Search Results (110)

The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata Lam. Since only P. indica is traditionally used in Thai polyherbal products, adulteration with other species could potentially compromise the therapeutic efficacy and overall effectiveness of these formulations. To address this issue, a MassARRAY iPLEX assay was developed to accurately identify and differentiate P. indica from its closely related species. Five single nucleotide polymorphism (SNP) sites—positions 18, 112, 577, 623, and 652—within the internal transcribed spacer (ITS) region were selected as genetic markers for species identification. The assay demonstrated high accuracy in identifying P. indica and was capable of detecting the species at DNA concentrations as low as 0.01 ng/µL. Additionally, the assay successfully identified P. zeylanica in commercial crude drug samples, highlighting potential instances of adulteration. Furthermore, it was able to distinguish P. indica in mixed samples containing P. indica, along with either P. zeylanica or P. auriculata. The developed MassARRAY iPLEX assay proves to be a reliable and effective molecular tool for authenticating P. indica raw materials. Its application holds significant potential for ensuring the integrity of herbal products by preventing misidentification and adulteration. Full article

Background: Trichophyton indotineae, a new emerging pathogen according to the WHO, is known to cause severe forms of tinea. Given that traditional identification methods rely on morphological characteristics, and the morphological distinctions among T. indotineae, T. mentagrophytes, and T. interdigitale are minimal, the adoption of alternative diagnostic techniques, such as RT-PCR or gene sequencing, has become critically important to prevent misidentification. The purpose of this study was firstly to analyze the local epidemiology of dermatophytes isolated and secondly to investigate the presence of T. indotineae among the isolated strains. Methods: Between January 2021 and June 2024, 1096 samples of skin adnexa were analysed. The isolated strains belonging to the genus Trichophyton were submitted to molecular identification by ITS sequencing, and T. indotineae strains were subjected to squalene epoxidase (SQLE) sequencing analysis. Results: Trichophyton rubrum and Trichophyton interdigitale appear to be the most prevalent pathogenic species. Molecular identification reveals four T. indotineae strains (4/87; 4.61%) from Asian patients, which were also characterized by gene mutations associated with terbinafine resistance. Conclusions: This study has made it clear that there is a need to implement basic mycological diagnostics with molecular methods to avoid misidentifications, ensure the correct identification, and evaluate the presence of mutations associated with antifungal drug resistance. Full article

Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment. Full article

Candida auris (C. auris) is an emerging multidrug-resistant fungal pathogen recognized by the World Health Organization (WHO) as a critical global health threat. Its rapid transmission, high mortality rate, and frequent misidentification in clinical laboratories present significant challenges for diagnosis and infection control. This review provides a comprehensive overview of current and emerging diagnostic methods for C. auris detection, including culture-based techniques, biochemical assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and molecular diagnostics such as PCR and loop-mediated isothermal amplification (LAMP). We evaluate each method’s sensitivity, specificity, turnaround time, and feasibility in clinical and surveillance settings. While culture remains the diagnostic gold standard, it is limited by slow turnaround and phenotypic overlap with related species. Updated biochemical platforms and MALDI-TOF MS with expanded databases have improved identification accuracy. Molecular assays offer rapid, culture-independent detection. Antifungal susceptibility testing (AFST), primarily using broth microdilution, is essential for guiding treatment, although standardized breakpoints remain lacking. This review proposes an integrated diagnostic workflow and discusses key innovations and gaps in current practice. Our findings aim to support clinicians, microbiologists, and public health professionals in improving early detection, containment, and management of C. auris infections. Full article

In this study, we combined automated annotation tools with targeted dereplication based on MS/MS fragmentation pathway studies to identify polycyclic polyprenylated acylphloroglucinols (PPAPs) in Hypericum species, using H. patulum and H. hookeranium as a case study. These species, extensively used in traditional medicine, exhibit morphological similarities that often result in misidentification. Following UHPLC-HRMS/MS analysis of plant extracts, a molecular network approach facilitated a comprehensive comparison of their chemical composition, assigning specific clusters to O-glycosylated flavonoids and PPAPs. Eight peaks, including quercitrin, isoquercitrin, procyanidins, chlorogenic acid, quercetin, and glycosylated derivatives, were annotated from the GNPS database. For PPAPs, despite the structural complexity posing challenges for automated annotation using public databases, our targeted-dereplication strategy, relying on in-house spectral data, led to the putative identification of 22 peaks for H. patulum and H. hookeranium. Key compounds such as hyperforin, hyperscabrone K, and garcinialliptone M were detected in both species, underscoring their chemical similarity. MS/MS fragmentation pathways, particularly the successive losses of isobutene and isoprenyl units, emerged as a consistent signature for PPAP detection and may be useful for selecting PPAP-enriched extracts or fractions for further phytochemical investigations. Full article

