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14 pages, 3747 KiB  
Article
Biocontrol Activity of Volatile Organic Compounds Emitted from Bacillus paralicheniformis 2-12 Against Fusarium oxysporum Associated with Astragalus membranaceus Root Rot
by Yan Wang, Jiaqi Yuan, Rui Zhao, Shengnan Yuan, Yaxin Su, Wenhui Jiao, Xinyu Huo, Meiqin Wang, Weixin Fan and Chunwei Wang
Microorganisms 2025, 13(8), 1782; https://doi.org/10.3390/microorganisms13081782 - 31 Jul 2025
Viewed by 254
Abstract
Root rot, mainly caused by Fusarium oxysporum, is one of the most destructive diseases and leads to significant economic loss of Astragalus membranaceus. To develop an effective strategy for the management of this serious disease, a bacterial strain 2-12 was screened [...] Read more.
Root rot, mainly caused by Fusarium oxysporum, is one of the most destructive diseases and leads to significant economic loss of Astragalus membranaceus. To develop an effective strategy for the management of this serious disease, a bacterial strain 2-12 was screened from A. membranaceus rhizosphere soil and identified as Bacillus paralicheniformis based on the phylogenetic analyses of gyrase subunit B gene (gyrB) and RNA polymerase gene (rpoB) sequences. Interestingly, the volatile organic compounds (VOCs) produced by B. paralicheniformis 2-12 exhibited potent antifungal activities against F. oxysporum, as well as fifteen other plant pathogens. Under scanning electron microscopy observation, hyphae treated with the VOCs exhibited abnormal variation such as distortion, twist, and vesiculation, leading to distinctive protoplasm shrinkage. After treatment with B. paralicheniformis 2-12 VOCs, the lesion diameter and disease incidence both reduced significantly compared to control (p < 0.05), thus demonstrating prominent biological efficiency. Moreover, B. paralicheniformis 2-12 VOCs were composed of 17 VOCs, including 9 alkanes, 3 alcohols, 3 acids and esters, 1 aromatic compound, and 1 alkyne compound. A total of 1945 DEGs, including 1001 up-regulated and 944 down-regulated genes, were screened via transcriptome analysis. These DEGs were mainly associated with membranes and membrane parts, amino acid metabolism, and lipid metabolism. The findings in this work strongly suggested that B. paralicheniformis 2-12 VOCs could be applied as a new candidate for the control of A. membranaceus root rot. Full article
(This article belongs to the Section Microbial Biotechnology)
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20 pages, 15855 KiB  
Article
Resistance Response and Regulatory Mechanisms of Ciprofloxacin-Induced Resistant Salmonella Typhimurium Based on Comprehensive Transcriptomic and Metabolomic Analysis
by Xiaohan Yang, Jinhua Chu, Lulu Huang, Muhammad Haris Raza Farhan, Mengyao Feng, Jiapeng Bai, Bangjuan Wang and Guyue Cheng
Antibiotics 2025, 14(8), 767; https://doi.org/10.3390/antibiotics14080767 - 29 Jul 2025
Viewed by 298
Abstract
Background: Salmonella infections pose a serious threat to both animal and human health worldwide. Notably, there is an increasing trend in the resistance of Salmonella to fluoroquinolones, the first-line drugs for clinical treatment. Methods: Utilizing Salmonella Typhimurium CICC 10420 as the test strain, [...] Read more.
