Fig. 3: Taxonomic identifications of Context-Seq sequences containing blaTEM and blaCTX-M. | Nature Communications

Fig. 3: Taxonomic identifications of Context-Seq sequences containing blaTEM and blaCTX-M.

From: Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance

Fig. 3

A The number of sequences containing blaTEM identified as each taxa by Kraken2 and confirmed by BLASTN. Plasmids (plasX ≥ 0.5) are indicated by a circle. B The number of sequences containing blaCTX-M identified as each taxa by Kraken2 and confirmed by BLASTN (supplemental data file 1). Plasmids (plasX ≥0.5) are indicated by a circle. C Comparison of Context-Seq to cultured and sequenced E. coli in the same sample. Coverage of the assembled contigs that resulted from 1.) the cultured E. coli using Illumina sequencing of the isolates and 2.) Context-Seq. Box shows interquartile range (25th to 75th percentiles) with the median and whiskers extending to 1.5 times the interquartile range. An open orange circle indicates that no blaTEM or blaCTX-M was identified in that sample using Illumina. D Taxonomic identification (color) and plasmid or chromosome designation (shape) in the 23 clusters ( > 80%ID over ≥3000 bp) that are shared between hosts (human, poultry, canine) and households. In some instances, more than one consensus sequence is shared between host and household. Taxonomy and plasmid are indicated for the highest percentage identity match. Source data are provided in the Source Data file.

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