Genomic characterization of asymptomatic Escherichia coli isolated from the neobladder

Abstract

The replacement of the bladder with a neobladder made from ileal tissue is the prescribed treatment in some cases of bladder cancer or trauma. Studies have demonstrated that individuals with an ileal neobladder have recurrent colonization by Escherichia coli and other species that are commonly associated with urinary tract infections; however, pyelonephritis and complicated symptomatic infections with ileal neobladders are relatively rare. This study examines the genomic content of two E. coli isolates from individuals with neobladders using comparative genomic hybridization (CGH) with a pan-E. coli/Shigella microarray. Comparisons of the neobladder genome hybridization patterns with reference genomes demonstrate that the neobladder isolates are more similar to the commensal, laboratory-adapted E. coli and a subset of enteroaggregative E. coli than they are to uropathogenic E. coli isolates. Genes identified by CGH as exclusively present in the neobladder isolates among the 30 examined isolates were primarily from large enteric isolate plasmids. Isolations identified a large plasmid in each isolate, and sequencing confirmed similarity to previously identified plasmids of enteric species. Screening, via PCR, of more than 100 isolates of E. coli from environmental, diarrhoeagenic and urinary tract sources did not identify neobladder-specific genes that were widely distributed in these populations. These results taken together demonstrate that the neobladder isolates, while distinct, are genomically more similar to gastrointestinal or commensal E. coli, suggesting why they can colonize the transplanted intestinal tissue but rarely progress to acute pyelonephritis or more severe disease.

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

“…The genome contents of the A. baumannii isolates were analyzed using LS-BSR (46). Generation of the LS-BSR matrix resulted in the reduction of 959,329 potential coding sequences present in the newly sequenced A. baumannii genomes to a nonredundant set of 13,585 centroids (see Data File S1 in the supplemental material).…”

“…For genomic DNA isolation, strains were grown overnight at 37°C with shaking at 250 rpm in Luria-Bertani broth, and the Sigma GenElute genomic kit (Sigma-Aldrich) was used to isolate DNA. Genomic DNA was extracted with standard methods (46) and sequenced on the Illumina HiSeq 2000 platform. The resulting 100-bp reads were assembled with the MaSurRCA Assembler (47) at the University of Maryland Institute for Genome Sciences, Genome Resource Center.…”

Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology

“…Genomic DNA was extracted with standard methods 55 and sequenced on the Illumina HiSeq 2000 platform at the University of Maryland School of Medicine, Institute for Genome Sciences, Genome Resource Center using established SOPs. The resulting 100 bp reads were assembled with the Celera Assembler 56 ; the resulting assemblies and corresponding accession numbers are shown in Table S1.…”

Asymptomatic Bacteriuria and Bacterial Interference

“…E. coli strains isolated from hospital-acquired asymptomatic bacteriuria possessed similar virulence profiles whether an indwelling catheter was present or not (87). Two E. coli isolates causing long-term ileal neobladder colonization genetically resembled commensal/ gastrointestinal adapted E. coli rather than UPEC, potentially explaining the persistence of these strains in the gut-derived neobladder (88).…”