Extensive data from O'ahu indicate that all streams on this island consistently exceed the USEPA standards (200 fecal coliform/100 ml, 33 enterococci/100 ml) for water quality. Soil was determined to be the source of the elevated counts of these bacteria. In tropical areas, as Hawai'i, these bacteria are able to survive and multiply in the soil. Thus, these bacteria can end up in nearby streams after heavy rains or due to erosion. As a result, the USEPA recommended indicator bacteria (fecal coliform, enterococci) cannot be used to reliably determine when waters in tropical areas are fecally contaminated. Several alternative indicators have been proposed for such areas such as C. perfringens and FRNA coliphages. Extensive monitoring data does not exist for the other islands of Hawai'i. Kaua'i differs from O'ahu in that it is older, wetter and contains an abundance of cesspools. The Nawiliwili Watershed, on the island of Kaua'i, was chosen for this study. Sampling was conducted over a period of one year, and all samples were assayed for the traditional USEPA indicators (fecal, coliform, enterococci) as well as two alternative indicators (C. perfringens, FRNA coliphages). Of the 14 sites sampled, 12 contained levels of fecal coliform and enterococci that exceeded the USEPA standards (200 fecal coliform/100 ml and 33 enterococci/100 ml. This is similar to what has been documented in O'ahu streams. Based on the concentrations of these indicator bacteria, the USEPA would deem these sites as sewage contaminated. However, monitoring of these same sites for C. perfringens indicated that there was no sewage contamination (geometric mean values fell below the proposed standard of 50 CFU/100 ml). FRNA coliphage data indicate that cesspools may be leaching into nearby streams. Two streams (Nawiliwili, Papakōlea) had geometric mean levels greater than the 50 PFU/100 ml (based on O'ahu streams). Other streams in the watershed may be sporadically contaminated by cesspool because elevated FRNA coliphage levels were detected on occasion. Genotyping these FRNA coliphage isolates furthered supported the theory that cesspools were contaminating these sites because 98% of the FRNA isolates were typed as human while only 2% were typed as of animal origin. Current USEPA standards (fecal coliform, enterococci) are not reliable indicators of sewage pollution in tropical areas, thus, alternative indicators such as C. perfringens and FRNA coliphages may prove to be better indicators in these areas.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2003. / Vita. Bibliography: 162-207.

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2005. / It is estimated by the World Health Organisation (WHO) that thousands of millions of cases of foodborne diseases occur world–wide every year. Enterobacter sakazakii is a member of the family Enterobacteriaceae and has been identified as an occasional contaminant of powdered infant formula milk (IFM). Enterobacter sakazakii is an opportunistic emerging pathogen and has the ability to cause a severe form of neonatal meningitis. This organism was referred to as “yellow pigmented Enterobacter cloacae” until 1980 after which it was renamed as E. sakazakii. The current method for the detection of E. sakazakii is very time consuming and includes pre–enrichment, enrichment in Enterobacteriaceae enrichment broth, subsequent plating on violet red bile glucose agar and subculturing on tryptone soy agar. In this study a polymerase chain reaction (PCR) method was developed for the identification of the presence of E. sakazakii in infant food products. A part of the 16S ribosomal RNA (rRNA) gene from E. sakazakii was amplified using the primer pair Esak2 and Esak3. An internal amplification control (IAC) was constructed as part of the PCR detection method. The 850 base pair (bp) E. sakazakii PCR product was digested with AluI and the two fragments containing the primer binding sites were ligated, resulting in a 240 bp IAC. During this study a positive band for both the target DNA (850 bp) and the IAC (240 bp) was simultaneously observed when the IAC was added to the PCR mixture at a concentration of 0.72 pg.ml-1. Four of 22 South African food products tested positive for the presence of E. sakazakii, using both the PCR and recommended culturing methods. The PCR method was used successfully for the detection of E. sakazakii within three days and thus provides a possible alternative and improvement on the recommended current culturing methods. Other microorganisms present in the products tested included Escherichia coli, Klebsiella pneumoniae, Raoultella terrigena (“Klebsiella terrigena”) and Chryseomonas luteola. Since E. sakazakii is usually present in low numbers in food products, it is possible that these few cells are unevenly distributed in the products, making it important to take multiple samples when evaluating IFM and thereby ensuring that even low numbers of this pathogen are detected.

