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Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application

Puspendu Sardar, Dana Elhottová, Eduardo Pérez-Valera

Data

The raw metagenomic data for this study have been deposited in the NCBI Sequence Read Archive under BioProject PRJNA743290.

To cite this work

Sardar, P., Elhottová, D., Pérez-Valera, E., 2023. Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application. FEMS Microbiology Ecology 99, fiad148. doi:10.1093/femsec/fiad148

Abstract

• Acinetobacter spp. and other non-fermenting Gram-negative bacteria (NFGNB) represent an important group of opportunistic pathogens due to their propensity for multiple, intrinsic, or acquired antimicrobial resistance (AMR). Antimicrobial resistant bacteria and their genes can spread to the environment through livestock manure. This study investigated the effects of fresh manure from dairy cows under antibiotic prophylaxis on the antibiotic resistome and AMR hosts in microcosms using pasture soil. We specifically focused on culturable Acinetobacter spp. and other NFGNB using CHROMagar Acinetobacter. We conducted two 28-days incubation experiments to simulate natural deposition of fresh manure on pasture soil and evaluated the effects on antibiotic resistance genes (ARGs) and bacterial hosts through shotgun metagenomics. We found that manure application altered the abundance and composition of ARGs and their bacterial hosts, and that the effects depended on the soil source. Manure enriched the antibiotic resistome of bacteria only in the soil where native bacteria had a low abundance of ARGs. Our study highlights the role of native soil bacteria in modulating the consequences of manure deposition on soil and confirms the potential of culturable Acinetobacter spp. and other NFGNB to accumulate AMR in pasture soil receiving fresh manure.

Funding

This work was supported by the Czech Science Foundation (1725660S and 20-28265Y) and the Czech Academy of Sciences (Strategy AV21, program number 19).