Background: MRSA or Methicillin-resistant Staphylococcus aureus consists of several strains in the bacterial species called Staphylococcus aureus. MRSA is resistant to methicillin but also to other types of antibiotics. Spread can occur both directly between humans and between humans and animals, but also indirectly through air. The number of positive bacterial cultures for MRSA in Sweden increases every year. The prevalence of MRSA of different types varies in different countries. LA-MRSA is a livestock-associated methicillin-resistant Staphylococcus aureus that was first discovered in the Netherlands in pigs. This bacterial type belongs to a specific clone called CC398 (clonal complex 398), were most belonged to a specific sequence type called ST398 (multi locus sequence type 398). The CC398 strain are constantly acquiring new features including virulence factors such as the PVL-gene has been reported and associated with serious infections in humans and animals. This specific bacterial clone is found primarily in food producing animals around Europe, and it can infect humans and cause infection. It occurs mainly in pigs and can be spread through contaminated pork or other meat products to humans. Purpose: This work was aimed to survey the prevalence of LA-MRSA in the countries from which Sweden imports most meat from and to review the spread from meat products. Method: This study is been based on information on antibiotic use among food producing animals and the proportion of reported cases of MRSA in the countries from which meat was imported. Scientific studies in all countries was used to obtain information on the prevalence of MRSA CC/ST 398 and on its characteristics. Results: The countries from which Sweden imports most meat are Germany, Denmark and the Netherlands, pork import dominates. In 2018 there were 27,260 tonnes of pork imported from Denmark and 45,197 tonnes from Germany, compared with imports from the Netherlands, which amounted to 6,888 tonnes. Germany has the highest antibiotic consumption and the highest proportion of reported cases of MRSA among these countries. In Denmark, the CC/ST 398-clone caused 17 blood infections and 700 skin and soft tissue infections between 2010 and 2015. In Germany, 166 of 330 pigs examined in 2012 were positive for the same clone, as was 77 of the 134 collected samples from the environment and 39 of the 63 animal caretakers. In Brazil, CC / ST398 was found in 6 of 1852 children, genotypic characterization indicated it was an MSSA (methicillin-sensitive S. aureus) CC398 that had acquired SCCmec genes in the health care system. In Italy 81 of 215 pig isolates collected were positive for MRSA where the dominant type was CC / ST398. Virulence genes associated with human MRSA strains such as enterotoxin and PVL genes were not present among the pig isolates. Resistance to tetracycline was seen in all pig isolates. In the Netherlands, MRSA CC / ST398 was linked to pigs in that sense that the humans that were infected were exposed to pigs on a daily basis. Conclusion: The prevalence of LA-MRSA CC / ST398 was high in all the countries surveyed. Resistance to tetracyclines was significantly higher among pig isolates compared to HA-MRSA isolates (healthcare-associated MRSA), whereas the virulence genes such as the PVL- gene usually not present detected in pig- isolates. Among strains identified as LA-MRSA CC / ST398 acquired SCCmec-genes were of types V and IV.  The spread from pigs or meat was through direct contact but also through air.

Next-generation sequencing technology provides high-resolution data for epidemiological surveillance of bacterial pathogens on local and global scales. This approach has been used for many species including Methicillin Resistant Staphylococcus aureus (MRSA). In this thesis I demonstrate the utility of these data for understanding the spread of the globally disseminated clone MRSA ST239. I focus both on local and national-level epidemiology through sequence data of 71 isolates recovered from four hospitals representing three cities in Turkey; Istanbul (x2). Ankara and Izmir. I analyse whole genome sequence data from a further 33 ST239 isolates from global sources. These data were combined with previously published data for phylogenetic analysis based only on the core genome. I demonstrate how transmission events can be inferred from this approach on multiple levels; within hospital, between hospitals and between countries. The data pointed to a European origin of ST239, and independent introductions from Europe to Turkey, South America and East Asia. I also demonstrate how whole genome sequence data can be used to develop bespoke PCR assays, based on phage variation, for rapid local epidemiology. Finally, I consider how the sequence data might be used to explain variation in virulence potential, and describe the distribution and transfer of an important phage-borne virulence determinant, sasX, within Europe. Finally, I identified a single isolate with very strong biofilm forming ability likely due to the over-expression of the important adhesion SasG.

Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / O Staphylococcus aureus resistente a meticilina (MRSA) foi inicialmente descrito como um patógeno associado a infecções relacionadas à assistência em saúde; porém, um clone de MRSA, o CA-MRSA emergiu na comunidade e está atualmente incrementando nos hospitais. O objetivo desta tese foi descrever aspectos relacionados com a epidemiologia das infecções por cepas CA-MRSA no Hospital Universitário Pedro Ernesto da Universidade do Estado do Rio de Janeiro (HUPE/UERJ), avaliando especificamente fatores de risco relacionado com as infecções por CA-MRSA. Usando informações das bases de dados do laboratório de microbiologia, da farmácia e da Comissão para Controle da Infecção Hospitalar do HUPE/UERJ foi realizado um estudo retrospectivo de infecções/colonizações por cepas de S. aureus (fevereiro 2005 a Julho 2011). Foi realizado um estudo caso e controle, utilizando como casos os pacientes com infecções por cepas CA-MRSA. Na avaliação da susceptibilidade aos antimicrobianos usados em infecções graves por MRSA (vancomicina, teicoplanina, daptomicina e linezolida), foram determinadas as concentrações inibitórias mínimas (CIM) das amostras por diferentes metodologias (testes de difusão em agar, microdiluição em caldo e E-test). Nas analises das tendências temporais da apresentação dos subtipos de MRSA, usando um critério fenotípico para classificação das cepas MRSA, foi observada uma diminuição do número de cepas de MRSA multirresistente (HA-MRSA) (p<0.05). Também foi observada uma tendência ao aumento de cepas não-multirresistentes (CA-MRSA), mas sem alcançar a significância estatística (p = 0.06) igual que os S. aureus sensíveis a meticilina (MSSA) (p = 0.48). Não houve associação entre o subtipo de MRSA e a mortalidade devida à infecção por cepas MRSA. Uma idade acima de 70 anos (OR: 2.46, IC95%: 0.99 - 6.11), a presença de pneumonia adquirida no hospital (OR: 4.94, IC95%: 1.65 -14.8), a doença pulmonar obstrutiva crônica (OR: 6.09, IC95% 1.16 31.98) e a leucemia (OR: 8.2, IC95%: 1.25 54.7) foram fatores de risco associadas à mortalidade nas infecções por cepas de S. aureus. Usando curvas de Kaplan-Meier, foi observada uma tendência ao aumento da mortalidade em infecções causadas por MSSA na primeira semana, porém sem alcançar significância estatística (p = 0.07). Não foram observadas amostras MRSA com susceptibilidade intermediaria a vancomicina, linezolida, daptomicina ou teicoplanina. A dinâmica das infecções por S. aureus no HUPE/UERJ mudou durante o período de estudo, com menor número de episódios infecciosos causados por cepas de MRSA multirresistentes. Existe uma tendência ao aumento das cepas não-multirresistentes de MRSA entanto que a taxa de infecções por MSSA permaneceu estável no período do estudo. O perfil de resistência dos estafilococos não teve associação com a mortalidade / The methicillin-resistant Staphylococcus aureus (MRSA) was described initially like a health-care associated pathogen. However, an MRSA clone called community-adquired S. aureus emerged with success in the community and now has a worring increasing frequency in hospital settings. The aim of this study was to descript issues related to the epidemiology of infections due tu CA-MRSA isolates at the Pedro Ernesto Universitary Hospital (HUPE/UERJ) in Rio de Janeiro, Brazil from february 2005 to june 2011, analyzing risk factors related to these infections. Thus, using databases of the microbiology laboratory, pharmacia department and the infection control committee of the HUPE-UERJ, was realized an restrospective study of S. aureus isolates obtained from infected/colonizated patients hospitalized from February 2005 to July 2011. To evaluate risk factors related to CA-MRSA infections was conduced a case-control study, using patients with true infections due to MRSA like cases and patients with methicillin susceptible S. aureus (MSSA) like