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

Varney, A.M., Mannix-Fisher, E., Thomas, J.C. ORCID: 0000-0002-1599-9123 and McLean, S. ORCID: 0000-0001-8551-4307, 2024. Evaluation of phenotypic and genotypic methods for the identification and characterisation of bacterial isolates recovered from catheter-associated urinary tract infections. Journal of Applied Microbiology: lxae155. ISSN 1364-5072

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Abstract

Aims

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.

Methods and results

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.

Conclusions

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.

Item Type:	Journal article
Publication Title:	Journal of Applied Microbiology
Creators:	Varney, A.M., Mannix-Fisher, E., Thomas, J.C. and McLean, S.
Publisher:	Oxford University Press
Date:	26 June 2024
ISSN:	1364-5072
Identifiers:	Number Type 10.1093/jambio/lxae155 DOI 1909424 Other
Rights:	© The Author(s) 2024. This is a pre-copyedited, author-produced version of an article accepted for publication in the Journal of Applied Microbiology following peer review. The version of record [Adam M Varney, Eden Mannix-Fisher, Jonathan C Thomas, Samantha McLean, Evaluation of phenotypic and genotypic methods for the identification and characterisation of bacterial isolates recovered from catheter-associated urinary tract infections, Journal of Applied Microbiology, 2024;, lxae155] is available online at: https://doi.org/10.1093/jambio/lxae155.
Divisions:	Schools > School of Science and Technology
Record created by:	Melissa Cornwell
Date Added:	04 Jul 2024 12:42
Last Modified:	04 Jul 2024 12:42
URI:	https://irep.ntu.ac.uk/id/eprint/51688

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