We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within

Tularemia, caused by the bacterium

Groups A.I and A.II differ in virulence, as do subgroups within A.I, although clinical signs and symptoms can be similar. Human infections involving A.I strains are associated with a higher fatality rate than that for infections involving A.II strains (

Because PFGE lacks the phylogenetic resolution of some other testing methods (

Neighbor-joining tree of 14

Strain ID† | Original strain ID‡ | Original laboratory | State/province of exposure | Region§ | Year | CDC PFGE type¶ | Subclade# | Major group | Subgroup |
---|---|---|---|---|---|---|---|---|---|

AR01-0903 | AR01-0903 | CDC | AR | C | 2001 | A1 | A.I.1/2 | A.I.12 | A.I.12/2 |

AR01-1117 | AR01-1117 | CDC | AR | C | 2001 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

AR03-1002 | AR03-1002 | CDC | AR | C | 2003 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

AR97-0782 | AR97-0782 | CDC | AR | C | 1997 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

AR98-2146 | AR98-2146 | CDC | AR | C | 1998 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

AR99-3840 | AR99-3840 | CDC | AR | C | 1999 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

CA04-2148 | CA04-2148 | CDC | CA | W | 1983 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

CA04-2149 | CA04-2149 | CDC | CA | W | 2004 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

CA04-2258 | CA04-2258 | CDC | CA | W | 2004 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

CA95-1135 | CA95-1135 | CDC | CA | W | 1995 | A1 | A.I.1/2 | A.I.8 | A.I.9 |

DE03-1544 | DE03-1544 | CDC | DE | E | 2003 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

F0003 | FSC 043 | FOI | OH | E | 1941 | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0005 | FSC 041 | FOI | BC | W | 1935 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0008 | FSC 046 | FOI | OH | E | 1940 | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0061 | KS00-0948 | CDC | KS | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

F0069 | OK00-2731 | CDC | OK | C | 2000 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

F0071 | OK00-2733 | CDC | OK | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0076 | OK-ADA | OKDH | OK | C | 2000 | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0077 | OK-CAN | OKDH | OK | C | 1993 | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0078 | OK-CHK | OKDH | OK | C | 2000 | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0079 | OK-HUG | OKDH | OK | C | 1993 | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0080 | OK-OKL-1 | OKDH | OK | C | 1994 | NA | A.I.SchuS4 | A.I.12 | A.I.2/13/14/15 |

F0084 | OK-TUL-2 | OKDH | OK | C | 1996 | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0085 | OK-TUL-3 | OKDH | OK | C | 1993 | NA | A.I.1/2 | A.I.8 | A.I.11 |

F0244 | 83A-5698 | CADH | CA | W | 1983 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0246 | 93A-5254 | CADH | CA | W | 1993 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0272 | 92A-4575 | CADH | CA | W | 1992 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0276 | 94A-3325 | CADH | CA | W | 1994 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0281 | MO01-2148 | CDC | MO | C | 2001 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0282 | KS00-1817 | CDC | KS | C | 2000 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

F0287 | AR99-3448 | CDC | AR | C | 1999 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

F0297 | FSC 047 | FOI | AK | W | UNK | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0298 | FSC 052 | FOI | AK | W | UNK | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0307 | ND00-0952 | CDC | ND | C | 2000 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

F0308 | MA01-2505 | CDC | MA | E | 1978 | NA | A.I.4 | A.I.3 | A.I.4 |

F0312 | CO99-1817 | CDC | CO | W | 1999 | A1 | A.I.1/2 | A.I.12 | A.I.12/2 |

F0314 | MO01-4055 | CDC | MO | C | 2001 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

F0315 | MO01-1907 | CDC | MO | C | 2001 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

F0332 | NY98-1732 | CDC | NY | E | 1998 | A1b | A.I.4 | A.I.3 | A.I.4 |

F0347 | GA02-5426 | CDC | MA | E | 1981 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

F0348 | AR03-1800 | CDC | AR | C | 2003 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

F0357 | SD97-2107 | CDC | SD | C | 1997 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

