Dataset Information

Novel gene discovery in up to 10 ETEC strains and production of species microarray. Discovery of conserved and unique ETEC genes by comparative genome hybridization studies.

ABSTRACT: PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. Infectious diarrhea is a leading worldwide cause of infant mortality and secondary malnutrition. Enterotoxigenic E. coli (ETEC) is a principal etiology of travelers?diarrhea and a major endemic health threat, especially among children in developing nations where it is estimated to cause hundreds of thousands of deaths each year. Vaccine development for ETEC has been significantly hampered by the remarkable genetic plasticity of E. coli, a comparatively modest understanding of the basic pathogenesis of these organisms, and an uncertainty regarding the degree to which any given antigenic target might be conserved. While experimental and epidemiologic data suggest that a broadly protective vaccine can be achieved, this will most effectively be accomplished in a research environment that fosters sharing of vital resources and open, collaborative interactions among multiple investigators. The proposed project is aimed at providing critical leverage to ongoing international investigative efforts pertaining to ETEC pathogenesis and vaccinology. The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a species DNA microarray to better understand the ancestral relationships among its members. Based on preliminary MLST genotyping, 11 diverse ETEC strains were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for ETEC group members. The availability of the ETEC species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of ETEC group.

ORGANISM(S): Escherichia coli

PROVIDER: GSE25601 | GEO | 2010/12/07

SECONDARY ACCESSION(S): PRJNA134243

REPOSITORIES: GEO

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Project description:The PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. Clostridium botulinum produces botulinum neurotoxin (BoNT)and is classified as a “Category A” select agent. BoNT can be classified into seven serotypes designated A-G. There is considerable genetic variation within these serotypes, as demonstrated by the recognition of at least 47 subtypes. The most studied serotype, BoNT/A, has been found in a large and diverse group of clostridia, most of which express the subtype BoNT/A1. The BoNT/A1 producing C. botulinum strain ATCC 3502, used to obtain an initial annotated genome sequence, is not representative of the diverse clostridia group producing BoNT. Nearly 50% of C. botulinum strains producing BoNT/A1 have been shown to also encode unexpressed variants of BoNT/B with a distinct cluster arrangement. This nucleotide cluster is completely absent from the published genome sequence. In addition, a recently identified novel BoNT/A1 strain lacks the gene cluster seen in the genome sequence of ATCC 3502. Furthermore, a strain designated Hall A Hyper differs greatly from the sequenced strain as indicated by its ability to produce higher quantities of BoNT/A1. The genetic and phenotypic basis for this difference in BoNT expression is currently unknown, and the sequences of the BoNT gene and the cluster are identical in both strains. This observation supports the hypothesis that genes outside the toxin cluster are involved in the regulation and maturation of BoNT. The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a “species” DNA microarray to better understand the ancestral relationships among its members. Based on preliminary genotyping (MLST, and CGH using a single-genome-based array), 20 diverse C. botulinum strains were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for C. botulinum group members. The availability of the C. botulinum species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of C. botulinum group.

Project description:Enterotoxigenic Escherichia coli (ETEC) strains that produce both heat-stable (ST) and heat-labile (LT) enterotoxins cause severe post-weaning diarrhea in piglets. However, the relative importance of the individual enterotoxins to the pathogenesis of ETEC infection is poorly understood. In this study, we investigated the effect on virulence of an F4+ ETEC strain when removing some or all of its enterotoxins. Several isogenic mutant strains were constructed that lack the expression of LT in combination with one or both types of ST enterotoxins (STa and/or STb). Host early immune responses induced by these mutant strains 4h after infection were compared to the wild type strain GIS26 Â (O149:F4ac+, Â LT+ Â STa+ Â STb+). At the same time, the immune response of this wild type ETEC strain was compared to the mock-infected control, demonstrating the expression of porcine inflammatory response genes. For these purposes, the small intestinal segment perfusion (SISP) technique and microarray analysis were used and results were validated by qRT-PCR. We also measured net fluid absorption of pig small intestinal mucosa 4h after infection with wild type ETEC, the mutant strains and PBS (mock-infected). These data indicate an important role for STb in inducing small intestinal secretion early after infection. The microarray analysis of the different mutant strains also revealed an important role for STb in ETEC-induced immune response by the significant differential regulation of immune mediators like matrix metalloproteinase 3, interleukin 1 and interleukin 17. We conclude that STb can play a prominent role in ETEC-induced secretion and early immune response. In three pigs, 6 different treatments were performed. These treatments consisted of 4 mutant enterotoxigenic Escherichia coli GIS26 strains, GIS26 wild type strain, or PBS control. Per pig, the small intestine was divided into 6 loops with an interloop in between to avoid cross-contamination. In conclusion, every pig received each of the 6 treatments ad random.

Project description:The PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. Many infectious agents that cause emerging and re-emerging diseases appear to evolve from non-virulent forms. We still lack a clear understanding about the natural history of various microbial agents that cause human infectious diseases and the events leading to acquisition of their pathogenic potential. There have been seven pandemics of V. cholerae throughout the history of the mankind. To date, the world population is still experiencing the seventh one which started in the early 1960s. From almost 200 recognized V. cholerae serotypes, the majority of these epidemics are associated with primarily O1 serotype. However there is evidence that this species is undergoing some phenotypic changes during the last decades. Such examples include shifts in some metabolic pathways used for biotyping, phage sensitivity profiling and the acquisition of plasmids that carry multiple genes conferring antimicrobial resistance. Furthermore, the recent emergence of a non-O1 serotype (‘Bengal strain’, classified serologically as O139) has prompted the experts to think that perhaps this genotype will be the predominant one in the upcoming (eighth) pandemic. Besides the O1 and O139, the non-O1 and non-O139 V. cholerae stains are occasionally associated with other severe forms of gastrointestinal disease in humans. Interestingly, many of these non-canonical strains lack the genes encoding the typical virulence factors for this species such as the Cholera-toxin (ctx) and toxin co-regulated pilus (tcpA). Therefore it has been hypothesized that this group of non-canonical V. cholerae pathogens consist of several sub-clones that elicit disease via unknown virulence determinants and underlying mechanisms. The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a "species" DNA microarray to better understand the ancestral relationships among its members. Based on preliminary genotyping (MLST, and CGH using a single-genome-based array), 10 diverse V. cholerae and one V. mimicus were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for V. cholerae group members. The availability of the V. cholerae species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of V. cholerae group.

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Novel gene discovery in up to 10 ETEC strains and production of species microarray. Discovery of conserved and unique ETEC genes by comparative genome hybridization studies.

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