Journal Description
Bacteria
Bacteria
is an international, peer-reviewed, open access journal on bacteriology published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus and other databases.
- Journal Rank: CiteScore - Q2 (Immunology and Microbiology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 25.4 days after submission; acceptance to publication is undertaken in 8.8 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Bacteria is a companion journal of Pathogens and Microorganisms.
Latest Articles
Gene Regulatory Network Inference Relating to Glycolysis in Escherichia coli with Causal Discovery Method Based on Machine Learning
Bacteria 2025, 4(4), 60; https://doi.org/10.3390/bacteria4040060 (registering DOI) - 13 Nov 2025
Abstract
Escherichia coli LS5218 is an attractive host for producing polyhydroxybutyrate. The strain, however, strongly requires heterologous gene expressions like phaC for efficient production. For enhancing the production, the whole gene expressions relating to end product-producing flow should be optimized so that not only
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Escherichia coli LS5218 is an attractive host for producing polyhydroxybutyrate. The strain, however, strongly requires heterologous gene expressions like phaC for efficient production. For enhancing the production, the whole gene expressions relating to end product-producing flow should be optimized so that not only heterologous induced-genes but also other relating genes are comprehensively analyzed on the transcription levels, resulting in normally time-consuming mutant-creation. Additionally, the explanation for each transcriptional relationship is likely to follow the relationships on known metabolic pathway map to limit the consideration. This study aimed to infer gene regulatory networks within glycolysis, a central metabolic pathway in LS5218, using machine learning-based causal discovery methods. To construct a directed acyclic graph representing the gene regulatory network, we employed the NOTEARS algorithm (Non-combinatorial Optimization via Trace Exponential and Augmented lagRangian for Structure learning). Using transcription data of 264 time-resolved sampling points, we inferred the gene regulatory network and identified several distal regulatory relationships. Notably, gapA, a key enzyme controlling the transition between the preparatory and rewarding phases in glycolysis, was found to influence pgi, the enzyme at the pathway’s entry point. These findings suggest that inferring such nonlocal regulatory interactions can provide valuable insights for guiding genetic engineering strategies.
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(This article belongs to the Topic Bioinformatics, Machine Learning and Risk Assessment in Food Industry)
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Open AccessArticle
Computational Analysis of the Effect of Dietary Interventions on the Gut Microbiome Composition in Parkinson’s Disease
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López Franyer, García Macias Adrian, Beltran Oscar, González Janneth and Pinzón Andrés
Bacteria 2025, 4(4), 59; https://doi.org/10.3390/bacteria4040059 - 3 Nov 2025
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Parkinson’s disease (PD) is a neurodegenerative disorder characterized by motor symptoms like tremor, rigidity, and bradykinesia. The WHO estimates that 10 million people currently have PD, with its prevalence expected to double to 20 million by 2050. Key risk factors include age, male
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Parkinson’s disease (PD) is a neurodegenerative disorder characterized by motor symptoms like tremor, rigidity, and bradykinesia. The WHO estimates that 10 million people currently have PD, with its prevalence expected to double to 20 million by 2050. Key risk factors include age, male sex, environmental contaminants, and family history. Emerging evidence links gut microbiota dysbiosis to PD, suggesting it contributes to neuroinflammation and disease progression, though the role of dietary interventions remains unclear. This study used computational simulations with genome-scale metabolic models (GEMs) to analyze how diet impacts the gut microbiota in PD patients. Fecal microbiota from PD patients and healthy controls were compared across three diets: high-fiber, Mediterranean, and vegan. Simulations revealed increased pro-inflammatory bacteria (e.g., Escherichia coli O157) in PD patients, likely due to reduced bacterial competition, alongside the decreased production of beneficial metabolites like butyrate, phenylalanine, and cysteine. The Mediterranean diet showed higher short-chain fatty acid production, potentially benefiting PD patients. These findings underscore the importance of dietary interventions in modulating the gut microbiome and suggest that targeted diets may complement PD therapies, improving patient outcomes.
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Open AccessBrief Report
RTGill-W1 Cells Response to Salmonella enterica Metabolites
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Abdulhusein Jawdhari, Robert Wolff, Bianca-Maria Tihăuan, Irina-Tania Ghitoc and Nicolae Crăciun
Bacteria 2025, 4(4), 58; https://doi.org/10.3390/bacteria4040058 - 2 Nov 2025
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This report investigates the interaction between the metabolites of the highly virulent bacteria Salmonella enterica and RTGill-W1 cells, a cell line derived from rainbow trout gills. As a facultative intracellular pathogen, Salmonella enterica infects both animals and humans through many routes. Upon entering
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This report investigates the interaction between the metabolites of the highly virulent bacteria Salmonella enterica and RTGill-W1 cells, a cell line derived from rainbow trout gills. As a facultative intracellular pathogen, Salmonella enterica infects both animals and humans through many routes. Upon entering an organism it can cause severe infection and pathology, which is also influenced by the bacterial metabolites. Although no intracellular presence of the pathogen in the exposed cell line could be detected, a dose-dependent effect of the metabolites on the cell line was observed, as exposure to 5%, 10%, and 20% concentrations led to enhanced metabolic activity and increased cytoplasmic neutral lipid droplets accumulation, whereas the lower dosage of 2.5% induced a lower metabolic rate compared to control and no significant intracellular lipid accumulation. The combination of all of the metabolites might be speculated to have increased the metabolic rate and lipid droplet production at higher concentrations due to possessing a growth factor or an endocrine effect, or as a response to a toxin. This paper may be the first report investigating the effect of a complete bacterial metabolite mixture in cultured cells.