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Em nosso meio, a resistência às cefalosporinas de amplo espectro em enterobactérias tem sido associada à produção de β-lactamases de espectro ampliado (ESβL). Porém, nos últimos anos, a produção de cefalosporinases do tipo AmpC mediadas por genes plasmídiais (pAmpC) também tem sido responsabilizada pela resistência a essas drogas. O objetivo deste estudo foi avaliar a presença de pAmpCs entre amostras de enterobactérias isoladas de pacientes internados no Hospital São Paulo que apresentaram infecção de corrente sangüínea, entre janeiro e julho de 2006. Foram estudadas 133 amostras de enterobactérias identificadas como K. pneumoniae (65 amostras), K. oxytoca (5 amostras), E. coli (41 amostras), P. mirabilis (18 amostras) e Salmonella spp. (4 amostras). O perfil de sensibilidade aos antimicrobianos selecionados foi avaliado pela técnica de diluição em ágar, segundo as recomendações do CLSI. A detecção fenotípica da produção de pAmpC foi realizada pelos testes tri-dimensional e de Hodge modificado. Adicionalmente, foi realizada a detecção fenotípica da produção de ESβL. A pesquisa e identificação dos genes que codificam pAmpC foram realizados pela técnica de reação em cadeia da polimerase (PCR) e seqüenciamento. Entre os antimicrobianos testados, imipenem (99,2%) apresentou a maior taxa de sensibilidade, seguido pela cefoxitina (80,5%). De forma geral, os isolados de K. pneumoniae apresentaram alto grau de resistência aos β- lactâmicos e os isolados de P. mirabilis apresentaram a menor taxa de sensibilidade para ciprofloxacino (27,8%). Entre as 133 amostras estudadas, 59 (44,4%) foram classificadas fenotipicamente como produtoras de ESβL pela metodologia de disco aproximação. Foi observada discordância entre os resultados dos testes fenotípicos para detecção de pAmpC. A produção de pAmpC foi observada em seis isolados de acordo com o teste tri-dimensional, enquanto, o método de Hodge modificado classificou 19 isolados como possíveis produtores de pAmpC. Além disso, resultados duvidosos foram observados em ambas as técnicas. Um único isolado de K. pneumoniae foi identificado como produtor de CMY-2. Este isolado foi corretamente identificado como produtor de pAmpC por ambos métodos fenotípicos empregados. / The broad-spectrum cephalosporins are the main therapeutic options to Enterobacteriaceae infections and the resistance to these agents has been associated to ESβL production. However, plasmid-mediated AmpC β-lactamases (pAmpC) have been associated with this resistance phenotype. The aim of this study was to determine the occurrence of pAmpC among clinical isolates recovered from bloodstream from patients hospitalized at a Brazilian teaching hospital, collected between January and July 2006. A total of 133 non-repetitive Enterobacteriaceae per patients (65 K. pneumoniae, 41 E. coli, 18 P. mirabilis, 05 K. oxytoca and 04 Salmonella spp.) were studied. The antimicrobial susceptibility profile was determined by CLSI agar dilution method. ESβL phenotype was detected by doubledisk diffusion method while pAmpC production was evaluated by two phenotypic methods: modified three-dimensional and modified Hodge tests and the presence of pAmpC genes was confirmed by PCR and sequencing. Among tested antimicrobial, imipenem showed the highest susceptibility rate (99.2%), followed by cefoxitin (80.5%). K. pneumoniae presented high resistance to β-lactams. P. mirabilis isolates showed the lower susceptibility rate to ciprofloxacin (27.8%). Fifty-nine (44.4%) of studied isolates were phenotypically classified as ESβL producers. Modified threedimensional and Hodge methods classified 06 and 19 Enterobacteriaceae strains as pAmpC producers, respectively. Discordant results were observed between phenotypic pAmpC detection methods. Of those, a single K. pneumoniae isolate was confirmed as CMY-2 producer. / TEDE / BV UNIFESP: Teses e dissertações

Capes / Uma superfície mal higienizada em um ambiente produtivo, somada à capacidade de adesão de um microrganismo, pode se tornar uma fonte potencial de contaminação e levar à formação de biofilmes. Estes, uma vez formados, são de difícil remoção e podem proliferar para a contaminação de alimentos. A preocupação com a segurança dos alimentos é um desafio, visto que problemas a ela relacionados podem comprometer a saúde do consumidor. O objetivo deste trabalho foi isolar microrganismos patogênicos potenciais produtores de biofilme microbiano presentes no processamento industrial de um frigorífico bovino. O desenvolvimento do trabalho se resume em três fases: entrevista com o coordenador de qualidade de um frigorífico da região dos Campos Gerais; diagnóstico de pontos críticos no controle de qualidade do processamento industrial desse frigorífico, por meio de um diagrama decisório e coleta de amostras durante o processo industrial através de swabs, utilizados no isolamento por microbiologia. Em seguida, foi identificado o perfil genético das amostras, por meio do isolamento de DNA, seguida de amplificação por Reação em Cadeia da Polimerase com os primers universais rD1 e fD1. Os dados gerados na primeira fase indicam os programas de controle de qualidade aplicados na indústria frigorífica em estudo. A entrevistada, responsável pelo controle de qualidade da indústria, salientou o uso de Boas Práticas de Fabricação (BPF), Análise de Perigo e Pontos Críticos de Controle (APPCC), Procedimento Padrão de Higiene Operacional (PPHO), Monitoramento de Pragas (MIP) e Folha de Verificação (FV). A partir do diagrama