Table 3.

Confirmation of putative F-specific amplicon sequences

Source strainaPutative F type of ampliconUnambiguous nucleotides in sequenced amplicon (no.)BLAST search result
Best match2nd best match
% Identity with best matchF type of best matchAccession no. of best match% Identity with 2nd best matchF type of 2nd best matchAccession no. of 2nd best match
CFT073F7-134699.4F7-1 X02921 39.6F14 Y08928
CFT073F7-215896.2F7-2 M12861 67.1F16 Y08930
C351-82F822797.8F8 Y08931 83.7ECOR 48e AF051811
C483-82F933992.6F9 M68059 14.2F14 Y08928
3669b F10b 27593.1F10 Y08927 60.7F13 X61239
IA2F1125895.3F11 L07420 77.1ECOR 48e AF051811
C1979-79F1235998.3F12 X62157 91.9F15 Y08929
C1979-79F12/15c 15498.7F12 X62157 98.1F15 Y08929
CP9F1336794.3F13 X61239 45.0F10 Y08927
CP9b F14b 301100F14 Y08928 70.4F7-1 X02921
C372-82F1542799.7F15 Y08929 92.7ECOR 46e AF051810
C372-82F12/15d 15697.4F12 X62157 96.8F15 Y08929
IA2b F16b 22097.3F16 Y08930 89.1F15 Y08929
  • a Strains are as shown in Table 1.

  • b The F10, F14, and F16 amplicons from strains 3669, CP9, and IA2, respectively, represented extra F types. Extra F10 amplicons from F8 and F15 control strains C1254-77 and C1805-79 also were confirmed as representing authentic F10 sequence (data not shown).

  • c From F12.

  • d From F15.

  • e F = antigen type not defined.