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Open AccessArticle
Comparative Antimicrobial Effects of Dimethylsulfoxide and Dimethylsulfone on the Planktonic Growth and Viability of Porphyromonas gingivalis and Their Cytotoxic Effects on Human Oral Epithelial Cells
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Dominic L. Palazzolo, Andrea Jorratt, Deneil Patel, Makenna Hoover, Debasis Mondal, Maya Tabakha, Cathy Tran, Juliette R. Amram and Giancarlo A. Cuadra
Bacteria 2025, 4(4), 57; https://doi.org/10.3390/bacteria4040057 - 1 Nov 2025
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Background: Past studies have documented the antimicrobial effects of dimethyl sulfoxide (D.M.SO). However, the side effects and toxicity profiles of DMSO in vivo have been a significant deterrent for its wide-ranging clinical use. Dimethyl sulfone (DMSO-2), a natural metabolite of DMSO, is
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Background: Past studies have documented the antimicrobial effects of dimethyl sulfoxide (D.M.SO). However, the side effects and toxicity profiles of DMSO in vivo have been a significant deterrent for its wide-ranging clinical use. Dimethyl sulfone (DMSO-2), a natural metabolite of DMSO, is currently used as a safe dietary supplement due to its antioxidant properties and multimodal mechanisms of action. While DMSO displays antimicrobial activity, little is known concerning DMSO-2’s antimicrobial effect. Thus, this investigation compares the antimicrobial effects of DMSO and DMSO-2 on the growth and viability of the pathogenic anaerobic bacteria, Porphyromonas gingivalis, and their cytotoxic effect on human oral epithelial (OKF6/TERT-2) cells. Methods: P. gingivalis was grown in TSBY media in the presence of DMSO or DMSO-2 (0–4%) for planktonic growth and viability determinations. OKF6/TERT-2 cells were expanded in vitro and similarly exposed to DMSO or DMSO-2 for viability studies. Results: After 24 h exposure to DMSO or DMSO-2, growth of P. gingivalis is inhibited by 57% and 77%, respectively, while viability is inhibited by 55% and 62%. In contrast, 24 h exposure to similar concentrations of DMSO or DMSO-2 induces 5% and 2% cytotoxicity in OKF6/TERT-2 cells, respectively. Conclusions: Both DMSO and DMSO-2 inhibit the growth and viability of P. gingivalis but show minimal toxic effect on OKF6/TERT-2 cells. Therefore, the utility of these two natural compounds as antimicrobial agents against anaerobic pathogens should be further investigated.
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Open AccessArticle
Dual Action of Bacillus and Lactobacillus spp.: Promoting Bean Cultivar Development and Suppressing Xanthomonas axonopodis pv. phaseoli
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Ibrahim Isse Ali and Kubilay Kurtulus Bastas
Bacteria 2025, 4(4), 56; https://doi.org/10.3390/bacteria4040056 - 1 Nov 2025
Abstract
Common bacterial blight (CBB) is a significant disease caused by the seed-borne pathogen Xanthomonas axonopodis pv. phaseoli (Xap), which devastates global bean production. This study evaluated the effects of Bacillus subtilis (Bst26), Lactobacillus plantarum (Lpkb10), their combination (Bst26 + Lpkb10), copper hydroxide (CH),
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Common bacterial blight (CBB) is a significant disease caused by the seed-borne pathogen Xanthomonas axonopodis pv. phaseoli (Xap), which devastates global bean production. This study evaluated the effects of Bacillus subtilis (Bst26), Lactobacillus plantarum (Lpkb10), their combination (Bst26 + Lpkb10), copper hydroxide (CH), and an untreated control on controlling CBB in three bean cultivars (Göynük, Saltan, and Tezgeldi). Disease incidence (CI), disease severity index (DSI), severity score (SC), area under disease progress curve (AUDPC), and disease control (DC), along with agronomic traits such as plant height, number of primary branches, root length, and fresh root weight, were recorded to assess both infection rates and plant health under each treatment. The findings revealed significant differences in DI, DSI, SC, AUDPC, and DC (p ≤ 0.01) among the bean cultivars for CBB. Among the cultivars, the Bst26 treatment and the combination of Bst26 and Lpkb10 showed the highest control effectiveness, with DI values of 33.11% and 33.46% in Saltan, 35.65% and 44.16% in Göynük, and 37.71% and 42.43% in Tezgeldi, respectively, at 21 days after inoculation (DAI). Bst26 alone and in combination with Lpkb10 effectively controlled CBB, with disease reduction of 56.80% and 46.49% in Göynük, 57.08% and 56.62% in Saltan, and 52.18% and 46.19% in Tezgeldi, respectively. Disease progression was highest in the untreated control, with DI ranging from 77.15% to 82.54% across Göynük, Saltan, and Tezgeldi cultivars. Significant differences (p ≤ 0.01) in plant height, root length, and root weight were observed among treatments and cultivars. Disease parameters were negatively correlated with plant growth traits, and multi-treatment analysis demonstrated that combining bacterial strains effectively reduced disease severity in susceptible cultivars, highlighting their potential for improved CBB management.
