As infecções em pacientes submetidos a transplantes de órgãos sólidos são importante causa de morbidade, além de serem definidoras da sobrevida desta população. A maioria das infecções que ocorre nos dois primeiros meses pós-transplante é relacionada à assistência à saúde (IRAS). O objetivo deste trabalho é identificar fatores de risco para IRAS por bactérias Gram-negativas (BGN) multi-droga resistentes (MDR) em pacientes submetidos a transplante de fígado (TF), nos dois primeiros meses após o transplante. Os objetivos secundários são: identificar fatores de risco para aquisição por MDR GNB em pacientes submetidos a TF, e determinar o impacto das IRAS por MDR GNB na sobrevida desses pacientes. Foram avaliados os TF consecutivos realizados em pacientes adultos no Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) no período de novembro de 2009 a novembro de 2011. A vigilância microbiológica foi realizada no dia do TF, e semanalmente até a alta hospitalar ou 60 dias após o transplante. Os sítios de coleta foram swab de orofaringe ou secreção traqueal, swab retal e swab axilar. Foram pesquisadas as seguintes bactérias: A. baumannii. P. aeruginosa e Enterobactérias resistentes a carbapenêmico, e K. pneumoniae e E. coli produtoras de betalactamase de espectro estendido (ESBL). Posteriormente, as amostras clínicas foram comparadas com as cepas da mesma espécie isoladas em culturas de vigilância por tipagem molecular. A análise de fatores de risco foi realizada por tipo de infecção e espécie de bactéria. Na análise estatística utilizou-se o teste qui-quadrado ou teste exato de Fisher para variáveis dicotômicas, e teste de Mann-Whitney para variáveis ordenáveis. A análise multivariada foi realizada por regressão logística. A análise de sobrevida foi realizada por regressão de Cox. O nível de significância de P considerado foi 0,05. Foram realizados, no período, 229 transplantes em 202 pacientes, e analisados 214 transplantes em 195 pacientes. O motivo de indicação do transplante mais frequente foi cirrose pelo vírus C, 33%. Foram identificados no período do estudo 110 pacientes (56,4%) com IRAS pós-TF, e um total de 201 infecções. Em 76,3% dos pacientes com IRAS (84/110) foi isolado MDR GNB em alguma amostra clínica relacionada à infecção. Os dois principais sítios de infecção foram infecção de sitio cirúrgico (32%) e infecção primária de corrente sanguínea (27%). Os dois microrganismos mais frequentemente isolados das IRAS foram A. baumannii e K. pneumoniae, e a proporção de infecções por cepas resistentes a carbapênemico foi, respectivamente, 100% e 48,9%. Os fatores de risco para infecções por MDR GNB pós-TF foram: retransplante precoce, volume de concentrados de hemácias transfundidos no intra-operatório da cirurgia do TF, colonização por MDR GNB no pré-transplante, tempo prolongado de internação em UTI e tempo prolongado de isquemia fria. Cento e cinco pacientes adquiriram algum MDR GNB nos 60 dias pós-TF, e o único fator de risco detectado para aquisição de MDR GMB no pós-TF foi tempo prolongado de sonda vesical de demora. A análise de clonalidade demonstrou que as cepas de MDR identificadas pré-TF eram fortemente relacionadas às cepas isoladas das infecções no pós-TF para A. baumannii e K. pneumoniae resistente a carbapenêmico. As infecções por MDR GNB apresentaram uma tendência a aumentar o risco de óbito nos 60 primeiros dias pós-TF, mas esta / Bacterial infections among patients submitted to liver transplantation (LT) are an important cause of morbidity and have huge impact on patients\' survival. The majority of infections in the first two months after LT are related to healthcare assistance. The aim of this study has been to identify risk factors for healthcare-associated infections (HAI) caused by multidrug-resistant Gram-negative bacteria (MDR GNB) in liver transplant patients in the first two months after LT. The secondary aims have been to identify risk factors for acquisition of MDR BGN among liver transplant patients and analyze the survival rate during the first two months after LT. We analyzed consecutive liver transplantations performed at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) from November 2009 to November 2011. Surveillance cultures were performed on a weekly basis, starting on the day of the LT until the hospital discharge or 60 days after the LT. We collected surveillance cultures through swab from oropharynx (or tracheal secretion), axillary and inguinal rectal sites. We surveyed the following bacteria: carbapenem-resistant A. baumanni, P. aeruginosa, Enterobacteriaceae, ESBL-producing K. pneumoniae, and E. coli. The strains isolated from surveillance culture were compared to strains isolated from clinical cultures through PFGE. The risk factor analysis was performed for each type of MDR bacterium for risk of colonization and infection. The statistical analysis was carried out for dichotomous variables using chi-square tests or Fisher\'s exact tests when appropriate; Mann-Whitney tests were used for continuous variable and step-wise logistic regression was used for multivariate analysis. The survival rate analysis was performed using Cox regression. The significant value of P was 0.05. During the study period, 229 liver transplantations were performed in 202 patients and we analyzed 214 LT performed in 195 patients. The main baseline disease that warranted LT was virus C cirrhosis, 33%. 