Beyond the usual suspects: emerging uropathogens in the microbiome age

Area of Science:

• Microbiology
• Genomics
• Urology

Background:

• The human urinary tract harbors a complex microbial community, the urinary microbiome.
• Standard clinical microbiology methods focus on a limited set of known uropathogens, potentially overlooking other causative agents.
• Recurrent urinary tract infections (UTIs) and symptoms in patients with "no growth" cultures suggest current diagnostic approaches are insufficient.

Purpose of the Study:

• To review emerging and suspected uropathogens identified by advanced culture-independent methods.
• To highlight the limitations of traditional culture-based diagnostics in capturing the full spectrum of the urinary microbiome.
• To stimulate research into the role of underappreciated microbes in urinary tract health and disease.

Main Methods:

• Utilized enhanced culture (metaculturomic) and culture-independent DNA-based (metagenomic) techniques.
• Analyzed urine samples from patients with lower urinary tract symptoms.
• Reviewed literature on microbial species detected by advanced methods but missed by standard cultures.

Main Results:

• Metagenomic and metaculturomic methods have identified hundreds of microbial species in the urinary tract, far exceeding those detected by standard methods.
• Fastidious, slow-growing, or anaerobic microbes, often missed by traditional cultures, are frequently detected in patients with UTI symptoms.
• Some of these newly identified microbes are also implicated in non-urinary tract infections, suggesting opportunistic pathogenicity.

Conclusions:

• The current focus on a narrow range of uropathogens is likely too limited for diagnosing and understanding UTIs.
• Advanced molecular techniques are crucial for uncovering the true diversity of the urinary microbiome and its role in health and disease.
• Further research is needed to understand the biology of emerging uropathogens and their transition from commensals to pathogens.