Table 2 Details of epidemiological clusters defined within the S. sonnei population.
New genotyping framework | Previously defined as | Description | ||
|---|---|---|---|---|
Genotype | Name | Name | Study | |
Lineage II | ||||
2.8 | Korea II | Korea II | Holt 2012 | Associated with Korea |
2.9, 2.10, 2.11 | Latin America II | South America II LA sublineage IIa & IIb | Holt 2012 Baker 2017 | Associated with Latin America |
Lineage III | ||||
3.4 | Latin America III | South America III LA sublineage IIIa & IIIb | Holt 2012 Baker 2017 | Associated with Latin America |
3.6 | Central Asia III | Central Asia IIIa | Holt 2012 | Associated with Central Asia |
3.6.1 | CipR parent | – | This study | Subclade from which ciprofloxacin-resistant sublineage emerged |
3.6.1.1 | CipR | Ciprofloxacin-resistant Pop2 | The 2015 The 2019 | Ciprofloxacin-resistant triple mutation sublineage |
3.6.1.1.1 | CipR.SEA | - | This study | Ciprofloxacin-resistant isolates associated with South East Asia |
3.6.1.1.3.1 | CipR.MSM1 | MSM clade 1 | Baker 2018 | MSM-linked ciprofloxacin resistant isolates |
3.6.1.1.2 | CipR.MSM5 | BAPS1 MSM Clade 5 | Ingle 2019 Bardsley 2020 | MSM-linked ciprofloxacin resistant isolates |
3.7.25 | MSM4 | MSM Clade 4 | Baker 2018 | MSM-linked |
3.7.29 | Vietnam III | VN clone | Holt 2012 | Associated with South East Asia |
3.7.29.1 | VN2 | VN clone, sweep 2 | Holt 2013 | Clonal group originating from genetic sweep 2 |
3.7.29.1.1 | VN3 | VN clone, sweep 3 | Holt 2013 | Clonal group originating from genetic sweep 3 |
3.7.29.1.1.1 | VN3.KH2 | KH2 | Holt 2013 | Kanh Hoa subclone 2, emerging from sweep 3 |
3.7.29.1.1.2 | VN4 | VN clone, sweep 4 | Holt 2013 | Clonal group originating from genetic sweep 4 |
3.7.29.1.2 | VN2.MSM2 | MSM Clade 2 | Bardsley 2020 | MSM-linked strains, emerging from sweep 2 |
3.7.29.1.2.1 | VN2.MSM2.Aus | - (part of BAPS3) | This study Ingle 2019 | Australian MSM-linked, emerging from sweep 2 |
3.7.29.1.3 | VN2.Hue | Hue2 | Holt 2013 | Hue subclone 2, emerging from sweep 3 |
3.7.29.1.4 | VN2.KH1 | KH1 | Holt 2013 | Kanh Hoa subclone 1, emerging from sweep 2 |
3.7.29.1.4.1 | VN2.KH1.Aus | - (part of BAPS3) | This study Ingle 2019 | Australian isolates, emerging from KH1 |
3.7.30 | Middle East III | Middle East III | Holt 2012 | Associated with Middle East |
3.7.30.4 | Israel III | Israel III | This study | Associated with Israel |
3.7.30.4.1 | OJC | OJC-associated | Baker 2016 | Associated with the Orthodox Jewish communities in Israel, UK, USA and Europe |
