ILRI BecA articles

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Next generation sequencing and genetic analyses reveal factors driving evolution of sweetpotato viruses in Uganda
(Journal Article, 2024-10-01) Adero, Joanne; Wokorach, G.; Stomeo, Francesca; Yao, Nasser; Machuka, Eunice; Njuguna, Joyce; Byarugaba, D.K.; Kreuze, J.; Yencho, G.C.; Otema, M.A.; Yada, B.; Kitavi, M.
Sweetpotato (Ipomoea batatas L.) is an essential food crop globally, especially for farmers facing resource limitations. Like other crops, sweetpotato cultivation faces significant production challenges due to viral infections. This study aimed to identify and characterize viruses affecting sweetpotato crops in Uganda, mostly those associated with sweetpotato virus disease (SPVD). Infected leaf samples were collected from farmers’ fields in multiple districts spanning three regions in Uganda. MiSeq, a next-generation sequencing platform, was used to generate reads from the viral nucleic acid. The results revealed nine viruses infecting sweetpotato crops in Uganda, with most plants infected by multiple viral species. Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. The sweet potato virus C carried more codons under positive diversifying selection than the closely related sweet potato feathery mottle virus, particularly in the P1 gene. This study provides valuable insights into the viral species infecting sweetpotato crops, infection severity, and the evolution of sweet potato viruses in Uganda.
Genome-wide association study for the level of prolificacy in Cameroon’s native goat
(Journal Article, 2024-12-31) Kouam Simo, Jaures; Meutchieye, Felix; Wouobeng, Patrick; Tarekegn, Getinet Mekuriaw; Mutai, Collins; Nandolo, Wilson; Pelle, Roger; Djikeng, Appolinaire; Manjeli, Yacouba
Income from goats highly depends on prolificacy, which is difficult to improve by traditional breeding methods. The study aimed to identify SNP markers for prolificacy, using a case–control genome-wide association study (GWAS) on 111 genotyped Cameroon native goat (CNG) does, based on the 50 K single nucleotide polymorphism (SNP) chip panel. None of the top SNPs reached the significant p-value of 5 × 10−8. The highest p-value was 0.0009. Despite the number of cases being about a quarter of the number of controls, the highest allele frequency of some of the top 20 variants in the cases was indicative of their potential role in the trait. These top variants included the following 15: rs268285661, rs268235169, rs268236449, rs268235135, rs268240394 in Sphingosine-1-phosphate phosphatase 2 (SGPP2) gene, rs268283635 in Solute carrier family 24 member 2 (SLC24A2) gene, rs268251678 in Androgen-induced gene 1 (AIG1) gene, rs268267018, rs268239617, rs268281364, rs268273029, rs268286941, rs268236144, rs268233233 in CEP126 gene and rs268278159, respectively. Our findings indicate that GWAS enable the identification of some loci within genes, with known biological functions and pathways in human being and mice animal model but far-ranging to what was previously hypothesized and tested in goat.
Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations
(Journal Article, 2024-05-30) Nantongo, Ziwena; Birungi, Josephine; Opiyo, S.O.; Shirima, G.; Mugerwa, S.; Mutai, Collins; Kyalo, Martina; Munishi, L.; Agaba, M.; Mrode, Raphael A.
Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources.
The effect of cutting regime and genotype on growth, seed yield, seed quality and herbage yield of seven Urochloa (syn. Brachiaria) grass genotypes in the Adamawa region of Cameroon
(Journal Article, 2024) Ojong, N.; Takor, M.; Egbe, A.; Bechem, E.; Etchu, K.; Mutai Collins, K.