Background: Salmonella infections pose a serious threat to both animal and human health worldwide. Notably, there is an increasing trend in the resistance of Salmonella to fluoroquinolones, the first-line drugs for clinical treatment. Methods: Utilizing Salmonella Typhimurium CICC 10420 as the test strain, ciprofloxacin was used for in vitro induction to develop the drug-resistant strain H1. Changes in the minimum inhibitory concentrations (MICs) of various antimicrobial agents were determined using the broth microdilution method. Transcriptomic and metabolomic analyses were conducted to investigate alterations in gene and metabolite expression. A combined drug susceptibility test was performed to evaluate the potential of exogenous metabolites to restore antibiotic susceptibility. Results: The MICs of strain H1 for ofloxacin and enrofloxacin increased by 128- and 256-fold, respectively, and the strain also exhibited resistance to ceftriaxone, ampicillin, and tetracycline. A single-point mutation of Glu469Asp in the GyrB was detected in strain H1. Integrated multi-omics analysis showed significant differences in gene and metabolite expression across multiple pathways, including two-component systems, ABC transporters, pentose phosphate pathway, purine metabolism, glyoxylate and dicarboxylate metabolism, amino sugar and nucleotide sugar metabolism, pantothenate and coenzyme A biosynthesis, pyrimidine metabolism, arginine and proline biosynthesis, and glutathione metabolism. Notably, the addition of exogenous glutamine, in combination with tetracycline, significantly reduced the resistance of strain H1 to tetracycline. Conclusion: Ciprofloxacin-induced Salmonella resistance involves both target site mutations and extensive reprogramming of the metabolic network. Exogenous metabolite supplementation presents a promising strategy for reversing resistance and enhancing antibiotic efficacy. Full article
(This article belongs to the Section Mechanism and Evolution of Antibiotic Resistance)
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20 pages, 489 KiB  
Article
Genomic Analysis of Antibiotic Resistance and Virulence Profiles in Escherichia coli Linked to Sternal Bursitis in Chickens: A One Health Perspective
by Jessica Ribeiro, Vanessa Silva, Catarina Freitas, Pedro Pinto, Madalena Vieira-Pinto, Rita Batista, Alexandra Nunes, João Paulo Gomes, José Eduardo Pereira, Gilberto Igrejas, Lillian Barros, Sandrina A. Heleno, Filipa S. Reis and Patrícia Poeta
Vet. Sci. 2025, 12(7), 675; https://doi.org/10.3390/vetsci12070675 - 17 Jul 2025
Viewed by 395
Abstract
Sternal bursitis is an underexplored lesion in poultry, often overlooked in microbiological diagnostics. In this study, we characterized 36 Escherichia coli isolates recovered from sternal bursitis in broiler chickens, combining phenotypic antimicrobial susceptibility testing, PCR-based screening, and whole genome sequencing (WGS). The genetic [...] Read more.
Sternal bursitis is an underexplored lesion in poultry, often overlooked in microbiological diagnostics. In this study, we characterized 36 Escherichia coli isolates recovered from sternal bursitis in broiler chickens, combining phenotypic antimicrobial susceptibility testing, PCR-based screening, and whole genome sequencing (WGS). The genetic analysis revealed a diverse population spanning 15 sequence types, including ST155, ST201, and ST58. Resistance to tetracycline and ciprofloxacin was common, and several isolates carried genes encoding β-lactamases, including blaTEM-1B. Chromosomal mutations associated with quinolone and fosfomycin resistance (e.g., gyrA p.S83L, glpT_E448K) were also identified. WGS revealed a high number of virulence-associated genes per isolate (58–96), notably those linked to adhesion (fim, ecp clusters), secretion systems (T6SS), and iron acquisition (ent, fep, fes), suggesting strong pathogenic potential. Many isolates harbored virulence markers typical of ExPEC/APEC, such as iss, ompT, and traT, even in the absence of multidrug resistance. Our findings suggest that E. coli from sternal bursitis may act as reservoirs of resistance and virulence traits relevant to animal and public health. This highlights the need for including such lesions in genomic surveillance programs and reinforces the importance of integrated One Health approaches. Full article
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15 pages, 4191 KiB  
Article
Whole-Genome Sequencing of a Potentially Novel Aeromonas Species Isolated from Diseased Siberian Sturgeon (Acipenser baerii) Using Oxford Nanopore Sequencing
by Akzhigit Mashzhan, Izat Smekenov, Serik Bakiyev, Kalamkas Utegenova, Diana Samatkyzy, Asset Daniyarov, Ulykbek Kairov, Dos Sarbassov and Amangeldy Bissenbaev
Microorganisms 2025, 13(7), 1680; https://doi.org/10.3390/microorganisms13071680 - 17 Jul 2025
Viewed by 384
Abstract
Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based [...] Read more.
Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation—differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966T) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings. Full article
(This article belongs to the Section Microbial Biotechnology)
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11 pages, 1671 KiB  
Article
Optimal Reference Gene Selection and Potential Target Gene Identification During Xanthomonas phaseoli pv. dieffenbachiaeAnthurium andreanum Infection
by Shu-Cheng Chuang, Shefali Dobhal, Teresita D. Amore, Anne M. Alvarez and Mohammad Arif
Methods Protoc. 2025, 8(4), 72; https://doi.org/10.3390/mps8040072 - 4 Jul 2025
Viewed by 312
Abstract
Xanthomonas phaseoli pv. dieffenbachiae (Xpd), the causal agent of bacterial blight in Anthurium within the Araceae family, is listed as an EPPO A2 quarantine organism. Although the whole genome of Xpd has been sequenced, the molecular mechanisms underlying anthurium bacterial blight (ABB) remain [...] Read more.
