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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #160337
Title: PHYLOGENY AND STRAIN TYPING OF ESCHERICHIA COLI INFERRED FROM VARIATION IN MONONUCLEOTIDE REPEAT (MNR) LOCI

Author
item DIAMANT, ERAN - THE TECHNION INST. ISRAEL
item Palti, Yniv
item HALLERMAN, ERIC - VIRGINIA TECH
item KASHI, YECHESKEL - TECHNION INST. ISRAEL

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2004
Publication Date: 4/1/2004
Citation: Diamant, E., Palti, Y., Hallerman, E., Kashi, Y. 2004. Phylogeny and strain typing of escherichia coli inferred from variation in mononucleotide repeat (mnr) loci. Applied and Environmental Microbiology. 70(4):2464-2473.

Interpretive Summary: Simple sequence repeats of mononucleotide repeating motifs in the E. coli genome were found to be highly polymorphic among strains and useful for phylogenetic analysis and identification of pathogenic isolates. This will enable devolvement of diagnostic tools for rapid identification of pathogenic E. coli in clinical samples as well as food for humans and in animal feed. This E. coli model for rapid identification of pathogenic strains can be adapted for bacterial pathogens of fish and live stock once the genome of such pathogens is sequenced.

Technical Abstract: Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships in Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of mononucleotide repeating motifs (mononucleotide repeats - MNRs) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven non-coding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including EHEC (with six isolates of O157:H7), EPEC, ETEC, B, and K12 strains. The four MNRs also were sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) amplified in the B2 group, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis (MLEE). The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing (MLST) should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria.