Evaluation of phenotypic and genotypic methods for the identification and characterisation of bacterial isolates recovered from catheter-associated urinary tract infections

• Published in: Journal of applied microbiology 2024-07, Vol.135 (7)
• Main Authors: Varney, Adam M, Mannix-Fisher, Eden, Thomas, Jonathan C, McLean, Samantha
• Format: Article
• Language: English
• ISSN: 1365-2672; 1365-2672
• DOI: 10.1093/jambio/lxae155

Urinary tract infections are the most common hospital-acquired infection, 80% are associated with catheterisation. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital. We compared five bacterial identification methods, including biochemical testing, MALDI biotyping, and genome sequencing, finding differences in genus or species level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design. This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.