Search Results (708)

This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of Salmonella enterica serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated genes were screened by PCR. Pulsed-field gel electrophoresis (PFGE) assessed clonal relatedness, and whole-genome sequencing (WGS) enabled multilocus sequence typing (MLST), core genome MLST (cgMLST), SNP phylogeny, resistance gene detection, and MGE analysis. Nine virulence profiles (VP1–VP9) were identified. VP1 (74.1%) was strongly associated with multidrug resistance (MDR), while VP2 (14.8%), which carried plasmid-encoded spv genes, remained largely susceptible. Overall, 83.7% of isolates were resistant to at least one antimicrobial, and 65.2% were MDR, with ampicillin and tetracycline consistently forming the backbone of MDR phenotypes. PFGE revealed high genetic diversity, with 72 pulsotypes, yet certain clones (e.g., SMOX01.006, SMOX01.012) were widely distributed and corresponded to VP2 isolates. WGS confirmed two dominant sequence types, ST34 (n = 24) and ST19 (n = 20), with SNP phylogeny showing VP1 isolates mainly clustered with ST34 and VP2 with ST19. Genotype–phenotype concordance showed strong agreement for most antimicrobials, except cefoxitin, ciprofloxacin, amikacin, and trimethoprim/sulfamethoxazole. MGE analysis revealed that tet(B) was consistently associated with ISVsa5, while ISEc59 was linked to multiple resistance genes, though only aac(3)-IV was phenotypically expressed. These findings demonstrate that MDR and virulence gene composition were closely associated with clonal clustering and that MGEs may contribute to resistance gene expression. This study provides a basis for understanding the dissemination of resistant and virulent Salmonella in the region and underscores the need for continuous genomic surveillance. Full article

Background: Escherichia coli strains associated with poultry are increasingly recognized as reservoirs of both virulence and resistance genes, posing significant zoonotic risks throughout the food production chain. However, the genotypic architecture and pathogenic potential of isolates from large-scale turkey farms remain under characterized, particularly in the context of extended-spectrum β-lactamase (ESBL) production. Methods: A total of 160 ESBL-producing E. coli isolates were collected from healthy turkeys on intensive Hungarian farms. Whole genome sequencing (WGS) was performed to characterize virulence factors. Functional annotation included screening for fimbrial adhesins, iron acquisition systems, secretion pathways, and autotransporter toxins, using VirulenceFinder and Prodigal-based genome annotations. Data analysis included assembly quality control with QUAST and BUSCO, and comprehensive virulome profiling. Results: The isolates exhibited a functionally diverse virulence profile encompassing classical ExPEC-associated colonization factors (type I, P, S fimbriae; curli; ECP), multiple iron acquisition systems (enterobactin, salmochelin, aerobactin, yersiniabactin, and heme uptake), and key secretion systems (LEE-associated T3SS and T2SS). Genetic hallmarks of avian pathogenic E. coli (APEC), uropathogenic pathogenic E. coli (UPEC), and enteropathogenic E. coli (EPEC) pathotypes co-occurred in 44% of the isolates, indicating a mosaic virulence landscape. Notably, serine protease autotransporters of Enterobacteriaceae (SPATE) toxins (Vat, Pic) and ColV-type plasmid-associated modules were frequently detected. All isolates were confirmed by ESBL producers, highlighting their antimicrobial resistance potential. Conclusions: This study reveals that E. coli strains isolated from turkeys possess a complex, host-adapted virulence repertoire capable of supporting both enteric and extraintestinal infections. The co-occurence of APEC-, UPEC-, and EPEC-like traits—combined with ESBL production—underscores their One Health relevance. These findings support the need for host-specific surveillance, functional validation, and integrative control strategies in poultry systems. Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat, with ST101 identified as a major circulating clone in Saudi Arabia. We used whole genome sequencing and plasmid reconstruction to investigate the molecular characteristics of CRKP ST101 isolates from Saudi Arabia (2018–2021), analyzing antimicrobial resistance genes (ARGs), virulence factors, and plasmid structure and replicon types. Clinical isolates were obtained from the Ministry of National Guard Health Affairs (MNGHA) hospitals in Saudi Arabia between 2018 and 2021. Whole-genome sequencing was performed using the Illumina MiSeq^® platform, followed by comprehensive bioinformatic analysis of ARGs, virulence factors, and plasmid content. All ten isolates belonged to ST101 and harbored extensive antimicrobial resistance (AMR) and virulence determinants. Nine isolates (90%) carried bla_OXA-48, with three co-harboring bla_NDM-1, representing dual-carbapenemase producers. These carbapenemase genes were located on plasmids with distinct replicon types, including IncL/M, IncHI1B/IncFIB, and IncFIA/IncR. All isolates were multidrug-resistant (MDR), with half classified as extensively drug-resistant (XDR). Four isolates exhibited hypervirulent profiles, harboring aerobactin and yersiniabactin siderophores. This study provides comprehensive genomic characterization of CRKP ST101 in Saudi Arabia, revealing complex resistance mechanisms mediated by diverse plasmid types. The findings highlight the importance of genomic surveillance to track the evolution and dissemination of high-risk MDR and XDR lineages and inform targeted infection control strategies. Full article

