Explore the vast range of titles available.

Brucellosis is a neglected zoonotic disease in most developing countries, including South Sudan. Precise identification of Brucella species is crucial for addressing public health and epidemiological concerns associated with brucellosis. The study aimed to identify Brucella species using real-time polymerase chain reaction (qPCR) from seropositive samples that were acquired from an earlier investigation. A total of 143 genomic DNA samples were extracted from brucellosis Rose Bengal plate test (RBPT) seropositive samples from humans (n = 7), cattle (n = 103) and goats (n = 33). The samples were collected from Terekeka and Juba counties, Central Equatoria State (CES), South Sudan. The qPCR targeting the Brucella-specific IS711 insertion gene at the genus level was performed. Samples with a cycle threshold (Ct) of ≤ 35 were considered positive and subjected to further Brucella speciation assays. Out of 143 DNA samples tested for genus-specific Brucella, 15 (10.5%) were positive including 4 (2.8%) from humans, 10 (6.9%) from cattle, and 1 (0.7%) from goats. Brucella abortus was identified in 5 (33.3%) of the positive samples at the genus level. The overall individual species infection rates with B. abortus were 6.6% (1/15) in humans, 20% (3/15) in cattle, and 6.6% (1/15) in goats. There was no B. melitensis detected in this study. This study identified B. abortus in cattle, goats and humans in CES, South Sudan. The findings suggest that cattle are probably the primary reservoirs for transmission of B. abortus, with infections occurring in goats and humans primarily resulting from cattle spillover.

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis) , Brucella spp. ( Brucella ) and Coxiella burnetii ( Coxiella ). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis , Brucella , and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.

Background Brucellosis poses serious public health implications and substantial economic losses in pastoral rural settings in South Sudan. In humans, brucellosis is almost always originating from animals. Current literature provides scant data regarding the seroprevalence of brucellosis in South Sudan. This cross-sectional study investigates the seroprevalence of brucellosis among the pastoral community and livestock and identifies risk factors for the disease from two Counties, Terekeka and Juba in Central Equatoria State (CES), South Sudan. Methodology A total of 986 sera; from humans (n = 143), cattle (n = 478), sheep (n = 86), and goats (n = 279) were randomly collected from 17 cattle camps in CES. Sera for the humans, cattle and goats were screened for Brucella-specific antibodies using Rose Bengal plate test (RBPT) and further confirmed by competitive enzyme-linked immunosorbent assay (c-ELISA) in series due to the cost of testing. All the sera from sheep were tested in parallel using RBPT and c-ELISA as the sheep samples were few and were all tested negative on the RBPT. A camp was considered positive when at least one animal of either species tested positive on the c-ELISA. A structured questionnaire was used to collect information on potential individual and herd level risk factors. Univariate analysis using binary logistic regression with a confidence interval of 95% at a p-value of ≤ 0.05 was used to identify the association between the potential individual risk factors and Brucella seropositivity. The investigated risk factors for livestock included age, sex, species, prior abortion history, retained placenta, parity, and reproductive status. Variables found to have associations in univariate analysis (p = 0.25) with Brucella seropositivity were further included in multivariable logistic regression. The risk factors investigated for humans included, gender, age, educational level, occupation, marital status, drinking of raw milk, aiding female animals during delivery, eating undercooked meat and blowing of air into the cow’s uterus through the vagina, a practice in South Sudan. Results The study revealed seroprevalence of 21.7%, 11.8%, and 4.8% in cattle, goats, and humans, respectively. Our results indicated that all sheep serum samples were negative on both RBPT and c-ELISA. The seropositive in the 13 camps from Terekeka County was 100.0% (13/13) compared to 50.0% (2/4) seropositive from 4 camps in Juba County. All the variables investigated in the univariate analysis of risk factors in cattle were significantly associated with Brucella seropositivity: sex (OR:4.5, 95% CI: 2.2–8.9, p<0.001), age (OR:6.6, 95% CI: 2.3–19.1, p:<0.001), abortion history (OR:3.1, 95% CI: 1.8–5.2, p:<0.001), retained placenta (OR:2.5, 95% CI: 1.4–4.4, p = 0.001), parity (OR:2.3, 95% CI: 1.1–4.7, p = 0.020), However, in small ruminants, none of the potential risk factors were associated with Brucella seropositivity. In humans, blowing air through a cow’s vagina (OR: 1.4, 95%CI: 0.782–2.434, p = 0.035) was the only variable found to be significantly associated with Brucella seropositivity in the univariate analysis. The forceful blowing of air into a cow’s vagina to induce milk letdown is a common practice among the pastoral communities in South Sudan. The multivariable logistic regression model identified sex, age, and abortion history as statistically significant factors for Brucella seropositivity in cattle. The odds of seropositivity were nearly threefold (OR: 2.8; 95% CI: 1.3–5.8, p = 0.006) higher in cows compared to bulls (male cattle). Cattle over two years old had higher odds of Brucella seropositivity than young animals (OR: 3.5, 95% CI: 1.2–10.3-, p: 0.025). Cows with a history of abortion had higher odds of Brucella seropositivity (OR: 2.8, 95% CI: 1.6–4.7, p = 0.001). Conclusion This study reports the occurrence of brucellosis in goats and its absence in sheep in (CES), South Sudan. The present study also shows the occurrence of brucellosis in cattle, goats and people in the pastoral community and recommends for the implementation of the One Health approach and awareness campaigns for effective mitigation of this disease.

Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.

