Search Results (110)

×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (trnK–rps16, ndhF) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S–ITS1–5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from Triticum aestivum; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from T. aestivum. In contrast, ETS sequence analysis showed phylogenetic affinity to Elytrigia intermedia, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of T. aestivum-like ribotypes in the hybrid’s rDNA pool, with only a minor fraction identical to the main ribotype of E. intermedia. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of E. intermedia populations. The predominance of the wheat genome in ×T. cziczinii is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins. Full article

Objective: Although Las Vegas is a major tourist hub, it is not among the counties that are under CDC surveillance for Clostridioides difficile infection (CDI), a major nosocomial infection. To determine the distribution of C. difficile ribotypes in the Las Vegas area, we collected stool samples from CDI-positive patients at the University Medical Center (UMC). Methods: We included adult patients diagnosed with CDI and provided informed consent. C. difficile was isolated from the stool samples and ribotyped. Demographic information was also obtained and analyzed. All information was compared to the surveillance data from the CDC. Results: We identified more frequently in male patients than in the CDC data. Less than half of the patients used antibiotics prior to the infection. We observed several comorbidities in our patient sample pool, with cardiovascular disease and diabetes being the most prevalent comorbidities. Hypervirulent C. difficile strain 027 was the most prevalent ribotype. Except for two samples of ribotype 076, all other samples represented unique singlet ribotypes. Four of these ribotypes (160, 302, 363, and 813) have not been explicitly reported in humans. Conclusions: Due to the unique environment created by the tourism industry in Las Vegas, this population is exposed to national and international visitors. This study shows the pre-COVID landscape of C. difficile ribotypes in Las Vegas and offers valuable insights into the varieties of C. difficile that are currently infecting this community. Full article

The bloom-forming dinoflagellates and euglenophyceae were observed in the coastal waters of Hammam-Lif (Southern Mediterranean), during a green tide event on 3 June 2023. The bloom was dominated by Lepidodinium chlorophorum, identified through ribotyping with densities reaching 2.3 × 10⁷ cells·L⁻¹. Euglena spp. and Eutrepsiella spp. contributed to the discoloration, with abundances up to 2.9 × 10⁷ cells·L⁻¹. Environmental data revealed significant depletion of nitrite and nitrate, coinciding with a rapid increase in sunlight duration, likely promoting the proliferation of L. chlorophorum and euglenophyceae. By 5 June, two days after the bloom, nutrient stocks were exhausted. Diatoms appeared limited by low silicate concentrations (<0.05 µmol·L⁻¹), while dissolved inorganic phosphate and Nitrogen-ammonia were elevated during the bloom (0.88 and 4.8 µmol·L⁻¹, respectively), then decreased significantly afterward (0.23 and 1.06 µmol·L⁻¹, respectively). Low salinity (34.0) indicated substantial freshwater input from the Meliane River, likely contributing to nutrient enrichment and bloom initiation. After the event, phytoplankton abundance and chlorophyll levels declined, with a shift from dinoflagellates to diatoms. The accumulation of pigments (chlorophyll b and carotenoids) and the presence of Mycosporine-like amino acids (MAAs) during and after the bloom suggest that UV radiation and Nitrogen-ammonia were key drivers of this green tide. Full article

Clostridioides difficile was first identified in 1935 and subsequently emerged over the next several decades as the predominant bacterial cause of healthcare-associated gastrointestinal infections, placing a significant burden on healthcare systems worldwide. A major driver of the rapid rise in the incidence of C. difficile infection (CDI) was the emergence and spread of a hypervirulent strain, which became known as PCR ribotype 027 (RT027). The C. difficile RT027 strain produced not just the typical toxin A and toxin B virulence factors but also expressed a third toxin called binary toxin that enhanced pathogenicity. Interestingly, the C. difficile RT027 strain apparently emerged at least twice in geographically distinct areas. The two lineages can be differentiated by their resistance or susceptibility to fluoroquinolones. Other ribotypes of C. difficile that also express binary toxin have emerged recently, some of which are highly related genetically to RT027. The aim of this study is to integrate genomic data and published literature to clarify the emergence, divergence, and apparent decline of C. difficile RT027. Full article

