I just had to blog about this fantastic paper I recently read in mBio titled “Insertion sequence IS26 reorganizes plasmids in clinically isolated multidrug-resistant bacteria by replicative transposition” by He at al. The title was intriguing, and the paper did not disappoint. It addresses a lot of observations we have had about plasmids in Enterobacteriaceae, as I’ll describe below.
The paper starts by acknowledging that IS26, which is an insertion sequence, has been found all over conjugative plasmids. Why is this important? Well, it frequently carries or transposes genes associated with antibiotic resistance. Among the genes that it can transpose are those that define carbapenem-producing Enterobacteriaceae, or CRE. The CRE superbugs are bacteria that are resistant to carbapenem antibiotics, and are usually also resistant to most other antibiotics used in human and animal medicine. IS26 can mobilize resistance genes, genomic regions that include MULTIPLE resistance genes, and other gene clusters that provide fitness advantages to a bacteria. IS26 can move these gene clusters to another genomic location in a process called replicative transposition.
The impact of IS26 is illustrated below by an analysis I am working on of plasmids of E. coli ST131, which is the predominant E. coli lineage causing urinary tract infections that has emerged worldwide in the past ten years. The plasmid below is a defining trait of multidrug-resistant ST131, and it confers resistance to numerous antibiotics. Note how there are eight copies of IS26 on this plasmid, and it is pretty clear that they have carried with them a variety of genes associated with antibiotic resistance, and genes encoding other possible traits such as iron acquisition (the enhanced ability to acquire iron in the host gives bacteria like ST131 a fitness advantage during its colonization).
Now back to the paper – here’s just a few things I love about it:
1. It begins to delve into the mechanisms by which IS26 is able to reorganize plasmids. We have known for a long time that these elements are highly prevalent on some of the most dangerous plasmids of Enterobacteriaceae; however, this paper starts to better explain the broad and immediate impact they can have on plasmid evolution! It shows that IS26 not only drives the mobilization of accessory genes, it can also mediate deletions of large fragments of DNA or reorientation of said regions. This explains so much of what I have been seeing in ST131 plasmids, where strains belonging to a “clonal” lineage have the same plasmids, but these plasmids are drastically different in orientation and accessory gene content. The conclusions from the paper help to explain what we have been seeing on these plasmids – IS26 tends not to transpose frequently via replicative transposition, but instead duplicates through inversion of DNA within an element, thus changing the landscape of the plasmid and creating additional copies of IS26.
2. As the authors state, “This study also provides a method to trace the evolution of resistance plasmids based on TSD (target site duplication) patterns.” This, for the first time in such a fashion, presents a concept by which to trace the evolutionary history of these transposition events and improves our ability to reconstruct the history of plasmid rearrangements within clonal lineages. Using TSDs following the plasmids of CREs in the NIH outbreak, the authors were able to demonstrate that TSDs served as a “tracer” of the history of IS26 activity! A key point also mentioned by the authors is that “When the disruptions are caused by IS26, deletions are often observed at the antibiotic resistance gene locus. We suspect that these observations indicate ongoing plasmid streamlining that continues even after the acquisition of resistance determinants.” This is important because it highlights not only the additive capacity of IS26, but its ability to further modify a genome through reduction events that might enhance bacterial fitness.
3. Tn4401. This is an extremely important transposon that often carries KPC, making a bacteria CRE. The authors state that “As there are many more copies of IS26 than of Tn4401, we speculate that this composite element may have higher transposition activity than the original Tn4401 and could be an example of IS26-mediated mobility enhancement of a critical resistance determinant.” This suggests that not only can IS26 act alone to modify a genome, it can act on other mobile elements within a plasmid to further enhance their capacity to transpose. This synergistic activity would have major implications for bacterial genome evolution. Tn4401 is also thought to be “restricted” from further transposition (transposition immunity), limiting its duplication within a genetic element. However, in concert with other IS elements, it can be duplicated within the same plasmid. Again, I see a similar phenomenon in a plasmid I am analyzing from a CRE Enterobacter cloacae (image below). I need to look at this in more detail, but it explains yet another mechanism conferred through IS cooperation.
In short, this paper shows how detailed analysis of plasmid genomes can be used to better understand the molecular mechanisms driving their evolution, in the absence of any experimental data. Yes, experimental data is still needed to validate. But it shows that we can use rapid sequencing and subsequent analysis to understand the events driving rapid changes in bacterial genomes. Awesome paper!