Search Results (160)

Entoloma is a species-rich and taxonomically complex genus in Entolomataceae, characterised by pink to pinkish-brown spore prints and angular basidiospores. Within this genus, Entoloma sect. Madida, corresponding to the Prunuloides lineage in recent infrageneric treatments, includes several morphologically similar taxa related to the E. bloxamii–prunuloides complex. However, this lineage remains poorly documented from subtropical eastern China. In this study, we examined Entoloma collections from the Huangshan region of Anhui Province, China, using macromorphological observations, micromorphological characters, scanning electron microscopy (SEM) of basidiospores, and multilocus phylogenetic analyses based on ITS, LSU and rpb2. We recognised two independent and well-supported species-level lineages, described here as Entoloma theobrunneum and E. ochrorubrum. Entoloma theobrunneum is phylogenetically close to E. corneri but differs in its smoky grey to tea-brown pileus, snakeskin-like stipe pattern, higher basidiospore Q values, larger basidia, and the presence of pleurocystidia and caulocystidia. Entoloma ochrorubrum is associated with taxa of the E. bloxamii complex but is distinguished by its darker iron-red to ochre-brown pileus, blackish-brown central papilla, cracking pileus margin, longitudinally fibrillose stipe, higher basidiospore Q values, and basidia with granular contents. SEM observations are provided only as supplementary documentation of the three-dimensional architecture of basidiospores. These findings add two phylogenetically supported Chinese species to the current framework of E. sect. Madida, help fill a regional documentation gap in subtropical eastern China, and provide additional East Asian data relevant to future evaluation of the current infrageneric framework of Entoloma. Full article

The genus Xylaria (Xylariaceae, Ascomycota) comprises a morphologically and ecologically diverse group of fungi with a predominantly saprobic lifestyle, widely distributed in forest ecosystems worldwide. Despite its global occurrence, its diversity in European Atlantic laurel forests (laurisilva), both insular and continental, remains poorly understood. In this study, we examined more than 80 collections of Xylaria from laurisilva forests in Madeira and the Azores (Portugal), the Canary Islands (Spain), and relict laurel woodlands in mainland Iberia, documenting at least 13 species. Several collections could not be successfully sequenced, suggesting that additional taxa may occur. Among the identified species, eight are described here as new to science and are supported by morphological differences and multilocus phylogenetic analyses. Species delimitation was based on an integrative approach combining detailed morphological observations with phylogenetic inference from ITS, LSU, RPB2, and TUB2 loci. Our results reveal a substantially higher diversity of Xylaria in these ecosystems than previously recognized and confirm the importance of multilocus frameworks for resolving species boundaries, particularly in morphologically cryptic lineages. This study expands the known diversity of Xylaria in Europe and identifies Atlantic laurel forests as important reservoirs of fungal diversity and evolutionary novelty. Full article

The spongy moth (Lymantria dispar) is a significant defoliator of broadleaf forests and fruit trees, but its population genetic structure in Central Asia remains poorly defined. We analyzed 153 specimens collected from ten populations across Kazakhstan between 2023 and 2024, using a combination of diagnostic real-time PCR, RAPD genotyping, and mitochondrial COI sequencing. Subspecies identification and Asian introgression were initially assessed with the COI/FS1 TaqMan assay. All samples carried the European mitochondrial type L. dispar dispar, while the nuclear FS1 locus indicated Asian introgression in 92.8% of specimens, including eleven heterozygotes for the Asian allele. RAPD amplification with five polymorphic primers produced 107 variable bands, which we converted into a presence/absence matrix for population genetics analysis. Principal coordinate analysis showed weak but detectable population structure, and Bayesian clustering (STRUCTURE) supported the presence of two primary nuclear clusters. Populations from Ketpentau, Sumbe, Kazachka, Butakovka, and Pavlodar were assigned predominantly to one cluster, whereas most individuals from Almaty, Ile-Alatau, Koksu, North Kazakhstan, and Tekeli were assigned predominantly to the other, with limited admixture in several localities. COI sequences formed a single, minimally differentiated L. dispar clade, with no evidence of distinct mitochondrial lineages. Overall, these findings reveal extensive Asian nuclear introgression in populations retaining European mitochondrial haplotypes, supporting the interpretation of Kazakhstan as part of a broad contact zone within the larger dispar–asiatica gradient. The observed mito-nuclear discordance has important implications for quarantine diagnostics and highlights the need for multilocus molecular assays in regional biosurveillance. Full article

