Isolation, characterization, and genome analysis of novel bacteriophage - Stenotrophomonas phageCM1.

A common environmental bacteria called Stenotrophomonas maltophilia has become an organism responsible for significant nosocomial infection, mortality in immunocompromised patients, and significantly increasing morbidity and is challenging to treat due to the antibiotic resistance activity of the organism. and bacteriophage therapy is one of the promising treatments against the organism. In this research, we isolated, identified, and characterized Stenotrophomonas phage CM1 against S. maltophilia. Stenotrophomonas phage CM1 head was measured to have a diameter of around 224.25 nm and a tail length of about 159 nm. The phage was found to have noticeable elongated tail spikes around 125 nm in length, the Myoviridae family of viruses, which is categorized under the order Caudovirales. The ideal pH for growth was around 7, demonstrated good thermal stability when incubated at 37-60 °C for 30 min or 60 min, and phage infectivity decreased marginally after 30 min of incubation at 1-5% chloroform concentration. Phage was 3,19,518 base pairs long and had an averaged G + C composition of 43.9 %; 559 open-reading frames (ORFs) were found in the bacteriophage genome, in which 508 of them are hypothetical proteins, 22 of them are other known proteins, 29 of them are tRNAs, and one of them is restriction enzyme. A phylogenetic tree was reconstructed, demonstrating that CM1 shares a close evolutionary relationship with other Stenotrophomonas phages.

Study of Cadmium Metal Resistance in Stenotrophomonas maltophilia.

Metal-resistant bacteria are recommended for metal removal applications due to their rapid multiplication and growth rates. To ensure safety replenishment in contaminated areas frequently hampered by heavy metal toxicity, it is crucial to comprehend their coping mechanisms under heavy metal stress. This study primarily examines the role of EPS (exopolysaccharide) in Stenotrophomonas maltophilia, a Gram-negative, aerobic, and rod-shaped bacteria, in response to Cd, as well as the binding behavior and biosorption mechanism between EPS and Cd, using SEM and FTIR. The studies showed that Stenotrophomonas maltophilia, can resist up to 150 µM of Cd due to the binding of Cd to EPS. SEM analysis showed significant morphological changes and FTIR was to identify main structural groups like carboxyl and hydroxyl which confirms the presence of EPS. The study will also describe the mechanism of cross-reactivity between exopolysaccharide and siderophore production in metal-tolerant Stenotrophomonas maltophilia. This study proved that siderophore-mediated metal detoxification and effective absorption have been linked to metal chelation.

Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database.

Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.

Identification of natural inhibitor against L1 ß-lactamase present in Stenotrophomonas maltophilia.

Antibiotic resistance is threatening the medical industry in treating microbial infections. Many organisms are acquiring antibiotic resistance because of the continuous use of the same drug. Gram-negative organisms are developing multi-drug resistance properties (MDR) due to chromosomal level changes that occurred as a part of evolution or some intrinsic factors already present in the organism. Stenotrophomonas maltophilia falls under the category of multidrug-resistant organism. WHO has also urged to evaluate the scenario and develop new strategies for making this organism susceptible to otherwise resistant antibiotics. Using novel compounds as drugs can ameliorate the issue to some extent. The ß-lactamase enzyme in the bacteria is responsible for inhibiting several drugs currently being used for treatment. This enzyme can be targeted to find an inhibitor that can inhibit the enzyme activity and make the organism susceptible to ß-lactam antibiotics. Plants produce several secondary metabolites for their survival in adverse environments. Several phytoconstituents have antimicrobial properties and have been used in traditional medicine for a long time. The computational technologies can be exploited to find the best compound from many compounds. Virtual screening, molecular docking, and dynamic simulation methods are followed to get the best inhibitor for L1 ß-lactamase. IMPPAT database is screened, and the top hit compounds are studied for ADMET properties. Finally, four compounds are selected to set for molecular dynamics simulation. After all the computational calculations, withanolide R is found to have a better binding and forms a stable complex with the protein. This compound can act as a potent natural inhibitor for L1 ß-lactamase.

Present and pioneer methods of early detection of food borne pathogens.

