Progress and Challenges in the Antibiotic Treatment of Infections

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

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 12704

Special Issue Editor


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Guest Editor
1. Department of Clinical Microbiology, Clinical Hospital Center Rijeka, Kresimirova 42, 51000 Rijeka, Croatia
2. Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia
Interests: antibiotics; antimicrobial resistance (AMR); clinical microbiology; infectious disease diagnostics; medical education

Special Issue Information

Dear Colleagues,

The excessive and inappropriate use of antibiotics has led to increasing antimicrobial resistance (AMR), which undermines the effectiveness of antibiotics in the treatment of infectious diseases. Infections that were once easy to treat are now increasingly difficult to manage. The lack of effective antibiotics is making routine medical procedures such as surgery, chemotherapy, and organ transplantation a major health concern. An alarming increase in multi-drug resistant pathogens is making it more difficult to treat infections, prolonging hospital stays, and driving up healthcare costs. Improvements in diagnostics and antimicrobial stewardship are important strategies to combat AMR. The appropriate and effective use of existing antibiotics in combination with the use of rapid diagnostic tools is of paramount importance. Prioritising the development of novel antimicrobial therapeutic strategies can help to preserve the efficacy of antibiotics for future generations.

This Special Issue aims to explore the multifaceted challenges of antibiotic treatment in the context of increasing antimicrobial resistance. Submissions related to advances in the timely and accurate diagnosis of infectious diseases, AMR, and the judicious use of antibiotics are particularly encouraged. The aim of this Special Issue is to collect the latest experiences of all professionals working in this field.

Prof. Dr. Marina Bubonja-Sonje
Guest Editor

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Keywords

  • antimicrobial therapy
  • antimicrobial stewardship
  • antimicrobial resistance
  • rapid microbiological diagnostics

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Published Papers (8 papers)

