Molecular analysis of inflammatory mechanisms associated with Escherichia coli and inflammatory bowel diseases

Inflammatory bowel diseases (IBD), encompasses a range of chronic, immune-mediated inflammatory disorders that are usually classified under two major relapsing conditions, Crohn’s Disease (CD) and ulcerative colitis (UC). Extensive studies in the last decades have suggested that the etiology of IBD involves environmental and genetic factors that lead to dysfunction of epithelial barrier with consequent deregulation of the mucosal immune system and inadequate responses to gut microbiota.Over the last decade, the microbial species that has attracted the most attention, with respect to CD etiology, is Eschericia coli. In CD tissue, E. coli antigens have also been identified in macrophages within the lamina propria, granulomas, and in the germinal centres of mesenteric lymph nodes of patients. They have been shown to adhere to and invade intestinal epithelial cells whilst also being able to extensively replicate within macrophages. Through the work of genome-wide association studies (GWAS), there is growing evidence to suggest that the microbial imbalance between commensal and pathogenic bacteria in the gut is aided by a defect in the innate immune system. Autophagy represents a recently investigated pathway that is believed to contribute to the pathogenesis of CD, with studies identified a variant of the autophagy gene, ATG16L1, as a susceptibility gene. The aim of my thesis was to study the cellular and molecular mechanism promoted by E.coli strains in epithelial cells and to assess their contribution to IBD pathology. To achieve this we focused on developing both an in vitro and in vivo model of AIEC infection. This allowed us to further our knowledge on possible mechanisms utilised by AIEC that promoted their survival, as well as developing a better understanding of host reactions. We demonstrate a new survival mechanism promoted by E.coli HM605, whereby it induces the expression of the anti-apoptotic proteins Bcl-XL and BCL2, all of which is exacerbated in an autophagy deficient system. We have also demonstrated the presence of AIEC-induced inflammasome responses in epithelial cells which are exacerbated in an autophagy deficient system and expression of NOD-like receptors (NLRs) which might mediate inflammasome responses in vivo. Finally, we used the Citrobacter rodentium model of infectious colitis to identify Pellino3 as an important mediator in the NOD2 pathway and regulator of intestinal inflammation. In summary, we have developed robust and versatile models of AIEC infection as well as provide new insights into AIEC mediated survival pathways. The collected data provides a new perception into why AIEC bacteria are able to prosper in conditions associated with Crohn’s disease patients with a defect in autophagy.

Estudo de resistência da bactéria Escherichia Coli a antibióticos em infecções urinárias na população da Região Autónoma da Madeira

