Orientador: João Pessoa Araujo Junior / Resumo: A segurança dos alimentos é essencial para o desenvolvimento da sociedade e as doenças transmitidas por alimentos (DTAs) acometem milhares de pessoas todos os anos. Dentre os agentes de DTA, Salmonella se destaca como a principal causa de hospitalizações e mortes. A carne suína é uma importante fonte de nutrientes, sendo a mais consumida no mundo. Vários relatos apontaram o isolamento de Salmonella multidrogas resistentes (MDR) associados com a cadeia produtiva dos suínos, e a ocorrência de elementos que possibilitam a transferência de genes de resistência entre populações bacterianas estão diretamente relacionados a essa característica. O presente trabalho objetivou determinar os genes associados com resistência a antimicrobianos de 9 isolados de Salmonella MDR provenientes de linfonodos mesentéricos de suínos, além de aplicar um protocolo in silico para predizer a localização de cada gene (plasmidial ou cromossomal) e detectar e caracterizar a presença de Integrons de resistência. Diversos genes de resistência para a mesma classe de antimicrobianos foram encontrados em cada cepa, e a localização presumida dos genes foi heterogênica, com exceção para os genes de resistência a sulfonamidas, todos classificados como plasmidiais. Cinco cepas apresentaram integrons classe 1, agrupados em três diferentes perfis. A comparação destes perfis com sequências do GenBank revelou que bactérias de diversas espécies, isoladas em diversos países e proveniente de diferentes fontes, inclusive... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Food safety is essential for society development, and foodborne diseases affect thousands of people every year. Among the main foodborne disease agents, Salmonella stands out as the most associated with hospitalizations and deaths. Pork products are an important source of nutrients for population and the most consumed meat in the world. Several reports reveal the presence of Multidrug Resistant (MDR) Salmonella strains in the pork production chain, and the occurrence of elements that allows transference of resistance genes between bacterial populations is related to this characteristic. The present study aimed to determinate the genetic bases associated with Antimicrobial Resistance (AMR) in nine MDR Salmonella strains isolated from swine mesenteric lymph-nodes, beside applying an in-silico protocol to determinate location of the AMR genes (chromosomal or plasmidial) and characterize resistance integrons. Different resistance genes for the same antimicrobial class were present in each strain, and gene localization was heterogenous, except for sulphonamides resistance genes, where all were classified as plasmidial. Five isolates harbored Class 1 ix integrons, which were classified in three distinct Integron Profiles (IPs). Comparison of IPs with sequences of GenBank database revealed that different species of bacteria, from different countries and isolation sources, including human clinical isolates had the same integrons. The diversity of resistance mechanisms for the same an... (Complete abstract click electronic access below) / Doutor

Introdução. A resistência bacteriana é facilitada pela pressão seletiva do uso de antimicrobianos na clínica e em outras atividades, como a agricultura e pecuária, além de poder ser disseminada para a natureza por meio do lançamento inadequado do esgoto ou pela aplicação do lodo de esgoto na agricultura. As -lactamases de espectro estendido (ESBL) são uma das formas mais prevalentes de resistência em Gram negativos no mundo, e seus genes codificadores são disseminados por meio de diversos elementos genéticos, principalmente transposons e integrons mobilizados para plasmídios. Objetivo. Identificar e caracterizar genes codificadores de ESBL, bem como suas prováveis formas de mobilização, em enterobactérias isoladas de fontes ambientais e clínicas. Material e Métodos. Quarenta e cinco cepas isoladas de um hospital público em 2004 e 2005, responsáveis por infecções hospitalares (14), infecções comunitárias (7) e colonizações (24), e 7 isoladas de estações de tratamento de esgoto (ETE) em 2009, em São Paulo, geneticamente distintas e produtoras de ESBL da família Enterobacteriaceae, foram estudadas. A técnica de PCR seguida de sequenciamento foi utilizada para a identificação dos genes blaESBL, triagem de elementos móveis e mapeamento do ambiente genético de blaESBL. A identificação dos grupos de incompatibilidade plasmidial (Inc) foi realizada pela técnica de PBRT, e a determinação dos tamanhos dos plasmídios pela técnica de S1-PFGE. Resultados. Os genes blaESBL identificados foram: amostras clínicas - blaTEM-15, blaTEM-197, blaSHV-5, blaSHV-12, blaSHV-27, blaSHV-28, blaSHV-45, blaSHV-55, blaSHV-110, blaCTX-M-2, blaCTX-M-59 e blaCTX-M-131; amostras ambientais blaSHV-28, blaCTX-M-15 e blaCTX-M-8. Os genes blaTEM- 15 e blaTEM-197 estavam associados aos elementos Tn2* e Tn3, respectivamente. Os genes blaSHV-5 e blaSHV-12 estavam associados à IS26, e não foi possível determinar o ambiente genético dos demais genes blaSHV. Os genes blaCTX-M-2, blaCTX-M-59 e blaCTXM- 131 estavam inseridos em integrons de classe 1 complexos, blaCTX-M-15 estava associado à ISEcp1 interrompida pela IS26, e blaCTX-M-8 estava associado à IS10, também interrompida pela IS26. Os principais grupos Inc detectados foram IncA/C (37 por cento ) e IncF (30,4 por