Although its highly infectious nature has led to its classification as a potential bio-terror threat, very little is known about the pathogenesis of Francisella. A complete understanding of the mechanisms employed by Francisella to gain residence and replicate within macrophages will provide valuable insight into the means by which F. tularensis, and other intracellular pathogens such as M. tuberculosis and L. pneumophila, invade host cells, secrete effectors, alter phagosome biogenesis and disrupt vesicle traficking. The overall theme of this dissertation is the analysis of genes encoded within a recently identified Francisella pathogenicity island (FPI). In particular, the chapters will focus on the identification, mutagenesis, and phenotypic analysis of Pathogenicity determinant protein D (pdpD), a ~135 kDa protein encoded within the FPI. Chapter 2 addresses the identification of the Francisella pathogenicity island, and the intramacrophage growth of several mutants found within this loci. One of the greatest strengths in determining the roles of putative virulence genes is the ability of researchers to alter and amplify nucleic acids in a highly developed model platform and subsequently introduce the altered genetic material into a pathogen. Although genetic transformation has been well developed and optimized in E. coli, where it is regularly used in cloning experiments, the introduction of DNA into Francisella has been a major deterrent in the mutagenesis of putative virulence factors. Chapter 3 focuses on engineered genetic elements and methods for transformation, antibiotic selection, deletion mutagenesis, and complementation in Francisella strains. The chromosomes of F. tularensis strains carry two identical copies of the Francisella pathogenicity island, and the FPI of North American-specific biotypes contain two genes, anmK and pdpD, that are not found in biotypes distributed over the entire Northern Hemisphere. Furthermore, unlike other known intracellular pathogens, F. tularensis lacks a functional type III or type IV secretion system, which are necessary for other bacterium to arrest maturation of their respective phagosomes. Chapter 4 focuses on the virulence contribution of anmK and pdpD using F. novicida, which is very closely related to F. tularensis but carries only one copy of the FPI. In addition, the outer membrane localization of PdpD is examined in deletions of FPI genes encoding proteins that are homologues of known components of Type VI secretion systems. Although each chapter is a continuum of research related to the Francisella pathogenicity island, each will be treated as a distinct work consisting of an introduction, materials and methods, results, and a discussion. Chapter 5 of this dissertation will consist of an overall conclusion section which will tie the 3 research chapters together as well as focus on future studies.

MENEZES, Francisca Gleire Rodrigues de. Caracterização fenotípica e genotípica de bactérias do gênero Vibrio isoladas em alguns estuários do Estado do Ceará. 2011. 94 f. : Tese (doutorado) - Universidade Federal do Ceará, Centro de Ciências Agrárias, Departamento de Engenharia de Pesca, Fortaleza-CE, 2011 / Submitted by Nádja Goes (nmoraissoares@gmail.com) on 2016-07-26T13:27:46Z No. of bitstreams: 1 2011_tese_fgrmenezes.pdf: 2453594 bytes, checksum: 0370cb8f6e2c333d91e3ccc575df6f2b (MD5) / Approved for entry into archive by Nádja Goes (nmoraissoares@gmail.com) on 2016-07-26T13:28:01Z (GMT) No. of bitstreams: 1 2011_tese_fgrmenezes.pdf: 2453594 bytes, checksum: 0370cb8f6e2c333d91e3ccc575df6f2b (MD5) / Made available in DSpace on 2016-07-26T13:28:01Z (GMT). No. of bitstreams: 1 2011_tese_fgrmenezes.pdf: 2453594 bytes, checksum: 0370cb8f6e2c333d91e3ccc575df6f2b (MD5) Previous issue date: 2011 / The frequent association of environmental aquatic contamination with vibriosis in humans suggests the need for systematic monitoring and study of environmental vibrio strains and their pathogenic potential and clinical significance. The objective of this study was to evaluate the diversity of vibrio species in four estuaries (Pacoti, Choró, Pirangi and Jaguaribe) in Ceará, Northeastern Brazil. Nineteen vibrio species were identified in 32 water samples and 32 sediment samples collected between January and April 2009. Overall, V. parahaemolyticus and V. alginolyticus were the most abundant (the former in Choró, the latter in Pacoti). The isolated strains were submitted to antibiogram testing with 15 antibiotics. All strains (n=197) were susceptible to sulfametoxazol-trimetoprim, ciprofloxacin, nalidixic acid and chloramphenicol. Resistance was observed to penicillin G (n=163; 82%), ampicillin (n=108; 54%), cephalothin (n=15; 7%), aztreonam (n=3; 1%), gentamicin, cefotaxime, ceftriaxone (1 each; 0.5%). Partial resistance was observed to cefalotin (n=52; 25%), ampicillin (n=28; 14%), aztreonam (n=10; 5%), tetracycline (n=8; 4%), oxytetracycline (n=2; 1%), and florfenicol, cefotaxime, ceftriaxone, streptomycin and gentamicin (1 each; 0.5%). Five species known to be pathogenic to humans were chosen for analysis of factors of pathogenicity. Strains belonging to the species V. parahaemolyticus (n=64) and V. cholerae (n=9) were submitted to molecular analysis using genes to confirm the species and indicate virulence. Sixty-three strains of V. parahaemolyticus were positive for species-specific tl, 57 were positive for tdh and 20 for trh. Five strains of V. cholerae were positive for species-specific ompW, but no strains presented the genes ctxA, zot, tcp or rfbO1. In conclusion, the