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Transmission analysis

YX Yue Xiao
CY Chao Yang
LY Leilei Yu
FT Fengwei Tian
YW Yarong Wu
JZ Jianxin Zhao
HZ Hao Zhang
RY Ruifu Yang
WC Wei Chen
CH Colin Hill
YC Yujun Cui
QZ Qixiao Zhai
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By setting pairwise SNP distances less than 2500, we defined 31 semi-clonal groups (SCG) with each SCG containing 2–146 isolates for the 418 B. longum subsp. longum strains. As the number of used assemblies can affect the size of the core genome and the number of detected SNPs, we recalled SNPs for each SCG and used the recombination detection tool (Gubbins) [61] to identify the recombination sites for each SCG. After removing recombination regions, we re-analyzed the pairwise SNP distances between strains of each SCG to identify clonal groups (CGs). A pairwise SNP distance of less than 10 was set as the CG threshold, according to a previous study [62]. Isolates in each CG are the decedents of a common ancestor, and thus are considered as valid candidates to reflect transmission events.

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