Development and immunological evaluation of an mRNA-based vaccine targeting Naegleria fowleri for the treatment of primary amoebic meningoencephalitis

More than 95% of patients fall victim to primary amoebic meningoencephalitis (PAM), a fatal disease attacking the central nervous system. Naegleria fowleri, a brain-eating microorganism, is PAM's most well-known pathogenic ameboflagellate. Despite the use of antibiotics, the fatality rate continues to rise as no clinical trials have been conducted against this disease. To address this, we mined the UniProt database for pathogenic proteins and selected assumed epitopes to create an mRNA-based vaccine. We identified thirty B-cell and T-cell epitopes for the vaccine candidate. These epitopes, secretion boosters, subcellular trafficking structures, and linkers were used to construct the vaccine candidate. Through predictive modeling and confirmation via the Ramachandran plot (with a quality factor of 92.22), we assessed secondary and 3D structures. The adjuvant RpfE was incorporated to enhance the vaccine construct's immunogenicity (GRAVY index: 0.394, instability index: 38.99, antigenicity: 0.8). The theoretical model of immunological simulations indicated favorable responses from both innate and adaptive immune cells, with memory cells expected to remain active for up to 350 days post-vaccination, while the antigen was eliminated from the body within 24 h. Notably, strong interactions were observed between the vaccine construct and TLR-4 (- 11.9 kcal/mol) and TLR-3 (- 18.2 kcal/mol).

Screening, biochemical characterization and antibiotics resistance/susceptibility of bacteria isolated from native soil and water samples

Abstract The present study was conducted to isolate and characterize bacteria from water and soil sample taken from the Lahore Canal at different sites i.e. Mall Road, Mohlanwal and Khera site. Isolated bacterial strains were identified on the basis of morphological and biochemical tests. Identification was confirmed by culturing bacteria on selective media. Antibiotic resistance test was also performed to observe the resistance of bacteria against different antibiotics. Blood agar test was performed for identification of different pathogenic bacteria. The result revealed that water and soil samples of Lahore Canal Lahore from different sites were contaminated with Escherichia coli, Salmonella sp., Vibrio sp., Bacillus spp., Enterococcus sp. and Staphylococcus spp. Due to presence of these pathogens, this water is not suitable for any domestic and irrigation use. Study also revealed that water of the Lahore Canal is harmful for human health as it is contaminated with bacteria that can cause severe disease e.g., Escherichia coli can cause gastroenteritis, Bacillus spp. can cause nausea and vomiting, Enterococcus may infect urinary tract, Salmonella sp. is responsible for Bacteremia, Staphylococcus spp. can cause mild fever and Vibrio sp. can be the reason of cholera. Thus it is rendered unfit for any kind of human use even other than drinking like swimming, bathing, washing etc., until and unless some remedial measures are employed to eradicate pathogenic microorganisms by WASA and LWMS according to standards of WHO. Similarly, it is quite harmful, when and where ever it is used for irrigation without proper treatment.

Whole proteome analysis of MDR Klebsiella pneumoniae to identify mRNA and multiple epitope based vaccine targets against emerging nosocomial and lungs associated infections

Klebsiella pneumonia is a Gram negative facultative anaerobic bacterium involved in various community-acquired pneumonia, nosocomial and lungs associated infections. Frequent usage of several antibiotics and acquired resistance mechanisms has made this bacterium multi-drug resistance (MDR), complicating the treatment of patients. To avoid the spread of this bacterium, there is an urgent need to develop a vaccine based on immuno-informatics approaches that is more efficient than conventional method of vaccine prediction or development. Initially, the complete proteomic sequence of K. pneumonia was picked over for specific and prospective vaccine targets. From the annotation of the whole proteome, eight immunogenic proteins were selected, and these shortlisted proteins were interpreted for CTL, B-cells, and HTL epitopes prediction, to construct mRNA and multi-epitope vaccines. The Antigenicity, allergenicity and toxicity analysis validate the vaccine's design, and its molecular docking was done with immuno-receptor the TLR-3. The docking interaction showed a stronger binding affinity with a minimum energy of -1153.2 kcal/mol and established 23 hydrogen bonds, 3 salt bridges, 1 disulfide bond, and 340 non-binding contacts. Further validation was done using In-silico cloning which shows the highest CAI score of 0.98 with higher GC contents of 72.25% which represents a vaccine construct with a high value of expression in E. coli. Immune Simulation shows that the antibodies (IgM, IgG1, and IgG2) production exceeded 650,000 in 2 to 3 days but the response was completely neutralized in the 5th day. In conclusion, the study provides the effective, safe and stable vaccine construct against Klebsiella pneumonia, which further needs in vitro and in vivo validations.Communicated by Ramaswamy H. Sarma.

Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir

The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.

Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens

Serratia marcescens, a Gram-negative bacterium, is one of the known disease-causing pathogens. It is resistant to ampicillin, macrolides, cephalosporins, cefotaxime, and ceftazidime. The only antibiotic that has been proven to be effective against S. marcescens is gentamicin. By causing epigenetic alterations, bacteria can also become resistant to all antibiotics. Many epigenetically related proteins were studied, and four proteins were selected in this regard for epitope evaluation and their subsequent use in the development of a messenger ribonucleic acid (mRNA) vaccine. A series of immune-informatics tools used to build this mRNA vaccine elicited cellular and humoral immunity. Molecular docking between epitopes and alleles of the major histocompatibility complex (MHC) was performed. The vaccine was developed using 37 epitopes, an adjuvant that is a TLR-4 agonist known as resuscitation-promoting factor E (RpfE), subcellular trafficking structures, secretion boosters, and linkers. This proposed architecture was found to cover 99.6% of the population during testing. During testing, it was proven that it was both effective and safe. To confirm our idea, we performed an in silico immunological simulation of vaccination. The codon was also optimized to ensure that the mRNA reached the cytoplasm of a human host and underwent efficient translation. TLR-4 and TLR-3 were also docked against the secondary and tertiary structures of the vaccine peptide. Furthermore, the vaccine's stability was confirmed by molecular dynamics simulation. In summary, this vaccine construct can be a potential candidate against S. marcescens and is suitable for in vitro analyses to validate its effectiveness.

Immunoinformatics Approach to Design Multi-Epitope-Based Vaccine against Machupo Virus Taking Viral Nucleocapsid as a Potential Candidate

The family members of Arenaviridae include members of the genus Machupo virus, which have bi-segmented negative sense RNA inside the envelope and can be transferred to humans through rodent carriers. Machupo virus, a member of the mammarenavirus genus, causes Bolivian hemorrhage fever, its viral nucleocapsid protein being a significant virulence factor. Currently, no treatment is available for Bolivian hemorrhage fever and work to develop a protective as well as post-diagnosis treatment is underway. Adding to these efforts, this study employed a reverse-vaccinology approach to design a vaccine with B and T-cell epitopes of the viral nucleocapsid protein of the Machupo virus. Five B-cell specific, eight MHC-I restricted, and 14 MHC-II restricted epitopes were finalized for the construct based on an antigenicity score of >0.5 and non-allergenicity as a key characteristic. The poly-histidine tag was used to construct an immunogenic and stable vaccine construct and 50S ribosomal 46 protein L7/L12 adjuvant with linkers (EAAAK, GPGPG, and AYY). It covers 99.99% of the world’s population, making it highly efficient. The physicochemical properties like the aliphatic index (118.31) and the GRAVY index (0.302) showed that the vaccine is easily soluble. The overall Ramachandran score of the construct was 90.7%, and the instability index was 35.13, endorsing a stable structure. The immune simulations demonstrated a long-lasting antibody response even after the excretion of the antigen from the body in the first 5 days of injection. The IgM + IgG titers were predicted to rise to 6000 10 days post-injection and were illustrated to be stable (around 3000) after a month, elucidating that the vaccine would be effective and provide enduring protection. Lastly, the molecular interaction between the construct and the IKBKE receptor was significant and a higher eigenfactor value in MD simulations confirmed the stable molecular interaction between the receptor and the vaccine, validating our construct.

