Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.

First Report on Ovine Paratuberculosis in the Sudan: Diagnosis Using Different Techniques.

Paratuberculosis (PTB) has been reported in the Sudan in cattle and goats for more than 50 years but has never been reported in sheep. However, suspicion of the disease in a breeding flock of sheep in Khartoum North locality was made due to a history of unknown cause of loss of weight. Blood and faecal samples were collected from all animals (N = 59): harvested sera were tested for anti-Mycobacterium avium subsp. paratuberculosis (MAP) antibodies by Enzyme Linked Immunosorbent Assay (ELISA); faeces were screened for acid-fast bacilli by Ziehl-Neelsen staining, tested for MAP DNA by recombinase polymerase amplification (RPA) and some faecal samples were cultured for MAP isolation. Typical MAP acid-fast bacilli were seen in 10.2% (6/59) of the faecal smears, 37.5% of the tested faecal samples (12/32) were positive for MAP DNA and only 3 (5.1%) animals were seropositive for MAP. MAP positive cultures were obtained from 2 out the 6 samples showing typical MAP acid-fast bacilli; the isolates were confirmed by real-time PCR and sequencing. As sheep are animals of utmost economic importance as the main export animals for the country, this first report of ovine PTB warrants special considerations and more investigations for planning control programmes of the disease.

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan.

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease in animals with zoonotic potential; it has been linked to many chronic diseases in humans, especially gastrointestinal diseases (GID). MAP has been extensively studied in Europe and America, but little reports were published from Africa. Sudan is a unique country with close contact between humans and livestock. Despite such interaction, the one health concept is neglected in dealing with cases of humans with GID. In this study, patients admitted to the reference GID hospital in the Sudan over a period of 8 months were screened for presence of MAP in their faeces or colonic biopsies. A total of 86 patients were recruited for this study, but only 67 were screened for MAP, as 19 did not provide the necessary samples for analysis. Both real-time PCR and culture were used to detect MAP in the collected samples and the microbial diversity in patients´ faecal samples was investigated using 16S rDNA nanopore sequencing. In total, 27 (40.3%) patients were MAP positive: they were 15 males and 12 females, of ages between 21 and 80 years. Logistic regression analysis revealed no statistical significance for all tested variables in MAP positive patients (occupation, gender, contact with animal, milk consumption, chronic disease, etc.). A unique microbiome profile of MAP-positive patients in comparison to MAP-negative was found. These findings suggest that a considerable proportion of the population could be MAP infected or carriers. Therefore, increase awareness at community level is urgently needed to decrease the risk of MAP at human/animal interface. This study represents the first report of MAP in humans in the Sudan; nevertheless, a better view of the situation of MAP in humans in the country requires a larger study including patients with other conditions.

Paratuberculosis: The Hidden Killer of Small Ruminants.

Paratuberculosis (PTB) is a contagious and chronic enteric disease of ruminants and many non-ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), and is characterised by diarrhoea and progressive emaciation with consequent serious economic losses due to death, early culling, and reduced productivity. In addition, indirect economic losses may arise from trade restrictions. Besides being a production limiting disease, PTB is a potential zoonosis; MAP has been isolated from Crohn's disease patients and was associated with other human diseases, such as rheumatoid arthritis, Hashimoto's thyroiditis, Type 1 diabetes, and multiple sclerosis. Paratuberculosis in sheep and goats may be globally distributed though information on the prevalence and economic impact in many developing countries seem to be scanty. Goats are more susceptible to infection than sheep and both species are likely to develop the clinical disease. Ingestion of feed and water contaminated with faeces of MAP-positive animals is the common route of infection, which then spreads horizontally and vertically. In African countries, PTB has been described as a "neglected disease", and in small ruminants, which support the livelihood of people in rural areas and poor communities, the disease was rarely reported. Prevention and control of small ruminants' PTB is difficult because diagnostic assays demonstrate poor sensitivity early in the disease process, in addition to the difficulties in identifying subclinically infected animals. Further studies are needed to provide more insight on molecular epidemiology, transmission, and impact on other animals or humans, socio-economic aspects, prevention and control of small ruminant PTB.

Seroprevalence of Mycobacterium avium subsp. paratuberculosis in Dairy Cattle in Khartoum State, Sudan.

Paratuberculosis, caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic wasting disease mainly of domestic and wild ruminants. It occurs worldwide, causing significant economic losses through decreased productivity, low fertility, increased cull rates and mortality. It is listed by the OIE (World Organization for Animal Health) as a disease of concern to trade in animals. Prevalence of this disease can be studied by detecting anti-MAP antibodies by Enzyme linked immunosorbent Assay (ELISA). The aim of this study was to investigate the current prevalence of MAP infection in cattle in Khartoum State. The overall apparent prevalence of MAP infection was found to be 6.3% and 18.9% at animal and herd levels, respectively. All seropositive animals were cross-bred females of good body condition; most of them (>90%) were >3 years old and >50% were from medium-sized herds in Omdurman. No significant association (p > 0.05) was found between seropositivity and animal herd size. The prevalence of MAP infection in Khartoum State is still low to medium compared to other parts of the world, but it is comparable to those reported from other African countries. Further studies with the view of designing nationwide surveys in domestic ruminants and camels in other states of the country are needed for establishing control programmes.

