Acinetobacter baumannii is an important microorganism involved in hospital-acquired infections with a remarkable ability to develop resistance to multiple antibiotics (multidrug-resistance, MDR) which makes it a highly troublesome pathogen in many hospitals around the world. Third-generation cephalosporins (such as ceftazidime) and carbapenems (such as imipenem and meropenem) represent important treatment options for infections caused by this microorganism. Nevertheless, the number of strains resistant to these antibiotics has been increasing during the last decade. The ability to capture, mobilise and regulate the expression of resistance-genes of this microorganism is a cornerstone factor in the development of the MDR, where the Mobilome, defined as “all the mobile genetic elements in a cell”, is responsible for its genetic plasticity. The aim of this work was to analyse the role of insertion sequences (ISs), transposon-like structures, resistance-plasmids and ISCR1-like elements in the resistance to carbapenems and ceftazidime in A. baumannii. Fifteen carbapanem-resistant strains of Acinetobacter baumannii isolated from Chile and two ceftazidime-resistant strains from the United Arab Emirates were studied. Different ceftazidime- and carbapenem-resistance genes were analysed and their genetic environments were characterised. The Mobilome in the carbapenem-resistant strains was composed of insertion sequences (ISs), specifically by ISAba1 associated with blaOXA-51-like, ISAba3 associated to blaOXA-58, which in turn was detected in two different plasmids, and ISAba15 interrupting ISAba3. In the case of the ceftazidime-resistant strain, the presence of an ISCR1 element was harbouring the blaPER-7, which was detected in a megaplasmid. The Mobilome, in the strains analysed, was composed of a wide variety of genetic elements, such as plasmids, insertion sequences, ISCR-like elements, which reflects the ability of A. baumannii to use different genetic platforms to capture and use resistance genes, making the Mobilome an important contributor in the resistance and the dissemination of resistance genes among nosocomial pathogens around the world.