110 (56.4%) patients developed healthcare-associated infections after the LT and a total of 201 infections were identified; 84 (76.3%) patients had MDR GNB isolated from clinical cultures related to HAI. Surgical wounds (31%) and primary bloodstream (27%) were the most prevalent infection sites. The risk factors for HAI by MDR GNB after the LT were: re-transplantation, volume of blood units transfused during the LT surgery, colonization by MDR GNB before the LT, prolonged time of ICU stay, and prolonged time of cold ischemia. 105 patients acquired MDR GNB during the first 60 days after the LT; the only risk factor identified was the prolonged use of urinary drain. The clonal analysis showed that strains isolated in the period before the LT were closely related to strains isolated from clinical culture after the LT for carbapenem-resistant A. baumannii e K. pneumoniae. The infections by MDR GNB have been shown to increase the risk of death in the first 60 days after LT

Bakgrund: Kolonisering och spridning av multiresistenta bakterier (MRB) är ett ökande problem både i samhället och i sjukvården idag. MRB smittar genom kontaktsmitta, genom direkt personkontakt eller kontakt av kontaminerade ytor. Frågor rörande patientsäkerhet påverkar alla inom hälso- och sjukvårdens organisationer, men huvudansvaret att utveckla ledningssystem för att ett systematiskt kvalitetsarbete ska kunna bedrivas, ligger på vårdorganisationen- och vårdgivaren. Kunskapsbrist om MRB hos vårdpersonal samt brist på tydliga riktlinjer i vården i det kliniska arbetet kan påverka attityder till och bemötande av patienter med MRB. Syfte: Att belysa vårdorganisationers ansvar, sjuksköterskans kunskaper om MRB samt hens attityder till och bemötande av patienter med MRB- smitta. Metod: Studien gjordes som en litteraturöversikt där tio vetenskapliga artiklar analyserades för att framställa resultatet. Resultat: I resultatet framkom att vårdorganisationen och ledarskapet var av stor vikt för sjuksköterskans förutsättningar att ge god och säker vård till patienter med MRB. Kunskaperna om MRB var oftast låga. Attityder och bemötande visade sig i de flesta fall också påverkas av kunskapsnivån. Dålig kunskap och brist på erfarenhet av patienter med MRB kunde även relateras till ökade rädslor hos sjuksköterskor att smittas av MRB. Diskussion: Resultatet diskuterades mot Travelbee´s teori om mellanmänskliga relationer och konsensusbegreppet vårdande. Vårdorganisationens ansvar och kunskaper hos sjuksköterskor om MRB tycks vara de faktorer som mest påverkade bemötandet gentemot och attityderna till patienter med MRB. / Background: Colonization and transmission of MDRB is an increasing problem today, both in society and in health care settings. MDRB is most commonly transmitted through cross-contamination through personal contact and contact with contaminated surfaces. Patient safety affects everybody within health care settings. Main responsibility lies with healthcare organizations and caregivers, to develop management systems for systematic quality improvement. Knowledge deficiency of MDRB among health care personnel and lack of clear guidelines in health care settings may influence the attitudes and behaviour towards patients with MDRB. Aim: To illustrate healthcare organizations responsibilities, nurses’ knowledge of MDRB and nurses’ attitudes and behaviour towards patients with MDRB. Method: The study was conducted as a literature review and ten scientific papers were analysed to generate the results. Results: The results showed that healthcare organizations and leadership were of great importance for the nurses’ ability to provide good and safe care for patients with MDRB. Knowledge about MDRB was also proved to be low. Deficient knowledge and lack of experience of caring for patients with MDRB among nurses might also influence their own fears of contracting MDRB. Discussions: The results were discussed against Travelbee’s Intrapersonal relationship- theory and the concept of caring. Healthcare organizations responsibility and nurses’ knowledge of MDRB seemed to be the eminent factors that influenced both behaviour and attitudes towards patients with MDRB.

