Antimicrobial resistance genes in weaned pigs: individual quantitative abundance and group dynamics as determined by qPCR

Megarsa Bedasa Jaleta^1*Vera Junker²Christina Susanne Hölzel³Jürgen Zentek⁴Thomas Amon^1,5Ulrich Nübel^2,6,7Tina Kabelitz¹

• ¹Leibniz-Institut fur Agrartechnik und Biookonomie eV, Potsdam, Germany
• ²Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Brunswick, Germany
• ³Christian-Albrechts-Universitat zu Kiel Agrar- und Ernahrungswissenschaftliche Fakultat, Kiel, Germany
• ⁴Institut für Tierernährung, Freie Universitat Berlin, Berlin, Germany
• ⁵Institut für Tier- und Umwelthygiene, Freie Universitat Berlin, Berlin, Germany
• ⁶Deutsches Zentrum fur Infektionsforschung eV, Brunswick, Germany
• ⁷Technische Universitat Braunschweig Institut fur Mikrobiologie, Brunswick, Germany

Antibiotic resistance genes (ARGs) associated with the selection of resistant bacteria in intensive commercial livestock production require regular surveillance. This study aimed to measure ARG abundances in weaner pigs, focusing on inter-individual variation and temporal trends of ARG dynamics over eight weeks in weaner pigs flat-deck. Fecal samples from 103 individual pigs and 53 pooled pen-floor collections were analyzed. Broad-spectrum ARG profiling of pooled DNA from both sample types was conducted using high-throughput qPCR (SmartChip), while standard qPCR quantified eight ARGs (aadA1, blaTEM, dfrA12, erm(B), lnu(F), qnrS, sul2, tet(A)) and the 16S rRNA gene in all samples. Among the quantified ARGs, erm(B) and aadA1 were the most abundant, while qnrS was least frequently detected. Substantial inter-individual variation was observed for most ARGs, despite pigs living together under the same management conditions. Pooled pen-floor feces exhibited significantly higher ARG loads than individual fecal samples, suggesting that resistome profiles at the pen-floor level cannot be accurately inferred from fresh feces of individual animals. Temporal analysis revealed that 16S rRNA gene copies increased during the later period, while tet(A) and sul2 decreased, suggesting age-related effects. These findings demonstrate high intra-cohort variability in ARG abundance in weaner pigs, highlighting the influence of weaning-related factors on resistome composition. Future studies should investigate the role of gut microbiome dynamics and dietary interventions in stabilizing ARG profiles and mitigating resistance development.