controls. To test the antimicrobial susceptibility of the antibiotics used in MRSA severe infections (Vancomycin, teicoplanin, daptomycin and linezolid), were determinated the minimal inhibitory concentration (MIC) of MRSA isolates using differents methods (disk-difusion test, microdilution in broth and E-test strips). The trend analyses of the MRSA types, using a phenotypic criteria to classificate the MRSA isolates, found a decrease in the infections due to multi-resistant MRSA isolates (HA-MRSA) in our hospital (p<0.05). Also was observed and increase in non-multi-resistant MRSA strains (CA-MRSA), but without reach statistic significancy (p = 0.06), similar to MSSA (p = 0.48). There is not association between the MRSA phenotype and the mortality due to S. aureus infection. In the multivariate analysis, were observed that an older age than 70 years (OR: 2.46, IC95%: 0.99 - 6.11), health-care pneumonia (OR: 4.94, IC95%: 1.65 -14.8), chronic obstructive pulmonary disease (OR: 6.09, IC95% 1.16 31.98) and leucaemia (OR: 8.2, IC95%: 1.25 54.7) were risk factors associated with mortality due to S. aureus infections. The Kaplan-Meier analysis, found a trend to high mortality due to MSSA infections in the first week, but without get statistic significancy (p = 0.07). We dont found any MRSA isolated with resistance or intermediary resistance to vancomycin, linezolid, daptomycin or teicoplanin. There is good correlation between both MICs determinations, with broth microdiluiton and E-Test strips metodhology. Its were concluded that the dynamic of the S. aureus infections at the HUPE/UERJ is changing, with less number of infectious episodes due to multi-resistant MRSA isolates. Moreover, there are an increasing number of infections due to non-multi-resistant MRSA isolate. The prevalence of infections due to MSSA dont have change in the time of period study. The kind of the S. aureus phenotype dont has association with all-causes-mortality

Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / O Staphylococcus aureus resistente a meticilina (MRSA) foi inicialmente descrito como um patógeno associado a infecções relacionadas à assistência em saúde; porém, um clone de MRSA, o CA-MRSA emergiu na comunidade e está atualmente incrementando nos hospitais. O objetivo desta tese foi descrever aspectos relacionados com a epidemiologia das infecções por cepas CA-MRSA no Hospital Universitário Pedro Ernesto da Universidade do Estado do Rio de Janeiro (HUPE/UERJ), avaliando especificamente fatores de risco relacionado com as infecções por CA-MRSA. Usando informações das bases de dados do laboratório de microbiologia, da farmácia e da Comissão para Controle da Infecção Hospitalar do HUPE/UERJ foi realizado um estudo retrospectivo de infecções/colonizações por cepas de S. aureus (fevereiro 2005 a Julho 2011). Foi realizado um estudo caso e controle, utilizando como casos os pacientes com infecções por cepas CA-MRSA. Na avaliação da susceptibilidade aos antimicrobianos usados em infecções graves por MRSA (vancomicina, teicoplanina, daptomicina e linezolida), foram determinadas as concentrações inibitórias mínimas (CIM) das amostras por diferentes metodologias (testes de difusão em agar, microdiluição em caldo e E-test). Nas analises das tendências temporais da apresentação dos subtipos de MRSA, usando um critério fenotípico para classificação das cepas MRSA, foi observada uma diminuição do número de cepas de MRSA multirresistente (HA-MRSA) (p<0.05). Também foi observada uma tendência ao aumento de cepas não-multirresistentes (CA-MRSA), mas sem alcançar a significância estatística (p = 0.06) igual que os S. aureus sensíveis a meticilina (MSSA) (p = 0.48). Não houve associação entre o subtipo de MRSA e a mortalidade devida à infecção por cepas MRSA. Uma idade acima de 70 anos (OR: 2.46, IC95%: 0.99 - 6.11), a presença de pneumonia adquirida no hospital (OR: 4.94, IC95%: 1.65 -14.8), a