The evolution of class 1 integrons and the rise of antibiotic resistance

Abstract

Class 1 integrons are central players in the worldwide problem of antibiotic resistance, because they can capture and express diverse resistance genes. In addition, they are often embedded in promiscuous plasmids and transposons, facilitating their lateral transfer into a wide range of pathogens. Understanding the origin of these elements is important for the practical control of antibiotic resistance and for exploring how lateral gene transfer can seriously impact on, and be impacted by, human activities. We now show that class 1 integrons can be found on the chromosomes of nonpathogenic soil and freshwater Betaproteobacteria. Here they exhibit structural and sequence diversity, an absence of antibiotic resistance genes, and a phylogenetic signature of lateral transfer. Some examples are almost identical to the core of the class 1 integrons now found in pathogens, leading us to conclude that environmental Betaproteobacteria were the original source of these genetic elements. Because these elements appear to be readily mobilized, their lateral transfer into human commensals and pathogens was inevitable, especially given that Betaproteobacteria carrying class 1 integrons are common in natural environments that intersect with the human food chain. The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species.

FIG. 1.

Schematic maps of class 1 integrons and associated elements, including Tn6008 from Enterobacter cloacae JKB7 (A), an example of a Tn402 integron (B), and a typical clinical class 1 integron (C). Below these, class 1 integrons from Hydrogenophaga strain PL2G6 (D), Aquabacterium strain PL1F5 (E), Acidovorax strain MUL2G8 (F), Imtechium strain PL2H3 (G), Azoarcus strain MUL2G9 (H), Thauera strain B4 (I), and Thauera strain E7 (J) are shown. Symbols are as follows: red diamonds, attI1 sites; blue circles, 59-be; block arrows, genes (showing the direction of transcription, with diagonal blue stripes indicating transposases, recombinases, or IS elements and solid colors indicating cassette-encoded genes or the class 1 integron-integrase gene intI1); colored arrowheads, inverted repeat regions, including IRi and IRt associated with Tn402 (yellow) and those found in Thauera chromosomal integrons (pink, blue and green); shaded regions, nucleotide homology between elements. Where this homology falls below 99%, the percent identity is given. The vertical arrow indicates the breakpoint for sequence homology between clinical and chromosomal class 1 integrons and is also the insertion point for ISPa7. Selected genes outside the integron are named. Generally, these genes have phylogenetic relationships that are consistent with vertical inheritance from a common betaproteobacterial ancestor. Other symbols are defined in the text.

FIG. 2.

Model for the origin and subsequent divergence of the class 1 integrons that are now widely disseminated in pathogens and human commensals. Stages in the hypothetical evolution are as follows. (A and B) The common ancestor of clinical class 1 integrons was a member of an integron pool that was repeatedly acquired by diverse Betaproteobacteria but not other lineages (Fig. 1) (21). (C and D) One betaproteobacterial chromosomal integron inserted/recombined into a Tn402-like element. This event occurred prior to, or concomitant with, the antibiotic era. Capture of qacE probably occurred around the same time. (E) sul1 and orf5 were captured. (F) Deletions, insertions, and other rearrangements involving qacE, sul1, and adjacent sequence generated the 3′-conserved segment (3′-CS). (G) Deletions and insertions involving tni generated Tn402 transposition-incompetent integrons, which conferred various antibiotic resistance phenotypes due to their diverse cassette arrays. (H) trans-mediated Tn402-like transposition events moved integrons into diverse plasmids and other transposons, such as the Tn21 family (22). These events generated further diversity and accelerated the penetration of class 1 integrons into a wide variety of pathogens and commensals.