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Research

9 pages, 536 KB  
Article
Detecting erm-Mediated Inducible Macrolide–Lincosamide–Streptogramin B Resistance in Anaerobic Clinical Isolates
by Fabio Daniel Thalmann, Claudio Neidhöfer, Pascal Schläpfer, Christopher Field, Karoline Leuzinger, Claudia Lang and Peter M. Keller
Antibiotics 2026, 15(4), 360; https://doi.org/10.3390/antibiotics15040360 - 1 Apr 2026
Viewed by 605
Abstract
Background: Inducible macrolide–lincosamide–streptogramin B (iMLSB) resistance is well defined in Gram-positive aerobes but remains poorly characterized in anaerobes, where standardized detection strategies are lacking. Following withdrawal of EUCAST guidance to infer clindamycin resistance from erythromycin resistance in Peptostreptococcus and Bacteroides spp. because [...] Read more.
Background: Inducible macrolide–lincosamide–streptogramin B (iMLSB) resistance is well defined in Gram-positive aerobes but remains poorly characterized in anaerobes, where standardized detection strategies are lacking. Following withdrawal of EUCAST guidance to infer clindamycin resistance from erythromycin resistance in Peptostreptococcus and Bacteroides spp. because of inconsistent species-specific performance, a diagnostic gap persists. Methods: We therefore assessed the accuracy of the D-test for detecting iMLSB resistance in anaerobes by correlating phenotypic results with whole-genome sequencing data. Fifty clinical anaerobic isolates, including Finegoldia magna, Peptostreptococcus anaerobius, and Bacteroides spp., were included in the analysis. Antimicrobial susceptibility testing was performed using gradient diffusion to determine minimum inhibitory concentrations of erythromycin and clindamycin, complemented by D-test analysis for phenotypic detection of inducible resistance. Whole-genome sequencing was undertaken to identify erm genes encoding ribosomal methyltransferases associated with the iMLSB phenotype. Results: Among the 50 isolates, erm genes were detected in 16 strains (32.0%). The prevalence of erm positivity was highest among Gram-positive cocci (50%), followed by Gram-positive rods (35.3%) and Gram-negative rods (11.8%). Five erm-positive isolates exhibited a characteristic D-shaped growth pattern, with high erythromycin MICs (>256 mg/L) and low clindamycin MICs (≤2 mg/L), consistent with an inducible iMLSB phenotype, whereas the remaining eleven demonstrated constitutive resistance. Conclusions: The D-test accurately identified inducible iMLSB resistance among Gram-positive anaerobic cocci and, if confirmed in larger studies, could form the basis of an accessible and pragmatic screening strategy for this subgroup. Integration of molecular analyses seems essential for the evidence-based refinement of diagnostic algorithms, particularly in the absence of robust, species-specific guidance. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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14 pages, 1327 KB  
Article
Synergistic Antimicrobial and Antibiofilm Activity of Nitroxoline in Combination with Hydroquinone Against Uropathogenic Enterococcus faecalis
by Davorka Repac Antić, Silvestar Mežnarić, Marko Kolenc, Irena Brčić Karačonji and Ivana Gobin
Antibiotics 2026, 15(4), 333; https://doi.org/10.3390/antibiotics15040333 - 25 Mar 2026
Viewed by 628
Abstract
Background: Enterococcus faecalis is a major cause of complicated urinary tract infections (UTIs), characterized by intrinsic resistance and pronounced biofilm formation. Nitroxoline (NTX), a metal-chelating uroantiseptic, accumulates in urine and exhibits antibiofilm activity. Hydroquinone (HQ), the active urinary metabolite of arbutin-containing herbal [...] Read more.
Background: Enterococcus faecalis is a major cause of complicated urinary tract infections (UTIs), characterized by intrinsic resistance and pronounced biofilm formation. Nitroxoline (NTX), a metal-chelating uroantiseptic, accumulates in urine and exhibits antibiofilm activity. Hydroquinone (HQ), the active urinary metabolite of arbutin-containing herbal preparations, is also excreted into urine and may contribute to antimicrobial activity in situ. This study investigated the antimicrobial and antibiofilm effects of NTX and HQ, individually and in combination, against uropathogenic E. faecalis isolates. Methods: Minimum inhibitory (MIC), bactericidal (MBC), and anti-adhesion (MAC) concentrations were determined using broth microdilution. Interaction was assessed by the checkerboard method and expressed as the fractional inhibitory concentration index (FICI). Biofilm inhibition was quantified by colony-forming unit (CFU) enumeration following exposure to subinhibitory concentrations. Ultrastructural alterations of E. faecalis following exposure to NTX and HQ were examined by transmission electron