Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections

Abstract

Uropathogenic Escherichia coli (UPEC) UTI89 is a well-characterized strain, which has mainly been used to study UPEC virulence during urinary tract infection (UTI). However, little is known on UTI89 key fitness-factors during growth in lab media and during UTI. Here, we used a transposon-insertion-sequencing approach (TraDIS) to reveal the UTI89 essential-genes for in vitro growth and fitness-gene-sets for growth in Luria broth (LB) and EZ-MOPS medium without glucose, as well as for human bacteriuria and mouse cystitis. A total of 293 essential genes for growth were identified and the set of fitness-genes was shown to differ depending on the growth media. A modified, previously validated UTI murine model, with administration of glucose prior to infection was applied. Selected fitness-genes for growth in urine and mouse-bladder colonization were validated using deletion-mutants. Novel fitness-genes, such as tusA, corA and rfaG; involved in sulphur-acquisition, magnesium-uptake, and LPS-biosynthesis, were proved to be important during UTI. Moreover, rfaG was confirmed as relevant in both niches, and therefore it may represent a target for novel UTI-treatment/prevention strategies.

Phage Resistance Accompanies Reduced Fitness of Uropathogenic Escherichia coli in the Urinary Environment

“…Phage-resistant UPEC strains were equally capable of growth in LB as parental strains but grew poorly in urine. This result echoes recent work by García et al who demonstrated that several genes involved in LPS biosynthesis are important for bacterial growth in urine ( 66 ). The addition of yeast extract to urine rescued bacterial growth to levels resembling growth in LB, suggesting that this phenotype may be due ineffective nutrient acquisition or utilization under deplete conditions.…”

“…While the LPS mutations assessed by this group are not identical to those observed in our study, the functional consequences (e.g., outer membrane truncation and inner membrane truncation) are likely similar. In addition, García et al have shown recently that rfaG , another gene involved in LPS biosynthesis, is important for colonization of the murine bladder ( 66 ). Of note, we did not investigate all phage-resistant strains isolated from this study in vivo , and it remains possible that alternative phenotypes may be present in other phage-resistant UPEC strains.…”

Proteomes of Uropathogenic Escherichia coli Growing in Human Urine and in J82 Urinary Bladder Cells

“…To assess whether there was a link between level of regulation and importance during growth in urine/the outcome of infection (UTI), we identified growth and virulence scores from literature of the genes encoding the upregulated proteins ( Supplementary Files S2—Table S3 ). Global analysis by TraDIS (transposon directed differential insertion sequencing) has recently been carried out with UPEC strains CFT073 and the strain used in the current study, UTI89 [ 47 , 48 ], to identify factors important for growth in urine and for infection. TraDIS compares mutants in all non-essential genes to the wild type strain, in this case resulting in a relative score for the ability to grow in urine and to infect in an UTI model in mice.…”

“…For 10 of the proteins, no attenuation score was reported for the relevant gene. According to Garcia et al [ 48 ], none of the proteins were significantly associated with attenuation in the mouse model. Seven of the proteins were, however, significantly depleted, but they did not reach the cut-off.…”

“…Recently, global analysis of importance of genes in UPEC for growth in urine and during UTI in mice has been investigated using TraDIS (random transposon) libraries made in the strains CFT073 and UTI89 [ 47 , 48 ]. This allowed us to compare the gene pool encoding the most highly upregulated protein in our study to growth and attenuation scores given to mutants in the genes encoding these proteins.…”