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(This article belongs to the Special Issue New Insights into Microbial Biocontrol: Strategies for Sustainable Aquaculture and Agriculture)
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Open AccessArticle
Genomic Mapping of Brazilian Escherichia coli: Characterizing Shiga Toxin-Producing, Enteropathogenic, and Diffusely Adherent Strains Using an In Silico Approach
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Vinicius Silva Castro, Emmanuel W. Bumunang, Kim Stanford and Eduardo Eustáquio de Souza Figueiredo
Bacteria 2025, 4(4), 55; https://doi.org/10.3390/bacteria4040055 - 26 Oct 2025
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Background: Diarrheagenic Escherichia coli (DEC) remains relevant to public health and agri-food chains. The context in Brazil, as a major food producer and exporter, reinforces the need for genomic surveillance. Objective: We aimed to characterize Brazilian diffusely adhering (DAEC), enteropathogenic (EPEC), and
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Background: Diarrheagenic Escherichia coli (DEC) remains relevant to public health and agri-food chains. The context in Brazil, as a major food producer and exporter, reinforces the need for genomic surveillance. Objective: We aimed to characterize Brazilian diffusely adhering (DAEC), enteropathogenic (EPEC), and Shiga toxin-producing E. coli (STEC) sequences in silico across O-serogroups, in addition to sequence-type (ST), virulence, resistome, and phylogenomic relationships. Methodology: We retrieved 973 genomes assigned to Brazil from NCBI Pathogen Detection Database and performed virtual-PCR screening for key DEC-genes. We then typed O-serogroups (ABRicate/EcOH), Multi-Locus Sequencing Type (MLST), virulome (Ecoli_VF), resistome (ResFinder), and characterized stx genes. Results: DEC represented 18.7% of genomes, driven primarily by EPEC. In EPEC, the eae β-1 subtype was most common; we detected, for the first time in Brazilian sequences, ξ-eae subtype and ST583/ST301. Seventy-eight percent of DAEC isolates were multidrug-resistant (MDR), and two ST were newly reported in the country (ST2141/ST500). In STEC, O157 formed a largely susceptible clade with uniform eae γ-1, whereas 57% of non-O157 were MDR. New STs (ST32/ST1804) were observed, and three genomes were closely related to international isolates. Conclusions: Despite the low DEC representation in the dataset, new STs and eae subtypes were detected in Brazil. Also, MDR in DAEC and non-O157 STEC reinforces the need for antimicrobial-resistance genomic surveillance.
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Open AccessBrief Report
Community Surveillance of MRSA and Staphylococcus aureus in Rural Portugal: The BI-STAPH Project—Phase 1: Sertã
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Ainhoa Cordero, Francisco Ferreira, Patrícia Coelho, João Belo, João Metello, Carina Santos, Sónia Mateus, Miguel Castelo-Branco and Francisco José Barbas Rodrigues
Bacteria 2025, 4(4), 54; https://doi.org/10.3390/bacteria4040054 - 13 Oct 2025
Abstract
Introduction: Colonization by Staphylococcus aureus—including methicillin-resistant strains (MRSA)—represents a growing public health concern, particularly in community and rural settings. In Portugal, limited data are available regarding its prevalence in populations with agricultural or animal-related exposures. Objectives: To determine the prevalence of S.
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Introduction: Colonization by Staphylococcus aureus—including methicillin-resistant strains (MRSA)—represents a growing public health concern, particularly in community and rural settings. In Portugal, limited data are available regarding its prevalence in populations with agricultural or animal-related exposures. Objectives: To determine the prevalence of S. aureus and MRSA nasal colonization among adults residing in the municipality of Sertã, Portugal, and to explore potential sociodemographic and behavioral factors associated with colonization. Methods: A cross-sectional study was conducted with 292 adult participants from multiple parishes of Sertã. Nasal swabs were collected for microbiological identification of S. aureus and MRSA. Data on sociodemographic characteristics, occupational exposure, animal contact, and recent antibiotic use were collected via structured questionnaires. Descriptive statistics and inferential analyses (chi-square and Fisher’s exact tests) were performed, and odds ratios were estimated. Results: The overall prevalence of S. aureus colonization was 19.9% (58/292), with MRSA detected in 4.8% (14/292) of participants, representing 24.1% of all S. aureus carriers. Colonization by S. aureus was slightly more frequent among females (51.7%) and predominantly observed in individuals aged 35–59 years. MRSA was more frequent in participants aged ≥ 60 years and was equally distributed between sexes. 57% of MRSA cases reported recent antibiotic use and all MRSA cases reported daily contact with animals—primarily domestic species. No statistically significant associations were identified between colonization and the analyzed variables, although trends suggested increased risk among individuals with animal contact and moderate to high-risk occupations. Conclusions: This study revealed a notable prevalence of S. aureus and MRSA colonization in a rural Portuguese population. Although no statistically significant associations were found, with animal contact, occupational exposure, and recent antibiotic use emerged as relevant epidemiological factors. These findings highlight the need for strengthened surveillance and further investigation into zoonotic transmission and occupational risk in rural environments.
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Open AccessCommunication
Survival of Pathogenic Escherichia coli Strains in Sand Subjected to Desiccation
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Rocío de la Cuesta, Mariana S. Sanin, Florencia Battaglia, Sandra L. Vasquez Pinochet, Cecilia C. Cundon, Adriana B. Bentancor, María P. Bonino and Ximena Blanco Crivelli
Bacteria 2025, 4(4), 53; https://doi.org/10.3390/bacteria4040053 - 2 Oct 2025
Abstract
Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are E. coli pathovars of particular relevance to infant health. While the intestinal tract of humans and animals constitutes their primary habitat, these bacteria can also persist in natural environments such as sand.
