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

Abstract

CrpP enzymes have been recently described as a novel ciprofloxacin-resistance mechanism. We investigated by whole genome sequencing the presence of crpP-genes and other mechanisms involved in quinolone resistance in MDR/XDR-Pseudomonas aeruginosa isolates (n = 55) with both ceftolozane-tazobactam susceptible or resistant profiles recovered from intensive care unit patients during the STEP (Portugal) and SUPERIOR (Spain) surveillance studies. Ciprofloxacin resistance was associated with mutations in the gyrA and parC genes. Additionally, plasmid-mediated genes (qnrS2 and aac(6′)-Ib-cr) were eventually detected. Ten chromosomal crpP-like genes contained in related pathogenicity genomic islands and 6 different CrpP (CrpP1-CrpP6) proteins were found in 65% (36/55) of the isolates. Dissemination of CrpP variants was observed among non-related clones of both countries, including the CC175 (Spain) high-risk clone and CC348 (Portugal) clone. Interestingly, 5 of 6 variants (CrpP1-CrpP5) carried missense mutations in an amino acid position (Gly7) previously defined as essential conferring ciprofloxacin resistance, and decreased ciprofloxacin susceptibility was only associated with the novel CrpP6 protein. In our collection, ciprofloxacin resistance was mainly due to chromosomal mutations in the gyrA and parC genes. However, crpP genes carrying mutations essential for protein function (G7, I26) and associated with a restored ciprofloxacin susceptibility were predominant. Despite the presence of crpP genes is not always associated with ciprofloxacin resistance, the risk of emergence of novel CrpP variants with a higher ability to affect quinolones is increasing. Furthermore, the spread of crpP genes in highly mobilizable genomic islands among related and non-related P. aeruginosa clones alert the dispersion of MDR pathogens in hospital settings.

New Sequence Type ST3449 in Multidrug-Resistant Pseudomonas aeruginosa Isolates from a Cystic Fibrosis Patient

“…The acquisition of the crpP gene, coding for a ciprofloxacin-modifying enzyme [ 63 ] was detected in our strains, all of them bearing the non-synonymous mutations K4R and G7D in CrpP, when compared with the CrpP (GenBank accession: NG_062203). A very recent study conducted on a large number of P. aeruginosa isolates from Portugal and Spain showed that CrpP proteins with the amino acid substitutions K4R and G7D were the most predominant variants among the population analyzed [ 64 ]. A reduced activity of CrpP on ciprofloxacin was previously observed when missense mutations occurred in the amino acid position G7, indicating that this is an essential residue for the enzymatic activity of CrpP [ 65 ].…”

The First Saudi Report of Novel and Common Mutations in the gyrA and parC Genes Among Pseudomonas Spp. Clinical Isolates Recovered from Taif Area

“…As mentioned above, quinolones’ resistance is either chromosomally or plasmid-mediated through different mechanisms. 11 , 12 These mechanisms act separately or in combination leading to various degrees of quinolone resistance that range from reduced susceptibility to complete resistance. 13 …”

“…Unfortunately, due to the irrational use of quinolones, resistance to this group has been increasing over the last years with the emergence of multi-drug resistant (MDR) P. aeruginosa . 5 , 6 …”

“…Chromosomally mediated quinolone resistance in P. aeruginosa may arise from (i) mutational alterations in the gyrA and/or parC genes with subsequent alteration in the binding affinity to GyrA and ParC proteins (target modification) that altogether forms the quinolone resistance determining region (QRDR), (ii) efflux pumps overexpression, and (iii) downregulation of certain outer membrane proteins (OMPs). 11 , 12 These chromosomal mechanisms act separately or together leading to various degrees of quinolone resistance that range from reduced susceptibility to complete resistance. 13 In this regard, and due to the fact that the pre-2019 Clinical Laboratory Standards Institute (CLSI) breakpoints for ciprofloxacin and levofloxacin against P. aeruginosa were too high to detect low level quinolone resistance, 14 , 15 these breakpoints were recently amended.…”

“…Unfortunately, due to the irrational use of quinolones, resistance to this group has been increasing over the last years with the emergence of multi-drug resistant (MDR) P. aeruginosa. 5,6 Quinolones work by inhibiting the bacterial DNA supercoiling and relaxation process, which are crucial for the replication and transcription of DNA. 7 Quinolones exert their effect via non-covalent binding and inhibition of two target enzymes namely, DNA gyrase and topoisomerase IV with some variations in the affinity of different quinolones to both enzymes.…”