cento ). Exceto por 7 cepas clínicas, todas apresentavam plasmídios de alto peso molecular, entre 48,5kb e 388kb. Conclusões. Este estudo detectou 15 genes blaESBL diferentes, dos quais dois são genes novos (blaTEM-197 e blaCTX-M-131) e três são inéditos no Brasil (blaTEM-15, blaSHV-55 e blaSHV-110). A maioria das cepas deste estudo possuía genes blaESBL associados a elementos mobilizáveis, bem como continham plasmídios de grupos Inc envolvidos na disseminação da resistência antimicrobiana. Além disso, carreavam plasmídios provavelmente conjugativos. Os resultados deste estudo mostram genes de resistência associados a elementos mobilizáveis em cepas contendo elementos transferíveis. As cepas foram isoladas tanto em uma instituição de saúde como nas ETEs da Grande São Paulo, mostrando o potencial de disseminação da resistência da clínica para o ambiente em nossa região. / Introduction. Bacterial resistance is facilitated by selective pressure of antimicrobial use in clinical and other activities, as agriculture and livestock, and can be spread to nature through the inadequate discharge of sewage or by the use of sludge in agriculture. Extended-spectrum -lactamases (ESBL) are the most prevalente forms of resistance in Gram-negative bacteria in the world, and their encoding genes are disseminated through several genetic elements, especially transposons and integrons mobilized to plasmids. Objective. To identify and characterize ESBL-encoding genes, as well as their probable mobilization pathways, in enterobacteria isolated from clinical and environmental sources. Material and Methods. Forty-five strains isolated from a public hospital in 2004 and 2005, responsible for hospital infections (14), community-acquired infections (7) and colonizations (24), and 7 isolated from sewage treatment plants (ETE) in 2009, in São Paulo, genetically distinct and ESBL producers from Enterobacteriaceae family, were studied. PCR technique followed by sequencing was used for blaESBL genes identification, mobile elements screening and blaESBL genetic environment mapping. Plasmid incompatibility groups (Inc) were identified by PBRT technique, and plasmid sizes were determined by S1-PFGE technique. Results. The blaESBL genes identified were: clinical samples - blaTEM-15, blaTEM-197, blaSHV-5, blaSHV-12, blaSHV-27, blaSHV-28, blaSHV-45, blaSHV-55, blaSHV-110, blaCTX-M-2, blaCTX-M-59 and blaCTX-M-131; environmental samples blaSHV-28, blaCTX-M-15 and blaCTX-M-8. Genes blaTEM-15 and blaTEM-197 were associated to the elements Tn2* and Tn3, respectivelly. Genes blaSHV-5 and blaSHV-12 were associated to IS26, and it was not possible to detect the genetic environment of the other blaSHV genes. Genes blaCTX-M-2, blaCTX-M-59 and blaCTX-M-131 were inserted in complex class 1 integrons, blaCTX-M-15 was associated to ISEcp1 interrupted by IS26, and blaCTX-M-8 was associated to IS10, also interrupted by IS26. The most common Inc grups detected were IncA/C (37 per cent ) and IncF (30,4 per cent ). Except for 7 clinical strains, all isolates showed high molecular weight plasmids, rangng from 48,5kb to 388kb. Conclusions. This study detected 15 different blaESBL genes, from which 2 are new genes (blaTEM-197 e blaCTX-M-131) and 3 are still unpublished in Brazil (blaTEM-15, blaSHV-55 and blaSHV-110). Most of the strains from this study had blaESBL genes associated to mobile elements, as well as they had plasmids from Inc groups involved in the spread of antimicrobial resistance. Moreover, the strains probably carried conjugative plasmids. Results from the present work show resistance genes associated to mobile elements in strains carrying transferable elements. The strains were isolated either from a healthcare institution or from ETEs in São Paulo, which shows the spread potential of resistance from the clinic to the environment in our region.

Introdução. A resistência bacteriana a antibióticos é aceita como um dos maiores problemas de saúde pública. As tetraciclinas são antibióticos de amplo espectro, e após seu uso indiscriminado observou-se o surgimento de bactérias resistentes, levando médicos e veterinários a diminuírem seu uso. Objetivos. Verificar o perfil de sensibilidade a tetraciclinas em isolados clínicos e ambientais de Escherichia coli, Klebsiella pneumoniae e Aeromonas spp., bem como pesquisar os principais genes tet associados à resistência a esta classe de antibióticos e determinar a potencial forma de disseminação destes genes através da caracterização de seu ambiente genético. Material e Métodos. Os perfis de sensibilidade à tetraciclina (TET), doxiciclina (DOX), minociclina (MIN) e tigeciclina (TGC) de 572 isolados foram obtidos através das técnicas de Disco-Difusão e Concentração Inibitória Mínima. Os isolados não-sensíveis à tetraciclina foram submetidos a reações de PCR para pesquisa de grupos Inc, genes tet e para a caracterização de seu ambiente genético pela pesquisa das integrases de classes 1, 2, 3 e 4, e dos elementos genéticos móveis Tn1721, IS26, Tn10 e ISAS5. Perfis de similaridade genética dos isolados foram obtidos através das técnicas de ERIC-PCR e PFGE. Após análise destes resultados 33 cepas foram selecionadas para as técnicas de S1-PFGE e transformação. Resultados. A partir dos 572 isolados 18,5 por cento foram resistentes à TET, 13,5 por cento à DOX, 8 por cento à MIN e nenhum à TGC. Vinte e dois por cento dos isolados clínicos e 16,3 