decisório, foram identificados 25 pontos para a coleta de amostras para a identificação de microrganismos patogênicos. Dentre esses, dez pontos amostrais foram isolados por microbiologia convencional com meio de cultura EMB, indicando contaminação de conteúdo gastrointestinal por coliformes fecais. Em dez pontos, nem sempre distintos, houve crescimento em meio de cultura SS – Salmonella Shigella, indicando contaminação durante o abate a partir da manipulação da carne pelos funcionários, uma vez que esses podem ser portadores sadios de microrganismos patogênicos. Para identificação genotípica das amostras sequenciadas, os resultados chegaram a nível de gênero, sendo Escherichia, Proteus, Hafnia e Bacillus, todos pertencentes ao grupo de Enterobactérias, com exceção de Bacillus. Verificou-se através da identificação genotípica, relacionada com os locais de coleta das amostras no fluxograma, que há contaminação cruzada no ambiente produtivo do presente frigorífico, na maioria dos pontos, relacionadas com o manipulador. / An unhygienic surface in a productive environment, added to the adhesion capacity of a microorganism, can become a potential source of contamination and lead to the formation of biofilms. These, once formed, are difficult to remove and can proliferate for food contamination. Concern about food safety is a challenge, as related problems can compromise consumer health. The objective of this work is to select potential pathogenic microorganisms producing microbial biofilms present in the industrial processing of a beef cattle. The development of the work is summarized in three phases: interview with the quality coordinator of a refrigerator in the Campos Gerais region; diagnosis of critical points in the quality control of the industrial processing of this refrigerator, through a decision diagram and sample collection during the industrial process through swabs, used in the isolation by microbiology. Then, the genetic profile of the samples was identified through DNA isolation, followed by amplification by Polymerase Chain Reaction with the universal primers rD1 and fD1. The data generated in the first phase indicated the quality control programs in the refrigeration industry under study. The interviewee, responsible for the quality control of the industry, emphasized the use of Good Manufacturing Practices (GMP), Hazard Analysis and Critical Control Points (HACCP), Standard Operating Procedures (PPHO), Pest Monitoring (IPM) And Verification Sheet (FV). From the decision diagram, 25 points were identified for the collection of samples for the identification of pathogenic microorganisms. Among these, ten sample points were isolated by conventional microbiology with EMB culture, indicating contamination of gastrointestinal contents by fecal coliforms. At ten points, not always distinct, there was growth in the SS - Salmonella Shigella culture, indicating contamination during slaughter from the handling of the meat by the employees, since they may be healthy carriers of pathogenic microorganisms. For genotypic identification of the sequenced samples, the results reached the species level, being Escherichia, Proteus, Hafnia and Bacillus, all belonging to the group of Enterobacteria, except for Bacillus. It was verified through the genotypic identification, related to the sample collection sites in the flowchart, that there is cross contamination in the productive environment of the present refrigerator, in most of the points, related to the manipulator.

Capes / Uma superfície mal higienizada em um ambiente produtivo, somada à capacidade de adesão de um microrganismo, pode se tornar uma fonte potencial de contaminação e levar à formação de biofilmes. Estes, uma vez formados, são de difícil remoção e podem proliferar para a contaminação de alimentos. A preocupação com a segurança dos alimentos é um desafio, visto que problemas a ela relacionados podem comprometer a saúde do consumidor. O objetivo deste trabalho foi isolar microrganismos patogênicos potenciais produtores de biofilme microbiano presentes no processamento industrial de um frigorífico bovino. O desenvolvimento do trabalho se resume em três fases: entrevista com o coordenador de qualidade de um frigorífico da região dos Campos Gerais; diagnóstico de pontos críticos no controle de qualidade do processamento industrial desse frigorífico, por meio de um diagrama decisório e coleta de amostras durante o processo industrial através de swabs, utilizados no isolamento por microbiologia. Em seguida, foi identificado o perfil genético das amostras, por meio do isolamento de DNA, seguida de amplificação por Reação em Cadeia da Polimerase com os primers universais rD1 e fD1. Os dados gerados na primeira fase indicam os programas de controle de qualidade aplicados na indústria frigorífica em estudo. A entrevistada, responsável pelo controle de qualidade da indústria, salientou o uso de Boas Práticas de Fabricação (BPF), Análise de Perigo e Pontos Críticos de Controle (APPCC), Procedimento Padrão de Higiene Operacional (PPHO), Monitoramento de Pragas (MIP) e Folha de Verificação (FV). A partir do diagrama decisório, foram identificados 25 pontos para a coleta de amostras para a identificação de microrganismos patogênicos. Dentre esses, dez pontos amostrais foram isolados por microbiologia convencional com meio de cultura EMB, indicando contaminação de conteúdo gastrointestinal por coliformes fecais. Em dez pontos, nem sempre distintos, houve crescimento em meio de cultura SS – Salmonella Shigella, indicando