In veterinary hospitals, the risk of C. difficile nosocomial acquired infections remains largely unknown, and only a few studies surveyed the environmental prevalence of C. difficile in these facilities. The aim of this study was to determine the prevalence of C. difficile in the Ontario Veterinary College large animal hospital environment and to characterize the recovered isolates. Methods. The environment of the large animal clinic of a university veterinary hospital was tested for the presence of C. difficile. Samples were collected from 157 surface sites and cultured using selective enriched broth and selective agar media. Multiplex PCR method for the detection of C. difficile toxin A (tcdA), toxin B (tcdB) binary toxin (cdtA⁄cdtB) genes; high-resolution capillary gel-based electrophoresis PCR-Ribotyping; multilocus sequence typing (MLST) and antimicrobial resistance predictions from sequenced genome were performed. Results. Thirteen isolates were recovered from 157 (8.3%) of multiple sampled sites of the main hospital. Ten distinct ribotypes, of which 7 were positive for toxin genes A and B, and all were negative for binary toxin genes. The two most common PCR ribotypes were 014 and 010. Isolates belong to the MLST Clade 1 and were further divided into 5 different sequence types. A high prevalence of AMR genes was observed in some isolates. Conclusions. C. difficile is present in different areas of the large animal hospital environment, particularly areas of high traffic and surfaces difficult to clean. Active surveillance and biosecurity measures should be in place to maintain a low environmental contamination and prevent nosocomial infections. Full article

The unarmored dinoflagellate Akashiwo sanguinea is a cosmopolitan harmful algal species known for forming intense blooms leading to mass mortality of fish, shellfish, and seabirds. Globally distributed populations of A. sanguinea have been classified into four ribotypes based on their characteristic sequences in LSU rRNA gene and primary geographic distributions. In this study, we compared the bacterial communities co-existing with the six strains of A. sanguinea from China and the USA (belonging to two ribotypes) using high-throughput sequencing of 16S rRNA gene amplicons. Generally, a bacterial microbiome with high diversity was found to be associated with laboratory-cultured A. sanguinea strains from different geographic origins. Based on ribotype classification, the six samples were divided into two groups (ribotype A: AsCHINA; ribotype C: AsUSA) for subsequent comparative analyses of their bacterial communities. Beta diversity analysis revealed a clear separation between the two groups, reflecting significant differences in bacterial community composition between the two ribotypes. Significantly higher abundance of nitrogen-fixing bacteria was found in the AsUSA group, suggesting that ribotype C may benefit from external nitrogen sources provided by their bacterial associates. If this also holds true in natural environments, this nitrogen-fixing partnership likely confers a competitive advantage to ribotype C in oligotrophic offshore waters, and potentially extends bloom duration when environmental nitrogen is depleted. Our study raised the possibility that different ribotypes of A. sanguinea may harbor distinct prokaryotic microbiomes in their phycospheres under stable cultivation conditions. Further comprehensive comparison among more isolates across all four ribotypes is highly necessary to validate this hypothesis. Full article

