an epidemic increases the infection pressure on those remaining susceptible, hence infection outbreak data are serially dependent. Statistical methods that assume independence of infection events are misleading and prone to over-estimating the impact of infection control interventions. Structured mathematical models that include transmission pressure are essential. Mathematical models can also give insights into the potential impact of interventions. The complex interaction of different infection control strategies, and their likely impact on transmission can be predicted using mathematical models. This dissertation uses modified or novel mathematical models that are specific to the pathogen and dataset being analysed. The first study estimates MRSA transmission in an Intensive Care Unit, using a structured four compartment model, Bayesian inference and a piecewise hazard methods. The model predicts the impact of interventions, such as changes to staff/patient ratios, ward size and decolonisation. A comparison of results of the stochastic and deterministic model is made and reason for differences given. The second study constructs a Hidden Markov Model to describe longitudinal data on weekly VRE prevalence. Transmission is assumed to be either from patient to patient cross-transmission or sporadic (independent of cross-transmission) and parameters for each mode of acquisition are estimated from the data. The third study develops a new model with a compartment representing an environmental reservoir. Parameters for the model are gathered from literature sources and the implications of the environmental reservoir are explored. The fourth study uses a modified Susceptible-Exposed-Infectious-Removed (SEIR) model to analyse data from a SARS outbreak in Shanxi province, China. Infectivity is determined before and after interventions as well as separately for hospitalised and community symptomatic SARS cases. Model diagnostics including sensitivity analysis, model comparison and bootstrapping are implemented.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance. The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits. This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups. A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy. To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing. The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform.

Submitted by Priscila Nascimento (pnascimento@icict.fiocruz.br) on 2012-11-28T19:21:24Z No. of bitstreams: 1 rodrigo-muller.pdf: 1238864 bytes, checksum: 6c267fda3ccb992508b5424e77147783 (MD5) / Made available in DSpace on 2012-11-28T19:21:24Z (GMT). No. of bitstreams: 1 rodrigo-muller.pdf: 1238864 bytes, checksum: 6c267fda3ccb992508b5424e77147783 (MD5) Previous issue date: 2009 / Fundação Oswaldo Cruz. Instituto de Tecnologia em Imunobiológicos. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil. / As infecções causadas por Staphylococcus aureusresistentes à meticilina (MRSA) são temidas em virtude da dificuldade de seu tratamentoe da elevada morbidade associada. A PBP2a (penicillin binding protein 2a), enzima responsável pela síntese da parede celular em MRSA, apresenta baixíssima afinidade porbeta-lactâmicos. Pelo fato de a PBP2a estar localizada na superfície externa, a mesma seria acessível ao sistema imune. Durante as infecções causadas por MRSA, pouco se sabe se o hospedeiro infectado ou colonizado desenvolve anticorpos anti-PBP2a e se osmesmos seriam protetores ou não. O presente projeto tem por finalidade avaliar a presença e níveis de anticorpos anti-PBP2a em um grupo de 56 pacientes colonizados por MRSA e investigar se estes anticorpos seriam protetores ou não. Os resultados gerados permitiram observar que 71% das amostras analisadas apresentaram anticorposanti-PBP2a pelo teste ELISA. Estas amostras foram submetidas à Western blot paraconfirmação, demonstrando que 46% das amostras possuíram anticorpos anti-PBP2a. Após estes resultados, as amostras positivas foram submetidas à purificação para avaliar a cinética de crescimento de MRSA. Foi observado que houve ligeira redução do crescimento bacteriano entre amostras de soro com anticorpos MRSA comparadas comas de soro com anticorpos anti-MSSA (PBP2a negativos). Por conseguinte avaliamos a curva de crescimento de MRSA em presença de imunoglobulinas purificadas de soro de pacientes colonizados por MRSA, (quantificação bacteriana). Observamos que houve uma redução drástica do crescimento bacteriano em presença destas imunoglobulinas. Os resultados obtidos indicaram que: (i) pacientes colonizados por MRSA podem produzir anticorpos anti-PBP2a e (ii) estes anticorpos podem conferir proteção contra MRSA. Estes dados parecem indicar que uma potencial vacina anti-PBP2apoderia ser efetiva para prevenção de infecções causadas por MRSA, como também para o emprego de imunoterapia passiva para o tratamento de pacientesinfectados por este patógeno. / Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are feared because of the difficulty of their treatment and the high associated morbidity. The PBP2a (penicillin binding protein 2a), the enzyme responsible for cell wall synthesis in MRSA, presents low affinity for beta-lactams. Because of the PBP2a is located on the external surface, it would be accessible to the immune system. During the MRSA infections, little is known whether the infected orcolonized host can produce antibodies anti-PBP2a and whether these antibodies would be protective or not. This project aims to assess the presence and levels of anti-PBP2a in a group of 56 patients colonized by MRSA and investigate whether these antibodies wouldbe protective or not. The results showed that 71% of the samples presented anti-PBP2aantibodies in ELISA. These samples which were subjected to Western blot for confirmation, it was demonstrated that 46% of the samples presented antibodies anti-PBP2a. After these results, the positive samples were subjected to purification to assess the MRSA growth kinetics. It was observed that there was a slight reduction in bacterial growth between serum samples with antibodies and MRSA compared to those of the serum with anti-MSSA (PBP2a negative). Therefore, the curve of growth ofMRSA was evaluated in the presence of purified immunoglobulins from the serumof patients colonized by MRSA (bacterial quantification). We observed that there was a drastic reduction in bacterial growth in the presence of immunoglobulins, thus demonstrating that these antibodies could have a protective action. These results indicated that: (i) MRSA colonized patients can produce antibodies against PBP2a and (ii) these antibodies can be protective against MRSA. These data suggest that a potential vaccine anti-PBP2a could be effective for prevention of infections caused byMRSA and for the use of passive immunotherapy in the treatment of patients infectedby this pathogen.