F0359 | NC01-5379 | CDC | NC | E | 2001 | A1b | A.I.4 | A.I.3 | A.I.4 |

F0368 | KS03-2487 | CDC | KS | C | 2003 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

F0375 | MO02-1911 | CDC | MO | C | 2002 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0379 | PA03-3835 | CDC | PA | E | 2003 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0383 | OSU-1 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0384 | OSU-2 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.12 | A.I.12/2 |

F0385 | OSU-3 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.8 | A.I.11 |

F0386 | OSU-4 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0387 | OSU-5 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0388 | OSU-6 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.16 |

F0389 | OSU-7 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.8 | A.I.11 |

F0390 | OSU-8 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0391 | OSU-9 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0392 | OSU-10 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0393 | OSU-11 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0394 | OSU-12 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.16 |

F0395 | OSU-13 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0396 | OSU-14 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0397 | OSU-15 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0398 | OSU-16 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0399 | OSU-17 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0401 | OSU-19 | OSU | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0402 | OSU-20 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0403 | OSU-21 | OSU | OK | C | UNK | NA | A.I.1/2 | A.I.12 | A.I.12/2 |

F0404 | OKH-1 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0405 | OKH-2 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.2/13/14/15 |

F0406 | OKH-3 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0407 | OKH-4 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0408 | OKH-5 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0409 | OKH-6 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0410 | OKH-7 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.13 |

F0411 | OKH-8 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0412 | OKH-9 | OSU/OKDH | OK | C | UNK | NA | A.I.SchuS4 | A.I.12 | A.I.14 |

F0413 | OKH-10 | OSU/OKDH | OK | C | UNK | NA | A.I.1/2 | A.I.8 | A.I.11 |

F0414 | NC-1 | OSU | NC | E | 1998 | NA | A.I.4 | A.I.3 | A.I.4 |

F0415 | NC-2 | OSU | NC | E | 1998 | NA | A.I.4 | A.I.3 | A.I.4 |

F0685 | 80700069 | LLNL | UT | W | 2007 | NA | A.I.1/2 | A.I.12 | A.I.12/2 |

F0690 | 1100558 | IAB | AK | W | 2003 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0691 | 1133496 | IAB | AK | W | 2004 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0693 | 1211988 | IAB | AK | W | 2006 | NA | A.I.1/2 | A.I.8 | A.I.8/9/10 |

F0694 | 1211990 | IAB | AK | W | 2006 | NA | A.I.1/2 | A.I.8 | A.I.8/9/10 |

F0695 | 1213860 | IAB | AK | W | 2006 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0696 | 1213861 | IAB | AK | W | 2006 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0697 | 0916900084 | IAB | AK | W | 2009 | NA | A.I.1/2 | A.I.8 | A.I.9 |

F0717**†† | OK01-2528 | CDC | OK | C | 2001 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

F0718**†† | MO02-4195 | CDC | MO | C | 2002 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0723**‡‡ | MD00-2970 | CDC | DE | E | 2000 | A1b | A.I.4 | A.I.3 | A.I.4 |

F0724**‡‡ | MA00-2987 | CDC | MA | E | 2000 | A1b | A.I.4 | A.I.3 | A.I.4 |

GA00-3376 | GA00-3376 | CDC | GA | E | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.2/13/14/15 |

GA02-5347 | GA02-5347 | CDC | MS | C | 1980 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5351 | GA02-5351 | CDC | LA | C | 1981 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5353 | GA02-5353 | CDC | TN | E | 1992 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5360 | GA02-5360 | CDC | KY | E | 1973 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5373 | GA02-5373 | CDC | NY | E | 1977 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

GA02-5381 | GA02-5381 | CDC | AR | C | 1979 | A1b | A.I.1/2 | A.I.8 | A.I.10/11 |

GA02-5386 | GA02-5386 | CDC | OR | W | 1978 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5388 | GA02-5388 | CDC | SD | C | 1985 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

