Project description:Eperythrozoonosis is a small ruminant disease caused by the bacterium Mycoplasma ovis (formerly known as Eperythrozoon ovis). Whilst acute infection in sheep may result in an anaemia and ill thrift syndrome, most animals do not develop clinical signs. Molecular methods were used to compare and evaluate the prevalence of infection with M. ovis in sheep and goats in Tunisia. A total of 739 whole blood samples from 573 sheep and 166 goats were tested for the M. ovis 16S rRNA gene using PCR. The overall prevalence was 6.28% ± 0.019 (36/573). Only sheep were infected with M. ovis (p < 0.001), and the prevalence was significantly higher in central Tunisia (29.2%) compared with other regions (p < 0.05). The prevalence revealed significant differences according to breed and bioclimatic zones (p < 0.001). Furthermore, the prevalence in young sheep (35/330; 10.6%) was higher than in adults (1/243; 0.41%) (p < 0.001). Only sheep of the Barbarine breed were infected, with a prevalence of 11.8% (p < 0.001). This is the first molecular study and genetic characterisation of M. ovis in North African sheep breeds.
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism.
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism. Investigate the influence of genetic variances on blood DNA methylation patterns in the human genome of 96 subjects from 22 pedigrees by using different approaches, including mid-parent offspring analysis (MPO), methylation quantitative trait loci (mQTL) analysis and allele-specific DNA methylation (ASM) Raw data not provided since the files contain genetic information of the human subject that should be protected.
Project description:Background and Aim:Cronobacter sakazakii (C. sakazakii) has attracted considerable attention as an emerging neonatal pathogen and has been associated with outbreaks of life-threatening septicemia, necrotizing enterocolitis, and meningitis in neonates and infants globally. No data about the role of C. sakazakii as a cause of neonatal sepsis in North Africa is availale. Herein, we aimed to study the incidence of C. sakazakii in cases of neonatal sepsis, its distribution in different food samples in Egypt, antimicrobial profile, and the ability of the strains to form biofilms. Methods:A total of 100 positive blood cultures from cases of neonatal sepsis admitted to the neonatal ICU at Assiut University Children's Hospital, Egypt, were analyzed. In addition, 1,100 food samples, including 400 powdered infant formula (PIF), 500 herbs, and 200 water samples were screened for the presence of C. sakazakii. We evaluated the antimicrobial profile and the ability of the strains to form biofilms. Results:Cronobacter sakazakii was detected in 12 out of 100 cases of neonatal sepsis. The organism was also isolated from PIF, herbs, and water in percentages of 17.5, 9.2, and 7.5%, respectively. Regarding the antimicrobial sensitivity, all strains were resistant to ampicillin, amoxicillin, ampicillin/sulbactam, clindamycin, cephalothin, and cephalexin. In addition, C. sakazakii strains showed the ability to form biofilms, but with variable degrees of cell density. Conclusion:We reported, for the first time, cases of neonatal sepsis caused by the emerging life-threatening pathogen C. sakazakii in Egypt. The organism was also detected in contaminated PIF, herbs, and water, which may be sources of infection for neonates, especially in countries where natural herbs are widely used as an alternative medicine. Finally, collective efforts by the parents, manufacturers of PIF, and healthcare personnel are essential to prevent serious infections caused by C. sakazakii, particularly in infants.
Project description:Recent studies have shown that mtDNA background could affect the clinical expression of Leber hereditary optic neuropathy (LHON). We analyzed the mitochondrial DNA (mtDNA) variation of 304 Chinese patients with m.11778G>A (sample #1) and of 843 suspected LHON patients who lack the three primary mutations (sample #2) to discern mtDNA haplogroup effect on disease onset. Haplogroup frequencies in the patient group was compared to frequencies in the general Han Chinese population (n?=?1,689; sample #3). The overall matrilineal composition of the suspected LHON population resembles that of the general Han Chinese population, suggesting no association with mtDNA haplogroup. In contrast, analysis of these LHON patients confirms mtDNA haplogroup effect on LHON. Specifically, the LHON sample significantly differs from the general Han Chinese and suspected LHON populations by harboring an extremely lower frequency of haplogroup R9, in particular of its main sub-haplogroup F (#1 vs. #3, P-value?=?1.46×10(-17), OR?=?0.051, 95% CI: 0.016-0.162; #1 vs. #2, P-value?=?4.44×10(-17), OR?=?0.049, 95% CI: 0.015-0.154; in both cases, adjusted P-value <10(-5)) and higher frequencies of M7b (#1 vs. #3, adjusted P-value?=?0.001 and #1 vs. #2, adjusted P-value?=?0.004). Our result shows that mtDNA background affects LHON in Chinese patients with m.11778G>A but not suspected LHON. Haplogroup F has a protective effect against LHON, while M7b is a risk factor.