contaminação durante o abate a partir da manipulação da carne pelos funcionários, uma vez que esses podem ser portadores sadios de microrganismos patogênicos. Para identificação genotípica das amostras sequenciadas, os resultados chegaram a nível de gênero, sendo Escherichia, Proteus, Hafnia e Bacillus, todos pertencentes ao grupo de Enterobactérias, com exceção de Bacillus. Verificou-se através da identificação genotípica, relacionada com os locais de coleta das amostras no fluxograma, que há contaminação cruzada no ambiente produtivo do presente frigorífico, na maioria dos pontos, relacionadas com o manipulador. / An unhygienic surface in a productive environment, added to the adhesion capacity of a microorganism, can become a potential source of contamination and lead to the formation of biofilms. These, once formed, are difficult to remove and can proliferate for food contamination. Concern about food safety is a challenge, as related problems can compromise consumer health. The objective of this work is to select potential pathogenic microorganisms producing microbial biofilms present in the industrial processing of a beef cattle. The development of the work is summarized in three phases: interview with the quality coordinator of a refrigerator in the Campos Gerais region; diagnosis of critical points in the quality control of the industrial processing of this refrigerator, through a decision diagram and sample collection during the industrial process through swabs, used in the isolation by microbiology. Then, the genetic profile of the samples was identified through DNA isolation, followed by amplification by Polymerase Chain Reaction with the universal primers rD1 and fD1. The data generated in the first phase indicated the quality control programs in the refrigeration industry under study. The interviewee, responsible for the quality control of the industry, emphasized the use of Good Manufacturing Practices (GMP), Hazard Analysis and Critical Control Points (HACCP), Standard Operating Procedures (PPHO), Pest Monitoring (IPM) And Verification Sheet (FV). From the decision diagram, 25 points were identified for the collection of samples for the identification of pathogenic microorganisms. Among these, ten sample points were isolated by conventional microbiology with EMB culture, indicating contamination of gastrointestinal contents by fecal coliforms. At ten points, not always distinct, there was growth in the SS - Salmonella Shigella culture, indicating contamination during slaughter from the handling of the meat by the employees, since they may be healthy carriers of pathogenic microorganisms. For genotypic identification of the sequenced samples, the results reached the species level, being Escherichia, Proteus, Hafnia and Bacillus, all belonging to the group of Enterobacteria, except for Bacillus. It was verified through the genotypic identification, related to the sample collection sites in the flowchart, that there is cross contamination in the productive environment of the present refrigerator, in most of the points, related to the manipulator.

Orientador: Pilar Rodriguez de Massaguer / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-15T20:08:51Z (GMT). No. of bitstreams: 1 Chaves_RafaelDjalma_M.pdf: 1221605 bytes, checksum: 39b07012e6e51d1b792777e7b85fb78b (MD5) Previous issue date: 2010 / Resumo: Este trabalho teve como objetivos avaliar a microbiota de carnes embaladas a vácuo, em específico bactérias ácido lácticas (BAL) e enterobactérias. Para tanto foram analisadas 12 amostras de carne bovina brasileira embaladas a vácuo, sendo 7 deterioradas (5 contra-filé, 1 cupim e 1 picanha) e 5 não deterioradas (contra-filé). As amostras foram cedidas por 2 frigoríficos do estado de são Paulo, com exceção de 3 amostras não deterioradas adquiridas em mercado localizado na cidade de Campinas. Foi realizada a avaliação visual e sensorial das amostras, bem como a enumeração e identificação dos isolados recuperados, para posterior utilização no ensaio de reprodução do defeito. Foi analisada também a contaminação na linha de produção do frigorífico parceiro, desde o local de confinamento do gado até as esteiras de embalagem. As contagens da superfície da carne e do exsudato foram realizadas em meios específicos para cada grupo estudado: de Mann, Rogosa & Sharpe (MRS Agar, Difco) para BAL e Violet Red Bile Agar (VRBA, Oxoid) acrescido de 1% de glicose para enterobactérias. A incubação se deu a 30°C por 4 dias. As médias das contagens de BAL encontradas para as carnes deterioradas ficaram em torno de 108UFC/mL para o exsudato e 107UFC/100cm2 para a superfície da peça. Já para as enterobactérias, 106UFC/mL e 104UFC/100cm2, respectivamente. Para as carnes não deterioradas as medias de BAL ficaram em 107UFC/mL para o exsudato e 105UFC/100cm2 para a superfície e para as enterobactérias, 102UFC/mL e 102UFC/100cm2 respectivamente. A diferença entre as médias das contagens do exsudato proveniente das amostras deterioradas e não deterioradas, assim como entre as médias da superfície também provenientes dos 2 tipos de amostra, foram consideradas significativamente diferentes (p < 0.01). Os isolados foram identificados pelo sistema API (bioMérieux®), sendo API 50CHL para BAL como: Lactobacillus brevis (1 isolado), Lactobacillus pentosus (2 isolados), Lactococcus lactis (2 isolados) e Leuconostoc mesenteroides (2 isolados) e API 20E para enterobactérias identificadas como: Hafnia alvei (4 isolados), Serratia marcescens (2 isolados), Serratia odorifera (1 isolado), Yersinia