WGS permet d'analyser et de déchiffrer l'étude de résistances de bactéries multirésistantes(MDR), en comprenant les différents mécanismes de résistance, les annuaires génétiques. Au cours de ma thèse de doctorat, j'ai réalisé: 1 revue de la littérature sur l'utilisation de nouveaux outils de diagnostic contemporains et les capacités dans la détection des foyers dans les maladies infectieuses causées par MDR. L'identification et l'analyse de résistances de bactéries multirésistantes Comme étant des Shewanellalgae, normalement de l'environnement marin, dans notre cas une souche clinique isolée du lavage bronchoalvéolaire d'un patient hospitalis avec pneumonie et Chryseobacteriumin dologenes, isolé d'une fibrose kystique du patient. Dans cette analyse, nous pouvons montrer que les bactéries environnementales telles que les S.algae peuvent être un réservoir de gènes de résistance aux antibiotiques. L'analyse exhaustive de ces bactéries a montré leur capacité à s'adapter à leurs écosystèmes, y compris l'acquisition de nouveaux éléments génétiques par transfert latéral de gènes. La détection des gènes impliqués dans la synthèse de peptides synthetasenon ribosomale et de polycétide synthétase peut avoir un rôle dans leur capacité à survivre dans des environnements hostiles tels que le tractus respiratoire des patients atteints de fibrose kystique ou leur présence chez des patients ayant subi plusieurs antibiotiques. Nous avons réalisé une analyse standardisée «insilico» afin de déterminer la résistance de ces bactéries et la présence de métabolites secondaires associés aux bactériocines et aux NRPS/PKS. L'application du NTS pour le séquençage du génome bactérien de nouvelles espèces bactériennes isolées dans le microbiome humain nous a permis de développer une plateforme capable d'analyser ces nouvelles espèces dans les 48heures. Ce travail permet de mieux comprendre la biodiversité des bactéries isolées dans le microbiome humain. / Theuse of WG Sallows to analyze and to decipherthe study of resistome of Multi Drug Resistant bacteria (MDR), understanding the different resistance mechanisms, genetic directories and their dissemination mechanisms at global level. During them y thesis I have achieved: 1. A literature review on the use of new contemporary diagnostic tools and capabilities in detecting out breaksin infectious diseases caused by MDR. 2: The identification and the analysis of resistome of multidrug resistant bacteria from clinical isolates suchasShewanellaalgae, normally marine environmental, in our case clinical strain isolated from the broncho alveolar lavage of a hospitalized patient with pneumonia and Chryseobacteriumin dologenes, isolated from a patient cysticfibrosis. In this analysis, we can show that environment albacteria suchas S.algae can be a reservoir of antibiotic resistance genes. The exhaustive analysis of these bacteria showed their ability to a dapttotheirecosystemsincludingtheacquisitionofnewgeneticelementsbylateralgenetransfer. The detection of genes in volved in the synthesis of nonribosomal peptide synthetase and polyketide synthases may have a role in their ability to survive in hostile environments suchas therespiratorytractofCFpatients or their presence inpatients having suffered multipleofantibiotic. 3:In this work,through theuse of the NTS onnew bacterial species isolated from human microbiome,we have a chieveda standardized analysis"insilico"to determine there sistome of these bacteria and the presence of secondary metabolites associated bacteriocins and the NRPS/PKS. The application of the NTS for sequenc in go bacterial genome of new bacterial species isolated in the human microbiome, allowe dus to develop a platform capable of analyzing the senew species within 48

Les infections associées aux soins représentent un enjeu majeur de santé publique dans le monde. Les bactéries multirésistantes (BMR) sont responsables d’une grande partie de ces infections. Mieux comprendre leur dissémination dans les établissements de soins est indispensable pour élaborer des mesures de contrôle et de prévention.L’objectif de cette thèse est d’utiliser des données détaillées sur les réseaux de contacts interindividuels, couplées à des méthodes de modélisation mathématique, pour étudier la dissémination des BMR à l’hôpital afin d’améliorer leur contrôle. Pour répondre à cette problématique, les données de l’étude i-Bird ont été analysées. Cette étude prospective longitudinale a eu lieu dans l’hôpital maritime de Berck-sur-Mer durant 4 mois en 2009. Pendant cette période, les interactions de proximités