ICEs are the main reservoirs of the ciprofloxacin-modifying crpP gene in Pseudomonas aeruginosa

• Type: Other Publications
• Date: 2020

Authors

Botelho, J (Author) Other; Grosso, F (Author) Other; Luisa Peixe (Author) FFUP

Other information

Authenticus ID: P-00S-6MH

DOI: 10.1101/2020.03.13.991208

Abstract (EN): <jats:title>Abstract</jats:title><jats:p>The ciprofloxacin-modifying <jats:italic>crpP</jats:italic> gene was recently identified in a plasmid isolated from a clinical <jats:italic>Pseudomonas aeruginosa</jats:italic> clinical isolate. Homologues of this gene were also identified in <jats:italic>Escherichia coli, Klebsiella pneumoniae</jats:italic> and <jats:italic>Acinetobacter baumannii</jats:italic>. We set out to explore the mobile genetic elements involved in the acquisition and spread of this gene in publicly available and complete genomes of <jats:italic>Pseudomonas</jats:italic>. The <jats:italic>crpP</jats:italic> gene was identified only in <jats:italic>P. aeruginosa</jats:italic>, 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 <jats:italic>crpP</jats:italic>-harboring ICEs, with 93.4% belonging to the mating-pair formation G (MPF<jats:sub>G</jats:sub>) family. The ICEs were integrated at the end of a tRNA<jats:sup>Lys</jats:sup> gene and were all flanked by highly conserved 45-bp direct repeats. The core ICEome contains 26 genes (2.2% of all genes), which are present in 99% or more of the <jats:italic>crpP</jats:italic>-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work reveals that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying <jats:italic>crpP</jats:italic> gene in <jats:italic>P. aeruginosa</jats:italic>.</jats:p><jats:sec><jats:title>Author Notes</jats:title><jats:p>All supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.</jats:p></jats:sec><jats:sec><jats:title>Impact Statement</jats:title><jats:p>A high proportion of <jats:italic>Pseudomonas aeruginosa</jats:italic> clinical isolates are resistant to ciprofloxacin. Resistance to this antibiotic is often mediated by chromosomal mutations, but recently horizontally transferred genes have been identified. We assessed the repartition of the ciprofloxacin-modifying <jats:italic>crpP</jats:italic> gene among <jats:italic>Pseudomonas</jats:italic> genomes and we characterized the mobile elements associated with its acquisition. We found that this gene is prevalent in <jats:italic>P. aeruginosa</jats:italic> and frequently associated with integrative and conjugative elements (ICEs). Importantly, we also identified highly conserved direct repeats that can be used to accurately delimit <jats:italic>crpP</jats:italic>-carrying ICEs in <jats:italic>P. aeruginosa</jats:italic> genomes.</jats:p></jats:sec><jats:sec><jats:title>Data Summary</jats:title><jats:p>All the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The newick files used to create the trees in Figures 1 and 4 are deposited on figshare at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://figshare.com/projects/ICEs_are_the_main_reservoirs_of_the_ciprofloxacin-modifying_crpP_gene_in_Pseudomonas_aeruginosa/79308">https://figshare.com/projects/ICEs_are_the_main_reservoirs_of_the_ciprofloxacin-modifying_crpP_gene_in_Pseudomonas_aeruginosa/79308</jats:ext-link>.</jats:p></jats:sec>

Language: English

Type (Professor's evaluation): Scientific