estuaries surveyed presented a great diversity of vibrio species, the most abundant of which were V. parahaemolyticus and V. alginolyticus. Resistance to penicillin and ampicillin was elevated and positivity for virulence factors was considerable among strains of species pathogenic to humans. V. parahaemolyticus strains presented virulence genes indicating risk to public health. V. cholerae was identified in samples of both water and sediment / Muitas pesquisas têm associado contaminação aquática ambiental com infecções de Vibrio em humanos, sugerindo que a importância do monitoramento sistemático das cepas ambientais se faz necessário para definir seu possível potencial patogênico e sua significância clínica. O objetivo dessa pesquisa foi estudar a diversidade do gênero Vibrio isolado de quatro regiões estuarinas no Estado do Ceará, (Pacoti, Choró, Pirangi e Jaguaribe). As coletas realizadas resultaram num total de 32 amostras de água e 32 de sedimento, durante os meses de janeiro a abril de 2009. Foram catalogadas 19 espécies de bactérias pertencentes ao gênero Vibrio, das quais Vibrio parahaemolyticus e Vibrio alginolyticus foram as mais abundantes nos quatro estuários: V. parahaemolyticus no Rio Choró e V. alginolyticus no Rio Pacoti. As cepas identificadas foram submetidas a testes de susceptibilidade a quinze antimicrobianos. Todas as cepas analisadas (197) apresentaram susceptibilidade a sulfazotrim, ciprofloxacin, ácido nalidíxico e cloranfenicol, sendo que cento e sessenta e três (82%) apresentaram resistência a penicilina G, cento e oito (54%) a ampicilina, quinze (7%) a cefalotina, três (1%) a aztreonam, uma (0,5%) a gentamicina, a cefotaxima e a ceftriaxona. Cinquenta e uma cepas (25%) apresentaram comportamento intermediário frente à cefalotina, vinte e oito cepas (14%) a ampicilina, dez (5%) a aztreonam, oito (4%) a tetracilina, duas (1%) a oxitetraciclina e uma (0,5%) a florfenicol, a cefotaxima, a ceftriaxona, a estreptomicina e a gentamicina. Foram escolhidas cinco espécies patógenas ao homem para verificação de seus fatores de patogenicidade. As cepas identificadas como V. parahaemolyticus (64) e V. cholerae (9) foram analisadas através de técnicas de biologia molecular, usando genes que confirmam as espécies e genes que indicam virulência. Das 64 amostras de V. parahaemolyticus analisadas, 63 foram positivas para o gene tl, específico para espécie, 57 para o gene tdh e 20 para o trh, genes que indicam patogenicidade. Das nove cepas de V. cholerae, cinco foram positivas para o gene ompW, gene específico para espécie, porém, nenhuma amostra apresentou os genes de virulência ctxA, zot, tcp e rfbO1. Com isso conclui-se que os estuários dos rios analisados apresentam uma elevada abundância de espécies, tendo V. parahaemolyticus e V. alginolyticus como as mais abundantes. O antibiograma das cepas isoladas mostrou uma elevada resistência à penicilina e a ampicilina. Foram encontradas elevada positividade para a presença dos fatores de virulência nas cepas pertencentes às espécies de Vibrio patógenas a humanos. As cepas de V. parahaemolyticus apresentaram genes de virulência indicando que as cepas podem acarretar danos à saúde pública. A presença do V. cholerae foi confirmada nas águas e sedimento dos estuários

Orientador: José Moacir Marin / Banca: Maria de Fátima Martins / Banca: Tammy Priscilla Chioda Delfino / Resumo: A resistência antimicrobiana em bactérias de origem animal tem se caracterizado como importante problema de saúde pública. No Brasil, muitos trabalhos têm verificado a presença de fatores de virulência e resistência em cepas de Escherichia coli isoladas de animais de produção, porém há poucos estudos avaliando estes aspectos em animais de companhia. O presente trabalho verificou o perfil de sensibilidade microbiana e a presença dos genes codificadores de adesinas (pap, sfa, afa), de intimina (eae) e de Shiga toxina (stx1, stx2) em cepas fecais de E. coli obtidas através de swabs retais de gatos diarréicos e de saudáveis, e em cepas urinárias de gatos com sintomas de infecção do trato urinário (ITU) apresentados para consultas e vacinação em clínicas veterinárias da região de Ribeirão Preto. Entre Janeiro e dezembro de 2009 foram isoladas 205 cepas de E. coli que foram caracterizadas quanto à presença de genes codificadores de fatores de virulência por PCR e sensibilidade microbiana pelo método de difusão em discos. O gene sfa ocorreu em maior abundância (35,6%) sendo mais freqüente entre animais com diarréia e ITU que entre os saudáveis. O gene eae foi verificado apenas entre os diarréicos (2,4%) e sempre associado ao sfa. O gene pap ocorreu em todos os grupos (22,43%). Genes stx1,stx2 e afa não foram encontrados. As resistências predominantemente observadas foram para cefalotina (42,1%), tetraciclina (20%) e ampicilina (15,8%) entre os isolados dos gatos diarréicos enquanto nos dos saudáveis as resistências mais freqüentes foram tetraciclina (30,5%), cotrimoxazol (17,9%) e ampicilina (20,0%). Gatos com ITU apresentaram maiores resistências para ampicilina (46,7%), cefalotina (13,3%) e ácido nalidíxico (13,3%). Multiresistência foi encontrada... