Within-cycle dynamics of acquired antibiotic resistance genes in semi-intensive broiler production systems in Kenya

Abstract Background Longitudinal analysis of temporal patterns of antibiotic resistance genes (ARGs) across the poultry production cycle is crucial to understand how resistance emerges and persists within flocks, and to identify critical windows for targeted stewardship. Methods We used high-throughput quantitative PCR to characterise within-cycle patterns of ARGs in flock-level samples from 41 Kenyan semi-intensive broiler farms across three timepoints: flock placement (T1; day 0), using faecally soiled day-old chick transport liners; mid-growth (T2; day 14 ± 1), and pre-slaughter (T3; day 26–42) using pooled fresh faecal samples. DNA was extracted and screened for 48 ARGs, selected from an initial screen of 384 targets. Results All 48 ARGs were detected. Alpha diversity was lower in samples collected at flock placement than at T2 and T3 (median 28 vs. 39 and 41; p < 0·001), with no significant difference between T2 and T3. Likewise, beta diversity differed by production stage (PERMANOVA R²=0·09, p = 0·001), driven primarily by differences between T1 and both T2 and T3, whereas T2 and T3 were not significantly different ( p = 0·18). Relative ARG abundance (normalised to 16S rRNA) similarly increased between flock placement and later production stages, being higher at T2 (β = 0·007, p < 0·001) and T3 (β = 0·005, p = 0·004) compared with T1. Conclusion ARGs were widely detected at flock placement, establishing an arrival-associated ARG profile before on-farm rearing. ARG richness and relative abundance were higher at mid-production and pre-slaughter, indicating substantial changes after flock placement. Together, these findings demonstrate that resistance determinants are present at farm entry and that the flock-associated ARG profile changes substantially during the production cycle.