Background/Objectives: Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Oman, this study aimed to characterize the genomic epidemiology, serotype distribution, and antimicrobial resistance (AMR) of Streptococcus pneumoniae causing invasive pneumococcal disease (IPD). Methods: All IPD isolates collected through national laboratory-based surveillance between 2018 and 2021 were analyzed using Whole-Genome Sequencing (WGS). Bioinformatics tools determined serotypes, multilocus sequence types (MLSTs), and Global Pneumococcal Sequence Clusters (GPSCs). Clinical correlates and predictors of mortality were assessed via multivariate logistic regression. Results: A total of 129 IPD isolates were included. Serotype 3 (11.6%) was the most prevalent, followed by 23B and 9N (10.8% each), and 8 (8.5%). PCV13 serotypes accounted for only 26.4% of isolates, while PCV20 coverage reached 59.7%. Significant clonal diversity was observed, with GPSC12 (Serotype 3) and GPSC699 (Serotype 9N/13) being prominent lineages. Multidrug resistance (MDR) was identified in 36.4% of isolates, primarily driven by GPSC6 and GPSC699. The case fatality rate was 23.0%. Advanced age (≥65 years) and clinical presentation with bacteremia were significant independent predictors of death, whereas bacterial genotype and AMR status were not. Conclusions: The findings demonstrate significant serotype replacement in Oman after the introduction of PCV13. The high prevalence of non-vaccine serotypes and emerging MDR clones justifies the transition to higher-valency vaccines like PCV20. Sustained genomic surveillance remains essential to monitor the evolving landscape of invasive pneumococcal lineages. Full article

Accurate species delimitation is fundamental yet challenging, particularly in recently diverged, phenotypically conservative taxa such as bats. The “Rhinolophus macrotis group” represents one of the most taxonomically contentious groups among horseshoe bats. During field surveys in Southwest China, we discovered an unidentified Rhinolophus sp. occurring sympatrically with R. osgoodi and R. episcopus, sharing broad morphological affinities with recognized species of the “R. macrotis group.” To explore its taxonomic status, we employed an integrative approach combining morphological, acoustic, and multi-locus genetic (mitogenomic and nuclear) data. Phenotypically, Rhinolophus sp. closely resembles R. osgoodi but can be distinguished by its divergent echolocation resting frequency. Genetically, while mitochondrial data deeply nested Rhinolophus sp. within R. osgoodi with a shallow divergence time, phylogenies based on two nuclear introns positioned it closer to two other species, R. episcopus and R. siamensis. Species delimitation based on these genetic markers revealed a pattern of mitochondrial subdivision contrasted by overly conservative nuclear signals. Such mito-nuclear discordance suggests a complex evolutionary history that complicates taxonomic assignments. Given that only three specimens of Rhinolophus sp. were available, which precludes a robust assessment of intraspecific variation, we provisionally designate it as a candidate lineage within the “R. macrotis group,” warranting future validation with additional comprehensive evidence. This study highlights the indispensable utility of integrative taxonomy in uncovering hidden diversity and provides insights into chiropteran evolutionary history. Full article

