Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan.

The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).

Aptamers targeting SARS-CoV-2 nucleocapsid protein exhibit potential anti pan-coronavirus activity.

Emerging and recurrent infectious diseases caused by human coronaviruses (HCoVs) continue to pose a significant threat to global public health security. In light of this ongoing threat, the development of a broad-spectrum drug to combat HCoVs is an urgently priority. Herein, we report a series of anti-pan-coronavirus ssDNA aptamers screened using Systematic Evolution of Ligands by Exponential Enrichment (SELEX). These aptamers have nanomolar affinity with the nucleocapsid protein (NP) of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and also show excellent binding efficiency to the N proteins of both SARS, MERS, HCoV-OC43 and -NL63 with affinity KD values of 1.31 to 135.36 nM. Such aptamer-based therapeutics exhibited potent antiviral activity against both the authentic SARS-CoV-2 prototype strain and the Omicron variant (BA.5) with EC50 values at 2.00 nM and 41.08 nM, respectively. The protein docking analysis also evidenced that these aptamers exhibit strong affinities for N proteins of pan-coronavirus and other HCoVs (-229E and -HKU1). In conclusion, we have identified six aptamers with a high pan-coronavirus antiviral activity, which could potentially serve as an effective strategy for preventing infections by unknown coronaviruses and addressing the ongoing global health threat.

The landscape of nanoparticle-based siRNA delivery and therapeutic development.

Five small interfering RNA (siRNA)-based therapeutics have been approved by the Food and Drug Administration (FDA), namely patisiran, givosiran, lumasiran, inclisiran, and vutrisiran. Besides, siRNA delivery to the target site without toxicity is a big challenge for researchers, and naked-siRNA delivery possesses several challenges, including membrane impermeability, enzymatic degradation, mononuclear phagocyte system (MPS) entrapment, fast renal excretion, endosomal escape, and off-target effects. The siRNA therapeutics can silence any disease-specific gene, but their intracellular and extracellular barriers limit their clinical applications. For this purpose, several modifications have been employed to siRNA for better transfection efficiency. Still, there is a quest for better delivery systems for siRNA delivery to the target site. In recent years, nanoparticles have shown promising results in siRNA delivery with minimum toxicity and off-target effects. Patisiran is a lipid nanoparticle (LNP)-based siRNA formulation for treating hereditary transthyretin-mediated amyloidosis that ultimately warrants the use of nanoparticles from different classes, especially lipid-based nanoparticles. These nanoparticles may belong to different categories, including lipid-based, polymer-based, and inorganic nanoparticles. This review briefly discusses the lipid, polymer, and inorganic nanoparticles and their sub-types for siRNA delivery. Finally, several clinical trials related to siRNA therapeutics are addressed, followed by the future prospects and conclusions.

Expression of concern: Influence of chemical composition on the amount of second phases precipitates and transformation temperatures of TiNiPdCu shape memory alloys prepared through novel powder metallurgy route.

Expression of concern for 'Influence of chemical composition on the amount of second phases precipitates and transformation temperatures of TiNiPdCu shape memory alloys prepared through novel powder metallurgy route' by Abid Hussain et al., RSC Adv., 2023, 13, 29376-29392, https://doi.org/10.1039/D3RA05513B.

Comprehensive multi-level expression profiling of key biomarkers in breast cancer patients.

