Direct Extraction and Assessment of Genomic DNA of Mycetoma Fungi from Black-grains Specimen

Background: Direct isolation of genomic DNA of mycetoma fungi from black-grains achieve rapid diagnosis and may overcome culture disadvantages. Objectives: This study aimed to isolate and assess the DNA of mycetoma fungi using black-grains and to apply amplification of ITS region and nucleotide sequences. Methods: CTAB method was followed by manual homogenization alternatively to liquid nitrogen and glass beads disruption to obtain the genomic DNA. Results: Yielded DNA concentrations vary from 1.50 to 47.97 μg/ml (mean 10.09 μg/ml) while the optimum DNA purity recorded with 75.8% of specimens (n=69/91).Successful amplification of ITS region was done using pan-fungal primers (ITS4/5) with 90.1 (n=82/91)percentage. Species nucleotide sequences were detected with 67 (94.4%) amplicons from a total of 71.Conclusion: The study recommended using of black-grain specimens for DNA extraction of mycetoma fungi parallel with culture to insure rabid diagnosis and identification

Plasmodium vivax Diversity and Population Structure across Four Continents

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations

Concomitant malaria among visceral leishmaniasis in-patients from Gedarif and Sennar States, Sudan: a retrospective case-control study

In areas where visceral leishmaniasis (VL) and malaria are co-endemic, co-infections are common. Clinical implications range from potential diagnostic delay to increased disease-related morbidity, as compared to VL patients. Nevertheless, public awareness of the disease remains limited. In VL-endemic areas with unstable and seasonal malaria, vulnerability to the disease persists through all age-groups, suggesting that in these populations, malaria may easily co-occur with VL, with potentially severe clinical effects

Prevalence and identification of arthropod-transmitted viruses in Kassala state, Eastern Sudan

Vector-borne diseases are responsible for more than 20% of the infectious diseases worldwide. The prevalence of arboviruses transmit diseases to humans in Sudan has not been investigated. Mosquito-borne viral diseases increase globally incidence, including the Sudan. Frequent unknown fever outbreaks have been reported in eastern region, Sudan. However, diagnosis was based exclusively on clinical signs and symptoms without confirmatory laboratory investigations. However, for accurate detection of these viruses in outbreaks, molecular technique is considered. The objective of this study was to determine the prevalence of six arboviruses in the Kassala state of east Sudan during unknown fever outbreak. A cross sectional hospital-based study was conducted in the Kassala, Teaching Hospital. Blood samples from 119 patients suffering from unknown fever were used for screening of six arboviruses, hepatitis E virus and malarial using molecular techniques and serology. The overall arboviruses seroprevelance was 61.3% (73/119). The highest positivity rate was 73.1% (52/73) chikungunya virus; 29 males and 20 females patients were chikungunya positive. Other arboviruses were circulating in low rate 20.5% (15/73), and 6.8% (5/73) for sindbis and rift valley fever viruses respectively. Hepatitis E virus was negative in all cases and malaria positivity rate 13.4% (16/119). The prevalence of arboviruses among unknown fever patients present to Kassala teaching hospital of eastern region in Sudan is significantly high (61.3%). The chikungunya virus is the predominant causative agent of arboviruses. Molecular techniques such as PCR are important for accurate and rapid diagnosis of this viral outbreak

Informed decision-making before changing to RDT: a comparison of microscopy, rapid diagnostic test and molecular techniques for the diagnosis and identification of malaria parasites in Kassala, eastern Sudan

Rapid diagnostic tests (RDTs) are promoted for the diagnosis of malaria in many countries. The question arises whether laboratories where the current method of diagnosis is microscopy should also switch to RDT. This problem was studied in Kassala, Sudan where the issue of switching to RDT is under discussion. Two hundred and three blood samples were collected from febrile patients suspected of having malaria. These were subsequently analysed with microscopy, RDT (SD Bioline P.f/P.v) and PCR for the detection and identification of Plasmodium parasites. Malaria parasites were detected in 36 blood samples when examined microscopically, 54 (26.6%) samples were found positive for malaria parasites by RDT, and 44 samples were positive by PCR. Further analysis showed that the RDT used in our study resulted in a relatively high number of false positive samples. When microscopy was compared with PCR, an agreement of 96.1% and k = 0.88 (sensitivity 85.7% and specificity 100%) was found. However, when RDT was compared with PCR, an agreement of only 81.2 and k = 0.48 (sensitivity 69% and specificity 84%) was found. PCR has proven to be one of the most specific and sensitive diagnostic methods, particularly for malaria cases with low parasitaemia. However, this technique has limitations in its routine use under resource-limited conditions, such as our study location. At present, based on these results, microscopy remains the best option for routine diagnosis of malaria in Kassala, eastern Suda

Effect of Plasmodium vivax malaria and their density on some Haematological parameters in infected patients admitted to Wad Medani teaching hospital in Gezira state, Sudan

Background: Despite the great effort of the malaria control program in Sudan, Plasmodium vivax malaria has remained a major challenge recently, causing significant morbidity with a variety of haematological changes. Objective: This study aims to investigate the effect of Plasmodium vivax malaria and their density on some haematological parameters in patients admitted to Wad Medani teaching hospital in Gezira state, Sudan. Methods: Some haematological parameters of 160 participants, 80 infected with vivax malaria (47 male and 33 female) and 80 non-infected with malaria, who were admitted to Wad Medani teaching hospital in Gezira state, Sudan during high transmission season between August and November 2018, were evaluated for some haematological parameters. Results: The parameters (haemoglobin, haematocrit, counts of red blood cells, platelets, white blood cells, lymphocytes, monocytes and eosinophils) were significantly lower in infected patients than malaria negatives. The platelets and haemoglobin were inversely correlated to parasite density in positive cases. Conclusion: The exhibition of some haematological parameters changes was closely related to patients infected with vivax malaria versus non-infected, and these changes could be used as a diagnostic criterion for vivax malaria diagnosis in endemic regions

Infection of <i>Leishmania donovani</i> in <i>Phlebotomus orientalis</i> Sand Flies at Different Microhabitats of a Kala-Azar Endemic Village in Eastern Sudan

A study was carried out to compare the infection rates of Leishmania donovani in Phlebotomus orientalis sandflies at different microhabitats of a VL endemic village in Gedarif state, Sudan. DNA extracts of 1078 P. orientalis sand fly females sampled by CDC light traps from indoor, outdoor, peri-domestic, and sylvatic sites, in three transmission seasons, March–June 2016–18, in Helat-Belo village, were subjected to independent PCR amplifications targeting Leishmania kDNA and the cpb gene followed by ITS1 region sequencing. Leishmania kDNA was detected in 1.4% of the 1078 P. orientalis females captured in the area. Two of these specimens showed a characteristic 741 bp band of L. donovani after cpb gene amplification. The DNA sequence of the ITS1 region of the parasites matched the ITS1 L. donovani genotype F. There were no signficant differences between rates of infection of L. donovani in P. orientalis captured at different sites. Blood meals found in infected flies origninated from human (5 specimens), cattle (4 specimens) and donkey (2 specimens). The finding of fresh cow and donkey blood in the infected flies suggests the possible role of these animals in the zoopotentiation and/or zooprophylaxis against VL. The study provides important information for VL transmission models and control programs in East Africa