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Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are E. coli pathovars of particular relevance to infant health. While the intestinal tract of humans and animals constitutes their primary habitat, these bacteria can also persist in natural environments such as sand. The aim of this study was to evaluate the persistence of STEC and EPEC strains in sand microcosms under controlled conditions of heat and desiccation in order to estimate their viability in this matrix and provide evidence regarding the potential risks associated with the use of sandboxes in public spaces. The study included STEC strains belonging to clinically important serotypes (O26:H11, O103:H2, O111:H8, O121:H19, O145:NM, O157:H7 and O174:H28), animal-derived EPEC strains, and a non-pathogenic E. coli strain (NCTC 12900). The strains were inoculated into sterile sand microcosms and maintained at 37 °C. Death curves, persistence in the matrix, presence of virulence genes, and ability to produce biofilm were evaluated. The death and persistence curves varied by serotype; some strains remained viable in the viable but non-culturable state for extended periods. All strains retained their virulence-associated genetic markers throughout the assays. None of the STEC strains was classified as a biofilm producer under the experimental conditions, whereas the two EPEC strains were identified as weak and moderate biofilm producers. However, no association was found between biofilm formation and persistence in the matrix. The findings provide an initial approach and provide relevant evidence of the capacity of STEC and EPEC strains to survive in sand, which could represent a potential risk in recreational environments.
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Open AccessArticle
Shiga Toxin Genes Detected in Fecal Samples of Illinois Finisher Pigs
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Kathryn L. Lauder, Shafiullah M. Parvej, Yiyang Shen, Chongyang Zhang, Jehadi Osei-Bonsu, James F. Lowe and Weiping Zhang
Bacteria 2025, 4(4), 52; https://doi.org/10.3390/bacteria4040052 - 2 Oct 2025
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(1) Background: Pigs can be another host of Shiga toxin-producing E. coli (STEC), suggesting that pork products could be a potential risk to public health. A USDA National Animal Health Monitoring System (NAHMS) study revealed that Shiga toxin genes were detected in more
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(1) Background: Pigs can be another host of Shiga toxin-producing E. coli (STEC), suggesting that pork products could be a potential risk to public health. A USDA National Animal Health Monitoring System (NAHMS) study revealed that Shiga toxin genes were detected in more than half of samples nationwide but only about a quarter of samples from the state of Illinois. To characterize the presence of STEC in Illinois pigs better and to explore the discrepancy between Illinois and other swine-producing states, we increased the sampling size and collected samples in different regions of the state and in different months to detect Shiga toxin genes in Illinois finisher pigs and subtyped the Shiga toxin genes further to assess any potential risk of STEC originating from Illinois pigs to human health. (2) Methods: Fecal samples were collected from 471 Illinois finisher pigs at different locations from October 2021 to September 2022. DNA samples were extracted from individual fecal samples and PCR-tested for Shiga toxin genes (stx1, stx2) and then toxin subtypes (stx2a, stx2c, stx2d, and stx2e). (3) Results: The data showed that the stx2 gene was detected in 61% of the fecal samples (285/471), whereas stx1 was detected only in 0.4% of the samples (2/471). The data also indicated a lower prevalence of stx genes in the samples collected in certain cold months (36% in October and 19% in March) compared to that in those from warm months (56% to 100% from April to September). Stx2d, a subtype associated with severe human illness, was detected in 2% of the samples (10/471); in contrast, stx2e, which is expressed by E. coli strains causing diarrhea and edema disease in pigs, was the most detected (49%; 229/471). (4) Conclusions: The high prevalence of Shiga toxin genes in the fecal samples from Illinois finisher pigs suggests that Stx-positive E. coli strains circulate in Illinois pig farms. However, the highly detected stx2e-positive STEC (or enterotoxigenic E. coli, ETEC) strains are associated with diarrhea and edema disease in pigs, indicating the need for disease prevention or control for pigs but unlikely a safety concern for Illinois pork products or a major risk of human illnesses.
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Open AccessArticle
Antitumor Potential of Bioactive Crude Extracts Derived from Actinomycetes
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Hassan K. Dhaini, Bahaa Fahed Hassanieh, Rana El Hajj and Mahmoud I. Khalil
Bacteria 2025, 4(4), 51; https://doi.org/10.3390/bacteria4040051 - 1 Oct 2025
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Marine actinomycetes constitute a vigorous source of bioactive compounds with potential anti-tumor activity. This study investigates the antitumor activity and classification of actinomycetes isolated from 32 marine soil samples collected across four seasons from Tyr City Beach, Lebanon. A total of 80 morphologically
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Marine actinomycetes constitute a vigorous source of bioactive compounds with potential anti-tumor activity. This study investigates the antitumor activity and classification of actinomycetes isolated from 32 marine soil samples collected across four seasons from Tyr City Beach, Lebanon. A total of 80 morphologically diverse isolates were recovered and characterized, with dominant genera including Streptomyces, Kocuria, and Micrococcus. Among these, three promising strains—Kocuria rosea, Micrococcus luteus, and Streptomyces longisporoflavus—were selected for further analysis. Crude extracts were tested against human colorectal adenocarcinoma (Caco-2) and human hepatocellular carcinoma (HepG-2) cancer cell lines using MTT and Western blot assays. At the highest concentration (8 µg/µL), the extracts reduced cell viability to 24–37% in Caco-2 and 12–25% in HepG-2. The IC50 values ranged from 1.72 to 3.53 µg/µL, depending on the extract and cell line. Western blot analysis showed dose-dependent increases in the Bax/Bcl-2 ratio, with fold changes reaching 4.35 (Kocuria), 11.39 (Micrococcus), and 14.25 (Streptomyces) in HepG-2 cells. The p53 protein expression also increased significantly, with fold changes up to 7.79 in Caco-2 and 3.0 in HepG-2 cells. These results indicate that marine actinomycetes from the Lebanese coastline hold strong potential as a source of antitumor agents targeting apoptosis pathways.
