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  • MLST Schemes for Pathogenic E. coli
    Three MLST schemes based on different combinations of 15 house keeping genes are supported within the system. The main MLST scheme uses internal fragments of the seven house-keeping genes listed in Table 1. The associated sequence type is defined as st7. Some isolates are only characterized using internal fragments of two of the seven house-keeping genes: mdh and uidA. The associated sequence type is defined as st2. Some isolates are further characterized using internal fragments of the eight additional house-keeping genes listed in Table 2. The associated sequence type is defined as st15.
    Table 1. Seven house keeping genes defined st7 of pathogenic E. coli
    Gene Gene Product Gene Size (bp) PCR Primers Amplicon (bp) Amplicon Range Allele Sequence (bp)
    aspC aspartate aminotransferase 1191
    594 57..650 513
    clpX ATP-dependent Clp protease 1275
    672 292..933 567
    fadD cyl-CoA synthetase 1686
    580 768..1347 492
    icdA isocitrate dehydrogenase 1251
    669352..1020 567
    lysP lysine-specific permease 1470
    628 36..663 477
    mdh malate dehydrogenase 939
    650 130..779 549
    uidA beta-D-glucuronidase 1812
    658 277..934 588
    Table 2. Eight additional house keeping genes, together with the seven genes listed in Table 1, defined st15 of pathogenic E. coli
    Gene Gene Product Gene Size (bp) PCR Primers Amplicon (bp) Amplicon Range Allele Sequence (bp)
    arcA Aerobic respiration control protein ArcA 717
    552 99..650 435
    aroE dehydroshikimate reductase 819
    362 238..599 291
    cyaA adenylate cyclase 2547
    571 312..882 498
    dnaG DNA primase 1746
    512 868..1397 444
    grpE heat shock protein GrpE 594
    488 39..526 417
    mtlD mannitol-1-phosphate dehydrogenase 1149
    658 22..679 543
    mutS methyl-directed mismatch repair protein MutS 2562
    596 1488..2083 507
    rpoS RNA polymerase, sigma factor RpoS 993
    618 274..891 585
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    Operated by the STEC Center at Michigan State University
    National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) Food and Waterborne Diseases Integrated Research Network (FWD IRN) Microbiology Research Unit (MRU) Reference Center to Facilitate the Study of Shiga Toxin-Producing Escherichia Coli