Les bactéries pathogènes opportunistes (BPO) sont responsables d'une grande part de la pathologie infectieuse bactérienne. Les BPO d'origine environnementale doivent subir des changements profonds de mode de vie pour s'adapter et coloniser l'homme. Comprendre les conditions de cette adaptation permettra de préciser la notion d'opportunisme infectieux et le rôle des BPO environnementales dans l'émergence des pathogènes.Les genres Ochrobactrum et Agrobacterium regroupent des bactéries présentant une grande variété de modes de vie et établissant différentes relations avec la cellule eucaryote. Ces bactéries connues pour vivre dans l'environnement sont par ailleurs des pathogènes opportunistes de l'homme principalement responsables d'infections chez les individus immunodéprimés. Dans le cadre de ce travail nous avons entrepris une étude populationnelle par une approche de génétique multilocus sur des collections de souches cliniques et environnementales de différentes origines géographiques. Les structures de population obtenues ont été confrontées à divers caractères phénotypiques reliés à la virulence et/ou l'adaptation chez l'homme, la température de croissance, la formation de biofilm et la virulence vis-à-vis des modèles Caenorhabditis elegans et macrophages humains.Ochrobactrum anthropi et Ochrobactrum intermedium sont les deux principales espèces d'intérêt médical du genre Ochrobactrum. La population d'O. anthropi est de type épidémique qui s'organise en deux complexes clonaux (CCs). Si le CC1 regroupe à la fois des souches de diverses origines, le CC4 ne contient que des souches cliniques. Cette sous-population apparait associée à l'homme même si les caractères phénotypiques étudiés ne révèlent pas de différences entre ces deux sous populations. De la même façon, ces deux CCs ne se distinguent pas par leur comportement en modèle macrophage ou par leur diversité génomique. O. intermedium, tout comme O. anthropi, présente une forte diversité génétique toutefois, aucun regroupement des souches en fonction de leur origine n'est mis en évidence pour cette espèce. La diversité des souches cliniques apparait aussi importante que celle de l'ensemble de la population. Plusieurs arguments suggèrent une niche étroite pour cette espèce, notamment une faible diversité génomique. Par ailleurs, le faible nombre de souches environnementales associé à une meilleure croissance planctonique à 37°C qu'à 25°C et 30°C suggèrent que l'homme pourrait constituer cette niche. L'étude de la virulence d'O. intermedium en modèle macrophage ou C. elegans met en évidence différents comportements, pour autant ceux-ci ne semblent pas liés à la structure de population. Certaines souches sont capables de se multiplier dans le modèle macrophage.L'étude du genre Agrobacterium par une approche multilocus sur une collection représentative des différents modes de vie de ces bactéries met en évidence, tout comme pour O. anthropi, une sous population clinique qui regroupe près de 80% des souches de cette origine. D'autres arguments tels que la croissance à 42°C confirment que le génovar A7 peut correspondre à une sous-population associée à l'homme. Les données obtenues seront confrontées aux connaissances sur d'autres bactéries pathogènes opportunistes d'origine environnementale comme Pseudomonas aeruginosa, Stenotrophomonas maltophilia et les bactéries du complexe Burkholderia cepacia qui présentent également des sous populations associées à l'homme et/ou à certaines pathologies humaines. L'existence de ces sous populations suggère une spécialisation qui sera discutée dans le contexte de la spéciation des bactéries pathogènes afin de revisiter le concept d'opportunisme infectieux. / The opportunistic bacterial pathogens (OBP) cause the main part of bacterial infectious diseases. Environmental-borne OBP should encounter dramatic changes in lifestyle in order to colonize human beings. The conditions of this adaptation should precise concepts about OBP and emerging pathogens.The genera Ochrobactrum and Agrobacterium groups bacteria with versatile lifestyles that establish diverse relationships with the eukaryotic cells. These environmental-borne OBP caused diverse infectious diseases in immune-compromised patients. In this study, we undertook an approach of multilocus genetic on large population of environmental and clinical strains of Ochrobactrum and Agrobacterium. The population structures were compared to phenotypic traits related to adaptation and virulence in man, such as growth temperature, biofilm formation and virulence tested in Caenorhabditis elegans and human macrophages models.Ochrobactrum anthropi and Ochrobactrum intermedium are the two main Ochrobactrum species to be involved in human diseases. O. anthropi displays an epidemic population structure organized in two large clonal complexes (CCs). CC4 groups only human associated strains whereas CC1 contain environmental and clinical strains. Population genetics suggested that CC4 is a human-associated clone although phenotypic, genomic and virulence traits do not differ between CC1 and CC4 strains.As O. anthropi, O. intermedium displays a high genetic diversity without correlation between the genetic structure and the origin of strains. The level of genetic diversity among clinical strains appears as high as observed in the whole population. Several data such as a low level of genomic diversity suggested that O. intermedium is associated to a narrow ecological niche. The low number of environmental strains described for this species as well as an optimal growth at 37°C suggested that human beings could be the main niche for O. intermedium. Virulence in macrophage and C. elegans models showed diverse behaviour whereas some strains are able to survive and multiply in macrophages model.Multilocus genetics in a population of Agrobacterium spp. that displays diverse lifestyles, revealed a human associated population as observed for O. anthropi. The clinical genovar A7 groups 80% of the clinical strains included in the study, this strains growing at 42°C. Data obtained in this study will be confronted to the knowledge about other environmental-borne OBP such as Pseudomonas aeruginosa, Stenotrophomonas maltophilia and bacteria belonging to the species complex Burkholderia cepacia. All these bacteria displayed sub-populations associated to man or to a particular human disease. These sub-populations suggest a specialization process that will be described in the context of the speciation of bacterial pathogen in order to revisite the concept of « opportunisme infectieux ».

Magister Public Health - MPH / Introduction: Despite ongoing training provided to healthcare workers (HCWs) on tuberculosis infection prevention and control (TB IPC), at the health institution and implementation of TB IPC precautions, nosocomial TB infection within the hospital persist. The facility’s 2017 Occupational Infection & Needle Prick Report showed the proportions of new nosocomial TB infection cases among HCWs rose steadily from (5.6%) n=2 in 2013/14, (7.8%) n= 4 2015/16 and (9%) n=7, to (11%) n=11 cases in 2017/18. Study findings confirmed high new nosocomial TB infections among HCWs and a likelihood that these cases were usually under- reported meaning the problem of nosocomial TB infection among HCWs was actually bigger than understood at the hospital. In fact during the period of the mini-thesis study (July 2018) alone, three (3) cases of nosocomial TB infections were reported among HCWs (a porter and 2 nurses). Aim: The aim of this study was to explore the factors which are perceived to be contributing to nosocomial TB infection amongst doctors and nurses in a Level 2 referral hospital in the Free State Province of South Africa.