As infecções do tracto urinário (ITU) são doenças infecciosas comuns e distinguem-se em dois grandes grupos: o das infecções do tracto urinário superior e o das infecções do tracto urinário inferior. O principal agente etiológico envolvido nas ITU é a bactéria Escherichia coli (E. coli), representando 80-95% dos invasores do tracto urinário na população em geral. É mais comum entre os adultos do sexo feminino, principalmente com actividade sexual, embora as crianças, mulheres grávidas e idosos também apresentam grande susceptibilidade. Paralelamente, a problemática da resistência aos antimicrobianos é um tema actual e muito debatido internacionalmente. Como tal, o presente estudo teve como principal objectivo contribuir para a identificação fiável da bactéria E. coli em infecções urinárias bem como a determinação do seu perfil de resistência a antibióticos. Os dados apresentados referem-se a um estudo efectuado entre Outubro de 2008 e Junho de 2009 no Laboratório de Análises Clínicas Castro Fernandes – MMC. Foram analisadas 6522 amostras de urina, das quais 390 corresponderam a uroculturas positivas. Verificou-se que o sexo feminino tem uma maior propensão para infecções urinárias, havendo uma tendência para o aumento das ITU com a idade. Na interpretação da cultura revelou-se importante a informação dada pelo exame cultural acerca do número de leucócitos. Concluiu-se que nas uroculturas cujo número de colónias foi superior a 105 com menos de três espécies de colónias diferentes na cultura, o número de leucócitos foi superior a 30 milhares de células por μL, o que sugere a existência de infecção urinária. No estudo do perfil de sensibilidade da bactéria E. coli isolada, para a família dos betalactâmicos (Ampicilina (AMP), Amoxicilina/Ácido Clavulânico (AMC), Piperacilina/Tazobactam (PIP/TZP)), família das cefalosporinas (Cefalotina (KF), Cefuroxima (CXM), Cefuroxima Acetil (CA), Cefotaxima (CTX), Ceftazidima (CAZ), Cefepima (FEP)), família dos aminoglicosídeos (Amicacina (AM), Gentamicina (GM), Tobramicina (TOB)) e para as nitrofurantoínas (F), verificou-se uma grande sensibilidade e pouca resistência em termos quantitativos, mas para a família das quinolonas (Ciprofloxacina (CIP), Levofloxacina (LEV), Norfloxacina (NOR)) e para os Trimetoprim/Sulfametoxazol (TMP/SMX) verificou-se resistências quantitativamente superiores aos das famílias anteriormente referidas, sugerindo valores convergentes aos da tendência europeia. Foram identificados famílias de fenótipos tais como: os beta-lactâmicos, os aminoglicosídeos, quinolonas, tetraciclinas, furanos e trimetoprim/sulfamidas.E. coli é um microganismo cujo fenótipo selvagem não tem resistências intrínsecas. Todas as resistências são adquiridas. Actualmente, a realização dos antibiogramas para E. coli tornou-se fundamental tendo em vista os factores ecológicos, genéticos, ambientais e pelo facto de que mais isolados são resistentes à maioria dos antibióticos. Como conclusão, este estudo permitirá alertar para um problema sério que é uma grande ameaça à Saúde Pública.

Escherichia coli from Crohn’s disease patient displays virulence features of enteroinvasive (EIEC), enterohemorragic (EHEC), and enteroaggregative (EAEC) pathotypes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of management strategies on the performance of ruminant livestock production systems and the safety of plant and animal products in the city of Sikasso, Mali

