Current trends in antimicrobial resistance of ESKAPEEc pathogens from bloodstream infections - Experience of a tertiary care centre in North India.

INTRODUCTION: Bloodstream infections (BSI) due to ESKAPEEc pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanni, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli), cause significant mobility and mortality worldwide and are among the most common healthcare associated infections. Rising rates of antimicrobial resistance (AMR) in India are alarming, because of the high infection rates and poor control of antibiotic use. This single-centre, retrospective study was undertaken to identify the patterns of distribution and antimicrobial resistance of ESKAPEEc pathogens in bloodstream infections. METHODOLOGY: Blood samples from patients with suspected BSI were cultured and antimicrobial susceptibility testing was performed on automated systems (BD Bactec Fx/BactAlert 3D and Vitek2). The microbiological data on bacterial BSI was retrieved from the laboratory records and antimicrobial resistance profiles were analysed. RESULTS: 10.7% of the blood culture samples showed bacterial growth during the study period (adult > paediatric and intensive care unit (ICU) > ward > outpatient department (OPD)). E. coli (24%) and K. pneumoniae (20.5%) were the predominant species isolated, followed by S. aureus (9.5%) and A. baumanni (9%). High rates of resistance to third generation cephalosporins, ß-lactam-ß-lactamase inhibitor combinations (BL-BLI) and carbapenems was observed, in Gram-negative isolates, especially from ICU patients. Methicillin-resistant S. aureus (MRSA) isolates increased from 67% to 88% over the five-year period. Vancomycin-resistance among Enterococcus isolates also escalated to 40% in 2022 with 11% linezolid resistance. CONCLUSION: The study revealed that more than 77% of bloodstream infections were caused by ESKAPEEc pathogens, with high rates of resistance to most antimicrobials. This reinforces the importance of monitoring the frequency of bacteria and antibiograms in individual treatment and hospital infection control programs.

Candidate effectors for leaf rust resistance gene Lr28 identified through transcriptome and in-silico analysis.

Puccinia spp. causing rust diseases in wheat and other cereals secrete several specialized effector proteins into host cells. Characterization of these proteins and their interaction with host's R proteins could greatly help to limit crop losses due to diseases. Prediction of effector proteins by combining the transcriptome analysis and multiple in-silico approaches is gaining importance in revealing the pathogenic mechanism. The present study involved identification of 13 Puccinia triticina (Pt) coding sequences (CDSs), through transcriptome analysis, that were differentially expressed during wheat-leaf rust interaction; and prediction of their effector like features using different in-silico tools. NCBI-BLAST and pathogen-host interaction BLAST (PHI-BLAST) tools were used to annotate and classify these sequences based on their most closely matched counterpart in both the databases. Homology between CDSs and the annotated sequences in the NCBI database ranged from 79 to 94% and with putative effectors of other plant pathogens in PHI-BLAST from 24.46 to 54.35%. Nine of the 13 CDSs had effector-like features according to EffectorP 3.0 (≥0.546 probability of these sequences to be effector). The qRT-PCR expression analysis revealed that the relative expression of all CDSs in compatible interaction (HD2329) was maximum at 11 days post inoculation (dpi) and that in incompatible interactions (HD2329 + Lr28) was maximum at 3 dpi in seven and 9 dpi in five CDSs. These results suggest that six CDSs (>0.8 effector probability as per EffectorP 3.0) could be considered as putative Pt effectors. The molecular docking and MD simulation analysis of these six CDSs suggested that candidate Lr28 protein binds more strongly to candidate effector c14094_g1_i1 to form more stable complex than the remaining five. Further functional characterization of these six candidate effectors should prove useful for a better understanding of wheat-leaf rust interaction. In turn, this should facilitate effector-based leaf rust resistance breeding in wheat.

Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species.

