Christopher K. Rode

Transmission of Uropathogens between Sex Partners

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.

Discovery of Disseminated J96-like Strains of Uropathogenic Escherichia coli O4:H5 Containing Genes for Both PapGJ96 (Class I) and PrsGJ96 (Class III) Gal(α1-4)Gal-Binding Adhesins

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.

Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites.

A transposon-based method of introducing unique restriction sites was used for subdivision of the Escherichia coli genome into a contiguous series of large non-overlapping segments spanning 2.5Mb. The segments, sizes ranging from 150 to 250kb, were isolated from the chromosome using the inserted restriction sites and shotgun cloned into an M13 vector for DNA sequencing. These shotgun sizes proved easily manageable, allowing the genomic sequence of E. coli to be completed more efficiently and rapidly than was possible by previously available methods. The 9bp duplication generated during transposition was used as a tag for accurate splicing of the segments; no further sequence redundancy at the junction sites was needed. The system is applicable to larger genomes even if they are not already well-characterized. We present the technology for segment sequencing, results of applying this method to E. coli, and the sequences of the transposon cassettes.

Integrated Genomic Map from Uropathogenic Escherichia coli J96

ABSTRACT Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratoryE. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis inNotI digests. However, because the plasmid lacks restriction sites for the enzymes BlnI and I-CeuI, it was visualized in BlnI and I-CeuI digests only of derivatives carrying plasmid inserts artificially introducing these sites. Owing to an I-SceI site on the transposon, the plasmid could also be visualized and sized from plasmid insertion mutants after digestion with this enzyme. The insertional strains generated in construction of the integrated genomic map provide useful physical and genetic markers for further characterization of the J96 genome.

New ultrarare restriction site-carrying transposons for bacterial genomics.

Electrophoretic separation of macrorestriction fragments containing a particular genomic interval has until recently depended on fortuitously placed native rare restriction sites. We present new IS10-based transposons carrying the yeast intron-encoded I-SceI restriction site which is absent from most prokaryotic and eukaryotic genomes. Construction of the plasmid vectors containing them is described. Analysis by conventional or Pulsed Field gel electrophoresis of the DNA fragments generated by the I-SceI digestion reveals the physical distance between genomic insertions of these transposons: use of the same approach to subdivide the chromosome of Escherichia coli K-12 into equivalently sized contiguous/nonoverlapping I-SceI fragments is demonstrated. Because coordinates for the loci delimited by their insertions can be readily determined in different isolates by either physical or genetic manipulations, these transposons allow sufficient flexibility for species-wide bacterial genomics.