20 research outputs found
Designing T-cell epitope-based vaccine against Eimeria infection in chicken using immunoinformatics approach.
No full textMasters Degree. University of KwaZulu-Natal, Durban.Chicken coccidiosis is the most significant ubiquitous, intestinal parasitic disease known to infect chickens globally. It is recognised for incurring significant production loss to the poultry industry, caused by single or multiple Eimeria spp. infections which threaten chicken welfare and productivity. The emergence of drug resistance in parasites and pathogenicity reversion has put pressure on the poultry industry to reduce chemoprophylactic drugs and live vaccines as preventive measures against coccidiosis. Recombinant DNA vaccines have shown promising results as an alternative option, but complete protection has not been reported highlighting the need for the design of new vaccine against this disease. In this study, Eimeria antigens Immune Mapped Protein-1(IMP1) and Microneme Protein-2(MIC2) were explored using reverse vaccinology and immunoinformatics tool to predict and design potential multiepitope vaccine candidate against coccidiosis. A total of 28 and 19 antigenic T-cell epitopes were predicted and used to construct two multiepitope vaccines with 610 and 512 amino acids for IMP1 and MIC2, respectively. The produced vaccines exhibited favoured characteristics for an ideal vaccine candidate; they were antigenic (Vaxijen score of 0.5989 and 0.5103), immunogenic (scores: 10.15 and 9 419), thermostable (instability index <40 ), and non-allergic. The presence of IFN-gamma and IL-4 inducing epitopes in the constructed vaccine enables vaccine to trigger a cellular and humoral response within the host. Molecular docking of designed vaccines with toll-like receptors (TLR4 and TLR5) to determine vaccine interaction and stability was confirmed by molecular dynamics simulation root-mean square deviation (RMDS) and root-mean-square fluctuation (RMSF) analysis. The designed vaccines induced immune response through production of cytokines and antibodies associated with tertiary response. When exposed to online immune simulation C-ImmSim, both vaccines produced potent immune response through production of IgG, Tc and Th cell and memory Bcells. The constructed multiepitope vaccine in this present study is highly promising and as such further experimental work should be done to confirm its suitability against chicken coccidiosis
Prevalence of Staphylococcus aureus and its antimicrobial resistance and virulence genes in pet dogs of Durban: the risks of reservoir populations.
No full textMasters Degree. University of KwaZulu-Natal, Westville.Abstract available in pdf
Effects of lactic acid bacteria as putative probiotics and host genetic profile on rumen microbial ecology of two South African goat breeds.
No full textDoctoral Degree. University of KwaZulu-Natal, Durban.Over a decade ago, the use of antibiotics as feed additives has been banned in most European Union countries because of the following risks: development of antibiotic resistance in pathogenic microbiota, release of unmanageable antibiotics into the environment and antibiotic or chemical residues in animal products. Due to consumer’s pressure and worries towards harmful effects of antibiotics as growth promoters, there was a need to think of alternatives to antibiotics. In recent years, probiotics have been preferred as a superior alternative to antibiotics because they no harmful attributes associated with antibiotics and also have the ability to stabilize the microbial diversity in the digestive tract, and promotes animal yield while preserving consumer’s health. Probiotics have also been observed to improve the functions of rumen microflora, fermentation processes and improve digestion in ruminants. The study therefore aimed to evaluate the effect of supplementation of putative probiotics- Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination for two South African goat breeds. The first objective of the study was to determine the effects of probiotics on feed intake and growth performance of Boer and Speckled goats. To achieve the first objective, a total of 18 Speckled and 18 