OBJECTIVES: In this comprehensive breast cancer (BC) study, we aimed to identify, validate, and characterize key biomarkers with significant implications in BC diagnosis, prognosis, and as therapeutic targets. METHODS: Our research strategy involved a multi-level methodology, combining bioinformatic analysis with experimental validation. RESULTS: Initially, we conducted an extensive literature search to identify BC biomarkers, selecting those with reported accuracies exceeding 20% in specificity and sensitivity. This yielded nine candidate biomarkers, which we subsequently analyzed using Cytoscape to identify a few key biomarkers. Based on the degree method, we denoted four key biomarkers, including progesterone receptor (PGR), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), and Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2). Expression analysis using The Cancer Genome Atlas (TCGA) dataset revealed that PGR and EGFR exhibited significant (p-value < 0.05) down-regulation in BC samples when compared to controls, while ESR1 and ERBB2 showed up-regulation. To strengthen our findings, we collected clinical BC tissue samples from Pakistani patients and performed expression verification using real-time quantitative polymerase chain reaction (RT-qPCR). The results aligned with our initial TCGA dataset analysis, further validating the differential expression of these key biomarkers in BC. Furthermore, we utilized receiver operating characteristic (ROC) curves to demonstrate the diagnostic use of these biomarkers. Our analysis underscored their accuracy and sensitivity as diagnostic markers for BC. Survival analysis using the Kaplan-Meier Plotter tool revealed a prognostic significance of PGR, ESR1, EGFR, and ERBB2. Their expression levels were associated with poor overall survival (OS) of BC patients, shedding light on their roles as prognostic indicators in BC. Lastly, we explored DrugBank to identify drugs that may reverse the expression patterns , and estradiol, decitabine, and carbamazepine were singled out. CONCLUSION: Our study gives valuable insight into BC biomarkers, for diagnosis and prognosis. These findings have implications for BC management using personalized and targeted therapeutic approaches for BC patients.

Influence of chemical composition on the amount of second phases precipitates and transformation temperatures of TiNiPdCu shape memory alloys prepared through novel powder metallurgy route.

The chemical composition of TiNiPdCu high temperature shape memory alloys (HTSMAs) affects their microstructure and martensitic transformations. In TiNiPdC HTSMAs, second phase precipitates were found. Extremely high densities of nanoscale precipitates of TiPdCu and Ti2Pd of particle size 0.8-4.4 µm were found to be produced by the TiNiPdCu alloys. It was found that the TiPdCu-type precipitates were favoured by the preferential migration of Cu atoms towards the heterogeneous nucleation sites, which in turn favoured the fine Ti2Pd-type precipitates. Due primarily to their high-temperature stability, these precipitates significantly strengthened the resistance against transformation-induced plasticity and creep deformation, especially at high loads and high temperatures. High concentrations of these nanoscaled precipitates led to a significant rise in transformation temperatures by 12% and a small decrease in thermal hysteresis by 30%. It was anticipated that the current research findings will have a significant positive impact on the creation of HTSMAs that maintain their benefits of simplicity of manufacture. The HTSMAs developed in current research are beneficial for high temperature sensors and actuators at optimum cost.

Hollow Mesoporous Silica Nanoparticles for Dual Chemo-starvation Therapy of Hepatocellular Carcinoma.

PURPOSE: This study aims at chemotherapy and starvation therapy of HCC via starvation and apoptosis. METHODS: Hollow mesoporous organosilica nanoparticles (HMONs) with the thioether-hybrid structure were developed using an organic/inorganic co-templating assembly approach. Hydrofluoric acid was used to remove the internal MSN core for yielding large radial mesopores for loading drug cargos. The morphology and structure of NPs were determined using TEM and SEM. HMONs were stepwise surface modified with glucose oxidase (GOx), oxygen (O2) and Doxorubicin (DOX), and cancer cell membrane (CCM) for yielding CCM-coated HMONs (targeted stealth biorobots; TSBRs) for starvation, apoptotic, and enhanced cell uptake properties, respectively. The surface area and pore size distribution were determined via BET and BJH assays. The catalytic ability of GOx-modified NPs was measured using in vitro glucose conversion approach authenticated by H2O2 and pH determination assays. MTT assay was used to determine the cytotoxicities of NPs. Cell uptake and apoptotic assay were used for the NPs internalization and apoptosis mechanisms. The subcutaneous HepG2 tumor model was established in mice. The long-term in vivo toxicity was determined using blood assays. RESULTS: The prepared NPs were spherical, hollow and mesoporous with excellent surface area and pore size distribution. The GOx-modified NPs exhibited excellent catalytic activity. The TSBRs showed better cytotoxicity and reduce the tumor size and weight. The NPs showed long-term safety in vivo. CONCLUSION: TSBRs destroyed cancer cells by starvation and chemotherapy in both in-vitro and in-vivo settings which demonstrates its anti-cancer potential.

Loratadine oral bioavailability enhancement via solid dispersion loaded oro-dispersible films: Formulation, characterization and pharmacokinetics.