por cento ambientais foram resistentes à TET. Os genes codificadores de bomba de efluxo tet(A), tet(B), tet(C), tet(D) e tet(E), foram observados em 25,5 por cento , 33 por cento , 6,5 por cento , 18,9 por cento e 23,5 por cento dos isolados, respectivamente. Noventa e cinco por cento, 100 por cento , 100 por cento e 4,5 por cento das cepas carreando o gene tet(A), tet(B), tet(D) e tet(E), foram não-sensíveis à DOX, nesta ordem. Resistência à MIN foi observada em 4,2 por cento , 78,8 por cento e 100 por cento dos isolados carreando tet(A), tet(B) e tet(D), respectivamente. O gene tet(A) estava associado a Tn1721, tet(B) à Tn10 e tet(C) e tet(D) à IS26. Nenhuma das integrases pesquisadas estavam associadas aos genes tet detectados. Os grupos IncF, IncFIB e IncA/C foram observados em 54,8 por cento , 41,1 por cento e 28,7 por cento dos isolados, respectivamente. Uma cepa de Aeromonas spp. carreava um plasmídio do grupo IncP. Através dos perfis de similaridade genética foi observado que dentre os isolados hospitalares de K. pneumoniae houve a ocorrência de perfis genéticos idênticos, no entanto nos demais isolados do estudo os perfis genéticos observados eram distintos. Das 33 cepas selecionadas para os experimentos de linearização plasmidial e de transformação, 8 foram transformadas com sucesso, nas quais foi observada a presença dos genes tet em plasmídios. Conclusões. Uma baixa porcentagem de resistência à TET foi detectada. Verificou-se que a TGC foi a tetraciclina mais ativa, seguida da MIN. Os genes tet(A) e tet(B) foram os mais prevalentes. Todas as cepas carreando tet(B) e tet(D) foram não-sensíveis a DOX e MIN. Plasmídios dos grupos IncF, FIB e A/C foram os mais detectados neste estudo. Os resultados sugerem que os genes tet(A), (B), (C) e (D) são disseminados por meio de plasmídios e estão associados aos transposons Tn1721, IS10 e IS26. Estudos adicionais com isolados mais recentes e outros gêneros bacterianos são necessários, para contribuir com informações da resistência bacteriana a tetraciclinas. / Introduction. The antibiotic resistance is accepted as one of the major problems for public health. Tetracyclines are broad spectrum antibiotics, and its indiscriminate use promoted the emergence of resistant bacteria, leading physicians and veterinarians to decrease its use. Objectives. Verify the susceptibility of clinical and environmental isolates of Escherichia coli, Klebsiella pneumoniae and Aeromonas spp. to tetracyclines, and also search for the main tet genes associated with resistance to these antibiotics and determine the potential mechanism of tet genes dissemination by characterizing their genetic context. Material and Methods. Disk-Diffusion and Minimum Inhibitory Concentration tests were carried out in 572 isolates using tetracycline (TET), doxycycline (DOX), minocycline (MIN) and tigecycline (TGC). PCR was carried out in TET non-susceptible isolates for the detection of Inc groups, tet genes and its genetic context determination through the search of classes 1, 2, 3, and 4 integrases, and Tn1721, Tn10, IS26 and ISAS5 mobile genetic elements. Genetic similarities patterns were determined by ERIC-PCR and PFGE techniques. After analyzing the results 33 strains were selected for the S1-PFGE and transformation experiments. Results. From 572 isolates, 18.5 per cent were TET-resistant, 13.5 per cent DOX-resistant, 8 per cent MIN-resistant and none resistant to TGC. Twenty-two per cent and 16.3 per cent of clinical and environmental isolates were TET-resistant, in that order. Genes tet(A), tet(B), tet(C), tet(D) and tet(E), coding for efflux pump mechanism, were found in 25.5 per cent , 33 per cent , 6.5 per cent , 18.9 per cent and 23.5 per cent of the isolates, respectively. Ninety-five per cent, 100 per cent , 100 per cent and 4.5 per cent of the isolates carrying tet(A), tet(B), tet(D) and tet(E) were non-susceptible to DOX, respectively. Resistance to MIN was observed in 4.2 per cent , 78.8 per cent and 100 per cent of isolates carrying tet(A), tet(B) and tet(D), in that order. The gene tet(A) was associated with Tn1721, tet(B) with Tn10, and tet(C) and (D) with IS26. None of the searched integrases were associated with the tet genes detected. Groups IncF, IncFIB and IncA/C were respectively observed in 54.8 per cent , 41.1 per cent and 28.7 per cent of the isolates. One Aeromonas spp. was carrying an IncP plasmid. The genetic similarities patterns demonstrated that there were identical genetic patterns among the hospital K. pneumoniae isolates, however all the remaining isolates possessed distinct genetic patterns. Of the 33 strains selected for plasmid linearization and transformation experiments, 8 were successfully transformed, in which the presence of tet genes in plasmids were observed. Conclusions. A low level of tetracycline resistance was detected. TGC was the most active tested antibiotic, followed by MIN. Genes tet(A) and tet(B) were the most prevalent among the isolates. All strains carrying tet(B) and tet(D) were non-susceptible to DOX and MIN. Groups IncF, IncFIB and IncA/C were the most detected in this study. The results suggest that tet(A), (B), (C) and (D) are disseminated by plasmids and are associated with Tn1721, Tn10 and IS26. Additional studies assembling recent isolates and other genera are necessary in order to contribute with information about the bacteria resistance to tetracyclines.

