Genome Sequences Of Avian Pathogenic Escherichia Coli Strains Isolated From Brazilian Commercial Poultry.

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. The disease might present as different local infections or as septicemia. Here, we present the draft genome sequences of three Brazilian APEC strains isolated from different kinds of infections. The availability of these APEC genome sequences is important for gaining a thorough understanding of the genomic features of E. coli, particularly those of this pathotype.1e001101

Detection of genes under positive selection in Avian Pathogenic Escherichia coli (APEC) and humans pathogenic strains

Orientador: Wanderley Dias da SilveiraTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: A bactéria Escherichia coli coloniza o trato intestinal de aves e humanos, de maneira comensal sem causar processos infecciosos. No entanto alguns clones adquiriram fatores de virulência específicos, permitindo o desenvolvimento de diferentes doenças como infecção do trato urinário, diarréia e meningite em humanos e colibacilose em aves. As linhagens que causam doença em aves são tipicamente denominadas APEC (Avian Pathogenic Escherichia coli). Neste trabalho foram sequenciados e anotados os genomas de quatro linhagens APECs (SCI-07, SEPT362, S17 e O8)que, juntamente com mais nove genomas referentes a linhagens de Escherichia coli patogênicas para aves e patogênicas para humanos foram utilizados para a busca de genes sob seleção positiva. Os genes homólogos foram agrupados,e posteriormente submetidos ao alinhamento de códons e das sequencias protéicas correspondentes. Uma árvore filogenética foi gerada para cada grupo de proteínas homólogas. Testes estatísticos determinaram qual entre os modelos de seleção neutra ou seleção positiva melhor explicou os dados existentes (alinhamentos de códons e árvores filogenéticas). Essas análises detectaram duzentas e cinquenta e quatro grupos de genes homólogos com evidência de seleção positiva. Para cada grupo foi realizado um teste de recombinação para verificar se o aumento na variação das sequencias não era devido à conversão gênica, resultando em cento e dezesseis grupos de genes homólogos sob seleção positiva. A proteína correspondente a um gene de cada grupo de genes homólogos foi identificada, por meio da ferramenta Blast. Diversos fatores de virulência, já conhecidos, e proteínas regulatórias puderem ser detectados. Os genes sob seleção positiva, também foram submetidos à anotação considerando o termo GO (Gene Ontology),apenas da categoria processo biológico. Dos cento e dezesseis genes apenas cinquenta e sete puderam ser identificados por meio dessa metodologia. O resultado da classificação dos genes dentro da classe GO, considerando o terceiro nível hierárquico,mostrou que a maioria dos genes anotados (31) tinha relação com o metabolismo primário.As proteínas cuja identificação, por meio do blast, não foi possível (proteínas hipotéticas)foram submetidas à análise de predição de localização subcelular e de peptídeo sinal. Essas análises revelaram que três proteínas desconhecidas (hypothetical proteinECIAI39_1028, hypothetical proteinZ0639e hypothetical proteinEC042_3791) são potenciais alvos para estudos que visam à busca de novos fatores de virulência de Escherichia coli patogênicasAbstract: The bacterium Escherichia coli colonizesthe intestinal tract of birds and humans, in a commensal relationship without causing infection. However, some clones have acquired specific virulence factors allowing the development of various diseases such as urinary tract infection, diarrhea and meningitis in humans and colibacillosis in poultry. The strains that cause disease in birds are typically named APEC (Avian Pathogenic Escherichia coli). In this study we sequenced and annotated the genomes of four APECs strains (SCI-07, SEPT362, S17 and O8). These genomes and nine others avian pathogenic Escherichia coli and humans pathogenic strains genomes were used for studying genes under positive selection. The homologous genes were grouped and then subjected to codons and corresponding protein sequences alignment. A phylogenetic tree was generated for each group of homologous proteins. Statistical tests determined which among neutral or positive selection models best explains the existing data (codon alignments and phylogenetic trees). This analyzes detected two hundred fifty-four groups of homologous genes with positive selection evidence. For each group a recombination test was conducted to verify if the variation increase in the sequences was not due to gene conversion, resulting in one hundred and sixteen groups of homologous genes under positive selection. The protein corresponding to a gene of each group of homologous genes under positive selection was identified through Blast tool. Genes under positive selection were annotated considering the GO term (Gene Ontology), just for the biological process category. Only fifty-seven genes could be identified using this methodology. The gene classification within the GO classes, considering only the third hierarchical level showed that most of the annotated genes (31) were related with the primary metabolism. Proteins which blast identification was not possible (hypothetical proteins) were subjected to sub cellular localization and signal peptide prediction analyzes. These analyzes revealed that three unknown proteins (hypothetical protein ECIAI39_1028, hypothetical protein Z0639e hypothetical protein EC042_3791) are potential targets for studies, in order to search for new virulence factors of pathogenic Escherichia coliDoutoradoMicrobiologiaDoutora em Genética e Biologia Molecula

Draft genome of a Brazilian avian-pathogenic Escherichia coli strain and in silico characterization of virulence-related genes

Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying hen with swollen head syndrome

Draft Genome of a Brazilian Avian-Pathogenic Escherichia coli Strain and In Silico

Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying hen with swollen head syndrome

Avian extraintestinal Escherichia coli exhibits enterotoxigenic-like activity in the in vivo rabbit ligated ileal loop assay.