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Antimicrobial resistance in animal origin bacteria has been characterized as an important public health problem. In Brazil, many studies have verified the presence of antimicrobial virulence factors and resistance in strains of Escherichia coli isolated from livestock, however there are few studies evaluating these aspects in pets. The current work verified the sensibility profile and the presence of genes encoding adhesins (pap, sfa, afa) intimin (eae) and Shiga toxin (stx1, stx2) in E. coli fecal strains obtained from rectal swabs from diarrheic and healthy cats and urinary strains from cats with symptoms of urinary tract infection (UTI) presented to be consulted and get vaccination in veterinary clinics in the region of Ribeirão Preto. Between January and December 2009 were isolated 205 strains of E. coli that have been characterized for the presence of genes encoding virulence factors by PCR and microbial sensitibility by disc diffusion method. The sfa gene occurred in greatest abundance (35.6%) was more common among animals with diarrhea and UTI than among the healthy. The eae gene was found only among diarrheic (2.4%) and always associated with sfa. The pap gene occurred in all groups (22.43%). Genes stx1, stx2 and afa were not found. The predominantly observed resistance was to cephalothin (42.1%), tetracycline (20%) and ampicillin (15.8%) among the isolates from diarrheic cats while in the healthy the tetracycline resistance was most frequent (30.5%), allowed by cotrimoxazol (17.9%) and ampicillin (20.0%). Cats with UTI showed greater resistance to ampicillin (46.7%), cephalothin (13.3%) and nalidixic acid (13.3%). Multidrug resistance was found in 8.4%, 17.9% and 33.3% of strains isolated from diarrheic healthy and with symptoms of UTI cats, respectively. The phenotype of resistance extended to beta-lactams (ESBL) was not... (Summary complete electronic access click below) / Mestre

Made available in DSpace on 2014-08-20T13:42:05Z (GMT). No. of bitstreams: 1 Tese_Elen_Silveira_Nalerio.pdf: 599740 bytes, checksum: f430564f38cd6d98d1788d137e38ed1e (MD5) Previous issue date: 2009-11-17 / Listeria monocytogenes is the causative agent of listeriosis which may cause a range of diseases from gastroenteritis, meningitis and death. In fact, disease outcome can be related to strain serotype/lineage thus molecular analyses has demonstrated that L. monocytogenes is a highly diverse species which can be grouped into three lineages. Whole-genome microarray can be employed to study phylogenetic relationships among Listeria strains either species or serotype level, in addition to demonstrate differences on their virulence potential and/or environmental adaptation. The aim of this study was the whole genome comparison of L. monocytogenes strains from different origins. Ninety-nine L. monocytogenes strains from different geographical origins (Brazil, Denmark, Austria, Ireland, USA and unknown), including clinical strains (humans and animals), food and food industries strains were analysed. DNA from all strains were competitively hybridized on to a L. monocytogenes DNA microarray based on the whole-genome sequence L. monocytogenes EGD-e. DNA labeling and hybridization protocol were followed according to Dorrell et al., (2001). Data acquisition, processing and comparative phylogenomics were performed as previously described by Stabler et al. (2006). Comparative phylogenomics clustered the L. monocytogenes strains into two central clades which is representative of the two main lineages of this species. In addition each of these clades were divided into two further subclades. Clade formation was independent of the geographical origin of strains with the exception of the clade containing persistent strains (strains that persist in food-processing environment), where none of the Brazilian strains were present. It was found 18 specific genes for lineage I strains (1/2a and 1/2c serotypes). These genes are related to carbohydrate metabolism, two component regulatory system, ABC transporter complex and bvrB and bvrC genes. Significantly all persistent strains clustered together in the same lineage I clade. We achieved a set of unique genes belonging exclusively to L. monocytogenes persistent strains pointing to be responsible for its adaptation profile. The genes are involved in stress resistance and are related to carbohydrate transport and metabolism, environmental information processing, signal transduction mechanisms, cell surface protein, amino acid transport and metabolism, nucleotide transport and metabolism, translation, cell wall biogenesis, replication, recombination and repair, transport of small molecules similar to ABC transporter, metabolism of lipids and unknown function. Interestingly from 14 virulence listed genes most of them were present in all studied L. monocytogenes strains with exception of inlE and inlG genes. These findings indicate that genetic variability of L. monocytogenes strains point to niche adaptation instead virulence differentiation despite of different origins. Persistent strains clustered suggesting genetic origin to survival in this environment. / Listeria monocytogenes é o agente causador da listeriose, uma infecção severa que pode cursar com sintomas que variam desde gastroenterites, meningites e até mesmo a morte. De fato, o desenvolvimento da doença pode ser relacionado a determinados sorotipos/linhagens das cepas de Listeria. Análises moleculares dos diferentes sorotipos/linhagens de L. monocytogenes, demonstraram que esta espécie é amplamente diversa, a qual pode ser agrupada em três linhagens. O estudo completo de genomas, baseado na técnica de microarray, pode ser empregado para estudar a relação filogenética entre cepas de Listeria tanto em nível de espécie, quanto em nível de sorotipo. Não obstante, a técnica de microarray visa evidenciar as diferenças no potencial patogênico e/ou adaptativo das cepas. O objetivo deste estudo foi a comparação filogenética