Xanthomonas phaseoli pv. dieffenbachiae (Xpd), the causal agent of bacterial blight in Anthurium within the Araceae family, is listed as an EPPO A2 quarantine organism. Although the whole genome of Xpd has been sequenced, the molecular mechanisms underlying anthurium bacterial blight (ABB) remain unknown. Selecting an optimal reference gene is crucial for obtaining accurate and reliable gene expression profiles during the initial interactions between Xpd and Anthurium. The stability of four reference genes was evaluated by applying three statistical methods—BestKeeper, geNorm, and delta Ct (ΔCt)—using reverse-transcription quantitative PCR (RT-qPCR) data. The rpoD and gyrB genes exhibited the most consistent gene expression profiles, whereas atpD and thyA were less stable at four time points (0, 0.5, 1, and 2 h) during the interactions between Xpd and susceptible A. andreanum cultivar ‘Marian Seefurth.’ The suitability of these reference gene candidates was validated by normalizing the gene expression levels of four pathogenicity-related genes. The highly upregulated expression of gumD, which encodes xanthan biosynthesis glycosyltransferase, observed after 1 h of interaction, suggests it may be a key virulence determinant in the Xpd–Anthurium pathosystem. The stable reference genes identified here will facilitate more accurate and comprehensive gene expression studies in the Xpd–Anthurium pathosystem going forward. Full article
(This article belongs to the Section Molecular and Cellular Biology)
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9 pages, 734 KiB  
Proceeding Paper
Comparative Evaluation of 16S rRNA and Housekeeping Gene-Specific Primer Pairs for Rhizobia and Agrobacteria Metagenomics
by Romain Kouakou Fossou and Adolphe Zézé
Biol. Life Sci. Forum 2025, 46(1), 1; https://doi.org/10.3390/blsf2025046001 - 2 Jul 2025
Viewed by 306
Abstract
Of many housekeeping genes, gyrB and rpoB are used as alternative markers to 16S rDNA to analyze Rhizobia and Agrobacteria communities. However, the extent to which the targeted genes and their corresponding primers could be suitable in metagenomic studies within communities belonging to [...] Read more.
Of many housekeeping genes, gyrB and rpoB are used as alternative markers to 16S rDNA to analyze Rhizobia and Agrobacteria communities. However, the extent to which the targeted genes and their corresponding primers could be suitable in metagenomic studies within communities belonging to the two taxa remains elusive. This work evaluates in silico the taxonomic resolution of partial regions of two housekeeping and 16S rRNA genes in differentiating between Rhizobia and Agrobacteria. The study confirmed V5–V7 as the best 16S rDNA variable region for differentiating all the genera at a 100% threshold. However, rpoB and gyrB markers outcompeted the 16S rDNA in terms of taxonomic resolution regardless of the threshold, possibly replacing the use of 16S rDNA V-regions in metagenomics studies of Rhizobia and Agrobacteria. Full article
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15 pages, 1547 KiB  
Article
Screening and Validation of Reference Genes for Normalization of qRT-PCR in Rice BLB Pathogen Xanthomonas oryzae pv. oryzae Under Tetramycin Stress
by Feiyan Fang, Xinli Miao, Tong Mou, Zian Wang, Yanhe Guo, Yingfen Yang, Shunyu Gao, Zhenji Wang, Chengdong Xu and Jun Yang
Genes 2025, 16(7), 788; https://doi.org/10.3390/genes16070788 - 30 Jun 2025
Viewed by 482
Abstract
Background: Xanthomonas oryzae pv. oryzae (Xoo) causes rice leaf blight (BLB) and poses a major threat to global rice production. In rice production, tetramycin agents provide good control of rice leaf blight, while the standardization of the reference genes of Xoo [...] Read more.
