Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites

Abstract

Integrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites (attCs) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attCs from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attCs that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attCs cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For example, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons.

The Natural History of Integrons

“…This can be inferred from the phylogeny of IntI protein sequences, which cluster according to the environment of origin rather than bacterial phylogeny. IntIs encoded by marine and soil/freshwater bacteria form the two distinct clades [7,10,16,25]. The same is true for attCs.…”

“…The clinical variants mainly carry gene cassettes that contain antimicrobial resistance genes, and because these cassettes have been acquired from diverse sources, they have highly variable attC sites [9,10]. In contrast, sedentary chromosomal integrons carry gene cassettes that encode genes that are mostly of unknown function and tend to have attC sites that are conserved in sequence and a secondary structure [10][11][12][13][14]. Lastly, clinical class 1 integrons have relatively short gene cassette arrays, usually comprising one to six cassettes, which are expressed from a single promoter embedded in the intI sequence (P c ).…”

“…Interestingly, integrons that share homologous IntIs and attCs are often found in divergent bacterial lineages that inhabit similar environments [10]. This can be inferred from the phylogeny of IntI protein sequences, which cluster according to the environment of origin rather than bacterial phylogeny.…”

“…The same is true for attCs. Based on their sequence and structure, attCs also cluster according to their environment [10]. They form three major clades (Figure 2): One is a distinctly marine clade, the second is a soil/freshwater clade, and a third clade that has been named 'Xanthomonadales-like', as it is almost exclusively (>99%) comprised of attCs from the Xanthomonadales order.…”

“…Clinical class 1 integrons are associated with plasmids and transposons, while the majority of integrons are found on bacterial chromosomes [8]. The clinical variants mainly carry gene cassettes that contain antimicrobial resistance genes, and because these cassettes have been acquired from diverse sources, they have highly variable attC sites [9,10]. In contrast, sedentary chromosomal integrons carry gene cassettes that encode genes that are mostly of unknown function and tend to have attC sites that are conserved in sequence and a secondary structure [10][11][12][13][14].…”