Urinary tract infections (UTIs) are one of the most common bacterial infections. Conventional approaches to diagnose these infections rely on microbial urine culture, urine sediment microscopy and basic molecular urinalysis tests, in combination with assessments of patient symptoms that are indicative of UTI. The last decade has seen a more widespread clinical use of standardized MALDI-TOF methods to identify UTI-causing microbial agents. Shotgun proteomics methods to determine the extent of inflammation and types of immune cell effectors in urine have not become part of routine clinical tests. However, such methods are useful to investigate UTI pathogenesis, identify difficult-to-culture pathogens and understand antimicrobial effector mechanisms. The present chapter describes these approaches in order to gain quantitative and qualitative insights into inflammation and immune responses in patients with UTI and simultaneously profile the causative agents. The methods are also applicable to examine catheter-associated UTIs and vaginal infections from urine samples. Protocols provided here pertain to direct analyses of clinical specimens including urine sediments and urethral catheter biofilms.
Keywords: FASP; Inflammation; LC-MS/MS; Mass spectrometry; Metaproteomics; Pathogen identification; Proteomics; Urinary tract infection; Urine.