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Antibiotics
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From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms
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From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms

A Special Issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: 31 January 2027 | Viewed by 2761

Editor

Dr. Silvia Di Lodovico

E-Mail Website
Guest Editor
Department of Pharmacy, “G. d’Annunzio” University, 66100 Chieti, Italy
Interests: antimicrobial resistance; anti-biofilm and anti-virulence activities of natural compounds alone and combined with antibiotics against multi drug-resistant strains (Helicobacter pylori, Staphylococcus spp., Pseudomonas aeruginosa, Candida albicans, Mycobacterium abscessus and other fast-growing mycobacteria)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The global rise of multidrug‑resistant (MDR) microorganisms represents one of the most important challenges regarding public health. Understanding their epidemiology is essential for finding effective ways to counteract infection associated with MDR strains. MDR pathogens spread through complex networks involving hospitals, communities, animals, and the environment, driven by factors such as inappropriate antibiotic use, inadequate infection control practices, and global mobility. Epidemiological surveillance—combining molecular typing, real‑time data analysis, and risk factor assessment—enables researchers to track transmission routes and identify emerging hotspots. A new multifaceted approach from a One Health perspective is therefore necessary. Key strategies include strengthening antimicrobial stewardship programs, improving hygiene and sanitation, implementing rapid diagnostic tools, and promoting evidence‑based infection prevention measures. Bridging epidemiology and new therapeutical solutions could reduce the spread of MDR microorganisms and help to safeguard global health.

Dr. Silvia Di Lodovico
Guest Editor

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-anonymized 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

  • multidrug-resistant microorganisms
  • antimicrobial resistance
  • epidemiological surveillance
  • infection prevention and control
  • antimicrobial stewardship
  • one health
  • public health interventions

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Published Papers (5 papers)