GA02-5389 | GA02-5389 | CDC | IA | C | 1979 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5390 | GA02-5390 | CDC | MS | C | 1981 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5392 | GA02-5392 | CDC | LA | C | 1983 | A1a | A.I.SchuS4 | A.I.12 | A.I.15/16 |

GA02-5393 | GA02-5393 | CDC | TN | E | 1980 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

GA02-5395 | GA02-5395 | CDC | NE | C | 1982 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5403 | GA02-5403 | CDC | OR | W | 1984 | A1b | A.I.1/2 | A.I.8 | A.I.11 |

GA02-5404 | GA02-5404 | CDC | GA | E | 1986 | A1b | A.I.SchuS4 | A.I.3 | A.I.5/6 |

GA02-5406 | GA02-5406 | CDC | DE | E | 1987 | A1a | A.I.SchuS4 | A.I.12 | A.I.2/13/14/15 |

GA02-5407 | GA02-5407 | CDC | AR | C | 1980 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5408 | GA02-5408 | CDC | SD | C | 1983 | A1b | A.I.SchuS4 | A.I.12 | A.I.12/2 |

GA02-5409 | GA02-5409 | CDC | KS | C | 1980 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

GA02-5410 | GA02-5410 | CDC | SD | C | 1984 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5412 | GA02-5412 | CDC | TX | C | 1980 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5422 | GA02-5422 | CDC | TX | C | 1983 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5425 | GA02-5425 | CDC | GA | E | 1986 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5427 | GA02-5427 | CDC | OH | E | 1986 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5428 | GA02-5428 | CDC | MO | C | 1980 | A1b | A.I.1/2 | A.I.8 | A.I.11 |

GA02-5435 | GA02-5435 | CDC | LA | C | 1984 | A1b | A.I.1/2 | A.I.8 | A.I.10/11 |

GA02-5441 | GA02-5441 | CDC | LA | C | 1983 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5444 | GA02-5444 | CDC | TX | C | 1980 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5445 | GA02-5445 | CDC | TN | E | 1992 | A1a | A.I.SchuS4 | A.I.12 | A.I.2/13/14/15 |

GA02-5446 | GA02-5446 | CDC | NC | E | 1992 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

GA02-5449 | GA02-5449 | CDC | TN | E | 1989 | A1a | A.I.1/2 | A.I.12 | A.I.16 |

GA02-5454 | GA02-5454 | CDC | MO | C | 1987 | A1b | A.I.1/2 | A.I.8 | A.I.10/11 |

GA02-5462 | GA02-5462 | CDC | OK | C | 1984 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5465 | GA02-5465 | CDC | IL | C | 1985 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5469 | GA02-5469 | CDC | OK | C | 1981 | A1b | A.I.1/2 | A.I.8 | A.I.11 |

GA02-5470 | GA02-5470 | CDC | MO | C | 1981 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5476 | GA02-5476 | CDC | KS | C | 1982 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5482 | GA02-5482 | CDC | IN | E | 1981 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA02-5497 | GA02-5497 | CDC | VA | E | 1982 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

GA02-5499 | GA02-5499 | CDC | MD | E | 1982 | A1b | A.I.SchuS4 | A.I.3 | A.I.4 |

GA02-5500 | GA02-5500 | CDC | MO | C | 1982 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

GA02-5501 | GA02-5501 | CDC | LA | C | 1982 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

GA02-5512 | GA02-5512 | CDC | MA | E | 1981 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

GA99-2584 | GA99-2584 | CDC | GA | E | 1999 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

F0719** | AR00-0028 | CDC | AR | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0720** | NE03-1457 | CDC | NE | C | 2003 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

F0721** | IL00-4351 | CDC | IL | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

F0722** | GA02-5383 | CDC | GA | E | 2002 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

F0725** | MI01-2654 | CDC | MI | E | 2001 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

F0726** | AK96-2888 | CDC | AK | W | 1996 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

F0727** | OK00-2732 | CDC | OK | C | 2000 | A1b | A.I.1/2 | A.I.8 | A.I.11 |

F0728** | CO00-3111 | CDC | CO | W | 2000 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

