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.

Prevalence and Associated Symptoms of Helicobacter pylori Infection among Schoolchildren in Kassala State, East of Sudan.

This study aimed to determine the prevalence of H. pylori infections among schoolchildren and investigate the associations between H. pylori seropositivity and existence of gastrointestinal symptoms. Methods. A prospective cross-sectional study was conducted during a period from January to December 2012 at Kassala state, east of Sudan. Schoolchildren from different primary schools were enrolled in the study. Sociodemographic characteristics and gastrointestinal symptoms were recorded from each child. A rapid immunochromatographic test was performed for the detection of H. pylori IgG antibodies. Data on patient demographic characteristics, clinical diagnosis, and findings of H. pylori infection were analyzed by simple descriptive statistics. Results. Among 431 schoolchildren, H. pylori seropositivity was found to be 21.8%. The majority of children (79; 84%) had BMI below the normal range. The most frequent symptoms associated with H. pylori infections were nausea (25.5%), followed by gastric pain (24.5%) and heart pain (20.2%). There were statistically significant differences in H. pylori seropositivity between boys and girls (p = 0.003). Conclusions. The prevalence of H. pylori infection among schoolchildren in Kassala city has been documented. Although the majority of the disease was associated with several gastrointestinal symptoms, the role of infection in the etiology of abdominal symptoms needs further investigations.

Bovine tuberculosis in South Darfur State, Sudan: an abattoir study based on microscopy and molecular detection methods.

Bovine tuberculosis (BTB) is a widespread zoonosis in developing countries but has received little attention in many sub-Saharan African countries including Sudan and particularly in some parts such as Darfur states. This study aimed to detect bovine tuberculosis among caseous materials of cattle slaughtered in abattoirs in South Darfur State, Sudan by using microscopic and PCR-based methods. The study was a cross-sectional abattoir-based study which examined a total of 6,680 bovine carcasses for caseous lesions in South Darfur State between 2007 and 2009. Collected specimens were examined for the presence of acid-fast bacilli (AFB) by using microscopic and culture techniques. Isolated mycobacteria were identified by selected conventional cultural and biochemical tests in comparison to a single tube multiplex PCR (m-PCR) assay which detect Mycobacterium bovis-specific 168-bp amplicons. Of the total 6,680 slaughtered cattle examined in South Darfur, 400 (6 %) showed caseations restricted to lymph nodes (86.8 %) or generalized (13.2 %). Bovine tuberculosis was diagnosed in 12 (0.18 %), bovine farcy in 59 (0.88 %), unidentified mycobacteria in 6 (0.09 %), and missed or contaminated cultures in 7 (0.1 %). Out of 18 cultures with nonbranching acid-fast rods, 12 amplified unique 168-bp sequence specific for M. bovis and subsequently confirmed as M. bovis. With the exception of the reference M. tuberculosis strains, none of the remaining AFB amplified the 337-bp amplicon specific for M. tuberculosis. It could be concluded that bovine tuberculosis is prevalent among cattle in South Darfur representing 4.5 % from all slaughtered cattle with caseous lesions. The study sustains microscopy as a useful and accessible technique for detecting AFB. m-PCR assay proved to be valuable for confirmation of BTB and its differentiation from other related mycobacteriosis, notably bovine farcy.

Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence.

Staphylococcus aureus subsp. anaerobius is responsible for Morel's disease in animals and a cause of abscess in humans. It is characterized by a microaerophilic growth, contrary to the other strains of S. aureus. The 2,604,446-bp genome (32.7% GC content) of S. anaerobius ST1464 comprises one chromosome and no plasmids. The chromosome contains 2,660 open reading frames (ORFs), 49 tRNAs and three complete rRNAs, forming one complete operon. The size of ORFs ranges between 100 to 4,600 bp except for two ORFs of 6,417 and 7,173 bp encoding segregation ATPase and non-ribosomal peptide synthase, respectively. The chromosome harbors Staphylococcus phage 2638A genome and incomplete Staphylococcus phage genome PT1028, but no detectable CRISPRS. The antibiotic resistance gene for tetracycline was found although Staphylococcus aureus subsp. anaerobius is susceptible to tetracycline in-vitro. Intact oxygen detoxification genes encode superoxide dismutase and cytochrome quinol oxidase whereas the catalase gene is impaired by a stop codon. Based on the genome, in-silico multilocus sequence typing indicates that S. aureus subsp. anaerobius emerged as a clone separated from all other S. aureus strains, illustrating host-adaptation linked to missing functions. Availability of S. aureus subsp. anaerobius genome could prompt the development of post-genomic tools for its rapid discrimination from S. aureus.

Ovine clone ST1464: a predominant genotype of Staphylococcus aureus subsp. anaerobius isolated from sheep in Sudan.

BACKGROUND: The aim of the present study was to examine the phenotypic and genotypic relatedness of 17 Staphylococcus aureus subsp. anaerobius isolates recovered from sheep abscesses in Khartoum state, Sudan, during the period 2007-2008. METHODOLOGY: This sample was characterised using antibiogram typing, biochemical typing with the commercial PhenePlate system (PhP-CS) and multilocus sequence typing (MLST). RESULTS: Low levels of resistance were noted to the 11 antimicrobial agents tested. All the isolates corresponded to a single PhP type, and to a single, novel, multilocus sequence type, designated ST1464. CONCLUSION: These results demonstrate that the vast majority of cases of sheep abscess disease in Khartoum state are caused by a single novel clone of S. aureus subsp. anaerobius.