The regional population growth in West Africa, and especially its urban centers, will bring about new and critical challenges for urban development policy, especially in terms of ensuring food security and providing employment for the growing population. (Peri-) urban livestock and vegetable production systems, which can contribute significantly to these endeavours, are limited by various constraints, amongst them limited access to expensive production factors and their (in)efficient use. To achieve sustainable production systems with low consumer health risks, that can meet the urban increased demand, this doctoral thesis determined nutrient use efficiencies in representative (peri-) urban livestock production systems in three West African cities, and investigated potential health risks for consumers ensuing from there. The field study, which was conducted during July 2007 to December 2009, undertook a comparative analysis of (peri-) urban livestock production strategies across 210 livestock keeping households (HH) in the three West African cities of Kano/Nigeria (84 HH), Bobo Dioulasso/Burkina Faso (63 HH) and Sikasso/Mali (63 HH). These livestock enterprises were belonging to the following three farm types: commercial gardening plus field crops and livestock (cGCL; 88 HH), commercial livestock plus subsistence field cropping (cLsC; 109 HH) and commercial gardening plus semi-commercial livestock (cGscL; 13 HH) which had been classified in a preceding study; they represented the diversity of (peri-) urban livestock production systems in West Africa. In the study on the efficiency of ruminant livestock production, lactating cowsand sheep herd units were differentiated based on whether feed supplements were offered to the animals at the homestead (Go: grazing only; Gsf: mainly grazing plus some supplement feeding). Inflows and outflows of nutrients were quantified in these herds during 18 months, and the effects of seasonal variations in nutrient availability on animals’ productivity and reproductive performance was determined in Sikasso. To assess the safety of animal products and vegetables, contamination sources of irrigated lettuce and milk with microbiological contaminants, and of tomato and cabbage with pesticide residues in (peri-) urban agriculture systems of Bobo Dioulasso and Sikasso were characterized at three occasions in 2009. Samples of irrigation water, organic fertilizer and ix lettuce were collected in 6 gardens, and samples of cabbage and tomato in 12 gardens; raw and curdled milk were sampled in 6 dairy herds. Information on health risks for consumers of such foodstuffs was obtained from 11 health centers in Sikasso. In (peri-) urban livestock production systems, sheep and goats dominated (P<0.001) in Kano compared to Bobo Dioulasso and Sikasso, while cattle and poultry were more frequent (P<0.001) in Bobo Dioulasso and Sikasso than in Kano. Across cities, ruminant feeding relied on grazing and homestead supplementation with fresh grasses, crop residues, cereal brans and cotton seed cake; cereal grains and brans were the major ingredients of poultry feeds. There was little association of gardens and livestock; likewise field cropping and livestock were rarely integrated. No relation existed between the education of the HH head and the adoption of improved management practices (P>0.05), but the proportion of HH heads with a long-term experience in (peri-) urban agriculture was higher in Kano and in Bobo Dioulasso than in Sikasso (P<0.001). Cattle and sheep fetched highest market prices in Kano; unit prices for goats and chicken were highest in Sikasso. Animal inflow, outflow and dairy herd growth rates were significantly higher (P<0.05) in the Gsf than in the Go cattle herds. Maize bran and cottonseed expeller were the main feeds offered to Gsf cows as dry-season supplement, while Gsf sheep received maize bran, fresh grasses and cowpea pods. The short periodic transhumance of Go dairy cows help them maintaining their live weight, whereas Gsf cows lost weight during the dry season despite supplement feeding at a rate of 1506 g dry matter per cow and day, resulting in low productivity and reproductive performance. The daily live weight gains of calves and lambs, respectively, were low and not significantly different between the Go and the Gsf system. However, the average live weight gains of lambs were significantly higher in the dry season (P<0.05) than in the rainy season because of the high pressure of gastrointestinal parasites and of Trypanosoma sp. In consequence, 47% of the sheep leaving the Go and Gsf herds died due to diseases during the study period. Thermo-tolerant coliforms and Escherichia coli contamination levels of irrigation water significantly exceeded WHO recommendations for the unrestricted irrigation of vegetables consumed raw. Microbial contamination levels of lettuce at the farm gate and the market place in Bobo Dioulasso and at the farm gate in Sikasso were higher than at the market place in Sikasso (P<0.05). Pesticide residues were detected in only one cabbage and one tomato sample and were below the maximum residue limit for consumption. Counts of thermo-tolerant coliforms and Escherichia coli were higher in curdled than in raw milk (P<0.05). From 2006 to x 2009, cases of diarrhea/vomiting and typhoid fever had increased by 11% and 48%, respectively, in Sikasso. For ensuring economically successful and ecologically viable (peri-) urban livestock husbandry and food safety of (peri-) urban foodstuffs of animal and plant origin, the dissemination and adoption of improved feeding practices, livestock healthcare and dung management are key. In addition, measures fostering the safety of animal products and vegetables including the appropriate use of wastewater in (peri-) urban agriculture, restriction to approve vegetable pesticides and the respect of their latency periods, and passing and enforcement of safety laws is required. Finally, the incorporation of environmentally sound (peri-) urban agriculture in urban planning by policy makers, public and private extension agencies and the urban farmers themselves is of utmost importance. To enable an efficient (peri-) urban livestock production in the future, research should concentrate on cost-effective feeding systems that allow meeting the animals’ requirement for production and reproduction. Thereby focus should be laid on the use of crop-residues and leguminous forages. The improvement of the milk production potential through crossbreeding of local cattle breeds with exotic breeds known for their high milk yield might be an accompanying option, but it needs careful supervision to prevent the loss of the local trypanotolerant purebreds.

