Fig. 2
Strain analysis, uropathogenic genes, and antimicrobial resistance genes in paired urine-fecal specimens. a Among 34 urine and fecal specimens profiled, 20 consensus strains for E. coli could be constructed using StrainPhlAn. A phylogenetic tree was constructed based on the E. coli strain alignment (24 markers) and the proportion of sequences that are different between strains is noted on the x-axis. Each point represents an E. coli strain from a urine or fecal specimen with different colors representing different subjects. b Among 34 urine and fecal specimens profiled, 10 consensus strains for E. faecalis could be constructed using StrainPhlAn. A phylogenetic tree was constructed based on the E. faecalis alignment (200 markers) and the proportion of sequences that are different between strains is noted on the x-axis. Each point represents an E. faecalis strain from a urine or fecal specimen with different colors representing different subjects. c Among 34 urine and fecal specimens profiled, 5 consensus strains for E. faecium could be constructed using StrainPhlAn. A phylogenetic tree was constructed based on the E. faecium alignment (200 markers) and the proportion of sequences that are different between strains is noted on the x-axis. Each point represents an E. faecium strain from a urine or fecal specimen with different colors representing different subjects. d Bacterial genes were determined using HUMAnN219 and relative abundance was estimated for each of the following uropathogenic E. coli associated genes: FimH, PapG, CsgBAC, BarA, and UvrY. A heatmap was constructed with the uropathogenic genes on the X-axis and the E. coli associated urine specimens and paired stool specimens on the Y-axis. The abundance is colored by blue intensity, log scaled. e Antibiotic resistance genes were determined using Bowtie221 on the MEGARES antibiotic resistance database22 and RPKM was estimated for genes that confer resistance to beta-lactams, fosfomycin, glycopeptides, sulfonamides, and trimethoprim. A heatmap was constructed with antibiotic resistance gene classes on the X-axis and the E. coli associated urine specimens and paired stool specimens on the Y-axis. The abundance is colored by blue intensity, log scaled. Source data are provided as a source data file.