Molecular and in-silico analysis of single nucleotide polymorphism targeting human TP53 gene exon 5-8 in Sudanese esophageal cancer patients.

Background: The protein product of the normal TP53 gene performs an essential function in cell cycle control and tumor suppression, and the mutation of a TP53 gene is an essential step in the development of many cancers. Despite the reported association of TP53 gene mutations with many human cancers, the comprehensive computational analysis of single nucleotide polymorphisms (SNPs), and their functional impacts, still remains rare. Methods: In this study DNA were extracted from formalin fixed paraffin embedded samples followed by the conventional polymerase chain reaction and DNA sequencing. Computational analysis was performed using different algorithms to screen for deleterious SNPs. Results: The results demonstrate that there are synonymous SNPs (sSNPs) and non-synonymous SNPs (nsSNPs) in the TP53 gene that may be deleterious to p53 structure and function. Additionally, TP53 gene mutations were found in 40% of samples. Six out of ten of TP53 gene mutations occurred in exon 5, two mutation in exon 6 and other two were present in exon 8. Only one SNP in position E298Q was predicted to have a neutral effect and other SNPs were predicted to be disease related according to Mutation Taster software. A total of 37.2% of squamous cell carcinoma (SCC) samples were found to be mutated, 87.5% of them exist in exon 5, 12.5% in exon 6 and 6.3% in exon 8, whereas adenocarcinoma (AC) achieved a higher rate of mutation (57.1%) with 100% exon 5 involvement. Conclusions: Mutation of TP53 exon 5 in esophageal cancer patients were the most frequent. Genomic results have identified a higher TP53 mutation rate in esophageal AC in contrast to SCC.

The pulmonary involvement in Theileria lestoquardi naturally infected sheep.

Malignant Ovine Theileriosis (MOT) caused by Theileria lestoquardi is considered a major constraint for sheep production in many areas of the world including Sudan. Pulmonary oedema is thought to be the main cause of animal death, but the mechanism, the cell types involved and/or the probable cause of this pneumonia has yet to be defined. The present study was carried out to investigate the pulmonary involvement post T. lestoquardi infection and to identify the cell types involved in pneumonia. Apparently healthy sheep were exposed to ticks challenge in T. lestoquardi endemic area. Lungs impression smears and tissue sections for histopathology were processed. At necropsy, fifteen infected sheep revealed severe pneumonia associated with oedema and accumulation of creamy-grayish frothy exudates. The microscopic findings of examined lungs showed emphysema, congestion, collapse and proliferation of immense amount of different kinds of cells. The current study indicates that T. lestoquardi infections are accompanied with remarkable pulmonary involvements and may lead to respiratory failure and death.

Molecular identification of different Theileria and Babesia species infecting sheep in Sudan.

The epidemiological aspects of sheep piroplasmosis in Sudan are poorly studied, and further investigations using sensitive and precise techniques are required. In this study, the Reverse Line Blot (RLB) hybridization assay was used to detect and simultaneously differentiate between Theileria and Babesia species. DNA was extracted from blood collected on filter paper (n=219) from apparently healthy sheep from six different geographical localities in Sudan. Results indicated that Theileria ovis (88.6%), T. separata (20.1%), T. lestoquardi (16.4%) and T. annulata (16.4%) DNA could be detected in the blood samples. Single and mixed Theileria infections were detected in 74 (33.8%) and 124 (56.6%) respectively and T. ovis being the most prevalent species in the country. T. ovis and T. separata were reported for the first time in sheep in Sudan.

Natural in utero infection of neonatal calves with bovine viral diarrhoea virus on a large dairy farm in Saudi Arabia.

The dairy industry is a large and important business in Saudi Arabia. Although farms are administered to high international standards, some reproduction problems, of uncertain aetiology, are encountered. The most frequently seen are conception failures, abortions, stillbirths and the birth of weak or malformed calves. These conditions are suggestive of bovine viral diarrhoea virus (BVDV) infection. Unfortunately, very little published information is available regarding the impact of this disease on cattle populations in Saudi Arabia. As a consequence, the present study was carried out and is the first of its kind in Saudi Arabia and the Gulf region. The aim of the study was to elucidate the role of in utero BVDV infection leading to the birth of weak or malformed calves on a large dairy farm in Saudi Arabia. The study was divided into two parts. Firstly, apparently healthy neonatal calves were sampled for the detection of pre-colostral serum antibodies to BVDV. The presence of these antibodies indicates exposure of the foetus to BVDV during the last two trimesters of gestation. Secondly, tissue samples from malformed neonatal calves were examined for the presence of BVDV antigens. Detection of such antigens confirms exposure of the foetus to the virus during the first trimester of gestation. The results of the investigation indicated that 36.1% of the neonatal calves were exposed to BVDV infection in utero. This is higher than what has been reported in the literature and suggests that dairy farmers in the Arabian Peninsula need to be made aware of the dangers of BVDV infections in their herds. The epidemiological significance of the results is discussed.