Volume 16, Number 4—April 2010
Research
Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987–2008
Christian Jenke, Dag Harmsen, Thomas Weniger, Jörg Rothgänger, Eija Hyytiä-Trees, Martina Bielaszewska, Helge Karch, and Alexander Mellmann
Table 1
VNTR characteristics of enterohemorrhagic Escherichia coli, Germany, 1987–2008*
| VNTR locus | Alternative name† | Repeat length, bp | Inside ORF (no.)‡ | No. repeats |
No. alleles§ | Null alleles | Null allele frequency, % | ID | Typeability, %¶ | |
|---|---|---|---|---|---|---|---|---|---|---|
| Minimum | Maximum | |||||||||
| 3 | Vhec3, TR5 | 6 | + (Z0268) | 3 | 23 | 22 | + | 2.0 | 0.86 | 98.0 |
| 34 | Vhec2, TR6 | 18 | + (Z5865) | 4 | 12 | 8 | – | – | 0.66 | 100.0 |
| 9 | Vhec4, TR1 | 6 | + (Z3935/Z3936) | 6 | 23 | 15 | + | 31.7 | 0.90 | 68.3 |
| 25 | TR4 | 6 | – | 2 | 15 | 6 | – | – | 0.74 | 100.0 |
| 17 | TR3 | 6 | + (Z5935) | 2 | 19 | 10 | – | – | 0.80 | 100.0 |
| 19 | TR7 | 6 | + (Z3274) | 3 | 11 | 9 | – | – | 0.76 | 100.0 |
| 36# | Vhec7 | 7 | – | 3 | 15 | 13 | + | 44.1 | 0.87 | 55.9 |
| 37# | – | 6 | + (L7083) | 3 | 17 | 11 | + | 2.0 | 0.82 | 98.0 |
*VNTR, variable number tandem repeat; ORF, open reading frame; ID, index of diversity without null alleles.
†Vhec loci as explained by Lindstedt et al. (15). TR loci are from Noller et al. (14).
‡Number is based on current EDL933 genome data. ORF encoding VNTR loci encoded either hypothetical proteins or proteins with unknown function.
§Including null alleles.
¶Typeability determines the proportion of all alleles without null alleles.
#Located on plasmid pO157 of reference strain EDL933.
