Sequencing and comparative genomic analysis of pK29, a 269-kilobase conjugative plasmid encoding CMY-8 and CTX-M-3 beta-lactamases in Klebsiella pneumoniae

Abstract

A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3 extended-spectrum beta-lactamases in the common backbone of IncHI2 plasmids. Mechanisms for dissemination of the resistance genes are highlighted in comparative genomic analyses.

FIG. 1.

Map of pK29 and comparison of pK29 with the other two IncHI2 plasmids, pR478 and pAPEC-O1-R. The lines between the three plasmids indicate the homologous sequence blocks which are >99% identical (white squares). Inversion between the homologous regions is shaded. The important features are indicated, as follows: repHIA and repHI2, replication origins; trh and tra, conjugal transfer genes; parAB, plasmid partitioning genes; muc, mucAB mutagenesis genes. The ter, ars, cop, sil, and mer genes encode products conferring tellurite, arsenic, copper, silver, and mercury resistance, respectively. Other genes and their products are as follows: adhC, alcohol dehydrogenase; cat, putative chloramphenicol acetyltransferase; aphA1-Iab, aminoglycoside phosphotransferase; tet, tetracycline resistance proteins; aadA, putative streptomycin adenyltransferase; aac3-VI, gentamicin resistance protein; sul-1, dihydropteroate synthetase; and qacEdelta1, quaternary ammonium transporter protein. The two regions unique to pK29 (regions 1 and 2) are shown in black.

FIG. 2.

Schematic diagram of regions 1 and 2, which are unique to pK29. The boundaries between the regions and the known sequence from pR478 are indicated by dashed lines. The ORFs are shown as arrows, with the arrowheads indicating the direction of transcription. The β-lactamase genes are shown in black. The ORFs related to IS are shown in gray. Unmarked white arrows are hypothetical genes. IR, inverted repeats; IR*, incomplete inverted repeats. The genes and their products are as follows: sul-1, dihydropteroate synthetase; qacEdelta1, quaternary ammonium transporter protein; aadA2, streptomycin adenyltransferase; putative aac, putative aminoglycoside 6′-N-acetyltransferase (80% identical to AAC6-II of Acinetobacter baumannii [GenBank accession no. ABL95928]); catB2, chloramphenicol acetyltransferase; and intl1, integrase. In region 2, the ISEcp1 element to the left of bla_CTX-M-3 is truncated (tnpA*). The region homologous to plasmid pCTX-M-3 is indicated.