enterocolitica (1 isolado), Klebsiella pneumoniae (1 isolado), Escherichia coli (4 isolados), Ewingella americana (1 isolado), Buttiauxella agrestis (1 isolado), Enterobacter sakazakii (1 isolado) e Flavimonas oryzihabitans (1 isolado) sendo que a Hafnia alvei predominou em 50% das amostras de carne embalada a vácuo, já no ambiente de frigorífico a E. coli predominou no corredor de abate. Para a realização do teste de reprodução do defeito, 3 peças de contrafilé foram cortadas, assepticamente, em bifes de 10x5x2cm e inoculadas individualmente com suspensão de células vegetativas pré-ajustada de 108UFC/mL (Densimatic) de 6 diferentes isolados de enterobactérias, 4 de BAL e 1 Pseudomonas sp. O vácuo aplicado nas sacolas plásticas présoldadas (EVA multicamadas) com os bifes inoculados foi de 6mBar, praticado normalmente pela industria, seguido de termo-encolhimento por 4 segundos a 83°C. A incubação foi procedida por 4 semanas a 4 e 15°C. Após 7 dias de incubação a 15°C, foi observado estufamento nas embalagens inoculadas com Hafnia alvei. Todas as outras embalagens inoculadas com enterobactérias, assim como com BAL, iniciaram o estufamento das embalagens com 15 dias de incubação. Com incubação a 4°C e somente após 6 semanas, aconteceu perda de vácuo e início de estufamento na embalagem inoculada com H. alvei. Apesar de que, de acordo com a literatura, os Clostridium psicrotróficos estão envolvidos nos episódios de estufamento de embalagens, nesta pesquisa concluímos que linhagens de BAL (homo e heterofermentativas) e enterobactérias também causam este defeito. Além disso, o abuso de temperatura (15°C) reportado ao longo da linha de produção do frigorífico em estudo pode aumentar a contaminação inicial destes organismos, fazendo com que o acondicionamento a vácuo não se torne uma barreira tão eficiente ao desenvolvimento de micro-organismos deterioradores e patogênicos / Abstract: This work aimed to evaluate the bacteria flora of vacuum packed meat, particularly lactic acid bacteria (LAB) and Enterobacteriaceae. For both microorganisms, 12 samples of red vacuum packaged meat were analyzed, seven of which were deteriorated (5 striploin, 1 hump and 1 rump cap) and 5 fresh (striploin). The samples were donated by 2 slaughterhouses located in São Paulo State, except 3 samples which were purchased in a market located in Campinas city. Enumeration and identification of the recovered isolates were performed, followed by inoculation tests to verify the defect. Contamination of slaughterhouse production line was also analyzed, from the stockyard area until the conveyor belt after packaging. Surface and purge counts were made with specific culture medium: de Mann, Rogosa & Sharpe (MRS agar, Difco) for LAB and Violet Red Bile Agar (VRBA, Oxoid), 1% glucose added, for Enterobacteriaceae. Incubation was conducted at 30°C for 4 days, LAB average counts found for deteriorated samples were ~ 108CFU/mL in purge and 107CFU/cm2 in meat surface and 106UFC/mL and 104CFU/100cm2 for Enterobacteriaceae, respectively. For fresh samples, the values for LAB were 107CFU/mL in purge and 105CFU/100cm2 of LAB in the meat surface and for Enterobacteriaceae, 102CFU/mL for purge and 102CFU/100cm2 for meat surface. Mean counts between purge from deteriored and non deteriored samples and mean counts between meat surface from both samples were considered significantly different (p <0.01). Isolates were identified with API system (bioMérieux®): API 50 CHL for LAB: Lactobacillus brevis (1 isolate), Lactobacillus pentosus (2 isolates), Lactococcus lactis (2 isolates) and Leuconostoc mesenteroides (2 isolates) and API 20E for Enterobacteriaceae identified as: Hafnia alvei (4 isolates), Serratia marcescens (2 isolates), Serratia odorifera (1 isolate), Yersinia enterocolitica (1 isolate), Klebsiella pneumoniae (1 isolate), Escherichia coli (4 isolates), Ewingella americana (1 isolate), Buttiauxella agrestis (1 isolate), Enterobacter sakazakii (1 isolate) and Flavimonas oryzihabitans (1 isolate). Hafnia alvei was the dominant species in 50% samples of vacuum packed meat while in the abattoir environment, E. coli was dominant at the slaughter blood conveyor. For the inoculation test to verify the defect, 3 fresh vacuum pack strip loins were aseptically cut in 10x5x2cm beefs and inoculated individually with pre adjusted bacterial suspension 108CFU/mL (Densimatic) of 6 different Enterobacteriaceae isolates, 4 LAB and 1 Pseudomonas sp. were used individually. The applied vacuum in individual packs (EVA multilayer) was 6mBar, as industrial practice, followed by heat-shrinking of 83°C, 4s. Incubation was about 4 weeks at 4 and 15°C. After 7 days incubation at 15°C, blown pack was observed in samples with Hafnia alvei inoculated. In all other samples, the blown pack started after 15 days incubation. After 6 weeks at 4°C, was observed vacuum loss in the sample inoculated with H. alvei. Although, according to literature, the psychrotrophic clostridia are involved in blown pack cases, in this research it is concluded that LAB strains (homo ¿ heterofermentative) and Enterobacteriaceae also cause the defect. Besides, temperature abuse along the slaughterhouse production line (15°C) may increase initial contamination of these organisms, becoming the vacuum packaging a non so efficient barrier against spoilage and pathogenic microorganisms development / Mestrado / Mestre em Ciência de Alimentos