entre cepas de L. monocytogenes isoladas de diferentes fontes. Foram analisadas 99 cepas de L. monocytogenes de diferentes origens geográficas (Brasil, Dinamarca, Áustria, Irlanda, Estados Unidos da América e fontes desconhecidas), incluindo cepas clínicas (humanas e animais), de alimentos e de indústrias alimentícias. O DNA das cepas teste foi hibridizado em DNA microarrays de L. monocytogenes baseado em seqüências do genoma de L. monocytogenes EGD-e. Os protocolos para marcação e hibridização do DNA seguiram as recomendações de Dorrell et al., (2001). A aquisição de dados, o processamento e as comparações filogenômicas foram realizadas conforme previamente descrito por Stabler et al. (2006). Comparações filogenômicas agruparam as cepas de L. monocytogenes em dois clades centrais, os quais são representativos das duas principais linhagens desta espécie. Além disso, cada um destes clades foram subdivididos em mais dois sub-clades. A formação dos clades foi independente da origem geográfica das cepas, com exceção do clade contendo cepas persistentes (cepas que persistem no ambiente de processamento de alimentos), onde nenhuma cepa Brasileira esteve presente. Foram identificados 18 genes específicos para as cepas da linhagem I (sorotipos 1/2a e 1/2c). Esses genes são relacionados ao metabolismo de carboidratos, sistema regulatório two component, complexo de transporte ABC e aos genes bvrB e bvrC. A grande maioria das cepas persistentes se agrupou no mesmo clade pertencente à linhagem I. Foi obtido um conjunto de genes únicos pertencentes exclusivamente às cepas persistentes de L. monocytogenes, os quais sugerem serem os responsáveis pelo perfil adaptativo destas cepas. Os genes são envolvidos em resistência ao estresse e são relacionados ao transporte e metabolismo de carboidratos, processamento de informação ambiental, mecanismos de transdução de sinais, proteína de superfície celular, transporte e metabolismo de aminoácidos, transporte e metabolismo de nucleotídeos, tradução, biogênese de parede celular, replicação, recombinação e reparo, transporte de pequenas moléculas similar ao transportador ABC, metabolismo de lipídios e de função desconhecida. Dos 14 genes de virulência listados a maioria deles esteve presente em todas as cepas de L. monocytogenes estudadas, com exceção dos genes inlE e inlG. Estes dados sugerem que, apesar das distintas origens de isolamento, a variabilidade genética das cepas de L. monocytogenes é direcionada para adaptação ambiental, ao invés da diferenciação visando virulência.

A carne está exposta à contaminações em todas as fases do seu processamento tecnológico, particularmente nas operações em que é mais manipulada e sempre que não são tomados cuidados especiais em relação às Boas Práticas de Higiene. O patógeno mais importante em carne bovina é Salmonella spp, o principal agente causador de doenças transmitidas por alimentos no mundo. Vários estudos têm relatado a ocorrência de Salmonella spp em carne bovina in natura disponível no mercado, mas pouco se sabe sobre este patógeno em carne bovina produzida no Brasil para exportação. O presente estudo objetivou verificar a prevalência, o perfil de susceptibilidade antimicrobiana, a presença de genes de virulência e o perfil de macrorrestrição por PFGE em cepas de Salmonella spp isoladas em diferentes pontos da cadeia de produção. A pesquisa foi realizada em um abatedouro de grande porte que produz carne bovina para exportação. Amostras de superfície foram coletadas de 200 animais, em três pontos do processo do abate: no couro (CO), na carcaça após a esfola (CA1) e na carcaça após a lavagem, antes da refrigeração (CA2), com um total de 600 amostras. A metodologia utilizada para detecção de Salmonella spp foi a preconizada pela ISO 6579:2002, confirmando-se os resultados de identificação pela técnica de PCR e sorotipagem completa. O patógeno foi encontrado no CO de 31 animais (15,5%), na CA1 de 7 animais (3,5%) e na CA2 de 6 animais (3%). Houve a prevalência do sorovar S. Infantis (54,5%), seguido de S. Enteritidis (13,6%). Pesquisou-se a presença dos genes de virulência invA, sitC, spaN, sifA e msgA por PCR nos isolados de Salmonella spp de cada ponto amostrado positivo, em um total de 44 isolados. Observou-se que 59,1% dos isolados apresentaram todos os genes pesquisados e que os demais apresentaram pelo menos dois dos cinco genes de virulência estudados. Os mesmos isolados foram analisados quanto à susceptibilidade aos antimicrobianos, empregando-se as fitas M.I.C Evaluator (Oxoid) com os antimicrobianos ampicilina, cefotaxima, ciprofloxacina, gentamicina, imipenem e tetraciclina. Dos 44 isolados estudados, todos foram sensíveis a cefotaxima, ciprofloxacina, gentamicina e imipenem, enquanto que 5 (11,4%) foram resistentes à ampicilina e à tetraciclina simultaneamente. O perfil de macrorrestrição, feito por FPGE, mostrou que os isolados expressaram 26 perfis genéticos distintos, sendo que maioria dos perfis (92,3%) foi constituída por apenas um ou dois isolados. Os resultados indicam que Salmonella spp está presente no abatedouro estudado. A ocorrência de isolados pertencentes ao mesmo sorovar e ao mesmo perfil de macrorrestrição no couro de animais e também nas carcaças CA1 e CA2 indica possível contaminação cruzada durante o processo de abate, reforçando a necessidade da adoção de Boas Práticas de Higiene para evitar a disseminação do patógeno na cadeia de produção da carne bovina. / Beef is exposed to contamination at all stages of the production chain, particularly in operations where it is more manipulated and when Good