Mitogen-activated protein kinase (MAPK) cascades are critical for fungal development, stress adaptation. and virulence. However, their dynamic and stress-specific regulatory networks in entomopathogenic fungi remain largely unresolved. This study systematically investigates the roles of all three key MAPKs—BbHog1, BbSlt2, and BbMpk1—in insect pathogenic fungus Beauveria bassiana. A combination of detailed phenotypic profiling of deletion mutants (ΔBbHog1, ΔBbSlt2, and ΔBbMpk1) and time-course transcriptomics (RNA-seq at 0, 0.5, and 12 h) under osmotic, cell-wall, oxidative, and thermal stress conditions was employed, followed by weighted gene co-expression network analysis (WGCNA). This approach delineated twelve stress-responsive gene modules regulated by those MAPKs that were highly associated with fungal stress adaptation, including membrane repair, redox balance, cell-wall remodeling, and core metabolism. Functional analyses showed that Hog1 orchestrates osmoadaptation through coordinated control of osmolyte metabolism, glycolytic flux, and cell-wall remodeling; Slt2 protects against thermal damage by sustaining membrane integrity, ergosterol homeostasis, and redox balance; and Mpk1 directs oxidative stress responses by tuning mitochondrial activity, metabolic suppression, and detoxification pathways. In summary, this work outlines a concise, systems-level framework of MAPK-mediated stress regulation in B. bassiana, providing mechanistic insight into fungal environmental resilience and identifying molecular targets for the engineering of robust biocontrol strains. Full article

Escherichia ruysiae is a recently characterized species within the Escherichia genus, often misclassified as E. coli due to limitations in existing operating procedures and diagnostic databases. In this study, we report the first isolation and genomic characterization of E. ruysiae in Togo, from a five-year-old female patient who was hospitalized with gastroenteritis and bloody diarrhea and subsequently died after eight days. Biochemical tests and MALDI-TOF initially identified the microorganism as E. coli, but phylogenomic and Average Nucleotide Identity (ANI) analysis confirmed it to be E. ruysiae, Clade IV with enteroaggregative associated genes. Whole genome sequencing of the strain FK53-34 enables the identification of resistance genes, including bla_EC-15, eptA, and pmrF. The virulence profile of the strain included, but was not limited to aap, aatABC, and senB genes, which may support its pathogenicity and virulence. Multilocus sequence typing (MLST) did not match any known sequence type, which is obvious for a newly characterized microorganism. This study highlights the critical need for enhanced diagnostic tools and surveillance systems to identify emerging pathogens, including Escherichia ruysiae. Full article

