First evaluation and detection of ivermectin resistance in gastrointestinal nematodes of sheep and goats in South Darfur, Sudan.

In Sudan, resistance to benzimidazoles has been reported recently in cattle and goats from South Darfur. Herein, ivermectin efficacy against gastrointestinal nematodes (GINs) was evaluated in sheep and goats in three study areas in South Darfur. The faecal egg count reduction test (FECRT) was used to evaluate the efficacy of ivermectin in sheep and goats naturally infected with GINs in the region of Bulbul (goats: n = 106), Kass (goats: n = 40) and Nyala (Domaia (sheep: n = 47, goats: n = 77) and the University farm (goats: n = 52)), using different treatment plans, and the efficacy was evaluated 12 days after treatment. Ivermectin efficacy was also evaluated in goats experimentally infected using local Haemonchus contortus isolates from Kass and Nyala. Nematodes surviving ivermectin treatment in goats in Bulbul and Nyala were harvested and larvae used to infect worm-free male sheep (n = 6, ≤6 months old). Infected sheep were dosed subcutaneously with ivermectin every eight days with increasing doses from 0.2 mg/kg to 1.6 mg/kg bodyweight (bw). Reduced ivermectin efficacy was identified in sheep and goats in the four study locations. Using a paired statistic, the efficacy of a therapeutic dose in sheep was 75.6% (90% upper credible limit (UCrL): 77.5%), while twice the recommended dose led to a reduction of 92.6% (90% UCrL: 93.3%). In goats, the FECRs of a therapeutic dose were 72.9-95.3% (90% UCrL range: 73.6-95.7%) in Bulbul, Nyala Domaia, Nyala University farm and Kass. Twice the dose recommended for goats in Bulbul revealed a 90% UCrL of 87.6%. All post-treatment faecal cultures contained only Haemonchus spp. larvae. The experimental infection trials in sheep and goats supported our findings from field trials and calculated upper 90% CrL of below 98.9%. For the first time highly ivermectin resistant H. contortus populations have been identified in sheep and goats in Sudan, and resistance was experimentally confirmed.

COVID-19 anomaly detection and classification method based on supervised machine learning of chest X-ray images.

The term COVID-19 is an abbreviation of Coronavirus 2019, which is considered a global pandemic that threatens the lives of millions of people. Early detection of the disease offers ample opportunity of recovery and prevention of spreading. This paper proposes a method for classification and early detection of COVID-19 through image processing using X-ray images. A set of procedures are applied, including preprocessing (image noise removal, image thresholding, and morphological operation), Region of Interest (ROI) detection and segmentation, feature extraction, (Local binary pattern (LBP), Histogram of Gradient (HOG), and Haralick texture features) and classification (K-Nearest Neighbor (KNN) and Support Vector Machine (SVM)). The combinations of the feature extraction operators and classifiers results in six models, namely LBP-KNN, HOG-KNN, Haralick-KNN, LBP-SVM, HOG-SVM, and Haralick-SVM. The six models are tested based on test samples of 5,000 images with the percentage of training of 5-folds cross-validation. The evaluation results show high diagnosis accuracy from 89.2% up to 98.66%. The LBP-KNN model outperforms the other models in which it achieves an average accuracy of 98.66%, a sensitivity of 97.76%, specificity of 100%, and precision of 100%. The proposed method for early detection and classification of COVID-19 through image processing using X-ray images is proven to be usable in which it provides an end-to-end structure without the need for manual feature extraction and manual selection methods.

Susceptible trichostrongyloid species mask presence of benzimidazole-resistant Haemonchus contortus in cattle.