Boer randomly selected goats were separated into five treatment groups according to gender and breed. The trial lasted for 30 days. The goats were fed with pellets. Also, fresh water and hay were provided ad libitum. The treatment groups were as follows: (T1) basal diet + Lactobacillus rhamnosus SCH; (T2) basal diet + Enterococcus faecalis 25a; T3 basal diet + probiotic Lactobacillus rhamnosus SCH and Enterococcus faecalis 25a; T4 (positive control) basal diet + antibiotic; and T5 (negative control) basal diet with no antibiotics and no probiotics. The animals were weighed before and after the trial to determine their growth performance. Ruminal contents were collected before and after trial to examine the changes in the ruminal pH. All the data collected were processed and analyzed using one-way analysis of variance (ANOVA) procedure of Statistical Analysis System (SAS, version 9.4). The efficiency of oral administration of putative probiotics on growth performance of South African goats showed the best performance in weight gain, final body weight and feed conversion ratios. Gender and breed affected weight gain and body weight, showing that male (18.4 kg) goats were heavier than females (15.3 kg) and that Boer goat had a faster percentage growth rate of 24% than Specked (18%). This indicates that Boer goats will reach the market weight faster; this is due to the effect of probiotics. Supplementation of probiotics had no effect on feed intake. The pH across all treatment groups decreased averagely from 7.01 to 6.18. The lowest pH of 6.18 was observed in treatment group 3 (combination of probiotics). The findings in this study suggest that probiotics may have beneficial effects in goats’ nutrition by increasing weight gain and lowering pH. The second aim of the study was to determine the effect of host genetic profile on rumen ecology and performance characteristics of two South African goat breeds. Gut microbiota compositions were determined by sequencing the V3-V4 region of the 16S rRNA gene from ruminal contents of 36 goats. A total of 1,260 operational taxonomic units were obtained and grouped in 19 Phyla and 97 Genera. Bacteroidetes, Firmicutes, Proteobacteria and Fibrobacters were the most dominant Phyla in all the treatment groups, while Prevotella and Anaerofustis were the most abundant Genera. Archaeal genus Vadin CA11, decreased in Treatment 1, 2, 3 and 5, while an increase was observed only in treatment 5. The presence of this genus has potential to allow the microbiome to adapt quickly to environmental stress like diet changes. However, the abundance of this genus must be controlled because it can produce additional ammonium through methanogenesis. The presence of Chlamydiae was observed only in Treatment 5 showing that probiotics and antibiotics eliminate obligate pathogens. Our result indicates that probiotics promote microbial diversity. The final objective was to examine the alterations triggered by the probiotics on the rumen microbial profiles of Boer and Speckled goats using the 50K SNP bead chip. Genome-wide association study was explored between genotype and the rumen microbiome composition. A total of 44 single-nucleotide polymorphisms dispersed across the goat genome were associated with the relative abundance of six microbial Genera: BF311, Clostridium, Fibrobacter, Methanobrevibacter, Prevotella, and Ruminococcus. A total of 47 candidate genes were identified within 1-Mb windows of the goat genome; CPT1A, STC2, AGPAT3 and ACSF3 genes were associated with fatty acid metabolism, while GH, BMP, MSTN, GHR and STMN1 were associated with regulation of developmental growth. Our results suggest that 47 candidate genes may positively shape the microbiome and elucidate the association between gastrointestinal (GI) microbiome and the host genome in two South African goat breeds used for this study
Genetic characterization of robustness and fitness traits in South African indigenous chickens.
No full textMaster of Science in Microbiology. University of KwaZulu-Natal, Durban, 2016.Abstract available in PDF file
Genetic characterization of resistance and virulence genes in Enterococcus species from animal isolates in Durban.
