Dentre as espécies do gênero Yersinia, Yersinia enterocolitica é a espécie mais prevalente como causa de doença em humanos e animais. Y. enterocolitica é dividida em seis biotipos. Os biotipos 1B, 2, 3, 4 e 5 compreendem linhagens associadas à doença em humanos e animais, enquanto o biotipo 1A consiste de linhagens consideradas não patogênicas. Apesar de Y. enterocolitica biotipo 2 ser de importância clínica, há uma escassez de estudos no país, o que dificulta avaliar o envolvimento dessa bactéria como causa de doença em humanos e em animais, bem como, determinar o impacto de sua presença no meio-ambiente. O objetivo deste trabalho foi investigar o potencial patogênico, determinar o perfil de suscetibilidade a antimicrobianos e verificar a diversidade genotípica de linhagens de Y. enterocolitica biotipo 2 isoladas no Brasil. Foram estudadas 40 linhagens de Y. enterocolitica biotipo 2, isoladas de humanos (5), ambiente (34) e animal (1), entre os anos de 1979 e 1998. Ademais, nas análises filogenéticas, foram acrescidas 26 linhagens de Y. enterocolitica pertencentes aos outros biotipos, com o intuito de comparar as linhagens de Y. enterocolitica biotipo 2 aos biotipos 1A, 1B, 3, 4 e 5. As linhagens de humanos e animal foram sensíveis a todos os 14 antimicrobianos testados. Dentre as 34 linhagens de ambiente, sete (20,6%) foram resistentes a um ou dois antimicrobianos, sendo esses, amicacina, cefoxitina, gentamicina, e sulfametoxazol - trimetoprima. Todas as linhagens apresentaram os genes inv, ail, ystA, hreP, tccC e myfA. Os genes fepD e fes foram detectados em 39 (97,5%) linhagens, o gene virF foi encontrado em três (7,5%) linhagens, os genes ystB e fepA não foram detectados em nenhuma linhagem. Todas as linhagens apresentaram comportamento relacionado à virulência frente aos testes fenotípicos de atividade da pirazinamidase, hidrólise da esculina e fermentação da salicina. O dendrograma de similaridade genética de Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) agrupou as linhagens de Y. enterocolitica biotipo 2 em cinco grupos denominados A, B, C, D e E. Todas as linhagens, com exceção de duas, apresentaram similaridade genética superior a 88,3%. O dendrograma de similaridade genética de Pulsed field gel electrophoresis (PFGE) agrupou as linhagens de Y. enterocolitica biotipo 2 em três grupos denominados I, J e K. A maioria das linhagens (72,5%) apresentou similaridade ii genética superior a 78,3%. O dendrograma de similaridade genética de Multilocus variable number tandem repeat analysis (MLVA) agrupou as linhagens de Y. enterocolitica biotipo 2 em dois grupos denominados O e P com similaridade genética superior a 37,7%. Pode-se concluir que o potencial patogênico das linhagens de Y. enterocolitica biotipo 2 foi evidenciado pela prevalência da maioria dos marcadores de virulência, bem como, pelo comportamento relacionado à virulência frente aos testes fenotípicos pesquisados. Algumas linhagens apresentaram-se resistentes a antimicrobianos de primeira escolha no tratamento de yersiniose, o que pode acarretar em falha terapêutica. Os resultados de ERIC-PCR e PFGE mostraram a alta similaridade entre as linhagens de Y. enterocolitica biotipo 2, sugerindo que as mesmas pouco se diferenciaram ao longo dos 19 anos e que possivelmente o meio ambiente tem sido uma fonte de contaminação para humanos e animais no Brasil. A técnica de MLVA agrupou as linhagens de Y. enterocolitica biotipo 2 quanto à sua origem e a técnica de ERIC-PCR agrupou as linhagens de Y. enterocolitica biotipos 1A, 1B, 2, 3, 4, e 5 quanto às diferentes patogenicidades características de cada biotipo. / Among the species of the genus Yersinia, Yersinia enterocolitica is the most prevalent species that cause illness in humans and animals. Y. enterocolitica is divided into six biotypes. Biotypes 1B, 2, 3, 4 e 5 comprise strains associated to illness in humans and animals, while biotype 1A comprise strains considered nonpathogenic. Despite of the fact that Y. enterocolitica biotype 2 is of clinical importance, there is a paucity of studies in this country, which makes difficult to assess the involvement of this bacteria as a cause of illness in humans and animals, as well as to determine the impact of its presence in the environment. The aim of this work was to investigate the pathogenic potential, to determine the antimicrobial resistance profile and to verify the genetic diversity of Y. enterocolitica biotype 2 strains isolated in Brazil. Forty strains of Y. enterocolitica biotype 2 isolated from humans (5), environment (34) and animal (1), between 1979 and 1998 were studied. Besides, in the phylogenetic analyzes it was added 26 Y. enterocolitica strains belonging to the other biotypes, in order to compare the Y. enterocolitica biotype 2 strains to biotypes 1A, 1B, 3, 4 e 5. Humans and animals strains showed susceptibility to all 14 antibiotics tested. Among the 34 environment strains, seven (20.6%) were resistant to one or two antibiotics used such as amikacin, cefoxitin, gentamicin and sulfamethoxazole-trimethoprim. All the strains presented the genes inv, ail, ystA, hreP, tccC and myfA. Genes fepD and fes were detected in 39 (97.5%) strains, virF was found in three (7.5%) strains, and ystB and fepA were not detected in any strains. All