Acne vulgaris is a prevalent chronic inflammatory dermatosis primarily affecting the pilosebaceous units. Current therapeutic approaches often exhibit limited efficacy and high recurrence rates. To investigate the microbiome-related mechanisms of acne vulgaris, facial skin samples from 19 patients with moderate acne and 20 healthy individuals were analyzed using an integrated metagenomic and lipidomic profiling strategy. Metagenomic analysis revealed a significant reduction in microbial diversity (Chao index) in acne-affected skin compared to healthy controls (p < 0.001). The relative abundance of Staphylococcus, particularly Staphylococcus epidermidis, was significantly elevated in acne group (p < 0.05), while Cutibacterium acnes levels remained unchanged. Carbon metabolism pathways were enriched in the acne group (p < 0.05), predominantly driven by Cutibacterium, whereas other enriched metabolic pathways, such as ABC transporters and glycine, serine, and threonine metabolism (p < 0.05), showed a greater contribution from Staphylococcus. Virulence factors enriched in acne samples were primarily offensive in nature and largely attributed to Staphylococcus. Moreover, acne-associated microbiome exhibited a significantly higher prevalence of resistance genes against fluoroquinolones, fosfomycin, and triclosan (p < 0.05). Untargeted lipidomic analysis demonstrated significantly elevated total serum and triglyceride levels, along with a reduction in fatty acid chain length and a higher degree of saturation compared to the healthy group (p < 0.01). Specific triglycerides significantly enriched in the acne group, such as TG (15:0_14:0_16:0) + NH₄, exhibited a significant positive correlation with Staphylococcus. This correlation is associated with elevated clinical erythema and melanin indices, suggesting that Staphylococcus is implicated in the development of acne-related inflammation. Additionally, Thermus exhibits negative correlations with acne-associated lipids and inflammatory parameters, potentially exerting a protective role. These findings suggest that Cutibacterium and Staphylococcus play differential yet synergistic roles in acne pathogenesis. The observed skin microbiome dysbiosis and lipid metabolic alterations provide novel insights into the pathophysiology of acne vulgaris, which may inform the development of targeted therapeutic strategies. Full article

This study aimed to characterize the transcriptional response of Porphyromonas gingivalis biofilms to treatment with xanthohumol and curcumin. A validated dynamic in vitro biofilm model, based on microbial growth under flow and shear conditions resembling the oral cavity, was used to develop mature biofilms of P. gingivalis on sterile ceramic calcium hydroxyapatite discs. Transcriptional profiles of biofilms, treated and untreated with both extracts, were obtained through RNA-Sequencing (RNA-Seq). The biofilm development and the lack of phenotypic effects from sublethal concentrations of xanthohumol and curcumin were confirmed via Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM). Reverse transcription quantitative PCR (RT-qPCR) was employed to verify differentially expressed genes identified by RNA-Seq. Xanthohumol and curcumin caused extensive reprogramming of P. gingivalis biofilm gene expression. Out of 1,973 genes, xanthohumol activated 173 and repressed 286, whereas curcumin activated 170 and repressed 163. These changes affected genes involved in membrane integrity, oxidative stress, transmembrane transport, and virulence, suggesting a mechanism of action that involves membrane disruption. Full article

Background: Infections caused by antimicrobial-resistant bacteria are difficult to treat and increase the risk of death in animals. This report describes a fatal case of diarrhea in a horse that, despite intensive treatment including surgery and broad-spectrum antimicrobials (ceftiofur and amikacin), experienced a worsening of its condition and subsequent death. Methods: A fecal swab sample was subjected to microbiological culture for the identification of bacteria and assessment of their phenotypical antimicrobial susceptibility profiles using the disk-diffusion and broth microdilution methods. The double-disk synergy test, polymerase chain reactions for the detection of genes encoding extended-spectrum β-lactamases, and whole-genome sequence-based analysis were also performed. Results: Strains of Salmonella enterica and Escherichia coli were isolated, with the E. coli strain DSL-HVUVV-2025 presenting resistance to a third-generation cephalosporin. Accordingly, the bla_CTX-M-2 gene was identified in the DSL-HVUVV-2025 strain, which was submitted to whole-genome sequencing. Genomic analysis showed several antimicrobial resistance determinants, as well as virulence genes, including those associated with the enteroaggregative pathotype. The bla_CTX-M-2 gene was surrounded by an ISCR1 element and embedded in a complex class 1 integron that is part of the Tn7337 transposon. Strain DSL-HVUVV-2025 belonged to a novel sequence type. Conclusions: This case highlights the importance of monitoring antimicrobial resistance and performing genomic characterization of bacteria involved in equine diarrhea to guide effective clinical management in veterinary hospitals. It also reinforces the role of horses as potential carriers of WHO critical priority pathogens and the need for responsible antimicrobial use. Full article

