ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

Abstract

The ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas spp. All Pseudomonas complete genomes were downloaded from NCBI’s Refseq library and were inspected for the presence of the crpP gene. The mobile elements carrying this gene were further characterized. The crpP gene was identified only in P. aeruginosa, in more than half of the complete chromosomes (61.9%, n = 133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136 crpP-harboring integrative and conjugative elements (ICEs), with 93.4% belonging to the mating-pair formation G (MPFG) family. The ICEs were integrated at the end of a tRNALys gene and were all flanked by highly conserved 45-bp direct repeats. The crpP-carrying ICEs contain 26 core genes (2.2% of all 1193 genes found in all the ICEs together), which are present in 99% or more of the crpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work suggests that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying crpP gene in P. aeruginosa.

Diversification and prevalence of the quinolone resistance crpP genes and the crpP-carrying Tn6786-related integrative and conjugative elements in Pseudomonas aeruginosa

“…Although crpP was originally identified in plasmid pUM505 [2], ICEs were identified as a major reservoir of crpP genes in P. aeruginosa [14]. Our results revealed that all the fully sequenced crpP-carrying ICEs had the highly conserved 45-bp terminal attL/attR pairs and displayed similar backbone gene organizations, and thus were assigned into a newly identified Tn6786 family.…”

“…S1). Additionally, all these ICEs were integrated at the end of the tRNA Lys gene as described in a previous report [14].…”

“…An ICE element can transfer between cells because of their self-encoded conjugation function, and it is typically composed of attL (attachment site at the left end), int (integrase), xis (excisionase), rlx (relaxase), oriT (origin of conjugative replication), cpl (coupling protein), a P (TivB)-or F (TivF)-type T4SS gene set (mating pair formation), and attR (attachment site at the right end). While ICEs have been identified as a major crpP reservoir in P. aeruginosa [14], there are still no reports on systematic classification and detailed genetic dissection of crpPcarrying ICEs.…”

Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain

“…crpP gene was first detected in 2018 as encoded within the pUM505 plasmid in a P. aeruginosa clinical isolate from Mexico [ 9 ]. Since then, ciprofloxacin-modifying crpP genes have been identified in P. aeruginosa as part of different mobile integrative and conjugative elements (ICEs) that frequently transfer horizontally [ 10 ]. However, homologous crpP genes have also been located in chromosomal pathogenicity genomic islands (PAGI) of P. aeruginosa clinical isolates recovered in France and Switzerland between 2000 and 2015 [ 11 ].…”

Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity

“…Nearly half of the ICEs/IMEs carried at least one AMR gene (228/553), with the ciprofloxacin-modifying crpP gene and the sulphonamide-resistance sul1 gene being most frequent ( Table S13 ). Indeed, the crpP gene was recently shown to be widely dispersed across ICEs from P. aeruginosa (42). Around one third of the ICEs/IMEs (193/553) carried at least one defence system, resulting in a total of 250 defence systems across the ICEs/IMEs and including 27 different types ( Figure S10 and Table S13 ).…”