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Open AccessReview
Beyond Genes: Non-Canonical Mechanisms Driving Antimicrobial Resistance in Bacteria
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Leonard Koolman, Chijioke Emenike, Debasis Mitra and Sourav Chattaraj
Bacteria 2025, 4(4), 50; https://doi.org/10.3390/bacteria4040050 - 1 Oct 2025
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Antimicrobial resistance (AMR) is traditionally discussed in the context of horizontally acquired resistance genes and point mutations at target loci. However, this gene-centred model fails to account for a large number of clinically important modalities of resistance. There is now substantial evidence implicating
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Antimicrobial resistance (AMR) is traditionally discussed in the context of horizontally acquired resistance genes and point mutations at target loci. However, this gene-centred model fails to account for a large number of clinically important modalities of resistance. There is now substantial evidence implicating bacteria in the ability to escape the effects of antibiotics in a variety of non-canonical ways, which are not considered in traditional diagnostic and surveillance pipelines. Among these factors, we can list those arising from global regulatory networks, phase variability, epigenetic tuning, small RNAs, genome structural variability, and phenotypic states like tolerance and persistence. This review will blend the current knowledge on these alternative pathways of resistance and underscore how they intersect with canonical genetic determinants. We will highlight cases where resistance emerges in the absence of known resistance genes, analyse the role of regulatory plasticity in efflux pump expression and membrane remodelling, and examine the contributions of bacterial stress responses and post-transcriptional control. Additionally, we will address methodological gaps in the detection of these mechanisms and their implications for clinical treatment failure, resistance surveillance, and drug development. By integrating insights from molecular microbiology, systems biology, and genomics, this review aims to offer a framework for understanding AMR as a multifaceted, context-dependent phenotype, not merely a genotype. We conclude by identifying knowledge gaps and suggesting priorities for research and diagnostic innovation in this evolving field.
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Open AccessReview
Bacterial Biosurfactants as Bioactive Ingredients: Surfactin’s Role in Food Preservation, Functional Foods, and Human Health
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Zainab Hussain Abdul Wahab and Shayma Thyab Gddoa Al-Sahlany
Bacteria 2025, 4(4), 49; https://doi.org/10.3390/bacteria4040049 - 25 Sep 2025
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Biosurfactants are amphiphilic compounds synthesized by microorganisms, providing environmentally sustainable alternatives to synthetic surfactants owing to their biodegradability and minimal toxicity. This review examines bacterial origins of biosurfactants, with a focus on surfactin derived from Bacillus species including B. subtilis, B. amyloliquefaciens
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Biosurfactants are amphiphilic compounds synthesized by microorganisms, providing environmentally sustainable alternatives to synthetic surfactants owing to their biodegradability and minimal toxicity. This review examines bacterial origins of biosurfactants, with a focus on surfactin derived from Bacillus species including B. subtilis, B. amyloliquefaciens, B. licheniformis, and B. pumilus. The cyclic lipopeptide structure of surfactin, which consists of a heptapeptide attached to a β-hydroxy fatty acid chain, imparts remarkable surface-active characteristics, such as a reduced surface tension of 27 mN/m and a low critical micelle concentration of 20 µM. In medical applications, surfactin demonstrates antimicrobial, antiviral, and anticancer properties through mechanisms such as apoptosis induction and metastasis inhibition, as well as promoting wound healing by enhancing angiogenesis and decreasing fibrosis. In the realm of food processing, it functions as a natural antimicrobial agent against pathogens such as Listeria and Salmonella, improves emulsion stability in products like mayonnaise, prolongs shelf life, and influences gut microbiota composition. The safety profiles correspond with the Generally Recognized as Safe (GRAS) status for compounds derived from Bacillus; however, it is essential to optimize dosing to reduce the risks associated with hemolysis. Challenges encompass production expenses, scalability issues, and regulatory obstacles, with genetic engineering suggested as a means to achieve improved yields. Surfactin demonstrates potential as a sustainable bioactive component within the food and health industries.