Background: Xanthomonas oryzae pv. oryzae (Xoo) causes rice leaf blight (BLB) and poses a major threat to global rice production. In rice production, tetramycin agents provide good control of rice leaf blight, while the standardization of the reference genes of Xoo under tetramycin stress has not been reported. The aim of this study was to identify the most stable reference genes for quantitative PCR analysis of Xoo under tetramycin stress. Methods: Six candidate reference genes, gyrB (RNA polymerase β gene), GADPH (glyceraldehyde-3-phosphate dehydrogenase gene), recA (recombinase A gene), gyrA (citrate synthase encoding gene), dnaK (molecular chaperone protein gene), and 16S rRNA (16S ribosomal RNA gene) were selected and their expression stability was assessed under tetramycin stress conditions using real-time quantitative PCR (qRT-PCR). GeNorm, NormFinder, BestKeeper and RefFinder were used to assess the expression stability, the relative expression values of the eight genes involved QS (Quorum sensing) pathway under tetramycin stress were used to validate by the rpf (regulation of pathogenic factors) gene family. Results: 16S rRNA expression was most stable under tetracycline stress, whereas GADPH was the least. The rpf gene family showed a highly stable expression level, confirming the reliability of 16S r RNA as a reference gene in the study of Xoo under tetramycin stress. Conclusions: 16S rRNA was identified as the best reference gene for Xoo gene expression analysis under tetramycin stress. It provides a reliable support for the molecular research on the control strategy of rice BLB. Full article
(This article belongs to the Section Genes & Environments)
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13 pages, 1186 KiB  
Article
Determination of Phylogroups, Pathotypes and Antibiotic Resistance Profiles of E. coli Isolates from Freshwater and Wastewater in the City of Panama
by Gabriela A. Rodríguez Guevara, Emmanuel Michelangelli, Juan R. Medina-Sánchez, Fermín Mejía-Meléndez, Carmen Indira Espino, José E. Moreno P., Alex O. Martínez Torres and Jordi Querol-Audí
Pathogens 2025, 14(7), 617; https://doi.org/10.3390/pathogens14070617 - 20 Jun 2025
Viewed by 689
Abstract
Untreated water bodies are critical ecological niches where environmental conditions can drive the adaptive evolution of bacterial populations, enabling them to acquire new traits such as antibiotic-resistance genes. Escherichia coli is typically a commensal bacterium but can evolve into a pathogenic form, known [...] Read more.
Untreated water bodies are critical ecological niches where environmental conditions can drive the adaptive evolution of bacterial populations, enabling them to acquire new traits such as antibiotic-resistance genes. Escherichia coli is typically a commensal bacterium but can evolve into a pathogenic form, known as Diarrheagenic E. coli, responsible for both intestinal and extraintestinal diseases. This study focuses on the characterization of E. coli isolates from water samples collected from the Matasnillo River and the influence of the Juan Díaz Wastewater Treatment Plant (WWTP). While isolates from the Matasnillo River were classified as commensal, 18% of the isolates from the WWTP belonged to either phylogroups D or B2. Pathotype analysis revealed the presence of Entero-Toxigenic and Entero-Hemorrhagic E. coli in the WWTP. Moreover, Matasnillo River isolates exhibited resistance mainly to the quinolone ciprofloxacin, whereas those from the WWTP influent showed resistance to multiple broad-spectrum antibiotics. Sequencing analysis revealed the prevalence of the transmissible quinolone resistance qnrB19 among the Matasnillo River isolates and mutations conferring resistance to quinolone in gyrA, parC, and parE. These findings highlight the importance of monitoring antibiotic-resistant bacterial contamination in both freshwater and wastewater to mitigate the risk of the spread of resistant pathogens and potential epidemic outbreaks. Full article
(This article belongs to the Special Issue Current Progress on Bacterial Antimicrobial Resistance)
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18 pages, 963 KiB  
Article
Accuracy of Analytic Potentials for Orbits of Satellites Around a Milky Way-like Galaxy: Comparison with N-Body Simulations
by Rubens E. G. Machado, Giovanni C. Tauil and Nicholas Schweder-Souza
Universe 2025, 11(6), 191; https://doi.org/10.3390/universe11060191 - 17 Jun 2025
Viewed by 288
Abstract
To study the orbits of satellites, a galaxy can be modeled either by means of a static gravitational potential or by live N-body particles. Analytic potentials allow for fast calculations but are idealized and non-responsive. On the other hand, N-body simulations [...] Read more.
