pEl1573 Carrying blaIMP-4, from Sydney, Australia, is closely related to other IncL/M plasmids

Abstract

Complete sequencing of pEl1573, a representative IncL/M plasmid carrying bla(IMP-4) from Sydney, Australia, revealed an ∼60-kb backbone almost identical to those of IncL/M plasmids pCTX-M3, from Poland, and pCTX-M360, from China, and less closely related to pNDM-HK, pOXA-48a, and pEL60, suggesting different lineages. The ∼28-kb Tn2-derived multiresistance region in pEl1573 is inserted in the same location as those in pCTX-M3 and pNDM-HK and shares some of the same components but has undergone rearrangements.

Fig 1

(A) Tn2 and Tn2-derived MRR in IncL/M plasmids. IS are labeled with their number or name, with the pointed end indicating IR_R or oriIS for ISCR1. Tall bars represent the 38-bp IR of Tn2 (designated IR_TEM and IR_tnp) and the 38-bp IR of the transposon carrying the chrA gene (IR_chrA) (16), as labeled. Shorter pink bars represent the 25-bp IR of class 1 integrons (IRi, IR at intI1 end; IRt, at tni end). The extents and directions of antibiotic resistance (thick arrows) and other selected genes are indicated. Cassette arrays in class 1 integrons are indicated by letters in boxes: A, dfrA12-gcuF-aadA2; B, bla_IMP-4-qacG-aacA4-catB3; BΔ, bla_IMP-4Δ-intron-ΔcatB3. Filled circles on stalks represent DRs (black, TTATT; blue, GTGAC). The extent of Tn1548 in pCTX-M3 is indicated. pNDM-HK is missing 563 bp of the Tn2 tnpA gene next to IS26, as indicated, which may be the result of an IS26-mediated deletion (16). The solid line below the pEl1573 diagram indicates the region mapped in reference , in which the IS interrupting the 38-bp IR_chr was erroneously reported as IS4321 (97% identical to IS5075); both pEl1573 and pJIBE401 have IS5075. (B) Rearrangements in the pEl1573 MRR could give a configuration more closely related to pCTX-M3. The two copies of the 135-bp segment of the IR_TEM end of Tn2 present in inverse orientation at both ends of the MRR are indicated by red horizontal lines. Dotted lines indicate the extent of segments inverted by homologous recombination (HR) between inverse repeats. (C) Related MRR in pJIE137. (D) Related partial structure carrying bla_IMP-4 in pIMP-4. Diagrams were drawn from sequences available under the GenBank accession numbers listed in Table 1 plus EF219134 for pJIE137 and FJ384365 for pIMP-4.

Fig 2

Comparison of the pNDM-HK, pOXA-48a, and pEL60 backbones with the pEl1573 backbone. The pCTX-M3 backbone is almost identical to the pEl1573 backbone, and the pCTX-360 backbone is also closely related to these two, except that a short region downstream of the ssb gene (shown as a small black box) is missing. The extents and directions of selected genes in the pEl1573 sequence are shown by labeled arrows, with tra genes indicated by the appropriate letters and open reading frames of unknown function indicated by numbers. Percentages on the right indicate the range of identity. Vertical arrows indicate the insertion points of mobile elements and/or MRR that were removed, along with one copy of any DR, before alignment. The triangle above the primase gene in the pEl1573 diagram indicates the repeat region. Sequences were obtained from the accession numbers listed in Table 1. The figure was drawn using mVISTA (http://genome.lbl.gov/vista/mvista/submit.shtml) (7) using a calculation window of 100 bp.