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Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low-and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this "core genome" confirmed the diverse history of the ETEC pathovar and provides a finer resolution of the E. coli relationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETEC E. coli genomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Typical EPEC isolates are differentiated from other types of pathogenic E. coli by two distinctive phenotypes, attaching effacement and localized adherence. The genes specifying these phenotypes are found on the locus of enterocyte effacement (LEE) and the EPEC adherence factor (EAF) plasmid. To describe how typical EPEC has evolved, we characterized a diverse collection of strains by multilocus sequence typing (MLST) and performed restriction fragment length polymorphism (RFLP) analysis of three virulence genes (eae, bfpA, and perA) to assess allelic variation. Among 129 strains representing 20 O-serogroups, 21 clonal genotypes were identified using MLST. RFLP analysis resolved nine eae, nine bfpA, and four perA alleles. Each bfpA allele was associated with only one perA allele class, suggesting that recombination has not played a large role in shuffling the bfpA and perA loci between separate EAF plasmids. The distribution of eae alleles among typical EPEC strains is more concordant with the clonal relationships than the distribution of the EAF plasmid types. These results provide further support for the hypothesis that the EPEC pathotype has evolved multiple times within E. coli through separate acquisitions of the LEE island and EAF plasmid.Enteropathogenic E. coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations (31, 37). A key characteristic of EPEC strains is the ability to intimately attach to intestinal epithelial cells and create attaching and effacing (AE) lesions (24). The AE phenotype is specified by genes of the locus of enterocyte effacement (LEE), a ϳ35-kb pathogenicity island located in the bacterial chromosome (23, 41). The LEE island comprises approximately 40 genes and encodes the components of a type III secretion system, various effector molecules, and the intimin adhesin (23,33,68). Intimin plays a crucial role in AE lesion formation (15) and is encoded by the highly polymorphic eae gene (1, 72), which can be divided into periplasmic, transmembrane, and extracellular domains (39). To date, more than 25 major allelic variants of eae have been described (36).Most typical EPEC strains fall into one of two phylogenetically distinct groups or clonal lineages, designated EPEC 1 and EPEC 2 (69), and differ from atypical EPEC and other types of pathogenic E. coli by their ability to form microcolonies on the surface of intestinal epithelial cells (4). This phenotype, termed localized adherence (LA), correlates with the presence of a large virulence plasmid called the EPEC adherence factor (EAF) plasmid (18). The EAF plasmids from different EPEC strains show considerable variation in size (ϳ85 to 110 kb) (48) and, presumably, gene content. Comparison of the complete EAF plasmid sequences from two prototypical EPEC strains (O127:H6 EPEC 1 strain E2348/69 and O111:NM EPEC 2 strain B171) indicates that the EPEC 2 plasmid of B171 carries fewer genes (80 v...

To study the natural history of rotavirus infection and to determine the protection it confers against reinfection and diarrhea, 200 newborns in Guinea-Bissau were prospectively followed for up to 2 years. Rotavirus was detected in stool specimens collected weekly. By age 2 years, the incidence of primary rotavirus infection was 74%. In the first 3 months of life, 17% of the infections were diarrhea associated, compared with 60% at 9-11 months; after age 18 months, all infections were asymptomatic. A primary infection conferred 52% (95% confidence interval [CI], 16% to 73%) and 70% (95% CI, 29% to 87%) protection against subsequent rotavirus infection and rotavirus diarrhea, respectively. The protection was 66% (95% CI, 24% to 85%) against reinfection within the same epidemic, compared with 34% (95% CI, -29% to 67%) against reinfection in any subsequent epidemic. The high level of protection against symptomatic rotavirus infection provides an important incentive for development of a rotavirus vaccine.

We recruited 200 children shortly after birth and collected stool specimens weekly, irrespective of whether the children had diarrhea, until up to 2 years of age. All children were recruited during the first year of the study and were monitored for a median of 18.4 months. To measure pathogenicity, the odds ratio for diarrhea, adjusted for age, sex, and coinfections with other enteropathogens, was determined by logistic regression. Standard estimation of the population attributable risk indicated that rotavirus, enterotoxigenic Escherichia coli that produced only the heat-stable toxin ST, Isospora spp., Cryptosporidium parvum, Shiga toxin (Stx)-producing E. coli (STEC), and Shigella spp. or enteroinvasive E. coli were the most important contributors to diarrhea in this population. Stx2-but not Stx1-producing STEC strains were pathogenic. Enteroaggregative E. coli, diffusely adherent E. coli, and attaching-and-effacing E. coli strains, which were the most commonly isolated microorganisms, were not associated with diarrhea. For most of the microorganisms, primary infections did not confer protection against reinfection with the same organism, but some conferred protection against diarrhea from reinfection.Diarrheal diseases remain a major cause of childhood mortality and morbidity in developing countries. Although the mortality from diarrheal diseases is declining, diarrheal morbidity is not (27,48). In order to target preventive measures, it is essential to describe the natural history and the relative importance of the various diarrheagenic agents. Moreover, to guide vaccine development, it is important to estimate the protection against reinfection and disease that natural infections with the various enteropathogens may confer.Prospective cohort studies that investigate infections with diarrheal pathogens have been carried out for rotavirus (54), Campylobacter spp. (12)., Shigella spp. (20), Giardia lamblia (37), enterotoxigenic Escherichia coli (ETEC) (2), and other diarrheagenic E. coli strains (7,28,44). Longitudinal studies that describe a wide range of potential enteropathogens are few and were undertaken before the recognition of more recently described diarrheagenic agents, such as enteroaggregative E. coli (EAggEC) and diffusely adherent E. coli (DAEC) (14, 32).We used DNA-DNA colony hybridization to identify diarrheagenic E. coli, Salmonella, and Shigella spp. in a cohort of newborn children who were monitored until up to 2 years of age with weekly stool specimen collection. Furthermore, examinations for rotavirus, Yersinia spp., Campylobacter spp., and enteric parasites, including Cryptosporidium parvum, were undertaken. Our objectives were to identify from a wide range of potential enteropathogens those that were associated with diarrhea, to determine the age of primary infection, to quantify any protection that was induced by natural infection, and to estimate their relative contribution to the incidence of diarrhea in children of a developing country. MATERIALS AND METHODSStudy design and assembly ...