Hygiene Practices are not properly followed. The most relevant pathogen in bovine meat is Salmonella spp, the major causative agent of foodborne diseases in the world. Several studies have shown that Salmonella spp can occur in raw bovine meat at retail level, but little is known about this pathogen in meat produced for export. The present study aimed to determinate the prevalence, antimicrobial susceptibility test, the presence of virulence genes and PFGE macrorestriction profiles of Salmonella spp isolates obtained at different points of the production chain. The survey was conducted in a large slaughterhouse that produces bovine meat for export. Surface samples were collected from 200 animals, at three points of the slaughtering process: hide right (CO), carcass after removal of the hide (CA1) and carcass after cleaning but before chilling (CA2), with a total of 600 samples. The methodology used for detection of Salmonella spp was that recommended by ISO 6579:2002, and results were confirmed by PCR and complete serotyping. The pathogen was found in CO of 31 animals (15.5%), in CA1 of 7 animals (3.5%) and CA2 of 6 animals (3%). The prevalent serovar was S. Infantis (54.5%), followed by S. Enteritidis (13.6%). The presence of virulence genes invA, sitC, spaN, sifA and msgA was investigated by PCR in 44 isolates. All these genes were detected in 59.1% of the isolates, and the others had at least two of these virulence genes. The same isolates were tested for antimicrobial susceptibility using the MIC Evaluator strips (Oxoid) with the antimicrobials ampicillin, cefotaxime, ciprofloxacin, gentamicin, imipenem and tetracycline. All 44 isolates were sensitive to cefotaxime, ciprofloxacin, gentamicin and imipenem, whereas five (11.4%) were resistant to ampicillin and tetracycline simultaneously. The macrorestriction profiles, determined by PFGE, the 44 isolates expressed 26 different genetic profiles, and most profiles (92.3%) contained only one or two isolates. The results indicate that Salmonella spp is present in the studied abattoir. The occurrence of isolates belonging to the same serovar and presenting the same macrorestriction profile in the hides and in the carcasses indicates possible cross contamination during the slaughtering process, strengthening the need of adoption of Good Hygiene Practices to avoid dissemination of the pathogen in beef the production chain.

Les Escherichia coli pathogènes de la volaille (APEC) font partie des E. coli extra-intestinaux pathogènes (ExPEC) et seraient un réservoir possible de gènes de virulence et de résistance aux antimicrobiens (RAM) des ExPEC chez l’humain. L’objectif de cette étude était d’évaluer l’effet d’un prébiotique et d’un mélange d’acide organique et d’huiles essentielles encapsulés sur la prévalence des gènes de virulence des ExPEC et de RAM, ainsi que les associations entre ces gènes chez E. coli de l’intestin du poulet sain. Des échantillons de contenus caecaux de poulets de 29 jours d’âge ayant reçu un de ces ingrédients alimentaires comparativement à des témoins ont été analysés pour la présence des gènes de virulence iucD, tsh, papC et des gènes de RAM blaTEM, blaSHV, tetA, tetC, blaCMY-2, aadA1, aac3 par PCR. La prévalence d’iucD était supérieure dans le groupe témoin comparativement aux groupes «prébiotique» et «acide organique» et la prévalence de papC était affectée dans le groupe «acide organique». La prévalence d’isolats d’E.coli positifs pour blaCMY-2 était supérieure dans le groupe témoin comparée aux groupes «prébiotique» et «acide organique», tel que démontré par la technique d’hybridation de l’ADN sur HGMF (Hydrophobic Grid Membrane Filter). De plus, la prévalence des isolats d’E. coli positifs pour tetA, blaTEM, aadA1 ou tsh était affectée par les ingrédients alimentaires. Dans l’ensemble, des associations entre la présence de tsh et iucD, blaTEM et aadA1, et iucD et blaCMY-2 ont été observées. .Cette étude démontre l’utilité de certains ingrédients alimentaires pour dimunier le risque d’exposition en santé publique. / Avian Pathogenic E. coli (APEC) belong to the extra-intestinal pathogenic E. coli (ExPEC) pathotype, and may be a virulence and antimicrobial resistance (AMR) gene reservoir for ExPEC in humans. The aim of this study was to evaluate the effect of addition to the feed of a prebiotic or an organic acid on the prevalence of ExPEC-associated virulence genes and antimicrobial resistance (AMR) genes and the association between these genes in E. coli of the intestinal microflora of healthy chickens. Caecal contents from 29-day-old chickens having received one of these feed ingredients in comparison to a control group were examined for the presence of virulence genes iucD, tsh, and papC and AMR genes blaTEM, blaSHV, tetA, tetC, blaCMY-2, aadA1, and aac3 by PCR. The prevalence of iucD was significantly higher in the control group than in the prebiotic and organic acid groups and prevalence of papC was affected by the use of the organic acid. The prevalence of blaCMY-2-positive E. coli isolates was higher in the control group than the prebiotic or organic acid groups, as demonstrated by Hydrophobic–grid membrane filter (HGMF) DNA probe colony hybridization. In addition, the prevalence of E. coli isolates positive for tetA, blaTEM, aadA1 or tsh was affected by the use of these feed ingredients. Overall, associations between the presence of iucD and tsh, blaTEM and aadA1, and iucD and blaCMY-2 were observed. This study demonstrates that the use of certain feed ingredients could reduce the risk of exposure in a public health perspective.