microscopy (TEM). Results: NTX demonstrated MIC values ranging from 0.002–0.016 mg/mL (MIC50/MIC90: 0.004/0.008 mg/mL), while HQ exhibited MIC values of 0.78–1.56 mg/mL (MIC50/MIC90: 0.78/1.56 mg/mL). Synergistic interactions (FICI ≤ 0.5) were observed in selected isolates, with up to eightfold and sixteenfold reductions in NTX and HQ concentrations, respectively. Additive effects predominated in the remaining isolates without antagonism. The combination achieved 3–5 log10 reductions in adherent bacterial counts compared to untreated controls and up to 4 log10 reductions compared to single-agent exposure. In several strains, complete inhibition of adhesion was observed. TEM analysis revealed marked envelope disruption, cytoplasmic condensation, and structural collapse following combined treatment. Conclusions: Given that both NTX and HQ are active within the urinary environment, their combination may represent a pharmacologically relevant strategy targeting both bacterial growth and early biofilm establishment in enterococcal UTIs. These findings support further in vivo and pharmacokinetic investigations to evaluate the clinical applicability of this combination. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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20 pages, 3501 KB  
Article
Target Fidelity and Failure: Structure–Activity Relationship of High-Molecular-Mass Penicillin-Binding Proteins (HMM-PBPs) in Refractory Granulicatella adiacens Endocarditis
by Paola Conti, Alberto Pagotto, Sebastiano A. Fortuna, Alessandra Giardina, Grete F. Privitera, Ester Rosa, Assunta Sartor, Carlo Tascini and Floriana Campanile
Antibiotics 2026, 15(2), 168; https://doi.org/10.3390/antibiotics15020168 - 5 Feb 2026
Viewed by 945
Abstract
Background/Objectives: Granulicatella adiacens infective endocarditis is conventionally managed with penicillin, ampicillin, or ceftriaxone in combination with gentamicin, although double beta-lactam regiments have been proposed a safer alternative to reduce aminoglycoside-associated nephrotoxicity. To date, the High-Molecular-Mass Penicillin-Binding Proteins (HMM-PBPs) of G. adiacens and [...] Read more.
Background/Objectives: Granulicatella adiacens infective endocarditis is conventionally managed with penicillin, ampicillin, or ceftriaxone in combination with gentamicin, although double beta-lactam regiments have been proposed a safer alternative to reduce aminoglycoside-associated nephrotoxicity. To date, the High-Molecular-Mass Penicillin-Binding Proteins (HMM-PBPs) of G. adiacens and their affinities for beta-lactam antibiotics have not been previously characterized. This study investigated the HMM-PBP profile of G. adiacens, with particular interest on sequence alterations and beta-lactam binding properties, both as single agents and in combination. Methods: Beta-lactam activity, synergistic interactions and PBP binding affinities were evaluated in a clinical isolate (IS 48) and compared with those in the reference strain ATCC 49175. Binding of PBPs to ampicillin, ceftriaxone, and ceftobiprole, alone or in combination, was investigated by Bocillin-FL labeling. PBP homology and conserved active-sites motifs were assessed by sequence alignment, and pbp gene mutations were identified by whole-genome sequencing. Results: The clinical isolate was non-susceptible to ampicillin, resistant to ceftriaxone and exhibited higher minimum inhibitory concentrations (MICs) for ceftobiprole relative to the fully susceptible ATCC reference strain. Five HMM PBPs with high enterococcal homology, were identified. In the IS 48 isolate, the class A PBP showed distinct amino acid substitutions in proximity to the catalytic centers. Despite these alterations, PBP1A and PBP2A were strongly inhibited by the tested beta-lactams, whereas PBP2 and PBP2B demonstrated low acylation rates. Combination of ampicillin with either ceftobiprole or ceftriaxone resulted in enhanced acylation of the three bifunctional HMM PBPs compared with monotreatment. IC50 values were consistently higher for the IS 48 clinical isolate, suggesting decreased target availability and/or reduced beta-lactam affinity under clinical conditions. Conclusions: The resistance phenotype of G. adiacens clinical isolate appears to be primarily associated with altered PBP beta-lactam interactions. Nonetheless, beta-lactam combination regimes remain effective by achieving substantial inhibition of key HMM-PBPs involved in peptidoglycan synthesis, thereby supporting the rationale for dual beta-lactam therapy in this setting. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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13 pages, 343 KB  
Article
Timing of Antimicrobial Lock Replacement for Gram-Positive Port Infections: Results of a Randomized Trial
