Table 2:
Studies combining whole-genome sequencing and spatial data to address research questions beyond spatial distribution
| Study duration | Study area | Definition of genomic clusters | Spatial approaches | Types of questions addressed | Focus on DR-TB | |
|---|---|---|---|---|---|---|
|
| ||||||
| Yang et al (2018)19 | 2009–15 | Shanghai, China | SNP (10) and transmission probability | KDE | a, b, d | ·· |
| Jiang et al (2020)44 | 2013–17 | Shenzhen, China | SNP (12) | KDE | a, b | ✓ |
| Lin et al (2020)45 | 2018 | Guangxi, China | SNP (12) | NA | a, d | ·· |
| Bui et al (2021)26 | 2016–17 | Lima, Peru | SNP (5) | KDE | a, b, c, d | ✓ |
| Huang et al (2022)46 | 2009–12 | Lima, Peru | SNP (1, 5, 10) | Other | a, b, d | ·· |
| Yin et al (2022)47 | 2018–20 | Beijing, China | SNP (12) and transmission probability | KDE | a, b | ✓ |
| Yang et al (2022)48 | 2018–19 | Moldova | SNP (5), patristic distance, and transmission probability | NA | a, d | ·· |
| Zhao et al (2022)49 | 2018–20 | Chongqing, China | SNP (12) | NA | a, d | ✓ |
| Baker et al (2023)42 | 2012–16 | Gaborone, Botswana | SNP (5) | KDE, K function | a, b, d | ·· |
| Li et al (2023)41 | 2011–20 | Shanghai, China | SNP (12) and transmission probability | KDE | a, b, d | ·· |
| Miyahara et al (2023)50 | 2017–20 | Chiang Rai province, Thailand | SNP (12) | Nearest neighbour index | a, b | ·· |
| Che et al (2024)51 | 2020–23 | Ningbo, China | SNP (12) | KDE | a, b, d | ✓ |
| Lan et al (2024)37 | 2018–19 | Moldova | SNP (5), patristic distance, and transmission probability | Spatial Bayesian modelling | a, b, c | ·· |
| Liu et al (2024)52 | 2015–21 | Zhejiang, China | SNP (12) | KDE | a, b, d | ·· |
| Utpatel et al (2024)53 | 2017–19 | Callao, Peru | SNP (5) | KDE | a, b | ✓ |
| Yang et al (2024)54 | 2016–21 | Urumqi City, China | SNP (12) | Scan statistics | a, b | ✓ |
| Yuen et al (2024)55 | 2011–12 and 2020–21 | Peru | SNP (5, 10) | NA | a, d | ·· |
A checkmark in the DR-TB column indicates a study that focuses on at least one drug-resistant phenotype, including multidrug-resistant and extensively drug-resistant phenotypes. DR-TB=drug-resistant tuberculosis. KDE=kernel density estimation. NA=not applicable. SNP=single nucleotide polymorphism. Question a=spatial description. Question b=hotspot detection and localisation. Question c=hotspot explanation.
Question d=association between proximity and genetic relatedness.