No full textMasters Degree. University of KwaZulu-Natal, Durban.Misuse of antimicrobials in animal agriculture has given rise to strains of bacteria that are resistant to multiple antibiotics. Enterococci bacteria have emerged among such antibiotic-resistant strains of bacteria and infections due to antibiotic-resistant bacteria is one of the world’s critical health challenge. Enterococci are gut commensal bacteria but are currently confirmed pathogenic bacteria responsible for so many hospital-acquired infections like urinary tract infections. The aim of this research was to detect the occurrence of Enterococcus species in chickens, cats, and dogs; their phenotypic and genotypic resistance to antibiotic drugs and virulence genes. Isolation of Enterococcus species was done using microbiological culture methods and confirmed using specific primers through Polymerase Chain Reaction (PCR). Presumptive Enterococcus growth on bile esculin agar was positive for 94% of all the isolates. Overall, 77.3% of the isolates were positive for Tuf gene (Enterococcus genus-specific gene). Enterococcus faecalis was detected at a higher frequency (40.4%; P <0.05) compared to Enterococcus faecium (8.5%). All the Enterococcus isolates were susceptible to High-Level Gentamicin on antimicrobial susceptibility test. Enterococcus species in chickens exhibited higher resistance to the antibiotics than the pets. Highest resistance was observed in Quinupristin/Dalfopristin (89.4%) followed by Vancomycin (87.9%), Rifampicin (85%), Ampicillin (76.6%), Erythromycin (72.3%), and Tetracycline (64.5%). Chloramphenicol (24.8%), High-Level Streptomycin Resistance (24.1%), and Ciprofloxacin (14.2%). Eighty-four percent (84%) of the Enterococcus isolates expressed multidrug resistance (MDR). Three of the four resistance genes screened were detected: 21.3%, 7.8% and 4.3% for Kanamycin, Streptomycin, and Vancomycin resistance genes respectively. Gentamicin resistance gene was absent in all the isolates. PCR detection of virulence gene showed highest prevalence in EfaA gene at 88.7% frequency followed by GelE (82.3%), ccf (81.6%), Esp (26.2%) and CylA (25.5%). All E. faecalis and E. faecium detected harbored multiple virulence genes. These findings show that chickens, cats, and dogs can be colonized by pathogenic Enterococci which harbor resistance and virulence genes and are multidrug resistant. It is therefore important that antibiotics are used prudently in animal husbandry to mitigate emergence and transfer of Enterococci pathogens to humans via food chain and direct contact of pets by their owners
Diversity of Eimeria tenella apical membrane antigen-1 from chickens in Mpumalanga province and its in silico epitope prediction as a vaccine candidate.
No full textMasters Degree. University of KwaZulu-Natal, Durban.Coccidiosis has been a significant challenge in the poultry industry. There is a high request for the modification of a cost-effective immunizing agent to curtail this disease. Apical membrane antigen 1 (AMA1) has been reported as a protective antigen in sub-unit vaccine development against several apicomplexan parasites such as Plasmodium falciparum, Eimeria tenella and Eimeria maxima. However, knowledge of genetic diversity in this vaccine candidate is imperative. Also, to minimize the cost and time involved in producing a vaccine, computational vaccine design has received much attention through the immunoinformatics method. Therefore, screening for the potential vaccine epitopes in AMA1 that can induce cellular and humoral immune response through the immunoinformatics technique looks promising. This investigation aimed to detect the level of genetic diversity amid Eimeria tenella Apical Membrane Antigen 1(EtAMA1) in selected farms in Mpumalanga province and predict vaccine epitopes from this antigen. Four hundred fresh faecal samples were collected from 10 selected broiler chicken farms in Mpumalanga. The samples were screened for Eimeria oocyst using a compound microscope, and samples containing oocyst were further screened for E. tenella using molecular methods. AMA1 (n=103) was amplified from positive samples for E. tenella, and resulted amplicons were sent to Inqaba Biotec for sequencing and analyzed using MEGA6.06 and DnaSP programs. The results revealed low levels of genetic diversity among Mpumalanga EtAMA1 sequences which were measured by nucleotide diversity (0.0007) diversity, haplotype diversity (0.113) and haplotype number (3). Correspondingly, the haplotype network revealed 4 haplotypes, 3 of which consist of samples from Mpumalanga. Identification of immunogenic B- and T-cell epitopes from EtAMA1 sequences was further carried out and were used to construct a multiepitope vaccine (MEV) using immunoinformatics approaches. The constructed MEV is 311 amino acids long. It was constructed by linking 6 B-cell, 3 CD8+ epitopes and 6 CD4+ epitopes with appropriate adjuvant and linkers. Both adjuvant and linkers were used to increase the immunogenicity of the MEV. The designed MEV was highly antigenic and non-allergenic. The results showed a strong binding affinity of MEV with TLR4. These results suggest that the predicted vaccine could be a significant vaccine candidate against chicken coccidiosis through further experimental validation is still necessary
Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review
