Low-cost rapid diagnostics and typing for clinical microbiology using FT-IR

Abstract

Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) represent urgent challenges for global public health, with impactful consequences in patient outcomes and hospital resources. However, current diagnostic tools present limitations in terms of speed, accuracy and simplicity, critical for early pathogen detection, effective treatment decisions, infection prevention and dissemination in clinical settings. This thesis focused on specific diagnostic challenges to improve accurate, quick and simple pathogen detection and antimicrobial resistance mechanisms and extend Fourier transform infrared (FT-IR) spectroscopy applications for the detection of clinically relevant EcSC, MDR-Kp and Hv-Kp. To accomplish this task, we i) used a real clinical case to identify limitations associated with routine molecular methods for detection of rare mechanisms of resistance (production of IMP-22 in Klebsiella pneumoniae); ii) assessed the potential of FT-IR spectroscopy to differentiate and identify clinically-relevant Enterobacter cloacae species compared to reference methods; iii) extended FT-IR application to detect hypervirulent K. pneumoniae. Phenotypic, genotypic and molecular methods were combined with FT-IR spectroscopy and multivariate data analysis, used to interpret spectral patterns and build classification models. This work underscored the need to integrate phenotypic and targeted molecular approaches for comprehensive carbapenemase surveillance. It further demonstrated FT-IR's effectiveness in species and subspecies differentiation, underscoring its role as a rapid and reliable diagnostic tool for prompt treatment, minimizing the spread of multidrug-resistant pathogens, and improving patient care.

Date of Award	16 Oct 2025
Original language	English
Awarding Institution	Universidade Católica Portuguesa
Supervisor	Ângela Patrícia da Silva Novais Amorim (Supervisor)