Antimicrobial Therapies Affect the Microbial Ecosystems Within Our Body: The Urinary Microbiome and Urolithiasis

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Pharmacology".

Deadline for manuscript submissions: 25 November 2025 | Viewed by 353

Special Issue Editor


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Guest Editor
1. Clinical Laboratory of Medical Microbiology, Marius Nasta Institute of Pneumology, 050159 Bucharest, Romania
2. Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
Interests: virology; microbiology; respiratory infections; HIV
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Special Issue Information

Dear Colleagues,

This Special Issue brings together works that reconsider how we think about infectious diseases at a time of escalating complexity regarding host–microbe–drug interactions. We welcome contributions that consider the aspects of medicine beyond simply the use of antibiotics, illustrating how antimicrobial therapies affect the microbial ecosystems within our body (whether temporary or more permanent), influence immune responses, or provoke chronic disease states. Drug treatments may influence infection management via resistance, microbiome disruption, or unexpected adverse events. Submissions may explore such topics as microbial ecology, precision medicine, and their pharmacological effects on health. We strongly encourage interdisciplinary submissions engage with elements of microbiology, pharmacology, clinical assessments, imaging, and/or leveraged computational models. We expect submissions on topics, for example, that concern a role for bacteria in non-traditional disease processes. Stone disease is an obvious example of a non-infectious process that is heavily influenced by bacteria. Ultimately, our goal is to showcase differing perspectives on tackling the treatment of infectious diseases by integrating therapeutic outcomes with an understanding of broader human biology and pathophysiology.

Dr. Loredana Sabina Cornelia Manolescu
Guest Editor

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Keywords

  • antibiotics
  • antimicrobials
  • resistance
  • microbiome
  • urolithiasis
  • biofilms
  • infections
  • pathogens
  • pharmacotherapy
  • inflammation

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Published Papers (1 paper)

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Review

21 pages, 1217 KiB  
Review
Beyond Infection: How Antimicrobial Therapies Influence the Urinary Microbiome and Stone Disease
by Oana Nicu-Canareica, Vlad-Octavian Bolocan, Loredana Sabina Cornelia Manolescu, Petru Armean, Cosmin Medar, Liliana Burlibașa, Maria-Luiza Băean and Viorel Jinga
Pharmaceuticals 2025, 18(7), 1038; https://doi.org/10.3390/ph18071038 - 12 Jul 2025
Viewed by 269
Abstract
The discovery of a resident urinary microbiome has significantly altered the understanding of urolithiasis, expanding its etiology beyond metabolic and dietary factors to include microbial contributions. This review highlights how specific uropathogens—particularly Proteus mirabilis, Klebsiella pneumoniae, and Escherichia coli—facilitate stone [...] Read more.
The discovery of a resident urinary microbiome has significantly altered the understanding of urolithiasis, expanding its etiology beyond metabolic and dietary factors to include microbial contributions. This review highlights how specific uropathogens—particularly Proteus mirabilis, Klebsiella pneumoniae, and Escherichia coli—facilitate stone formation through mechanisms such as urease activity, citrate degradation, urine alkalinization, biofilm development, and inflammatory signaling. We critically examine how antibiotic therapies, while essential for treating urinary tract infections (UTIs), disrupt microbial homeostasis by depleting beneficial taxa like Lactobacillus and enabling colonization by lithogenic and resistant strains. Recurrent or broad-spectrum antibiotic use is linked to persistent dysbiosis and increased risk of stone recurrence. Additionally, this paper explores emerging microbiome-targeted strategies—such as probiotics, prebiotics, bacteriotherapy, and precision antimicrobials—as potential interventions to restore microbial balance and mitigate stone risk. Recognizing the urinary microbiome as a therapeutic target opens new avenues for personalized, microbiota-conscious strategies in the prevention and management of kidney stone disease. Full article
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