Campylobacter jejuni é a espécie bacteriana mais comumente relacionada como causa de gastroenterite em humanos em vários países. Porém, o isolamento e o estudo de C. jejuni não são muito frequentes no Brasil, o que dificulta avaliar a dimensão dessa bactéria como causadora de doença em humanos e animais, bem como, determinar o impacto de sua presença em alimentos e no meio-ambiente. O objetivo desse trabalho foi avaliar a diversidade genética por cinco diferentes técnicas de tipagem molecular, o potencial patogênico pela pesquisa de 16 genes de virulência por PCR e o perfil de resistência pela concentração inibitória mínima por Etest® frente a quatro antimicrobianos e pela análise in silico de genes de resistência e pontos de mutação de linhagens de C. jejuni isoladas no Brasil. Foram estudadas 121 linhagens de C. jejuni isoladas de humanos (51), animais (35), alimentos (33) e ambiente (02) nos estados de Minas Gerais, São Paulo, Rio de Janeiro e Rio Grande do Sul, no período de 1996 a 2016. Todas as linhagens apresentaram os genes flaA, flhA, iamA, docA, ciaB, cdtA, cdtB, cdtC, racR, dnaJ, pldA, cadF, sodB e csrA. O gene wlaN foi detectado em 15 linhagens, e uma linhagem apresentou o gene virB11. Dentre as 121 linhagens estudadas, 68 linhagens foram resistentes a pelo menos um dos antimicrobianos testados. A resistência à ciprofloxacina, doxiciclina, tetraciclina e eritromicina foi observada em 43,8%, 34,7%, 34,7% e 4,9% das linhagens, respectivamente. O dendrograma de similaridade genética de Pulsed field gel electrophoresis (PFGE) agrupou as 121 linhagens estudadas em três grupos com similaridade genômica de 46,9% entre eles. Apesar da alta diversidade genômica entre as linhagens estudadas, algumas linhagens isoladas de diferentes fontes, locais e anos, apresentaram uma similaridade genotípica acima de 80% entre elas e, foram agrupadas em 21 subgrupos. Pelas sequências da SVR do gene flaA as linhagens estudadas foram agrupadas em dois grupos com linhagens isoladas de fontes clínicas e não clínicas e de humanos e animais com similaridade acima de 80,9 % entre elas e tipadas em 40 SVR-flaA alelos, sendo os alelos 57, 49 e 45 os mais frequentemente detectados. A análise do locus CRISPR por HRMA tipou as linhagens de C. jejuni em 23 diferentes variantes sendo que algumas variantes continham linhagens de origem clínica e não clínica e de humanos e animais. A árvore de SNPs gerada a partir dos dados do sequenciamento do genoma completo alocou as 116 linhagens sequenciadas em dois principais grupos. O grupo SNP-A agrupou 97 linhagens e o grupo SNP-B agrupou 19 linhagens, com linhagens de fontes clínicas e não clínicas e de humanos e animais, respectivamente. A técnica de Multilocus sequence typing (MLST) tipou as 116 linhagens de C. jejuni em 46 STs, e não foi observada a predominância de um ST. O índice de discriminação das metodologias de análise de SNPs no genoma completo, PFGE, MLST, sequenciamento das SVR do gene flaA e análise do locus CRISPR por HRMA foi 1,0, 0,982, 0,941, 0,939 e 0,874, respectivamente. Na análise in silico de genes de resistência e pontos de mutação, 95 linhagens apresentaram ao menos um gene de resistência ou ponto de mutação conhecido, sendo que a porcentagem de correlação entre os resultados de resistência fenotípicos e genotípicos foi maior que 66,7%; 94,6% e 96,8% para eritromicina, tetraciclina e ciprofloxacina, respectivamente. Conclui-se que a alta frequência da maioria dos genes de virulência pesquisados evidenciou o potencial patogênico das linhagens de C. jejuni estudadas. A resistência a antimicrobianos de primeira escolha utilizados para o tratamento da campylobacteriose encontrada nas linhagens estudadas é preocupante, podendo levar à falha terapêutica quando o tratamento é necessário. Os resultados obtidos pelas metodologias de tipagem molecular realizadas sugerem que uma possível contaminação possa ter ocorrido entre fontes clínicas e não clínicas e entre humanos e animais, ao longo de 20 anos no Brasil. Pelo índice de discriminação, foi observado que as metodologias de análise de SNPs no genoma completo e PFGE, em comparação com as outras técnicas de tipagem, foram as mais eficientes em discriminar as linhagens