The Virulent Hypothetical Proteins: The Potential Drug Target Involved in Bacterial Pathogenesis

Abstract:

Hypothetical proteins (HPs) are non-predicted sequences that are identified only by open reading frames in sequenced genomes but their protein products remain uncharacterized by any experimental means. The genome of every species consists of HPs that are involved in various cellular processes and signaling pathways. Annotation of HPs is important as they play a key role in disease mechanisms, drug designing, vaccine production, antibiotic production, and host adaptation. In the case of bacteria, 25-50% of the genome comprises of HPs, which are involved in metabolic pathways and pathogenesis. The characterization of bacterial HPs helps to identify virulent proteins that are involved in pathogenesis. This can be done using in-silico studies, which provide sequence analogs, physiochemical properties, cellular or subcellular localization, structure and function validation, and protein-protein interactions. The most diverse types of virulent proteins are exotoxins, endotoxins, and adherent virulent factors that are encoded by virulent genes present on the chromosomal DNA of the bacteria. This review evaluates virulent HPs of pathogenic bacteria, such as Staphylococcus aureus, Chlamydia trachomatis, Fusobacterium nucleatum, and Yersinia pestis. The potential of these HPs as a drug target in bacteria-caused infectious diseases along with the mode of action and treatment approaches have been discussed.

Utility of the microcolony method for evaluation of multidrug-resistant tuberculosis patients in Karachi, Pakistan

OBJECTIVE: To compare the microcolony method (MCM) with the reference culture method to evaluate culture conversion in multidrug-resistant tuberculosis (MDR-TB) patients.MATERIAL AND METHODS: Adult patients with Mycobacterium tuberculosis culture-positive MDR-TB undergoing second-line anti-tuberculosis treatment were recruited from two tertiary care chest clinics from January 2013 to October 2014. The MCM was performed in addition to MGIT™ and Löwenstein-Jensen medium (reference method) on sputum samples submitted on a monthly basis.RESULTS: Of 140 patients, culture conversion could be evaluated in 95 patients. The MCM showed 100% agreement with the reference M. tuberculosis culture in 83 of 95 patients who achieved culture conversion. In smear-positive and smear-negative cases, the mean time to positivity was 9.1 and 11.4 days for the MCM and 16.1 and 23.2 days for the reference M. tuberculosis culture respectively. The contamination rate for the MCM was 4.5% in comparison with 6.1% for the reference M. tuberculosis culture. The cost of MCM was estimated to be 30% that of the reference method.CONCLUSION: The MCM can be used in non-urban laboratories as a safe, rapid and cost-effective substitute for the reference M. tuberculosis culture to assess culture conversion in MDR-TB patients.Note: Abstract has been published in International Journal of Mycobacteriology 2015; 4: 159-160.

Invasive candidiasis in Pakistan: clinical characteristics, species distribution and antifungal susceptibility