F0729** | NC98-3428 | CDC | NC | E | 1998 | A1b | A.I.1/2 | A.I.3 | A.I.6 |

IA00-3490 | IA00-3490 | CDC | IA | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

ID04-2686 | ID04-2686 | CDC | ID | W | 2004 | A1b | A.I.1/2 | Basal | A.I.1/3/7 |

IL01-3022 | IL01-3022 | CDC | IL | C | 2001 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

KS01-4799 | KS01-4799 | CDC | KS | C | 2001 | A1b | A.I.1/2 | A.I.8 | A.I.9 |

KS03-2455 | KS03-2455 | CDC | KS | C | 2003 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

KS82-0004 | KS82-0004 | CDC | KS | C | 1982 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

KS89-0548 | KS89-0548 | CDC | KS | C | 1989 | A1b | A.I.SchuS4 | A.I.12 | A.I.14 |

KY00-2794 | KY00-2794 | CDC | KY | E | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

LA95-0751 | LA95-0751 | CDC | LA | C | 1995 | A1 | A.I.SchuS4 | A.I.12 | A.I.14 |

MA04-2790 | MA04-2790 | CDC | MA | E | 2004 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

MD01-1249 | MD01-1249 | CDC | MD | E | 2001 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

MD04-2528 | MD04-2528 | CDC | MD | E | 2004 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

NC05-1521 | NC05-1521 | CDC | NC | E | 2005 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

NC98-3687 | NC98-3687 | CDC | NC | E | 1998 | A1 | A.I.1/2 | A.I.3 | A.I.4 |

ND00-1213 | ND00-1213 | CDC | ND | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.16 |

ND01-1900 | ND01-1900 | CDC | ND | C | 2001 | A1a | A.I.1/2 | Basal | A.I.1/3/7 |

NE82-0001 | NB82-0001 | CDC | NE | C | 1982 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

NE88-5553 | NB88-5553 | CDC | NE | C | 1988 | A1b | A.I.1/2 | A.I.8 | A.I.10/11 |

NE95-1835 | NE95-1835 | CDC | NE | C | 1995 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

NE97-2086 | NE97-2086 | CDC | NE | C | 1997 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

NJ04-3009 | NJ04-3009 | CDC | NJ | E | 2004 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

NY04-2564 | NY04-2564 | CDC | NY | E | 2004 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

NY96-3369 | NY96-3369 | CDC | NY | E | 1996 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

OK82-0005 | OK82-0005 | CDC | OK | C | 1982 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

PA84-0001 | PA84-0001 | CDC | PA | E | 1984 | A1a | A.I.SchuS4 | A.I.12 | A.I.13 |

SD00-3147 | SD00-3147 | CDC | SD | C | 2000 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

SD04-0857 | SD04-0857 | CDC | SD | C | 2003 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

TX05-5417 | TX05-5417 | CDC | TX | C | 2005 | A1b | A.I.1/2 | Basal | A.I.1/3/7 |

UT07-4262 | UT07-4262 | CDC | UT | W | 2007 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

