Genomic and Phenotypic Inconsistencies in Pseudomonas aeruginosa Resistome among Intensive Care Patients

Objective Pseudomonas aeruginosa, a difficult-to-manage nosocomial pathogen, poses a serious threat to clinical outcomes in intensive care (ICU) patients due to its high antimicrobial resistance. To promote effective management, it is essential to conduct a study of the genomic and phenotypic resistance expression in the isolates. Methods A prospective observational study was conducted at Liepaja Regional Hospital, Latvia. The study included all adult patients who were admitted to the ICU from July 2022 to April 2023 and had documented P. aeruginosa infections during standard laboratory microbiological testing and short-read sequencing. In addition to the clinical samples, environmental samples were also collected and analysed. Results The cohort consisted of 29 ICU patients with 33 samples and three environmental samples. Infection with P. aeruginosa was associated with unfavourable clinical outcomes. One third of isolates met the criteria for multi-drug resistant strains. However, significant variations were observed when comparing phenotypic data to genotypic data. The aminoglycoside resistance prediction of ResFinder showed a major error value of 3.03% for Amikacin, marginally meeting the FDA threshold. Furthermore, there were significant discrepancies in all other antibiotic categories, except for Colistin, to which all samples were susceptible. Financial impact analysis of P. aeruginosa as a nosocomial infection revealed that an ICU patient with P. aeruginosa infection costed 3.17 times more than a regular ICU patient. Conclusions The study emphasizes the genetic diversity of P. aeruginosa at our centre. Utilizing a combination of diagnostic methods can aid clinical microbiologists in identifying resistance mechanisms and clusters while minimizing errors in interpretation. Keywords: Pseudomonas; epidemiology; molecular; intensive care; resistance; antimicrobial; finance; sequencing.