No abstract

In a cohort study of 200 young children in Guinea-Bissau, it was previously found that some enterotoxigenic Escherichia coli (ETEC) strains were more pathogenic than others, depending on the type of toxin that they could produce, and that natural ETEC infections induced substantial protection against new infections with ETEC strains that had the same combination of toxins and colonization factors (CFs). We wanted to describe the clonal relatedness of the ETEC strains isolated during this study and to investigate whether the protective antigens and the virulence factors that were responsible for the pathogenic traits were common to strains that were clonally closely related or whether they were more likely to be encoded by the ETEC virulence plasmids that normally encode the toxins and the CFs. By performing repetitive sequence-based PCR analysis of strains representing 452 infections, we found that strains that had the same toxin-CF profile were usually closely related, although a few were unrelated. Strains that did not have the same toxin-CF profiles but that were positive for a given toxin or for a given CF were not consistently more closely related to each other than to strains that were negative for the same toxin or CF. Our results indicate that the pathogenic traits of ETEC were mainly attributed to genes carried on the ETEC virulence plasmids. Because most strains that had the same toxin-CF profile were closely related, it seems likely that the toxin-CF-specific protection was clonal and was not targeting antigens encoded by the virulence plasmids. These results are of relevance to the ETEC vaccine development effort.

Enterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea among children living in and among travelers visiting developing countries. Human ETEC strains represent an epidemiologically and phenotypically diverse group of pathogens, and there is a need to identify natural groupings of these organisms that may help to explain this diversity. Here, we sought to identify most of the important human ETEC lineages that exist in the E. coli population, because strains that originate from the same lineage may also have inherited many of the same epidemiological and phenotypic traits. We performed multilocus sequence typing (MLST) on 1,019 ETEC isolates obtained from humans in different countries and analyzed the data against a backdrop of MLST data from 1,250 non-ETEC E. coli and eight ETEC isolates from pigs. A total of 42 different lineages were identified, 15 of which, representing 792 (78%) of the strains, were estimated to have emerged >900 years ago. Twenty of the lineages were represented in more than one country. There was evidence of extensive exchange of enterotoxin and colonization factor genes between different lineages. Human and porcine ETEC have probably emerged from the same ancestral ETEC lineage on at least three occasions. Our findings suggest that most ETEC strains circulating in the human population today originate from well-established, globally widespread ETEC lineages. Some of the more important lineages identified here may represent a smaller and more manageable target for the ongoing efforts to develop effective ETEC vaccines.Enterotoxigenic Escherichia coli (ETEC) infections are an important cause of childhood diarrhea and diarrheal deaths among young children in developing countries (59) and of diarrhea among travelers to these countries (6, 54). Human ETEC strains are E. coli that produce one or more of three plasmid-encoded protein enterotoxins called human heat-stable toxin (STh or STaII), porcine heat-stable toxin (STp or STaI), and heat-labile toxin (LT or LT-I). The enterotoxins induce secretion of salts and water into the intestinal lumen (29). Many ETEC strains also produce surface appendages, called colonization factors (CFs), which help anchor the bacteria to the small intestinal wall (20). The toxins and all but one known CF are plasmid encoded (20,34).Human ETEC strains are phenotypically and epidemiologically diverse: more than 20 different CFs have thus far been described (20), the characterization of ETEC strains collected from different parts of the world has yielded 117 different serotypes (57), and some ETEC strains appear to be more pathogenic than others (9,36,46). This diversity poses a challenge for the ongoing efforts to develop effective ETEC vaccines (7). Many studies have shown that ETEC have emerged from E. coli on several occasions, probably through horizontal transfer of the enterotoxin-encoding virulence plasmids, and that some of these ETEC lineages appear to be widespread (4, 11, 31-33, 37, 38, 43, 47, 51). Because strains that originate from the s...