by César Bustos, José R. Yuste, Aitziber Aguinaga, Asunción Parra, Francisco Carmona-Torre, José R. Azanza, Carlos Lacasa and José L. Del Pozo
Antibiotics 2026, 15(2), 157; https://doi.org/10.3390/antibiotics15020157 - 2 Feb 2026
Viewed by 1197
Abstract
Background: Conservative management of port-related bacteremia often includes locally administered antimicrobials, known as antimicrobial lock therapy (ALT). Current guidelines recommend daily replacement of antimicrobial lock solutions (ALSs). We aimed to evaluate whether ALSs could remain effective with extended dwell times of up [...] Read more.
Background: Conservative management of port-related bacteremia often includes locally administered antimicrobials, known as antimicrobial lock therapy (ALT). Current guidelines recommend daily replacement of antimicrobial lock solutions (ALSs). We aimed to evaluate whether ALSs could remain effective with extended dwell times of up to 10 days. Methods: In this randomized clinical trial, patients with noninfected, recently implanted ports were assigned to one of five ALS dwell-time groups, ranging from 1 to 10 days. Each ALS contained heparin plus an antimicrobial at standard intraluminal concentrations: vancomycin 2 mg/mL, teicoplanin 10 mg/mL, linezolid 1.8 mg/mL, daptomycin 5 mg/mL, or tigecycline 4.5 mg/mL. The primary endpoint was the time at which intraluminal drug concentrations decreased below 1 mg/mL (ClinicalTrials.gov NCT01592032). Results: Vancomycin and linezolid concentrations fell significantly below 1 mg/mL after 3 days of dwell time. Daptomycin and tigecycline concentrations decreased significantly after 7 days but remained above 1 mg/mL. Teicoplanin concentrations did not decline significantly after 7 days. Conclusions: Optimal ALS dwell time depends on the antimicrobial agent. Vancomycin and linezolid locks require daily replacement, whereas daptomycin, tigecycline, and teicoplanin locks maintain therapeutic concentrations for up to 7 days. These findings support individualized ALS replacement strategies, potentially reducing the need for daily interventions. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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16 pages, 1189 KB  
Article
Molecular Epidemiology, Antimicrobial Resistance, and Clinical Characteristics of Streptococcus pneumoniae Isolated from Adult Patients with Invasive Pneumococcal Disease
by Kristina Franjić Amančić, Bojana Mohar-Vitezić, Đurđica Cekinović Grbeša, Tanja Grubić Kezele, Maja Abram and Marina Bubonja-Šonje
Antibiotics 2025, 14(11), 1158; https://doi.org/10.3390/antibiotics14111158 - 15 Nov 2025
Viewed by 1999
Abstract
Background/Objectives: Streptococcus pneumoniae is a major human pathogen causing illnesses that range from mild respiratory infections to severe invasive diseases. More than 100 known S. pneumoniae serotypes differ in their virulence, prevalence, and levels of drug resistance. Additionally, different clonal types within [...] Read more.
Background/Objectives: Streptococcus pneumoniae is a major human pathogen causing illnesses that range from mild respiratory infections to severe invasive diseases. More than 100 known S. pneumoniae serotypes differ in their virulence, prevalence, and levels of drug resistance. Additionally, different clonal types within the same serotype may exhibit varying disease potential and genetic characteristics. This study aimed to determine phenotypic and molecular characteristics of S. pneumoniae isolated from patients with invasive pneumococcal disease (IPD). Methods: The serotypes of invasive S. pneumoniae isolates collected between 2022 and 2025 from adult patients hospitalized in a tertiary hospital were determined. Multilocus sequence typing (MLST) was performed on isolates with reduced susceptibility to penicillin to assess their molecular epidemiology. Results: Serotype 3 was the most common among all invasive isolates (29/85; 34.1%), followed by serotype 19A (22/85; 25.9%). Most penicillin-resistant isolates belonged to serotypes 19A and 19F. Three of the eight 19A isolates with reduced penicillin susceptibility were assigned to ST320 (37.5%), a clinically significant clone due to its high virulence and antibiotic resistance. While 15.3% of all isolates were multidrug-resistant (MDR), nearly half of the isolates with reduced penicillin susceptibility were MDR, most frequently exhibiting the erythromycin–clindamycin–tetracycline resistotype. Conclusions: This study highlights the predominance of serotype 19A, particularly the highly virulent and resistant ST320 clone, among invasive isolates with reduced penicillin susceptibility. These findings underscore the ongoing threat of antimicrobial resistance in IPD and the importance of continued surveillance of serotype distribution and resistance patterns to guide treatment strategies and vaccination policy decisions. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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12 pages, 1894 KB  
