Complete sequence of pJIE143, a pir-type plasmid carrying ISEcp1-blaCTX-M-15 from an Escherichia coli ST131 isolate

Abstract

pJIE143 (34 kb), from an Escherichia coli ST131 isolate, carries bla(CTX-M-15) but could not be typed using the standard PCR-based replicon-typing primer set. Complete sequencing revealed a backbone with similarity to IncX plasmids, including a pir-like gene encoding a π-like replication protein and iterons related to those of other IncX plasmids. The 2.971-kb ISEcp1-bla(CTX-M-15)-orf477Δ transposition unit often found within Tn2 is inserted just beyond the end of pir, flanked by 5-bp direct repeats.

Fig. 1.

(A) Comparison of backbones of pBS512_33 (CP001059), pJIE143, pCROD2 (FN543504), and pOLA52 (EU370913) (GenBank accession numbers are in parentheses). Darker shading indicates regions with 99% nucleotide identity, and lighter shading 97% identity. The extents and directions of various genes are shown as arrows labeled with the gene name (as described in the text, plus dpp3, DNA distortion polypeptide; actX, antiterminator; and dnaJ, chaperone) or the number for pilx genes. The insertion point of the ISEcp1-bla_CTX-M-15-orf477Δ transposition unit in pJIE143 is indicated. The vertical arrow labeled IS above pCROD2 indicates the site of insertion of IS102. The arrow labeled ME above pOLA52 indicates the region where several mobile elements and resistance genes are inserted. The approximate positions of proposed oriV (small vertical bars labeled V) and oriT (small diamonds labeled T) of pJIE143 and pOLA52 are indicated. (B) oriV iterons of R6K and proposed oriV iterons of pOLA52 (all taken from reference , except oriV-α of R6K, which appears to have an extra T in reference 16) and pJIE143. Bases conserved in the majority of sequences in each set are in boldface, and bases which differ are in lowercase. (C) Sequences surrounding the proposed oriV/oriT β (top) and α (bottom, reverse orientation to part A) regions of pJIE143. Proposed iterons shown in panel B are indicated by doubled-headed arrows. Stop and start codons of various genes are underlined. Vertical arrows indicate nic sites (1). The 5 bp duplicated by insertion of ISEcp1-bla_CTX-M-15-orf477Δ are indicated by an oval. The DnaG site in the α region is boxed (16), and “74” indicates 74 bp corresponding to the distance between this site and one end of the oriV-α iteron in R6K and pOLA52 (15). Sequences are continuous from one line to the next but have been broken to enable the 94-bp oriT repeats (shown in boldface on the lower lines) to be aligned.