An annotated list of liverworts of the Murmansk Region is compiled based on a critical compilation of publications and label data available in the information system CRIS (L.). It includes 210 species, 2 subspecies and 8 varieties, which is 59 species more than in the list of species published in 1982. Ten taxa were excluded through comparison with the previous list and later publications, due to misidentifications or new taxonomical treatments. Annotations for each species include the synonyms under which they were listed for the region; the category of threat in the Red Data Books of Europe, Russia and the Murmansk Region; links to the most representative publications on occurrence in each of nine accepted biogeographic provinces of the region; and at least one specimen number of the KPABG or INEP herbaria in the case of the absence of published data. In total, we provide 259 new records for different provinces based on herbaria KPABG (205 records) and INEP (52 records). Additionally, there are links to publications on the nucleotide sequence data of 149 specimens obtained for 82 species and for 1 variety from the Murmansk Region, including 14 specimens (11 species), published here for the first time. Species threatened in Europe, Russia and the Murmansk Region are discussed and future perspectives of liverwort study in the Murmansk Region are outlined. Full article

The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specimens and 31 egg cases from 26 skate species were barcoded. NJ and ML analyses showed that nearly all species exhibited unique barcodes or clusters of closely related haplotypes, except for Psammobatis normani/P. rudis and Dipturus trachyderma/D. argentinensis. The first pair was discriminated by NCD. BIN analysis recovered 17 groups, whereas ABGD recovered 23, better reflecting taxonomic diversity. In summary, 24 species were resolved by COI. Phylogeographic signals were observed for Amblyraja doellojuradoi and Zearaja brevicaudata. Compiling our results with data from BOLD, almost all the species occurring in the area possess barcodes, contributing to completing and curating the BOLD reference library, which constitutes an important tool for resolving taxonomic issues, tracing fishery products, and performing eDNA biomonitoring. Full article

Archaeognatha (bristletails) represent an evolutionarily significant but understudied insect group. Notably, the morphological identification method proposed by Mendes for Archaeognatha has certain limitations, which may lead to the underestimation or misidentification of some cryptic species. To address this issue, we employed an integrated strategy that combines morphological and molecular identification methods. Therefore, this study aimed to (1) identify cryptic diversity within Pedetontus silvestrii using mitogenomic data; (2) clarify phylogenetic relationships among Archaeognatha lineages; and (3) estimate divergence times for key taxonomic splits. We analyzed mitochondrial genomes from six P. silvestrii populations (Liaoning, Jilin, and Hebei Provinces) alongside 14 published Archaeognatha genomes. Key findings include the following: (1) Integrative analyses of genetic distances, phylogenetic reconstruction, bPTP-based molecular species delimitation, and divergence time estimation collectively revealed four evolutionarily distinct lineages within P. silvestrii. (2) Machilidae and Machilinae were non-monophyletic, whereas Petrobiellinae showed close affinity to Meinertellidae. (3) Archaeognatha originated ~301.19 Mya (Late Carboniferous); the Machilinae–Petrobiinae split occurred approximately 153.99 Mya (Jurassic). This study underscores the critical importance of mitogenomic analysis in elucidating cryptic biodiversity, while emphasizing the necessity of integrating morphological identification with molecular characterization for comprehensive species delineation in future taxonomic investigations. Full article

The genus Dendrobium (Orchidaceae) is highly renowned for its great medicinal and ornamental values. However, due to morphological similarities among closely related taxa within this genus, certain species are frequently subject to misidentification and adulteration in the market. Traditional morphological taxonomy and limited DNA markers prove challenging in effectively differentiating among them. Here, we generated an extensive single nucleotide polymorphism (SNP) dataset through whole genome re-sequencing (WGRS) of 41 Dendrobium species to evaluate its effectiveness in species identification. The phylogenetic relationships of 41 Dendrobium species were explored based on the SNP dataset, and then divergence times at each node were estimated. We found that the whole genome re-sequencing method achieved a 100% identification rate for all 41 species examined, indicating that whole genome re-sequencing could be employed to accurately authenticate Dendrobium species. Furthermore, phylogenetic analysis revealed that the sect. Dendrobium was polyphyletic. In addition, the divergence time analysis suggested that Dendrobium originated since the Oligocene. These findings provide valuable genetic data resources for further systematic studies of the rare and endangered Dendrobium species. Full article