the strains exhibited behavior related to virulence against the phenotypic tests of pyrazinamidase activity, esculin hydrolysis and salicin fermentation. The dendrogram of genetic similarity of Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) grouped the Y. enterocolitica biotype 2 strains in five groups, designated A, B, C, D and E. All the strains, except two, showed a genetic similarity of more than 88.3%. The dendrogram of genetic similarity of Pulsed field gel electrophoresis (PFGE) grouped the Y. enterocolitica biotype 2 strains in three groups, designated I, J and K. The majority of the strains (72.5%) showed a genetic similarity of more than 78.3%. The dendrogram of genetic similarity of Multilocus variable number tandem repeat analysis (MLVA) grouped the Y. enterocolitica iv biotype 2 strains in two groups, designated O and P with a genetic similarity of more than 37.7%. It is possible to conclude that the pathogenic potential of the Y. enterocolitica biotype 2 strains was highlighted by the prevalence of the majority of the virulence markers searched, as well as by the behavior related to virulence against the phenotypic tests. Some strains were resistant to antimicrobials that are the first choice for yersiniosis treatment, which can result in therapeutic failure. The results of ERIC-PCR and PFGE showed a high genetic similarity between the Y. enterocolitica biotype 2 strains, suggesting that the strains differed little over 19 years, and that the environment has been possibly a source of humans and animals infections in Brazil. The MLVA technique grouped the Y. enterocolitica biotype 2 strains according their origins, and the ERIC-PCR technique grouped the Y. enterocolitica biotypes 1A, 1B, 2, 3, 4 and 5 strains according to the different pathogenicity characteristics of each biotype.

Black rot caused by Xanthomonas campestris pv. campestris (X. c pv. campestris) is a major disease constraint to cabbage production. The control of black rot is difficult and resistant cultivars could play an important role in reducing the losses due to the disease. Information on the distribution and diversity of X. c pv. campestris is critical before any meaningful disease resistance screening can be done. However, little is known about the diversity and international significance of South African X. c pv. campestris strains. To assess the genetic diversity and international significance of X. c pv. campestris strains in South Africa, strains of the pathogen were obtained from cabbage growing districts in Gauteng, Mpumalanga and North West Provinces of South Africa in 2010. International strains were obtained from international culture collections. Isolates from South Africa were purified and race typed using differential sets of Brassica spp according to Nickerson–Zwaan protocols. Four races, race 1(14%), race 3 (7%), race 4 (68%) and race 6 (10%) of the pathogen were identified. Repetitive DNA polymerase chain reaction–based fingerprinting using Eric– and Box–primers were used to assess the genetic diversity. Polyacrylamide gel electrophoresis allowed clear and reproducible differentiation of the PCR products. Of the amplified loci for South African isolates 5 loci were present in at least 90 % of the isolates for Eric–profiles and 6 in at least 80% of the isolates for Box–profiles. Of these prominent loci, none had corresponding high presence in international isolates. While no loci had a presence greater than 51% and 61% for Eric– and Box– profiles in international isolates, respectively, several loci among South African isolates were unique to isolates from specific geographic origin. Generated fingerprints of X. c pv. campestris were similar for the South African isolates and distinguishable from those of X. c pv. armoraciae and X. c pv. raphani reference strains. However, when international X. c pv. campestris were considered, no profile pattern was observed to be unique to international X. c pv. campestris isolates as was the case with South African isolates. Eric– and Box–PCR profiles of international isolates varied widely with some isolates having profile patterns similar to those of reference strains. Cluster analysis divided X. c pv. campestris into two major groups, the South African group and the international isolates group. The South African group could be divided into subgroups, which clustered according to the geographical origin of the isolates. The same was observed for international isolates, which generally clustered isolates according to country of origin. However, isolates from different countries also clustered together. A few X. c pv. campestris strains of international origin clustered with the South African isolates group. Furthermore, a few South African isolates were clustered in the international isolate group. Although X. c pv. campestris distribution may be unique to its geographical origin, our findings, based on the present data set, suggest wide spread of the pathogen both at national and international level. The existence of different races, genetic variability and international distribution of the pathogen should be considered when resistant crucifer cultivars are bred to control black rot of crucifers / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2011.