PhD (Microbiology) / Department of Microbiology / Background: Diarrheal diseases have a major effect on human health, Globally; it is second only to pneumonia as a leading cause of death among children under five. They are due to a variety of infectious and non-infectious agents; including Entamoeba spp. Entamoeba histolytica is an invasive enteric protozoan parasite that causes amebiasis. Amebiasis is frequent in communities without clean water and poor sanitation, which include low-income South African populations in Giyani and Pretoria. In these populations, the amount of diarrhea caused by Entamoeba histolytica inclusive of all ages, sexes and HIV status is uncertain. Diagnosis of the parasite is usually by microscopy. However, microscopy lacks sensitivity and specificity, therefore it is not reliable. Fortunately, molecular diagnostic tests have been developed to detect different Entamoeba species in humans. It is known that the parasite E. histolytica causes asymptomatic and symptomatic diseases. However, the transition from colonization to disease is still unclear. While parasite and host factors, as well as environmental conditions influence the infection outcome, there is currently no clear explanation of wide variation in the presentation of the disease. This could suggest that there are other factors affecting the disease outcome. A better understanding of these factors as well as their role in disease remains target objectives of modern scientists and it will definitely help in the fight against the disease. In spite of the emerging evidence that the host microbiome, parasite burden and the inflammatory response contribute to the virulence of E. histolytica, their roles have never been defined in developing regions such as Giyani and Pretoria. In addition, the present study hypothesized that co-infections with E. histolytica and secretion of extracellular vesicles/exosomes have a significant impact on the virulence of E. histolytica. Little has been explored or elucidated about responses triggered by other enteropathogens/ameba interplay that could be important in the induction of tissue invasion and disease and also how E. histolytica/enteropathogens interplay in these infections has not been determined. Therefore, the knowledge of this interplay could help in understanding how this modifies disease manifestations by modulating pathogen virulence and the host response. The use of secretion systems is an essential biological process exploited by pathogenic microorganisms to promote survival and spread of the pathogen, which in turn exacerbate the infection. The study of extracellular vesicles (EVs) released by pathogens is a new and exciting field that may realistically contribute to a better understanding of the pathogenic process of E. histolytica and provide alternate control strategies. Aim and objective of the study: The overall aim of the study was to determine the impact of enteric pathogens and secreted extracellular vesicles on amebic virulence and the outcome of infection. This aim was addressed in through a series of six primary objectives, which were: a. To investigate the distribution and prevalence of protozoan parasites in South Africa. b. To investigate novel species of Entamoeba circulating in the South African population. ix c. To elucidate the impact of gut microbiota and immune response during amebic infection. d. To determine the role of Entamoeba histolytica macrophage inhibitory factor (EhMIF) during amebic infection. e. To investigate the impact of co-infections on the outcome of amebiasis. f. To determine the presence of secreted extracellular vesicles/exosomes in Entamoeba histolytica. Brief methodology and results: A modified and validated Taqman qPCR assay (with taqman probes and genus specific primers) was used for amplification and target detection. This assay was used to investigate the distribution and prevalence of protozoan parasites (Cryptosporidium spp and Giardia lamblia) in South Africa, the assay was considered superior for this project because it is more sensitive than conventional PCR and it can be used to detect multiple infection targets. This assay allows fast, accurate, and quantitative detection of a broad spectrum of enteropathogens and is well suited for surveillance or clinical purposes. A total of 484 stool samples collected from diarrheal and non-diarrheal patients from rural and urban communities of South Africa were studied. The overall prevalence of parasites (Giardia lamblia and Cryptosporidium spp) in rural and urban patients were found to be 49% (112/227) and 21% (54/257) respectively (p= < 0.0001). The distribution of specific pathogens in rural areas was Cryptosporidium spp (20%) and Giardia lamblia (14%). Our findings showed no significant difference in parasitic infections between gender and the age of the participants (Chapter 3). The discovery of novel species is of great importance to human health. We have recently discovered stools positive for Entamoeba organisms by microscopy but PCR negative for known Entamoeba species. This led to the hypothesis that novel species of Entamoeba are present in the South African population. A comprehensive assay was used which included probes to identify Entamoeba bangladeshi from diarrheal and non-diarrheal participants. A sensitive qPCR assays and amplicon sequencing was used to detect Entamoeba spp, Prevotella copri and Enterobacteriaceae. Interestingly, E. bangladeshi was identified in the South African population. Entamoeba was present in 27% (E. histolytica 8.5% (41/484), E. dispar 8% (38/484), and E. bangladeshi 4.75% (23/484) E. moshkovskii was not detected in the present study. We were also