Clonal Relatedness on the Basis of Single-Nucleotide Polymorphisms

We performed single-nucleotide polymorphism (SNP) calling for genome sequences to untangle the clonal relatedness of ST171 strains and to investigate whether the ST171 strains in this study are clonally related to strains recovered elsewhere. All genome sequences of ST171 Enterobacter strains (n = 102), regardless of types of the host source (human, nonhuman, or unknown) and source (blood, nonblood, or unknown), were retrieved from GenBank. We used the complete chromosome sequence of ST171 strain 34798 (GenBank accession no. CP012165), which was recovered from a bile sample in the United States in 2011, as our reference for mapping. Genome sequences of the strains were mapped against the reference genome by using Snippy version 4.3.6 (https://github.com/tseemann/snippy) at default settings. The resulting core SNPs (n = 1,918) were concatenated and used to infer a phylogenomic tree by using RAxML version 8.2.12 (17) under the general time-reversible plus gamma model with a 1,000-bootstrap test.

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