Differential regulation of MMP-13 expression in two models of experimentally induced periodontal disease in rats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

ANTIMICROBIAL ACTIVITY of CARPOLOBIA LUTEA EXTRACTS and FRACTIONS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Expressão de MMP-13 e ativação de vias de sinalização intracelular em dois modelos de doença periodontal induzida experimentalmente em ratos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Resonadores piezoeléctricos de cizalladura: estudio de la formación de biofilms y caracterización de fluidos magneto‐reológicos

La presente tesis revisa y analiza algunos aspectos fundamentales relativos al comportamiento de los sensores basados en resonadores piezoeléctricos TSM (Thickness Shear Mode), así como la aplicación de los mismos al estudio y caracterización de dos medios viscoelásticos de gran interés: los fluidos magnetoreológicos y los biofilms microbianos. El funcionamiento de estos sensores está basado en la medida de sus propiedades resonantes, las cuales varían al entrar en contacto con el material que se quiere analizar. Se ha realizado un análisis multifrecuencial, trabajando en varios modos de resonancia del transductor, en algunas aplicaciones incluso de forma simultánea (excitación pulsada). Se han revisado fenómenos como la presencia de microcontactos en la superficie del sensor y la resonancia de capas viscoelásticas de espesor finito, que pueden afectar a los sensores de cuarzo de manera contraria a lo que predice la teoría convencional (Sauerbrey y Kanazawa), pudiéndonos llevar a incrementos positivos de la frecuencia de resonancia. Además, se ha estudiado el efecto de una deposición no uniforme sobre el resonador piezoeléctrico. Para ello se han medido deposiciones de poliuretano, modelándose la respuesta del resonador con estas deposiciones mediante FEM. El modelo numérico permite estudiar el comportamiento del resonador al modificar distintas variables geométricas (espesor, superficie, no uniformidad y zona de deposición) de la capa depositada. Se ha demostrado que para espesores de entre un cuarto y media longitud de onda aproximadamente, una capa viscoelástica no uniforme sobre la superficie del sensor, amplifica el incremento positivo del desplazamiento de la frecuencia de resonancia en relación con una capa uniforme. Se ha analizado también el patrón geométrico de la sensibilidad del sensor, siendo también no uniforme sobre su superficie. Se han aplicado sensores TSM para estudiar los cambios viscoelásticos que se producen en varios fluidos magneto-reológicos (FMR) al aplicarles distintos esfuerzos de cizalla controlados por un reómetro. Se ha podido ver que existe una relación directa entre diversos parámetros reológicos obtenidos con el reómetro (fuerza normal, G’, G’’, velocidad de deformación, esfuerzo de cizalla…) y los parámetros acústicos, caracterizándose los FMR tanto en ausencia de campo magnético, como con campo magnético aplicado a distintas intensidades. Se han estudiado las ventajas que aporta esta técnica de medida sobre la técnica basada en un reómetro comercial, destacando que se consigue caracterizar con mayor detalle algunos aspectos relevantes del fluido como son la deposición de partículas (estabilidad del fluido), el proceso de ruptura de las estructuras formadas en los FMR tanto en presencia como en ausencia de campo magnético y la rigidez de los microcontactos que aparecen entre partículas y superficies. También se han utilizado sensores de cuarzo para monitorear en tiempo real la formación de biofilms de Staphylococcus epidermidis y Eschericia coli sobre los propios resonadores de cristal de cuarzo sin ningún tipo de recubrimiento, realizándose ensayos con cepas que presentan distinta capacidad de producir biofilm. Se mostró que, una vez que se ha producido una primera adhesión homogénea de las bacterias al sustrato, podemos considerar el biofilm como una capa semi-infinita, de la cual el sensor de cuarzo refleja las propiedades viscoelásticas de la región inmediatamente contigua al resonador, no siendo sensible a lo que sucede en estratos superiores del biofilm. Los experimentos han permitido caracterizar el módulo de rigidez complejo de los biofilms a varias frecuencias, mostrándose que el parámetro característico que indica la adhesión de un biofilm tanto en el caso de S. epidermidis como de E. coli, es el incremento de G’ (relacionado con la elasticidad o rigidez de la capa), el cual viene ligado a un incremento de la frecuencia de resonancia del sensor. ABSTRACT This thesis reviews and analyzes some key aspects of the behavior of sensors based on piezoelectric resonators TSM (Thickness Shear Mode) and their applications to the study and characterization in two viscoelastic media of great interest: magnetorheological fluids and microbial biofilms. The operation of these sensors is based on the analysis of their resonant properties that vary in contact with the material to be analyzed. We have made a multi-frequency analysis, working in several modes of resonance of the transducer, in some applications even simultaneously (by impulse excitation). We reviewed some phenomena as the presence of micro-contacts on the sensor surface and the resonance of viscoelastic layers of finite thickness, which can affect quartz sensors contrary to the conventional theory predictions (Sauerbrey and Kanazawa), leading to positive resonant frequency shifts. In addition, we studied the effect of non-uniform deposition on the piezoelectric resonator. Polyurethane stools have been measured, being the resonator response to these depositions modeled by FEM. The numerical model allows studying the behavior of the resonator when different geometric variables (thickness, surface non-uniformity and deposition zone) of the deposited layer are modified. It has been shown that for thicknesses between a quarter and a half of a wavelength approximately, non-uniform deposits on the sensor surface amplify the positive increase of the resonance frequency displacement compared to a uniform layer. The geometric pattern of the sensor sensitivity was also analyzed, being also non-uniform over its surface. TSM sensors have been applied to study the viscoelastic changes occurring in various magneto-rheological fluids (FMR) when subjected to different controlled shear stresses driven by a rheometer. It has been seen that there is a direct relationship between various rheological parameters obtained with the rheometer (normal force, G', G'', stress, shear rate ...) and the acoustic parameters, being the FMR characterized both in the absence of magnetic field, and when the magnetic field was applied at different intensities. We have studied the advantages of this technique over the characterization methods based on commercial rheometers, noting that TSM sensors are more sensitive to some relevant aspects of the fluid as the deposition of particles (fluid stability), the breaking process of the structures formed in the FMR both in the presence and absence of magnetic field, and the rigidity of the micro-contacts appearing between particles and surfaces. TSM sensors have also been used to monitor in real time the formation of biofilms of Staphylococcus epidermidis and Escherichia coli on the quartz crystal resonators themselves without any coating, performing tests with strains having different ability to produce biofilm. It was shown that, once a first homogeneous adhesion of bacteria was produced on the substrate, the biofilm can be considered as a semi-infinite layer and the quartz sensor reflects only the viscoelastic properties of the region immediately adjacent to the resonator, not being sensitive to what is happening in upper layers of the biofilm. The experiments allow the evaluation of the biofilm complex stiffness module at various frequencies, showing that the characteristic parameter that indicates the adhesion of a biofilm for the case of both S. epidermidis and E. coli, is an increased G' (related to the elasticity or stiffness of the layer), which is linked to an increase in the resonance frequency of the sensor.

