Corrigendum: Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

摘要

In the original article, there was a mistake in Table 1 as published. Our collection stock of EIEC-O152 (1) contained low level of ExPEC-O25:H16 which was sequenced in the study instead of EIEC. The corrected Table 1 appears below. Table 1 Number of bacterial isolates and serotypes. Tree label Description Isolates Serotypes EIEC Enteroinvasive E. coli 32 15 EAEC Enteroaggregative E. coli 3 3 STEC Shiga-toxin producing E. coli 1 1 ExPEC Extraintestinal E. coli 6 3 EPEC Enteropathogenic E. coli 3 2 EHEC Enterohemorrhagic E. coli 5 5 E. fergusonii E. fergusonii 2 1 SD Shigella dysenteriae 23 14 SF Shigella flexneri 36 6 SB Shigella boydii 32 20 SS Shigella sonnei 26 1 S. enterica Salmonella enterica 2 1 Total 171 72 The ExPEC cluster contains the ExPEC-O25:H16 instead of the one EIEC isolate but this cluster was not discussed in the original manuscript. The NCBI accession has been updated as well.Labels for EIEC-O152 (1) were modified to ExPEC-O25:H16 on the phylogenetic trees displayed in Figures 1 , 3 , and in Supplementary Figures 1 , 4 – 6 , and in Supplementary Tables 1 , 3 . Figure 1 A maximum-likelihood (ML) phylogeny of Shigella , enteroinvasive E. coli (EIEC) and non-invasive E. coli strains based on 7,062 core SNPs using kSNP (Gardner and Hall, 2013). The ML tree was generated using GARLI v. 2.0.1019 under the GTR + I + Γ model and other default settings (Zwickl, 2006). Trees were visualized with Figtree v. 1.3.1 (Rambaut and Drummond, 2009). The best tree was chosen from 1,000 runs of the data set and bootstrap values (1,000 iterations) are reported above each node. Bootstrap values <80% are not shown. A tree that includes the Salmonella outgroup can be found in Supplementary Figure 1 . Figure 3 Hierarchical clustering and heat map illustrating the differences in predicted protein homologs between genomes. Manhattan distances were calculated from a pairwise abundance matrix of 3,777 predicted protein homologs that were identified using the default BLASTP bidirectional best hit approach (75% amino acid sequence coverage, 1e-05 E-value and 60% sequence identity) within the program GET_HOMOLOGUES (Contreras-Moreira and Vinuesa, 2013). Only genes shared by at least two samples were included. Blue cells on the heat map indicate that genomes share more similar genes. The dendrogram on y-axis indicates hierarchical clustering of the abundance matrix using the average linkage method and Manhattan distances with bootstrap probabilities (BP, only values of ≥80 shown in black) and approximately unbiased p -values (AU, only values of ≥95 shown in red) from 10,000 replicates. The phylogenetic group of each genome from Figure 1 is represented as a colored bar in between the dendrogram and the heat map. Additionally, the text in the Phylogeny subsection in Results, first paragraph, should be written as:One hundred and seventy-one genomes were selected to encompass a large selection of EIEC strains and represent the diversity of the Shigella genus. Genomes from 35 isolates were in-house sequenced draft genomes while 136 were available in public databases (Supplementary Table 1 ). We used 23 isolates of SD, including a minimum of 14 serotypes, 36 SF isolates, including at least six serotypes, 32 SB isolates, covering all 20 serotypes, 26 SS isolates, 32 EIEC isolates with 15 different serotypes, 18 isolates of non-invasive E. coli composed of 14 different serotypes, two isolates of E. fergusonii . The genomes of two Salmonella isolates were used for an outgroup (Table 1 ).In the original article, there was a mistake in Table 2 as published. A coding mistake led to incorrect identification of lineage-specific SNPs. We reported 404 diagnostic SNPs, but the correct count is 254. The corrected Table 2 appears below and Supplementary Table 2 with the sequences of the regions containing the diagnostic SNPs has been modified. Table 2 Phylogenetic group name (from Figure 1 ), number of individuals within each group ( N ) and the number of diagnostic SNPs ( D _( snps )). Group N D_( snps ) EIEC/EHEC/EAEC 12 6 EIEC large 16 0 EIEC small 3 31 ExPEC 6 71 SB/SD large 38 7 SB/SD small 15 21 SD serotype 1 3 1 SD serotype 10 3 37 SD serotype 8/EHEC/EPEC 10 1 SF 33 34 SS 26 45 Total 165 254 The abstract should read “Lastly, we identified a panel of 254 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC.” Similarly, the second line in the Lineage-Specific SNP Identification and Evaluation of Previously Described Molecular Assays for the Differentiation of Shigella and EIEC subsection in Results should read: “From 7,062 core SNPs, we found 254 SNP positions that were diagnostic for each of the clusters (Supplementary Table S2 ).”The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way.The original article has been updated. Conflict of interest statement The authors declare that t