The emergence of antimicrobial resistance (AMR) in Clostridium difficile (C. difficile), particularly to last-line antibiotics such as linezolid, represents a critical challenge in clinical settings. This study investigates the genomic epidemiology of linezolid-resistant C. difficile, focusing on the distribution and mutational patterns of the chloramphenicol–florfenicol resistance (cfr) gene and its association with multidrug resistance. We analyzed 514 clinical isolates (354 from NCBI Pathogen Detection, 160 from EnteroBase), revealing distinct prevalence patterns among cfr subtypes: cfr(C) was dominant (156/354 NCBI strains; 101/160 EnteroBase strains), whereas cfr(B) frequently harbored missense mutations (p.R247K, p.V294I, and less commonly p.A334T). The cfr(E) subtype was exclusively identified in ribotype 027 (RT027) strains. Notably, cfr(C) exhibited a strong association with RT017, correlating with a conserved 99 bp genomic deletion. Phylogenetic analysis linked cfr-carriage to predominant sequence types (ST1 in NCBI strains, ST37 in EnteroBase isolates). Furthermore, the co-occurrence of cfr with additional AMR genes conferred resistance to macrolides (erythromycin, azithromycin) and tetracyclines, indicating a convergent evolution toward multidrug resistance. These findings underscore the interplay between cfr mutations, hypervirulent ribotypes, and AMR dissemination, necessitating enhanced surveillance to mitigate the spread of resistant C. difficile lineages. Full article

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal transcribed spacer ITS1 and the 5.8S rRNA gene in the cultivated species was studied with next-generation sequencing (NGS), and the patterns of occurrence and distribution of the ribotypes were compared among them and with those of the wild species. According to these data diploid, A. strigosa is more closely related to the diploid A. hirtula than to polyploid oats, and it could have evolved independently of polyploid cultivated species. The tetraploid Avena abyssinica could be a cultivated derivative of A. vaviloviana. Two hexaploid cultivated species, A. byzantina and A. sativa, could have a different origin; A. sativa could be the cultivated form of A. fatua, whereas A. byzantina could originate independently. It was found that the oat species with the A and C subgenomes, even with strong morphological and karyological differences, could intercross and pass the further stages of introgression producing a new stable combination of genomes. Our data show that almost all species of Avena could form an introgressive interspecies complex. Full article

In recent decades, ships’ ballast water and associated sediments have been recognized globally as significant vectors for the dissemination of non-indigenous species, which has attracted extensive attention due to its ecological and economic impacts. The characteristics of production of resting cysts in the dinoflagellate life cycle further increases the risk of biological invasions through ballast tank sediments. Despite extensive research which has characterized the species diversity of dinoflagellate cysts within ballast tank sediments, the possibility and importance of invasions caused by different ribosomal types of the same species have been paid little attention. In this study, two cultures of dinoflagellates were established through cyst germination from the ballast tank sediments collected from two ships (“THETIS” and “WARIYANAREE”) arriving at the Jiangyin Port (China) and identified as Wangodinium sinense Z. Luo, Zhangxi Hu, Yingzhong Tang and H.F. Gu by comprehensive phylogenetic analysis of rDNA sequences (including LSU, SSU, and ITS1-5.8S-ITS2). Despite the rDNA sequences of the isolates showing a generally high similarity to reference sequences, the LSU D1-D6 sequences contained up to 11 stable single nucleotide polymorphisms (SNPs), while SSU and ITS1-5.8S-ITS2 sequences exhibited up to five and two divergence sites, respectively. Moreover, phylogenetic analyses based on partial LSU and SSU rDNA sequences further indicated that strains germinated from ships’ ballast tank sediments formed a strongly supported sister clade to the strains previously isolated from Chinese and Korean waters, representing a novel ribo-type distinct from Chinese and Korean strains. Detailed morphological observations using light microscopy (LM) and scanning electron microscopy (SEM) did not find differences between our isolates and the holotype of the species in key diagnostic characteristics including the position and shape of the nucleus and chloroplasts, as well as the ASC structure, which suggested that no significant morphological divergence has occurred among these ribo-types. Acute toxicity exposure assays indicated that this ribo-type of W. sinense posed no lethal effect on rotifers at concentrations ≤ 10⁴ cells/mL, yet it remains necessary to maintain vigilance regarding the potential risk of algal blooms resulting from higher cell density or environmental changes in the invaded ecosystems. This study reports the first successful germination of W. sinense cysts from ballast tank sediments, indicating that its cysts may be widely transferred through ballast tank sediments, and presents a potential risk of bio-invasions of new genotypes of species to a region where other genotypes of the same species have been present as indigenous species. Full article

