Fig 1.
First line H. pylori eradication therapy consisted of esomeprazolum 40 mg, clarithromycinum 500 mg and amoxicillinum 1000 mg, each twice per day for ten days.
Table 1.
Descriptive summary of the patient-specific parameters.
Fig 2.
Relative abundance and proportion of common ESBL coding genes between the experimental, validation-targeted, and validation-shotgun groups.
Section A-C: relative ESBL coding gene prevalence profile in the pre- and post-eradication samples of the analyzed datasets. For each dataset ESBL counts were normalized against 16S rRNA gene V3 region bacterial counts and summarized by treatment state. For visualization purposes, for the experimental (A) and targeted validation (B) groups, the abundance threshold was set to 0.1%, and for the shotgun validation (C) group it was 0.0001%. Section D-F: Venn diagram of the ESBL gene cluster counts observed in the experimental group and the validation group of shotgun and targeted sequencing. Only gene clusters that appear at least once in the respective sample group were included in the analysis. Abbreviations: ESBL–extended spectrum beta lactamases, BL–beta lactamases, Exp–experimental group, Vtr–targeted validation group, Vsh–shotgun validation group, Exp-pre–pre-eradication sample set of experimental group, Exp-post–post-eradication sample set of experimental group, Vtr-pre–pre-eradication sample set of targeted validation group, Vtr-post–post-eradication sample set of targeted validation group, Vsh-pre–pre-eradication sample set of shotgun validation group, Vsh-post–post-eradication sample set of shotgun validation group.
Table 2.
Significant distribution of BL genes among annotated bacterial sources from patients comparing the pre- and post-eradication states.
Fig 3.
Significantly associated microbial species between the pre- and post-eradication states (at a significance level p<0.05).
Section A–differentially abundant microbial species between pre- and post-eradication states; Section B–the significance of the enrichment calculated by a Wilcoxon test with FDR multiple hypothesis correction; Section C–generalized fold change of each significantly associated microbial species; Section D–the prevalence shift of each significantly associated microbial species; Section E–the Area Under the Receiver Operating Characteristics Curve (AU-ROC) as a non-parametric measure of the enrichment.
Fig 4.
Top 50 most abundant gene products obtained by shotgun metagenomic sequencing between the pre- and post-eradication states.