Abstract
Integrons are hot spots for acquiring gene cassettes from the environment and play a major role in the bacterial evolution and dissemination of antimicrobial resistance (AMR), thus posing a serious threat. There are currently studies on integrons and antibiotic resistance genes; however, the presence and association of integrons in different agricultural crops and their subsequent dissemination and role in AMR have not been reported previously. This study examines the abundance of integrons, their gene cassette diversity in various crop soils, and their role in the dissemination of AMR in the southern region of China. Samples from different agri-crop soil, such as rice (R.S), sugarcane (S.S), citrus (C.S), banana (B.S), agricultural runoff (the point where the runoff of all sites meet (R.O)), and wild (non-agricultural) soil (W.S), were collected. Quantitative PCR was used to determine the abundance of integrons, and clone libraries were constructed to examine the gene cassette arrays. All the tested samples were found positive for Class-I (CL1) integrons and revealed a higher concentration and higher relative abundance of R.S than the others, with the least found at the W.S site. The W.S CL1 cassette arrays were found empty, and no putative conserved domains were found. The R.O was found to contain a high number of gene cassettes with various functions, while the smallest number of gene cassettes was found in the S.S among the crop soils. Most of the gene cassettes presented by the R.O were primarily shared with other sites, and the antibiotic-resistant genes were consistently observed to be dominant. The constructed clone libraries represented a diverse gene cassette array with 16% novel gene cassettes that play a vital role in pathogenesis, transportation, biosynthesis, and AMR. Most resistance-related gene cassettes were associated with the genes encoding resistance to quaternary ammonium compound (QAC) and aminoglycosides. This study highlights the significant differences in the abundance of integrons among various agricultural soils and offers deep insight into the pools of gene cassettes that play a key role in the dissemination of integrons and AMR.
Highlights
Bacterial genomes contain versatile gene accretion systems called integrons, which are commonly found in most gram-negative bacteria
Bacterial evolution is greatly advanced by integrons and between integrons
The present study investigated the role of agriculture in the dissemination of integrons and determined their role in the development of antimicrobial resistance
Summary
Bacterial genomes contain versatile gene accretion systems called integrons, which are commonly found in most gram-negative bacteria. The 5’ conserved region (5’C.S) consists of an integron integrase (intI) gene, an integron-associated recombination site (attI), and an integron-associated promoter (Pc) site. This platform captures and expresses GCs that are non-replicative mobile elements in the bacterial genome. These GCs consist of one or more open reading frame (ORF) and recombination cassette, joining the attC site. Integrons play a key role in bacterial evolution through the adaptation of GCs and the expression of their different ORFs along with their subsequent role in developing adaptive antibiotic resistance [5,6]. Hundreds of GCs carried by integrons have demonstrated their role in resistance to different classes of antibiotics, such as amino glycosides, beta-lactams, chloramphenicol, trimethoprim, and streptothricin [12,13]
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