Article
Current Clinical Practice on the Management of Invasive Streptococcus Pyogenes Infections in Children: A Survey-Based Study
by Maia De Luca, Costanza Tripiciano, Carmen D’Amore, Marta Luisa Ciofi Degli Atti, Lorenza Romani, Federica Pagano, Daniele Zama, Silvia Garazzino, Giangiacomo Nicolini, Samantha Bosis, Elena Chiappini, Claudia Colomba and Andrea Lo Vecchio
Antibiotics 2025, 14(10), 970; https://doi.org/10.3390/antibiotics14100970 - 26 Sep 2025
Viewed by 2231
Abstract
Background/Objectives: Streptococcus pyogenes (Group A Streptococcus, GAS) is a major human pathogen that causes a wide spectrum of diseases. While mild infections like pharyngitis and impetigo are common, severe and invasive infections, though less frequent, pose significant health risks, particularly in children. [...] Read more.
Background/Objectives: Streptococcus pyogenes (Group A Streptococcus, GAS) is a major human pathogen that causes a wide spectrum of diseases. While mild infections like pharyngitis and impetigo are common, severe and invasive infections, though less frequent, pose significant health risks, particularly in children. In recent years, the re-emergence of hypervirulent GAS strains has heightened global concern. Nowadays, the absence of universally accepted guidelines compels clinicians to rely on a combination of clinical judgment, microbiological data and available evidence to manage these infections effectively. Our aim was to assess the current management of invasive GAS (iGAS) infections in Italy and the variability in therapeutic and preventive approaches. Methods: A web-based current clinical practice survey about invasive and severe GAS infections was designed according to the Checklist for Reporting of Survey Studies (CROSS) methodology and circulated among the members of the Italian Society of Pediatric Infectious Diseases (SITIP). Results: The survey reveals that while many practices are commonly shared among clinicians, particularly regarding first-line therapies (penicillin or ceftriaxone depending on the infection site), significant uncertainties remain, particularly about the use of combined antibiotic regimens and supportive treatments. The use of combined antibiotic regimens was considered appropriate as first-line therapy for STSS, NF and brain abscesses. Clindamycin was the preferred agent for combination with beta-lactam for most infections, except for brain abscesses, where linezolid was favored. However, there was disagreement regarding the optimal timing for de-escalation to beta-lactam monotherapy. Responses varied widely concerning the indications and dosages for IVIG, as well as the use of corticosteroids. Conclusions: Addressing the burden of invasive GAS (iGAS) infections in children requires enhanced surveillance, early recognition, prompt treatment and preventive strategies. Further work to increase surveillance, e.g., developing national registries, and to standardize the management of the disease, e.g., developing country-specific guidelines, is essential to build solid evidence on the most effective approaches. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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17 pages, 958 KB  
Article
First Report of CTX-M-32 and CTX-M-101 in Proteus mirabilis from Zagreb, Croatia
by Branka Bedenić, Josefa Luxner, Gernot Zarfel, Andrea Grisold, Mirela Dobrić, Branka Đuras-Cuculić, Mislav Kasalo, Vesna Bratić, Verena Dobretzberger and Ivan Barišić
Antibiotics 2025, 14(5), 462; https://doi.org/10.3390/antibiotics14050462 - 30 Apr 2025
Cited by 1 | Viewed by 1508
Abstract
Background/Objectives: Proteus mirabilis is a frequent causative agent of urinary tract and wound infections in community and hospital settings. It develops resistance to expanded-spectrum cephalosporins (ESC) due to the production of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC β-lactamases (p-AmpC). Here, we report the [...] Read more.
Background/Objectives: Proteus mirabilis is a frequent causative agent of urinary tract and wound infections in community and hospital settings. It develops resistance to expanded-spectrum cephalosporins (ESC) due to the production of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC β-lactamases (p-AmpC). Here, we report the characteristics of ESBLs and p-AmpC β-lactamases encountered among hospital and community isolates of P. mirabilis in two hospitals and the community settings in Zagreb, Croatia. Methods: Antibiotic susceptibility testing was performed using disk-diffusion and broth dilution methods. The double-disk-synergy test (DDST) and inhibitor-based test with clavulanic and cloxacillin were applied to screen for ESBLs and p-AmpC, respectively. PCR