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. 2020 Oct 19;11:564103. doi: 10.3389/fmicb.2020.564103

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Copyright © 2020 van den Beld, Reubsaet, Pijnacker, Harpal, Kuiling, Heerkens, Hoeve-Bakker, Noomen, Hendriks, Borst, van der Heide, Kooistra-Smid and Rossen.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Core genome MLST tree of S. sonnei, including context isolates. 203 isolates, distance based on comparing 2315 alleles using the Enterobase Escherichia/Shigella cgMLST v1 scheme. Missing values are an own category. Red text = MSM-associated clusters. Black text = serotype; prov = provisional Shigella. Qnr genes left to right = qnrB19, qnrB4, qnrS1; SHI-1 left to right = sigA, pic, set; SHI-2 left to right = iucA, iucB, iucC, iucD, iutA, shiA, shiB, shiD, shiE; and T3SS effectors left to right = ipa-ipg operon, virA, ospB, ospC1, ospC3, ospD3, ospE1, ospE2, ospF, ospG. Further features are explained in the legend within Figure 2.