This study reports for the first time, to our knowledge, descriptive epidemiological data for 188 invasive Candida isolates from Pakistan, including species identification and antifungal susceptibility against fluconazole, itraconazole, voriconazole, caspofungin, micafungin, anidulafungin and amphotericin. Risk factors for invasive candidiasis (IC) were determined for 96 patients from Karachi, Pakistan. In adults and neonates, Candida tropicalis (38 and 36 %, respectively) was the most common species, followed in adults by Candida parapsilosis (17.8 %), Candida glabrata (15.9 %) and Candida albicans (12.3 %). C. albicans (21 %) was the second most common in neonates. In children, C. albicans (31.9 %), C. tropicalis (26.4 %) and C. parapsilosis (19.4 %) were the most common. C. albicans IC was significantly associated with paediatric age [crude odds ratio (COR) 3.46, 95 % confidence interval (CI) 1.63-7.32]. Rare species made up 17.5 % of the total isolates studied. Resistance to fluconazole was seen in C. glabrata (15 .0%) and Candida krusei (100 .0%). Only one isolate (C. glabrata) was resistant to all three echinocandins. Low MICs of fluconazole for 98 % (184/188) of isolates tested support its continued use as an empiric therapy for IC. Non-C. albicans IC was associated with the use of β-lactam inhibitor combinations (COR 3.16, 95 % CI 1.05-9.57). Use of healthcare devices was documented in 85.4 % of IC patients, whilst 75 .0% had been admitted to special care units. Surprisingly, 66.7 % of patients with IC were not obviously immunosuppressed. The high frequency of modifiable risk factors in this population indicates that candidaemia can be reduced with stringent antibiotic and infection control measures. These data will be useful for empiric selection of antifungals in Karachi, and contribute to global assessments of antifungal resistance.

Use of p-nitrobenzoic acid in 7H10 agar for identification of Mycobacterium tuberculosis complex: a field study

We report the efficiency and cost-effectiveness of p-nitrobenzoic acid (PNB) testing in Middlebrook 7H10 agar medium for the identification of Mycobacterium tuberculosis complex (MTC). PNB-7H10 was compared with PNB-MGIT and BACTEC-NAP using 200 clinical mycobacterial isolates. PNB-7H10 showed 100% agreement with PNB-MGIT and BACTEC-NAP tests, and reduced the cost of PNB-MGIT test by 80%. PNB-7H10 agar is therefore an effective alternative to the costly PNB-MGIT and BACTEC-NAP tests, especially in resource-poor settings.

Increased isolation of Vibrio cholerae O1 serotype Inaba over serotype Ogawa in Pakistan

Although the predominant Vibrio cholerae serotype in Pakistan is Ogawa and serotype Inaba is rare, there has been a significant increase in the isolation of Inaba in our referral laboratory in Karachi. This paper reports this observation and further analysis of previous cholera data from 1993 to 2005 to assess the trend of occurrence and resistance pattern of V. cholerae strains. From January to September 2005, 245/3292 (7.4%) specimens yielded growth of V. cholerae. Of these, 243 were serotype Inaba, outnumbering serotype Ogawa. This recent Inaba strain is 100% resistant to cotrimoxazole, 3% resistant to chloramphenicol and not resistant to ampicillin, tetracycline and ofloxacin. This sensitivity pattern is almost similar to that of the previous predominant serotype Ogawa.

Comparison of double disc and combined disc method for the detection of extended spectrum beta lactamases in enterobacteriaceae

OBJECTIVE

To compare double disc approximation and combined disc method for their ability to detect extended spectrum b lactamase (ESBL) production in enterobacteriaceae and determine the percentage of isolates which are falsely reported as sensitive in absence of ESBL detection, in a clinical microbiology laboratory of a tertiary care hospital between September-October 2002.

METHODS

Selected isolates were identified according to standard biochemical tests. Disc susceptibility tests were performed according to NCCLS. ESBL detection by combined disc [cefotaxime (30 ug) versus cefotaxime plus clavulanate (30+10 ug)] was compared with detection using double discs [amoxy-clavulanic acid (20+10 ug) and aztreonam (30 ug) applied 10 mm apart]. Results were interpreted according to NCCLS and analysed on SPSS version 10.

RESULTS

ESBL production was detected in 140 (30%) isolates by combined disc method and 139 (29.5%) by double disc method. There was no significant difference between two methods. Of the ESBL positive isolates 41 (29%) gave zone diameters that were within the sensitivity range cutoff and would have been falsely reported as being beta lactam sensitive in absence of ESBL detection.

CONCLUSION

ESBL detection should be routinely performed in clinical laboratories as false reporting would result in treatment failure despite in vitro sensitivity. No difference was found between the combined disc and double disc methods hence either of two could be used.