BACKGROUND: Benzimidazole (BZ) anthelmintics are widely used to control infections with parasitic nematodes, but BZ resistance is an emerging threat among several nematode species infecting humans and animals. In Sudan, BZ-resistant Haemonchus contortus populations were recently reported in goats in South Darfur State. The objective of this study was to collect data regarding the situation of BZ resistance in cattle parasitic nematodes in South Darfur using phenotypic and molecular approaches, besides providing some epidemiological data on nematodes in cattle. METHODS: The faecal egg count reduction test and the egg hatch test (EHT) were used to evaluate benzimidazole efficacy in cattle nematodes in five South Darfur study areas: Beleil, Kass, Nyala, Rehed Al-Birdi and Tulus. Genomic DNA was extracted from pools of third-stage larvae (L3) (n = 40) during trials, before and after treatment, and pools of adult male Haemonchus spp. (n = 18) from abattoirs. The polymorphisms F167Y, E198A and F200Y in isotype 1 ß-tubulin genes of H. contortus and H. placei were analysed using Sanger and pyrosequencing. RESULTS: Prevalence of gastro-intestinal helminths in cattle was 71% (313/443). Reduced albendazole faecal egg count reduction efficacy was detected in three study areas: Nyala (93.7%), Rehed Al-Birdi (89.7%) and Tulus (88.2%). In the EHT, EC50 values of these study areas ranged between 0.032 and 0.037 µg/ml thiabendazole. Genus-specific PCRs detected the genera Haemonchus, Trichostrongylus and Cooperia in L3 samples collected after albendazole treatment. Sanger sequencing followed by pyrosequencing assays did not detect elevated frequencies of known BZ resistance-associated alleles in codon F167Y, E198A and F200Y in isotype 1 ß-tubulin gene of H. placei (≤ 11.38%). However, polymorphisms were detected in H. contortus and in samples with mixed infections with H. contortus and H. placei at codon 198, including E198L (16/58), E198V (2/58) and potentially E198Stop (1/58). All pooled L3 samples post-albendazole treatment (n = 13) were identified as H. contortus with an E198L substitution at codon 198. CONCLUSIONS: To the knowledge of the authors, this is the first report of reduced albendazole efficacy in cattle in Sudan and is the first study describing an E198L substitution in phenotypically BZ-resistant nematodes collected from cattle.

New codon 198 ß-tubulin polymorphisms in highly benzimidazole resistant Haemonchus contortus from goats in three different states in Sudan.

BACKGROUND: Benzimidazole (BZ) resistance in gastrointestinal nematodes is a worldwide problem for livestock production, particularly in small ruminants. Assignment of the emergence of resistance using sensitive and reliable methods is required to adopt the correct strategies for control. In Sudan, BZ resistant Haemonchus contortus populations were recently reported in goats in South Darfur. This study aimed to provide additional data regarding albendazole efficacy and to describe the prevailing molecular BZ resistance mechanisms. METHODS: Faecal egg count reduction and egg hatch tests (EHT) were used to evaluate albendazole efficacy in three different areas of South Darfur using naturally (Rehed Al-Birdi and Tulus) and experimentally infected (Tulus and Um Dafuq) goats. Using samples from Central, East and South Darfur, pyro- and Sanger sequencing were used to detect the polymorphisms F167Y, E198A and F200Y in H. contortus isotype 1 ß-tubulin in DNA extracted from pooled third-stage larval (L3) samples (n = 36) on days 0 and 10 during trials, and from pooled adult male H. contortus (treated goats, n = 14; abattoirs, n = 83) including samples from populations previously found to be resistant in South Darfur. RESULTS: Albendazole efficacies at 5, 7.5 and 10 mg/kg doses were 73.5-90.2% on day 14 in natural and experimental infections while 12.5 mg/kg showed > 96.6% efficacy. EC50 in the EHT were 0.8 and 0.11 µg/ml thiabendazole in natural and experimental infection trials, respectively. PCRs detected Haemonchus, Trichostrongylus and Cooperia in L3 samples from albendazole-treated goats. Haemonchus contortus allele frequencies in codons 167 and 200 using pyrosequencing assays were ≤ 7.4% while codon 198 assays failed. Sanger sequencing revealed five novel polymorphisms at codon 198. Noteworthy, an E198L substitution was present in 82% of the samples (L3 and adults) including all post-treatment samples. Moreover, E198V, E198K and potentially E198I, and E198Stop were identified in a few samples. CONCLUSIONS: To our knowledge, this is the first report of E198L in BZ resistant H. contortus and the second where this is the predominant genotype associated with resistance in any strongyle species. Since this variant cannot be quantified using pyrosequencing, the results highlight important limitations in the general applicability of pyrosequencing to quantify BZ resistance genotypes.