Recombination UVB (sensitivity) like (RuvBL) helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought. We identified nine wheat RuvBL genes, one each on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. The lengths of genes ranged from 1647 to 2197 bp and exhibited synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare, and B. distachyon. The gene sequences were associated with regulatory cis-elements and transposable elements. Two genes, namely TaRuvBL1a-4A and TaRuvBL1a-4B, also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATP-dependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that the proteins were localized mainly in the cytoplasm. A representative gene, namely TaRuvBL1a-4A, was also shown to be involved in protein-protein interactions with ten other proteins. On the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classified into clusters and sub-clusters. In silico studies suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis confirmed that expression of TaRuvBL genes differed among wheat cultivars, which differed in the level of thermotolerance. The present study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat including use of RuvBL genes in breeding thermotolerant wheat cultivars.

Diagnostic Efficacy of New Xpert Ultra for Extrapulmonary Tuberculosis Using Culture and Composite Reference Standard.

Introduction: Xpert Ultra (Cepheid, USA) is recently introduced with an extra category of trace-positive results and higher sensitivity for tuberculosis (TB) diagnosis. Objective: The objective of the study was to assess the diagnostic accuracy of Xpert Ultra for extrapulmonary samples using culture and composite reference standard (CRS) as the gold standard. Materials and Methods: In a 1-year (March 2021-22) prospective observational study, samples of suspected extrapulmonary TB (EPTB) patients were subjected to Ziehl-Neelsen staining, culture, and Xpert Ultra (Cepheid, Sunnyvale, CA) tests. Relevant clinical and treatment information was noted. The diagnostic accuracy of Xpert Ultra compared with culture and CRS was calculated. Results: Out of 1720 suspected patients of EPTB, 223 (13%), predominantly males 135 (60%), with a mean age of 41.46 ± 19.81 years, were diagnosed as TB positive following CRS criteria. The maximum cases were of pleural TB (35.4%), followed by central nervous system TB (17.9%), gastrointestinal TB (17.5%), and lymph node TB (12.1%). Of all samples, 150 (8.7%) were microbiologically confirmed, including 141 detected by Xpert ultra, 67 culture positive, and only 16 smear positive. Among the Xpert Ultra-positive samples, 35 showed trace results, including six false-positive results. Considering culture and CRS as the gold standard, the sensitivity (86.57%, 59.64%) and specificity (94.98%, 99.47%) of Xpert Ultra were calculated, respectively. Rifampicin resistance was detected in 1 (0.70%) sample. Conclusion: Diagnosis of EPTB is a challenge and Xpert Ultra may detect TB at a very early stage. However, it is essential to rule out false-positive results. Additional studies are needed on Xpert Ultra to interpret trace results better.

Role of (1-3)-Β-D-Glucan Test in the Diagnosis of Invasive Fungal Infections among High-Risk Patients in a Tertiary Care Hospital.

Background Invasive fungal infections (IFI) are associated with high mortality. Serum fungal biomarkers offer an advantage over the traditional methods in early diagnosis and better clinical outcomes. The aim of the study was to evaluate the role of (1-3)-ß-D-glucan (BDG) assay in the patients suspected of IFI. Materials and Methods This prospective study was conducted in the Department of Microbiology, Dayanand Medical College and Hospital, Ludhiana, over a period of 1 year. A total of 862 serum samples were received from patients suspected of IFI, for the BDG test (Fungitell, Associates of Cape Cod Inc., USA). The test was performed as per kit protocol. Appropriate samples were processed for KOH fungal smear and fungal culture. Blood culture was done by Bactec (Biomerieux). Statistical Analysis Results were analyzed using descriptive statistical methods. Sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) were calculated at different cutoffs. In addition, the receiver operating characteristic (ROC) curve using SPSS 21.00 software was calculated and the diagnostic accuracy was shown by the area under the ROC curve (AUC). Results Among 862 patients, 546 (63.3%) were males. The predominant age group (25.6%) was between 61 and 70 years. The most common risk factor (54.8%) was prolonged intensive care unit stay. Out of the total samples, 455 (52.8%) samples were found positive for BDG. Fungal elements were seen in 48 (10.5%) KOH smears and fungal growth was obtained in 81 (17.8%) cultures. Comparison of BDG assay and culture at different cutoffs yielded AUC-0.823. Sensitivity (100%), specificity (51.3%), accuracy (55.6%), PPV (15.8%), and NPV (100%) were observed at the kit cutoff of 80 pg/mL. Optimum sensitivity and specificity of 79.2% and 70.3%, respectively, were observed at a cutoff of 142.4pg/mL. A significant correlation was observed between BDG positivity and piperacillin-tazobactam use and dialysis. Among BDG positive patients, 38(8.4%) succumbed to death. Conclusion Detection of BDG helps in the early diagnosis of IFI in critically ill patients. As the assay has a high NPV, a negative test can be used to stop the empirical antifungal drugs. The use of a higher cutoff can be useful to avoid false-positive results.