Moricandia moricandiodes is an endemic species found in the south and east of the Iberian Peninsula. Five subspecies have been recognized, and all exist as fragmented populations on limestones and marls with salt and gypsum intrusions under a continental Mediterranean climate, except for one of the subspecies, which inhabits semi-arid and hotter environments. In this study, we sampled populations covering the distribution area of the species and performed a population and phylogeographic study to assess the evolutionary history of populations and the taxonomic relationships of subspecies. ISSR markers, nrITS, and plastid sequences were used in the analyses. The results revealed that, in general, southern populations showed higher genetic diversity than northern populations, suggesting that the former are located in glacial refugia. Furthermore, we did not find clear differences between subspecies, except for M. moricandioides subsp. pseudofoetida, which showed exclusive haplotypes and an exclusive ribotype. Isolation and rapid divergence are discussed as the probable causes of differentiation, whereas bottlenecks and secondary contact between populations would explain the absence of differentiation among the other subspecies. Finally, we propose a few guidelines for the conservation of M. moricandioides. Full article

Clostridioides difficile Infection (CDI) continues to be a major cause of antibiotic-associated diarrhea and pseudomembranous colitis, fueled in large measure by virulence factors TcdA and TcdB. These giant glucosyltransferase toxins interfere with host cytoskeletal integrity and inflammatory signaling by inhibiting Rho GTPase; however, the detailed structural dynamics, receptor selectivity, and subcellular trafficking mechanisms remain in part unspecified. This review integrates recent insights from cryo-electron microscopy (cryo-EM) and X-ray crystallography to describe the quaternary architecture of TcdA/B, emphasizing conformational changes key to pore formation and endosomal escape. We also examine the genomic heterogeneity of hypervirulent C. difficile strains (e.g., ribotype 027), correlating toxin gene polymorphisms (e.g., tcdC mutations) with increased toxin production and virulence. Mechanistic explanations of toxin-driven inflammasome activation and epithelial barrier dysfunction are situated within host immune evasion mechanisms, including microbiota-derived bile acid regulation of toxin stability. Subsequent innovative therapeutic strategies, encompassing the utilization of engineered neutralizing antibodies that specifically target the autoprocessing domain alongside structure-guided small-molecule inhibitors, are subjected to a rigorous evaluation. By integrating structural biology, systems-level omics, and clinical epidemiology, this review establishes a comprehensive framework for understanding C. difficile toxin pathogenesis and guiding next-generation precision antimicrobials. Full article

Background: Clostridioides difficile infection (CDI) remains a significant public health challenge in the United States, with limited treatment options currently available. Objectives: This study investigated the antimicrobial efficacy of a fungal-based fermentate derived from Aspergillus oryzae, cultivated in a proprietary food-grade medium, against toxigenic strains of C. difficile. Methods and Results: The ethyl acetate extract of A. oryzae fermentate (fungal extract) exhibited potent bactericidal activity, producing a significant zone of inhibition across all tested C. difficile strains, including hypervirulent Ribotype 027. Notably, 80% of the tested strains (four out of five) exhibited greater susceptibility to the fungal extract than to 5 µg vancomycin discs. Inner colony formation within the zone of inhibition was observed for all strains treated with vancomycin but only one strain was exposed to fungal extract. Time kill assays further confirmed the rapid bactericidal effect of the fungal extract, achieving complete C. difficile eradication within six hours. Mechanistic studies using scanning electron microscopy (SEM) and flow cytometry revealed that the fungal extract induced severe membrane disruption, leading to intracellular leakage and complete lysis. Flow cytometry analysis confirmed membrane depolarization and permeability loss on C. difficile cells. Conclusions: These findings highlight that the fungal extract of A. oryzae exhibits a promising antimicrobial activity against C. difficile. Future studies will focus on identifying its active components, evaluating its efficacy in vivo, and assessing its impact on gut microbiota to establish its potential clinical application in managing CDI. Full article