This dissertation examines risk factors and outcomes associated with bloodstream infection (BSI). In Chapter One, the problems of BSI are introduced and their significance described. In Chapter Two, the results of a systematic review and meta-analysis synthesizing the prevalence of one of the most rapidly emerging causes of BSI among nursing home residents, multidrug resistant-gram negative bacteria are described. In Chapter Three, a retrospective cohort study identifying the prevalence and risk factors for BSI present on hospital admission (POA) is reported, including an assessment of antimicrobial resistance in isolates causing BSI-POA by admission source (i.e. private homes, other hospitals and skilled nursing facilities). In Chapter Four, a retrospective cohort study explaining risks for hospital-associated infections (HAIs) among the BSI-POA cohort is described. Length of stay and mortality among patients with a BSI-POA who develop HAI and those who do not are reported. Finally, in Chapter Five, findings of the previous chapters are synthesized and the conclusion is provided including strengths, limitations and implications for policy and practice.

Patients who experience multiple hospitalizations over short periods of time may be at greater risk of hospital-acquired infections (HAIs). While it is known that prior hospitalizations are associated with HAIs, there is a gap in knowledge regarding which factors of prior hospitalizations have an impact on the risk of HAIs in subsequent hospitalizations. HAIs caused by gram-negative bacteria (GNB) are of particular concern due to their propensity to develop drug resistance and the limited antibiotics available to treat them. The aims of this dissertation are to: 1) examine clinical and patient risk factors associated with acquiring at least one gram-negative hospital-acquired infection in adult patients with multiple hospitalizations; 2) systematically review the literature assessing the association between repeat gram-negative bacterial infections and changes in antibiotic susceptibility patterns; and 3) assess the association between repeat infections with three common gram-negative pathogens and risk of subsequent drug resistant infections with the same species among patients with multiple hospitalizations. A retrospective cohort study was conducted to identify risk factors from prior hospitalizations associated with incident HAIs caused by three common GNB. Of the 129,372 patients with multiple hospitalizations, 1,672 (1.3%) acquired K. pneumoniae, 1,127 (0.9%) acquired P. aeruginosa, and 262 (0.2%) acquired A. baumannii infections. In survival analyses, older age, mechanical ventilation, history of chronic diseases, and increasing days of use of antibiotics decreased the time to infection for all 3 pathogens. This study highlights potential modifiable risk factors for infection control. Patients with multiple hospitalizations are also inherently at greater risk for repeat HAIs which may result in decreased antibiotic susceptibility, making them more difficult to treat. A systematic review was conducted to evaluate if there is an association between repeat GNB HAIs and drug resistance. From 2000 to 2015, only seven studies explicitly examined repeat GNB HAIs and change in antibiotic susceptibility, five of which reported decreased susceptibility in later infections. The association between repeat GNB HAIs and risk of drug resistance among patients with multiple hospitalizations was then investigated with available electronic medical record data. The risk of a drug-resistant K. pneumoniae HAI increased by 1.14 times (95%CI: 1.04-1.24) with each prior K. pneumoniae HAI, after adjusting for potential confounders and antibiotic use. Similarly, patients with repeat P. aeruginosa infections had a 1.23 times increased risk of a subsequent drug-resistant infection (95%CI: 1.12-1.36) with each prior P. aeruginosa HAI as compared to patients with only one infection. Repeat A. baumannii infections were not analyzed due to limited sample size. The studies in this dissertation demonstrate that patients with multiple hospitalizations are a high-risk population for GNB HAIs. Prevention of GNB HAIs in this group is critical in order to reduce complications to medical care and limit transmission of infections to others in healthcare facilities and the community. Patient medical history can be used for infection risk assessment and to guide future medical care to reduce risk of infection in patients with multiple hospitalizations.

