IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates

Abstract

The whole sequence of plasmid pENVA carrying the extended-spectrum β-lactamase gene blaCTX-M-15 was determined. It was identified from a series of clonally related Klebsiella pneumoniae sequence type 274 strains recovered from companion animals. This plasmid was 253,984 bp in size and harbored, in addition to blaCTX-M-15, a large array of genes encoding resistance to many antibiotic molecules, including β-lactams (blaTEM-1, blaDHA-1), aminoglycosides (aacA2, aadA1), tetracycline (tetA), quinolones (qnrB4), trimethoprim (dfrA15), and sulfonamides (two copies of sul1). In addition, genes encoding resistance to mercury, tellurium, nickel, and quaternary compounds were identified. It also carried genes encoding DNA damage protection and mutagenesis repair and a locus for a CRISPR system, which corresponds to an immune system involved in protection against bacteriophages and plasmids. Comparative analysis of the plasmid scaffold showed that it possessed a structure similar to that of only a single plasmid, which was pNDM-MAR encoding the carbapenemase NDM-1 and identified from human K. pneumoniae isolates. Both plasmids possessed two replicons, namely, those of IncFIB-like and IncHIB-like plasmids, which were significantly different from those previously characterized. The blaCTX-M-15 gene, together with the other antibiotic resistance genes, was part of a large module likely acquired through a transposition process. We characterized here a new plasmid type carrying the blaCTX-M-15 gene identified in a K. pneumoniae isolate of animal origin. The extent to which this plasmid type may spread efficiently and possibly further enhance the dissemination of blaCTX-M-15 among animal and human isolates remains to be determined.

FIG 1

Genetic map of the fully sequenced plasmid pENVA. The circles (from the innermost to the outermost) represent (i) GC skew, (ii) GC content, (iii) annotated coding sequences as arrows, and (iv) plasmid modules. These modules are colored depending on their functional assignments, as shown by the labeling.

FIG 2

(A) Major structural features of pENVA and comparison with the reference plasmid pNDM-MAR. White boxes indicate plasmid backbone regions that commonly occur in plasmids. The tra locus (conjugative transfer) is indicated by white boxes with capital letters, which indicate the respective tra genes. Resistance genes are indicated by orange boxes, except for the β-lactamase genes, which are indicated by red boxes. Transposon-specific genes (tnpA, tnpR, tnpM) and insertion sequences are indicated by green boxes, and class 1 integrase genes are indicated by dark gray boxes. Other genes are indicated by colored boxes, as follows: violet, replicase genes; light gray, partitioning systems and DNA methylase genes; blue, heavy metal resistance clusters. (B) Schematic representation of the multidrug resistance module of plasmid pENVA. The genes and their annotations are indicated by arrows and colored according to their functions.