Functional cloning and characterization of antibiotic resistance genes from the chicken gut microbiome

Abstract

Culture-independent sampling in conjunction with a functional cloning approach identified diverse antibiotic resistance genes for different classes of antibiotics in gut microbiomes from both conventionally raised and free-range chickens. Many of the genes are phylogenetically distant from known resistance genes. Two unique genes that conferred ampicillin and spectinomycin resistance were also functional in Campylobacter, a distant relative of the Escherichia coli host used to generate the genomic libraries.

Fig 1

Phylogenetic relationship of β-lactamases from different sources. Unrooted phylogenetic trees were generated from ClustalW2 alignments using the neighbor-joining algorithm. FRAmp1.1, discovered in this study, was analyzed together with 25 identified β-lactamases. *, the novel β-lactamases belonging to different families that were discovered from the human gut microbiome by Sommer et al. (21); **, the β-lactamases that were discovered from the human microbiome by Sommer et al. (21) that share high similarity to the previously characterized β-lactamase families; ***, the β-lactamases representing previously characterized common β-lactamase families that were not analyzed by Sommer et al. (21) (SHV [25], OXA-10 [accession number AY841859], IMP [15], VIM [9], and KPC [31]); ****, the β-lactamases identified in different C. jejuni strains, including Cj0299 (accession number YP_002343737), CJE0344 (accession number AAW34933), CJS3_0285 (accession number ADT72049), and Cam1 (accession number AAT01092).