What’s in a Name? ISSwi1 Corresponds to Transposons Related to Tn2 and Tn3

LETTER

With the rapid expansion in generation of DNA sequence data, including data from long-read methods that greatly simplify assembly, it is increasingly important to address annotation issues. In bacteria, exactly the same mobile genetic element may be found in different locations, and consistent annotation greatly simplifies comparative analyses. Registries such as ISfinder (https://www-is.biotoul.fr/) (1), which includes a searchable database of insertion sequences (IS) and assigns IS names, are important resources in achieving this. Nomenclature is becoming more complex as the traditional distinction between IS (containing essentially only transposition functions for their own movement) and unit transposons (Tn; larger, more complex elements that also carry “passenger” gene[s]) is becoming blurred: elements closely related to known IS families but carrying passenger gene(s) are being identified (2), as well as elements closely related to known transposons that lack passenger genes.

As their numbers suggest, Tn1, Tn2, and Tn3 were among the earliest transposons to be identified (3–5). Their sequences are closely related overall, but identity is lower in short regions adjacent to the resolution (res) site, suggesting generation by different recombination events (6). Tn3 and Tn2 each carry a bla_TEM-1 gene encoding the TEM-1 β-lactamase, but with different “frameworks” (i.e., patterns of synonymous single nucleotide changes [7]) designated 1a and 1b, respectively. Tn1 carries bla_TEM-2, which encodes TEM-2 with a single amino acid change. All known TEM enzymes (n > 200) (http://www.lahey.org/Studies/), including “extended-spectrum” variants conferring resistance to clinically important third-generation cephalosporin antibiotics, are derived from TEM-1 or TEM-2. Correctly identifying these transposons is important in understanding resistance epidemiology, but Tn2, the most common variant in antibiotic resistance plasmids, is often misannotated as Tn3 (8), as are other members of the larger Tn3 family (9).

In a recent paper (10), He and colleagues, in their Fig. 5a, used the name ISSwi1 for transposons that correspond to Tn2, Tn3, or different “hybrids” of these (Fig. 1a). Reference 10 also discusses an “ISSwi1 derivative, ISSwi1-m1 (also called Tn1331).” Tn1331 is a well-described derivative of Tn3 that contains the aacA4-aadA1a-bla_OXA-9 cassette array from a class 1 integron (11). “ISSwi-m1” in pNJST258N5 and “ISSwi-m2” (with a deletion) in pNJST258C2 include different regions that match Tn2 rather than Tn3 (Fig. 1b). Other “ISSwi-m2” elements shown in Fig. 5a of reference 10 are almost identical to the corresponding parts of Tn1331 (Fig. 1b), suggesting this as the direct ancestor. A minor variant of Tn1331, with differences including two nucleotide changes in aacA4 [aac(6′)-Ib] that lead to a ciprofloxacin-resistant variant (Fig. 1b), has been designated Tn6238 (12). Reference 10 also used the name ISAcsp1 for Tn5403, a Tn3 family element without passenger genes (13).

FIG 1 .

Comparison of transposon sequences. Vertical black lines indicate differences from the reference sequence (top). Genes are shown by labeled arrows, 38-bp terminal inverted repeats are shown as black triangles, and the res site is a gray box (the vertical arrow shows the recombination site). Gene cassettes are shown as white boxes labeled with the cassette name, with small black boxes indicating attC sites (truncated in the case of aadA1a). The 3′ indicates a 111-kb fragment of the class 1 integron 3′-conserved segment. Positions of possible sequence errors (e.g., an A missing from a run of As in pKPC-272 and pKPC-f91; a G missing from two short runs of Gs in Tn1331; and 3 bases missing from pNJST258N5) and of various insertions/deletions (1, IS26 in pKPN-068; 2, Tn5403 in pKPN-068; 3, Tn4401 in pKPC-272 and pKPC-f91; 4, ISEcp1-bla_CTX-M-15 in Tn2 in pHg; 5, IS26 truncating Tn2 in pHg; 6, Tn4401 in pNJST258C2) are indicated, with selected IS26 elements shown (pointed end, IR_R). (a) Comparison of ISSwi1 (from ISfinder) with Tn3 (GenBank accession number HM749966; the Tn in pKPN-068 CP007733 is identical), Tn2 (GenBank AY123253; the Tn in pHg CP006662 is identical), and the Tn from pNJST258N4 (N4; CP006928), pKPC-272 (pKPC; CP008825; the Tn in pKPCf-91 CP008826 is identical), and pNJST258C1 (C1; CP006922). (b) Comparison of Tn3, Tn1331 (GenBank AF479774), Tn6238 (KJ511462), ISSwi1-m1 in pNJST258N5 (N5; CP006924), ISSwi1-m2 in pNJST258C2 (C2, CP006919), and the identical ISSwi1-m2 sequences (Δ) in pAAC154-a50 (CP007728 and CP008828), pKPN-294 (CP008832 and CP009873), pKPN-819 (CP008799), and pKPC-484 (CP008798). This figure was compiled from alignments created using Geneious (Biomatters, New Zealand).

Developing consistent nomenclature for bacterial mobile genetic elements, deciding on meaningful identity cutoffs for whether elements should be considered the same or different, as well as dealing with “hybrids” are clearly important. While the historic nomenclature may not be perfect, using names based on those already established for elements such as Tn1, Tn2, Tn3, Tn1331, and Tn5403 seems sensible in order to avoid adding to the already considerable confusion in nomenclature related to antibiotic resistance.