Introdução. A resistência bacteriana a antibióticos é aceita como um dos maiores problemas de saúde pública. As tetraciclinas são antibióticos de amplo espectro, e após seu uso indiscriminado observou-se o surgimento de bactérias resistentes, levando médicos e veterinários a diminuírem seu uso. Objetivos. Verificar o perfil de sensibilidade a tetraciclinas em isolados clínicos e ambientais de Escherichia coli, Klebsiella pneumoniae e Aeromonas spp., bem como pesquisar os principais genes tet associados à resistência a esta classe de antibióticos e determinar a potencial forma de disseminação destes genes através da caracterização de seu ambiente genético. Material e Métodos. Os perfis de sensibilidade à tetraciclina (TET), doxiciclina (DOX), minociclina (MIN) e tigeciclina (TGC) de 572 isolados foram obtidos através das técnicas de Disco-Difusão e Concentração Inibitória Mínima. Os isolados não-sensíveis à tetraciclina foram submetidos a reações de PCR para pesquisa de grupos Inc, genes tet e para a caracterização de seu ambiente genético pela pesquisa das integrases de classes 1, 2, 3 e 4, e dos elementos genéticos móveis Tn1721, IS26, Tn10 e ISAS5. Perfis de similaridade genética dos isolados foram obtidos através das técnicas de ERIC-PCR e PFGE. Após análise destes resultados 33 cepas foram selecionadas para as técnicas de S1-PFGE e transformação. Resultados. A partir dos 572 isolados 18,5 por cento foram resistentes à TET, 13,5 por cento à DOX, 8 por cento à MIN e nenhum à TGC. Vinte e dois por cento dos isolados clínicos e 16,3 por cento ambientais foram resistentes à TET. Os genes codificadores de bomba de efluxo tet(A), tet(B), tet(C), tet(D) e tet(E), foram observados em 25,5 por cento , 33 por cento , 6,5 por cento , 18,9 por cento e 23,5 por cento dos isolados, respectivamente. Noventa e cinco por cento, 100 por cento , 100 por cento e 4,5 por cento das cepas carreando o gene tet(A), tet(B), tet(D) e tet(E), foram não-sensíveis à DOX, nesta ordem. Resistência à MIN foi observada em 4,2 por cento , 78,8 por cento e 100 por cento dos isolados carreando tet(A), tet(B) e tet(D), respectivamente. O gene tet(A) estava associado a Tn1721, tet(B) à Tn10 e tet(C) e tet(D) à IS26. Nenhuma das integrases pesquisadas estavam associadas aos genes tet detectados. Os grupos IncF, IncFIB e IncA/C foram observados em 54,8 por cento , 41,1 por cento e 28,7 por cento dos isolados, respectivamente. Uma cepa de Aeromonas spp. carreava um plasmídio do grupo IncP. Através dos perfis de similaridade genética foi observado que dentre os isolados hospitalares de K. pneumoniae houve a ocorrência de perfis genéticos idênticos, no entanto nos demais isolados do estudo os perfis genéticos observados eram distintos. Das 33 cepas selecionadas para os experimentos de linearização plasmidial e de transformação, 8 foram transformadas com sucesso, nas quais foi observada a presença dos genes tet em plasmídios. Conclusões. Uma baixa porcentagem de resistência à TET foi detectada. Verificou-se que a TGC foi a tetraciclina mais ativa, seguida da MIN. Os genes tet(A) e tet(B) foram os mais prevalentes. Todas as cepas carreando tet(B) e tet(D) foram não-sensíveis a DOX e MIN. Plasmídios dos grupos IncF, FIB e A/C foram os mais detectados neste estudo. Os resultados sugerem que os genes tet(A), (B), (C) e (D) são disseminados por meio de plasmídios e estão associados aos transposons Tn1721, IS10 e IS26. Estudos adicionais com isolados mais recentes e outros gêneros bacterianos são necessários, para contribuir com informações da resistência bacteriana a tetraciclinas. / Introduction. The antibiotic resistance is accepted as one of the major problems for public health. Tetracyclines are broad spectrum antibiotics, and its indiscriminate use promoted the emergence of resistant bacteria, leading physicians and veterinarians to decrease its use. Objectives. Verify the susceptibility of clinical and environmental isolates of Escherichia coli, Klebsiella pneumoniae and Aeromonas spp. to tetracyclines, and also search for the main tet genes associated with resistance to these antibiotics and determine the potential mechanism of tet genes dissemination by characterizing their genetic context. Material and Methods. Disk-Diffusion and Minimum Inhibitory Concentration tests were carried out in 572 isolates using tetracycline (TET), doxycycline (DOX), minocycline (MIN) and tigecycline (TGC). PCR was carried out in TET non-susceptible isolates for the detection of Inc groups, tet genes and its genetic context determination through the search of classes 1, 2, 3, and 4 integrases, and Tn1721, Tn10, IS26 and ISAS5 mobile genetic elements. Genetic similarities patterns were determined by ERIC-PCR and PFGE techniques. After analyzing the results 33 strains were selected for the S1-PFGE and transformation experiments. Results. From 572 isolates, 18.5 per cent were TET-resistant, 13.5 per cent DOX-resistant, 8 per cent MIN-resistant and none resistant to TGC. Twenty-two per cent and 16.3 per cent of clinical and environmental isolates were TET-resistant, in that order. Genes tet(A), tet(B), tet(C), tet(D) and tet(E), coding for efflux pump mechanism, were found in 25.5 per cent , 33 per cent , 6.5 per cent , 18.9 per cent and 23.5 per cent of the isolates, respectively. Ninety-five per cent, 100 per cent , 100 per cent and 4.5 per cent of the isolates carrying tet(A), tet(B), tet(D) and tet(E) were non-susceptible to DOX, respectively. Resistance to MIN was observed in 4.2 per cent , 78.8 per cent and 100 per cent of isolates carrying tet(A), tet(B) and tet(D), in that order. The gene tet(A) was associated with Tn1721, tet(B) with Tn10, and tet(C) and (D) with IS26. None of the searched integrases were associated with the tet genes detected. Groups IncF, IncFIB and IncA/C were respectively observed in 54.8 per cent , 41.1 per cent and 28.7 per cent of the isolates. One Aeromonas spp. was carrying an IncP plasmid. The genetic similarities patterns demonstrated that there were identical genetic patterns among the hospital K. pneumoniae isolates, however all the remaining isolates possessed distinct genetic patterns. Of the 33 strains selected for plasmid linearization and transformation experiments, 8 were successfully transformed, in which the presence of tet genes in plasmids were observed. Conclusions. A low level of tetracycline resistance was detected. TGC was the most active tested antibiotic, followed by MIN. Genes tet(A) and tet(B) were the most prevalent among the isolates. All strains carrying tet(B) and tet(D) were non-susceptible to DOX and MIN. Groups IncF, IncFIB and IncA/C were the most detected in this study. The results suggest that tet(A), (B), (C) and (D) are disseminated by plasmids and are associated with Tn1721, Tn10 and IS26. Additional studies assembling recent isolates and other genera are necessary in order to contribute with information about the bacteria resistance to tetracyclines.

