FIG 5.

E. coli amplicon sequence variant fingerprints. (A) E. coli ASVs were inferred from longitudinal samples at the indicated weeks from reads classified as E. coli by SBanalyzer from twin pair A/B and twin pair Y/Z. Twins A and B were admitted simultaneously to hospital 1, and twins Y and Z were admitted simultaneously to hospital 2, as indicated. The 8 ASVs obtained from the samples using DADA2 were mapped to the NCBI database, and the closest-matching taxonomies were selected and are displayed to the right. ASVs in green text indicate perfect matches to the indicated NCBI region (reg.). “Novel” in bold text indicates an ASV that did not match perfectly to any sequence in the NCBI database but was present in multiple samples. The twin ID and the week that the sample was collected are indicated at the bottom. The relative number of each of the ASVs in each sample is indicated by shading, where dark red indicates more reads and blue indicates fewer. (B) E. coli ASV structure at the V6 stem-loop. E. coli ASVs were inferred from twin pair A/B and twin pair Y/Z using DADA2, and the eight resulting ∼2,300- to 2,400-base 16S-ITS-23S ASVs were aligned against each other in Jalview (40). A portion of the alignment from bases 948 to 1103 containing the V6 region is shown, with identical sequences across all ASVs in black text with dark blue highlighting and ASV-specific variations shaded in lighter colors. The yellow and red boxes above the alignment indicate the V6 stem-loop sequences shaded in the structures pictured immediately below the alignment in the middle. The 2-D structures of the aligned V6 regions of each ASV sequence were mapped to the E. coli 16S gene structure (41) from bases 988 to 1050; bases were numbered according to the alignment. Variant sequences from the alignment are depicted in bold red text. Yellow and red shading in the structures corresponds to the yellow and red boxes above the aligned sequences. The ASVs containing the exact stem-loop V6 sequence are listed below each structure. ASVs with NCBI BLAST searches that produced perfect matches to the entire V6 sequence are listed immediately below the structure in bold green underlined text. The NCBI BLAST strain ID, genomic region, and ASV length for the perfect full-length ASV match containing the V6 sequence are listed immediately below the bold green text. The individual twin samples containing ASVs that include each V6 sequence are listed at the bottom in the outlined boxes.