Loratadine (LRD) belongs to second-generation tricyclic H1 antihistamine class, known for its non-sedating properties in allergic reactions. H1 antihistamines avoid and block the responses to allergens or histamine in nose and conjunctivae, thereby abolishing itching, congestion and sneezing. LRD is a Biopharmaceutical Class System (BCS) class II drug with dissolution or solubility limited absorption which limited the oral bioavailability and therapeutic efficacy of LRD. To improve the oral bioavailability of LRD for allergic disease (urticaria) treatment, LRD solid dispersions (LRD-SDs) were integrating into oro-dispersible films (ODFs). LRD-SDs were prepared through hot-melt extrusion method (HME) using d-alpha-tocopherol polyethylene glycol 1000 succinate (TPGS-1000), and polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol graft copolymer (SP). Subsequently, LRD-SDs were incorporated in ODFs by solvent casting method. The physicochemical and mechanical properties of LRD solid dispersions-loaded oro-dispersible films (LRD-SDs-ODFs), were evaluated. The in-vitro dissolution, ex-vivo permeation, oral bioavailability, and pharmacodynamics studies were conducted to evaluate LRD-SDs-ODFs efficiency. LRD-SDs-ODFs showed superior solubility and in-vitro dissolution results compared to that of pure LRD (p < 0.05). The solubility of the LRD-SD coded as LTS-4 was 190 times higher than the pure drug in aqueous media. The average hydrodynamic particle size (PS), polydispersity index (PDI), and zeta potential (ZP) of SD particles were 76 ± 2.1 nm, 0.20 ± 0.08 and - 19.16 ± 1.4 mV, respectively. Moreover, differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results confirmed the amorphousness of LRD in LRD-SDs-ODFs. The permeability flux of LRD was 44.6 ± 3.1 µg/cm2/h from DPF-5 formulation. Likewise, in vivo oral bioavailability of DPF-5 in Sprague-Dawley rats was significantly increased (p < 0.05) compared to free LRD. Further, wheal area was reduced 20 % higher than LRD in 8 h (p < 0.05). Overall, LRD-SDs-ODFs considerably enhanced LRD solubility, dissolution rate, bioavailability, and antihistaminic efficacy. Our findings show that SDs-ODFs is an effective carrier system for delivering poorly soluble LRD.

Geostatistical analysis for spatial distribution of anemia (Hb level) among women of reproductive age and determinant factors.

The study was designed to assess the geostatistical spatial distribution of anemia and determinant factors among the women of reproductive age group (RAG) in Gilgit district, Pakistan. The Hb levels for 15-25 RAG, 26-35 RAG, and 36-45 group showed 10.22 g/dL, 10.41 g/dL, and 9.90 g/dL levels, respectively, while the Hb level showed a nugget/sill ratio of 0.21 inferring strong for the 15-25 group, weak for the 26-36, and moderate for 36-45 spatial dependence. Furthermore, 15-25 RAG showed 8% severe and 33.34% sufficient cases and 26-35 showed 12% severe and 29.33% sufficient results in their Hb level, whereas 36-45 had 9.34% severe and 29.33% sufficient.

Impact of perceived supervisor support and leader-member exchange on employees' intention to leave in public sector museums: A parallel mediation approach.

High staff turnover in certain public sector organizations in Pakistan is a challenging problem, and organizations strive to reduce this issue using different mechanisms. Therefore, this research investigates the parallel mediation impact of perceived organizational support (POS) and organizational citizenship behavior (OCB) on the relationships among perceived supervisor support (PSS), leader-member exchange (LMX), and employee's intention to leave (IL). Data were collected from 482 employees working in public sector museums in Pakistan in three waves. Structural equation modeling (SEM) with a two-step approach was used to evaluate the data. The research found that both POS and OCB mediate the negative relationship between PSS and IL and between LMX and IL in a parallel mediation mechanism. Public sector museums should focus on providing visible supervisory support and develop a healthy work environment where the exchange relationship between supervisors and subordinates strengthens to reduce the possibility of the employee's leave intentions.

Occurrence of antibiotics in wastewater: Potential ecological risk and removal through anaerobic-aerobic systems.

