Genomic context of the two integrons of ST-111 Pseudomonas aeruginosa AG1: A VIM-2-carrying old-acquaintance and a novel IMP-18-carrying integron

Abstract

Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections mainly in immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems, due to the activity of VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons located inone out of the 57 PaeAG1 genomic islands. However, the genomic context associated to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we rst assessed the transcriptional activity of VIM-2 and IMP-18 genes when exposed to imipenem (a carbapenem) by RT-qPCR. To select related genomes to PaeAG1, we implemented a pan-genome analysis to de ne and up-date the phylogenetic relationship among complete P. aeruginosa genomes. We also studied the PaeAG1 genomic islands content in the related strains and nally we described the architecture and possible evolutionary steps of the genomic regions around the VIM-2-and IMP-18-carrying integrons.Expression of VIM-2 and IMP-18 genes was demonstrated to be induced after imipenem exposure. In a subsequent comparative genomics analysis with 211 strains, the P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST pro le, including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to de ne a diverse presence/absence pattern among related genomes. Finally, landscape reconstruction of genomic regions showed that VIM-2carrying integron (In59-like) is an old-acquaintance element harbored in the same known region found in other two ST-111 strains. Also, PaeAG1 has an exclusive genomic region containing a novel IMP-18carrying integron (registered as In1666), with an arrangement never reported before. Altogether, we provide new insights about the genomic determinants associated with the resistance to carbapenems in this high-risk P. aeruginosa using comparative genomics.

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

“…The phytools implementation of this plotting method is called , and it has been used in numerous published articles ( e.g. , Goelen et al, 2020 ; Hultgren et al, 2021 ; Molina-Mora et al, 2021 ; Huang et al, 2022 ; Morales-Poole et al, 2022 ). For this example, we will use a phylogenetic tree and log-transformed morphological trait dataset for Anolis lizards from Mahler et al (2010) .…”

phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)

“…Here, I'll illustrate just one such method in which a color gradient is used to visualize trait values for a set of quantitative characters at the tips of the tree. The phytools implementation of this plotting method is called phylo.heatmap, and it's been used in numerous published articles (e.g., Goelen et al 2020;Hultgren et al 2021;Molina-Mora et al 2021;Huang et al 2022). For this example, we'll use a phylogenetic tree and morphological trait dataset for Anolis lizards from (Mahler et al 2010) Our trait data object, anole.data, is a data frame with six trait columns for various phylogenetic traits.…”

Molecular Determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach: A Review of 10 Years of Study

“…To describe the landscape of the genomic regions associated with the two integrons of PaeAG1, a comparative genomic strategy was performed as a second main step in the multi-omics approach. It was first demonstrated that VIM-2 and IMP-18 are inducible genes under exposure to carbapenems using RT-qPCR (Molina-Mora et al 2021b ). We then described the phylogenetic relationships among all the complete genomes of P. aeruginosa strains using a pan-genome analysis (Fig.…”

“…On the other hand, in the context of antibiotic resistance, different assays have been performed in PaeAG1 to study its resistance to antibiotics. Antibiotic susceptibility testing is reported in Table 1 (Toval et al 2015 ; Chinchilla 2018 ), and an MBLs’ differential expression has been tested not only to carbapenems as demonstrated (Molina-Mora et al 2021b ) but also to other antibiotics (Chinchilla 2018 ).…”