Black rot caused by Xanthomonas campestris pv. campestris (X. c pv. campestris) is a major disease constraint to cabbage production. The control of black rot is difficult and resistant cultivars could play an important role in reducing the losses due to the disease. Information on the distribution and diversity of X. c pv. campestris is critical before any meaningful disease resistance screening can be done. However, little is known about the diversity and international significance of South African X. c pv. campestris strains. To assess the genetic diversity and international significance of X. c pv. campestris strains in South Africa, strains of the pathogen were obtained from cabbage growing districts in Gauteng, Mpumalanga and North West Provinces of South Africa in 2010. International strains were obtained from international culture collections. Isolates from South Africa were purified and race typed using differential sets of Brassica spp according to Nickerson–Zwaan protocols. Four races, race 1(14%), race 3 (7%), race 4 (68%) and race 6 (10%) of the pathogen were identified. Repetitive DNA polymerase chain reaction–based fingerprinting using Eric– and Box–primers were used to assess the genetic diversity. Polyacrylamide gel electrophoresis allowed clear and reproducible differentiation of the PCR products. Of the amplified loci for South African isolates 5 loci were present in at least 90 % of the isolates for Eric–profiles and 6 in at least 80% of the isolates for Box–profiles. Of these prominent loci, none had corresponding high presence in international isolates. While no loci had a presence greater than 51% and 61% for Eric– and Box– profiles in international isolates, respectively, several loci among South African isolates were unique to isolates from specific geographic origin. Generated fingerprints of X. c pv. campestris were similar for the South African isolates and distinguishable from those of X. c pv. armoraciae and X. c pv. raphani reference strains. However, when international X. c pv. campestris were considered, no profile pattern was observed to be unique to international X. c pv. campestris isolates as was the case with South African isolates. Eric– and Box–PCR profiles of international isolates varied widely with some isolates having profile patterns similar to those of reference strains. Cluster analysis divided X. c pv. campestris into two major groups, the South African group and the international isolates group. The South African group could be divided into subgroups, which clustered according to the geographical origin of the isolates. The same was observed for international isolates, which generally clustered isolates according to country of origin. However, isolates from different countries also clustered together. A few X. c pv. campestris strains of international origin clustered with the South African isolates group. Furthermore, a few South African isolates were clustered in the international isolate group. Although X. c pv. campestris distribution may be unique to its geographical origin, our findings, based on the present data set, suggest wide spread of the pathogen both at national and international level. The existence of different races, genetic variability and international distribution of the pathogen should be considered when resistant crucifer cultivars are bred to control black rot of crucifers / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2011.