To study the orbits of satellites, a galaxy can be modeled either by means of a static gravitational potential or by live N-body particles. Analytic potentials allow for fast calculations but are idealized and non-responsive. On the other hand, N-body simulations are more realistic but demand higher computational cost. Our goal is to characterize the regimes in which analytic potentials provide a sufficient approximation and those where N-bodies are necessary. We perform two sets of simulations, using both Gala and Gadget, in order to closely compare the orbital evolution of satellites around a Milky Way-like galaxy. Focusing on the periods when the satellite has not yet been severely disrupted by tidal forces, we find that the orbits of satellites up to 108M can be reliably computed with analytic potentials to within 5% error if they are circular or moderately eccentric. If the satellite is as massive as 109M then errors of 9% are to be expected. However, if the orbital radius is smaller than 30 kpc then the results may not be relied upon with the same accuracy beyond 1–2 Gyr. Full article
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16 pages, 3234 KiB  
Article
An Emerging Bacterial Leaf Disease in Rice Caused by Pantoea ananatis and Pantoea eucalypti in Northeast China
by Guohua Duan, Xin Liu, Shaoqi Zhang, Mengzhu Chai, Zhao Peng, Zihan Lin, Dayong Li and Wenxian Sun
Microorganisms 2025, 13(6), 1376; https://doi.org/10.3390/microorganisms13061376 - 13 Jun 2025
Cited by 1 | Viewed by 960
Abstract
Rice production faces new challenges from emerging diseases due to intensive cultivation practices and climate warming in China. A new rice leaf bacterial disease has recently occurred in Northeast China. The symptoms of the disease are similar to those of bacterial leaf blight. [...] Read more.
Rice production faces new challenges from emerging diseases due to intensive cultivation practices and climate warming in China. A new rice leaf bacterial disease has recently occurred in Northeast China. The symptoms of the disease are similar to those of bacterial leaf blight. Disease lesions spread along leaf edges and are later dried up due to water loss. In this study, 17 bacterial isolates were identified as the causal agents of the new disease following Koch’s postulates. These strains are categorized into two groups based on colony morphology and molecular characterization. Phylogenetic analysis using the five housekeeping genes leuS, gyrB, fusA, pyrG, and rplB reveals that the two groups of the isolates belong to Pantoea ananatis and P. eucalypti, respectively. The new rice disease is caused by P. ananatis, P. eucalypti, or a combination of both bacterial species. A complete genome map has also been assembled for P. eucalypti. Meanwhile, some important virulence factors have been predicted based on gene annotation and determination of extracellular enzymes. Collectively, this study represents the first report of a new rice leaf disease caused by P. eucalypti and the first high-quality genome assembly of P. eucalypti that infects rice leaves. Full article
(This article belongs to the Special Issue Phytopathogens: Detection and Control)
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16 pages, 345 KiB  
Article
Use of Redshifts as Evidence of Dark Energy
by Jan Stenflo
Physics 2025, 7(2), 23; https://doi.org/10.3390/physics7020023 - 13 Jun 2025
Viewed by 591
Abstract
The large-scale dynamics of the universe is generally described in terms of the time-dependent scale factor a(t). To make contact with observational data, the a(t) function needs to be related to the observable [...] Read more.
The large-scale dynamics of the universe is generally described in terms of the time-dependent scale factor a(t). To make contact with observational data, the a(t) function needs to be related to the observable z(r) function, redshift versus distance. Model fitting of data has shown that the equation that governs z(r) needs to contain a constant term, which has been identified as Einstein’s cosmological constant. Here, it is shown that the required constant term is not a cosmological constant but is due to an overlooked geometric difference between proper time t and look-back time tlb along lines of sight, which fan out isotropically in all directions of the 3D (3-dimensional) space that constitutes the observable universe. The constant term is needed to satisfy the requirement of spatial isotropy in the local limit. Its magnitude is independent of the epoch in which the observer lives and agrees with the value found by model fitting of observational data. Two of the observational consequences of this explanation are examined: an increase in the age of the universe from 13.8 Gyr to 15.4 Gyr, and a resolution of the H0 tension, which restores consistency to cosmological theory. Full article
(This article belongs to the Special Issue Beyond the Standard Models of Physics and Cosmology: 2nd Edition)
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21 pages, 2694 KiB  
Article
Isolation and Identification of Endophytic Bacterium B5 from Mentha haplocalyx Briq. and Its Biocontrol Mechanisms Against Alternaria alternata-Induced Tobacco Brown Spot
by Qunying Qin, Boyu Liu, Baige Ma, Xihong Wei, Yi Zhou and Zhengxiang Sun
J. Fungi 2025, 11(6), 446; https://doi.org/10.3390/jof11060446 - 12 Jun 2025
Viewed by 1275
Abstract
The fungus Alternaria alternata, which causes tobacco brown spot disease, poses a serious threat to the tobacco industry. Beneficial microorganisms and their secondary metabolites have emerged as a promising green strategy for disease management. This study recovered 16 endophytic bacterial strains from [...] Read more.