Project description:Here, we determined the Toxoplasma gondii genotype in amniotic fluid, placenta, and cerebrospinal fluid samples from 14 congenital toxoplasmosis cases in Tunisia, North Africa. Direct genotypic characterization of T. gondii strains was performed by polymerase chain reaction (PCR) amplification of six genetic markers (3'SAG2, 5' SAG2, SAG3, BTUB, GRA6, and APICO) and thereafter, was analyzed by restriction fragment-length polymorphism (RFLP). Samples were sequenced to resolve strain type whenever there were unclear enzyme digestion results. Multilocus analysis revealed that only one specimen harbored the type I allele in all studied loci, whereas the 13 others gave mixed genotype results with different alleles at different markers. Seven specimens produced RFLP profile of the recombinant strains I/III, and three produced a profile of I/II recombinant strains. The last three specimens produced complex digestion patterns. In these cases, sequence analysis revealed double peaks at known polymorphic sites, indicating the presence of multiple alleles.
Project description:Genetic polymorphisms can shape the global landscape of DNA methylation, by either changing substrates for DNA methyltransferases or altering the DNA binding affinity of cis-regulatory proteins. The interactions between CpG methylation and genetic polymorphisms have been previously investigated by methylation quantitative trait loci (mQTL) and allele-specific methylation (ASM) analysis. However, it remains unclear whether these approaches can effectively and comprehensively identify all genetic variants that contribute to the inter-individual variation of DNA methylation levels. Here we used three independent approaches to systematically investigate the influence of genetic polymorphisms on variability in DNA methylation by characterizing the methylation state of 96 whole blood samples in 52 parent-child trios from 22 nuclear pedigrees. We performed targeted bisulfite sequencing with padlock probes to quantify the absolute DNA methylation levels at a set of 411,800 CpG sites in the human genome. With mid-parent offspring analysis (MPO), we identified 10,593 CpG sites that exhibited heritable methylation patterns, among which 70.1% were SNPs directly present in methylated CpG dinucleotides. We determined the mQTL analysis identified 49.9% of heritable CpG sites for which regulation occurred in a distal cis-regulatory manner, and that ASM analysis was only able to identify 5%. Finally, we identified hundreds of clusters in the human genome for which the degree of variation of CpG methylation, as opposed to whether or not CpG sites were methylated, was associated with genetic polymorphisms, supporting a recent hypothesis on the genetic influence of phenotypic plasticity. These results show that cis-regulatory SNPs identified by mQTL do not comprise the full extent of heritable CpG methylation, and that ASM appears overall unreliable. Overall, the extent of genome-methylome interactions is well beyond what is detectible with the commonly used mQTL and ASM approaches, and is likely to include effects on plasticity.
Project description:Non-O157 Shiga toxin-producing Escherichia coli (STEC) E. coli are emerging pathotypes that are frequently associated with diseases in humans around the world. The consequences of these serogroups for public health is a concern given the lack of effective prevention and treatment measures. In this study, ten bacteriophages (phages; SA20RB, SA79RD, SA126VB, SA30RD, SA32RD, SA35RD, SA21RB, SA80RD, SA12KD and SA91KD) isolated from cattle faeces collected in the North-West of South Africa were characterized. Activity of these phages against non-O157 STEC isolates served as hosts for these phages. All of the phages except SA80RD displayed lytic against non-O157 E. coli isolates. Of 22 non-O157 E. coli isolates, 14 were sensitive to 9 of the 10 phages tested. Phage SA35RD was able to lyse 13 isolates representing a diverse group of non-O157 E. coli serotypes including a novel O-antigen Shiga toxigenic (wzx-Onovel5:H19) strain. However, non-O157 E. coli serotypes O76:H34, O99:H9, O129:H23 and O136:H30 were insensitive to all phages. Based on transmission electron microscopy, the non-O157 STEC phages were placed into Myoviridae (n = 5) and Siphoviridae (n = 5). Genome of the phage ranged from 44 to 184.3 kb. All but three phages (SA91KD, SA80RD and SA126VB) were insensitive to EcoRI-HF and HindIII nucleases. This is the first study illustrating that cattle from North-West South Africa harbour phages with lytic potentials that could potentially be exploited for biocontrol against a diverse group of non-O157 STEC isolated from the same region.
Project description:BACKGROUND:The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. METHODS:A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters. RESULTS:At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p < 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p < 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences). CONCLUSIONS:We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region.
Project description:The presence of more than one non-severe pathogenic mutation in the same mitochondrial DNA (mtDNA) molecule is very rare. Moreover, it is unclear whether their co-occurrence results in an additive impact on mitochondrial function relative to single mutation effects. Here we describe the first example of a mtDNA molecule harboring three Leber's hereditary optic neuropathy (LHON)-associated mutations (m.11778G>A, m.14484T>C, m.11253T>C) and the analysis of its genetic, biochemical and molecular characterization in transmitochondrial cells (cybrids). Extensive characterization of cybrid cell lines harboring either the 3 mutations or the single classic m.11778G>A and m.14484T>C mutations revealed no differences in mitochondrial function, demonstrating the absence of a synergistic effect in this model system. These molecular results are in agreement with the ophthalmological characteristics found in the triple mutant patient, which were similar to those carrying single mtDNA LHON mutations.