Made available in DSpace on 2014-06-11T19:32:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-02-26Bitstream added on 2014-06-13T20:24:18Z : No. of bitstreams: 1 oliveira_ac_dr_jabo.pdf: 650394 bytes, checksum: 3022a3790349efbed366f6fa0374267e (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Foram estudadas 180 amostras de água de 45 consultórios odontológicos da cidade de Barretos-SP, com o objetivo de isolar, identificar, determinar a contagem de isolados de Pseudomonas aeruginosa UFC/mL, determinar o perfil clonal e avaliar a diversidade genômica dos isolados e a suscetibilidade das mesmas frente a diferentes antibióticos. As amostras de água foram filtradas em filtro Millipore® e a membrana colocada sobre o centro de uma placa de Petri contendo agar cetrimida, As colônias típicas de bactérias do gênero Pseudomonas foram identificadas pelo método de Gram, inoculação em TSI agar (Triple Sugar Iron), crescimento a 42ºC, produção de pigmento, produção de alginato, oxidase, motilidade e alcalinização da acetamida. O teste utilizado para análise genômica foi o ERIC-PCR. Dos 76 (42,2%) isolados de Pseudomonas aeruginosa, 15 eram provenientes das amostras de torneira de lavagem das mãos, 18 de reservatório de garrafa pet, 23 de seringa tríplice e 20 do motor de alta rotação. Todos os isolados de Pseudomonas aeruginosa foram submetidos ao teste de suscetibilidade segundo a técnica de Kirby- Bauer. Dos antibióticos testados o que apresentou melhor resultado quanto à sensibilidade (65,8%) foi a ciprofloxacina. Quanto à similaridade genética dos isolados dos diferentes pontos analisados, foram encontrados nove “clusters” de 100% de similaridade. / The biofilm found in water supplies and lines of hospitals and dental units is extremely important because it presents a large number of bacteria, leading to risk of infection in immunocompromised patients vulnerable to opportunistic pathogens such as the Pseudomonas aeruginosa. One hundred eighty water samples from dental units of the city of Barretos-SP were evaluated. The water samples filtered in Millipore® filter were incubated in plates containing Cetrimide ágar. The bacteria colonies were identified through the gram-staining test, inoculation in agar T.S.I (triple sugar Iron), growth at 42 ° C, pigment production, production of alginate, oxidase acetamide alkalization and motility observation. All Pseudomonas aeruginosa bacteria were submitted to the susceptibility test according to the Kirby-Bauer technique. The test used for genomic analysis was the ERIC-PCR. From the total microorganisms studied, 76 (42,2%) were positive for Pseudomonas aeruginosa, isolates from 180 water samples, where 15 strains were from hand washing incoming local water supplies, 18 from PET bottled water, 23 from 3-in-1 syringes and 20 from the high speed handpiece. In relation to the antibiotics tested, the one presenting the best result with regard to sensibility was ciprofloxacin with 65.8%. The genetic similarity of isolates from different points analyzed, there were nine clusters of 100% similarity.

Salmonella spp. é reconhecida como uma das bactérias que mais causam doenças de origem alimentar no mundo. Dentre as diversas sorovariedades de Salmonella, a Typhimurium é uma das sorovariedades de maior ocorrência no mundo. Várias metodologias de tipagem fenotípicas e genotípicas foram desenvolvidas com o intuito de se delinear a epidemiologia e diversidade genotípica de Salmonella Typhimurium. Entretanto, a tipagem fenotípica é muitas vezes limitada por sua baixa capacidade de diferenciação de subtipos pertencentes a uma mesma sorovariedade de Salmonella, um problema minimizado pelos métodos genotípicos. No Brasil, foram realizados poucos estudos que genotiparam linhagens de S. Typhimurium. Os objetivos deste estudo foram caracterizar linhagens de S. Typhimurium isoladas de humanos, alimentos, animais e ambiente do animal no Brasil quanto ao seu potencial patogênico, perfil de resistência a antimicrobianos e diversidade genotípica. Foram estudadas 119 linhagens de S. Typhimurium, isoladas de material clínico de humanos (43), alimentos diversos (49), material clínico de suínos (22) e do ambiente de suínos (5), entre 1983 e 2013, provenientes de várias Estados do Brasil. A presença de 12 genes de virulência foi pesquisada por PCR. O perfil de resistência a 13 antimicrobianos foi realizado pelo método de discodifusão. A tipagem molecular foi realizada por