Antibiotics are intensively used to improve public health, prevent diseases and enhance productivity in animal farms. Contrarily, when released, the antibiotics laden wastewater produced from pharmaceutical industries and their application sources poses a potential ecological risk to the environment. This study provides a discussion on the occurrence of various antibiotics in wastewater and their potential ecological risk in the environment. Further, a critical review of anaerobic-aerobic processes based on three major systems (such as constructed wetland, high-rate bioreactor, and integrated treatment technologies) applied for antibiotics removal from wastewater is performed. The review also explores microbial dynamics responsible for antibiotic biodegradation in anaerobic-aerobic systems and its economic feasibility at wider-scale applications. The operational problems and prospective modifications are discussed to define key future research directions. The appropriate selection of treatment processes, sources control, understanding of antibiotic fate, and adopting precise monitoring strategies could eliminate the potential ecological risks of antibiotics. Integrated bio-electrochemical systems exhibit antibiotics removal ≥95% by dominant Geobacter sp. at short HRT ∼4-10 h. Major process factors like organic loading rate, hydraulic loading rate (HRT), and solid retention time significantly affect the system performance. This review will be beneficial to the researchers by providing in-depth understanding of antibiotic pollution and its abatement via anaerobic-aerobic processes to develop sustainable wastewater treatment technology in the future.

A framework for multi-sensor satellite data to evaluate crop production losses: the case study of 2022 Pakistan floods.

In August 2022, one of the most severe floods in the history of Pakistan was triggered due to the exceptionally high monsoon rainfall. It has affected ~ 33 million people across the country. The agricultural losses in the most productive Indus plains aggravated the risk of food insecurity in the country. As part of the loss and damage (L&D) assessment methodologies, we developed an approach for evaluating crop-specific post-disaster production losses based on multi-sensor satellite data. An integrated assessment was performed using various indicators derived from pre- and post-flood images of Sentinel-1 (flood extent mapping), Sentinel-2 (crop cover), and GPM (rainfall intensity measurements) to evaluate crop-specific losses. The results showed that 2.5 million ha (18% of Sindh's total area) was inundated out of which 1.1 million ha was cropland. The remainder of crop damage came from the extreme rainfall downpour, flash floods and management deficiencies. Thus approximately 57% (2.8 million ha) of the cropland was affected out of the 4.9 million ha of agricultural area in Sindh. The analysis indicated expected production losses of 88% (3.1 million bales), 80% (1.8 million tons), and 61% (10.5 million tons) for cotton, rice, and sugarcane. This assessment provided useful tools to evaluate the L&D of agricultural production and to develop evidence-based policies enabling post-flood recovery, rehabilitation of people and restoration of livelihood.

Emerging technologies for COVID (ET-CoV) detection and diagnosis: Recent advancements, applications, challenges, and future perspectives.

In light of the constantly changing terrain of the COVID outbreak, medical specialists have implemented proactive schemes for vaccine production. Despite the remarkable COVID-19 vaccine development, the virus has mutated into new variants, including delta and omicron. Currently, the situation is critical in many parts of the world, and precautions are being taken to stop the virus from spreading and mutating. Early identification and diagnosis of COVID-19 are the main challenges faced by emerging technologies during the outbreak. In these circumstances, emerging technologies to tackle Coronavirus have proven magnificent. Artificial intelligence (AI), big data, the internet of medical things (IoMT), robotics, blockchain technology, telemedicine, smart applications, and additive manufacturing are suspicious for detecting, classifying, monitoring, and locating COVID-19. Henceforth, this research aims to glance at these COVID-19 defeating technologies by focusing on their strengths and limitations. A CiteSpace-based bibliometric analysis of the emerging technology was established. The most impactful keywords and the ongoing research frontiers were compiled. Emerging technologies were unstable due to data inconsistency, redundant and noisy datasets, and the inability to aggregate the data due to disparate data formats. Moreover, the privacy and confidentiality of patient medical records are not guaranteed. Hence, Significant data analysis is required to develop an intelligent computational model for effective and quick clinical diagnosis of COVID-19. Remarkably, this article outlines how emerging technology has been used to counteract the virus disaster and offers ongoing research frontiers, directing readers to concentrate on the real challenges and thus facilitating additional explorations to amplify emerging technologies.

mRNA-based modalities for infectious disease management.

