Diversity among blaKPC-containing plasmids in Escherichia coli and other bacterial species isolated from the same patients

Abstract

Carbapenem resistant Enterobacteriaceae are a significant public health concern, and genes encoding the Klebsiella pneumoniae carbapenemase (KPC) have contributed to the global spread of carbapenem resistance. In the current study, we used whole-genome sequencing to investigate the diversity of bla_KPC-containing plasmids and antimicrobial resistance mechanisms among 26 bla_KPC-containing Escherichia coli, and 13 bla_KPC-containing Enterobacter asburiae, Enterobacter hormaechei, K. pneumoniae, Klebsiella variicola, Klebsiella michiganensis, and Serratia marcescens strains, which were isolated from the same patients as the bla_KPC-containing E. coli. A bla_KPC-containing IncN and/or IncFII_K plasmid was identified in 77% (30/39) of the E. coli and other bacterial species analyzed. Complete genome sequencing and comparative analysis of a bla_KPC-containing IncN plasmid from one of the E. coli strains demonstrated that this plasmid is present in the K. pneumoniae and S. marcescens strains from this patient, and is conserved among 13 of the E. coli and other bacterial species analyzed. Interestingly, while both IncFII_K and IncN plasmids were prevalent among the strains analyzed, the IncN plasmids were more often identified in multiple bacterial species from the same patients, demonstrating a contribution of this IncN plasmid to the inter-genera dissemination of the bla_KPC genes between the E. coli and other bacterial species analyzed.

Figure 1

Analysis of the bla_KPC-3-containing plasmid pYDC107_70 from E. coli strain YDC107. The two outermost data tracks contain the predicted protein-coding genes on the forward (first track) or reverse (second track) strands of the plasmid. The gene colors indicate their predicted protein functions as follows: antibiotic resistance (red), plasmid replication (purple), plasmid stability (green), conjugative transfer (orange), transposition (yellow), and gray (unknown). The red line separating the gene tracks and the inner heat map tracks is the GC content of the plasmid, calculated on a 100 bp sliding window. The inner heat map tracks (numbered 1 to 5) contain BSR values from the in silico detection of each protein-coding gene in the genome sequences of K. pneumoniae strain YDC121 (track 1), S. marcescens strain YDC107-2 (track 2), both of which were isolated from the same patient as E. coli strain YDC107, as well as the previously sequenced bla_KPC-containing IncN plasmids pYD626E (GenBank accession no. KJ933392.1) from E. coli strain YD626 (track 3), pBK32602 (GenBank accession no. KU295134.1) from E. coli strain BK32602 (track 4), and pECN580 (GenBank accession no. KF914891.1) from E. coli strain ECN580 (track 5).

Figure 2

In silico detection of plasmid pYDC107_70 in the bla_KPC-containing E. coli, and other bacterial species analyzed in this study. The heat map contains BSR values indicating the presence (very light green) or absence (dark blue) of each plasmid gene in each of the genomes. The heat map containing values clustered by column (genomes) was constructed with the heatmap.2 function of gplots using R v.3.4.1. Rows represent each of the protein-coding genes of pYDC107_70, while each column represents a different genome. The label of the E. coli YDC107 genome is indicated in bold. The species and/or genus of each genome is indicated by a square at the top of the heat map (see inset legend). The patient number (see Table S1) corresponding to each of the strains is indicated in parentheses next to the strain number.