Background: The traditional model of infection control has failed to stop the spread of emerging infectious diseases such as Clostridium difficile-associated diarrhea (CDAD) in the acute care environment. Ecological models, which rely upon identification of susceptible hosts, offer an alternative to the prevention of deadly outbreaks. Previous epidemiological research has identified a number of risk factors associated with CDAD. Utilization of this body of research by nurses is limited due to methodological issues that introduce bias and confounding, and use of variables that have limited meaning to the practicing clinical nurse. Aim: The aim of this study was to develop an ecological model useful for nurses in predicting the susceptibility of individuals to CDAD during an acute care hospital stay. Method: A case-control study compared 66 cases with CDAD to 66 controls matched for the temporal and spatial risk factors of hospital admission date and geographic nursing care unit within the institution. The two subject groups were compared on variables of age, antibiotic burden, laxative or bowel preparation exposure, nutritional status, gastric acid suppression therapy, enteral feeding exposure, and severity of illness as measured on the Horn Severity of Illness index. All subjects were hospitalized between January 1, 2000 and December 31, 2006. Results: On univariate analysis, age, severity of illness, serum albumin levels, length of exposure, and proton pump inhibitor drug burden were significantly associated with CDAD status. Following multivariate analysis, only severity of illness, length of exposure, and decreased antibiotic drug burden were significantly associated with the development of hospital-acquired CDAD. Conclusions: This study supports the use of an ecological perspective in identifying risk factors and interventions to prevent the future spread of this infectious disease.

Master of Science / The role of the microbiology laboratory is (1) to provide infection control information, so that highly transmissible isolates may be identified and appropriate control measures instigated as rapidly as possible and (2) to provide adequate information to the clinician enabling correct antibiotic choices to be made, particularly in the critically ill. Microbiological data is by definition slow as it is culture dependent: this study focused on the development of genetic, culture-independent methods for detection of resistance in nosocomial pathogens that could be introduced into the routine microbiology department and would fit into the routine workflow with a consequent reduction in time to result. Initially a duplex real-time polymerase chain reaction was developed for the rapid identification and detection of S. aureus and methicillin-resistance. This was optimised for immediate as-needs testing of positive blood cultures signalling with “Gram positive cocci, possibly staphylococcus” evident on Gram stain, on a random access real-time PCR platform. This technology, allowing early identification of S. aureus and its susceptibility to methicillin, by simple automated methodology, may soon become the standard for all microbiology laboratories servicing the critically ill. The second part of the study involved the development of a selective broth and multiplex PCR for detection of three important nosocomial isolates at this institution, methicillin-resistant S. aureus (MRSA), carbapenem-resistant Enterobacteriaceae, and multi-resistant Acinetobacter baumannii (MRAB). A multiplex PCR using four primer sets was designed to detect low colonisation levels of these isolates after overnight incubation in selective broth, significantly reducing the time to result and associated costs. This potentially useful epidemiological screening tool is practical, reproducible and sensitive with the potential of moving to an automated test (using real-time PCR, for example) in the future. The availability of early negative results judged by simple visual scanning (or by densitometry), means that the result is less operator-dependent, potentially reducing error rate. The last part of the study dealt with an important resistance phenotype, aminoglycoside resistance. There had been no recent comprehensive local surveys performed to determine the frequency of aminoglycoside resistance amongst the Enterobacteriaceae, or to identify the genetic determinants and their transmissibility. The isolates collected for the study were all resistant to at least one of gentamicin, tobramycin or amikacin. Identification of integron cassette arrays and use of specific internal primers identified at least one genetic determinant for gentamicin and tobramycin resistance in 22 of 23 isolates. Three isolates had two aminoglycoside resistance genes, and three isolates had three aminoglycoside resistance genes identified (Table 6.1). Transferable gentamicin-resistant plasmids were predominant amongst Klebsiella spp., but less so amongst Enterobacter spp. and E. coli. Gentamicin-resistant Klebsiella spp. were often ESBL positive, the genetic determinants of which were typically co-transferred on a conjugative plasmid. The importance of screening at a local level was demonstrated by the unexpected predominance of aac(6')-IIc amongst Enterobacter spp. and the detection of a new gene (aac(6')-LT). This part of the study has provided an understanding of the primary aminoglycoside resistance genes present in the local setting and their association with other resistances. This knowledge will allow development of assays for patient screening (clinical isolates and colonising flora), to better understand the epidemiology of aminoglycoside resistance and to allow better choice of antibiotic therapy related to presence or absence of these genes.