Epidemiology of strongyle nematode infections and first report of benzimidazole resistance in Haemonchus contortus in goats in South Darfur State, Sudan.

BACKGROUND: Since pastoralists in South Darfur, Sudan, had complained about lack of albendazole (ABZ) efficacy to control nematodes in goats, the frequency of infection with gastrointestinal helminths was studied before in vivo faecal egg count reduction tests (FECRT) were conducted using ABZ orally either at the dose recommended for sheep, 5 mg/kg body weight (bw) or at 10 mg/kg bw. Experiments included goats naturally infected with gastrointestinal nematodes or experimentally infected with local Haemonchus contortus isolates. Three study areas (Nyala, Beleil and Kass) were visited in autumn or winter. RESULTS: Out of 478 screened goats, 82.4% were infected with gastrointestinal helminths and 82% were shedding eggs of strongyle nematodes with 90% of the strongyle larvae representing Haemonchus spp. A FECRT using naturally infected goats (n = 225: 71 untreated, 104 and 50 treated with 5 and 10 mg ABZ/kg bw, respectively) detected reduced ABZ efficacy in Nyala and Kass. Paired and unpaired FECRT calculations detected reductions of 72-92% with samples taken at 8 days post treatment with 5 mg ABZ/kg bw and of 85-94% with 10 mg ABZ/kg bw. The FECRT based on day 14 post treatment samples showed reductions of 69-77% with 5 mg/kg and of 75-87% with 10 mg ABZ/kg bw. In Beleil, ABZ efficacy was 95%. In the egg hatch test EC50 values for Nyala and Kass ranged from 0.12-0.24 µg thiabendazole/ml, corresponding to benzimidazole resistant phenotypes. Only Haemonchus spp. larvae were present after treatments in coprocultures. When the efficacy was evaluated experimentally using isolates of H. contortus from Nyala and Kass, the 5 mg ABZ/kg dose revealed reductions of 76-78% on day 8 and of 62-70% on day 14 with the unpaired method. Using 10 mg ABZ/kg, the FECR was still only 77-82%. CONCLUSIONS: Both, in vivo and in vitro methods detected resistant H. contortus populations in goats from South Darfur State. The time point 14 days post treatment was more sensitive for detection of ABZ resistance than 8 days post treatment. This is the first report on the occurrence of anthelmintic resistance in Sudan confirming that anthelmintic resistance selection is occurring in African subsistence farming systems.

A Survey of Seasonal Gastrointestinal Parasitic Infections in Donkeys from a Semiarid Sub-Saharan Region, Sudan.

Out of 92 donkeys examined for gastrointestinal parasites, 90 animals were found infected by one or more gastrointestinal parasites with an overall prevalence rate of 97.78%. The distributions of the recovered parasites in the different parts of the body were as follows: stomach, 92.4%, small intestine, 19.6%, caecum, 88%, colon, 80.4%, rectum, 73.9%, and cranial mesenteric artery, 64.1%. A significant difference was found between mean parasite counts and seasons. Hot wet season had higher mean parasites count (5411.5 ± 1694.4) in comparison with hot dry (1795.9 ± 399.6) and cool dry (1719.9 ± 522.4) seasons. Although there was no significant difference between age and mean parasite count, animals more than four years old had high mean count (3361.3 ± 921.8) in comparison with 2330 ± 744.3 and 2030.2 ± 873.1 for young and adults animals, respectively. No significant positive or negative correlation was found between total parasite counts of infected animals and any of the climatic factors. The parasites identified were Habronema spp. (40.2%), Trichostrongylus axei (30.4%), Parascaris equorum (18.5%), Anoplocephala perfoliata (4.35%), Gastrodiscus aegyptiacus (8.7%), large strongyles (84%), small strongyles (72%), and Oxyuris equi (1.1%).