able to observe changes in the host microbiome and the parasite burden associated with E. histolytica infections in S. African diarrhea cases versus asymptomatic controls but not with E. bangladeshi or E. dispar. In E. histolytica positive samples the level of both parasite and P. copri were lower in non-diarrheal samples (p=0.0034) (Chapter 4). There is accumulating evidence that the inflammatory response contributes to injury. Little is known about the key parasite mediators of host mucosal immunopathology. This study hypothesized that migration inhibitory factor (MIF) mediates the destructive host inflammatory response seen in amebic colitis. To determine the role of EhMIF during amebic infection, we used a genetic approach to test the effect of EhMIF on mucosal inflammation. We found that EhMIF induces IL-8 secretion from intestinal epithelial cells. Mice treated with antibodies that specifically block EhMIF had reduced chemokine expression and neutrophil infiltration in the mucosa. In addition to antibody-mediated neutralization, mice infected with parasites overexpressing EhMIF had increased chemokine expression, neutrophil influx and mucosal damage. We also found that the concentration of EhMIF correlated with the level of intestinal inflammation in persons with intestinal amebiasis. Together, our results reveal a novel parasite mediator of mucosal inflammation and support MIF homologs as potential immunomodulatory targets (Chapter 5). To investigate the impact of co-infections on the outcome of amebiasis, we analyzed the co-occurence of E. histolytica with other enteropathogens known to cause diarrheal infections, such as Shigella/EIEC (IpaH), Campylobacter (cadf), Enterotoxigenic E. coli (STh), Norovirus GII and Adenovirus (Hexon). The results were compared with those obtained with E. histolytica that were not interacted with enteropathogens and with E. histolytica interacted with enteropathogens. The impact of multiple infections on the outcome of the infection was compared between nondiarrheal and diarrheal stool samples. It was found that co-infections with two pathogens were associated with diarrhea compared to single infections. Moreover, Norovirus GII, Campylobacter (Cadf) and co-infections were associated with diarrhea in the study population. This study did not show any significant impact of pathogens co-infecting with E. histolytica on the outcome of amebic infection (Chapter 6). The presence of secreted extracellular vesicles/Exosomes in Entamoeba histolytica was determined by using the Pathogenic ameba strains (HM-1:IMSS or HM-1:IMSS (Sub-strain-US) from petri’s lab to purify exosomes using the commercially available kit to isolate exosomes (total exosomes isolation kit). Our study for the first time revealed that E. histolytica does secrete Evs. This finding increases the appreciation that all organisms are likely to secrete these EVs (Chapter 7). However, the impact of these EVs on the pathogenesis of E. histolytica needs further investigations. Conclusion: This study has contributed significantly to our knowledge on infectious diarrhea and the diversity of Entamoeba species by providing new data on the rate and prevalence of Entamoeba diarrheal infections and their distribution in the South African population. Our study describes for the first time the presence of E. bangladeshi in the South African population. Furthermore, our results reveal a novel parasite mediator of mucosal inflammation and support MIF homologs as potential immunomodulatory targets. This study also, for the first time revealed that E. histolytica does secrete EVs. The results from this work will undoubtedly open an exciting research to establish a deeper understanding of the function and role of these vesicles in amebic infection. We encourage public health interventions like health education programs and improvement of sanitation and hygiene in these populations. Molecular diagnostics should be used for specific diagnostic in clinical settings. / NRF

Thesis (M. Tech. (Biomedical Technology)) -- Central University of technology, Free State, 2013 / The objective of this study was to determine the prevalence of Listeria monocytogenes and also to assess the general hygiene of fresh milk in the Maseru area, Lesotho. A total of 200 milk samples (40 pasteurised and 160 raw milk samples) were used for the research. Raw milk samples were collected from the local farmers at the Dairy reception as they bring it for selling. Pasteurised milk samples were bought from different milk selling points in the Maseru area. The total aerobic plate count, total coliform count and total E. coli count for 160 raw milk samples and 40 pasteurised samples were performed to determine the quality of milk. Milk was enriched in selective broths to increase detection sensitivity and was directly plated on selective agars for direct bacterial enumeration. About 54.4% of the of the raw milk samples had total aerobic plate counts greater that 200 000 cfu/ml while 55.6% (89/160) of the raw samples had high counts of greater than 20 cfu/ml for total coliforms, and 21.9% (35/160) of the samples had higher than expected total E. coli counts. High total coliform count was detected in 17.5% (7/40) of the pasteurised milk samples and about 67.5% (27/40) of these samples exceeded the limit for total aerobic plate counts. The counts exceeded the milk standards for pasteurised milk. Phosphatase activity was detected in seven pasteurised milk samples, whereas 33 tested negative for phosphatase activity. Some pasteurised