UT07-4263 | UT07-4263 | CDC | UT | W | 2007 | A1a | A.I.1/2 | A.I.12 | A.I.12/2 |

UT98-3134 | UT98-3134 | CDC | UT | W | 1998 | A1a | A.I.SchuS4 | A.I.12 | A.I.14 |

VA00-1000 | VA00-1000 | CDC | VA | E | 2000 | A1b | A.I.1/2 | A.I.3 | A.I.5/6 |

VA00-2108 | VA00-2108 | CDC | VA | E | 2000 | A1 | A.I.1/2 | A.I.3 | A.I.4 |

VA98-5912 | VA98-5912 | CDC | VA | E | 1998 | A1b | A.I.1/2 | A.I.3 | A.I.3/4/5 |

VA99-2600 | VA99-2600 | CDC | VA | E | 1999 | A1b | A.I.1/2 | A.I.3 | A.I.4 |

*ID, identification; CDC, Centers for Disease Control and Prevention (Fort Collins, CO, USA); PFGE, pulsed-field gel electrophoresis; C, central; W, western; E, eastern; FOI, Swedish Defence Research Agency (Umeå, Sweden); NA, not applicable; BC, British Columbia, Canada; OKDH, Oklahoma State Department of Health (Oklahoma City, OK, USA); CADH, California Department of Health Services (Richmond, CA, USA); OSU, Oklahoma State University (Stillwater, OK, USA); LLNL, Lawrence Livermore National Laboratory (Livermore, CA, USA); IAB, Institute of Arctic Biology University of Alaska (Fairbanks, AK, USA).
†Strain ID from the Northern Arizona University (Flagstaff, AZ, USA) or CDC collections.
‡Strain ID from the originating laboratory.
§Region classification of state/province for genetic diversity calculation.
¶See (

Our whole-genome phylogeny revealed 3 major subgroups within

We observed several differences among the 3 subgroups in the whole-genome phylogeny (

To show more comprehensive phylogenetic patterns, we developed 16 canonical SNP (canSNP) assays as described (

SchuS4† position | SNP state, der/anc‡ | Primers, 5′ → 3′§ | Con¶ | Temp, °C# | ||
---|---|---|---|---|---|---|

