Fig. 3: Strain-level resistome analysis.

a Neighbour-joining tree of 195 representative bacterial strains (post-genome dereplication) aligned with clinical metadata, ARG profiles (by resistance class), and ARG counts, the original dataset comprises both isolate genomes (n = 89) and metagenome-assembled genomes (MAGs; n = 322), totalling 411 individual bacterial genomes. b Comparison of distinct ARG counts per strain across the ten most abundant genera. Statistical analysis was performed using the Kruskal–Wallis test followed by Dunn’s post hoc test (FDR-adjusted). Significance was compared against Bifidobacterium. **P < 0.01, ****P < 0.0001. Data are presented as mean ± SEM. n represents number of representative strain-level genomes (total n = 162). c Comparison of ARG counts per strain between the four most resistant genera: Enterococcus, Escherichia, Klebsiella and Staphylococcus. Cohort comparisons were made using two-sided Wilcoxon tests with Benjamini–Hochberg correction, no difference were statistically significant. The box plot represents median (line inside the box), interquartile range (IQR; middle 50% of the data, box height), data within 1.5 × IQR (whiskers), and outliers (points). n represents number of representative strain-level genomes (total n = 162). d Profiles of multidrug resistance (MDR) efflux pumps (n = 20) across genomes (n = 204) of the four most resistant genera: Enterococcus, Escherichia, Klebsiella and Staphylococcus. e (Top) Proportions of ARG resistance classes per genome (n = 204) in both NPS and PS cohorts. (Bottom) Proportions of MDR versus non-MDR genomes in NPS and PS cohorts. MDR was defined as harbouring predicted ARGs conferring resistance to three or more antibiotic classes. Statistical significance was assessed using two-sided Fisher’s exact test. ****P < 0.0001. f Multi-locus sequence typing (MLST) analysis of key pathobiont genomes (n = 193) from the four most resistant genera. Pie charts display genus-specific proportions of unique (non-shared) and shared sequence types between NPS and PS cohorts. Additional surface antigen typing (Kaptive) for Klebsiella spp. is shown in the inset box.