In-silico analysis of the resistome of compost
Abstract
Dissemination of antibiotic resistant genes (ARG) is a global health concern to which not only medical treatments but also agriculture contributes to. Composting is a waste management strategy for solid organic waste and compost is widely used as soil fertilizer. Studies show that composting can reduce ARGs, but results are inconsistent, influenced by different factors, and increase in abundance also got reported. The objective of this study was to analyze public available whole genome sequencing (WGS) data of compost for ARGs and explore their phylogenetic relationship. WGS data from 9 experiments were obtained from the European nucleotide archive. After de-novo assembly, 4 databases (ARG-annot, CARD, NCBI and Resfinder) were screened to identify ARGs. A phylogenetic tree was built from their reference sequences. In total 381 different ARGs were identified within 7 datasets. The most frequently detected genes were lnu(C), lnu(D), erm(G), erm(A), mef(A) and tet(X). However within the samples of known origin of finished compost, those genes were not detected; here, aadA1, aadA14, aadA31, aph(3')-Ia, aph(3'')-Ib, aph(6)-Id, blaCARB-8, blaCMY-8, blaTEM-150, blaTEM-171, sul1, sul2, tet(H), tet(W) and vanR-O were found. From the 24 antimicrobial drug classes the main contributors to the resistome were against aminoglycoside, tetracycline, macrolide and multi-drug, accounting for 60.8%. The taxonomic classification identified as dominant phyla overall Actinobacteria,…
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