No full textThe gastrointestinal tract in poultry harbours a diverse microbial community that serves a crucial role in digestion and protection. Disruption of the gut environment due to Eimeria spp. parasite infection causes an imbalance in intestinal homeostasis, driving the increment of pathogens such as Clostridium species. Coccidiosis infection affects the composition and integrity of gut microbiota, resulting in elevated susceptibility to diseases that pose a serious threat to the overall health and productivity of chickens. Anticoccidial drugs have proven effective in curbing coccidiosis but with concerning drawbacks like drug resistance and drug residues in meat. The exploration of natural alternative strategies such as probiotics and phytochemicals is significant in controlling coccidiosis through modification and restoration of gut microbiota, without inducing drug resistance. Understanding the interaction between Eimeria parasites and gut microbiota is crucial for the control and prevention of coccidiosis, and the development of novel alternative treatments
Simultaneous Bayesian modelling of skew-normal longitudinal measurements with non-ignorable dropout
No full textMost often in genetic improvement studies, repeated measurements are observed on an individual animal, and these repeated measurements are often skewed. From the practical viewpoint, logarithm transformations of variables are usually adopted to reduce skewness, and this works satisfactorily in many cases. In most longitudinal datasets, however, because of the high rate of missingness, skewness often remains after transformation, the achievement of joint normality for each component of separately transformed variables, which are often difficult to interpret, is unrealistic. For this purpose, a more general form of distributions for considering skewness in the model should be used. In this paper, we used Bayesian joint modelling of longitudinal and survival data when data set presents skewness. A skew-normal mixed-effects model for longitudinal measurements and a Cox proportional hazard model for time to event variable were considered. We performed some simulation studies to investigate the performance of the proposed method to skewness in random effects, different dropout rates and sample sizes. Furthermore, we illustrated the proposed method using Nigerian indigenous chickens (NIC) dataset. The longitudinal outcomes of NIC data set were skewed, and presented left censored dropout. We assumed different model structures for the analysis of this data set and considered two versions of the deviance information criteria: namely, the conditional criteria (given the random effects) and marginal criteria (averaging over the random effects) in selecting the true model. These criteria were computed using the importance sampling method
Association between host genetics of sheep and the rumen microbial composition
No full textA synergy between the rumen microbiota and the host genetics has created a symbiotic relationship, beneficial to the host’s
health. In this study, the association between the host genetics and rumen microbiome of Damara and Meatmaster sheep
was investigated. The composition of rumen microbiota was estimated through the analysis of the V3-V4 region of the 16S
rRNA gene, while the sheep blood DNA was genotyped with Illumina OvineSNP50 BeadChip and the genome-wide asso-
ciation (GWA) was analyzed. Sixty significant SNPs dispersed in 21 regions across the Ovis aries genome were found to be
associated with the relative abundance of seven genera: Acinetobacter, Bacillus, Clostridium, Flavobacterium, Prevotella,
Pseudomonas, and Streptobacillus. A total of eighty-four candidate genes were identified, and their functional annotations
were mainly associated with immunity responses and function, metabolism, and signal transduction. Our results propose
that those candidate genes identified in the study may be modulating the composition of rumen microbiota and further
indicating the significance of comprehending the interactions between the host and rumen microbiota to gain better insight
into the health of sheep
Subtractive Genomics Approach for Identification of Novel Therapeutic Drug Targets in <i>Mycoplasma genitalium</i>
No full textMycoplasma genitalium infection is a sexually transmitted infection that causes urethritis, cervicitis, and pelvic inflammatory disease (PID) in men and women. The global rise in antimicrobial resistance against recommended antibiotics for the treatment of M. genitalium infection has triggered the need to explore novel drug targets against this pathogen. The application of a bioinformatics approach through subtractive genomics has proven highly instrumental in predicting novel therapeutic targets against a pathogen. This study aimed to identify essential and non-homologous proteins with unique metabolic pathways in the pathogen that could serve as novel drug targets. Based on this, a manual comparison of the metabolic pathways of M. genitalium and the human host was done, generating nine pathogen-specific metabolic pathways. Additionally, the analysis of the whole proteome of M. genitalium using different bioinformatics databases generated 21 essential, non-homologous, and cytoplasmic proteins involved in nine pathogen-specific metabolic pathways. The further screening of these 21 cytoplasmic proteins in the DrugBank database generated 13 druggable proteins, which showed similarity with FDA-approved and experimental small-molecule drugs. A total of seven proteins that are involved in seven different pathogen-specific metabolic pathways were finally selected as novel putative drug targets after further analysis. Therefore, these proposed drug targets could aid in the design of potent drugs that may inhibit the functionality of these pathogen-specific metabolic pathways and, as such, lead to the eradication of this pathogen