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Open AccessArticle
Characterization and Biological Activity of Magnesium Nanoparticles Synthesized from Escherichia coli Metabolites Against Multidrug-Resistant Bacteria
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Malak Mezher, Salma Khazaal, Mahmoud I. Khalil, Dalia El Badan and Taymour A. Hamdalla
Bacteria 2025, 4(3), 48; https://doi.org/10.3390/bacteria4030048 - 10 Sep 2025
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(1) Background: This study evaluated the efficacy of magnesium nanoparticles (MgNPs) synthesized through a green method utilizing bacterial metabolites (BMs) produced by Escherichia coli. (2) Methods: BMs were tested for total phenolic content by high-performance liquid chromatography. MgNPs were characterized by X-ray
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(1) Background: This study evaluated the efficacy of magnesium nanoparticles (MgNPs) synthesized through a green method utilizing bacterial metabolites (BMs) produced by Escherichia coli. (2) Methods: BMs were tested for total phenolic content by high-performance liquid chromatography. MgNPs were characterized by X-ray diffraction, transmission electron microscopy, Fourier transform infrared spectroscopy, photoluminescence, and ultraviolet–visible spectroscopy. MgNPs and BMs were tested for antibacterial and antibiofilm potentials against multidrug-resistant clinical isolates by agar well diffusion, minimum inhibitory and bactericidal concentration assays, time–kill test, and inhibition of biofilm formation and destruction of pre-formed biofilm assays. Furthermore, they were tested for antioxidant potential by 2,2-diphenyl-1-picryhydrazyl radical scavenging assay. (3) Results: BMs included carbohydrates, reducing sugars, and phenols (gallic acid and catechin) with a total phenolic content of 0.024 mg GAE/g. MgNPs showed a pure crystalline structure with a spherical shape, 17.8 nm in size, and a 4.19 eV energy gap. Bacteria included Streptococcus pneumonia, Enterococcus faecium, Klebsiella pneumonia, and Salmonella Typhimurium. The antibacterial results showed inhibition zones ranging between 7.2 and 10.4 mm, a bactericidal effect of MgNPs, a bacteriostatic effect of BMs, and growth inhibition after 3 h. The antibiofilm results demonstrated significant inhibition of biofilm formation (inhibition percentages of 64.931% for MgNPs and 71.407% for BMs). However, the assays revealed modest biofilm destruction (eradication percentages of 48.667% for MgNPs and 37.730% for BMs). Antioxidant capacity revealed notable scavenging activity of MgNPs (scavenging activity of 41.482%) and weak activity of BMs (scavenging activity of 16.460%). (4) Conclusions: These findings support the application of MgNPs in biomedical fields.
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Open AccessArticle
Humoral Immune Activation Against Mycobacterium avium subsp. paratuberculosis Through Oral Immunization with Engineered Salmonella
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Azar Motamedi Boroojeni, Nikoo Veiskarami, Elena Rita Simula, Leonardo Antonio Sechi and Abdollah Derakhshandeh
Bacteria 2025, 4(3), 47; https://doi.org/10.3390/bacteria4030047 - 8 Sep 2025
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Attenuated Salmonella strains offer an opportunity for delivering DNA vaccines to antigen-presenting cells. DNA vaccines trigger cellular immune responses, making them suitable for targeting intracellular pathogens, such as Mycobacterium avium subspecies paratuberculosis (MAP). Since whole organism MAP vaccines interfere with tuberculosis diagnosis, innovative
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Attenuated Salmonella strains offer an opportunity for delivering DNA vaccines to antigen-presenting cells. DNA vaccines trigger cellular immune responses, making them suitable for targeting intracellular pathogens, such as Mycobacterium avium subspecies paratuberculosis (MAP). Since whole organism MAP vaccines interfere with tuberculosis diagnosis, innovative vaccine technologies have been introduced to elicit an immune response targeting species-specific antigens. Fibronectin attachment protein (FAP), a MAP surface antigen that is species-specific, can induce cellular immune responses. The present study aims to explore the immunogenic potential of a mammalian expression plasmid encoding the fap-P gene of MAP within a mouse model, utilizing a Salmonella vector for oral immunization using a fluorescent assay and Western blot analysis. The results proved the ability of the constructed plasmid to stimulate the humoral immune response in mice. Moreover, fluorescence microscopy of splenocytes confirmed the successful delivery of the plasmid to the immune system at 24, 48, and 72 h following oral administration. It can be concluded that FAP-P could be considered a candidate for further investigation in the context of MAP vaccine development. Additionally, the use of Salmonella as a delivery system not only improves the efficacy of DNA vaccines but also helps in the preliminary evaluation of the antigens’ immunogenic properties.
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Open AccessSystematic Review
Biotechnological Innovations to Combat Antimicrobial Resistance and Advance Global Health Equity
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Sima Rugarabamu and Gaspary Mwanyika
Bacteria 2025, 4(3), 46; https://doi.org/10.3390/bacteria4030046 - 5 Sep 2025
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Antimicrobial resistance (AMR) is a growing global health emergency that threatens the effectiveness of modern medicine, exacerbating healthcare costs, morbidity, and mortality, particularly in low- and middle-income countries (LMICs). Traditional approaches to antimicrobial development and stewardship have proven inadequate in curbing the rapid
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Antimicrobial resistance (AMR) is a growing global health emergency that threatens the effectiveness of modern medicine, exacerbating healthcare costs, morbidity, and mortality, particularly in low- and middle-income countries (LMICs). Traditional approaches to antimicrobial development and stewardship have proven inadequate in curbing the rapid emergence and spread of resistant pathogens. This review explores cutting-edge biotechnological innovations as sustainable, precision-based solutions to combat AMR and promote global health equity. A comprehensive narrative review was conducted using literature published between 2018 and 2023 from PubMed, ScienceDirect, and Web of Science. Peer-reviewed studies focusing on novel antimicrobial strategies were thematically analyzed, with attention to efficacy, feasibility, and translational readiness. Key innovations identified include nanotechnology-enhanced antimicrobial delivery, bacteriophage therapy, CRISPR-Cas gene editing, immunotherapy, and personalized medicine. These strategies demonstrated substantial in vitro and in vivo efficacy, such as >90% MRSA biofilm reduction via silver nanoparticles and 95% carbapenem susceptibility restoration in E. coli using CRISPR-Cas9. When integrated with machine learning and rapid diagnostics, these approaches enable precision-targeted therapies and data-informed stewardship, offering scalable solutions adaptable to diverse healthcare systems. Antimicrobial resistance demands urgent, equitable innovation. Integrating biotechnologies like CRISPR, phage therapy, and nanomedicine with data-driven tools offers promising solutions. To ensure real-world impact, we recommend establishing regionally tailored translational research platforms and public–private partnerships as the most effective strategy to scale innovations and strengthen AMR response in low-resource settings.