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Research

16 pages, 1218 KB  
Article
Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy
by Federica Di Timoteo, Emanuela Di Giulio, Marco Di Domenico, Barbara Secondini, Francesca Marotta, Giusy Matteucci, Katiuscia Zilli, Teresa Romualdi, Dalia Palmieri, Giuliano Garofolo and Anna Janowicz
Antibiotics 2026, 15(9), 850; https://doi.org/10.3390/antibiotics15090850 - 31 Aug 2026
Viewed by 115
Abstract
Background/Objectives: Wastewater-based epidemiology (WBE) has emerged as a valuable One Health approach for monitoring antimicrobial resistance (AMR) at the population level. Although quantitative PCR (qPCR) and shotgun (SG) metagenomics are widely used for wastewater surveillance, studies integrating these complementary approaches remain limited. This [...] Read more.
Background/Objectives: Wastewater-based epidemiology (WBE) has emerged as a valuable One Health approach for monitoring antimicrobial resistance (AMR) at the population level. Although quantitative PCR (qPCR) and shotgun (SG) metagenomics are widely used for wastewater surveillance, studies integrating these complementary approaches remain limited. This study aimed to investigate the occurrence, seasonal dynamics, and diversity of antimicrobial resistance genes (ARGs) in municipal wastewater from Central Italy by combining targeted qPCR and SG metagenomic sequencing. Methods: Influent wastewater samples were collected monthly from eight municipal wastewater treatment plants in Central Italy between April 2025 and March 2026. Clinically relevant antimicrobial resistance genes were quantified by quantitative real-time PCR, while SG metagenomic sequencing was used to characterize resistome composition, resistance gene families, and ARG sequence diversity using bioinformatic pipelines. Results: All investigated ARGs were detected in every sample. Significant seasonal variation was observed for all investigated markers, including qnrS, blaKPC, blaCTX-M and intI1. Metagenomic analysis revealed broadly similar resistome profiles across sampling sites and time points, dominated by resistance genes to macrolide–lincosamide–streptogramin, aminoglycosides, β-lactams, and fluoroquinolones. High sequence diversity was observed within the dominant ARG families, highlighting the complementary value of SG metagenomics for comprehensive resistome characterization. Conclusions: The integration of targeted qPCR and SG metagenomics provided a comprehensive characterization of antimicrobial resistance in municipal wastewater. While qPCR enabled sensitive quantification of clinically relevant ARGs and revealed seasonal trends, metagenomics expanded resistome characterization by identifying dominant resistance classes, gene families, and sequence variants. These findings support the implementation of integrated molecular approaches for routine wastewater-based AMR surveillance within a One Health framework. Full article
(This article belongs to the Special Issue From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms)
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18 pages, 1956 KB  
Article
Molecular and Structural Insights of carO Gene Variations in Carbapenem-Resistant Acinetobacter baumannii
by Ploychomphoo Poollak, Nattita Srichomthong, Kittaporn Yartirat, Phuchit Pooruk, Rachanon Kiewdee, Nitchawat Paiyabhroma, Sattaporn Weawsiangsang, Sittichai Urtgam, Nontaporn Rattanachak, Touchkanin Jongjitvimol and Jirapas Jongjitwimol
Antibiotics 2026, 15(9), 828; https://doi.org/10.3390/antibiotics15090828 - 26 Aug 2026
Viewed by 487
Abstract
Background/Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a WHO critical-priority pathogen, and variations in the outer membrane porin CarO are one mechanism implicated in carbapenem resistance. No prior study has characterized carO mutation patterns among A. baumannii in Tak, Thailand. This study aimed to [...] Read more.
Background/Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a WHO critical-priority pathogen, and variations in the outer membrane porin CarO are one mechanism implicated in carbapenem resistance. No prior study has characterized carO mutation patterns among A. baumannii in Tak, Thailand. This study aimed to characterize carO mutation patterns in clinical isolates, evaluate their association with CRAB, reconstruct phylogeny, and predict the structural consequences of CarO representatives relative to a crystallographic reference structure (PDB 4RL9). Seventy-seven A. baumannii isolates were recovered from Mae Sot Hospital, and re-confirmed by PCR based on the presence of blaOXA-51-like gene. Results: The carO gene was sequenced and mutations compared between CRAB and carbapenem-susceptible (CSAB) isolates. Of the 77 isolates, 70 yielded successfully carO sequence data by next-generation sequencing (NGS), including 64 CRAB (91.43%) and 6 CSAB isolates. Two overlapping mutation clusters were significantly associated among CRAB isolates (73.44% and 75.00%; p = 0.0008 and p = 0.0006) and were absent from all 6 CSAB isolates (8.57%). Phylogenetic analysis resolved 3 clinical lineages, with variant III predominating. AlphaFold2 models predicted structural divergence among CarO variants with the single variant IV isolate showing the most extensive predicted remodeling of the CarO barrel. Conclusions: carO mutation was strongly associated with carbapenem resistance in this Thai cohort. However, these findings do not establish a direct causal role of carO mutation in carbapenem resistance. Predicted structures were consistent with potential alterations of porin function. These findings provide a regional characterization of carO-mediated resistance and support further functional validation of CarO as a resistance marker. Full article