International audienceAvian pathogenic Escherichia coli (APEC) strains harbor a number of virulence genes and cause extraintestinal diseases, such as septicemia, swollen-head syndrome, salpingitis, and omphalitis in poultry. APEC strains are not known to cause intestinal diseases. Herein, for the first time, it is reported that APEC strains were able to induce an enterotoxigenic-like effect in rabbit ligated ileal loops. Strain SEPT362 caused cell detachment of the intestinal villi, which also showed a flattened and wilted appearance, but the integrity of the tight junctions was maintained. Additionally, this strain did not adhere to enterocytes in vivo, although adhesin encoding genes ( fimH, csgA, lpfA2-3, and ECP) were present while other lpfA types, sfa, afa, papC, and ral genes were not. This enterotoxigenic-like activity was conserved after thermal treatment of the supernatant at 65°C but not at 100°C. Moreover, experiments based on filtering with different molecular weight cut-off (MWCO) pore sizes demonstrated that the component associated with the observed biological effect has a molecular weight >100 kDa. Blast search and polymerase chain reaction assays for known E. coli virulence factors showed that strain SEPT362 harbors the gene encoding for the toxin EAST-1 and the serine protease autotransporter (SPATE) Tsh, but is negative for genes encoding for the toxins LT-I, STh, STp, Stx1, Stx2, CNF-1, CNF-2, CDT and the SPATEs Sat, Pic, Vat, SigA, SepA, EatA, EspP, or EspC. A cloned copy of the tsh gene in E. coli K-12 was also tested and was shown to have an enterotoxic effect. These results suggest that APEC might induce fluid accumulation in the rabbit gut. The Tsh autotransporter seems to be one of the factors associated with this phenotype

Overlapped Sequence Types (STs) and Serogroups of Avian Pathogenic (APEC) and Human Extra-Intestinal Pathogenic (ExPEC) <i>Escherichia coli</i> Isolated in Brazil

<div><p>Avian pathogenic <i>Escherichia coli</i> (APEC) strains belong to a category that is associated with colibacillosis, a serious illness in the poultry industry worldwide. Additionally, some APEC groups have recently been described as potential zoonotic agents. In this work, we compared APEC strains with extraintestinal pathogenic <i>E. coli</i> (ExPEC) strains isolated from clinical cases of humans with extra-intestinal diseases such as urinary tract infections (UTI) and bacteremia. PCR results showed that genes usually found in the ColV plasmid (<i>tsh</i>, <i>iuc</i>A, <i>iss</i>, and <i>hly</i>F) were associated with APEC strains while <i>fyu</i>A, <i>irp</i>-2, <i>fep</i>C <i>sit</i>D_chrom, <i>fim</i>H, <i>crl</i>, <i>csg</i>A, <i>afa</i>, <i>iha</i>, <i>sat</i>, <i>hly</i>A, <i>hra</i>, <i>cnf</i>1, <i>kps</i>MTII, <i>clpV</i>_Sakai and <i>mal</i>X were associated with human ExPEC. Both categories shared nine serogroups (O2, O6, O7, O8, O11, O19, O25, O73 and O153) and seven sequence types (ST10, ST88, ST93, ST117, ST131, ST155, ST359, ST648 and ST1011). Interestingly, ST95, which is associated with the zoonotic potential of APEC and is spread in avian <i>E. coli</i> of North America and Europe, was not detected among 76 APEC strains. When the strains were clustered based on the presence of virulence genes, most ExPEC strains (71.7%) were contained in one cluster while most APEC strains (63.2%) segregated to another. In general, the strains showed distinct genetic and fingerprint patterns, but avian and human strains of ST359, or ST23 clonal complex (CC), presented more than 70% of similarity by PFGE. The results demonstrate that some “zoonotic-related” STs (ST117, ST131, ST10CC, ST23CC) are present in Brazil. Also, the presence of moderate fingerprint similarities between ST359 <i>E. coli</i> of avian and human origin indicates that strains of this ST are candidates for having zoonotic potential.</p></div

Dendrogram showing similarity relationship among APEC (n = 76) and human ExPEC (n = 53).

<p>Similarity was established by the presence of virulence genes, using the Pearson correlation (centered). Isolates were clustered by the complete linkage method. Legends adopt the following pattern: STRAIN ID/CATEGORY (either APEC or human ExPEC)/ECOR/ST (ST COMPLEX – if applicable)/SEROTYPE. Darker spots indicate the presence of the referred genes.</p