Background/Objectives: Multidrug resistant (MDR) Salmonella represents a major global public health challenge within the One Health interface. This study aimed to characterize the genomic epidemiology of Salmonella isolates from Colombia and resolve the genetic architecture of novel MDR plasmids identified in foodborne strains. Methods: A total of 90 Salmonella isolates collected between 2002 and 2009 from various food sources and food-producing animals in Colombia were analyzed using whole-genome sequencing (WGS). Bioinformatics tools were employed for serotype prediction, multi-locus sequence typing (MLST), and resistome/virulome profiling. Long-read sequencing was utilized to close the complete sequences of representative MDR plasmids. Results: 45.6% of isolates exhibited antimicrobial resistance, with seven being classified as MDR. The major serotypes identified were Uganda (n = 20), Newport (n = 10), and Braenderup (n = 10). We characterized a novel 229,037 bp IncHI1 plasmid (pCFS0255-1) harboring a copper homeostasis and silver resistance island (CHASRI) integrated with tetracycline and macrolide resistance clusters. Additionally, a 99,288 bp IncI1 plasmid (pCFS0255-2) carrying a unique aminoglycoside resistance module was resolved. Conclusions: Our findings highlight the persistence of specific Salmonella lineages in the Colombian food chain and the role of hybrid plasmids in the co-selection of metal and antibiotic resistance. The study underscores the necessity of implementing WGS-based surveillance to track emerging MDR threats. Full article

Lactococcosis has emerged as an economically and ecologically significant disease in aquatic animals worldwide. This study employed multilocus sequence typing (MLST) to investigate the genetic diversity of Lactococcus spp. strains from Brazilian fish species and evaluate their phylogenetic relationships with global isolates to elucidate potential epidemiological connections involving multiple host species and distinct geographic regions. A total of 55 isolates from different laboratories had their DNA extracted, followed by the amplification and sequencing of the internal fragments of seven housekeeping genes (als, atpA, tuf, gapC, gyrB, rpoC and galP). Sequence types (STs) and clonal complexes (CCs) were defined. An unrooted neighbor-joining phylogenetic tree was generated using allele profiles from this study and those previously reported from other aquatic animal species. The isolates comprised 29 STs (11 previously reported, 18 novel ones), which were grouped into species-specific CCs: CC5 (L. formosensis); CC4, CC17, CC62 (L. garvieae); CC24, CC29, CC97 (L. petauri). Considerable genetic divergence was observed, with L. formosensis and L. garvieae forming heterogeneous populations, while L. petauri was more homogeneous. These findings describe the MLST structure of the sampled isolates and should be interpreted as hypothesis-generating rather than population-level estimates of genotype prevalence. Phylogenetics confirmed groupings within the CCs and revealed additional phylogenetic clustering patterns. In conclusion, the Brazilian Lactococcus spp. strains analyzed in this study constitute a genetically diverse population based on their STs. MLST and phylogenetic analysis demonstrated genetic relatedness between the L. garvieae and L. formosensis isolates from this study and those from other aquatic animal species. In contrast, all the STs identified for L. petauri in this study were unrelated to the MLST lineages responsible for outbreaks in Brazilian Nile tilapia (Oreochromis niloticus) and North American rainbow trout (Oncorhynchus mykiss). This suggests that piscine L. petauri populations in the Americas evolved from distinct ancestral origins. Full article

Reliable species-level information on elasmobranchs (sharks, rays, and skates) in the Arabian Gulf remains limited, despite these fish being among the most threatened marine vertebrates. Taxonomic uncertainty, driven by morphological similarities and incomplete reference datasets, continues to hinder accurate biodiversity assessments in the region. In this study, NADH dehydrogenase subunit 2 (NADH2) gene sequences were analyzed to assess the taxonomic status of elasmobranchs in United Arab Emirates waters, based on 182 specimens representing 31 species (15 sharks and 16 batoids) across 12 families. Shark lineages were consistently recovered and matched closely with published references, indicating a stable taxonomy. Batoids (rays), however, showed greater complexity, including misidentification among morphologically similar taxa, gaps in available reference sequences, and signs of possible cryptic diversity, reflecting persistent challenges in species identification and the need for more comprehensive molecular resources. Our findings highlight the value of genetic approaches in improving taxonomic resolution and establishing robust biodiversity baselines. Expanding reference databases, applying multi-locus genomic approaches, and broadening regional sampling will be essential to refining taxonomic frameworks and informing conservation management for elasmobranchs in the Arabian Gulf. Full article

