Table 5.
Analysis of the Complete Genomes of Salmonella Typhi Isolates From the Acute Index Cases and Their Household Chronic Carrier in 4 Household/Familial Clusters
| Cluster | Clinical Host | Isolate IDa | Date of Isolation | Days Between Index Case Isolate and Carrier Isolateb | Sex | Age | GenoTyphi Genotype |
SNP Distance Between the Index Case Isolate and Carrier Isolatec |
SNP Distance Between First and Subsequent Coproculture Isolates From Same Carrier | SNP Distance to the Nearest Isolate External to This Cluster |
|---|---|---|---|---|---|---|---|---|---|---|
| Cluster 1 | Index case 2 | 314-2017_CI | 28-01-2017 | - | F | 13 mo | 3.5 | … | … | 95 |
| Chronic carrier | 314-2017_CO_03 | 29-01-2019 | 731 d | F | 71 y | 3.5 | 7 | … | 96 | |
| Cluster 2 | Index case 4 | 1521-2017_CI | 02-06-2017 | - | F | 21 y | 1.2.1 | … | … | 293 |
| Chronic carrier | 1521-2017_CO_04 d | 12-02-2019 | 620 d | F | 71 y | 1.2.1 | 8 | … | 293 | |
| Cluster 3 | Index case 5 | 1698-2017_CI | 29-06-2017 | - | F | 9 mo | 2 | … | … | 52 |
| Temporary carrier | 1698-2017_CO_04 | 10-01-2019 | 560 d | F | 6 y | 2 | 1 | … | 53 | |
| Chronic carrier | 1698-2017_CO_06 d | 10-01-2019 | 560 d | F | 79 y | 2 | 0 | … | 52 | |
| Index case 15 | 424-2019_CI | 02-02-2019 | 583 d | M | 13 y | 2 | 4 | … | 56 | |
| Cluster 4 | Index case 18 | 2027-2019_CI | 19-07-2019 | - | F | 6 y | 3.5 | … | … | 58 |
| Chronic carrier | 2027-2019_CO_04 d,e | 29-09-2019 | 81 d | F | 73 y | 3.5 | 11 | … | 51 | |
| Repeat coproculture | _Copro2f | 30-09-2019 | 82 d | 3.5 | 10g | 3 | 50 | |||
| Repeat coproculture | _Copro3f | 01-10-2019 | 83 d | 3.5 | 11g | 0 | 51 | |||
| Repeat coproculture | _Copro4f | 02-10-2019 | 84 d | 3.5 | 5g | 8 | 55 | |||
| Repeat coproculture | _Copro5f | 07-10-2019 | 89 d | 3.5 | 14g | 7 | 54 |
Associations are shown in relation to calendar time and SNP distances.
Abbreviations: F, female; M, male; SNP, single-nucleotide polymorphism.
aCI = Index case (note that cluster 3 includes 2 index cases (case 5 and case 15) widely separated in dates of onset); CO = Household contact; Copro# = Day of collection of 5 daily consecutive coprocultures from 1 chronic carrier.
bThe number of days between the isolation of Salmonella Typhi from the index acute case and the isolation of S Typhi from the stool of the household contact collected during a case investigation.
cThe number of core genome SNPs difference between the stool culture isolate from a household contact and the index acute case isolate.
dThe chronic carriers, all women 71–79 years of age, are highlighted in bold.
eThis chronic carrier within cluster 4 had coprocultures collected on 5 consecutive days to assess SNP differences on multiple days in the same chronic carrier.
fCoprocultures 2–5 are draft genomes.
gThe first number is the SNP distance for each sequential coproculture with respect to the index case, and the following number in parentheses is the SNP distance from coproculture 1 to measure within-host variation over sequential coprocultures.