investigated the nature of ESBL, carbapenemases, and fluoroquinolone resistance determinants. Selected strains were subjected to molecular analysis of resistance traits by the Inter-Array CarbaResist Kit and whole-genome sequencing (WGS). Results: In total, 39 isolates were analyzed. Twenty-two isolates phenotypically tested positive for p-AmpC and seventeen for ESBLs. AmpC-producing organisms exhibited uniform resistance to amoxicillin-clavulanate, ESC, ciprofloxacin, and sulphamethoxazole-trimethoprim, and uniform susceptibility to carbapenems and piperacillin-tazobactam and all harbored blaCMY-16 genes. ESBL-positive isolates demonstrated resistance to amoxicillin-clavulanate, cefuroxime, cefotaxime, ceftriaxone, and ciprofloxacin but variable susceptibility to cefepime and aminoglycosides. They possessed blaCTX-M genes that belong to cluster 1 (n = 5) or 9 (n = 12), with CTX-M-14 and CTX-M-65 as the dominant allelic variants. Conclusions: The study demonstrated the presence of CTX-M ESBL and CMY-16 p-AmpC among hospital and community-acquired isolates. AmpC-producing isolates showed uniform resistance patterns, whereas ESBL-positive strains had variable degrees of susceptibility/resistance to non-β-lactam antibiotics, resulting in more diverse susceptibility patterns. The study found an accumulation of various resistance determinants among hospital and outpatient isolates, mandating improvement in detecting β-lactamases during routine laboratory work. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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21 pages, 783 KB  
Article
A Biosocial Perspective to Understand Antimicrobial Prescription Practices: A Retrospective Cross-Sectional Study from a Public Community Health Center in North India
by Rashmi Surial, Sundeep Sahay, Vinay Modgil, Arunima Mukherjee and Ritika Kondal Bhandari
Antibiotics 2025, 14(3), 213; https://doi.org/10.3390/antibiotics14030213 - 20 Feb 2025
Cited by 3 | Viewed by 2710
Abstract
Background: It is well established by research that large-scale and indiscriminate prescribing, dispensing, and use of antimicrobials drive antimicrobial resistance (AMR) endangering the health and well-being of people, animals, and the environment. In the context of low- and middle-income countries (LMICs), the prescribing [...] Read more.
Background: It is well established by research that large-scale and indiscriminate prescribing, dispensing, and use of antimicrobials drive antimicrobial resistance (AMR) endangering the health and well-being of people, animals, and the environment. In the context of low- and middle-income countries (LMICs), the prescribing of antimicrobials is often not based on biomedical rationality but involves alternative logic driven by social, cultural, and institutional factors. This paper seeks to develop a “biosocial” perspective, reflecting a unified perspective that treats the biomedical and social conditions as two sides of the same coin. Methods: This analysis is based on an empirical investigation of prescription slips that patients carry to buy drugs from the pharmacy following an outpatient department encounter with the clinician. Data collection involves mixed methods, including the quantitative analysis of the antimicrobials prescribed and a qualitative analysis of the underlying reasons for these prescriptions, as described by doctors, pharmacists, and patients. Data analysis involved triangulating quantitative and qualitative data, to develop a “biosocial” perspective, which can provide implications for the development of antimicrobial stewardship policies, particularly relevant for health institutions in low- and middle-income countries. Results: Our analysis of 1175 prescription slips showed that 98% contained antimicrobials, with 74% being broad-spectrum antimicrobials. Only 9% of cases were advised antimicrobial sensitivity testing (AST) before initiating treatment. Qualitative findings indicated that patients had poor awareness of antimicrobials and pharmacists played a crucial role in counseling. Conclusions: This study highlights that antimicrobial prescriptions in public health settings are influenced by both biomedical and social factors, supporting a biosocial perspective. Although AMS interventions are predominantly biomedical, adhering to clinical standards and best practices, this study underscores the necessity of integrating a biosocial viewpoint by incorporating the experiences of pharmacists and patient groups. Strengthening diagnostic support, patient education, and interprofessional collaboration could improve rational antimicrobial uses in low-resource settings. Full article
(This article belongs to the Special Issue Progress and Challenges in the Antibiotic Treatment of Infections)
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