Listeria monocytogenes is already a well-known foodborne bacterial pathogen, ubiquitously dispersed not only in the food production environment but also in the primary animal production environment as well. The present study performed whole-genome characterization of the multidrug-resistant (MDR) L. monocytogenes strain BF11, previously isolated from raw pet food and phenotypically described for antimicrobial resistance. To this end, the genomic analysis performed on the isolate confirmed the pathogen’s designation as a serotype 1/2b strain belonging to ST5 and CC5 (Lineage I), carrying multiple MDR genes, stress-related genes, and mobile genetic elements, despite the absence of plasmids. The strain is phylogenetically closely related to Lineage I epidemic strains (e.g., F2365), as it has a full-length inlA and a functional prfA, rendering it capable of invading human cells and marking its high virulence. Overall, this strain may represent a potentially novel genomic profile when core genome multilocus sequence typing (cgMLST) is used, although further data from additional isolates would be required to confirm its classification within a new Complex Type, while displaying a hybrid unique profile. It is an evolved ST5 L. monocytogenes strain that has acquired genetic material conferring a “clinical signature” (Lineage I-like) and an extensive resistance network. Therefore, presence of L. monocytogenes strain BF11 in pet food is alarming, since such hybrid strains often evade surveillance monitoring as they do not fit strictly into classical categories, posing a serious food safety and public health threat in the concept of One Health. Full article

Gibellula (Cordycipitaceae, Hypocreales) represents a group of highly specialized obligate fungal pathogens restricted to spider hosts. Species delimitation was conducted using morphological characteristics in combination with multilocus phylogenetic analyses (nrSSU, ITS, nrLSU, tef1-α, rpb1, rpb2), and we recognized nine spider-associated Gibellula species from specimens collected in the Lancang–Mekong biodiversity hotspot (China, Laos, Thailand, and Vietnam). Among them, four are described as new to science: Gibellula longiconidiophora sp. nov., G. mekongensis sp. nov., G. ovorum sp. nov., and G. pseudopilosa sp. nov. The other five species represent new national distributional records: G. yunnanensis (new to Laos), G. pseudopigmentosa (new to Thailand), G. trimorpha (new to Vietnam), G. penicillioides (new to Laos), and G. scorpioides (new to China and Laos). Phylogenetic analyses resolved these taxa into well-supported lineages. Notably, G. ovorum is a rare example of a Gibellula species parasitizing spider egg sacs rather than adult spiders, revealing an unusual substrate shift. Morphological distinctions among the new species include differences in conidiophore length, synnematal development, conidial size, and sporulation patterns. Detailed descriptions, illustrations, and taxonomic comparisons are provided. This study significantly expands the known diversity and geographic distribution of Gibellula in the Lancang–Mekong region and underscores the importance of integrative taxonomy for uncovering hidden diversity in spider-pathogenic fungi. Full article