Frankenia is a morphologically complex genus, with some species exhibiting a few diagnostic characters and significant morphological variability. This has led to misidentification or the synonymisation of many names based on one or a few diagnostic traits. This phenomenon affects the annual sea-heath, F. pulverulenta, a Eurasian–Mediterranean herb that has become subcosmopolitan, to which several entities have been included due to their shared features, namely their annual lifespan or their flattened leaves. However, this fact also extends to shrubby species, such as the Madeiran F. cespitosa. Here, integrative taxonomic studies, encompassing detailed morphological descriptions of macro- and microcharacters along with molecular phylogenetic analyses of both nuclear ribosomal (ITS1-5.8S-ITS2 region) and plastid (matK gene) DNA sequence data, and an analysis of biogeographic data were undertaken. This examination has resulted in the most complete phylogenetic trees of Frankenia to date, leading to the reinstatement of two African species broadly differing morphologically from F. pulverulenta. Firstly, F. florida L.Chevall., a name applied to a species occurring in the Saharan regions of Algeria, Morocco, Mali, and Mauritania, is often accepted as a variety or subspecies of the annual sea-heath. In contrast, F. densa Pohnert, a species endemic to southern Namibia and northern South Africa, has been synonymised with F. pulverulenta. However, since those two names were later homonyms of two Chilean and Australian plants, they were deemed illegitimate upon publication. Consequently, two new names are proposed for them: F. sahariensis and F. dinteri, respectively. Their substantiation as independent species is provided by data on their morphology, distribution, ecology, and molecular phylogenetics, which demonstrate their distinctiveness from F. pulverulenta. Nomenclatural synonymy and types are also presented for all concerned names, including the designation of two new lectotypes. Furthermore, the importance of an accurate description of the morphological variation in populations is emphasised for a precise identification of taxa in Frankenia. Full article

Background: Candidemia, associated with high morbidity and mortality, remains challenging to diagnose due to the limitations of blood cultures. Serological biomarkers offer faster detection, enabling earlier treatment and improving outcomes. Methods: This study, conducted at CHU UCL Namur (August 2023–January 2025), evaluated three diagnostic biomarkers for candidemia: CAGTA IgG VirClia Monotest, Wako β-D-glucan test, and CandId OLM RT-PCR. A total of 35 candidemia cases and 20 controls were included. Results: CAGTA IgG VirClia Monotest demonstrated low sensitivity (46%) and moderate specificity (75%). Both Wako β-D-glucan test and CandId OLM RT-PCR exhibited higher sensitivity (74% and 71%, respectively) and excellent specificity (100%). The combined use of Wako β-D-glucan test and CandId OLM RT-PCR further enhanced diagnostic performance, achieving 91% sensitivity and 100% specificity. Misidentification between Candida albicans and Candida dubliniensis was observed with CandId PCR, underlining a potential limitation in species-level discrimination. Conclusions: Both Wako β-D-glucan test and CandID OLM RT-PCR outperformed CAGTA IgG VirClia Monotest in diagnosing candidemia, and their combination significantly improved diagnostic accuracy, albeit at a higher cost. These findings highlight the potential of integrating multiple biomarkers into diagnostic workflows to optimize early detection, though further studies are needed to refine strategies and address challenges. Full article

The Achromobacter genus comprises 22 species and various genogroups. Some species with higher virulence or antibiotic resistance are more likely to cause chronic infections in people with cystic fibrosis (CF). Current identification methods often fail to accurately distinguish between the species or result in misidentifications due to biochemical similarities. This study aims to develop an accurate qPCR protocol for species-level identification that is applicable in clinical diagnostic laboratories. Whole-genome sequencing of clinical isolates from different Achromobacter species identified species-specific single-nucleotide polymorphisms (SNPs) in two 16S gene regions. Based on these SNPs, two sets of primers and qPCR probes were designed to generate unique identification profiles. Thermal profiles were optimized, and qPCR was performed on serial bacterial DNA dilutions to determine the detection limit (LOD). Four probes successfully identified three species: A. xylosoxidans, A. dolens, and A. insuavis. Two additional probes were designed for novel genotypes unrelated to publicly available sequences. The LOD ranged from 0.005 pg/µL to 1 pg/µL. Combined probes achieved 100% sensitivity, with specificity ranging from 97.95% to 100%. This qPCR protocol enables accurate species identification, overcoming the limitations of current methods, and represents a reliable tool for clinical diagnostics. Full article