Background One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking. Results We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline. Conclusions The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

Helminth infections and nutrition can independently alter the composition and abundance of the gastrointestinal microbiota, however, their combined effect is poorly understood. Here, we used the T. retortaeformis-rabbit system to examine how the helminth infection and host restriction from coprophagy/ready-to-absorb nutrients affected the duodenal microbiota, and how these changes related to the acquired immune response at the site of infection. A factorial experiment was performed where the bacterial community, its functionality and the immune response were examined in four treatments (Infect, Infect+Collar, Control+Collar and Control). Helminths reduced the diversity and abundance of the microbiota while the combination of parasites and coprophagic restriction led to a more diversified and abundant microbiota than infected cases, without significantly affecting the intensity of infection. Animals restricted from coprophagy and free from parasites exhibited the richest and most abundant bacterial community. By forcing the individuals to absorb nutrients from less digested food, the coprophagic restriction appears to have facilitated the diversity and proliferation of bacteria in the duodenum. Changes in the microbiota were more clearly associated with changes in the immune response for the infected than the nutrient restricted animals. The functional and metabolic characteristics of the duodenal microbiota were not significantly different between treatments. Overall, infection and diet affect the gut microbiota but their interactions and outcome can be complex. These findings can have important implications for the development of control measures to helminth infections where poor nutrition/malnutrition can also be a concern.

Newcastle disease virus (NDV) is a threat to the global poultry industry, but particularly for smallholder farmers in low- and middle-income countries. Previous reports suggest that some breeds of chickens are less susceptible to NDV infection, however, the mechanisms contributing to this are unknown. We here examined the comparative transcriptional responses of innate immune genes to NDV infection in inbred sublines of the Fayoumi and Leghorn breeds known to differ in their relative susceptibility to infection as well as at the microchromosome bearing the major histocompatability complex (MHC) locus. The analysis identified a set of five core genes, Mx1 , IRF1 , IRF7 , STAT1 , and SOCS1 , that are up-regulated regardless of subline. Several genes were differentially expressed in a breed- or subline-dependent manner. The breed-dependent response involved TLR3 , NOS2 , LITAF , and IFIH1 in the Fayoumi versus IL8 , CAMP , and CCL4 in the Leghorn. Further analysis identified subline-dependent differences in the pro-inflammatory response within the Fayoumi breed that are likely influenced by the MHC. These results have identified conserved, breed-dependent, and subline-dependent innate immune responses to NDV infection in chickens, and provide a strong framework for the future characterization of the specific roles of genes and pathways that influence the susceptibility of chickens to NDV infection.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic intestinal inflammatory disease of cattle and other ruminants. JD has a high herd prevalence and causes serious animal health problems and significant economic loss in domesticated ruminants throughout the world. Since serological detection of MAP infected animals during the early stages of infection remains challenging due to the low sensitivity of extant assays, we screened 180 well-characterized serum samples using a whole proteome microarray from Mycobacterium tuberculosis (MTB), a close relative of MAP. Based on extensive testing of serum and milk samples, fecal culture and qPCR for direct detection of MAP, the samples were previously assigned to one of 4 groups: negative low exposure (n = 30, NL); negative high exposure (n = 30, NH); fecal positive, ELISA negative (n = 60, F+E-); and fecal positive, ELISA positive (n = 60, F+E+). Of the 740 reactive proteins, several antigens were serologically recognized early but not late in infection, suggesting a complex and dynamic evolution of the MAP humoral immune response during disease progression. Ordinal logistic regression models identified a subset of 47 candidate proteins with significantly different normalized intensity values (p<0.05), including 12 in the NH and 23 in F+E- groups, suggesting potential utility for the early detection of MAP infected animals. Next, the diagnostic utility of four MAP orthologs (MAP1569, MAP2942c, MAP2609, and MAP1272c) was assessed and reveal moderate to high diagnostic sensitivities (range 48.3% to 76.7%) and specificity (range 96.7% to 100%), with a combined 88.3% sensitivity and 96.7% specificity. Taken together, the results of our analyses have identified several candidate MAP proteins of potential utility for the early detection of MAP infection, as well individual MAP proteins that may serve as the foundation for the next generation of well-defined serological diagnosis of JD in cattle.

Johne's Disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP), results in significant economic loss to livestock production. The early detection of MAP infection in animals with extant serological assays has remained challenging due to the low sensitivity of commercially available ELISA tests, a fact that has hampered the development of effective JD control programs. Our recent protein microarray-based studies identified several promising candidate antigens that are immunogenic during different stages of MAP infection. To evaluate these antigens for use in diagnostic assays and reliably identify animals with MAP infection, a multiplex (Luminex®) assay was developed using color-coded flourescent beads coupled to 6 MAP recombinant proteins and applied to screen 180 serum and 90 milk samples from cows at different stages of MAP infection including negative (NL), fecal test positive/ELISA negative (F+E-), and fecal positive/ELISA positive (F+E+). The results show that while serum antibody reactivities to each of the 6 antigens were highest in F+E+ group, antibody reactivity to three of the six antigens were identified in the F+E- group, suggesting that these three antigens are expressed and provoke antibody responses during the early infection stages with MAP. Further, antibodies against all six antigens were elevated in milk samples from both the F+E- and F+E+ groups in comparison to the NL group (p<0.01). Taken together, the results of our investigation suggest that multiplex bead-based assays are able to reliably identify MAP infection, even during early stages when antibody responses in animals are undetectable with widely used commercial ELISA tests.

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.