Background: Staphylococcus pseudintermedius is a major opportunistic pathogen of dogs and the primary cause of canine pyoderma and other infections. The global emergence of methicillin-resistant S. pseudintermedius (MRSP) represents a significant challenge in veterinary medicine due to its frequent multidrug-resistant phenotype and limited therapeutic options. Methods: We describe the phenotypic and genomic characterization of an MRSP isolate recovered from a vaginal swab of an 11-year-old dog diagnosed with vulvovaginitis in southern Italy. Antimicrobial susceptibility testing was performed using broth microdilution according to CLSI VET01S guidelines. Whole-genome sequencing was conducted to determine sequence type and antimicrobial resistance determinants. Results: The isolate was identified as S. pseudintermedius by MALDI-TOF MS and confirmed by genomic analysis. Multilocus sequence typing assigned the strain to sequence type ST2333. Phenotypically, the isolate exhibited multidrug resistance, including resistance to β-lactams, macrolides, lincosamides, tetracyclines, aminoglycosides, fluoroquinolones, and trimethoprim–sulfamethoxazole, while remaining susceptible to amikacin, rifampicin, florfenicol, and vancomycin. Whole-genome sequencing confirmed the presence of mecA and additional resistance determinants consistent with the observed phenotype. Conclusions: This report suggests the possible occurrence of an MDR MRSP ST2333 lineage in southern Italy and highlights the importance of combined phenotypic and genomic surveillance to support antimicrobial stewardship in veterinary medicine within a One Health framework. Full article

Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene bla_OXA-23 was detected in all CRAB isolates, together with clone-specific bla_OXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article

Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of Achromobacter sp. isolates recovered from root and foliar tissues of Citrullus colocynthis and Peganum harmala, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names Achromobacter colocynthi sp. nov., Achromobacter maghribensis sp. nov., and Achromobacter semiaridum sp. nov. Genome assemblies were highly complete (98.7–99.2%) with minimal contamination (<1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within Achromobacter sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of Achromobacter sp., establish C. colocynthis and P. harmala as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments. Full article

Tilia cordata Mill. is a long-lived, ecologically important broadleaved tree species that maintains high genetic diversity despite habitat fragmentation and historical range shifts. In this study, we assessed genetic diversity, clonal structure, and population differentiation in six genetic conservation units (GCUs) in Lithuania using nuclear microsatellite markers. A total of 1109 individuals were successfully genotyped, revealing 979 unique multi-locus genotypes, with 17% of individuals assigned to clonal lineages. Clonal groups were generally small and spatially restricted, indicating localized vegetative regeneration. Genetic diversity was high across all populations, with similar levels of observed and expected heterozygosity, consistent with predominantly outcrossing reproduction. Juvenile cohorts exhibited slightly higher allelic richness and latent genetic potential compared to mature trees, suggesting effective regeneration and maintenance of genetic variation. Genetic differentiation among populations was low but significant (F_ST = 0.013; G″_ST = 0.051), with evidence of clustering corresponding to provenance regions. High gene flow (Nm ≈ 10) likely contributes to weak population structure, although regional differentiation persists. The results demonstrate that Lithuanian T. cordata populations retain a robust genetic framework, combining high within-population diversity with moderate structuring. These findings highlight the importance of conserving multiple GCUs and implementing genetic monitoring to ensure long-term population viability under changing environmental conditions. Full article

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of invasive disease, yet contemporary genomic data from Canada remain scarce. We investigated 56 cases of invasive SDSE infection identified between 2018 and 2022 in two major tertiary care teaching hospitals in Toronto, Ontario, and characterized 49 corresponding isolates by whole-genome sequencing. Nearly three-quarters of infections were caused by the globally expanding ST20 emm type stG62647 lineage. Patients infected with this lineage were significantly older than those infected with non-ST20 lineages across both bloodstream and non-blood infections. Core-genome phylogenetic analysis revealed a highly clonal ST20 cluster, although two isolates had divergent emm types suggesting recombination at the emm locus. Non-ST20 lineages were numerically smaller and genetically more heterogeneous, including distinct sublineages within ST3 and ST34. All isolates were susceptible to β-lactams and vancomycin. Resistance to tetracycline, erythromycin, and clindamycin was detected in a subset of isolates and was associated with genes tetM, tetO, ermA, ermB, and msrD. Several antimicrobial resistance determinants were located on mobile genetic elements, including integrative and conjugative elements. Our findings provide a contemporary genomic view of invasive SDSE in Toronto, highlighting the dominance of the ST20 stG62647 lineage in agreement with recent global observations. Full article