Table 1. Summary of published studies and other data sources.
Details of research studies and public health laboratory data aggregated in this study.
| Published studiesPubMed ID or DOI (citation as per reference list) | Total genomes | *Representative cases 2010–2020 | †Travel associated |
|---|---|---|---|
| 11677608 (Parkhill et al., 2001) | 1 | 0 | 0 |
| 12644504 (Deng et al., 2003) | 1 | 0 | 0 |
| 18660809 (Holt et al., 2008) | 4 | 0 | 0 |
| 25392358 (Hendriksen et al., 2015a) | 22 | 0 | 0 |
| 25428145 (Hendriksen et al., 2015b) | 2 | 0 | 0 |
| 25961941 (Wong et al., 2015) | 1736 | 733 | 248 |
| 26411565 (Baker et al., 2015) | 30 | 0 | 0 |
| 26974227 (Pham Thanh et al., 2016a) | 77 | 77 | 0 |
| 27069781 (Ashton et al., 2016) | 489 | 432 | 356 |
| 27331909 (Pham Thanh et al., 2016b) | 1 | 1 | 0 |
| 27657909 (Wong et al., 2016b) | 128 | 111 | 0 |
| 27703135 (Wong et al., 2016a) | 99 | 43 | 43 |
| 28060810 (Dyson et al., 2017) | 44 | 0 | 0 |
| 28280021 (Rodrigues et al., 2017) | 3 | 0 | 0 |
| 28705963 (Kong et al., 2017) | 2 | 0 | 0 |
| 28931025 (Kuijpers et al., 2017) | 64 | 59 | 0 |
| 29051234 (Gul et al., 2017) | 1 | 0 | 0 |
| 29136410 (Phoba et al., 2017) | 1 | 0 | 0 |
| 29216342 (Day et al., 2018) | 5 | 4 | 3 |
| 29255729 (Matono et al., 2017) | 107 | 0 | 0 |
| 29463654 (Klemm et al., 2018) | 100 | 0 | 0 |
| 29616895 (Djeghout et al., 2018) | 1 | 0 | 0 |
| 29684021 (Britto et al., 2018) | 192 | 169 | 0 |
| 30425150 (Tanmoy et al., 2018) | 536 | 0 | 0 |
| 30504848 (Park et al., 2018) | 249 | 209 | 0 |
| 30236166 (Burnsed et al., 2018) | 30 | 0 | 0 |
| 31225619 (Oo et al., 2019) | 39 | 39 | 0 |
| 31513580 (Ingle et al., 2019) | 107 | 99 | 91 |
| 31730615 (Hooda et al., 2019) | 12 | 0 | 0 |
| 31872221 (Sah et al., 2019) | 2 | 0 | 0 |
| 31665304 (Britto et al., 2020) | 94 | 94 | 0 |
| 32003431 (Pragasam et al., 2020) | 194 | 0 | 0 |
| 32106221 (Rahman et al., 2020) | 202 | 147 | 0 |
| 32119918 (Chirico et al., 2020) | 1 | 0 | 0 |
| 32217683 (Tagg et al., 2020) | 5 | 0 | 0 |
| 32253142 (Liu et al., 2021) | 1 | 0 | 0 |
| 32732230 (Hao et al., 2020) | 1 | 0 | 0 |
| 32883020 (Rasheed et al., 2020) | 27 | 27 | 0 |
| 33079054 (Maes et al., 2020) | 7 | 7 | 0 |
| 33085725 (Thanh Duy et al., 2020) | 116 | 0 | 0 |
| 33347558 (Mashe et al., 2021) | 29 | 0 | 0 |
| 34223059 (Duy et al., 2020) | 4 | 0 | 0 |
| 33496224 (Octavia et al., 2021) | 15 | 15 | 12 |
| 33515460 (Carey et al., 2021) | 66 | 66 | 0 |
| 33593966 (Sajib et al., 2021) | 80 | 80 | 0 |
| 33651791 (Shin et al., 2021) | 8 | 0 | 0 |
| 33704480 (Nair et al., 2021) | 58 | 58 | 58 |
| 33965548 (Jacob et al., 2021) | 2 | 0 | 0 |
| 34370659 (Chattaway et al., 2021) | 631 | 604 | 584 |
| 34463736 (Gauld et al., 2022) | 262 | 262 | 0 |
| 34515028 (Kariuki et al., 2021) | 136 | 88 | 0 |
| 34529660 (Guevara et al., 2021) | 77 | 0 | 0 |
| 34543095 (Ingle et al., 2021) | 116 | 116 | 107 |
| 34626469 (Argimón et al., 2021b) | 92 | 92 | 0 |
| 34812716 (Kanteh et al., 2021) | 16 | 14 | 0 |
| 35344544 (Dyson et al., 2022) | 41 | 0 | 0 |
| 35750070 (da Silva et al., 2022) | 3402 | 3390 | 0 |
| 35767580 (Maes et al., 2022) | 203 | 90 | 0 |
| 35999186 (Lagrada et al., 2022) | 190 | 190 | 0 |
| 36026470 (Ikhimiukor et al., 2022a) | 22 | 14 | 0 |
| 36094088 (Sikorski et al., 2022) | 202 | 174 | 1 |
| 37327220 (Rutanga et al., 2023) | 51 | 26 | 0 |
| 37339282 (Smith et al., 2023) | 281 | 281 | 13 |
| DOI: 10.1101/2022.09.01.506167 (Thilliez et al., 2022) | 57 | 0 | 0 |
| DOI: 10.1101/2022.10.03.510628 (Carey et al., 2022) | 463 | 0 | 0 |
| DOI: 10.1101/2023.03.27.23287794 (Ashton et al., 2023) | 20 | 20 | 0 |
| DOI: 10.1101/2023.03.11.23286741 (Dyson et al., 2023) | 732 | 707 | 0 |
| Previously unpublished public health laboratory data | |||
| France (Institut Pasteur) | 23 | 23 | 17 |
| New Zealand (ESR) | 99 | 97 | 52 |
| USA (CDC) | 889 | 850 | 712 |
| Total | 13,000 | 9508 | 2297 |
*
Genomes associated with assumed acute typhoid cases, isolated from 2010 onwards from non-targeted sampling frames; this is the subset of data used to generate genotype prevalence distributions shown in Figures 1—3.
†
Genomes recorded as travel-associated and with known travel to a specific country in this region, associated with assumed acute typhoid isolated from 2010 onwards from non-targeted sampling frames.