Campylobacter jejuni and campylobacter coli genotyping by high-resolution melting analysis of a flaA fragment

The highly variable flagellin-encoding flaA gene has long been used for genotyping Campylobacter jejuni and Campylobacter coli. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The objective of this study was to apply HRM analysis to flaA-based genotyping. The initial aim was to identify a suitable flaA fragment. It was found that the PCR primers commonly used to amplify the flaA short variable repeat (SVR) yielded a mixed PCR product unsuitable for HRM analysis. However, a PCR primer set composed of the upstream primer used to amplify the fragment used for flaA restriction fragment length polymorphism (RFLP) analysis and the downstream primer used for flaA SVR amplification generated a very pure PCR product, and this primer set was used for the remainder of the study. Eighty-seven C. jejuni and 15 C. coli isolates were analyzed by flaA HRM and also partial flaA sequencing. There were 47 flaA sequence variants, and all were resolved by HRM analysis. The isolates used had previously also been genotyped using single-nucleotide polymorphisms (SNPs), binary markers, CRISPR HRM, and flaA RFLP. flaAHRManalysis provided resolving power multiplicative to the SNPs, binary markers, and CRISPR HRM and largely concordant with the flaA RFLP. It was concluded that HRM analysis is a promising approach to genotyping based on highly variable genes.

Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis

In total, 782 Escherichia coli strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal- and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.