Complex pathways to Ceftolozane-tazobactam resistance in clinical Pseudomonas aeruginosa isolates: a genomic epidemiology study

Abstract

Objectives: We aimed to conduct a comprehensive genomic analysis of ceftolozane/tazobactam (C/T) resistance mechanisms in Pseudomonas aeruginosa by combining novel institutional data with publicly available sequencing data. Methods: We analyzed 1,682 P. aeruginosa isolates, comprising 339 isolates from Alfred Hospital (Melbourne, Australia) and 1,343 isolates from six public datasets. All isolates underwent whole-genome sequencing and C/T broth microdilution (BMD) susceptibility testing. We assessed previously reported intrinsic and acquired resistance mechanisms. We then conducted a genome-wide association study (GWAS) and machine learning analysis to identify novel genes associated with resistance. We then evaluated the impact of mutations in these genes on MIC values and ceftolozane binding affinity. Results: Among 1,682 P. aeruginosa isolates representing 527 distinct sequence types, 343 (20.4%) were C/T-resistant. Carbapenemase genes were detected in 206/1,682 (12.2%) isolates. Mutations in previously reported resistance-associated genes (ftsI, mpl, ampD, ampC, ampR, oprD) were more frequent in resistant isolates but were also found in almost all susceptible isolates. Successive mutations conferred additive increases in MIC. Combined GWAS and machine learning analyses a priori identified five key genes significantly associated with resistance: ftsI, ampR, ampC, PA3329, and PA4311. Molecular docking simulation revealed that the R504C mutation in penicillin-binding protein 3 (PBP3), which is encoded by ftsI, reduced binding contacts and hydrogen bonds with ceftolozane, significantly decreasing binding affinity (P=0.016). Conclusions: Our analysis of 1,682 P. aeruginosa genomes demonstrated complex pathways to C/T resistance and showed that ftsI may play an underappreciated role. We discovered two previously unidentified genes associated with C/T resistance, whose function remains to be determined.

Competing Interest Statement

N.M. has received research support from GlaxoSmithKline, unrelated to the current study. A.Y.P. has received research funding from MSD through an investigator-initiated research project. All other authors declare no conflict of interest.

Funding Statement

This work was supported by the National Health and Medical Research Council of Australia (Emerging Leader 1 Fellowship APP1176324 to N.M. and Practitioner Fellowship APP1117940 to A.Y.P) and the Australian Medical Research Future Fund (FSPGN000048)

Author Declarations

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Ethics committee of Alfred Hospital gave ethical approval for this work

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Data Availability

The in-house sequence files have been deposited in NCBI project ID PRJNA1220180

Comments (0)

No login
gif