Subgroup | ||||||

Major | Minor | |||||

NA | A.I.7 | 1005448** | C/T | A: TATTTCAATTTTTGCGATGGTAgGT | 0.80 | 55 |

D: ggggcggggcggggcTATTTCAATTTTTGCGATGGTAcTC | 0.20 | |||||

C: AAGTATGTTGGCAAGTAAAGTGAGAAGA | 0.20 | |||||

A.I.12 | NA | 142781†† | C/G | A: GCTTATCGCCGACATTCATCtAC | 0.20 | 60 |

D: ggggcggggcggggcgggCTTATCGCCGACATTCATCcAG | 0.20 | |||||

C: GGTATGGCAAAAAATACTTATGGTACG | 0.20 | |||||

A.I.12 | A.I.13 | 1833651‡‡ | T/C | A: CTTTCAATCATGTAACCATCATTATTTAaGC | 0.80 | 60 |

D: cggggcggggcggggcggggCTTTCAATCATGTAACCATCATTATTTAgGT | 0.20 | |||||

C: CTTAATGAACTTGGTGTAATGGGTAGATA | 0.20 | |||||

A.I.12 | A.I.16 | 273622 | T/C | A: AAACTTAAAAAAGAGCAAGAACTTAATGATcTC | 0.60 | 60 |

D: ggggcggggcggggcgAAACTTAAAAAAGAGCAAGAACTTAATGATaTT | 0.15 | |||||

C: CATCTTCATTAAAAGTCTTATTGTTTAAACGC | 0.15 | |||||

A.I.12 | A.I.15 | 1210286 | A/G | A: TCTTAAAACATCGACACTCTCAACcTG | 0.80 | 60 |

D: ggggcggggcggggcGATCTTAAAACATCGACACTCTCAACtTA | 0.20 | |||||

C: | 0.20 | |||||

A.I.12 | A.I.14 | 1296147 | T/C | A: ATCATACTGGTTATATTGGCGGTcTC | 0.80 | 60 |

D: cggggcggggcggggcggggATCATACTGGTTATATTGGCGGTgTT | 0.20 | |||||

C: GATGAGTCGCTATTAGCTTCTCGAAAG | 0.20 | |||||

A.I.8 | NA | 1150298 | G/A | A: TAGTCAATCTTGGAACTCCAGAtAA | 0.75 | 60 |

D: ggggcggggcggggcTAGTCAATCTTGGAACTCCAGAaAG | 0.15 | |||||

C: TCTATTACTCTAGGGTCAGATAGAAATTC | 0.15 | |||||

A.I.8 | A.I.9 | 1453599 | C/T | A: GCTGCTGCTAGATTAGCTATgCT | 0.15 | 60 |

D: ggggcggggcggggcGCTGCTGCTAGATTAGCTATcCC | 0.15 | |||||

C: TCAAGCAATCAACAATAATTTTACTAT | 0.15 | |||||

A.I.8 | A.I.10 | 797599 | T/G | A: GATCAATTGGTGGTGTTcCG | 0.80 | 60 |

D: ggggcggggcggggcGTGATCAATTGGTGGTGTTtCT | 0.20 | |||||

C: AACGTTTTATCCTCTTGAATATCAACTAT | 0.20 | |||||

A.I.8 | A.I.11 | 1278606 | G/A | A: AAGGAACAAAAAACATCATCATTgCT | 0.20 | 60 |

D: ggggcggggcggggcAAAAGGAACAAAAAACATCATCATTaCC | 0.20 | |||||

C: TCATACTAACAACGGCTATTCAGGGA | 0.20 | |||||

A.I.3 | NA | 1233898 | T/G | A: GCTTGACAATATTAGCTTATAAAACTATAgTG | 0.15 | 60 |

D: ggggcggggcggggcGCTTGACAATATTAGCTTATAAAACTATAaTT | 0.15 | |||||

C: TTTTTTCCATATTTCTGTAAAAAATATACTATTATG | 0.15 | |||||

A.I.3 | A.I.4 | 830715§§ | T/C | A: GTTAAGTCGGTAAGTATCGACAAaTC | 0.60 | 60 |

D: ggggcggggcggggcGTTAAGTCGGTAAGTATCGACAAgTT | 0.20 | |||||

C: CAAATCTTCTAGTATCTCTTTATCTTCAG | 0.20 | |||||

A.I.3 | A.I.5 | 113671 | G/A | A: cgggcgggcgggcgggGCTTGAGTTTATTTTTTGTTTAATGTgTA | 0.20 | 60 |

D: GCTTGAGTTTATTTTTTGTTTAATGTaTG | 0.20 | |||||

C: GGACAAAACTGTGGACGTTAAGAA | 0.20 | |||||

A.I.3 | A.I.6 | 580153 | G/A | A: cgggcgggcgggcgggTATAATGGTAACTCATGATCAAGAAcAA | 0.20 | 60 |

D: TTATAATGGTAACTCATGATCAAGAAaAG | 0.20 | |||||

C: ATCTGTCATGATACCAATTCTTGTCG | 0.20 |

*Melt-MAMA, melt–mismatch amplification mutation assay; SNP, single nucleotide polymporphism; canSNP, canonical SNP; con, concentration, μmol/L; temp, annealing temperature, °C; NA, not applicable; der, derived SNP state; anc, ancestral SNP state; D, derived allele primer; A, ancestral allele primer; C, common primer.
†Genomic position in reference A.I SchuS4 strain (GenBank accession no. NC_006570).
‡SNP states are listed according to their orientation in the SCHU S4 reference genome (GenBank accession no. AJ749949.2).
§Melt-MAMA primer sequences; primer tails and antepenultimate mismatch bases are in lower case.
¶Final concentration of each primer in Melt-MAMA genotyping assays.
#Assay annealing temperature.
**Assay designed on the reverse complement.
††SNP from (

Geographic alignment of 179 geographically diverse

Each subgroup exhibited complex yet distinct phylogeographic patterns (

The occurrence of the A.I.3 subgroup in the eastern United States could be a recent or ancient event. The subgroup may have been introduced more recently from the central region to a naive niche in the eastern region through importation of rabbits (

If we assume that the greatest genetic diversity in a phylogenetic context implies ancient origins, our findings suggest that the central United States is the likely geographic origin of a common ancestor to

We thank Mia Champion for her assistance with initial analyses and Laurel Respicio-Kingry for her assistance with SNP genotyping.

This work was supported in part by the US Department of Homeland Security Science and Technology Directorate through award HSHQDC-10-C-00139, the Swedish Civil Contingencies Agency through TA#014-2010-01, the Laboratory for Molecular Infection Medicine Sweden , and Västerbotten County Council. M.G. was supported by the Lendület program of the Hungarian Academy of Sciences.

Dr Birdsell is a postdoctoral fellow at the Center for Microbial Genetics and Genomics, Northern Arizona University. Her primary research interest is the evolution of