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding.

In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress (DS), heat stress (HS), salinity stress (SS), water-logging stress (WS), pre-harvest sprouting (PHS), and aluminium stress (AS) which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 189 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.

Highly efficient poly(acrylic acid-co-aniline) grafted itaconic acid hydrogel: Application in water retention and adsorption of rhodamine B dye for a sustainable environment.

The present study used a free radical co-polymerization approach to synthesize a smart hydrogel of itaconic acid grafted poly(acrylic acid-co-aniline) (ItA-g-poly(AA-co-ANi)). ItA-g-poly(AA-co-ANi) hydrogel was characterized by Fourier transform infrared spectroscopy (FT-IR), Raman, X-ray diffraction (XRD), thermogravimetric analysis (TGA), field emission scanning electron microscope (FE-SEM), and X-ray photoelectron spectroscopy (XPS) analysis. Rhodamine B (RhB) dye was removed from an aqueous medium using ItA-g-poly(AA-co-ANi) hydrogel. To determine the maximum adsorption, the effect of parameters such as initial dye concentration, contact time, pH, and adsorbent dose were examined. The ItA-g-poly(AA-co-ANi) hydrogel had a high swelling percentage of 1755.3%. The high water penetration of ItA-g-poly(AA-co-ANi) hydrogel with a high swelling rate exposed the internal adsorption sites for RhB dye adsorption. The adsorption performance of ItA-g-poly(AA-co-ANi) hydrogel was explained by the pseudo-first-order and Freundlich adsorption isotherm models. Moreover, after four adsorption-desorption cycles, the ItA-g-poly(AA-co-ANi) hydrogel maintained an adsorption efficiency of 85.2%. The high water retention ability of ItA-g-poly(AA-co-ANi) hydrogel improved the moisture maintenance limit of soil for irrigation up to 23 days. As a result, ItA-g-poly(AA-co-ANi) hydrogel can be used in the elimination of toxic dyes as well as in irrigation systems.

WheatQTLdb V2.0: a supplement to the database for wheat QTL.

We recently developed a database for hexaploid wheat QTL (WheatQTLdb; www.wheatqtldb.net), which included 11,552 QTL affecting various traits of economic importance. However, that database did not include valuable QTL from other wheat species and/or progenitors of hexaploid wheat. Therefore, an updated and improved version of wheat QTL database (WheatQTLdb V2.0) was developed, which now includes information on hexaploid wheat (Triticum aestivum) and the following seven other related species: T. durum, T. turgidum, T. dicoccoides, T. dicoccum, T. monococcum, T. boeoticum, and Aegilops tauschii. WheatQTLdb V2.0 includes a much-improved list of QTL, including 27,518 main effect QTL, 202 epistatic QTL, and 1321 metaQTL. This newly released WheatQTLdb V2.0 also has additional valuable options to search and choose the QTL, category-wise, and trait-wise data for their use in research or breeding programs.

Synthesis of Bio-based monomers and polymers using microbes for a sustainable bioeconomy.