The fungus Alternaria alternata, which causes tobacco brown spot disease, poses a serious threat to the tobacco industry. Beneficial microorganisms and their secondary metabolites have emerged as a promising green strategy for disease management. This study recovered 16 endophytic bacterial strains from Mentha haplocalyx Briq., a therapeutic herb. The study revealed that strain B5, with an inhibition rate of 82.76%, exhibited the highest antifungal activity against A. alternata. This strain exhibited broad-spectrum antifungal activity, with inhibition rates ranging from 66.34% to 87.23%. Phylogenetic analysis of 16S rDNA and gyrA gene sequences identified it as Bacillus velezensis (GenBank: PV168970 and PV173738). Further characterization revealed that strain B5 can secrete cell wall-degrading enzymes, produce IAA, and synthesize siderophores. The growth of mycelium in A. alternata was greatly reduced by both the ethyl acetate extract and the filtered liquid from the sterile fermentation, resulting in marked morphological abnormalities. Multiple antifungal active substances were identified through liquid LC-MS analysis. Greenhouse experiments demonstrated that the B5 fermentation broth effectively suppressed the occurrence of tobacco brown spot disease, achieving a relative control efficacy of 60.66%, comparable to that of 10% difenoconazole water dispersible granule (WDG). Additionally, strain B5 enhances plant disease resistance by activating the activities of key defense enzymes. B. velezensis B5 serves as a safe alternative to chemical fungicides and is highly effective at controlling tobacco brown spot disease. Full article
(This article belongs to the Special Issue Biological Control of Fungal Plant Pathogens)
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22 pages, 2834 KiB  
Article
Antibiotic Resistance and Genetic Determinants of Helicobacter pylori in Oman: Insights from Phenotypic and Whole-Genome Analysis
by Amal Al-Hinai, Meher Rizvi, Said A. Al-Busafi, Masoud Kashoob, Zakariya Al-Muharrmi, Ahmed Al-Darmaki and Zaaima Al-Jabri
Int. J. Mol. Sci. 2025, 26(12), 5628; https://doi.org/10.3390/ijms26125628 - 12 Jun 2025
Viewed by 674
Abstract
Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic [...] Read more.
Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic susceptibility in 15 H. pylori isolates (from 169 clinical samples) from naïve and treatment-failed patients. Resistance to clarithromycin (CLA), amoxicillin (AMX), metronidazole (MTZ), tetracycline, rifampicin (RIF), and levofloxacin (LEV) was tested alongside genetic analysis of virulence and resistance-associated mutations by whole-genome sequencing (WGS). Among the 15 resistant isolates, 20% were resistant to one antibiotic, 33.3% to two, 20% to three, and 26.6% to four antibiotics. MTZ resistance was universal among single-drug resistant isolates (100%). AMX-MTZ dual resistance was present in 60%, while triple resistance (CLA-AMX-MTZ) was present in 66.7%. Quadruple resistance (CLA-AMX-MTZ-RIF) was present in 75%. WGS revealed 23S rRNA mutations in 33.3% of CLA-resistant strains and pbp-1 mutations in 66.6% of AMX-resistant strains. MTZ resistance was linked to rdxA/frxA mutations, while RIF and LEV resistance correlated with rpoB (65.7%) and gyrA (20%) mutations, respectively. The genotype–phenotype agreement was insignificant (p = 1). High mutation heterogeneity, virulence factors, and environmental influences contribute to resistance. Further studies on host–pathogen interactions are needed to understand resistance mechanisms. Full article
(This article belongs to the Special Issue Microbial Genomics in the Omics Era)
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9 pages, 850 KiB  
Article
Genetic Mechanisms of Antimicrobial Non-Susceptibility to Novel Fluoroquinolone Delafloxacin Among Bulgarian Clinical Isolates of Streptococcus agalactiae
by Vasil Boyanov, Alexandra Alexandrova and Raina Gergova
Curr. Issues Mol. Biol. 2025, 47(6), 446; https://doi.org/10.3390/cimb47060446 - 11 Jun 2025
Viewed by 485
Abstract
Delafloxacin is one of the newest fluoroquinolones with a unique structure, determining better pharmacokinetic and pharmacodynamic properties, a better safety profile, and a broader spectrum of activity compared to older quinolones. We aimed to examine the susceptibility rates of delafloxacin, the genetic mechanisms [...] Read more.