Pulsed-field gel electrophoresis (PFGE), Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), Multiple-locus variablenumber tandem-repeats analysis (MLVA), Clustered regularly interspaced short palindromic repeats - Multi-virulence locus sequence typing (CRISPR-MVLST), Multilocus sequence typing (MLST) e sequenciamento do genoma completo para 92 linhagens de S. Typhimurium isoladas de humanos (43) e alimentos (46). As metodologias PFGE, ERIC-PCR e MLVA foram realizadas para 70 linhagens de S. Typhimurium isoladas de humanos (43), animais (22) e ambiente do animal (5). Todas as 119 linhagens apresentaram os genes sipA, flgK, flgL e invA. O gene sipD e o gene sopE2 foram encontrados em 118 (99,2%) linhagens. O gene fljB foi encontrado em 117 (98,3%) linhagens. O gene sopD foi presente em 114 (95,8%) linhagens, o gene sopB em 111 (93,3%) linhagens, o gene ssaR em 102 (85,7%) linhagens, o gene sifA em 86 (72,3%) linhagens e 45 (37,8%) linhagens apresentaram o gene plasmidial spvB. De um total de 119 linhagens, 64 (62,2%) linhagens foram resistentes a pelo menos um dos 13 antimicrobianos testados, sendo que 36 (30,3%) linhagens foram multi-droga resistentes (MDR). Na comparação dos isolados de humanos e alimentos, as linhagens isoladas de humanos antes de meados 1990, ficaram alocadas nos grupos PFGE-A, PFGE-B1, PFGE-B2, ERIC-A, ERIC-B, MLVA-A, MLVA-B1, MLVA-B2 e G1, G2, H para CRISPRMVLST. As linhagens isoladas de humanos após esse período ficaram alocadas nos grupos PFGE-B1, ERIC-A, MLVA-B1, MLVA-B2 e G2. As linhagens isoladas de alimentos ficaram alocadas nos grupos PFGE-A, PFGE-B1, ERIC-A, ERIC-B, MLVA-A, MLVA-B1, MLVAB2, G1 e G2. Por MLST, do total de 92 linhagens isoladas de humanos e alimentos, 77 linhagens foram tipadas como ST19. Pelo sequenciamento do genoma completo, as linhagens isoladas de alimentos e humanos ficaram alocadas no grupos I e J independente das datas de isolamento. Na comparação dos isolados de humanos e animais, as linhagens das duas origens ficaram alocadas nos grupos PFGE-D1, PFGE-D2, ERIC-C1, MLVA-C1 e MLVA-D. ii Conclui-se que a grande prevalência de genes de virulência nas linhagens de S. Typhimurium estudadas reforça o potencial das mesmas causarem doenças em humanos, bem como, os riscos de sua presença em alimentos, animais para consumo humano e ambiente. A ocorrência de S. Typhimurium multi-droga resistentes isoladas de alimentos diversos e de suínos para consumo é um alerta para o possível risco de humanos ingerirem alimentos contaminados por tais linhagens. Em conjunto os resultados de PFGE, ERIC-PCR, MLVA, CRISPR-MVLST sugerem que as linhagens de S. Typhimurium isoladas de humanos eram geneticamente mais diversificadas antes de meados de 1990, o que pode sugerir a seleção de um subtipo de S. Typhimurium mais adaptado, depois que Salmonella Enteritidis tornou-se a sorovariedade de maior ocorrência no Brasil após esse período. Com relação às linhagens isoladas de alimentos, os resultados de PFGE, ERIC-PCR, MLVA e CRISPR-MVLST sugerem que durante o período estudado houve a circulação de mais de um subtipo no país. Os resultados de MLST sugerem que tais linhagens tenham uma origem filogenética comum. Os resultados do sequenciamento do genoma completo sugerem que houve a circulação de mais de um subtipo de S. Typhimurium no país, com relação às linhagens de humanos e alimentos. Também alerta para o possível risco de linhagens MDR isoladas de alimentos contaminarem humanos e/ou disseminarem genes de resistência a antibióticos para linhagens de origem clínica e não clínica. Na comparação dos isolados de humanos e animais, os resultados de PFGE, ERICPCR e MLVA sugerem que algumas linhagens isoladas de suínos e humanos podem descender de um subtipo comum. Ademais, as linhagens MDR isoladas de suínos e do ambiente de suínos alertam para o possível risco de porcos usados para consumo contaminarem humanos, o ambiente e outros porcos. / Salmonella spp. is recognized as one of the most involved bacteria that cause food-borne diseases in the world. Among the various serovars of Salmonella, Typhimurium is one of the most frequent serovars worldwide. Several phenotypic and genotypic typing methods have been developed in order to delineate the epidemiology and genotypic diversity of Salmonella Typhimurium. However, phenotypic typing is often limited by its low capacity to differentiate subtypes belonging to the same serovar of Salmonella, a problem minimized by genotypic