The attachment–invasion locus protein Ail of pathogenic Yersinia strains is an important virulence factor, both for invasion of eucaryotic cells and for serum resistance. In other Yersinia strains, e.g., those belonging to biotype (BT) 1A of Yersinia enterocolitica, ail has only occasionally been described. Sequence analysis of 370 BT 1A isolates in our laboratory revealed 41 (11.1%) which were ail-positive. Most of these isolates were recovered from minced meat and tonsils of wild boars, and belonged to 17 MLST allele profiles. A closer look at DNA sequences surrounding ail disclosed that the gene in most isolates is embedded in DNA regions encoding phage proteins. The genomes of four prophages belonging to four different phylogenetic clusters were determined and analyzed by in silico studies. These have sizes of 34.9 and 50.7 kb, and are closely related to each other but not to known phages. Unlike other regions of the prophages, the integrases and attachment sites of some of them diverge, leading to different integration sites in the isolates. In a fifth cluster, ail is relocated at a position on the Y. enterocolitica chromosome that is several hundred kilobases apart from those of the other clusters, but surrounded by prophage-related sequences. In addition, highly pathogenic 1B/O:8 strains contain a DNA segment which includes ail and is 65 to 94% identical to the prophage sequences determined in this study. Full article

Background: Escherichia coli is a cause of severe clinical bovine mastitis; however, it is not yet fully understood what makes mastitis-associated bacteria different from commensal strains at the genetic level. The goal of this study was to compare the genomic features, sequence types, virulence, and antibiotic resistance profiles of E. coli isolated from healthy cows and cows with clinical mastitis in Northern Italy. Methods: Between 2023 and 2024, 46 E. coli isolates, 23 from healthy animals and 23 from mastitis cases were recovered. Standard phenotypic approaches and Oxford Nanopore sequencing were used to investigate the genomic landscape of the strains. Results: Phylogroups A and B1 were the most common in both groups. MLST showed several types, with ST10 (19.6%), ST58 (13.0%), and ST69 (8.7%) being the most common. There was no lineage that was uniquely able to describe the isolates as Mammary Pathogenic Escherichia coli (MPEC); indeed, the ST distribution and phylogeny were the same in both groups. A total of 47.8% of isolates had antimicrobial resistance determinants, with β-lactamases (21.7%) and tetA (15.2%) being the most common. No significant differences in resistance rates were observed between mastitis and healthy isolates. Pangenome investigation found a large pool of accessory genes, but no genomic signature that distinguished mastitis from commensal isolates across the MPEC. Conclusions: Bovine E. coli isolated from milk of both healthy and mastitic cows share sequence types, resistance rates, and accessory genome content, supporting the absence of a unique MPEC pathotype and highlighting the ecological versatility of these bacteria. Full article

Avian pathogenic Escherichia coli (APEC) causes avian colibacillosis, a disease responsible for high morbidity and mortality in commercial poultry flocks, leading to devastating economic losses to the poultry industry worldwide. APEC may also act as a source of virulence and antibiotic resistance genes that can be transferred to other Escherichia coli pathotypes. Therefore, this study aimed to determine the serotypes, phylogenetic background, virulence genes, and antibiotic resistance profiles of APEC in Algeria. A total of 98 APEC strains were isolated from chicken samples with characteristic colibacillosis signs between 2019 and 2020. O-serotyping identified O157 (20.41%) and O78 (11.22%) as the predominant serotypes. The isolates were classified into groups B1 (43.87%), C (29.59%), A (12.24%), E (7.14%), F (5.10%), and B2 (2.04%). Virulence gene analysis revealed that among the 31 genes investigated, a high occurrence of mat, crlA (100% each), yijP (98.98%), fimC, ibeB, ompA (97.96% each), iucD (89.80%), iroN (81.63%), iss (80.61%), and eae (79.59%) was observed. The highest resistance rates were found for ampicillin (97.96%), amoxicillin–clavulanic acid (96.94%), nalidixic acid (94.90%), tetracycline (90.82%), and ciprofloxacin (79.59%). Additionally, 92.86% of APEC isolates were resistant to three or more antibiotics, reflecting extensive antimicrobial use in Algerian poultry farms and highlighting a major challenge for animal health management and a potential risk of zoonotic transmission. Our data provide valuable insights into the characteristics of the APEC populations in broiler chickens in Algeria. This may assist in understanding APEC pathogenesis and in developing effective control strategies. Full article