Background/Objectives: Clostridioides difficile infection (CDI) represents a significant public health challenge globally, driven by its increasing prevalence, hypervirulent strains like ribotype 027 (RT027), and growing antibiotic resistance. This study aimed to evaluate the prevalence of RT027 and analyze molecular markers of vancomycin and metronidazole resistance in stool samples from CDI patients hospitalized in Poland between 2017 and 2019. Methods: A total of 200 stool samples from confirmed CDI cases were analyzed for the presence of RT027, vanA (vancomycin resistance), and nim (metronidazole resistance) genes. DNA was extracted, and a polymerase chain reaction (PCR) was conducted using specific primers. Statistical associations between RT027 and resistance genes were evaluated using chi-square tests and logistic regression. Results: RT027 was detected in 14% of samples. The vanA gene, indicative of vancomycin resistance, was found in 52.5% of samples, while the nim gene, associated with metronidazole resistance, was present in 1.5% of cases. Co-occurrence of RT027 with vanA was not statistically significant. The study revealed no significant association between RT027 and vanA. Also, no significant association was observed between RT027 and nim due to the latter’s low prevalence. Conclusions: This study highlights a concerning prevalence of vanA among CDI cases, indicating widespread vancomycin resistance and challenging current treatment guidelines. While RT027 prevalence was moderate, no significant associations with vancomycin or metronidazole resistance were observed. These findings emphasize the need for molecular surveillance and improved antimicrobial stewardship to manage CDI effectively. Full article

Clostridioides difficile is the leading cause of antibiotic-associated diarrhea in hospitalized patients. In recent years, the incidence of C. difficile infection (CDI) has increased globally, with a notable rise in community-associated CDI (CA-CDI). The presence of the microorganism in animals, the environment, and food suggests that these sources may contribute to the spread of the infection in the community. This review applies a One Health approach, integrating human, animal, and environmental health, to provide a comprehensive strategy for understanding and managing this pathogen. Findings reveal the widespread dissemination of C. difficile in animals, the environment, and food. The predominant PCR ribotypes identified were RTs 078 and 014/020, followed by RTs 126, 001, 002, 009, 010, and 033. C. difficile strains exhibited resistance to multiple antimicrobial agents, including clindamycin, erythromycin, fluoroquinolones, cephalosporins, and tetracyclines. Discriminative typing methods, such as whole-genome sequencing, revealed clonal relationships between C. difficile strains from humans and animals, indicating either direct transmission or a common environmental source of infection. The high genetic similarity between isolates from the environment and humans indicates potential environmental contamination. Additionally, clusters of C. difficile strains found in food and humans indicate a possible foodborne transmission route. This review summarizes the current knowledge on the role of Clostridioides difficile within the One Health framework. Full article

Clostridioides difficile (C. difficile), once considered a predominantly nosocomial pathogen, is increasingly implicated in community-acquired infections (CA-CDIs). This study investigates the prevalence, ribotypes, and antimicrobial susceptibility of C. difficile in Irish pork products and abattoirs, with a focus on the potential public health implications. A total of 180 retail pork products and 150 pig carcase swabs from three abattoirs were examined, alongside 30 environmental lairage samples. The C. difficile isolates were characterised through ribotyping and tested in terms of antimicrobial susceptibility. No C. difficile was isolated from the retail pork, while the carcase swabs yielded a low recovery rate (0.66%). However, the lairage areas were contaminated with C. difficile (33%), and six different ribotypes were identified, including the clinically relevant RT078. The ribotypes exhibited susceptibility to the antibiotics used to treat C. difficile infection (CDI) (fidaxomicin, vancomycin, and metronidazole) but showed resistance to tetracycline (9%) and ciprofloxacin (100%). These findings align with the international findings on antimicrobial resistance in C. difficile and suggest that strict EU food safety standards could mitigate retail pork contamination risks. Nevertheless, the environmental exposure during slaughtering and handling processes presents potential transmission risks for workers. Full article