As a result of environmental concerns and the depletion of biomass assets, eco-friendly, renewable biomass-based chemical extraction has recently received significant attention. Bio-based chemicals can be prepared using different renewable feedstockbio-resources through microbial fermentation. Chemicals produced from renewable feedstockscan reduce ecological consequences from improper disposal and repurpose them into valuable products. Biodegradability, biocompatibility and non-toxicity, particularly in biomedical applications, have inspired researchers towards developing novel technologies that have social benefit. Among semi-synthetic and synthetic polymeric materials, utilization of natural bio-based monomeric materials can provide opportunities for sustainable development of novel non-toxic, biodegradable and biocompatible products. The purpose of this work is to give a summary of research into the generation of natural bio-based succinic acid (SA) monomer, the development of poly(butylene succinate) (PBS) as biodegradable polymer, PBS-based nanocomposites and their innovative uses.

WheatQTLdb: a QTL database for wheat.

During the last three decades, QTL analysis in wheat has been conducted for a variety of individual traits, so that thousands of QTL along with the linked markers, their genetic positions and contribution to phenotypic variation (PV) for concerned traits are now known. However, no exhaustive database for wheat QTL is currently available at a single platform. Therefore, the present database was prepared which is an exhaustive information resource for wheat QTL data from the published literature till May, 2020. QTL data from both interval mapping and genome-wide association studies (GWAS) have been included for the following classes of traits: (i) morphological traits, (ii) N and P use efficiency, (iii) traits for biofortification (Fe, K, Se, and Zn contents), (iv) tolerance to abiotic stresses including drought, water logging, heat stress, pre-harvest sprouting and salinity, (v) resistance to biotic stresses including those due to bacterial, fungal, nematode and insects, (vi) quality traits, and (vii) a variety of physiological traits, (viii) developmental traits, and (ix) yield and its related traits. For the preparation of the database, literature was searched for data on QTL/marker-trait associations (MTAs), curated and then assembled in the form of WheatQTLdb. The available information on metaQTL, epistatic QTL and candidate genes, wherever available, is also included in the database. Information on QTL in this WheatQTLdb includes QTL names, traits, associated markers, parental genotypes, crosses/mapping populations, association mapping panels and other useful information. To our knowledge, WheatQTLdb prepared by us is the largest collection of QTL (11,552), epistatic QTL (107) and metaQTL (330) data for hexaploid wheat to be used by geneticists and plant breeders for further studies involving fine mapping, cloning, and marker-assisted selection (MAS) during wheat breeding.

Green synthesis of silver nanoparticles using Ocimum canum and their anti-bacterial activity.

Green synthesis of nanoparticles is an important area in the field of nanotechnology, which has cost effective and environment friendly benefit over physical and chemical methods. The present study aims at preparation of silver nanoparticles through green route using leaves of Ocimum canum Sims, a widely distributed medicinal herb. The synthesized silver nanoparticles were characterized by SEM and XRD. The spherical and rod like morphological shapes were proven by SEM techniques. Crystallographic structure was confirmed by XRD and average particle size of synthesized silver nanoparticles was calculated which was found to be of 15.72 nm. The antibacterial activity of these prepared silver nanoparticles against pathogenic bacterium Escherichia coli (E. coli) has shown the highest ZOI of 2.45 cm at 30 ppm.

Development of Biodegradable Agar-Agar/Gelatin-Based Superabsorbent Hydrogel as an Efficient Moisture-Retaining Agent.

