A Phage-Like Plasmid Carrying blaKPC-2 Gene in Carbapenem-Resistant Pseudomonas aeruginosa

Abstract

Background: Lateral gene transfer plays a central role in the dissemination of carbapenem resistance in bacterial pathogens associated with nosocomial infections, mainly Enterobacteriaceae and Pseudomonas aeruginosa. Despite their clinical significance, there is little information regarding the mobile genetic elements and mechanism of acquisition and propagation of lateral genes in P. aeruginosa, and they remain largely unknown.Objectives: The present study characterized the genetic context of blaKPC-2 in carbapenem-resistant P. aeruginosa strain BH9.Methods: Pseudomonas aeruginosa BH9 sequencing was performed using the long-read PacBio SMRT platform and the Ion Proton System. De novo assembly was carried out using the SMRT pipeline and Canu, and gene prediction and annotation were performed using Prokka and RAST.Results: Pseudomonas aeruginosa BH9 exhibited a 7.1 Mb circular chromosome. However, the blaKPC-2 gene is located in an additional contig composed by a small plasmid pBH6 from P. aeruginosa strain BH6 and several phage-related genes. Further analysis revealed that the beginning and end of the contig contain identical sequences, supporting a circular plasmid structure. This structure spans 41,087 bp, exhibiting all the Mu-like phage landmarks. In addition, 5-bp direct repeats (GGATG) flanking the pBH6 ends were found, strongly indicating integration of the Mu-like phage into the pBH6 plasmid. Mu phages are commonly found in P. aeruginosa. However, for the first time showing a potential impact in shaping the vehicles of the dissemination of antimicrobial (e.g., plasmid pBH6) resistance genes in the Pseudomonas genus.Conclusion: pBH6 captured the Mu-like Phage BH9, creating a co-integrate pBH6::Phage BH9, and this phage-plasmid complex may represent novel case of a phage-like plasmid.

The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria

“…This is a 10-kb Tn3-based transposon, delimited by two 39-bp imperfect inverted repeat sequences, that harbors, in addition to the KPC-2 gene, a transposase gene, a resolvase gene, and two novel insertion sequences known as ISKpn6 and ISKpn7 [56]. Besides Enterobacteriaceae, KPC has been described in P. aeruginosa from Brazil [57] and China [58], as well as in A. baumannii from Puerto Rico [59] and Portugal [60]. KPC-producing K. pneumoniae isolates may be deficient in OmpK35 and OmpK36, which are porins for carbapenem entry.…”

RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning

“…Phages are often found on chromosomes, rarely on plasmids, therefore including a phage detection algorithm could certainly improve predictions, although that is out of scope for this study, as phage prediction has its own difficulties and complexities. Furthermore, phage-like plasmids have been detected (Galetti et al, 2019;Octavia et al, 2015) which would need to be investigated if it is possible to distinguish these from real phages. Smaller contigs which consisting solely of transposases (1-3 kb usually) are generally present on both chromosome and plasmid and these could be detected and marked as such.…”

Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine‐derived environment

“…Considering that the ARGs co‐occurred in the prophage regardless of the type of ‘ bla TEM‐1B type’ or ‘classic class 1 integron (IntI1) type’ is, these results further supported that horizontal gene transfers, including that of ARGs, might be pervasive in natural bacterial populations via transposable bacteriophages (Toussaint and Rice, 2017) and mainly via a highly conserved transposon or integron structure. Several previous studies have also reported plasmid‐encoded prophage sequences (Yang et al ., 2017; Galetti et al ., 2019) and a high correlation between transposon sequences and plasmids (Partridge et al ., 2018). It would be of great significance to comprehensively study the correlations among the plasmids, prophages and ARGs in horizontal gene transfers in the future.…”