methods. In Brazil, few studies have been conducted that genotyped S. Typhimurium strains. The aims of this study were to characterize S. Typhimurium strains isolated from humans, food, animals and animal\'s environment in Brazil regarding its pathogenic potential, antimicrobial resistance and genotypic diversity. We studied 119 S. Typhimurium strains isolated from human clinical material (43), different foods (49), clinical material from pigs (22) and pigs environment (5), between 1983 and 2013 from various States of Brazil. The presence of 12 virulence genes was investigated by PCR. The resistance profile against 13 antimicrobial was performed by the disk diffusion method. Molecular typing was performed by Pulsed-field gel electrophoresis (PFGE), Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), Multiple-locus variable-number tandem-repeats analysis (MLVA), Clustered regularly interspaced short palindromic repeats - Multi-virulence locus sequence typing (CRISPR-MVLST), Multilocus sequence typing (MLST) and whole genome sequencing for 92 S. Typhimurium strains isolated from humans (43) and food (46). PFGE, ERIC-PCR and MLVA methods were performed for 70 S. Typhimurium strains isolated from humans (43), animals (22) and the animal\'s environment (5). All 119 strains showed the sipA, flgK, flgL and invA genes. The sipD and sopE2 genes were found in 118 (99.2%) strains. The fljB gene was found in 117 (98.3%) strains. The sopD gene was present in 114 (95.8%) strains, the gene sopB in 111 (93.3%) strains, the ssaR gene in 102 (85.7%) strains, the gene sifA in 86 (72.3%) strains and 45 (37.8%) strains showed the plasmid gene spvB. From a total of 119 strains, 64 (62.2%) strains were resistant to at least one of the 13 antimicrobials tested, and 36 (30.3%) strains were multi-drug resistant (MDR). In the comparison of isolates from humans and food, the strains isolated from humans before mid-1990s were allocated in PFGE-A, PFGE-B1, PFGE-B2, ERIC-A, ERIC-B, MLVA-A, MLVA-B1, MLVA-B2 and G1, G2, H for CRISPR-MVLST. The strains isolated from humans after this period were allocated in PFGE-B1, ERIC-A, MLVA-B1, MLVA-B2 and G2 clusters. The strains isolated from food were allocated in PFGE-A, PFGE-B1, ERIC-A, ERIC-B, MLVA-A, MLVA-B1, MLVA-B2, G1 and G2 clusters. By MLST, of the total of 92 strains isolated from humans and food, 77 strains were typed as ST19. By whole genome sequencing, the strains isolated from food and humans were allocated in I and J clusters independently of its isolation date. In the comparison of isolates from humans and animals, strains of the two origins were allocated in PFGE-D1, PFGE-D2, ERIC-C1, MLVA-C1 and MLVA-D clusters. In conclusion, the high frequency of virulence genes in the S. Typhimurium strains studied reinforces their potential hazard to cause disease in humans, as well as the risk of its presence in food, animals for human consumption and the environment. The occurrence of S. Typhimurium multi-drug iv resistant isolated from various food and pigs for consumption is an alert of the possible risk for humans to ingest contaminated food with those strains. Together the results of PFGE, ERIC-PCR, MLVA e CRISPR-MVLST suggest that S. Typhimurium strains isolated from humans were genetically more diverse before mid-1990s, which might indicate the selection of a more adapted S. Typhimurium subtype after Salmonella Enteritidis became the most prevalent serovar in Brazil. Regarding the strains isolated from food, the results of PFGE, ERIC-PCR, MLVA and CRISPR-MVLST suggest that during the studied period there was circulation of more than one subtype in the country. The MLST results suggest that these strains have a common phylogenetic origin. The results of the whole genome sequencing suggest that there may be more than one subtype circulating in the country, with respect to the strains of human and food origins. Also, alerts for the possible risk of MDR strains isolated from food to contaminate humans and/or disseminate antibiotic resistance genes for strains of clinical and non-clinical origin. In the comparison of isolates from humans and animals, the results of PFGE, ERIC-PCR and MLVA suggest that some strains isolated from pigs and humans may descend from a common subtype. In addition, the MDR strains isolated from pigs and pig environment warn for the possible risk of pigs used for human consumption to contaminate humans, the environment and other pigs.