de C. jejuni do presente estudo. / Campylobacter jejuni is the most commonly bacterial species related as a cause of gastroenteritis in humans in several countries. However, the isolation and the study of C. jejuni have not been very frequently in Brazil, which makes it difficult to evaluate the involvement of this bacterium as a cause of diseases in humans and animals, as well as to determine the impact of its presence in food and the environment. The aim of this study was to evaluate the genetic diversity by five different molecular typing techniques, the pathogenic potential by searching for the presence of 16 virulence genes by PCR and the resistance profile by the minimum inhibitory concentration by Etest® against four antibiotics and by the in silico analyses of resistance genes and mutation points of C. jejuni strains isolated in Brazil. A total of 121 C. jejuni strains isolated from humans (51), animals (35), food (33) and the environment (02) in the States of Minas Gerais, Sao Paulo, Rio de Janeiro and Rio Grande do Sul, between 1996 to 2016 were studied. All strains presented the genes flaA, flhA, iamA, docA, ciaB, cdtA, cdtB, cdtC, racR, dnaJ, pldA, cadF, sodB and csrA. The wlaN gene was detected in 15 strains, and one strain presented the virB11 gene. Among the 121 strains studied, 68 strains were resistant to at least one of the antibiotics tested. Resistance to ciprofloxacin, doxycycline, tetracycline and erythromycin was observed in 43.8%, 34.7%, 34.7% and 4.9% of the strains, respectively. The Pulsed field gel electrophoresis (PFGE) dendrogram of genetic similarity clustered the 121 strains studied in three groups with a genomic similarity of 46.9% among them. Despite the high genomic diversity among the strains studied, some strains isolated from different sources, places and years, presented a genotypic similarity above 80% among them and were grouped into 21 subgroups. By flaA-SVR sequencing the strains studied were clustered into two groups with strains isolated from clinical and non-clinical sources and from humans and animals with a similarity above 80.9% among them and typed in 40 flaA-SVR alleles, being the alleles 57, 49 and 45 the most frequently detected. The analysis of the CRISPR locus by HRMA typed the C. jejuni strains in 23 different variants, with some variants containing strains from clinical and non-clinical origin and from humans and animals. The SNP tree generated from the whole genome sequencing data grouped the 116 strains sequenced into two major groups. SNP-A grouped 97 strains and SNP-B grouped 19 strains, with strains from clinical and non-clinical sources and from humans and animals, respectively. Multilocus sequence typing (MLST) technique typed the 116 C. jejuni strains in 46 STs, and it was not observed a predominant ST. The discrimination index of the analysis of SNPs in the whole genome, PFGE, MLST, flaA-SVR sequencing and analysis of the CRISPR locus by HRMA was 1.0, 0.982, 0.941, 0.939 and 0.874, respectively. In the in silico analyses of resistance genes and mutation points, 95 strains showed at least one resistance gene or known mutation point, and the percentage of correlation between phenotypic and genotypic resistance results was greater than 66.7%; 94.6% and 96.8% for erythromycin, tetracycline and ciprofloxacin, respectively. In conclusion, the high frequency of the majority of the virulence genes studied highlighted the pathogenic potential of the C. jejuni strains studied. Resistance to antimicrobials of first choice used for the treatment of campylobacteriosis found in the strains studied is worrying and may lead to therapeutic failure when treatment is required. The results obtained by the molecular typing methodologies performed suggest that a possible contamination may have occurred between clinical and non-clinical sources and between humans and animals over 20 years in Brazil. By the discrimination index, it was observed that the methodologies of analysis of SNPs in the whole genome and PFGE, in comparison to the other typing techniques, were the most efficients in discriminating the C. jejuni strains of the present study.

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.

