Phenotype–genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt

Catheter-associated urinary tract infections (CAUTIs) are among the most common healthcare-associated infections in low- and middle-income countries (LMICs), contributing to the clinical burden of antimicrobial resistance (AMR). In this study, phenotypic (EUCAST AMR profiles) and genomic data were generated for 132 isolates (67 Escherichia coli , 14 Pseudomonas aeruginosa , 11 Klebsiella pneumoniae , 9 Proteus mirabilis , 8 Providencia spp., 5 Enterobacter hormaechei , and 18 rare uropathogens) recovered from CAUTIs in an Egyptian hospital. Several (22/132, 16.6 %) isolates were multidrug-resistant, while almost half (62/132, 46.9 %) were extensively drug-resistant. Comparison of phenotypic data with genotypic data from three different AMR-profiling tools (ResFinder, CARD, AMRFinder) highlighted phenotype–genotype discordance as an important consideration in resistome studies in Egypt, with a total concordance of 88.4 %, 85.7 %, and 80.3 % ResFinder, CARD and AMRFinder, respectively. Pseudomonas, at the species level, exhibited the greatest discordance. At the antimicrobial level, meropenem was subject to greatest discordance. In addition to the findings from our comparative analyses, new AMR variants are reported for Egypt for Pseudomonas ( OXA-486 , OXA-488 , OXA-905 , IMP-43 , PDC-35 , PDC-45 , PDC-201 ) and Escherichia coli ( TEM-176 , TEM-190 ), along with several new multilocus sequence types (for Escherichia coli , Enterobacter cloacae , Klebsiella pneumoniae , Pseudomonas aeruginosa ) for the country. Two Pseudomonas aeruginosa isolates harbouring pBT2436-like megaplasmids were identified, encoding resistance genes ( aph(3’’)-Ib , aph(6)-Id ). In summary, we show that there is significant phenotype–genotype discordance in AMR profiling among CAUTI isolates, highlighting the need for comprehensive approaches in resistome studies. We also show the genomic diversity of Gram-negative uropathogens contributing to disease burden in a little-studied LMIC setting.