TABLE 1.
S. Saintpaul SNP clusters with significantly higher or lower proportions of human clinical isolates
| SNP cluster | Epi-typea | No. of isolates |
Odds ratiob | P valuec | ||
|---|---|---|---|---|---|---|
| Human | Nonhuman | Total | ||||
| PDS000006321.200d | HA | 388 | 13 | 401 | 12.933 | <0.001 |
| PDS000029281.36 | HA | 241 | 0 | 241 | Inf | <0.001 |
| PDS000004371.140d | HA | 203 | 6 | 209 | 13.885 | <0.001 |
| PDS000009466.139d | HA | 213 | 14 | 227 | 6.225 | <0.001 |
| PDS000031607.43 | HA | 108 | 0 | 108 | Inf | <0.001 |
| PDS000002536.90d | HA | 121 | 3 | 124 | 16.175 | <0.001 |
| PDS000006544.8 | HA | 71 | 0 | 71 | Inf | <0.001 |
| PDS000032614.60d | HA | 115 | 10 | 125 | 4.579 | <0.001 |
| PDS000003801.90 | HA | 117 | 13 | 130 | 3.577 | <0.001 |
| PDS000009725.44 | HA | 50 | 1 | 51 | 19.656 | <0.001 |
| PDS000002279.52 | HA | 66 | 4 | 70 | 6.503 | <0.001 |
| PDS000013987.46 | HA | 51 | 2 | 53 | 10.020 | <0.001 |
| PDS000028639.6 | HA | 44 | 1 | 45 | 17.266 | <0.001 |
| PDS000029315.14 | HA | 69 | 6 | 75 | 4.529 | <0.001 |
| PDS000022946.21 | HA | 33 | 0 | 33 | Inf | <0.001 |
| PDS000004376.21 | HA | 31 | 0 | 31 | Inf | <0.001 |
| PDS000029174.10 | HA | 30 | 0 | 30 | Inf | <0.001 |
| PDS000028163.22 | HA | 37 | 1 | 38 | 14.489 | <0.001 |
| PDS000029326.49 | HA | 96 | 14 | 110 | 2.706 | 0.001 |
| PDS000028460.3 | HA | 25 | 0 | 25 | Inf | 0.002 |
| PDS000042733.19 | HA | 23 | 0 | 23 | Inf | 0.003 |
| PDS000029489.19 | HA | 22 | 0 | 22 | Inf | 0.004 |
| PDS000001869.65 | HA | 73 | 11 | 84 | 2.607 | 0.005 |
| PDS000002283.9 | HA | 21 | 0 | 21 | Inf | 0.005 |
| PDS000014879.19 | HA | 21 | 0 | 21 | Inf | 0.005 |
| PDS000003803.30 | HA | 29 | 2 | 31 | 5.660 | 0.015 |
| PDS000030636.11 | HA | 17 | 0 | 17 | Inf | 0.018 |
| PDS000028687.19 | HA | 22 | 1 | 23 | 8.577 | 0.024 |
| PDS000029061.13 | HA | 16 | 0 | 16 | Inf | 0.024 |
| PDS000004383.106d | NHA | 2 | 366 | 368 | 0.002 | <0.001 |
| PDS000029303.44d | NHA | 70 | 164 | 234 | 0.148 | <0.001 |
| PDS000004385.43d | NHA | 9 | 90 | 99 | 0.036 | <0.001 |
| PDS000032619.10d | NHA | 1 | 72 | 73 | 0.005 | <0.001 |
| PDS000004163.70 | NHA | 20 | 63 | 83 | 0.118 | <0.001 |
| PDS000001868.151 | NHA | 140 | 146 | 286 | 0.345 | <0.001 |
| PDS000003800.23 | NHA | 14 | 43 | 57 | 0.123 | <0.001 |
| PDS000030862.1 | NHA | 1 | 25 | 26 | 0.015 | <0.001 |
| PDS000032172.2 | NHA | 2 | 13 | 15 | 0.059 | <0.001 |
| PDS000023865.11 | NHA | 10 | 17 | 27 | 0.226 | 0.001 |
| PDS000037793.7 | NHA | 10 | 17 | 27 | 0.226 | 0.001 |
| PDS000011234.6 | NHA | 0 | 6 | 6 | 0.000 | 0.003 |
| PDS000037718.2 | NHA | 0 | 6 | 6 | 0.000 | 0.003 |
| PDS000032576.18 | NHA | 18 | 21 | 39 | 0.329 | 0.003 |
| PDS000002534.6 | NHA | 1 | 7 | 8 | 0.055 | 0.005 |
| PDS000025969.3 | NHA | 0 | 5 | 5 | 0.000 | 0.009 |
| PDS000041109.2 | NHA | 2 | 7 | 9 | 0.110 | 0.014 |
| PDS000002533.6 | NHA | 0 | 4 | 4 | 0.000 | 0.025 |
| PDS000004372.6 | NHA | 0 | 4 | 4 | 0.000 | 0.025 |
| PDS000030850.1 | NHA | 0 | 4 | 4 | 0.000 | 0.025 |
| PDS000032145.1 | NHA | 0 | 4 | 4 | 0.000 | 0.025 |
| PDS000048106.3 | NHA | 0 | 4 | 4 | 0.000 | 0.025 |
| PDS000037705.8 | NHA | 2 | 6 | 8 | 0.129 | 0.031 |
Epi-type is assigned based on the significant over- or underrepresentation of human clinical isolates among all isolates assigned to a given SNP clusters. For HA, the SNP clusters show a significant overrepresentation of human clinical isolates; for NHA, the SNP clusters show a significant underrepresentation of human clinical isolates. Inf, infinity.
The odds ratio of a given SNP cluster refers to the ratio of the odds of human clinical isolates in the SNP cluster to the odds of human clinical isolates not in the SNP cluster.
BH-corrected P value of the Fisher’s exact tests.
SNP clusters that are included in the comparative genomic analyses in this study.