Genomic Analysis of a Pathogenicity Island in Uropathogenic Escherichia coli CFT073: Distribution of Homologous Sequences among Isolates from Patients with Pyelonephritis, Cystitis, and CatheterAssociated Bacteriuria and from Fecal Samples

Abstract

Urinary tract infection is the most frequently diagnosed kidney and urologic disease and Escherichia coli is by far the most common etiologic agent. Uropathogenic strains have been shown to contain blocks of DNA termed pathogenicity islands (PAIs) which contribute to their virulence. We have defined one of these regions of DNA within the chromosome of a highly virulentE. coli strain, CFT073, isolated from the blood and urine of a woman with acute pyelonephritis. The 57,988-bp stretch of DNA has characteristics which define PAIs, including a size greater than 30 kb, the presence of insertion sequences, distinct segmentation of K-12 and J96 origin, GC content (42.9%) different from that of total genomic DNA (50.8%), and the presence of virulence genes (hly and pap). Within this region, we have identified 44 open reading frames; of these 44, 10 are homologous to entries in the complete K-12 genome sequence, 4 are nearly identical to the sequences of E. coli J96 encoding the HlyA hemolysin, 11 encode P fimbriae, and 19 show no homology to J96 or K-12 entries. To determine whether sequences found within the junctions of the PAI of CFT073 were common to other uropathogenic strains ofE. coli, 11 probes were isolated along the length of the PAI and were hybridized to dot blots of genomic DNA isolated from clinical isolates (67 from patients with acute pyelonephritis, 38 from patients with cystitis, 49 from patients with catheter-associated bacteriuria, and 27 from fecal samples). These sequences were found significantly more often in strains associated with the clinical syndromes of acute pyelonephritis (79%) and cystitis (82%) than in those associated with catheter-associated bacteriuria (58%) and in fecal strains (22%) (P < 0.001). From these regions, we have identified a putative iron transport system and genes other than hly and pap that may contribute to the virulent phenotype of uropathogenic E. coli strains.

Phylogenetic group B2 Escherichia coli strains from the bowel microbiota of Pakistani infants carry few virulence genes and lack the capacity for long-term persistence

“…The malX gene, previously used as a marker for PAI‐I from strain CFT073 [2,12,25], was detected using PCR as previously described [2], but using a primer concentration of 0.6 μM. Carriage of the HPI was detected using a duplex PCR amplifying the genes fyuA and irp2 with previously published primer pairs [26].…”

“…Such virulence genes are commonly located on particular regions of the bacterial chromosome called pathogenicity islands (PAIs) [11]. Two pathogenicity islands associated with E. coli strains of extra‐intestinal pathogenicity are PAI‐I, first identified in the uropathogenic E. coli strain CFT073, and the high‐pathogenicity island (HPI), thought to have spread from Yersinia [2,12]. The HPI is the most prevalent PAI among Enterobacteriaceae [13], and has been suggested to have been acquired early during evolution.…”

Sequence microdiversity at the ribosomal RNA operons of Escherichia coli pyelonephritogenic strains

“…Previous studies using carboxylesterase B electrophoretic pattern (MLEE) indicated that they belong to the B2 group [17–21]. In this group, DNA fragments (named ‘pathogenicity‐associated islands’ or PAIs) have been recently identified, in or near [22] the tRNA genes, that encode P‐fimbria, 1‐fimbria, α ‐hemolysin, aerobactin and necrocytotoxic factor synthesis [23]. The presence of PAIs allows the bacteria to colonize squamous, transitional and renal tubular epithelia, avoid natural defense mechanisms, grow in adverse media, and provoke internalization by means of toxic actions on the epithelial cells.…”

Impact of pathogenicity islands in bacterial diagnostics

“…Some PAIs are even strain specific. This could be demonstrated, for example, for PAI I 536 and PAI III 536 of the uropathogenic E. coli (UPEC) strain 536 and for PAI I CFT073 of the UPEC strain CFT073 (5, 6). Other PAIs are indicators for the more virulent strains of a certain pathogenic species such as the cag PAI of the most pathogenic Helicobacter pylori strains (7).…”