Proteus mirabilis (P. mirabilis) serves as a multi-host–pathogen regarded as an alarming foodborne infectious disease, causing illnesses of variable severity in both livestock and human beings. The present study aimed to estimate the prevalence, antibiotic susceptibility profiles, and associated antimicrobial resistance genes (ARGs) of P. mirabilis isolates obtained from diseased broiler chickens and native Egyptian buffaloes in Kafr El-Sheikh and Dakahlia governorates, Egypt. In addition, this study investigated the antibacterial activity of chitosan (CS) and chitosan nanoparticles (CSNPs), including the estimation of the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of CS at concentrations of 1% and 2%, as well as CSNPs. Furthermore, the sub-MIC values were utilized to assess the inhibitory effects of CS and CSNPs on swarming motility. P. mirabilis was detected in 68% (34/50) of broiler chickens and 40.74% (11/27) of buffaloes. Interestingly, all P. mirabilis isolates were tested against 21 antimicrobial drugs and showed high resistance against either critical, highly important, or important antimicrobial drugs. For chicken-originated P. mirabilis, 50% (17/34) of isolates were revealed to be extensively drug-resistant (XDR) and 50% (17/34) of isolates were revealed to be pan-drug-resistant (PDR). Meanwhile, 9.09% (1/11) of buffalo-originated P. mirabilis isolates were revealed to be XDR and 90.91% (10/11) of the isolates were revealed to be PDR. Among P. mirabilis isolates from broiler chickens, the prevalence of resistance genes was as follows: int1 (97.06%), dfrA1 (100%), sul2 (97.06%), catA1 (44.12%), aadA1 (97.06%), tet(M) (81.82%), ermB (23.53%), msrA (0%), qnrA (47.06%), qnrS (0%), gyrA (0%), mcr-1 (11.76%), bla_TEM (97.06%), bla_CTX-M (26.47%), bla_OXA-10 (2.94%), bla_CMY-2 (41.18%), and bla_SHV (0%). The corresponding detection rates in buffalo-derived isolates were 100%, 100%, 90.91%, 63.64%, 100%, 70.59%, 18.18%, 0%, 9.09%, 0%, 0%, 18.18%, 81.82%, 18.18%, 18.18%, 63.64%, and 0%, respectively. Carbapenemase genes were found in none of the isolates from either species. CSNPs demonstrated superior antibacterial and anti-virulence activity against resistant P. mirabilis. CSNPs exhibited significantly lower MIC (0.067–0.081 mg/mL) and MBC (0.167–0.177 mg/mL) values compared with conventional CS formulations (MIC: 3.25–4.5 mg/mL; MBC: 6.67–9.08 mg/mL) in both broiler and buffalo isolates. In inhibition zone assays, the CSNPs + ciprofloxacin (CIP) combination showed the highest efficacy with a 50–58% increase in the inhibition area. Both CSNPs and CS 2% substantially reduced swarming motility by 45–52%, with CSNPs showing the strongest inhibitory effect. These outcomes highlight how P. mirabilis carries and disseminates antibiotic resistance, presenting serious threats to health policy and livestock. Also, CS or CSNPs, either alone or enhanced with CIP, are effective in vitro against resistant P. mirabilis, which promotes the treatment of Proteus infections to guarantee a bactericidal impact. Full article

