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Antibiotics
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New Advances in Antibiotic Therapy in the Gastroenterology Field
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New Advances in Antibiotic Therapy in the Gastroenterology Field

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotic Therapy in Infectious Diseases".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 2849

Special Issue Editors

Dr. Giuseppe Guido Maria Scarlata

E-Mail
Guest Editor
Department of Health Sciences, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
Interests: gut-liver axis; gut microbiota; fatty liver disease; viral hepatitis; COVID-19, antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals
Dr. Francesca Serapide

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Guest Editor
Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
Interests: antimicrobial resistance; bacterial infections; enterococcal infections; antimicrobial stewardship; sepsis; gram-negative infections
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic therapy plays a pivotal role in managing gastrointestinal (GI) infections, liver diseases, and microbiota-associated disorders. However, the rise of antimicrobial resistance, evolving gut microbiome research, and novel therapeutic approaches are reshaping the landscape of antibiotic use in gastroenterology. This Special Issue explores cutting-edge advancements, including targeted antibiotic strategies, microbiome-sparing therapies, and precision medicine approaches for GI infections and liver diseases. Additionally, we highlight the implications of gut dysbiosis, antimicrobial stewardship, and emerging alternatives such as bacteriophage therapy and microbiota-based interventions. By integrating microbiology, pharmacology, and clinical practice, this collection aims to provide insights into optimizing antibiotic use while mitigating resistance and preserving gut health. We invite contributions from researchers and clinicians to advance our understanding of the evolving role of antibiotics in gastroenterology and hepatology, paving the way for more effective and sustainable therapeutic strategies in this rapidly developing field.

Dr. Giuseppe Guido Maria Scarlata
Dr. Francesca Serapide
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • antibiotic therapy
  • antimicrobial resistance
  • gastroenterology
  • infectious diseases
  • microbiology
  • gut–liver axis
  • antimicrobial stewardship
  • infection control
  • biomarkers
  • diagnosis
  • epidemiology

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Published Papers (3 papers)

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Research

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14 pages, 276 KB  
Article
Antimicrobial Susceptibility of Clostridioides difficile in Spain: Multicenter Retrospective Cohort Study
by María-Paz Ventero, María-Dolores Valverde-Fredet, Esperanza Merino, Rocío Herrero, Iryna Tyschkovska Germak, Miguel Rodríguez-Fernández, Jose-Manuel Ramos-Rincón, Maria Garcia, Elisabet Delgado-Sánchez, Miguel Nicolás Navarrete-Lorite, Concepcion Gil, María Tasias, Juan Jose Caston, David Vinuesa-Garcia, Cristina Gomez-Ayerbe, Francisco J. Martínez Marcos, Nicolas Merchante and Juan Carlos Rodríguez
Antibiotics 2026, 15(2), 145; https://doi.org/10.3390/antibiotics15020145 - 2 Feb 2026
Viewed by 903
Abstract
Background/Objetives: The objective of this study was to determine the in vitro susceptibility profiles of clinical Clostridioides difficile isolates to metronidazole (MTZ), vancomycin (VAN), fidaxomicin (FDX), tigecycline (TGC), and eravacycline (ERV) in a multicenter Spanish cohort, and to evaluate their association with [...] Read more.
Background/Objetives: The objective of this study was to determine the in vitro susceptibility profiles of clinical Clostridioides difficile isolates to metronidazole (MTZ), vancomycin (VAN), fidaxomicin (FDX), tigecycline (TGC), and eravacycline (ERV) in a multicenter Spanish cohort, and to evaluate their association with clinical factors. Methods: Strains were obtained from prospectively included patients in the ICD-ANCRAID-SEICV cohort (ClinicalTrials.gov ID: NCT04801862) in Andalucía and the Valencian Community between 1 January 2020 and 30 April 2023. Antimicrobial susceptibility testing was performed using E-test for MTZ, VAN, TGC, and ERV, and agar dilution for FDX. Results: The results were interpreted following EUCAST clinical breakpoints and ECOFF criteria. A total of 107 patients were included (median age 70 years; 65.4% women). Nearly half of the cases were community-acquired, 30% nosocomial, and the remainder healthcare-associated. Most infections were non-severe, and 32.7% experienced recurrence. Overall resistance levels were low: VAN and TGC each showed resistance in 2.8% of isolates, followed by MTZ (1.9%). Only one isolate was resistant to FDX (0.9%), and none to ERV. MIC90 values were low for all agents. Some resistant isolates displayed co-resistance and were recovered from patients with prior antibiotic exposure. Among the seven patients carrying resistant strains, most were women, and the cases were predominantly community-acquired. Clinical characteristics, including age, comorbidity, infection origin, and severity, did not differ from those with susceptible isolates. All patients achieved clinical cure without recurrent infection. No association was found between elevated MIC values and recurrence or greater severity. Conclusions: FDX and ERV demonstrated excellent in vitro activity. Resistance to MTZ, VAN, and TGC was uncommon but detectable. Findings highlight the need for continued antimicrobial resistance surveillance and evaluation of its potential clinical impact. Full article
(This article belongs to the Special Issue New Advances in Antibiotic Therapy in the Gastroenterology Field)
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Review

