A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity.

Yi Ren,Agata Palusiak,Wei Wang,Zhi Yao,Yi Wang,Huiting Wei,Qingke Kong,Quan Wang,Antoni Rozalski,Xiao Li

doi:10.3389/fmicb.2016.00623

Abstract

Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates.

Highlights

Urinary tract infections (UTIs) are one of the commonest bacterial infections causing morbidity in humans
In order to identify the Chaperone-usher fimbrial operons present in Uropathogenic Escherichia coli (UPEC) strains, we used two sets of genome sequences, one included 11 UPEC strains whose complete genomes had been sequenced and published, and the other contained the sequences obtained in this study of eight clinical UPEC strains not closely related with the 11 UPEC strains with available genomes based on multilocus sequence typing (MLST) analysis and fimH sequences
By the calculation of discriminatory power of different typing methods using Simpson’s index of diversity (D), it was shown that the methods based on whole-genome sequence (WGS) data and the combination of four genes and fimbrial types had the greatest discriminatory power [D = 0.999; 95% confidence interval, 0.998–1.000], which is greater than methods based on the internal fragments of fimH and fumC (D = 0.997; 95% CI, 0.995–0.999), and four genes

Summary

Introduction

Urinary tract infections (UTIs) are one of the commonest bacterial infections causing morbidity in humans. It is estimated that 40% of women and 12% of men will experience a symptomatic UTI during their lifetime (Nielubowicz and Mobley, 2010); infants and children are susceptible (Foxman, 2003; Zorc et al, 2005; Guay, 2008). There are >100 million cases of UTIs annually worldwide, causing a serious economic and medical burden (Shaikh et al, 2008; Chakupurakal et al, 2010). In the US alone, UTIs cause about 10 million physician visits and more than 1 million emergency room visits, with a cost more than 3 billion dollars annually (Foxman and Brown, 2003; Scholes et al, 2005; Litwin and Saigal, 2007; DeFrances et al, 2008).

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Conclusion