Re-emergence of Vibrio cholerae O139 in Pakistan: report from a tertiary care hospital

OBJECTIVE

This study reports re-emergence of Vibrio cholerae O139 in Pakistan in 2000-2001 from a tertiary care hospital in Karachi, Pakistan.

METHODS

This descriptive study was conducted from 2000-2001. Stool samples were taken from inpatients or those referred to the laboratory from other hospitals, clinics and general practitioners. Samples were processed and Vibrio cholerae isolates were identified according to standard protocols. Tellurite Taurocholate Gelatin agar was used as a selective medium for Vibrio cholerae. Serogroups were identified by slide agglutination with polyvalent antisera. Antimicrobial sensitivities were performed by Kirby Bauer technique. Data was entered and analyzed using SPSS, p values were calculated using t test and two independent samples test.

RESULTS

During the study period, 144 samples were found to be infected with Vibrio cholerae O139 in comparison with 545 Vibrio cholerae O1. Infection with O139 was characteristically observed in the older population (mean age = 40 years) in contrast with Vibrio cholerae O1 strains (mean age = 23 years) (p. value = <0.001). Sensitivity pattern of 2000-2001 Vibrio cholerae isolates was markedly different to that of 1993-1994. The earlier isolates were resistant to Cotrimoxazole (99%) and Chloramphenicol (35%) whereas the recent isolates are almost 100% sensitive.

CONCLUSION

In conclusion this re-emergent strain seen 6 years after previous episode infected large number of people especially older population suggesting that prior infection with O1 does not provide immunity against O139 and therefore Vibrio cholerae O139 has a potential to cause a major epidemic in an immunologically naïve population.

Haemotoxicity to chicken (Gallus gallus domesticus) by technical and formulation grades of some phosphoric and synthetic pyrethroid esters

Acute toxicity was studied by administering an encapsulated single dose to chickens (G.g. domesticus) and observing them for 21 days. Azodrin-71 (Tech.) was found to be extremely toxic, whereas Cypermethrin-92 (Tech.), Cypermethrin-25 EC and Permasect-25 EC (Form.) were practically non-toxic based on LD50 value determinations. Sub-acute oral haemotoxicity of technical and formulation grades of these insecticides was also studied by administering encapsulated low, medium and high daily doses for 21 days to chickens and recording clinical symptoms, mortality and haematological parameters pre and post-dosing. Clinically high doses of Azodrin-71 (Tech.) caused tremors and ataxia among chicks on the 10th day after dosing. Synthetic pyrethroids caused slight tremours in the whole body accompanied by salivation. In general, hyperactivity to external stimuli and loss of appetite and body weight were also observed. With sub-acute oral doses, Permasect-25 EC (Form.) more potently affected haemoglobin (Hb), red cell (RBC) counts and chloride level. Cypermethrin-92 (Tech.) was most potent towards thrombocytes and clotting time. Azodrin-71 (Tech.) was more potent to white cell (WBC) counts and serum protein level. The present Haematological studies have disclosed the possible reaction of blood and blood forming organs to these insecticides.

Effect of dermal application of phosphamidon-92 (technical) on different tissues and hematobiochemical parameters in albino rat

The histological disturbances occurring from the dermal application of low, medium, and high doses of phosphamidon-92 (technical) to rats as observed by light microscope and analysis of hematobiochemical parameters of blood are presented. Groups of 10 male and 10 female albino rats (Wistar strain) were treated with the test material at dose levels of 0.48 (low), 2.2 (medium), and 3.98 (high) mg/kg X d for 3 wk, followed by a 2-wk observation period. During application, a reduction in food intake and in body weight was recorded with all three treatments. However, gain in body weight and food intake resumed during the observation period and was marked with the high-dose treatment only. Symptoms like hypersalivation and frothing were noticed in both the sexes, as well as a relative decrease in liver weight and gross pathological alterations on microscopical examination of skin, lung, kidney, and testis; significant alterations in some hematobiochemical parameters of blood were observed.