Delafloxacin is one of the newest fluoroquinolones with a unique structure, determining better pharmacokinetic and pharmacodynamic properties, a better safety profile, and a broader spectrum of activity compared to older quinolones. We aimed to examine the susceptibility rates of delafloxacin, the genetic mechanisms contributing to resistance, and the serotype distribution in both invasive and non-invasive Streptococcus agalactiae strains. A total of 301 streptococcal strains were tested for minimal inhibitory concentration (MIC) to delafloxacin. All delafloxacin-resistant strains were subjected to serotyping, PCRs for quinolone-resistant genes, and sequence analysis for missense and silent mutations. Among the tested isolates, we found a 5.6% non-susceptibility rate to delafloxacin. The MICs ranged between 0.09 and 0.38 µg/mL, with a breakpoint for nonsusceptibility set as >0.03 µg/L, according to EUCAST criteria. All resistant isolates harboured missense mutations that led to amino acid substitutions in both GyrA (S81L) and ParC (S79F). Two common serotypes were determined among the resistant isolates: V (47.1%) and III (41.2%). Two strains were non-typable (11.7%). A statistical significance in the distribution of serotypes between delafloxacin-resistant and delafloxacin-susceptible strains was found. These findings highlight a concerning pattern of drug resistance developing prior to the introduction of a new medication, attributed to the extensive use of current antibiotics. Full article
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13 pages, 862 KiB  
Article
Quinolone Resistance and Prevalence of the Related Genes in Photobacterium damselae subsp. damselae Recovered from Diseased Fish in Eastern China
by Xiangyun Yang, Chen Shen, Suming Zhou, Liyun Jin, Yajun Wang and Fei Yin
Fishes 2025, 10(6), 280; https://doi.org/10.3390/fishes10060280 - 7 Jun 2025
Viewed by 342
Abstract
Photobacterium damselae subsp. damselae is a well-recognized marine animal pathogen. Herein, 70 P. damselae subsp. damselae isolates were investigated for quinolone susceptibility and prevalence of the genes including quinolone resistance-determining regions (QRDRs) and plasmid-mediated quinolone resistance (PMQR) genes. A total of 18/70 isolates [...] Read more.
Photobacterium damselae subsp. damselae is a well-recognized marine animal pathogen. Herein, 70 P. damselae subsp. damselae isolates were investigated for quinolone susceptibility and prevalence of the genes including quinolone resistance-determining regions (QRDRs) and plasmid-mediated quinolone resistance (PMQR) genes. A total of 18/70 isolates exhibited high-level resistance, and 23/70 isolates exhibited moderate resistance according to the MIC values. QRDR analysis showed that double mutants in both GyrA (Ser83Ile) and ParC (6/17 Ser80Phe or 11/17 Ser80Tyr) were detected in 94.4% (17/18) high-level quinolone resistance P. damselae subsp. damselae strains. PMQR detection showed that 60.0% (42/70) carried at least one PMQR (1/42 qnrB coexistence with aac(6′)-Ib-cr, 1/42 qnrS coexistence with aac(6′)-Ib-cr, 44/46 qnrS). QnrA, QnrC, qnrD and qepA were not detected in all strains. Among the 42 PMQR-positive strains, 24 showed fluoroquinolones MICs ≤ 0.5 mg/L and 13 MICs ≥ 2 mg/L, all carrying QRDR mutations. For the twenty-eight non-PMQR strains, twenty-three showed fluoroquinolone MICs ≤ 0.5 mg/L without QRDR mutations, and five MICs ≥ 2 mg/L carrying QRDR mutations. In conclusion, qnrS (qnrS2 allele) is the major PMQR widespread in P. damselae subsp. damselae isolated from eastern China; however, QRDR mutation plays a marked role in mediating fluoroquinolone resistance. Full article
(This article belongs to the Section Fish Pathology and Parasitology)
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