No abstract

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.