milk samples tested positive for coliform counts which exceeded the maximum limits according to national standards for pasteurised milk. However, most of the pasteurised samples (82.5%) had acceptable counts of less than 20 cfu/ml. API and PCR were used for confirmation and amplification of the isolated Listeria strains. The prevalence of Listeria was found to be (3.75%). Listeria species were found in 6 out of 200 samples tested (160 raw milk samples and 40 pasteurised milk), and were only detected in the raw milk samples. Five species belonged to Listeria monocytogenes and one was Listeria innocua. None of the Listeria was detected in the pasteurised milk samples. Serotyping was done through multiplex PCR with D1, D2, FlaA and GLT primers to determine the serovar groups of L. monocytogenes. All six isolates revealed 214 bp gene which identifies the serotypes in Lineages I or III. The genetic fingerprinting of the isolated Listeria was also determined. Enterobacterial Repetitive Intergenic Consensus (ERIC) sequence-based PCR was used to generate DNA fingerprints with ERIC specific primers. On the basis of ERIC-PCR fingerprints, three different DNA patterns could be discriminated among the analysed isolates. Three L. monocytogenes isolates showed similar DNA banding patterns, while two isolates both had different profiles. A questionnaire was used to determine consumption of raw (unpasteurised) milk or pasteurised milk and its products and it was completed by 300 households from the community. Although there was no indicated prevalence of raw (unpasteurised) milk consumption from the community, participants indicated symptoms alleged to consumption of pasteurised milk and/or milk products. According to community perception some of the dairy products consumed were allegedly implicated in food poisoning illnesses experienced. Participants indicated more symptoms with both fresh and sour milk consumption than in cheese and yogurt consumption.

Les entérobactéries productrices de carbapénèmases peuvent être responsables d’impasses thérapeutiques puisque ces souches sont multirésistantes aux antibiotiques. La colistine, un antibiotique de la famille des polymyxines, fait partie des molécules de derniers recours potentiellement utilisables pour le traitement des patients infectés par ces souches. Son utilisation est ainsi en augmentation constante mais des résistances émergent.Ce travail a contribué à l’amélioration du diagnostic de la résistance à la colistine par le développement de deux nouveaux outils diagnostiques : un test rapide, le Rapid Polymyxin NP test et un milieu de culture sélectif, la gélose SuperPolymyxin. Il a permis d’identifier de nouvelles mutations chromosomiques au sein des gènes pmrA, pmrB, phoP, phoQ, mgrB et crrB responsables de l’acquisition de résistances et d’hétérorésistance à la colistine chez K. pneumoniae et K. oxytoca. Il a révélé que les mutations chromosomiques et les résistances plasmidiques étaient additionnelles et pouvaient entraîner l’acquisition d’un haut niveau de résistance à la colistine chez E. coli. Il a permis d’identifier une épidémie de souches de K. pneumoniae productrices de la carbapénèmase OXA-48 et résistantes à la colistine en France en 2014. Il a démontré que Hafnia était un genre d’entérobactéries présentant une résistance naturelle de bas niveau à la colistine. Enfin, il a permis de proposer une option thérapeutique, le ceftazidime/avibactam en association ou non avec l’aztréonam, pour traiter les patients infectés par les souches de K. pneumoniae productrices de carbapénèmases et résistantes à la colistine.Ce travail a ainsi contribué à améliorer les connaissances sur la résistance à la colistine chez les BGN au niveau du diagnostic, des mécanismes de résistance acquis, des résistances naturelles, et de l’épidémiologie et a permis de proposer des combinaisons d’antibiotiques actives in vitro sur les souches de K. pneumoniae productrices de carbapénèmases et résistantes à la colistine. / Carbapenemase-producing Enterobacteriaceae may be responsible for therapeutic impasses since these strains are multidrug-resistant. Colistin, an antibiotic of the polymyxin family, is one of the last-resort molecules potentially usable for the treatment of patients infected with these strains. Its use is thus constantly increasing but resistances emerge.This work contributed to improve the diagnosis of colistin resistance by developing two new diagnostic tools: a rapid test, the Rapid Polymyxin NP test and a selective culture medium, the SuperPolymyxin agar. It identified new chromosomal mutations within the pmrA, pmrB, phoP, phoQ, mgrB and crrB genes responsible for the acquisition of colistin resistance and heteroresistance in K. pneumoniae and K. oxytoca. It revealed that chromosomal mutations and plasmid resistance were additional and could lead to the acquisition of a high level of colistin resistance in E. coli. It identified an outbreak caused by colistin-resistant OXA-48-producing K. pneumoniae strains in France in 2014. It demonstrated that Hafnia was a genus of enterobacteria with low-level intrinsic resistance to colistin. Finally, it suggested a therapeutic option, the ceftazidime / avibactam in combination or not with aztreonam, to treat patients infected with colistin-resistant and carbapenemase-producing K. pneumoniae.This work has significantly contributed to improve the knowledge of colistin resistance in Gram negatives in diagnostic, in characterization of acquired or intrinsic resistance mechanisms, and in epidemiology.