This research project investigated the impact of an action research intervention implemented to reducing surgical wound infection in one of the acute care hospitals in India. The study aimed to develop and implement a clinical practice improvement program in reducing surgical wound infection by improving the hand washing and wound dressing practices of nurses. The study also aimed to identify the important contributing factors to a model that predicts surgical wound infection. Pre-post evaluation measures were taken to compare the results of surgical wound infection rate before and after the implementation of the intervention. Surgical wounds of two thousand patients (one thousand before the intervention and another one thousand after) were assessed to determine the wound infection rate and severity of wound infection. The hand washing and wound dressing practices of forty nurses were observed. These same nurses were involved in the intervention using a participatory action research process. The results of the study suggest that there was a marked, significant reduction in the rate and severity of wound infection following the implementation of the intervention. By increasing the hand washing facilities in the ward, educating nurses on the importance of better hygiene, pre-operative shaving and post-operative wound care, the hand washing and wound dressing practices of nurses improved considerably. These improvements resulted in a reduction in the number and severity of patients' surgical wound infections. The study also examined the contribution of different factors to surgical wound infection in a Indian hospital. Significant predictive factors were the patients' age, longer pre-operative hospital stay, extended pre-operative shaving time before surgery, wound class, and co-morbidity of the patient. The identification of risk factors that contributed to increased surgical wound infection for example pre-operative skin preparation, pre-operative hospital stay of the patient would help in taking appropriate measures at the ward level and organisation as a whole. Nosocomial infections extends to an unnecessary lengthy hospital stay, additional treatment increased mortality and morbidity, and increased cost to the patients and the nation as a whole. This project proved that educational mentoring, data surveillance processes and involving the nurses in an action research process were effective in enabling participants to improve their clinical practice and thereby reduce the incidence of patients' surgical wound infections. Establishing infection control teams, ongoing surveillance and feedback to staff of nosocomial infection rates is an urgent need in all Indian hospitals. Organisational management, as a priority, need to provide funding and staff dedicated to undertaking this essential work. Health care professionals can no longer plead ignorance of a situation for which all have a moral and professional responsibility.

<p>Syftet med denna litteraturstudie var att beskriva varför följsamheten gällande handhygien ofta är låg bland vårdpersonal, samt hur man kan öka följsamheten för handhygien bland vårdpersonal. Metoden som använts var en litteraturstudie. Datainsamling skedde via databaserna Medline (PubMed), Cinahl (EBSCO host) och Academic Search Elite. Sökorden som använts: prevention, hand disinfection, hand washing, infection control, nosocomial infection och education. Totalt användes 15 vetenskapliga artiklar. Resultatet delades in i två huvudrubriker: Orsaker till att följsamheten ofta är låg bland vårdpersonal och faktorer som kan öka följsamheten gällande handhygien bland vårdpersonal. De två huvudrubrikerna delades in i sex underrubriker: tidsbrist, hudbekymmer, kunskapsbrist, utbildning, affisch/posters och tillgänglighet. Resultatet visade att det finns många anledningar till att följsamheten för handhygien är låg. Studien visar att tidsbrist, hudbekymmer samt kunskapsbrist gällande hand hygien är de vanligaste orsakerna. Utbildning tillsammans med affischer/posters samt ökad tillgänglighet vad gäller material har visat sig vara det mest effektiva sättet att öka följsamheten av handhygien.</p><p><strong><p>Nyckelord</p><p>.</p>: prevention, hand disinfection, hand washing, infection control, nosocomial infection och education. </strong></p>

Syftet med denna litteraturstudie var att beskriva varför följsamheten gällande handhygien ofta är låg bland vårdpersonal, samt hur man kan öka följsamheten för handhygien bland vårdpersonal. Metoden som använts var en litteraturstudie. Datainsamling skedde via databaserna Medline (PubMed), Cinahl (EBSCO host) och Academic Search Elite. Sökorden som använts: prevention, hand disinfection, hand washing, infection control, nosocomial infection och education. Totalt användes 15 vetenskapliga artiklar. Resultatet delades in i två huvudrubriker: Orsaker till att följsamheten ofta är låg bland vårdpersonal och faktorer som kan öka följsamheten gällande handhygien bland vårdpersonal. De två huvudrubrikerna delades in i sex underrubriker: tidsbrist, hudbekymmer, kunskapsbrist, utbildning, affisch/posters och tillgänglighet. Resultatet visade att det finns många anledningar till att följsamheten för handhygien är låg. Studien visar att tidsbrist, hudbekymmer samt kunskapsbrist gällande hand hygien är de vanligaste orsakerna. Utbildning tillsammans med affischer/posters samt ökad tillgänglighet vad gäller material har visat sig vara det mest effektiva sättet att öka följsamheten av handhygien. Nyckelord . : prevention, hand disinfection, hand washing, infection control, nosocomial infection och education.