Food-borne pathogens are a severe threat to human illness and death world-wide. Researchers have reported more than 250 food-borne diseases. Most of these are infections caused by a wide variety of bacteria, viruses, and parasites. It has a significant economic impact also. Detection of pathogenic microbes is thus essential for food safety. Such identification techniques could meet the following parameters viz., the accuracy of detection techniques that are quick, efficient, economical, highly sensitive, specific, and non-labor intensive. The various available methods for detecting food pathogens are classified into different groups, each having its advantages and disadvantages. The conventional methods are usually the first choice of detection even though they are laborious. Modern techniques such as biosensors, immunological assays, and macromolecule-based (nucleic acid) methods are being developed and refined to overcome traditional methods' limitations. Early detection of pathogens and secure food safety at each stage of food processing to storage, utilizing improved methodologies are mandatory. This review summarizes the deadly food pathogens leading to significant outbreaks and discusses the importance of early detection methods and advanced detection methods in comparison.

Review on Stenotrophomonas maltophilia: An Emerging Multidrug- resistant Opportunistic Pathogen.

Stenotrophomonas maltophilia is an opportunistic pathogen that results in nosocomial infections in immunocompromised individuals. These bacteria colonize on the surface of medical devices and therapeutic equipment like urinary catheters, endoscopes, and ventilators, causing respiratory and urinary tract infections. The low outer membrane permeability of multidrug-resistance efflux systems and the two chromosomally encoded ß- lactamases present in S. maltophilia are challenging for arsenal control. The cell-associated and extracellular virulence factors in S. maltophilia are involved in colonization and biofilm formation on the host surfaces. The spread of antibiotic-resistant genes in the pathogenic S. maltophilia attributes to bacterial resistance against a wide range of antibiotics, including penicillin, quinolones, and carbapenems. So far, tetracycline derivatives, fluoroquinolones, and trimethoprim-sulfamethoxazole (TMP-SMX) are considered promising antibiotics against S. maltophilia. Due to the adaptive nature of the intrinsically resistant mechanism towards the number of antibiotics and its ability to acquire new resistance via mutation and horizontal gene transfer, it is quite tricky for medicinal contribution against S. maltophilia. The current review summarizes the literary data on pathogenicity, quorum sensing, biofilm formation, virulence factors, and antibiotic resistance of S. maltophilia.

Identification of Therapeutic Drug Target of Stenotrophomonas maltophilia Through Subtractive Genomic Approach and in-silico Screening Based on 2D Similarity Filtration and Molecular Dynamic Simulation.

BACKGROUND: Stenotrophomonas maltophilia is a multi-drug resistant, gram-negative bacterium that causes opportunistic infections and is associated with high morbidity and mortality in severely immunocompromised individuals. AIM: The study aimed to find out the drug target and a novel inhibitor for Stenotrophomonas maltophilia. OBJECTIVES: The current study focused on identifying specific drug targets by subtractive genomes analysis to determine the novel inhibitor for the specified target protein by virtual screening, molecular docking, and molecular simulation approach. MATERIALS AND METHODS: In this study, we performed a subtractive genomics approach to identify the novel drug target for S.maltophilia. After obtaining the specific target, the next step was to identify inhibitors that include calculating 2D similarity search, molecular docking, and molecular simulation for drug development for S.maltophilia. RESULTS: With an efficient subtractive genomic approach, out of 4386 proteins, five unique targets were found, in which UDP-D-acetylmuramic (murF) was the most remarkable target. Further virtual screening, docking, and dynamics analyses resulted in the identification of seven novel inhibitors. CONCLUSION: Further, in vitro and in vivo bioassay of the identified novel inhibitors could facilitate effective drug use against S.maltophilia.

In silico analysis of diversity, specificity and molecular evolution of Stenotrophomonas phages.

In this study, we have focused on the lytic phage proteins encoded by the Stenotrophomonas phages. A total of 60 lytic proteins were identified to be encoded by 19 different phages. Those proteins were characterized under eight classes: amidases, muramidases, pectate lyase, peptidases, holins and spanins. The phages encoding these proteins come under the family of Ackermannviridae, Autographiviridae, Myoviridae, Podoviridae and Siphoviridae. All the phages encoding those proteins were found to infect Stenotrophomonas maltophilia. Among the phages, about 50% were found to undergo a lytic lifecycle. The isolated proteins were clustered according to the similarity in the amino acid sequence. These clusters were used to make their phylogenetic tree. The co-occurrence of the amidase, pectate lyase and lipase genes in the phage genome was found using a correlation analysis.

In-silico virtual screening for identification of potent inhibitor for L2-ß-lactamase from Stenotrophomonas maltophilia through molecular docking, molecular dynamics analysis study.