Introdução. A resistência bacteriana é facilitada pela pressão seletiva do uso de antimicrobianos na clínica e em outras atividades, como a agricultura e pecuária, além de poder ser disseminada para a natureza por meio do lançamento inadequado do esgoto ou pela aplicação do lodo de esgoto na agricultura. As -lactamases de espectro estendido (ESBL) são uma das formas mais prevalentes de resistência em Gram negativos no mundo, e seus genes codificadores são disseminados por meio de diversos elementos genéticos, principalmente transposons e integrons mobilizados para plasmídios. Objetivo. Identificar e caracterizar genes codificadores de ESBL, bem como suas prováveis formas de mobilização, em enterobactérias isoladas de fontes ambientais e clínicas. Material e Métodos. Quarenta e cinco cepas isoladas de um hospital público em 2004 e 2005, responsáveis por infecções hospitalares (14), infecções comunitárias (7) e colonizações (24), e 7 isoladas de estações de tratamento de esgoto (ETE) em 2009, em São Paulo, geneticamente distintas e produtoras de ESBL da família Enterobacteriaceae, foram estudadas. A técnica de PCR seguida de sequenciamento foi utilizada para a identificação dos genes blaESBL, triagem de elementos móveis e mapeamento do ambiente genético de blaESBL. A identificação dos grupos de incompatibilidade plasmidial (Inc) foi realizada pela técnica de PBRT, e a determinação dos tamanhos dos plasmídios pela técnica de S1-PFGE. Resultados. Os genes blaESBL identificados foram: amostras clínicas - blaTEM-15, blaTEM-197, blaSHV-5, blaSHV-12, blaSHV-27, blaSHV-28, blaSHV-45, blaSHV-55, blaSHV-110, blaCTX-M-2, blaCTX-M-59 e blaCTX-M-131; amostras ambientais blaSHV-28, blaCTX-M-15 e blaCTX-M-8. Os genes blaTEM- 15 e blaTEM-197 estavam associados aos elementos Tn2* e Tn3, respectivamente. Os genes blaSHV-5 e blaSHV-12 estavam associados à IS26, e não foi possível determinar o ambiente genético dos demais genes blaSHV. Os genes blaCTX-M-2, blaCTX-M-59 e blaCTXM- 131 estavam inseridos em integrons de classe 1 complexos, blaCTX-M-15 estava associado à ISEcp1 interrompida pela IS26, e blaCTX-M-8 estava associado à IS10, também interrompida pela IS26. Os principais grupos Inc detectados foram IncA/C (37 por cento ) e IncF (30,4 por cento ). Exceto por 7 cepas clínicas, todas apresentavam plasmídios de alto peso molecular, entre 48,5kb e 388kb. Conclusões. Este estudo detectou 15 genes blaESBL diferentes, dos quais dois são genes novos (blaTEM-197 e blaCTX-M-131) e três são inéditos no Brasil (blaTEM-15, blaSHV-55 e blaSHV-110). A maioria das cepas deste estudo possuía genes blaESBL associados a elementos mobilizáveis, bem como continham plasmídios de grupos Inc envolvidos na disseminação da resistência antimicrobiana. Além disso, carreavam plasmídios provavelmente conjugativos. Os resultados deste estudo mostram genes de resistência associados a elementos mobilizáveis em cepas contendo elementos transferíveis. As cepas foram isoladas tanto em uma instituição de saúde como nas ETEs da Grande São Paulo, mostrando o potencial de disseminação da resistência da clínica para o ambiente em nossa região. / Introduction. Bacterial resistance is facilitated by selective pressure of antimicrobial use in clinical and other activities, as agriculture and livestock, and can be spread to nature through the inadequate discharge of sewage or by the use of sludge in agriculture. Extended-spectrum -lactamases (ESBL) are the most prevalente forms of resistance in Gram-negative bacteria in the world, and their encoding genes are disseminated through several genetic elements, especially transposons and integrons mobilized to plasmids. Objective. To identify and characterize ESBL-encoding genes, as well as their probable mobilization pathways, in enterobacteria isolated from clinical and environmental sources. Material and Methods. Forty-five strains isolated from a public hospital in 2004 and 2005, responsible for hospital infections (14), community-acquired infections (7) and colonizations (24), and 7 isolated from sewage treatment plants (ETE) in 2009, in São Paulo, genetically distinct and ESBL producers from Enterobacteriaceae family, were studied. PCR technique followed by sequencing was used for blaESBL genes identification, mobile elements screening and blaESBL genetic environment mapping. Plasmid incompatibility groups (Inc) were identified by PBRT technique, and plasmid sizes were determined by S1-PFGE technique. Results. The blaESBL genes identified were: clinical samples - blaTEM-15, blaTEM-197, blaSHV-5, blaSHV-12, blaSHV-27, blaSHV-28, blaSHV-45, blaSHV-55, blaSHV-110, blaCTX-M-2, blaCTX-M-59 and blaCTX-M-131; environmental samples blaSHV-28, blaCTX-M-15 and blaCTX-M-8. Genes blaTEM-15 and blaTEM-197 were associated to the elements Tn2* and Tn3, respectivelly. Genes blaSHV-5 and blaSHV-12 were associated to IS26, and it was not possible to detect the genetic environment of the other blaSHV genes. Genes blaCTX-M-2, blaCTX-M-59 and blaCTX-M-131 were inserted in complex class 1 integrons, blaCTX-M-15 was associated to ISEcp1 interrupted by IS26, and blaCTX-M-8 was associated to IS10, also interrupted by IS26. The most common Inc grups detected were IncA/C (37 per cent ) and IncF (30,4 per cent ). Except for 7 clinical strains, all isolates showed high molecular weight plasmids, rangng from 48,5kb to 388kb. Conclusions. This study detected 15 different blaESBL genes, from which 2 are new genes (blaTEM-197 e blaCTX-M-131) and 3 are still unpublished in Brazil (blaTEM-15, blaSHV-55 and blaSHV-110). Most of the strains from this study had blaESBL genes associated to mobile elements, as well as they had plasmids from Inc groups involved in the spread of antimicrobial resistance. Moreover, the strains probably carried conjugative plasmids. Results from the present work show resistance genes associated to mobile elements in strains carrying transferable elements. The strains were isolated either from a healthcare institution or from ETEs in São Paulo, which shows the spread potential of resistance from the clinic to the environment in our region.

