Table 1. Assembly statistics and genomic typing of S. Typhi isolates in this study.
| Isolate/Sample ID | Case | Clinical sample | Timeline of isolate recoverya | Number of contigsb | Assembly length (bases) | Assembly N50 | GenoTyphi lineage |
|---|---|---|---|---|---|---|---|
| CIDM-STyphi-A01 | Case A | Blood | D-7 | 91 (90) | 4,720,812 | 97,881 | 4.3.1.1 |
| CIDM-Styphi-B01 | Case B- Sample 1 | Faeces | D+0 | 93 (92) | 4,686,206 | 110,674 | 4.3.1.1 |
| CIDM-Styphi-B02 | Case B- Sample 2 | Faeces | D+15 | 81 (80) | 4,721,781 | 129,329 | 4.3.1.1 |
| CIDM-Styphi-B03 | Case B- Sample 3 | Faeces | D+63 | 80 (79) | 4,722,620 | 125,234 | 4.3.1.1 |
| CIDM-Styphi-B04 | Case B- Sample 4 | Faeces | D+65 | 80 (79) | 4,722,052 | 143,307 | 4.3.1.1 |
| CIDM-Styphi-B05 | Case B- Sample 5 | Bile fluid | D+142 | 78 (77) | 4,723,529 | 144,688 | 4.3.1.1 |
| CIDM-Styphi-B06 | Case B- Sample 6 | Intraoperative gall bladder swab | D+142 | 75 (74) | 4,722,683 | 153,670 | 4.3.1.1 |
aTimeline measured in days (designated by the letter ‘D’) relative to the isolation of the first sample from Case B
bNumber of contigs taxonomically classified as S. enterica listed in parenthesis