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J Med Microbiol 56 (2007), 1363-1369; DOI: 10.1099/jmm.0.47262-0
© 2007 Society for General Microbiology
ISSN 1473-5644

Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs)

Sara Y. Tartof1, Owen D. Solberg2 and Lee W. Riley1,3

1 Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA

2 Department of Integrative Biology, University of California, Berkeley, CA, USA

3 Division of Infectious Diseases, University of California, Berkeley, CA, USA

Correspondence
Lee W. Riley
lwriley{at}berkeley.edu

Received 28 February 2007
Accepted 25 June 2007

The application of genotyping techniques for subtyping uropathogenic Escherichia coli has contributed to better understanding of the epidemiology of community-acquired urinary tract infection (UTI). However, the current techniques are hampered by limited reproducibility, poor discriminatory power, labour-intensive performance or high cost. A screening test that is sequence-based would provide an inexpensive, reproducible way to subtype E. coli isolates. Such a test, if also discriminatory, would be highly useful for epidemiological studies. The discriminatory ability of 12 putative virulence genes (fimH, fliD, fliM, iha, motA, papA/H, kpsMTII, fepE, fimA, flgA, malG, purD) was evaluated based on single nucleotide polymorphisms (SNPs) in nine uropathogenic E. coli isolates, all previously found to belong to a single multilocus sequence type (MLST) complex (ST69). An additional 25 epidemiologically well-characterized E. coli isolates belonging to 12 distinct MLST clonal complexes were analysed for fimH SNP. None of the 12 genes except fimH were able to further discriminate the nine ST69-complex strains. Isolates belonging to the 12 non-ST69 MLST groups were separated into 10 fimH SNP subgroups. While fimH SNP analysis may not be an appropriate phylogenetic method, it offers discriminatory power similar to that of MLST and could be used as a simple, inexpensive screening test for epidemiological studies of uropathogenic E. coli.

Abbreviations: ERIC-PCR, Enterobacterial Repetitive Intergenic Consensus-PCR; ExPEC, extraintestinal pathogenic Escherichia coli; MLST, multilocus sequence type; SNP, single nucleotide polymorphism; UTI, urinary tract infection.




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