entre tous les individus de l’hôpital ont été enregistrées chaque jour grâce à des capteurs RFID (Radio Frequency Identification Devices) et des prélèvements microbiologiques ont été récoltés chaque semaineDans un premier temps, la structure des contacts interindividuels au sein de et entre les différentes catégories d’individus (patient, aide-soignant, infirmier, …) a été analysée. Cette première étude a souligné l’importance des contacts patient-patient en établissement de longue durée. De plus, certaines catégories de personnel hospitalier ont été identifiées comme de potentiels super-propagateurs, tel que les brancardiers et les médecins.Dans un deuxième temps, le rôle du réseau de contacts dans la dissémination de deux espèces (E. coli et K. pneumoniae) d’entérobactéries résistantes aux béta-lactamines à spectre étendue (BLSE) a été étudié. Cette étude a montré que le réseau d’interactions de proximités était suffisant pour expliquer la propagation des KP-BLSE. En revanche, il n’était pas suffisant pour retracer la dissémination des EC-BLSE.La dernière partie de la thèse a été consacrée au développement d’un modèle individu-centré de transmission de BMR à l’hôpital modélisant explicitement les contacts interindividuels. Ce modèle permet d’évaluer l’effet de mesures de contrôle ciblant la structure du réseau de contacts. A titre d’application, les données de l’étude i-Bird ont été utilisées pour simuler la transmission de Staphylococcus aureus résistant à la méticilline (SARM) durant les 4 mois de l’étude. La simulation de procédures de cohorting du personnel dans l’hôpital de Berck-sur-Mer suggère que la mise en place de telles mesures permet de réduire l’acquisition de SARM chez les patients.Cette thèse combine analyse de réseaux, épidémiologie des maladies infectieuses et modélisation dynamique. Elle apporte une meilleure compréhension de la diffusion et du contrôle des BMR dans les hôpitaux de longue durée. De plus, elle apporte un outil innovant, visant à être développé, pour la compréhension et le contrôle de la dissémination des BMR à travers les contacts en milieu hospitalier. / Healthcare-associated infections represent a huge public health issue worldwide. Multidrug resistant bacteria (MDR) are a major cause of these infections. Hence, better understanding their transmission routes in hospital settings is crucial to design efficient control measures.The purpose of this thesis is to use detailed data on interindividual contact networks, associated with mathematical modelling methods, to study MDR spread in hospitals and improve their control. To this end, data collected during the i-Bird study was used. This longitudinal prospective study took place at the Berck-sur-Mer hospital during 4 months in 2009. Close proximity interactions were recorded by the use of RFID (Radio Frequency Identification Devices) sensors everyday. Meanwhile, microbiological swabs were collected weekly.In a first part, interindividual contact patterns within and between each individual categories (patients, nurses, hospital porters, etc.) were analyzed. This first study notably underlined the importance of patient-to-patient contacts in long-term care facilities (LTCF). Moreover, some hospital staff categories, such as hospital porters and physicians, were identified as potential superspreaders based on their contact patterns.In a second part, we investigated the impact of the contact network on the spread of two species of Extended-spectrum beta-lactamases (ESBL) Enterobacteriaceae (E. coli and K. pneumoniae). This work showed that the contact network was an important driver of ESBL-K. pneumoniae dynamics, but not of ESBL-E. coli dynamics over the i-Bird study.The last part of the thesis was dedicated to the development of an agent-based model of MDR spread in hospital settings that explicitly formalizes detailed interindividual contacts. This model allows to assess control measures focused on contact patterns. The model was applied to the i-Bird data; we simulated methicillin-resistant Staphylococcus aureus (MRSA) transmission during the 4-month study over the reported contact network. Using our simations, we evaluated measures associated with hospital staff cohorting and showed it can lead to reduce the MRSA acquisition=.This thesis combines network analysis, epidemiology of infectious diseases and dynamic modeling. It allows a better understanding of MDR spread and control in LTCF. Moreover, it brings an innovative tool, intended to be developed, to understand and control BMR spread through contact networks in hospital settings.