Depuis quelques années et dans plusieurs pays, un nouveau type de Staphylococcus aureus résistant à la méthicilline (SARM), le séquence type (ST) 398, a été fréquemment retrouvé chez les porcs et chez les fermiers en contact avec ces porcs. Au Canada, très peu d’informations sont disponibles concernant le SARM d’origine porcine. Une première étude dans notre laboratoire a permis de récolter 107 isolats de SARM provenant de deux abattoirs porcins du Québec. Le présent travail vise à caractériser les gènes de virulence et de résistance aux antibiotiques de ces SARM, d’étudier leur formation de biofilm en relation avec la spécificité du groupe agr et de vérifier la localisation plasmidique et la transférabilité de ces gènes à des souches de SARM d’origine humaine. Plusieurs souches ont démontré différents patrons phénotypiques de résistance aux antibiotiques. Vingt-quatre souches représentatives de ces isolats ont été soumises à une caractérisation plus approfondie par une étude génotypique en utilisant une biopuce à ADN et un grand nombre de gènes de virulence a été détecté codant pour des entérotoxines staphylococcales, des leucocidines, des hémolysines, des auréolysines, des facteurs d’immunoévasion, des superantigènes, des facteurs d’adhésion et des facteurs impliqués dans la formation de biofilm. Des gènes de résistance envers les aminoglycosides, les macrolides, les lincosamides, les tétracyclines et les biocides ont été également détectés par biopuce et leur localisation plasmidique a par la suite été déterminée. La transférabilité de ces gènes de souches porcines à des souches de SARM d’origine humaine a été démontrée par conjugaison bactérienne; ainsi le transfert horizontal de certains gènes de résistance aux antibiotiques et de virulence a été observé. Ces travaux de recherche apportent une meilleure connaissance de la résistance aux antibiotiques et de la virulence des SARM d’origine porcine et de leur potentiel de contribution à l’émergence de certaines résistances et facteurs de virulence chez le SARM d’origine humaine. / In recent years and in several countries, a new type of methicillin-resistant Staphylococcus aureus (MRSA), the sequence type (ST) 398, has been frequently found in pigs and in farmers in contact with these pigs. In Canada, little information is available concerning MRSA from pigs. A previous study in our laboratory identified 107 MRSA isolates from two pig slaughterhouses in Quebec. This study was conducted to determine antimicrobial resistance and virulence genes of MRSA from abattoir pig, to study their biofilm formation in relation with agr specificity groups and to evaluate horizontal transfer of genes to a MRSA of human clinical origin. Different phenotypic patterns of antimicrobial resistance were observed in these MRSA and a representative subset of these isolates was selected for further characterization. Twenty-four porcine MRSA were characterized by a DNA microarray, the StaphyType of CLONDIAG. Our results demonstrated that the MRSA strains from the abattoirs contain several antimicrobial resistance genes responsible for macrolide and tetracycline resistance and virulence genes encoding staphylococcal enterotoxins, hemolysins, leukocidins, aureolysin, superantigens, immunoevasion, adhesion, and biofilm development. This study presents the first evidence that horizontal transfer of some of these genes can occur between MRSA of porcine and human origin. We also report for the first time biofilm formation in Livestock Associated-MRSA of porcine origin associated with agr group II. It is possible that biofilm formation favors colonization, persistence as well as zoonotic potential. This research provides a better understanding of antimicrobial resistance and virulence of MRSA from pigs and their potential contribution to the emergence of some resistance and virulence factors in MRSA of human origin.

Les Escherichia coli pathogènes de la volaille (APEC) font partie des E. coli extra-intestinaux pathogènes (ExPEC) et seraient un réservoir possible de gènes de virulence et de résistance aux antimicrobiens (RAM) des ExPEC chez l’humain. L’objectif de cette étude était d’évaluer l’effet d’un prébiotique et d’un mélange d’acide organique et d’huiles essentielles encapsulés sur la prévalence des gènes de virulence des ExPEC et de RAM, ainsi que les associations entre ces gènes chez E. coli de l’intestin du poulet sain. Des échantillons de contenus caecaux de poulets de 29 jours d’âge ayant reçu un de ces ingrédients alimentaires comparativement à des témoins ont été analysés pour la présence des gènes de virulence iucD, tsh, papC et des gènes de RAM blaTEM, blaSHV, tetA, tetC, blaCMY-2, aadA1, aac3 par PCR. La prévalence d’iucD était supérieure dans le groupe témoin comparativement aux groupes «prébiotique» et «acide organique» et la prévalence de papC était affectée dans le groupe «acide organique». La prévalence d’isolats d’E.coli positifs pour blaCMY-2 était supérieure dans le groupe témoin comparée aux groupes «prébiotique» et «acide organique», tel que démontré par la technique d’hybridation de l’ADN sur HGMF (Hydrophobic Grid Membrane Filter). De plus, la prévalence des isolats d’E. coli positifs pour tetA, blaTEM, aadA1 ou tsh était affectée par les ingrédients alimentaires. Dans l’ensemble, des associations entre la présence de tsh et iucD, blaTEM et aadA1, et iucD et blaCMY-2 ont été observées. .Cette étude démontre l’utilité de certains ingrédients alimentaires pour dimunier le risque d’exposition en santé publique. / Avian Pathogenic E. coli (APEC) belong to the extra-intestinal pathogenic E. coli (ExPEC) pathotype, and may be a virulence and antimicrobial resistance (AMR) gene reservoir for ExPEC in humans. The aim of this study was to evaluate the effect of addition to the feed of a prebiotic or an organic acid on the prevalence of ExPEC-associated virulence genes and antimicrobial resistance (AMR) genes and the association between these genes in E. coli of the intestinal microflora of healthy chickens. Caecal contents from 29-day-old chickens having received one of these feed ingredients in comparison to a control group were examined for the presence of virulence genes iucD, tsh, and papC and AMR genes blaTEM, blaSHV, tetA, tetC, blaCMY-2, aadA1, and aac3 by PCR. The prevalence of iucD was significantly higher in the control group than in the prebiotic and organic acid groups and prevalence of papC was affected by the use of the organic acid. The prevalence of blaCMY-2-positive E. coli isolates was higher in the control group than the prebiotic or organic acid groups, as demonstrated by Hydrophobic–grid membrane filter (HGMF) DNA probe colony hybridization. In addition, the prevalence of E. coli isolates positive for tetA, blaTEM, aadA1 or tsh was affected by the use of these feed ingredients. Overall, associations between the presence of iucD and tsh, blaTEM and aadA1, and iucD and blaCMY-2 were observed. This study demonstrates that the use of certain feed ingredients could reduce the risk of exposure in a public health perspective.