Downgrading in the yield of crop is due to the inadequate availability of water. The way out for this trouble is to construct synthetic resources dependent on natural polymers with great water absorption and preservation limits. The present study investigated the design of agar-agar (Agr) and gelatin (GE) copolymerized methyl acrylate (MA) and acrylic acid (AA) hydrogel (Agr/GE-co-MA/AA) as a soil conditioner for moisture maintenance in agriculture. Agr/GE-co-MA/AA hydrogel was prepared by utilizing microwave-assisted green synthesis following the most suitable reaction conditions to obtain a remarkable water swelling percentage. The fabricated Agr/GE-co-MA/AA hydrogel was investigated through field emission scanning electron microscopy (FESEM), fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). The water holding capacity of the soil and sand was examined by mixing Agr/GE-co-MA/AA hydrogel with soil and sand. The result demonstrates that the water holding time extended from 10 to 30 days for soil and 6 to 10 days for sand by using Agr/GE-co-MA/AA hydrogel. This synthesized biodegradable, low-cost and non-toxic Agr/GE-co-MA/AA hydrogel shows novelty as soil water maintaining material for irrigation in agriculture.

Synthesis and biological function of Nickel and Copper nanoparticles.

Nickel and Copper nanoparticles were synthesized by simple chemical method and studied for antimicrobial activities. The size of synthesized Nickel and Copper nanoparticles was found to be 24.00 nm and 13.13 nm respectively. The XRD analysis reveals the crystal system of Nickel and Copper nanoparticles. Copper nanoparticles were found orthorhombic whereas the nickel nanoparticles were monoclinic. The antimicrobial activities of Nickel and Copper nanoparticles dispersed in DMSO was investigated. Comparative sensitivity test of these synthesized nanoparticles was carried out against three pathogenic micro-organisms (Gram negative bacteria), viz. Escherichia coli, Klebsiella pneumoniae and Pneumonia Typhus, using agar diffusion cup plate method. Copper and Nickel nanoparticles have shown appreciable sensitivity at 100 µg/ml against all test micro-organisms. Comparatively, Copper nanoparticles were found to exhibit higher zone of inhibition (ZOI) than Nickel nanoparticles.

Progress in pectin based hydrogels for water purification: Trends and challenges.

Pectin is one of the finest natural polymer which has drawn great attention because of its applications in different fields. Due to the quintessential structure of pectin, it can be transformed into variety of useful products. It can be utilized as a blend in many polymers to make a mixture or a composite material. Owing to considerable collection in chemical conformation and cross-linking mechanism, different pectin based hydrogels have been prepared for different characteristics in pharmaceutical and bio-medical sites. Inventive properties of hydrogels like volubility, swellability, solvability and hydrophilicity make them better alternative for wastewater treatment. Recently, pectin based hydrogels have demonstrated excellent performance to eliminate various metal ions and dyes from the polluted water. The adsorption characteristics of pectin based hydrogels can be upgraded by using nanoparticles, which prompts to the development of hydrogel nano-composites. In this review article, we have summarized a comprehensive assessment in the direction of using pectin based hydrogels to remove toxic pollutants from aqueous solution. Sodium acrylate-co-N-isopropylacrylamide based pectin hydrogel has demonstrated the maximum adsorption capacities of 265.49, 137.43, 54.86, 53.86, 51.72 and 50.01 mg g-1 for the adsorption of methyl violet, methylene blue, Pb(II), Cu(II), Co(II) and Zn(II) respectively. We have also discussed the pectin structure, properties and applications in this article.

Strategic exploration of battery waste management: A game-theoretic approach.

Electronic waste or e-waste is the fastest growing stream of solid waste today. It contains both toxic substances as well as valuable resources. The present study uses a non-cooperative game-theoretic approach for efficient management of e-waste, particularly batteries that contribute a major portion of any e-waste stream and further analyses the economic consequences of recycling of these obsolete, discarded batteries. Results suggest that the recycler would prefer to collect the obsolete batteries directly from the consumer rather than from the manufacturer, only if, the incentive return to the consumer is less than 33.92% of the price of the battery, the recycling fee is less than 6.46% of the price of the battery, and the price of the recycled material is more than 31.08% of the price of the battery. The manufacturer's preferred choice of charging a green tax from the consumer can be fruitful for the battery recycling chain.