Bakgrund: Sjukdom kan innebära en påverkan på något mer än det fysiska, sjukdom kan även innebära något annat än ohälsa. Sjuksköterskans kunskap samt relationen mellan sjuksköterska och patient är en viktigdel i skapandet av trygghet i hälsoprocesserna. För somligakan sjukdom ha en positiv effekt på hälsan. Penicillinet kom med stora möjligheter att behandla infektioner, men snabbt började bakterier utveckla resistens. Idag är de vanligaste, anmälningspliktiga multiresistenta bakterierna i Sverige MRSA, ESBL och VRE. Det innebär förhållningsregler för patienter och gör att hälso-och sjukvården behöver genomföra smittskyddsåtgärder för att minska spridning. Sjuksköterskan kan känna osäkerhet och rädsla i omvårdnaden av dessa patienter vilket kan ha en inverkan på den jämlika vård som enligt lagen ska ges. Syfte: Syftet var att belysa patienters upplevelser av att leva med multiresistenta bakterier (MRSA, ESBL eller VRE). Metod: En litteraturöversikt där informationssökning har gjorts i PubMed, CINAHL och SwePub. Artiklar inkluderades om de svarade på syftet, var orginalartiklar, publicerade mellan 2010-2020, skrivna på engelska, hade kvalitativ eller mixad metod, var granskade av referenter och hade ett etiskt godkännande. Den insamlade datan analyserades av författarna och sammanställdes i tre teman och tillhörande underteman. Resultat: Tre teman vilka rubricerades som känslomässig påverkan, upplevelser i mötet med hälso-och sjukvård och förändringar i relationen till andra. Diskussion: Litteraturöversiktens resultat diskuteras gentemot Livsvärldsteorin, bakgrunden, andra referenser och författarnas egna tankar. / Background: Disease can have impact on something more than the physical, disease can be something else than illness. The nurse’s knowledge and the relationship between nurse and patient is an importantpart in creating safety in the health processes. For some, disease can have a positive effecton the health. The penicillin came with great possibilities in treating infections, but the bacteria quickly began to develop resistance. Today, the most common notifiable multidrug-resistant bacteria in Sweden are MRSA, ESBL and VRE. It induces instructions for patients and the health care has to conduct disease control to reduce spread. The nurse can feel uncertainty and fear in the caring of these patients, which can have an impact on the equal care which is to be given according to the law. Aim: The aim was to illustrate patients’ experiences of living with multidrug-resistant bacteria (MRSA, ESBL or VRE). Method: A literature review where the information search has been conducted in PubMed, CINAHL and SwePub. Articles were included if they answered to the aim, was original articles, published between 2010-2020, written in English, had qualitative or mixed method, were peer-reviewed and had an ethical approval. The collected data were analysed by the authors and compiled in to three themes and belonging sub-themes. Results: Three themes who were labelled emotional impact, experiences in the encounter with health care and change in the relationship with others. Discussion: The result of the literaturereview was discussed towards Life World Theory, the background, other references and the authors’ own thoughts.