The novel coronavirus disease 2019 (COVID-19) is still rampant all over the world, causing incalculable losses to the world. Major pharmaceutical organizations around the globe are focusing on vaccine research and drug development to prevent further damage caused by the pandemic. The messenger RNA (mRNA) technology has got ample of attention after the success of the two very effective mRNA vaccines during the recent pandemic of COVID-19. mRNA vaccine has been promoted to the core stage of pharmaceutical industry, and the rapid development of mRNA technology has exceeded expectations. Beyond COVID-19, the mRNA vaccine has been tested for various infectious diseases and undergoing clinical trials. Due to the ability of constant mutation, the viral infections demand abrupt responses and immediate production, and therefore mRNA-based technology offers best answers to sudden outbreaks. The need for mRNA-based vaccine became more obvious due to the recent emergence of new Omicron variant. In this review, we summarized the unique properties of mRNA-based vaccines for infectious diseases, delivery technologies, discussed current challenges, and highlighted the prospects of this promising technology in the future. We also discussed various clinical studies as well preclinical studies conducted on mRNA therapeutics for diverse infectious diseases.

Banned Sudan dyes in spices available at markets in Karachi, Pakistan.

Sudan dyes were investigated in branded and non-branded spices, commonly available in the markets of Karachi, Pakistan. High performance liquid chromatography (HPLC) with a variable wavelength detector (VWD) was applied to determine Sudan dyes I-IV. The non-branded samples had higher concentrations of Sudan dyes than the maximum limits of 0.1 mg/kg. The highest concentration of Sudan dye (I) was found in turmeric powder (8460 mg/kg) and the lowest concentration (1.50 mg/kg) of Sudan (IV) in Chaat Masala. This indicates that the use of non-branded spices is not safe, whereas no Sudan dye was found in the branded spice samples. Further studies regarding the higher carcinogenic risk posed by Sudan dye adulterated spices in Pakistan is strongly advised.

Anaerobic-aerobic treatment of wastewater and leachate: A review of process integration, system design, performance and associated energy revenue.

Hybrid anaerobic-aerobic biological systems are an environmentally sustainable way of recovering bioenergy during the treatment of high-strength wastewaters and landfill leachate. This study provides a critical review of three major categories of anaerobic-aerobic processes such as conventional wetland, high-rate and integrated bioreactor systems applied for treatment of wastewaters and leachate. A comparative assessment of treatment mechanisms, critical operating parameters, bioreactor configurations, process control strategies, efficacies, and microbial dynamics of anaerobic-aerobic systems is provided. The review also explores the influence of wastewater composition on treatment performance, ammonium nitrogen removal efficacy, impact of mixing leachate, energy consumption, coupled bioenergy production and economic aspects of anaerobic-aerobic systems. Furthermore, the operational challenges, prospective modifications, and key future research directions are discussed. This review will provide in-depth understanding to develop sustainable engineering applications of anaerobic-aerobic processes for effective co-treatment of wastewaters and leachate.

An integrated leachate bed reactor - anaerobic membrane bioreactor system (LBR-AnMBR) for food waste stabilization and biogas recovery.

This study developed an integrated LBR - AnMBR system for efficient stabilization and biogas recovery from food waste (FW) at room temperatures (21-22 °C). First, the leachate recirculation rate (4.4-13.2 L/h) was optimized to maximize hydrolysis and acidification yields. The maximum hydrolysis yield of 551 gSCOD/kg VSadded was achieved at recirculation rate of 13.2 L/h. The VFA concentrations in the FW leachate was as high as 12.5-16.0 g/L, resulting in a high acidification of 468 g CODVFA/kg VS. The solubilized FW was further stabilized by feeding the leachate to AnMBR. Different hydraulic (HRT) and solids retention times (SRT) were tested to achieve high COD removal and methane yields. High COD removal of 86 ± 3% was obtained in the AnMBR at HRT of 13 and SRT of 75 days. High biogas recovery of about 850 kWh per ton FWtreated was achieved along with high quality of AnMBR permeates containing low COD concentration but advantageously high concentration of nutrients (NH4+-N 317-403 mg/L, total phosphate 23-213 mg/L) without any particulates, which can be reused for landscape or liquid fertilizer.

Probing the impact of sustainable emerging sonication and DBD plasma technologies on the quality of wheat sprouts juice.

