Distinct epidemiology and resistance mechanisms affecting ceftolozane/tazobactam inPseudomonas aeruginosaisolates recovered from ICU patients in Spain and Portugal depicted by WGS

Abstract

Objectives To analyse the epidemiology, the resistome and the virulome of ceftolozane/tazobactam-susceptible or -resistant Pseudomonas aeruginosa clinical isolates recovered from surveillance studies in Portugal (STEP, 2017–18) and Spain (SUPERIOR, 2016–17). Methods P. aeruginosa isolates were recovered from intra-abdominal, urinary tract and lower respiratory tract infections in ICU patients admitted to 11 Portuguese and 8 Spanish hospitals. MICs were determined (ISO-standard broth microdilution, EUCAST 2020 breakpoints). A subset of 28 ceftolozane/tazobactam-resistant P. aeruginosa isolates were analysed and compared with 28 ceftolozane/tazobactam-susceptible P. aeruginosa strains by WGS. Results Clonal complex (CC) 235 (27%) and CC175 (18%) were the most frequent, followed by CC244 (13%), CC348 (9%), CC253 (5%) and CC309 (5%). Inter-hospital clonal dissemination was observed, limited to a geographical region (CC235, CC244, CC348 and CC253 in Portugal and CC175 and CC309 in Spain). Carbapenemases were detected in 25 isolates (45%): GES-13 (13/25); VIM type (10/25) [VIM-2 (4/10), VIM-20 (3/10), VIM-1 (2/10) and VIM-36 (1/10)]; and KPC-3 (2/25). GES-13-CC235 (13/15) and VIM type-CC175 (5/10) associations were observed. Interestingly, KPC-3 and VIM-36 producers showed ceftolozane/tazobactam-susceptible phenotypes. However, ceftolozane/tazobactam resistance was significantly associated with GES-13 and VIM-type carbapenemase production. Six non-carbapenemase producers also displayed ceftolozane/tazobactam resistance, three of them showing known ceftolozane/tazobactam resistance-associated mutations in the PBP3 gene, ftsI (R504C and F533L). Overall, an extensive virulome was identified in all P. aeruginosa isolates, particularly in carbapenemase-producing strains. Conclusions GES-13-CC235 and VIM type-CC175 were the most frequent MDR/XDR P. aeruginosa clones causing infections in Portuguese and Spanish ICU patients, respectively. Ceftolozane/tazobactam resistance was mainly due to carbapenemase production, although mutations in PBP-encoding genes may additionally be involved.

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

“…Note that prevalence of crpP genes was higher in the P. aeruginosa isolates recovered in Spain than in those recovered in Portuguese hospitals, and this finding could be related to a successful association between the PAGI-crpP1.1 and the CC175 high-risk clone. It should be noted that the CC175 is the most frequent P. aeruginosa clone in Spanish hospitals and that its extensive resistome has been found to be determined mainly by mutational events [16,28,29]. On the other hand, the presence of crpP genes was scarcely observed in the CC235 (1/15), the most frequent clone in the Portuguese collection.…”

“…Minimum inhibitory concentration (MIC) values were determined by standard broth microdilution and interpreted according to the EUCAST 2020 criteria (https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.pdf) (S, susceptible ≤ 0.001 mg/L; I, susceptible, increased exposure >0.001-0.5 mg/L; R, resistant > 0.5 mg/L) [14,15]. A subset of 55 P. aeruginosa isolates with susceptible and resistant ceftolozane-tazobactam profiles were subsequently analyzed by whole genome sequencing (WGS) (Table S1) [16].…”

“…Acquired quinolone resistance genes were screened using Abricate (v0.8.11) (ARG-ANNOT and ResFinder databases; threshold, 95% identity; 90% coverage). In addition, mutations from 34 chromosomal genes involved in fluoroquinolones resistance were also analyzed using SNIPPY software (v4.4.3) (https://github.com/tseemann/snippy) (Table S2) [16]. Briefly, all P. aeruginosa assembled sequences were mapped against the P. aeruginosa PAO1 reference genome (GenBank accession No.…”

“…A total of 55 MDR/XDR-P. aeruginosa isolates from 11 Portuguese and 8 Spanish hospitals were analyzed by WGS as a part of the STEP and SUPERIOR studies, respectively [16]. In this subset, 46 isolates (83.6%) showed a non-wild type ciprofloxacin susceptible phenotype (MICCIP = 1 -> 2 mg/L) ( Table 2, Table S2).…”

“…Our aim was to investigate the dissemination of crpP-like genes in MDR or extensively resistant (XDR) P. aeruginosa clinical isolates recovered in patients admitted in Spanish and Portuguese ICUs between 2016 and 2018. These isolates were obtained during surveillance studies to monitor the activity of ceftolozane-tazobactam, a novel β-lactam-β -lactamase combination with enhanced antimicrobial activity against P. aeruginosa, including MDR/XDR isolates [14][15][16].…”