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19 pages, 897 KB  
Review
Biliary Microbiota in Health and Disease: Clinical Implications in Lithiasis, Infection, and Antimicrobial Resistance
by Claudia Marinaccio, Marta Giovanetti, Benedetto Neri, Dario Biasutto, Andrea D’Amico, Annamaria Altomare, Francesco Branda, Laura Restaneo, Massimo Ciccozzi, Michele Cicala and Michele Pier Luca Guarino
Antibiotics 2026, 15(5), 445; https://doi.org/10.3390/antibiotics15050445 - 29 Apr 2026
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Abstract
The biliary tract, long considered a sterile environment, is now recognized to harbor a resident microbiota with important implications for health and disease. This review aims to summarize current knowledge on the composition and function of the biliary microbiota in physiological conditions, and [...] Read more.
The biliary tract, long considered a sterile environment, is now recognized to harbor a resident microbiota with important implications for health and disease. This review aims to summarize current knowledge on the composition and function of the biliary microbiota in physiological conditions, and its alterations in pathological states such as infection and lithiasis, with a particular focus on antimicrobial resistance. In healthy individuals, the biliary microbiota appears to be shaped by bile acids and gut–bile axis interactions, playing a role in local immune modulation. In disease, microbial dysbiosis contributes to conditions such as acute cholecystitis, cholangitis, and gallstone formation, with distinct microbial signatures linked to specific stone types. Common biliary pathogens, including E. coli, Enterococcus spp., Pseudomonas spp., and K. pneumoniae, often exhibit concerning resistance patterns, impacting therapeutic strategies. Emerging evidence highlights the interplay between intestinal and biliary microbiota, suggesting potential diagnostic and prognostic applications. Understanding these dynamics opens new avenues for microbiota-informed antibiotic stewardship, targeted microbiota modulation, and precision medicine approaches. Further research, particularly culture-independent and longitudinal studies, is crucial to fully elucidate the clinical significance of the biliary microbiota and to integrate microbiota profiling into patient management strategies. Full article
(This article belongs to the Special Issue New Advances in Antibiotic Therapy in the Gastroenterology Field)
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21 pages, 836 KB  
Review
Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy
by Giuseppe Guido Maria Scarlata, Andrej Belančić, Davor Štimac, Almir Fajkić, Tomislav Meštrović and Ludovico Abenavoli
Antibiotics 2026, 15(3), 317; https://doi.org/10.3390/antibiotics15030317 - 20 Mar 2026
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Abstract
Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and [...] Read more.
Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment. Full article
(This article belongs to the Special Issue New Advances in Antibiotic Therapy in the Gastroenterology Field)
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