Orientador: Fernando Antônio de Ávila / Banca: José Moacir Marim / Banca: Patricia Amoroso / Banca: Simone Barone Salgado Marques / Banca: Tammy Priscilla Chioda Delfino / Resumo: Foram estudadas 180 amostras de água de 45 consultórios odontológicos da cidade de Barretos-SP, com o objetivo de isolar, identificar, determinar a contagem de isolados de Pseudomonas aeruginosa UFC/mL, determinar o perfil clonal e avaliar a diversidade genômica dos isolados e a suscetibilidade das mesmas frente a diferentes antibióticos. As amostras de água foram filtradas em filtro Millipore® e a membrana colocada sobre o centro de uma placa de Petri contendo agar cetrimida, As colônias típicas de bactérias do gênero Pseudomonas foram identificadas pelo método de Gram, inoculação em TSI agar (Triple Sugar Iron), crescimento a 42ºC, produção de pigmento, produção de alginato, oxidase, motilidade e alcalinização da acetamida. O teste utilizado para análise genômica foi o ERIC-PCR. Dos 76 (42,2%) isolados de Pseudomonas aeruginosa, 15 eram provenientes das amostras de torneira de lavagem das mãos, 18 de reservatório de garrafa pet, 23 de seringa tríplice e 20 do motor de alta rotação. Todos os isolados de Pseudomonas aeruginosa foram submetidos ao teste de suscetibilidade segundo a técnica de Kirby- Bauer. Dos antibióticos testados o que apresentou melhor resultado quanto à sensibilidade (65,8%) foi a ciprofloxacina. Quanto à similaridade genética dos isolados dos diferentes pontos analisados, foram encontrados nove "clusters" de 100% de similaridade. / Abstract: The biofilm found in water supplies and lines of hospitals and dental units is extremely important because it presents a large number of bacteria, leading to risk of infection in immunocompromised patients vulnerable to opportunistic pathogens such as the Pseudomonas aeruginosa. One hundred eighty water samples from dental units of the city of Barretos-SP were evaluated. The water samples filtered in Millipore® filter were incubated in plates containing Cetrimide ágar. The bacteria colonies were identified through the gram-staining test, inoculation in agar T.S.I (triple sugar Iron), growth at 42 ° C, pigment production, production of alginate, oxidase acetamide alkalization and motility observation. All Pseudomonas aeruginosa bacteria were submitted to the susceptibility test according to the Kirby-Bauer technique. The test used for genomic analysis was the ERIC-PCR. From the total microorganisms studied, 76 (42,2%) were positive for Pseudomonas aeruginosa, isolates from 180 water samples, where 15 strains were from hand washing incoming local water supplies, 18 from PET bottled water, 23 from 3-in-1 syringes and 20 from the high speed handpiece. In relation to the antibiotics tested, the one presenting the best result with regard to sensibility was ciprofloxacin with 65.8%. The genetic similarity of isolates from different points analyzed, there were nine clusters of 100% similarity. / Doutor

Des études ont récemment mis en évidence le rôle des lipopolysaccharides (LPS) des bactéries à Gram négatif de la flore intestinale dans le processus de l’inflammation conduisant à l’obésité et au diabète de type 2.Le présent travail est réalisé dans le cadre d’une collaboration entre les équipes du Dr. Caroff (U. Paris-Sud, Orsay) et du Pr. Zhao (U. Jiao Tong, Shanghai). Les expériences présentées ont été réalisées lors de séjours dans les deux laboratoires.Il a été démontré en Chine que des bactéries Sulfato-réductrices (SRB) à Gram négatif étaient présentes en plus forte proportion dans la flore intestinale chez les souris suivant un régime gras. Les mêmes résultats ont été observés chez l'homme. L’hypothèse selon laquelle des SRB seraient à l’origine de grandes quantités d’endotoxines chez les obèses et les patients diabétiques a été émise. Plusieurs souches de SRB isolées de la flore intestinale humaine d’un sujet sain et d’un sujet diabétique ont été cultivées en Chine. Des études de relation structure/activité des LPS isolés de ces bactéries ont été réalisées dans le laboratoire Français pour déterminer leur rôle dans le développement des maladies métaboliques. Les souches isolées des deux sujets ont pu être classées dans le genre Desulfovibrio. Les LPS correspondants ont été extraits et purifiés par des méthodes mises au point dans l’équipe d’Orsay. La structure chimique a été élucidée par les méthodes suivantes : Electrophorèse, Chromatographie sur couche mince, Chromatographie en phase gazeuse et Spectrométrie de masse MALDI. C’est ainsi que des spectres de masse ont été obtenus et que la structure des lipides A, principes actifs des LPS, isolés de SRB a été décrite pour la première fois. Les activités biologiques testées (TNFα, IL-6) varient en fonction du nombre d’acides gras présents. Les LPS de SRB du patient sain ont une structure variable (Smooth versus