Phenotypic and genomic characterization ofPseudomonas aeruginosaisolates recovered from catheter-associated urinary tract infections in an Egyptian hospital

Abstract

Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, andPseudomonas aeruginosais a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31P. aeruginosaisolates recovered from CAUTIs in an Egyptian hospital over a 3-month period. Genomes of isolates were of good quality and were confirmed to beP. aeruginosaby comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which 357 and 773 are considered high-risk clones. Antimicrobial resistance (AMR) testing according to EUCAST guidelines showed the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)], and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422,938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms, and were predicted to encode virulence genes associated with adherence, antimicrobial activity, antiphagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems, and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles ofP. aeruginosacontributing to CAUTIs in Egypt.