(This article belongs to the Special Issue From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms)
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12 pages, 265 KB  
Article
Wet Environmental Surveillance of Antimicrobial Resistance Genes in High-Risk Hospital Units
by Morana Magaš, Bojana Mohar Vitezić, Kata Ivanišević and Maja Abram
Antibiotics 2026, 15(8), 807; https://doi.org/10.3390/antibiotics15080807 - 18 Aug 2026
Viewed by 263
Abstract
Background/Objectives: Hospital water and wastewater environments are potential reservoirs for antimicrobial resistance genes (ARGs), particularly in high-risk clinical units. This study examined site-specific ARG DNA detection patterns in wet and waste-associated sites of a haematology ward and an intensive care unit (ICU) [...] Read more.
Background/Objectives: Hospital water and wastewater environments are potential reservoirs for antimicrobial resistance genes (ARGs), particularly in high-risk clinical units. This study examined site-specific ARG DNA detection patterns in wet and waste-associated sites of a haematology ward and an intensive care unit (ICU) to identify environmental hotspots that may inform targeted infection prevention and control (IPC) interventions. Methods: A descriptive point-prevalence environmental study was conducted in May 2025 in a tertiary acute-care hospital. Samples were collected after routine cleaning and during usual clinical activity. Real-time PCR assays were used to detect blaTEM, blaSHV, blaCTX-M, blaOXA-48-like, blaVIM, blaNDM, blaIMP, blaKPC, and mcr-1. Analytical summaries included samples meeting predefined quality-control criteria. Ct signals were categorised descriptively; Ct values ≤ 40 were considered positive, with Ct values 36–40 classified as very low molecular signals, whereas Ct values > 40 were considered negative. Results: The analytical dataset comprised 60 samples: 31 from haematology and 29 from ICU. At least one included ARG signal was detected in 40/60 samples (66.7%), including 23/31 haematology samples (74.2%) and 17/29 ICU samples (58.6%), blaTEM (51.7%) and blaSHV (43.3%) were most frequent. Sink drains showed the broadest multi-gene profiles, especially combinations of ESBL- and carbapenemase-associated genes. Haematology showed broader carbapenemase-associated diversity, whereas ICU detections clustered in patient-room sink drains and sluice-room wastewater infrastructure. Conclusions: ARG DNA signals were unevenly distributed, with sink drains representing most frequently positive sampling sites for multi-gene detection. This molecular, single-timepoint environmental study does not demonstrate viable organisms, colonisation, or transmission; however, point-prevalence environmental assessments may identify wet and wastewater-associated hotspots that can inform targeted IPC interventions against the spread of multidrug-resistant microorganisms. Full article
(This article belongs to the Special Issue From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms)
15 pages, 1581 KB  
Article
Trends and Long-Term Mortality in Sepsis: Evidence from a Population-Based Retrospective Cohort Study of 13,994 Hospitalizations in the Abruzzo Region, Central Italy
by Annalisa Marotta, Cristiano Vicenti, Camillo Odio, Jacopo Vecchiet, Marta Di Nicola and Katia Falasca
Antibiotics 2026, 15(6), 608; https://doi.org/10.3390/antibiotics15060608 - 15 Jun 2026
Viewed by 408
Abstract
Background: Sepsis remains a leading cause of morbidity, mortality, and healthcare expenditure worldwide. Despite international guidelines and diagnostic criteria, real-world variability in coding, treatment, and outcomes persist. This retrospective study analyzed 13,994 coded sepsis-related hospitalizations identified through administrative ICD-9-CM algorithms between 2016 and [...] Read more.
Background: Sepsis remains a leading cause of morbidity, mortality, and healthcare expenditure worldwide. Despite international guidelines and diagnostic criteria, real-world variability in coding, treatment, and outcomes persist. This retrospective study analyzed 13,994 coded sepsis-related hospitalizations identified through administrative ICD-9-CM algorithms between 2016 and 2024 to evaluate the burden of sepsis, temporal trends, clinical outcomes, and healthcare costs within a regional health system. Methods: Hospitalization data across four local health authorities (ASL 201–204) over an 8-year period were analyzed. The coded sepsis cases were identified using validated ICD-9-CM-based algorithms and classified into four groups according to available microbiological coding: Gram-positive, Gram-negative, anaerobic and unspecified. Variables included patient demographics, length of stay, costs, outcomes (in-hospital and post-discharge mortality) and presence of septic shock. Comparative analyses were conducted using descriptive statistical methods and One-way ANOVA test and chi-squared tests were applied to evaluate the significance of differences. Multivariable logistic regression