The continuous emergence of drug-resistance pathogens is a global concern. As a result, substantial effort is being expended to develop new therapeutics and mechanisms for controlling microbial growth to avoid entering a "post-antibiotic" era in which commonly used antibiotics are no longer effective in treating infections. In this work, we investigate the efficacy and application of ceragenins as non-peptide mimics of antimicrobial peptides (AMPs). First, this work examines the susceptibility of drug-resistant Gram-negative bacteria. The susceptibility of colistin-resistant clinical isolates of Klebsiella pneumoniae to ceragenins and AMPs suggests that there is little to no cross-resistance between colistin and ceragenins/AMPs. Furthermore, Lipid A modifications are found in bacteria with modest changes in susceptibility to ceragenins and with high levels of resistance to colistin. Next, we investigated the potential for cross resistance between chlorhexidine, colistin, AMPs and ceragenins as repeated exposure of bacteria to chlorhexidine might result in cross resistance with colistin, AMPs or ceragenins. Furthermore, a proteomics study on the chlorhexidine-resistant strains showed that chlorhexidine resistance is associated with upregulation of proteins involved in the assembly of LPS for outer membrane biogenesis and virulence factors in Pseudomonas aeruginosa.Second, this dissertation describes the antifungal activity of ceragenins against an emerging multidrug-resistant fungus, Candida auris. We found that lead ceragenins displayed activities comparable to known antifungal agents against C. auris isolates. We also found that fungal cell morphology was altered in response to ceragenin treatment, that ceragenins exhibited activity against sessile organisms in biofilms, and that gel and cream formulations including CSA-44 and CSA-131 resulted in a significant log reduction against established fungal infections in ex vivo mucosal tissues. Finally, a hydrogel film containing CSA-131 was generated on endotracheal tubes (ETTs). ETTs provide an abiotic surface on which bacteria and fungi form biofilms that cause serious infections. In this study, the eluting ceragenin prevented fungal and bacterial colonization of coated ETTs for extended periods while uncoated tubes were colonized by bacteria and fungi. Coated tubes were well tolerated in intubated pigs. The ability of ceragenins to eradicate established biofilms make them attractive potential therapeutics for persistent infections in the lung, including those associated with cystic fibrosis. In ex vivo studies, we initially found that this ceragenin, at concentrations necessary to eradicate established biofilms, also causes loss of cilia function. However, by formulating CSA-131 in poloxamer micelles, cilia damage was eliminated and antimicrobial activity was unaffected. These findings suggest that CSA-131, formulated in micelles, may act as a potential therapeutic for polymicrobial and biofilm-related infections in the lung and trachea.

No description available.

Rising global antibiotic resistance has caused concerns over sources and pathways for the spread of contributing factors. Majority of the antimicrobials used in the U.S. are involved in veterinary medicine, primarily with livestock rearing. Animal manure land application integrates livestock farming and agroecosystems. This manure contains antibiotic resistant elements (AREs) (resistant bacteria, resistance genes, and veterinary antibiotics) that contribute towards antimicrobial resistance. Altering manure application techniques can reduce surface runoff of other contaminants such as excess N and P, pesticides, and hormones, that can impact water quality. Conventional tillage practices in the U.S. has reduced or stopped, making subsurface injection of manure a promising option when compared to surface application. Our research compared manure application methods, manure application seasons, cropping system, and manure-rainfall time gaps to gauge the impact on AREs in the environment. Two field-scale rainfall simulation studies were conducted along with one laboratory study. Using the injection method lowered concentrations of manure associated AREs entering surface runoff. When manure was surface applied and rainfall occurred 7 d after application, 9-30 times less resistant fecal coliform bacteria (FCB) entered surface runoff when compared to 1 d time gap for that broadcast method. Within a day of manure application, antibiotic resistance gene (ARG) profiles in soil began to differ from each other based on manure application and soil ARG richness in all manure-amended soil increased compared to the background. Runoff from injection plots contained 52 ARGs with higher abundance compared to runoff from surface applied plots. ARGs in the former were more correlated to soil and more correlated to manure in the latter. The highest antibiotic concentrations were in the injection slit soil of those plots. Antibiotic concentrations in samples corresponded positively to concentrations of resistant FCB and ARGs, and there was a positive correlation between resistant FCB and their associated ARGs (Spearman's ρ = 0.43-0.63). A CRIISPR-Cas12a assay for quantification of ARGs in environmental samples was just as precise as conventional methods. There is also potential for in-situ detection. These combined results can hopefully help farmers improve manure management practices that mitigate spread of AREs to surrounding water, crops, and soil. / Doctor of Philosophy / Rising global antibiotic resistance cause concerns over sources and pathways for the spread of contributing factors. Most of the antimicrobials used in the U.S. are involved in veterinary medicine, especially with livestock rearing. Overuse of antibiotics that are medically important to human medicine compromises the effectiveness of our medicines. Animal manure contains antibiotic resistant elements (AREs) such as resistant bacteria, resistance genes, and antibiotics) that contribute towards resistance issues. Once these AREs enter the environment, they can be taken up by crops, runoff into surface water or leached into ground water, or even reside within the animal products we consume. Altering manure application techniques is beneficial for nutrient conservation but also potentially for reducing ARE spread. With our research, we compared manure application methods, manure application seasons, cropping systems, and manure-rainfall time gaps to find ways to balance the need for manure application and the spread of resistance. We used two field-scale rainfall simulation studies along with one laboratory study. Overall, using the injection method resulted in significantly lower concentrations of manure associated AREs entering surface runoff. When manure was surface applied and rainfall occurred 7 d after application, less resistant fecal coliform bacteria (FCB) entered surface runoff when compared to the 1 d time gap for broadcast methods. Within a day of manure application, antibiotic resistance gene (ARG) profiles in soil began to differ from each other and soil ARG totals in all manure applied soil increased compared to the background. Runoff from injection plots contained more soil ARGs and runoff from surface applied plots containing more manure associated ARGs. The subsurface injection method also caused highest antibiotic concentrations in the injection slit soil of those plots. High antibiotic concentrations in samples generally meant high concentrations of resistant FCB and ARGs, and resistant FCB were also found with their associated ARGs as well. A CRISPR-Cas12a assay for quantification of ARGs in environmental samples was just as precise as conventional methods. There is also potential for onsite detection. These combined results can hopefully help farmers improve manure management practices that mitigate spread of AREs to surrounding water, crops, and soil.

