TABLE 2.
Estimated mutation rates at MLVA loci in Salmonella Typhimuriuma
| Locus | Gene | Gene function | Repeat length(s) (bp) | No. of changes observeda |
Mutation rate |
Diversityb |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| In vitro | In vivo | Per generation, in vitro | Per day, in vitro | Per day, in vivo | General (10) | General (20) | General (this study) | Outbreak (20) | Outbreak (this study) | ||||
| STTR9 | Intergenic | Upstream of mannitol dehydrogenase | 9 | 0 | 0 | <3.5E-5 | <1.0E-3 | <2.3E-3 | 5.10E-01 | 3.70E-01 | 3.10E-01 | 8.70E-03 | 0 |
| STTR5 | yohM | Nickel/cobalt efflux protein | 6 | 2 (+1, +1) | 1 (−3) | 7.00E-05 | 2.00E-03 | 2.30E-03 | 8.70E-01 | 9.20E-01 | 9.10E-01 | 4.50E-01 | 6.30E-01 |
| STTR6 | Intergenic | Phage related | 6 | 4 (+1, +1, −1, −2) | 2 (+1, −2) | 1.40E-04 | 4.00E-03 | 4.50E-03 | 9.00E-01 | 9.10E-01 | 9.00E-01 | 7.20E-01 | 4.80E-01 |
| STTR10 | Intergenic | pSLT plasmid | 6 | 4 (+1, +1, +1, −1) | 1 (−2) | 1.40E-04 | 4.00E-03 | 2.30E-03 | 9.20E-01 | 9.10E-01 | 8.40E-01 | 5.50E-01 | 2.10E-01 |
| STTR3 | bigA | Surface-exposed virulence protein | 27/33 | 0 | 0 | <3.5E-5 | <1.0E-3 | <2.3E-3 | 2.50E-01 | 6.80E-01 | 2.80E-01 | 2.80E-02 | 0 |
a
Total numbers of observed changes are given; sizes and directions of changes are given in parentheses (e.g., “+1” indicates a 1-copy increase).
b
Diversity measures are Simpson's diversity values; “Outbreak” refers to diversity measures within sets of isolates epidemiologically defined as belonging to the same outbreak; “General” refers to large isolate collections not limited to outbreaks.