doença pulmonar obstrutiva crônica (OR: 6.09, IC95% 1.16 31.98) e a leucemia (OR: 8.2, IC95%: 1.25 54.7) foram fatores de risco associadas à mortalidade nas infecções por cepas de S. aureus. Usando curvas de Kaplan-Meier, foi observada uma tendência ao aumento da mortalidade em infecções causadas por MSSA na primeira semana, porém sem alcançar significância estatística (p = 0.07). Não foram observadas amostras MRSA com susceptibilidade intermediaria a vancomicina, linezolida, daptomicina ou teicoplanina. A dinâmica das infecções por S. aureus no HUPE/UERJ mudou durante o período de estudo, com menor número de episódios infecciosos causados por cepas de MRSA multirresistentes. Existe uma tendência ao aumento das cepas não-multirresistentes de MRSA entanto que a taxa de infecções por MSSA permaneceu estável no período do estudo. O perfil de resistência dos estafilococos não teve associação com a mortalidade / The methicillin-resistant Staphylococcus aureus (MRSA) was described initially like a health-care associated pathogen. However, an MRSA clone called community-adquired S. aureus emerged with success in the community and now has a worring increasing frequency in hospital settings. The aim of this study was to descript issues related to the epidemiology of infections due tu CA-MRSA isolates at the Pedro Ernesto Universitary Hospital (HUPE/UERJ) in Rio de Janeiro, Brazil from february 2005 to june 2011, analyzing risk factors related to these infections. Thus, using databases of the microbiology laboratory, pharmacia department and the infection control committee of the HUPE-UERJ, was realized an restrospective study of S. aureus isolates obtained from infected/colonizated patients hospitalized from February 2005 to July 2011. To evaluate risk factors related to CA-MRSA infections was conduced a case-control study, using patients with true infections due to MRSA like cases and patients with methicillin susceptible S. aureus (MSSA) like controls. To test the antimicrobial susceptibility of the antibiotics used in MRSA severe infections (Vancomycin, teicoplanin, daptomycin and linezolid), were determinated the minimal inhibitory concentration (MIC) of MRSA isolates using differents methods (disk-difusion test, microdilution in broth and E-test strips). The trend analyses of the MRSA types, using a phenotypic criteria to classificate the MRSA isolates, found a decrease in the infections due to multi-resistant MRSA isolates (HA-MRSA) in our hospital (p<0.05). Also was observed and increase in non-multi-resistant MRSA strains (CA-MRSA), but without reach statistic significancy (p = 0.06), similar to MSSA (p = 0.48). There is not association between the MRSA phenotype and the mortality due to S. aureus infection. In the multivariate analysis, were observed that an older age than 70 years (OR: 2.46, IC95%: 0.99 - 6.11), health-care pneumonia (OR: 4.94, IC95%: 1.65 -14.8), chronic obstructive pulmonary disease (OR: 6.09, IC95% 1.16 31.98) and leucaemia (OR: 8.2, IC95%: 1.25 54.7) were risk factors associated with mortality due to S. aureus infections. The Kaplan-Meier analysis, found a trend to high mortality due to MSSA infections in the first week, but without get statistic significancy (p = 0.07). We dont found any MRSA isolated with resistance or intermediary resistance to vancomycin, linezolid, daptomycin or teicoplanin. There is good correlation between both MICs determinations, with broth microdiluiton and E-Test strips metodhology. Its were concluded that the dynamic of the S. aureus infections at the HUPE/UERJ is changing, with less number of infectious episodes due to multi-resistant MRSA isolates. Moreover, there are an increasing number of infections due to non-multi-resistant MRSA isolate. The prevalence of infections due to MSSA dont have change in the time of period study. The kind of the S. aureus phenotype dont has association with all-causes-mortality