Background/Objectives: Klebsiella pneumoniae ST258 and ST11 are global high-risk antimicrobial-resistant clones known for their virulence and resistance gene dissemination. This study aims to identify these clones in a Greek tertiary hospital and understand their resistance profiles and transmission dynamics. Methods: In January 2025, we isolated two distinct carbapenem-resistant K. pneumoniae in a Greek tertiary hospital: INT18S from an ICU patient’s bronchioalveolar lavage and INT20U from a urine sample in the emergency unit. Antimicrobial susceptibility testing (via Microscan system) and Whole-Genome Sequencing (WGS) were conducted on both isolates and their genomes were submitted to the NCBI. Results: The INT18S isolate carried the bla_KPC-2 gene and belonged to the ST258 clone. The INT20U isolate carried the bla_NDM-1 gene and belonged to the ST11 clone lineage. Both isolates contained at least one of the extended spectra β-lactamase genes tested (TEM, SHV, OXA-1 and CTX-M group). Conclusions: The co-existence of the high-risk K. pneumoniae clones ST258 and ST11 in different hospital departments increases the risk of resistance gene transfer and suggests potential intra-hospital transmission pathways. Understanding their resistance profiles is critical for guiding treatment strategies and preventing the spread of multidrug-resistant pathogens. Full article

Enterococcus faecalis (E. faecalis) is a significant zoonotic pathogen, primarily causing opportunistic infections in humans while often existing as a commensal in animal reservoirs, facilitating its dissemination. Current understanding of the resistance profiles, virulence mechanisms, and host–pathogen interactions of E. faecalis from ruminants, particularly unique species such as the plateau yak, remains limited. This knowledge gap hinders the accurate assessment of their transmission risk and the development of effective control strategies. This study presents a comprehensive analysis of a multidrug-resistant E. faecalis isolate from yak feces, integrating whole-genome sequencing (WGS), an animal challenge model, and transcriptomic profiling. Antimicrobial susceptibility testing revealed resistance to β-lactams, aminoglycosides, glycopeptides, tetracyclines, and fluoroquinolones. WGS identified numerous resistance genes (e.g., parC, gyrA, rpoB) and virulence-associated genes (e.g., prgB/asc10, cpsA/uppS). Phylogenetic analysis indicated a close relationship with a human urinary tract isolate (ASM3679337v1). Mouse challenge experiments demonstrated that this strain induced significant intestinal histopathological damage. A subsequent transcriptomic analysis of infected tissues identified the differential activation of key signaling pathways, including NF-κB and MAPK. Our findings provide crucial insights into the resistance and pathogenic mechanisms of ruminant-derived E. faecalis and establish an experimental foundation for optimizing clinical antimicrobial therapy against such strains. Full article

Background/Objectives: Bacteroides species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical Bacteroides isolates from southern Thailand. Methods: Sixteen isolates were collected from body fluids, tissues, and pus at Songklanagarind Hospital (2022–2024). Whole-genome sequencing was performed on the BGI platform, followed by genome assembly, annotation, average nucleotide identity (ANI), pairwise single-nucleotide polymorphism (SNP) analysis, antimicrobial resistance (AMR) gene profiling, plasmid prediction, virulence screening, and phylogenetic analysis. Results: ANI and SNP analysis revealed two clusters: one comprising B. ovatus, B. intestinigallinarum, and B. thetaiotaomicron, and another mainly B. fragilis with one B. hominis isolate. All isolates were resistant to ampicillin, cephalothin, and penicillin; six B. fragilis strains were resistant to all tested antibiotics. The β-lactamase gene cepA was detected in all B. fragilis isolates, and plasmids were predicted in two genomes. Three virulence types (capsule formation, lipopolysaccharide modification, and stress response) were identified. Phylogenomic analysis confirmed species-level assignments and revealed underrecognized lineages, emphasizing the value of genome-based approaches for accurate classification. Conclusions: Clinical Bacteroides isolates display diverse resistance and virulence profiles, highlighting the importance of strain-level genomic surveillance. Full article