models were used to identify independent predictors of 6- and 12-month mortality. Results: The dataset included 13,994 coded sepsis-related hospitalizations, with the largest subgroup being ‘unspecified’ (48.0%). Among cases with specified etiology, coded anaerobic sepsis categories, though rare (0.7%), were associated with higher in-hospital mortality (45.5%) and economic burden (avg. € 8563). Mortality remained high at 6 and 12 months across all types, exceeding 50% post-discharge. Increasing age (OR ≈ 1.06 per year) and septic shock (OR ≈ 4.5–4.8) were the strongest independent predictors of mortality. Differences across microbiological groups should be interpreted cautiously given the high proportion of cases without organism-specific coding. Despite a modest reduction in mortality over time, sepsis was associated with persistently high 6- and 12-month mortality, highlighting a substantial long-term burden beyond the acute phase of illness. These findings suggest that sepsis-related hospitalizations are associated with substantial long-term mortality beyond the acute phase of illness. Discussion: These findings underscore the clinical and economic impact of sepsis in hospitalized patients, across microbiological coding categories. The high mortality rate at 6–12 months may support the need for further investigation into structured post-discharge follow-up strategies. Sepsis represents a substantial clinical and economic burden within the regional healthcare system, with persistently elevated short- and mid-term mortality. Incomplete organism-level documentation limits direct etiologic comparisons and highlights the need for improved integration between clinical, microbiological, and administrative data systems. Future research should integrate clinical variables and lab results to enable risk stratification and intervention planning. Full article
(This article belongs to the Special Issue From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms)
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12 pages, 249 KB  
Article
Evaluating the Impact of Filmarray Pneumonia Plus Panel in Therapeutic Decision-Making in Critical Patients with Suspected Respiratory Infection
by Rosa Latorre Ibars, Sulamita Carvalho-Brugger, Paula Rodríguez Ibáñez, Montserrat Vallverdú Vidal, Silvia Iglesias Moles, Mar Miralbés Torner, Alba Bellés Bellés, Andrea Castellano, David Campi, Jesús Caballero and José Javier Trujillano Cabello
Antibiotics 2026, 15(5), 521; https://doi.org/10.3390/antibiotics15050521 - 21 May 2026
Viewed by 540
Abstract
Background: Respiratory infections in critically ill patients remain a major challenge in intensive care units (ICUs), with high morbidity and mortality. Conventional microbiological methods often fail to identify the causative pathogen promptly, particularly in patients previously exposed to antibiotics. Multiplex molecular platforms, such [...] Read more.
Background: Respiratory infections in critically ill patients remain a major challenge in intensive care units (ICUs), with high morbidity and mortality. Conventional microbiological methods often fail to identify the causative pathogen promptly, particularly in patients previously exposed to antibiotics. Multiplex molecular platforms, such as the BioFire FilmArray® Pneumonia Panel Plus (FAPP), allow rapid detection of multiple respiratory pathogens and resistance markers, potentially improving early therapeutic decision-making. The objective of this work is to evaluate the impact of implementing FAPP on antimicrobial therapeutic decisions in critically ill patients with suspected respiratory infection. Methods: We conducted a retrospective cohort study in two mixed ICUs between 2023 and 2024. All respiratory samples in which FAPP was requested were analyzed. The results were compared with conventional cultures, and changes in antimicrobial therapy following the FAPP results were assessed, classified as escalation/initiation or de-escalation/discontinuation. Concordance between FAPP and culture was evaluated, and clinical and demographic variables were analyzed. Differences between groups were assessed using p-values obtained from the chi-square test or the Mann–Whitney test. Results: A total of 363 respiratory samples were included, 88.4% from mechanically ventilated patients. FAPP was positive in 65.3% of samples, whereas cultures were positive in 23.1%. Overall concordance between FAPP and culture was 57.3%. In 42.4% of cases, pathogens were detected exclusively by FAPP. Antimicrobial therapy was modified in 29.8% of patients, predominantly through de-escalation or discontinuation (69.4% of changes). Therapeutic modifications were more frequent in nosocomial infections and in patients with a positive FAPP result. Conclusions: The use of FAPP in critically ill patients with suspected respiratory infection provides rapid microbiological information that significantly influences antimicrobial decision-making, particularly by facilitating antibiotic de-escalation. Although discrepancies with conventional cultures remain and require careful clinical interpretation, FAPP represents a valuable tool for antimicrobial stewardship in the ICU setting. Full article
(This article belongs to the Special Issue From Epidemiology to Intervention: Addressing the Spread of Multidrug-Resistant Microorganisms)
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