Background/Objectives: Illicium verum Hook. f. and Illicium difengpi K. I. B.et K. I. M. are two important medicinal plants which grow in the mountainous areas of Guangxi, China. Their similar morphological characteristics frequently lead to their misidentification. Chloroplast genome (cp)-based barcode technology has been used to effectively identify two closely related species; however, at present, there is no systematic comparative study of the cp genome sequences between I. verum and I. difengpi. Methods: Here, the cp genomes of the two plants were sequenced and analyzed. Results: The cp genome sizes were 142,689 and 142,689 bp for I. verum and I. difengpi, respectively. Each of the cp genomes annotated 122 genes, with 79 protein coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. Amino acid frequencies of 1.17–10.19% (I. verum) and 1.18–10.17% (I. difengpi) were found in the coding genes. There were also 104 and 96 SSRs as well as 26 and 25 long repeats identified in I. verum and I. difengpi, respectively, among which the most common were A/T base repeats. Both cp genomes had SSC/IRa junctions located in gene ycf1-trnN. The ycf1 and trnL-trnV-rps7 genes were positioned at the IRb/SSC and LSC/IR boundaries, respectively. A phylogenetic relationship was constructed and the two species were fully nested within the genus Illicium. Conclusions: The comparative cp genomes of I. verum and I. difengpi are presented in this study, and this provides valuable phylogenetic information for subsequent molecular marker development and research of I. verum and I. difengpi. Full article

Background: Three aconitine poisoning events occurred in two Canadian provinces in 2022: one in British Columbia (BC) and two in Ontario (ON). Aconitine is a potent alkaloid found in several species of the plant Aconitum, containing cardiotoxins and neurotoxins. It is used in traditional Chinese medicine (TCM) for pain management, and in powdered form, Aconitum is similar in appearance to sand ginger (Kaempferia galanga), which can lead to poisonings from misidentification and mislabeling. Methods: Aconitine poisoning is rare in Canada; here, we compare communications, collaborations, laboratory testing options and actions during investigations. Results: Fourteen cases occurred from the consumption of sand ginger: in BC (n = 2), purchased at an Asian health food store; in ON (n = 11), Kaempferia galanga powder (KGP) spices were used to prepare meals at a restaurant, and in one ON case, KGP was purchased. Traceback found product imported from China contained aconitine levels ranging from 1304 to 5500 ppm. Later investigations revealed mislabeling of Aconitum as KGP from the same imported lot (January 2020). Plant DNA testing found no KGP in any spice packets, including lots not linked to illness, suggestive of adulteration. Conclusion: Method development for aconitine in BC led to an improved response time for testing in ON. BC and ON updated outbreak response protocols and communications. Full article

Climate change is promoting the occurrence of Harmful Cyanobacterial Blooms (HCBs) across freshwaters, posing serious risks for the ecosystems and human health. Under these warmer conditions, particularly blooms of invasive Aphanizomenon-like species such as Cuspidothrix issatschenkoi and Sphaerospermopsis aphanizomenoides (previously known as Aphanizomenon issatschenkoi and Aphanizomenon/Anabaena aphanizomenoides, respectively) have been reported to spread to higher latitudes, leading to increased toxic risks. Aphanizomenon and Anabaena genera have undergone several taxonomical revisions in recent years due to their morphological ambiguity, also corroborated by a high phylogenetic diversity. Furthermore, there is also a high phenotypic and genotypic variability within each one of these species, leading to diverse physiological and ecological traits. Therefore, DNA-based information is crucial not only to overcome possible species misidentifications, but also to provide information at the strain level. However, for the invasive Cuspidothrix issatschenkoi and Sphaerospermopsis aphanizomenoides, there is still a lack of geographically dispersed strains with available nucleotide sequences in databases, limiting deeper ecological studies to better understand their ecology and invasive trend. This review aimed to compile and discuss the geographical distribution of Cuspidothrix issatschenkoi and Sphaerospermopsis aphanizomenoides strains found in the NCBI nucleotide database and make some recommendations on the need to increase these numbers under the exponential inputs from DNA-metabarcoding. The integration of DNA-based information in water quality monitoring programmes is crucial to identify reoccurring bloom-forming strains and better understand their physiology and invasive ecology, ultimately leading to their effective forecast, and mitigation of their potential massive growth in target freshwater bodies. Full article