Widespread use of antibiotics in livestock production can result in the dissemination of bacteria carrying antibiotic resistance genes (ARGs) to the broader environment. Within agroecosystems, ARGs can pose a risk to livestock handlers, farmers, and ultimately consumers. The overall goals of this dissertation are to examine the presence of resistance (antibiotic, metal) in agricultural soils and evaluate the most critical potential points of best management control of antibiotic resistance spread along the agricultural production chain. The relative impacts of agricultural practices, manure management, native soil microbiota, and type of crop grown and harvested on the agricultural resistome are multi-dimensional and cannot be captured via a single analytical technique or by focusing on one specific point in the agricultural process. Culture-, molecular "indicator"-, and next-generation sequencing- based methods were employed to characterize antibiotic resistance via taxonomic and functional profiles on the broader manure, soil, and vegetable surface microbial communities through 16S rRNA amplicon sequencing and shotgun metagenomics. Although antibiotic concentrations dissipated in the soil after 28 days after amendment application, antibiotic resistance presence was recoverable throughout the entire 120d growing season in the compost and manure amendments, the amended soil, and on vegetable surfaces. The addition of organic fertilizers increased antibiotic resistance presence compared to background levels. Further, metals and metal resistance were also measured in the amended soils and were found to be at greater levels in the inorganically fertilized soils compared to the manures and compost amended soils. Analysis of the widespread agroecosystem microbial community composition and broader metagenome has characterized varying genera profiles in the soil and on the vegetable surfaces and specific ARG and mobile genetic element (plasmid) co-occurrences. These co-occurrences highlight which ARGs may be most critical for future antibiotic resistance dissemination research. It is imperative to employ multiple methods when measuring agricultural resistance, as one method alone may miss significant patterns and lead to different best management recommendations. Linking the livestock manure, soil, and vegetable surface-associated ARBs, ARGs, resistomes, and microbiomes will help identify critical control points for mitigation of agricultural dissemination of antibiotic resistance to the environment and food production. / Doctor of Philosophy / By 2050, it is estimated that antibiotic resistant infections will be the leading cause of death worldwide. It is important to consider human, animal, and environmental health when researching antibiotic resistance, which is known as a "One Health" approach. In this dissertation work, I focus on the environmental side of antibiotic resistance in our agricultural systems. Agriculture is a known source of antibiotic resistance due to its use of antibiotics in livestock as a treatment for illness, and in some instances, as a growth promoter. Over one growing season, I measured antibiotic resistance in an agricultural setting using many techniques. First, I analyzed the effects of inorganic (chemical) versus organic (manure and compost) fertilization on antibiotic resistance in the soil. I measured antibiotic resistance by growing antibiotic resistant bacteria, quantifying specific antibiotic resistant genes (ARGs) using DNA amplification, and quantifying all the ARGs in the soil using a next-generation sequencing (NGS) technique called shotgun metagenomics. I found that adding manure to the soil increases ARGs compared to background soil levels, and that composting in an effective management strategy in decreasing ARGs in the soil over time. Second, I analyzed the same effects of fertilization on metal resistance in the soil. I was able to use the same NGS dataset to measure metal resistance genes (MRGs). I found that adding inorganic chemical fertilizer increases MRGs in the agricultural soils compared to the organic (manure or compost) fertilizer. Additionally, I studied the microbes that live in the agricultural soils using another kind of NGS data specific for microbial identification. I found that although there were small differences between the microbial populations in the soil when fertilizers were added, they returned to similar composition over the growing season. Lastly, I measured antibiotic resistance and microbes throughout the entire agricultural system. I picked the point of fertilization (manure management), soil, and the lettuce surface to evaluate if antibiotic resistance spreads from the farm to the vegetable that ends up on a consumer's plate. I found that at each point antibiotic resistance is present, but at different levels. Composting reduces ARGs compared to raw manure. Agricultural soils may act as a natural buffer to antibiotic resistance. Lettuce plants grown in compost fertilized soils have less ARGs than lettuce plants grown in manure. There are many agricultural management practices that effectively reduce antibiotic resistance and using all of them plus many measurement methods will ultimately help farmers and consumers reduce antibiotic resistance in our agricultural systems.

