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Source-tracking fecal contamination by genomic analysis of Escherichia coli from human and animal hosts

ABSTRACT: The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be “hot spots” for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers.

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE21115 | GEO | 2013/03/01

SECONDARY ACCESSION(S): PRJNA126467

REPOSITORIES: GEO

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Project description:The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be M-bM-^@M-^\hot spotsM-bM-^@M-^] for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers. Twelve isolates of E. coli ( 3 from bear, 3 from cattle, 3 from deer and 3 from humans) were isolated from feces and/or raw sewage. Genome content for each strain was assessed in duplicate using comparative genome hybridization with E. coli K12 MG1655 as the reference for a total of 24 arrays.

Project description:Crohn’s disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. Its pathogenesis mechanisms remain obscure. One of the factors of CD pathogenesis is reduced diversity of gut microbiota which is accompanied by the characteristic increase of representation of Escherichia coli strains, several of which are able to penetrate the mucin layer, adhere to the epithelial cells, cross the epithelial barrier, and colonize macrophages. During the internalization, these E. coli strains can modulate macrophages’ defensive functions in a way that allows them to survive in a presence of such negative factors as low pH, oxidative stress, proteolytic enzymes and antimicrobial solutions. These strains were collectively assigned to the adhesive–invasive group of E. coli (AIEC). Earlier we sequenced 28 E. coli isolates from 10 patients with CD [Rakitina DV et al. Genome analysis of E. coli isolated from Crohn disease patients. BMC Genomics. 2017, 18(1):544. doi: 10.1186/s12864-017-3917-x] It has been demonstrated that the majority of enteropathogens feature specific metabolic pathways allowing them to use alternative carbon sources which leads to survivability and enhaced competitiveness in the host organism. Previously, we demonstrated that virulent properties of CD isolates are dependent on the carbon source: prolonged growth on propionate containing medium stimulates virulent properties while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655 [Pobeguts OV et al. Propionate Induces Virulent Properties of Crohn’s Disease-Associated Escherichia coli. Frontiers in Microbiology. 2020, 11:1460. doi: 10.3389/fmicb.2020.01460]. Thus, cultivation of E. coli on different growth mediums: M9 supplied with propionate and glucose made it possible to distinguish two states of each CD isolate: active (aAIEC) and inactive (iAIEC). In order to identify the major changes that occur upon change of carbon source, we carried out LC–MS-based proteomic analysis of aAIEC and iAIEC states of three CD isolates of E. coli ZvL2 (RCE07), BruB2 (RCE03) and К5 (RCE06) grown on glucose and propionate.

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Source-tracking fecal contamination by genomic analysis of Escherichia coli from human and animal hosts

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