Stenotrophomonas maltophilia, a Multiple-Drug-Resistant proteobacterium found in healthy normal flora and fauna with an aerobic and non-fermentative respiratory process, is majorly involved in Healthcare-Associated Infections (HAI). The Multiple-Drug-Resistance takes place by secretion of the ß-Lactamase enzyme, which hydrolyzes the ß-Lactam antibiotics and currently serving as a significant clinical challenge by substantially effecting the mortality rate. In this study, involved 2D Similarity, Molecular docking, and Molecular Simulation for the commercially available ZINC database compounds to overcome this resistance mechanism and find out a proper potent inhibitor for the target L2-ß-Lactamase, which would not get cleaved by the hydrolytic activity of the L2-ß-Lactamase natural enzyme. The ZINC35053014 compound had the highest binding energy: -8.51Kcal/mol with hydrophobic interaction at THR235 and formation of hydrogen bonds at SER70, SER130, ASN170, LYS234, THR235, SER237, and ARG244. In total, 08 hit compounds subjected for the stability check of the protein-ligand complex (MD simulation) analysis which, concluded in the same RMSD, RMSF, and Rg values at the comparison between known compounds and the selected virtual hit compounds. These selected virtual hit compounds can be experimentally verified and used as lead compounds for the future search of ß-Lactamase potent inhibitors for S. maltophilia. Communicated by Ramaswamy H. Sarma.

Molecular docking studies of (4Z, 12Z)-cyclopentadeca-4, 12-dienone from Grewia hirsuta with some targets related to type 2 diabetes.

BACKGROUND: Management of diabetes without any side effects is still a challenge to the medical system. This leads to increasing demand for natural products with antidiabetic activity with fewer side effects. Grewia hirsuta (Tiliaceae) is a traditional herbal medicinal plant and is reported to possess a variety of pharmacological actions. In the present research, a compound (4Z, 12Z)-cyclopentadeca-4, 12-dienone isolated from Grewia hirsuta was taken as ligand for molecular docking studies. Evaluation of hypoglycemic activity through an extensive in silico docking approach with molecular targets such as aldose reductase, glucokinase, pyruvate dehydrogenase kinase isoform 2, peroxisome proliferator-activated receptor-gamma, glycogen synthase kinase-3, 11ß-Hydroxysteroid dehydrogenase, and glutamine: fructose-6-phosphate amidotransferase were performed. METHODS: Isolation of the (4Z, 12Z)-cyclopentadeca-4,12-dienone from the methanol extract of the leaves of Grewia hirsuta was performed by the column chromatography to yield different fractions. These fractions were then subjected to purification and the structure was elucidated and confirmed by spectroscopic methods including UV, FTIR, (1)H, (13)C NMR and the accurate mass determination was carried out using the Q-TOF mass spectrometer. In-vivo experimentation was performed with evaluation of α-glucosidase, α-amylase and MTT assay that had been reported by the author in the earlier paper. Molecular docking study was performed with GLIDE docking software. RESULTS: The docking studies of the ligand (4Z, 12Z)-cyclopentadeca-4, 12-dienone with seven different target proteins showed that this is a good inhibitor, which docks well with various targets related to diabetes mellitus. Hence (4Z, 12Z)-cyclopentadeca-4,12-dienone can be considered for developing into a potent anti-diabetic drug. CONCLUSION: The results of the current study have revealed that the leaves of the selected plant Grewia hirsuta contains a potential inhibitor for diabetes (4Z, 12Z)-cyclopentadeca-4,12-dienone. Thus enabling a possibility of this plant extract as a new alternative to existing diabetic approaches.

BiodEnz:A database of biodegrading enzymes.

UNLABELLED: Azo dyes, which re characterized by azo bonds, are a predominant class of colorants used in tattooing, cosmetics, foods, textile and consumer products. Laccases (EC 1.10.3.2), lignin peroxidases (EC 1.11.1.14) , Azo reductases (EC 1.7.1.6) of different micro organisms are mainly useful for the development of biodegradation systems as they catalyse reductive cleavage of azo groups (-N=N-) . Laccases have very broad substrate specificity with respect to the electron donor and is capable of oxidizing phenols and aromatic amines. Azoreductase belongs to the family of oxidoreductases, acting on other nitrogenous compounds as donors with NAD+ or NADP+ as acceptor. Lignin peroxidase enzymes are highly non-specific and are well reported to decolourize various dyes We have developed BiodEnz database by collecting information like strains that produce particular enzymes, azo dyes that are degraded , substrate specificity, molecular weight, the optimum temperature and pH, sequence data of the above enzymes ,as the most effective inoculants used for bioremediation are able to degrade dyes over a broad concentration range, tolerate a range of environmental conditions of temperature, pH, and activity of the enzymes. The database can be searched by using a user friendly web interface. AVAILABILITY: The database is available for free at http://www.biodenzdatabase.in.