Submitted by Caroline Xavier (caroline.xavier@pucrs.br) on 2017-05-30T17:13:22Z No. of bitstreams: 1 DIS_BELISA_AVILA_RODRIGUES_PARCIAL.pdf: 420085 bytes, checksum: 77f9b7ddcd1250899386df6d319c1934 (MD5) / Made available in DSpace on 2017-05-30T17:13:22Z (GMT). No. of bitstreams: 1 DIS_BELISA_AVILA_RODRIGUES_PARCIAL.pdf: 420085 bytes, checksum: 77f9b7ddcd1250899386df6d319c1934 (MD5) Previous issue date: 2016-07-29 / Acinetobacter calcoaceticus-baumannii (ACB) are opportunistic pathogens responsible for respiratory tract infections, wound infections, and bacteremia in intensive care units patients. These microorganisms became a problem in health care units due to their ability to acquire and accumulate resistance determinants. They are resistant to important antibiotics commonly used to treat infections caused by them. Thus, this study aimed to determine the antimicrobial susceptibility and detect resistance determinants in clinical ACB isolates. For this, 200 clinical ACB isolates, resistant to carbapenems, were collected from a hospital in Porto Alegre, Brazil. To determine susceptibility to antimicrobial agents, 16 antimicrobials were used in the disk diffusion technique and the minimum inhibitory concentration (MIC) for polymyxin B and meropenem was performed by broth microdilution. Additionally, MIC for polymyxin B in 17 isolates was determined using different methods in comparison with broth microdilution, adopted as reference method. The presence of blaOXA-23, blaOXA-51, blaIMP and blaNDM, as well as class 1 and 2 integrons, were detected by PCR. A total of 82.5% were extremely resistant (XDR) and 17.5% were multidrug resistant (MDR). Forty-six non-susceptibility patterns were found among the isolates, with polymyxins, tetracyclines, and aminoglycosides being the classes with higher rate of susceptibility. When different methods to determining MIC for polymyxin B were evaluated, very major errors and major errors were found in E-test and major errors in agar dilution, as compared with the reference method. The broth microdilution with polysorbate 80 showed a reduction of two or more dilutions in most isolates (82.3%). The blaOXA-23 and blaOXA-51 genes were found in 100% of the isolates, while 49% harbored blaIMP. The blaNDM gene was not found in any isolate. Class 1 and class 2 integrons were found in 68% and 88% of the isolates, respectively. The high percentage of XDR isolates, as well as the detection of important resistance determinants and the high rate of integrons found, reinforce the concern regarding ACB microorganisms and their spread in health care units. / Acinetobacter calcoaceticus-baumannii (ACB) s?o pat?genos oportunistas respons?veis por infec??es do trato respirat?rio, infec??es de feridas e bacteremia em pacientes internados em unidades de terapia intensiva. Esses microrganismos tornaram-se um problema nas unidades de assist?ncia ? sa?de devido ? sua capacidade de adquirir e acumular determinantes de resist?ncia a antimicrobianos, sendo respons?veis por altas taxas de resist?ncia aos principais antimicrobianos utilizados terapeuticamente. Desta forma, esse estudo teve por objetivo determinar a suscetibilidade a antimicrobianos, assim como detectar determinantes de resist?ncia em isolados cl?nicos de ACB. Para isso, foram utilizados 200 isolados cl?nicos, resistentes aos carbapen?micos, pertencentes ao complexo ACB, coletados de um hospital em Porto Alegre, Brasil, no per?odo de janeiro de 2012 a maio de 2015. Para determinar a suscetibilidade a antimicrobianos, 16 f?rmacos foram utilizados na t?cnica de disco-difus?o, assim como foi determinada a concentra??o inibit?ria m?nima (CIM) para polimixina B e meropenem por meio da t?cnica de microdilui??o em caldo. Adicionalmente, a CIM para polimixina B foi determinada em 17 isolados, empregando diferentes m?todos em compara??o com a microdilui??o em caldo, adotada como refer?ncia. Os genes blaOXA-23, blaOXA-51, blaIMP e blaNDM, bem como os integrons de classe 1 e 2 foram detectados por PCR. Um total de 82,5% dos isolados foram extremely resistant (XDR) e 17,5% foram multidrug resistant (MDR). Quarenta e seis padr?es de n?o-suscetibilidade foram encontrados entre os isolados, sendo que polimixinas, tetraciclinas e aminoglicos?deos foram as classes com maior taxa de suscetibilidade. Na determina??o de CIM para polimixina B com diferentes m?todos, very major errors e major errors foram encontrados em E-test, e major errors em dilui??o em ?gar, quando comparados com o m?todo de refer?ncia. A microdilui??o em caldo suplementado com polissorbato 80 mostrou redu??o de duas ou mais dilui??es na maioria dos isolados (82,3%). Os genes blaOXA-23 e blaOXA-51 foram encontrados em 100% dos isolados, enquanto 49% apresentaram blaIMP. O gene blaNDM n?o foi encontrado nos isolados analisados. Integrons de classe 1 foram encontrados em 68% dos isolados e integrons de classe 2 em 88%. O elevado percentual de isolados XDR, assim como a detec??o de importantes determinantes de resist?ncia e a alta taxa de integrons encontrada, refor?am a preocupa??o com microrganismos do complexo ACB e sua dissemina??o nas unidades de assist?ncia ? sa?de.

