Syphilis, a sexually transmitted infection, is a deadly disease caused by Treponema pallidum. It is a Gram-negative spirochete that can infect nearly every organ of the human body. It can be transmitted both sexually and perinatally. Since syphilis is the second most fatal sexually transmitted disease after AIDS, an efficient vaccine candidate is needed to establish long-term protection against infections by T. pallidum. This study used reverse-vaccinology-based immunoinformatic pathway subtractive proteomics to find the best antigenic proteins for multi-epitope vaccine production. Six essential virulent and antigenic proteins were identified, including the membrane lipoprotein TpN32 (UniProt ID: O07950), DNA translocase FtsK (UniProt ID: O83964), Protein Soj homolog (UniProt ID: O83296), site-determining protein (UniProt ID: F7IVD2), ABC transporter, ATP-binding protein (UniProt ID: O83930), and Sugar ABC superfamily ATP-binding cassette transporter, ABC protein (UniProt ID: O83782). We found that the multiepitope subunit vaccine consisting of 4 CTL, 4 HTL, and 11 B-cell epitopes mixed with the adjuvant TLR-2 agonist ESAT6 has potent antigenic characteristics and does not induce an allergic response. Before being docked at Toll-like receptors 2 and 4, the developed vaccine was modeled, improved, and validated. Docking studies revealed significant binding interactions, whereas molecular dynamics simulations demonstrated its stability. Furthermore, the immune system simulation indicated significant and long-lasting immunological responses. The vaccine was then reverse-transcribed into a DNA sequence and cloned into the pET28a (+) vector to validate translational activity as well as the microbial production process. The vaccine developed in this study requires further scientific consensus before it can be used against T. pallidum to confirm its safety and efficacy.

Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.

Urinary tract infections (UTIs) are healthcare problems that commonly involve bacterial and, in some rare instances, fungal or viral infections. The irrational prescription and use of antibiotics in UTI treatment have led to an increase in antibiotic resistance. Urine samples (145) were collected from male and female patients from Lower Dir, Khyber Pakhtunkhwa (KP), Pakistan. Biochemical analyses were carried out to identify uropathogens. Molecular analysis for the identification of 16S ribosomal RNA in samples was performed via Sanger sequencing. Evolutionary linkage was determined using Molecular Evolutionary Genetics Analysis-7 (MEGA-7). The study observed significant growth in 52% of the samples (83/145). Gram-negative bacteria were identified in 85.5% of samples, while Gram-positive bacteria were reported in 14.5%. The UTI prevalence was 67.5% in females and 32.5% in males. The most prevalent uropathogenic bacteria were Klebsiella pneumoniae (39.7%, 33/83), followed by Escherichia coli (27.7%, 23/83), Pseudomonas aeruginosa (10.8%, 9/83), Staphylococcus aureus (9.6%, 8/83), Proteus mirabilis (7.2%, 6/83) and Staphylococcus saprophyticus (4.8%, 4/83). Phylogenetic analysis was performed using the neighbor-joining method, further confirming the relation of the isolates in our study with previously reported uropathogenic isolates. Antibiotic susceptibility tests identified K. pneumonia as being sensitive to imipenem (100%) and fosfomycin (78.7%) and resistant to cefuroxime (100%) and ciprofloxacin (94%). Similarly, E. coli showed high susceptibility to imipenem (100%), fosfomycin (78.2%) and nitrofurantoin (78.2%), and resistance to ciprofloxacin (100%) and cefuroxime (100%). Imipenem was identified as the most effective antibiotic, while cefuroxime and ciprofloxacin were the least. The phylogenetic tree analysis indicated that K. pneumoniae, E. coli, P. aeruginosa, S. aureus and P. mirabilis clustered with each other and the reference sequences, indicating high similarity (based on 16S rRNA sequencing). It can be concluded that genetically varied uropathogenic organisms are commonly present within the KP population. Our findings demonstrate the need to optimize antibiotic use in treating UTIs and the prevention of antibiotic resistance in the KP population.

Aquatic pollution is a burning issue nowadays due to urbanization and industrialization. Industrial wastewater (IWW) contains pollutants that pose a great risk to the environment and human beings and is a big challenge for industries. The remediation of IWW by microorganisms is an environmentally friendly technique. This study was carried out to evaluate the pollution of IWW and to use consortia of Bacillus pakistanensis, Lysinibacillus composti, and Cladophora glomerata for bioremediation. The IWW was obtained from the Hayatabad Industrial Estate and was evaluated for physicochemical parameters and metal concentration. A pot experiment was carried out for two weeks to assess the efficiency of the developed consortia. The IWW and tap water (control) were treated with three different consortia (Bacillus pakistanensis-Cladophora glomerata (CT1, E1), Lysinibacillus composti-Cladophora glomerata (CT2, E2), and Bacillus pakistanensis-Lysinibacillus composti-Cladophora glomerata (CT3, E3). The three pots (CT1, CT2, and CT3) serving as the control were provided with tap water, and the three experimental pots (E1, E2, and E3) were provided with IWW. After treatment, substantial reductions were obtained in the following parameters and percentages: colour 85.7%, electrical conductivity (EC) 40.8%, turbidity 69.6%, sulphide 78.5%, fluoride 38.8%, chloride 62.9%, biological oxygen demand (BOD) 66%, chemical oxygen demand (COD) 81.8%, total suspended solids (TSSs) 82.7%, total dissolved solids (TDSs) 24.6%, Ca hardness 37.2%, Mg hardness 50%, and total hardness 39%. The samples of water were also examined for metal concentrations using atomic absorption spectrophotometry. The selected species removed 98.2% of Mn, 94% of Cu, 97.7% of Cr, 91.6% of Cd, 92.8% of Co, 79.6% of Ag, 82.6% of Ni, 98% of Ca, 90% of Mg, and 82.1% of Pb. The BCF values showed by the consortia for Mn, Cu, Cr, Cd, Co, Ag, Ni, Ca, Mg, and Pb were 91.8, 67, 97.5, 83.3, 85.7, 48.1, 80.4, 84.3, 82.5, and 80.3%, respectively. The t-test analysis showed that the treatment with the selected species significantly decreased the metal concentrations in the IWW (p ≤ 0.05). Overall, the study concludes that metal concentration in the water was decreased significantly by the consortia of algae-bacteria.