La résistance bactérienne aux antibiotiques dans les établissements de santé complique la prise en charge thérapeutique et entraîne une surmortalité des patients infectés. L'objectif de ce travail était d'évaluer différentes approches ayant pour finalité la prévention et la maîtrise des infections nosocomiales. Ce travail s'articule autour de trois questions : (i) Existe-t-il une stratégie de promotion d'un juste usage des antibiotiques à privilégier ? (ii) Comment évaluer la performance en matière d'hygiène des mains ? (iii) Quelles mesures pouvons-nous proposer pour limiter la diffusion de P. aeruginosa ?Nous avons d'abord montré que la diffusion de recommandations sous la forme de guides régionaux ou de messages de pharmacovigilance était suivie d'une modification des prescriptions antibiotiques conformes aux recommandations.Ensuite, nous avons évalué le niveau de performance des établissements de santé en matière d'hygiène des mains en étudiant plus particulièrement l'indicateur de consommation de solution hydro-alcoolique (ICSHA). Nous avons ainsi pu montrer que le nombre minimal d'opportunité d'hygiène des mains servant à son calcul, était sous-estime. Dans une autre étude, nous avons été confrontés aux limites liées à sa construction, ces dernières étant en partie responsable de l'absence de relation observée entre cet indicateur et la prévalence des infections associées aux dispositifs invasifs.Enfin, nous avons montré que la charge en soins et la contamination des réseaux d'eau propre des établissements de santé étaient des facteurs de risque contextuels d'acquisition du bacille pyocyanique. Un autre travail a mis en évidence que les réseaux d'eau usée étaient impliqués dans la diffusion extra-hospitalière de souches résistantes. Une étude est actuellement en cours pour évaluer l'intérêt d'une approche globale associant dépistage et précautions complémentaires chez les patients porteurs de P. aeruginosa.En conclusion, si ce travail confirme l'efficacité de certaines actions de prévention tout en mettant en avant les limites d'autres approches, il ne permet pas de privilégier une stratégie particulière. Il apparaît ainsi nécessaire de mettre en place des stratégies globales et transversales allant au-delà des seuls établissements de santé / Bacterial resistance to antibiotics in health care facilities complicates the therapeutic burden and increased mortality of infected patients. The objective of this work was to evaluate different approaches which aim was to prevent and control hospital-acquired infections. This work focuses on three issues: (i) Is there a strategy already in place to promote the appropriate use of antibiotics? (ii) How can we evaluate performance in terms of hand hygiene? (iii) What measures can we implement to limit the spread of P. aeruginosa?We first showed that the distributions of regional guidelines or drug monitoring alerts were followed by a change in the uptake of antibiotic prescriptions in line with such recommandations.Then we evaluated the performance of health care facilities for hand hygiene, focusing especially on the index of consumption of alcohol-base hand-rub solution. We showed that the number of alcohol-based hand-rub is far higher than that defined by the French Ministry of Health. In another study, we were faced with limitations in its construction, the latter being partly responsible for the lack of a relationship between this indicator and the prevalence of invasive devices associated with infections.Finally, we have shown that the burden of care and the contamination of clean water networks of health facilities were contextual risk factors for acquisition of Pseudomonas aeruginosa. Another study showed that wastewater networks were involved in extra-hospital spread of resistant strains. A study is currently underway to assess the value of a global approach combining screening and additional precautions in patients with P. aeruginosa.In conclusion, this study confirms the effectiveness of some preventive measures while underlining the limitations of other approaches. However it does not promote a particular strategy. Because in terms of BMR, it is necessary to define global and cross-sectorial strategies which go beyond the health care facilities