This study was conducted to examine the rate of contamination and molecular characteristics of enteric bacteria isolated from a selection of food sources in Vietnam. One hundred and eighty raw food samples were tested and 60.8% of meat and 18.0% of shellfish samples were found to be contaminated with Salmonella spp. which belonged to variety of serogroups and serotypes. More than 90% of all food sources contained Escherichia coli and 32% of 50 shellfish samples were contaminated with Vibrio parahaemolyticus. PFGE was used to determine the degree of relatedness of Salmonella spp. There were 33 distinct PFGE patterns from 51 Salmonella spp. isolates tested, indicating that PFGE could be used as an alternative method for serotyping for use in epidemiology of Salmonella spp. Susceptibility of the isolates to 15 antimicrobial agents was investigated. Moderate to high frequencies of resistance to antibiotics were observed in Salmonella spp. and E. coli isolates and multi-resistance, defined as resistance to at least 4 antibiotics, was observed. All of the V. parahaemolyticus isolates were resistant to ampicillin/amoxicillin but not to other antibiotics. Betalactam TEM gene and tetracycline resistance tetA, tetB genes were widely distributed in both E. coli and Salmonella spp. isolates. Other resistance genes, including sulI, cmlA, aadA, aphA1, dhfrV, and aac(3)-IV were also present at high to moderate levels. Identification and characterisation of the mobile genetic elements, including identification of class 1 integrons and plasmids were carried out for multi-resistance isolates. The integrons harboured varying gene cassettes, including aadA1, aadA2, aadA5, aacA4, dhfrXII, drfA1 and dhfrA17, blaPSE1 and catB3. Thirty-five percent of Salmonella spp. isolates and 76% of E. coli isolates harboured plasmids of more than 95 kb. Transfer of resistance phenotypes between the isolates via conjugation and phage transduction was also demonstrated. Salmonella genomic island 1 (SGI1), a 43-kb genomic region contains a 13-kb antibiotic resistance gene cluster, has been identified in an isolate of S. Albany from chicken. The presence of Salmonella spp. virulence genes was investigated to examine the pathogenicity potential of the isolates. The invA gene was present in all Salmonella spp. isolates and the plasmid virulence gene spvC was detected in one S. Typhimurium isolate only, on a 95 kb virulence plasmid. Invasion assays performed in vitro demonstrated that all Salmonella isolates were capable of invading human intestine INT407 cells. In addition, the investigation for the presence of 58 selected virulence genes showed that all the tested isolates contained at least one virulence gene and there were 16 genes which are associated with different pathotypes detected. The data obtained in this study indicates that raw food in Vietnam is a potential reservoirs for many pathogenic organisms, and confirms the role of food animals as a reservoir of multidrug resistant E. coli and Salmonella spp.

<p>Transposons of the Mu superfamily are widespread and have been shown to play an important role in the dissemination of antibiotic resistance among microorganisms. One of these elements, Tn<i>5090</i>/Tn<i>402</i> is the basal vehicle of the type 1 integrons in which mobile resistance gene cassettes are inserted to form clusters and operons. The transposon was shown to preferentially target recombination sites of the serine family of recombinases that occur in many plasmids and transposons. Mutation analysis revealed that DNA-binding of the targeting factor, a serine recombinase, is essential for efficient transposition, while the recombination activity is not required. Truncated elements were frequently observed and in one instance borne on a composite transposon flanked by IS<i>6100</i>. This new transposon, Tn<i>5089</i>, has allowed the translocation of the integron to small mobilizable IncQ-plasmids that lack the targeting factor and thus are incompetent for insertion of Tn<i>5090</i>/Tn<i>402</i>. Another small replicon, by contrast targeting-positive, was completely sequenced.</p><p>The transposon Tn<i>5090</i>/Tn<i>402 </i>carries arrayed transposase-binding sites at the ends, which are supposed to arrange the transposase TniA in the appropriate geometry in a recombinationally active complex with DNA. Footprinting showed that transposase, TniA, binds to four 19 bp repeats on one end and to two 19 bp repeats on the other end.</p><p>Site-specific resolution of Tn<i>5090</i>/Tn<i>402</i> co-integrates<i> </i>was analysed in an <i>in vitro </i>system. The<i> res</i> site was found to be composed of three unusually organized subsites and expression of TniC was shown to be autoregulated by TniC acting as repressor due to an overlap of the <i>res</i> site with the promoter. </p><p>The data presented show several aspects of cooperation between transposition and site-specific recombination. This cooperation has enriched genes and combinations of genes that mediate resistance to antibiotic drugs and promotes lateral transfer of these genes. The organization of sites and subsites in the DNA is a subtle genetic code for the formation of the molecule complexes controlling these genetic events. </p>

Transposons of the Mu superfamily are widespread and have been shown to play an important role in the dissemination of antibiotic resistance among microorganisms. One of these elements, Tn5090/Tn402 is the basal vehicle of the type 1 integrons in which mobile resistance gene cassettes are inserted to form clusters and operons. The transposon was shown to preferentially target recombination sites of the serine family of recombinases that occur in many plasmids and transposons. Mutation analysis revealed that DNA-binding of the targeting factor, a serine recombinase, is essential for efficient transposition, while the recombination activity is not required. Truncated elements were frequently observed and in one instance borne on a composite transposon flanked by IS6100. This new transposon, Tn5089, has allowed the translocation of the integron to small mobilizable IncQ-plasmids that lack the targeting factor and thus are incompetent for insertion of Tn5090/Tn402. Another small replicon, by contrast targeting-positive, was completely sequenced. The transposon Tn5090/Tn402 carries arrayed transposase-binding sites at the ends, which are supposed to arrange the transposase TniA in the appropriate geometry in a recombinationally active complex with DNA. Footprinting showed that transposase, TniA, binds to four 19 bp repeats on one end and to two 19 bp repeats on the other end. Site-specific resolution of Tn5090/Tn402 co-integrates was analysed in an in vitro system. The res site was found to be composed of three unusually organized subsites and expression of TniC was shown to be autoregulated by TniC acting as repressor due to an overlap of the res site with the promoter. The data presented show several aspects of cooperation between transposition and site-specific recombination. This cooperation has enriched genes and combinations of genes that mediate resistance to antibiotic drugs and promotes lateral transfer of these genes. The organization of sites and subsites in the DNA is a subtle genetic code for the formation of the molecule complexes controlling these genetic events.