Sonication and dielectric barrier discharge (DBD) plasma are sustainable emerging food processing technologies. The study investigates the impact of sonication, DBD-plasma, and thermal treatment (TT) on wheat sprout juice. The obtained results indicated a significant (p < 0.05) increase in chlorophyll, total phenolics, flavonoids, DPPH assay, and ORAC assay after DBD-plasma (40 V) and sonication (30 mins) treatment as compared to TT and untreated samples. Both emerging technologies significantly (p < 0.05) reduce the polyphenol oxidase and peroxidase activities, but the TT sample had the highest reduction. Moreover, the synergistic application of both technologies significantly reduced the E. coli/Coliform, aerobics, yeast and mold up to the 2 log reduction, but the TT sample had a complete reduction. DBD-plasma and sonication processing significantly decreased (p < 0.05) the particle size, reducing apparent viscosity (η) and consistency index (K); while increasing the flow behavior (n), leading to higher stability of wheat sprout juice. To assess the impact of emerging techniques on nutrient concentration, we used surface-enhance Raman spectroscopy (SERS) as an emerging method. Silver-coated gold nano-substrates were used to compare the nutritional concentration of wheat sprout juice treated with sonication, DBD-plasma, and TT-treated samples. Results showed sharp peaks for samples treated with DBD-plasma followed by sonication, untreated, and TT. The obtained results, improved quality of wheat sprout juice, and lower microbial and enzymatic loads were confirmed, showing the suitability of these sustainable processing techniques for food processing and further research.

Optimization of biofilm conductance measurement with two-electrode microbial electrochemical cells (MECs).

This study was conducted to develop a standardized and consistent method for biofilm conductance measurement for an improved comprehension of extracellular electron transfer. Biofilm conductance (2.12 ± 0.25 × 10-4 S) with and without a fixed anode potential did not show significant difference. The conductance showed a sigmoidal relationship with anode potential. The current-voltage profile of the tested biofilm at applied voltage larger than 100 mV showed deviation from Ohm's law. Up to 69% decrease in biofilm conductance and deviation from Ohm's law were observed in the current-voltage profile when the measurement time increased. By choosing the voltage range (0- 100 mV) and step (25 mV), measurement time (100-s at each voltage step), and anode control mode, these operation settings were found more suitable for consistent and accurate biofilm conductance measurement in the 2-Au MEC system. This represents the first study that comprehensively evaluated the environmental and instrumental parameters for biofilm conductance measurement.

Genomic Assembly of Clinical Candida glabrata (Nakaseomyces glabrata) Isolates Reveals within-Species Structural Plasticity and Association with In Vitro Antifungal Susceptibility.

The opportunistic human pathogen Candida glabrata has become an increasingly important threat to human health, with infections globally characterized by high mortality rates and multidrug resistance. To face this threat, more efficient diagnostic and therapeutic approaches are required, underpinning research to help define the intraspecies epidemiology, genetic variability, and therefore, diagnostic and therapeutic target stability. Previous comparative genetics studies conducted on limited numbers of strains only revealed partial resolution of chromosomal settings. In this study, by combining short- and long-read genome sequencing, phenotypic characterization, and comparative genomics over a large set of strains, we detected strict relationships between large chromosomal rearrangements and phylogenetic clades, genes subjected to different selective pressures, and new sets of genes associated with resistance to antifungals. Overall, these results not only provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology but may also lay the foundations for the future development of tailored therapeutic approaches. IMPORTANCE The human pathogen Candida glabrata has become a global threat to human health, with infections characterized by high mortality and multidrug resistance. We have obtained nine fully assembled genomes from clinical isolates through a combination of short- and long-read sequencing approaches. The quality and completeness of such genomes and their subsequent comparison to the broadest set of genomes so far allowed us to pinpoint chromosomal rearrangements in several genomes and detect phylogenetic clades that were not associated with geographic location or isolation source. We identified a new set of genes associated with resistance to antifungals coding for adhesin or adhesin-like proteins, suggesting C. glabrata resists antifungals by forming aggregates or adhering to the host tissue. These results, which provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology, may initiate the development of precision medicine interventions for patients with suspected or proven invasive fungal infections.