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Open AccessFeature PaperArticle
Machine Learning-Powered ATR-FTIR Spectroscopic Clinical Evaluation for Rapid Typing of Salmonella enterica O-Serogroups and Salmonella Typhi
by
Cesira Giordano, Francesca Del Conte, Maira Napoleoni and Simona Barnini
Bacteria 2025, 4(3), 45; https://doi.org/10.3390/bacteria4030045 - 2 Sep 2025
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Clinical manifestations of salmonellosis in humans typically include acute gastroenteritis, abdominal pain, diarrhea, nausea, and fever. Diarrhea and anorexia may persist for several days. In some cases, the organisms may invade the intestinal mucosa and cause septicemia, even in the absence of significant
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Clinical manifestations of salmonellosis in humans typically include acute gastroenteritis, abdominal pain, diarrhea, nausea, and fever. Diarrhea and anorexia may persist for several days. In some cases, the organisms may invade the intestinal mucosa and cause septicemia, even in the absence of significant gastrointestinal symptoms. Most clinical signs are attributed to hematogenous dissemination of the pathogen. As with other microbial infections, disease severity is influenced by the serotype of the organism, bacterial load, and host susceptibility. Serotyping analysis of Salmonella spp. using the White–Kauffmann–Le Minor scheme remains the gold standard for strain typing. However, this method is expensive, time-consuming, and requires significant expertise and visual interpretation by trained personnel, which is why it is typically restricted to regional or national reference laboratories. In this study, we evaluated a spectroscopic technique coupled with chemometrics and multivariate machine learning algorithms for its ability to discriminate the main Salmonella spp. serogroups in a clinical routine setting. We analyzed 95 isolates of Salmonella that were randomly selected, including four strains of S. Typhi. The I-dOne Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) system (Alifax S.r.l., Polverara, Italy) also shows promising potential for distinguishing Salmonella Typhi within the D serogroup. The I-dOne system enables simultaneous identification of both species and subspecies using the same workflow and instrumentation, thus streamlining the diagnostic process.
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Open AccessReview
Biodegradation of Petrochemical Plastics by Microorganisms: Toward Sustainable Solutions for Plastic Pollution
by
Luis Getino, José Antonio Revilla-Gómez, Luisa María Ariza-Carmona, Sofie Thijs, Claude Didierjean and Alejandro Chamizo-Ampudia
Bacteria 2025, 4(3), 44; https://doi.org/10.3390/bacteria4030044 - 1 Sep 2025
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Plastic pollution has emerged as a critical environmental challenge due to the widespread accumulation of petrochemical plastics in natural ecosystems. Conventional waste management strategies, including mechanical recycling and incineration, have demonstrated limited efficiency in addressing the persistence of plastics such as polyethylene, polypropylene,
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Plastic pollution has emerged as a critical environmental challenge due to the widespread accumulation of petrochemical plastics in natural ecosystems. Conventional waste management strategies, including mechanical recycling and incineration, have demonstrated limited efficiency in addressing the persistence of plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride. While incineration eliminates plastic material, it does not promote circularity and may generate toxic emissions. As a sustainable alternative, microbial biodegradation involves bacteria, fungi, and actinomycetes capable of degrading synthetic polymers through enzymatic processes. This review provides a comprehensive overview of microbial degradation of major plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride, highlighting key strains, degradation rates, and enzymatic mechanisms. Importantly, biodegradation research also informs the development of in situ remediation technologies and supports new recycling strategies. Advances in protein engineering and synthetic biology are discussed for enhancing degradation efficiency. However, scaling biodegradation to environmental conditions remains challenging due to variable temperature, pH, microbial competition, and potentially toxic intermediates. Despite these limitations, microbial biodegradation represents a promising ecofriendly approach to address plastic waste and promote a biobased circular economy. Future work should integrate microbial processes into existing recycling infrastructure and design robust consortia guided by omics tools.
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Open AccessArticle
Genetic Characterization of Salmonella and Analysis of Ciprofloxacin Resistance Using Sanger Technique in Romania, 2024
by
Elena Roxana Buzilă, Raluca Gatej, Cristina Trifan, Teodora Vremera, Mihaela Leustean, Adina David, Daniela Cosmina Bosogea, Georgiana Barbu, Adina Gatea, Ciprian Ilie and Luminița Smaranda Iancu
Bacteria 2025, 4(3), 43; https://doi.org/10.3390/bacteria4030043 - 1 Sep 2025
Abstract
Salmonella is a major foodborne pathogen, representing a significant public health concern across the European Union (EU), accounting for 39% of foodborne illness-related hospitalizations in 2022, with the highest rates observed in Romania, Cyprus, Greece, and Lithuania. This pilot study aimed to enhance
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Salmonella is a major foodborne pathogen, representing a significant public health concern across the European Union (EU), accounting for 39% of foodborne illness-related hospitalizations in 2022, with the highest rates observed in Romania, Cyprus, Greece, and Lithuania. This pilot study aimed to enhance the surveillance and characterization of Salmonella by implementing both phenotypic and genotypic methods for strain typing, as well as for the detection and confirmation of resistance to ciprofloxacin. Materials and methods: A total of 109 Salmonella strains from acute diarrheal cases in North-Eastern Romania were collected (January–August 2024). From these, 19 representative isolates were selected for molecular characterization, including Multi-Locus Sequence Typing (MLST) and the detection of ciprofloxacin resistance determinants. Whole-Genome Sequencing (WGS) was subsequently performed to confirm serotype identity and resistance markers. Results: The 19 isolates underwent Multi-Locus Sequence Typing (MLST) and ciprofloxacin resistance profiling, with Whole-Genome Sequencing (WGS) for confirmation. MLST identified S. Enteritidis (42.1%) as the predominant serotype, followed by S. Typhimurium, S. Livingstone, and S. Infantis. WGS confirmed serotypes in 15 isolates; 2 showed discrepancies with phenotypic results. Phenotypic resistance to ciprofloxacin was detected in 12/19 (63.2%) of the isolates, 6/12 presenting gyrA mutations (S83Y, D87G), and 2/12 strains presenting the plasmid-mediated qnrB19 gene.