Rough) en fonction de la quantité de fer présent dans le milieu, et ceux isolés du patient diabétique présentent des structures atypiques qui ne sont pas toutes inflamogènes. Une molécule membranaire inconnue, que nous avons nommée « Glycosyl’X » était co-extraite avec les LPS. Elle joue apparemment un rôle important dans la croissance des SRB et a été étudiée après des étapes de purification complexes. Les structures et le pouvoir inflammatoire de ces molécules dont la structure varie avec les souches, et qui chélatent le fer, ont été étudiées. Elles sont de nature principalement osidique et fixées à la membrane. La proportion de ces molécules par rapport aux LPS varie avec la quantité de fer disponible dans le milieu. Un milieu riche en fer favorise la croissance des Desulfovibrio portant les Glycosyl’X qui n’ont pas de pouvoir inflammatoire eux-mêmes, mais entrent en compétition avec les LPS, modulant ainsi indirectement l’activité de ces derniers. L’augmentation du nombre de Desulfovibrio conduisant à l’augmentation des molécules Glycosyl’X pourrait aussi moduler positivement (par présentation) ou négativement (par élimination des bactéries) l’adsorption du fer dans les intestins dont l’équilibre est essentiel pour l’homéostasie métabolique.Par ailleurs, la croissance des Desulfovibrio augmente la production d’Hydrogène Sulfuré connu pour son action délétère sur les cellules. Nous favorisons l’hypothèse selon laquelle son action sur la disjonction des cellules épithéliales permettrait le passage des différents LPS relargués par la flore Gram-négative intestinale, et même des bactéries entières, vers la circulation sanguine. / Recent studies have highlighted the role of lipopolysaccharide (LPS) in the intestinal flora (gut microbiota) which could contribute to the inflammation process leading to obesity and type 2 diabetes. This thesis is part of a collaborative project between the laboratories of Dr. Caroff (U. Paris -Sud, Orsay, France) and Prof. Zhao (U. Jiao Tong , Shanghai, China). It has been shown by Pr.Zhao’s team in 2010 that the Sulfate -Reducing Bacteria (SRB) were presented in greater proportion in the intestinal mice flora following a fat diet compared to mice following a normal diet. The same results were observed in humans. The starting hypothesis was that SRB could produce a large amount of endotoxin in obese and diabetic patients and play a role in the development of metabolic diseases. Several SRB strains isolated from the human intestinal flora of a healthy subject and of a diabetic subject were grown in the Chinese laboratory. Studies of their LPS structure / activity relationships were carried out in the French laboratory. The aim of this study was to determine their roles in the development of metabolic diseases.Strains isolated from the two subjects could be classified in the Desulfovibrio genus. The corresponding LPS were extracted and purified by the methods developed in the French laboratory. The chemical structure was elucidated by the following methods: Electrophoresis, Thin layer chromatography, Gas chromatography and MALDI mass spectrometry. The mass spectra were obtained and the structure of lipid A, the active part of LPS isolated from SRB was described here for the first time. The biological activities test (TNFα, IL-6) vary depending on the number of fatty acids present in their lipid A structure. The LPS of SRB isolated from the healthy patient had a variable structure (Smooth versus Rough) depending on the amount of iron present in the medium, and those isolated from diabetic patients had atypical structures are not all inflamogenic .An unknown membrane molecule, which we named "Glycosyl'X" was co-extracted with the LPS. It apparently plays an important role in the growth of SRB was investigated after complex purification steps. The structures and the inflammatory power of these molecules variying with strains chelating iron were studied. They are mainly of glycosidic nature and linked to the bacterial membrane.The proportion of these molecules relatively to LPS varies with the amount of iron in the medium. An environment rich in iron promotes the growth of Desulfovibrio Glycosyl'X, molecules but competes with LPS and indirectly modulates the activity of the latter. The increase number of Desulfovibrio leading to increased Glycosyl'X molecules may also modulate positively (by presentation) or negatively (by killing bacteria) the absorption of iron in the intestines which balance is essential for metabolic homeostasis.Furthermore, the growth of Desulfovibrio increasing the production of Hydrogen Sulfide is known for its deleterious effects on the cells. We favor the hypothesis that its action on the separation of epithelial cells favors the passage of different LPS released by the Gram- negative of intestinal flora and even whole cell bacteria into the bloodstream.