A consequence of antimicrobial use in food production systems is the potential for antimicrobial resistant (AMR) bacteria to develop and transfer to the human population via the food chain. Integrons have been identified as critical factors in the development of AMR. Despite Australia being amongst the world’s largest exporters of beef, there is a general lack of data on the prevalence of AMR in bacteria from Australian beef cattle. Consequently, the aim of this study has been to contribute to research strategies and knowledge of AMR by investigating integron-associated antimicrobial resistance in Australian beef cattle production systems. This study developed a protocol that targets resistance integrons. The protocol was trialled on 50 bovine faecal samples with a total of 39 integron-containing isolates recovered. Characterisation of the integrons was performed and it was determined that the majority of integrons harboured genes encoding resistance to trimethoprim (dfr) and streptomycin / spectinomycin (aad). The protocol provides an opportunity to rapidly interrogate populations of bacteria within a defined sample for resistance integrons. The protocol was used to investigate integron-associated AMR in Australian beef cattle production systems. Each production system was investigated for resistance integrons to determine if production practices were impacting on the prevalence and types of AMR present. The investigation found that the prevalence of integron-containing bacteria was higher in lot-fed cattle than grass-fed cattle which in turn were higher than organically produced cattle. However, the types of AMR differed very little across production systems and suggested that the higher prevalence of integrons in lot-fed samples may be a function of the intensive nature of this type of production system rather than a result of selective pressure caused by antibiotic use. Although there appeared to be no obvious trends in the types of gene cassettes carried by integrons from differing production systems, if lot-fed cattle continually arrive at slaughter with a higher prevalence of integron-containing bacteria then these cattle may be more likely to contribute to contamination of the final product. Samples from lot-fed, grass-fed and organically produced cattle at slaughter were collected. Despite the apparent unrelatedness of the cattle herds, there was little difference in the PCR prevalence of class 1 and class 2 integrase, the gene cassettes harboured by the integrons, and the host organism for the integron. Genes encoding resistance to streptomycin and chloramphenicol (catB8) dominated the majority of arrays regardless of production system, although two novel arrays were identified. One of the arrays, cmlA5-blaoxa-10-aadA1, was found in A. veronii biovar Sobria isolates from organic cattle thereby confirming the ability of multi-resistant integrons to persist in environments that have no obvious antimicrobial selection. The abattoir study revealed an unusually high prevalence of Aeromonas isolates carrying integrons. It appeared to implicate the abattoir environment as a direct contributor to the presence of integron-containing bacteria in each herd. Characterisation of each Aeromonas isolate determined that the isolates were not clonal in nature and not a result of persistent contamination at the abattoir. It seemed more probable that the Aeromonas isolates were present in the cattle prior to arrival and may have been acquired from the environment. To explore this further, soil samples from cattle associated and non-cattle associated areas were tested for the presence of resistance integrons. The prevalence of class 1 integrons was higher in cattle-associated soil samples than in non-cattle-associated soil samples, however the diversity of gene cassettes harboured by the integrons was greater in non-cattle-associated samples than cattle-associated samples. An array harbouring blaoxa-30 was isolated from a non-cattle-associated soil sample. Its presence continues to highlight the potential for multi-resistant integrons to exist in environments with no obvious antimicrobial selection pressure.The detection of seldom reported class 1 integron arrays in this study indicates the potential of the developed protocol to interrogate populations of bacteria for resistance integrons. This is highlighted further by the isolation of a novel class 2 integron. This novel class 2 integron from Providencia stuartii possesses a class 2 integrase that is predicted to be fully functional and has a variable region comprising nine ORFs that do not encode AMR genes. Overall, this study demonstrated that integrons are present in all cattle production systems employed in Australia and although the prevalence of integrons appeared to align with the anticipated use of antimicrobials in each system, differences in the integrons from each production system were not evident. As the similarities observed between integrons extend to isolates from organically produced cattle and from non-cattle associated soil samples it is suggested that the majority of integrons identified in this study are not present as a direct result of antimicrobial use in cattle production. Nevertheless, the potential of integrons to capture AMR genes remains and their presence in beef cattle highlights the need for the continued prudent use of antimicrobials.