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Open AccessHypothesis
POLETicians in the Mud: Preprokaryotic Organismal Lifeforms Existing Today (POLET) Hypothesis
by
Douglas M. Ruden and Glen Ray Hood
Bacteria 2025, 4(3), 42; https://doi.org/10.3390/bacteria4030042 - 29 Aug 2025
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The discovery of Asgard archaea has reshaped our understanding of eukaryotic origins, supporting a two-domain tree of life in which eukaryotes emerged from Archaea. Building on this revised framework, we propose the Pre-prokaryotic Organismal Lifeforms Existing Today (POLET) hypothesis, which suggests that relic
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The discovery of Asgard archaea has reshaped our understanding of eukaryotic origins, supporting a two-domain tree of life in which eukaryotes emerged from Archaea. Building on this revised framework, we propose the Pre-prokaryotic Organismal Lifeforms Existing Today (POLET) hypothesis, which suggests that relic pre-prokaryotic life forms—termed POLETicians—may persist in deep, anoxic, energy-limited environments. These organisms could represent a living bridge to the RNA world and other origin-of-life models, utilizing racemic oligoribonucleotides and peptides, non-enzymatic catalysis, and mineral-assisted compartmentalization. POLETicians might instead rely on radical-based redox chemistry or radiolysis for energy and maintenance. These biomolecules may be racemic or noncanonical, eluding conventional detection. New detection methods are required to determine such life. We propose generalized nanopore sequencing of any linear polymer—including mirror RNAs, mirror DNAs, or any novel genetic material—as a potential strategy to overcome chirality bias in modern sequencing technologies. These approaches, combined with chiral mass spectrometry and stereoisomer-resolved analytics, may enable the detection of molecular signatures from non-phylogenetic primitive lineages. POLETicians challenge the assumption that all life must follow familiar biochemical constraints and offer a compelling extension to our search for both ancient and extant forms of life hidden within Earth’s most extreme environments.
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Open AccessArticle
Prevalence, Antimicrobial Resistance Profiles, and Risk Factors Analysis of Campylobacter spp. from Dogs in Kelantan, Malaysia
by
Chinedu Amaeze Frank, Mohammed Dauda Goni, Nor Fadhilah Kamaruzzaman, Hafeez A. Afolabi, Mohammed S. Gaddafi, Aliyu Yakubu and Shamsaldeen Ibrahim Saeed
Bacteria 2025, 4(3), 41; https://doi.org/10.3390/bacteria4030041 - 8 Aug 2025
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Background: Campylobacter represents a significant global public health threat, with rising prevalence and increasing concern over antimicrobial resistance (AMR). This study aims to assess the prevalence, evaluate the antimicrobial resistance profiles, and identify risk factors associated with infection in dogs from Kelantan,
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Background: Campylobacter represents a significant global public health threat, with rising prevalence and increasing concern over antimicrobial resistance (AMR). This study aims to assess the prevalence, evaluate the antimicrobial resistance profiles, and identify risk factors associated with infection in dogs from Kelantan, Malaysia. To the best of our knowledge, this is the first comprehensive investigation of Campylobacter spp. in dogs within this region. Methods: Campylobacter was isolated from rectal swabs of 50 dogs using modified charcoal cefoperazone deoxycholate agar (mCCDA) and confirmed biochemically, with Campylobacter identified via polymerase chain reaction (PCR). Antimicrobial resistance profile of the isolates was determined using the Kirby–Bauer disk diffusion method. Data on risk factors were assessed through a semi-structured questionnaire. Results: The results revealed an overall prevalence of Campylobacter spp. 28.0% (14/50) in dogs. C. helveticus was the predominant species in dogs (40.7%). The resistance rates of Campylobacter isolates showed notable resistance to ampicillin (85.71%), amoxicillin (71.43%), erythromycin (64.29%), tetracycline (57.14%), and sulfonamides (50%), respectively. Overall, multiple antimicrobial resistance (MAR) indices for all Campylobacter isolates were consistently above the 0.2 threshold, signifying multidrug resistance. Risk factors such as dogs that are semi-roamers and those fed homemade /raw feed were found to be associated with higher risk of Campylobacter (odds ratios: 1.180, p-value = 0.025 semi-roamers; odds ratio: 1.196, p-value = 0.019 fed homemade/raw feed). Conclusions: This study reveals significant prevalence and a remarkable antimicrobial resistance profile, thus advocating the need for improved pet management, responsible antimicrobial use, and targeted interventions to mitigate the spread of multidrug-resistant Campylobacter in companion animals.
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