The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylase (LDC) activity is present in Ϸ90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these ''black holes,'' deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.

Escherichia coli causes most urinary tract infections (UTIs) in ambulatory populations. Several bacterial virulence factors occur more frequently among urinary E. coli isolates than among fecal isolates, but none have been reported to predict risk of second UTIs. DNA hybridization was used to characterize the bacterial virulence profiles of urinary E. coli isolates from 174 women with first UTI and compared for risk of second UTI. Of the women, 28 (16%) had a culture-confirmed second UTI within 6 months of a negative test-of-cure. Three virulence factors were associated with a significantly lower risk of second UTI: cytotoxic necrotizing factor (relative risk [RR] = 0.0; 95% confidence interval [CI], 0.0, 0.42); hemolysin (RR, 0.10; 95% CI, 0.01, 0.69), and S fimbrial adhesin (RR, 0.25; 95% CI, 0.06, 1.00). Dr binding was associated with a 2-fold increased risk of second UTI (RR, 2.30; 95% CI, 1.23, 4.29). Half of all paired first and second UTI isolates from the same subject were apparently the same.

The pyelonephritis-associated adhesin gene papG of Escherichia coli occurs in three variants. Whereas the class II and class III variants are common among human urinary tract infection isolates, the class I allele, despite being the first cloned, has previously been found only in source strain J96. Five strains have been discovered from geographically diverse locales that, like J96, contain both the class I and class III papG alleles. One strain caused bacteremia, whereas 4 caused cystitis. Like J96, all 5 had group III capsule genes, expressed the H5 flagellar antigen and the F13 fimbrial antigen, and exhibited similar genomic patterns and virulence factor profiles. These findings demonstrate that the class I papG allele is not unique to J96 but is present in a group of extraintestinal isolates of E. coli O4:H5 that represent a disseminated virulent clonal group.

Up to 80% of faecal Escherichia coli strains are able to produce type 1 pili. These filamentous bacterial surface organelles, which mediate mannose-sensitive attachment to mammalian epithelial cells, are also conserved throughout the Enterobacteriaceae. As a potential explanation for their prevalence among intestinal isolates of enteric bacteria, it has been widely speculated that type 1 pili are important for adherence to the host's intestinal mucosa. However, conclusive evidence for this idea is lacking, and there are reasonable grounds for doubting such an effect. Permanent interruption of type 1 piliation in previously pil+ E. coli (by directed mutagenesis of pilA, the gene coding for the major structural subunit of type 1 pili) does not diminish the density of intestinal colonization in individual animals. Rather, as we demonstrate here, this lesion results in a dramatic decrease in transmission of E. coli K1 from experimentally colonized neonatal rats to their littermates. The enhanced communicability associated with type 1 piliation suggests a heretofore unrecognized explanation for the prevalence of type 1 pili among intestinal E. coli; one that does not necessarily require the direct action of these organelles at the intestinal mucosa.

Epidemiologic evidence and several case reports suggest that Escherichia coli causing urinary tract infection (UTI) may be transmitted between sex partners. In order to test this hypothesis, urinary, vaginal, and fecal E. coli isolates from 19 women with UTI were compared with E. coli found in random initial voids from their most recent male sex partner. E. coli was isolated from 4 of 19 male sex partners. In each case, the E. coli isolated from the man was identical by pulsed-field gel electrophoresis and bacterial virulence profile to the urinary E. coli from his sex partner.

type 1 pilus-deficient mutant of a systemically invasive Escherichia coli Kl strain was constructed by directed mutagenesis of pilA, the gene that codes for the major structural subunit of type 1 pili. By comparing this mutant with an isogenic piL4A strain, we were able to assess the role of type 1 piliation in alimentary tract colonization and bloodstream invasion in neonatal rats. Intestinal colonization was not significantly affected by the pilA mutation; in contrast, loss of type 1 piliation correlated with a dramatic decrease in oropharyngeal colonization. Nevertheless, development of bacteremia after oral administration of E. coli Kl was not diminished by the mutation in piLA. Thus, loss of type 1 piliation correlated with a site-dependent effect on colonization within the alimentary tract while not interfering with bloodstream invasion.

Background: In 1982 Smith and Huggins showed that bacteriophages could be at least as effective as antibiotics in preventing mortality from experimental infections with a capsulated E. coli (K1) in mice. Phages that required the K1 capsule for infection were more effective than phages that did not require this capsule, but the efficacies of phages and antibiotics in preventing mortality both declined with time between infection and treatment, becoming virtually ineffective within 16 hours.