The use of natural products isolated from mushrooms against infection, cancer diseases and other oxidative-stress-related diseases is one of the cornerstones of modern medicine. Therefore, we tried to establish a combination of medicinal mushrooms and nanotechnology possibly with the field of medicine for the development of antibacterial agents against these MDR strains. The aim of the research was to understand the molecular identification, characterization and antibacterial action of Calvatia gigantea and Mycena leaiana. The identification of fruiting body species via morpho-anatomical and molecular methods was necessary to analyze the genetic variability and phylogenetic relationships of mushrooms. Phylogenetic analysis revealed that Calvatia from Hunza, Pakistan, exhibited 98% resemblance to the previously discovered Langermannia gigantean (DQ112623) and L. gigantean (LN714562) from northern Europe, and Mycena (Pakistan) showed a 97% similarity to M. leaiana (MF686520) and M. leaiana (MW448623) from the USA. UV-vis, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) were used for AgNPs’ characterization. The UV-vis absorption peak of 500–600 nm indicates the AgNPs’ presence. XRD results determined Calvatia gigantea AgNPs were nanocrystals and Mycena leaiana seems to be amorphous. In addition, SEM results showed the cubic morphology of C. gigantea with a diameter of 65 nm, and the FTIR spectra of fruiting body revealed the presence of functional groups—carboxyl, nitro, and hydroxyl—in AgNPs, which catalyzed the reduction of Ag+ to Ag0. Further antibacterial activity of mushrooms against MDR strains was determined via agar well diffusion assay, and Minimum Inhibitory Concentration (MIC) was estimated by qualitative experimentation using the broth dilution method. All experiments were conducted in triplicate. The results showed that the mushroom AgNPs, along with their synergy and nano-composites (with the exception of Ethyl-acetate), were shown to have zones of inhibition from 4 mm to 29 mm against multidrug-resistant pathogens such as Acinetobacter baumannii, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumonia, Proteus mirabilis, Enterobacter cloacae and Escherichia coli. The mushroom composites were active against most of the tested microorganisms whilst the lowest MIC value (10–40 mg/mL) was recorded against MDR strains. Hence, the present study suggested the possibility of employing compounds present in mushrooms for the development of new antibacterial agents, as well as efflux pump inhibitors.

Aquatic bodies contaminated by heavy metals (HMs) are one of the leading issues due to rapidly growing industries. The remediation of using algae and hydrophytes acts as an environmentally friendly and cost effective. This study was performed to investigate the pollution load, especially HMs, in the wastewater of the Gadoon Industrial Estate and to utilize the hydrophytes (Typha latifolia (TL) and Eicchornia crassipes (EI)) and algae (Zygnema pectiantum (ZP) and Spyrogyra species (SS)) as bioremediators. The wastewater was obtained and assessed for physiochemical parameters before treating with the selected species. The pot experiment was performed for 40 days. Then the wastewater samples and selected species were obtained from each pot to analyze the metal removal efficiency and assess for metal concentrations using atomic absorption spectrophotometry. The dissolved oxygen (DO; 114 mg/L), total suspended solids (TSS; 89.30 mg/L), electrical conductivity (EC; 6.35 mS/cm), chemical oxygen demand (COD) (236 mg/L), biological oxygen demand (BOD; 143 mg/L), and total dissolved solids (TDS; 559.67 mg/L), pH (6.85) were analyzed. The HMs were noted as Zn (5.73 mg/L) and Cu (7.13 mg/L). The wastewater was then treated with the species, and significant reductions were detected in physicochemical characteristics of the wastewater such as DO (13.15–62.20%), TSS (9.18–67.99%), EC (74.01–91.18%), COD (25.84–73.30%), BOD (21.67–73.42%), and TDS (14.02–95.93%). The hydrophytes and algae removed up to 82.19% of the Zn and 85.13% of the Cu from the wastewater. The study revealed that the hydrophytes and algae significantly decreased the HM levels in the wastewater (p ≤ 0.05). The study found TL, EI, ZP, and SS as the best hyper accumulative species for Zn and Cu removal from wastewater. The HMs were removed in the order of Cu > Zn. The most efficient removal for Cu was found by Typha latifolia and Zn by Zygnema pectiantum. It was concluded that bioremediation is an environmentally friendly and cost-effective technique that can be used for the treatment of wastewater due to the efficiency of algae and hydrophytes species in terms of HM removal.