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Clonal complex designation

Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). These central genotypes are identified by a number of heuristic means, including BURST and split decomposition, along with feedback from public health laboratories and epidemiologists.

For the Neisseria database, once a central genotype has been identified, clonal complexes are defined as including any ST that matches the central genotype at four or more loci unless it more closely matches another central genotype.

STs are assigned to clonal complexes automatically by a Perl script that runs against the database each evening.

Currently defined complexes

Central STComplex name
11ST-11 complex/ET-37 complex
8ST-8 complex/Cluster A4
41ST-41/44 complex/Lineage 3
44ST-41/44 complex/Lineage 3
32ST-32 complex/ET-5 complex
1ST-1 complex/subgroup I/II
4ST-4 complex/subgroup IV
5ST-5 complex/subgroup III
106ST-106 complex
116ST-116 complex
18ST-18 complex
198ST-198 complex
23ST-23 complex/Cluster A3
231ST-231 complex
254ST-254 complex
292ST-292 complex
334ST-334 complex
35ST-35 complex
364ST-364 complex
269ST-269 complex
376ST-376 complex
53ST-53 complex
549ST-549 complex
92ST-92 complex
22ST-22 complex
162ST-162 complex
213ST-213 complex
595ST-595 complex (lactamica)
613ST-613 complex (lactamica)
624ST-624 complex (lactamica)
640ST-640 complex (lactamica)
1494ST-1494 complex (lactamica)
1540ST-1540 complex (lactamica)
461ST-461 complex
226ST-226 complex
60ST-60 complex
174ST-174 complex
103ST-103 complex
167ST-167 complex
750ST-750 complex
1157ST-1157 complex
865ST-865 complex
4821ST-4821 complex
37ST-37 complex
175ST-175 complex
1117ST-1117 complex
1136ST-1136 complex
212ST-212 complex
178ST-178 complex
282ST-282 complex
181ST-181 complex
4240ST-4240/6688 complex
6688ST-4240/6688 complex
192ST-192 complex
10217ST-10217 complex
1572ST-1572 complex


Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Neisseria Multi Locus Sequence Typing website (https://pubmlst.org/ neisseria/) sited at the University of Oxford (Jolley et al. Wellcome Open Res 2018, 3:124 [version 1; referees: 2 approved]). The development of this site has been funded by the Wellcome Trust and European Union.