Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration manure management practices in either amplifying or attenuating potential for resistance spread. Here, we carried out a comprehensive parallel examination small-scale (> 55 °C × 3 days) static turned composting manures from dairy beef cattle collected during standard (cephapirin/pirlimycin sulfamethazine/chlortetracycline/tylosin, respectively), versus untreated cattle, on “resistomes” (total genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, indicator ARGs enumerated quantitative polymerase chain reaction. To gain insight into role thermophilic phase, compost was also externally heated > 15 days. Results Progression with time succession corresponding microbiota overarching driver resistome composition (ANOSIM; R = 0.424, p 0.001, respectively) all composts at small-scale. Reduction abundance (16S rRNA gene normalized) total finished (day 42) day 0 noted across conditions 0.728, 0.001), except when heated. Sul 1, int I1, beta-lactam ARGs, plasmid-associated increased as compared initial condition. External heating more effectively reduced certain clinically relevant ( bla OXA , CARB ), fecal coliforms, risk scores, which take account putative pathogen annotations. When administration, taxonomic distinct according nonmetric multidimensional analysis tet (W) decayed faster condition slower Conclusions This comprehensive, integrated study revealed that had dominant effect composition, while little difference function collecting administration. (W), suggested some spread, but increase persistence other indicators were concerning. indicate guidelines intended reduction do not necessarily provide barrier their mobility prior land application additional mitigation measures should be considered.