Multilocus-genotyping methods have shown that Escherichia coliO157:H7 is a geographically disseminated clone. However, highresolution methods such as pulse-field gel electrophoresis demonstrate significant genomic diversity among different isolates. To assess the genetic relationship of human and bovine isolates of E. coli O157:H7 in detail, we have developed an octamer-based genome-scanning methodology, which compares the distance between over-represented, strand-biased octamers that occur in the genome. Comparison of octamer-based genome-scanning products derived from >1 megabase of the genome demonstrated the existence of two distinct lineages of E. coli O157:H7 that are disseminated within the United States. Human and bovine isolates are nonrandomly distributed among the lineages, suggesting that one of these lineages may be less virulent for humans or may not be efficiently transmitted to humans from bovine sources. Restriction fragment length polymorphism analysis with lambdoid phage genomes indicates that phage-mediated events are associated with divergence of the lineages, thereby providing one explanation for the degree of diversity that is observed among E. coli O157:H7 by other molecular-fingerprinting methods.
Non-sorbitol-fermenting, -glucuronidase-negative Escherichia coli O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.
BackgroundIndividuality in the species composition of the vertebrate gut microbiota is driven by a combination of host and environmental factors that have largely been studied independently. We studied the convergence of these factors in a G10 mouse population generated from a cross between two strains to search for quantitative trait loci (QTLs) that affect gut microbiota composition or ileal Immunoglobulin A (IgA) expression in mice fed normal or high-fat diets.ResultsWe found 42 microbiota-specific QTLs in 27 different genomic regions that affect the relative abundances of 39 taxa, including four QTL that were shared between this G10 population and the population previously studied at G4. Several of the G10 QTLs show apparent pleiotropy. Eight of these QTLs, including four at the same site on chromosome 9, show significant interaction with diet, implying that diet can modify the effects of some host loci on gut microbiome composition. Utilization patterns of IghV variable regions among IgA-specific mRNAs from ileal tissue are affected by 54 significant QTLs, most of which map to a segment of chromosome 12 spanning the Igh locus. Despite the effect of genetic variation on IghV utilization, we are unable to detect overlapping microbiota and IgA QTLs and there is no significant correlation between IgA variable pattern utilization and the abundance of any of the taxa from the fecal microbiota.ConclusionsWe conclude that host genetics and diet can converge to shape the gut microbiota, but host genetic effects are not manifested through differences in IgA production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0552-6) contains supplementary material, which is available to authorized users.
The O157:H7 lineage of enterohemorrhagic Escherichia coli is a geographically disseminated complex of highly related genotypes that share common ancestry. The common clone that is found worldwide carries several markers of events in its evolution, including markers for acquisition of virulence genes and loss of physiological characteristics, such as sorbitol fermentation ability and -glucuronidase production. Populations of variants that are distinct with respect to motility and the sorbitol and -glucuronidase markers appear to have diverged at several points along the inferred evolutionary pathway. In addition to these variants, distinct subpopulations of the contemporary non-sorbitol-fermenting, -glucuronidase-negative O157:H7 clone were recently detected among bovine and human clinical isolates in the United Stares by using highresolution genome comparison. In order to determine if these recently described subpopulations were derived from a regional or ancestral divergence event, we used octamer-based genome scanning, marker sorting, and DNA sequence analysis to examine their phylogenetic relationship to populations of non-sorbitol-fermenting, -glucuronidase negative O157:H7 and O157:H؊ strains from Australia. The inferred phylogeny is consistent with the hypothesis that subpopulations on each continent resulted from geographic spread of an ancestral divergence event and subsequent expansion of distinct subpopulations. Marker sorting and DNA sequence analyses identified sets of monophyletic markers consistent with the pattern of divergence and demonstrated that phylogeographic variation occurred through emergence of regional subclones and concentration of regional polymorphisms among distinct subpopulations. DNA sequence analysis of representative polyphyletic markers showed that genome diversity accrued through random drift and bacteriophage-mediated events.Hemorrhagic colitis is caused by a number of serotypes of Shiga toxin-producing Escherichia coli (STEC) (14). Among the clinical STEC strains that have been isolated, a subset of enterohemorrhagic E. coli (EHEC) strains has been found which carry common sets of virulence genes that encode factors for attachment to host cells, elaboration of effector molecules, and production of two different types of Shiga toxins (22). The sets of virulence genes are found in the locus of enterocyte effacement (LEE) pathogenicity island, lambdoid bacteriophages, and a large virulence-associated plasmid (8,9,23,25,26,31,32). Population genetic analysis of EHEC and STEC strains has shown that EHEC strains comprise two divergent lineages, termed EHEC 1 and EHEC 2, that are only distantly related but apparently experienced similar pathways of virulence gene acquisition (24,28,38). The EHEC 1 lineage is comprised solely of a geographically disseminated cluster of strains with related genotypes bearing O157:H7 and O157:HϪ serotypes, while the EHEC 2 lineage is serotypically and genotypically more diverse.The O157 serotype can be found in genetically diverse populations of E...
Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.Listeria monocytogenes is a ubiquitous gram-positive bacterium that can cause life-threatening infections including meningitis, septicemia, abortion, and fetal death. Its primary route of transmission to humans is through contaminated food and despite the relatively low incidence of listeriosis in humans, outbreaks of listeriosis often have high associated morbidity, particularly among pregnant women, unborn fetuses, and immunocompromised individuals (24). These characteristics, coupled with its physiological durability and its ubiquitous distribution in nature have propelled L. monocytogenes to the forefront of food safety research and the regulatory arena.Pathogenesis of listeriosis is a consequence of the organism's ability to invade and replicate within several different cell types in mammalian tissues, including intestinal, liver, and neural tissues. During the course of food-borne infections, the bacteria penetrate the intestinal lining through cell invasion and translocation and use the lymphatic system as a conduit to reach the main target tissues within the liver and spleen (41). Prolonged replication in the liver, facilitated by depressed cell mediated immunity, is thought to be an antecedent to spread of the bacteria to brain tissue and breach of the placental barrier in pregnant wo...
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