The performance of seven Urochloa grass genotypes (three worldwide cultivars cv. Basilisk, cv. Piata, cv. Xaraes and four landrace cv. Adamaoua1, cv. Adamaoua2, cv. North1 and cv. North2) subjected to two cutting regimes (mid-June cut and mid-July cut) was evaluated for regrowth characteristics, seed yields, seed quality and herbage production in 2020 and 2021 cropping seasons at Wakwa, Ngaoundere, Cameroon. This divergence in harvesting practices raises concerns regarding the effectiveness and efficiency of forage utilization, as well as the potential impact on livestock productivity and sustainable farming systems. A split plot design with five replications and a 1-year-old sward was used for the study. In both years, genotypes were significantly different for plant height and tiller numbers at 12 weeks after cutting (P ≤ 0.007). In 2020, the dry matter yield (DMY) ranged between 8.78 t/ha (cv. Piata) and 12.75 t/ha (cv. Xaraes) for June cut regrowth and between 7.69 t/ha (cv. Piata) and 10.26 t/ha (cv. Xaraes) for July cut regrowth. In 2021, DMY ranged between 6.06 t/ha (Adamaoua2) and 13.95 t/ha (cv. Xaraes) for the June cut and between 6.55 t/ha (cv. Adamaoua2) and 10.47 t/ha (cv. Basilisk) for the July cut. For flowering behavior and seed yields, Basilisk flowered earliest while cv. Xaraes flowered latest. In 2020, seed yields were 74.80 kg/ha and 107.72 kg/ha for June cut and July cut regrowth, respectively, whereas in 2021, seed yields were 331 kg/ha and 431 kg/ha for June cut and July cut regrowth, respectively. cv. Adamaoua1 produced the highest seed yield in both years. The cutting regimes evaluated in this study were indifferent for DMY and seed yield.
The major histocompatibility complex region and diversity of the local chicken populations in Niger
(Journal Article, 2023-12-02) Hassan Ousseini, M.; Machuka, Eunice M.; Kyallo, Martina M.; Tiambo, Christian K.; Domelevo Entfellner, Jean-Baka; Pelle, Roger
Introduction: The major histocompatibility complex (MHC) of chicken is highly polymorphic, and it is linked to several disease resistance or susceptibility traits. Therefore, the current study aimed to analyze the genetic diversity in the MHC region of Nigerien local chicken (Dourgou, Goggori, Kolonto, Tchagara, Gouzou-gouzou, and Popular) using a high polymorphic microsatellite marker named LEI0258 to determine the diversity of chickens kept at the four agroecological zones in Niger. Materials and methods: A total of 601 chickens from six local Nigerien chickens were sampled. By capillary electrophoresis using LEI0258 marker, 403 samples with different fragment sizes were randomly chosen and sequenced. Results: The findings indicated 80 different alleles ranging in size from 181 to 474 bp. A total of 22 new alleles and 39 private alleles (that existed in only one breed) were detected. The alleles 309, 295, and 193 were the most predominant in the Nigerien local chicken population. Nine polymorphisms were observed along the LEI0258 sequence, including three in the upstream (one indel and two Single Nucleotide Polymorphism [SNP]), one in the repeat region at the last R12 (SNP), and five in the downstream (two indels and three SNPs). Conclusion: The chickens are not clustering according to their agroecological zone of origin. They are randomly distributed across the four investigated agroecological zones. The information found in this study is invaluable in breeding and conservation programs associated with several disease resistance or susceptibility traits.
Bridging the gap in African biodiversity genomics and bioinformatics
(Journal Article, 2023-09) Sharaf, A.; Ndiribe, C.C.; Omotoriogun, T.C.; Abueg, L.; Badaoui, B.; Badiane Markey, F.J.; Beedessee, G.; Diouf, D.; Duru, V.C.; Ebuzome, C.; Eziuzor, S.C.; Jaufeerally Fakim, Y.; Formenti, G.; Ghanmi, N.; Guerfali, F.Z.; Houaga, I.; Ideozu, J.E.; Katee, Sally M.; Khayi, S.; Kuja, J.O.; Kwon-Ndung, E.H.; Marks, R.A.; Moila, A.M.; Mungloo-Dilmohamud, Z.; Muzemil, S.; Nigussie, H.; Osuji, J.O.; Ras, V.; Tchiechoua, Y.H.; Zoclanclounon, Y.A.B.; Tolley, K.A.; Ziyomo, Cathrine; Mapholi, N.; Muigai, A.W.T.; Djikeng, Appolinaire; Ebenezer, T.E.
The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientific knowledge and innovation and drive economic growth.
Genome segment ratios change during whitefly transmission of two bipartite cassava mosaic begomoviruses
(Journal Article, 2023-06-21) Kennedy, G.G.; Sharpee, W.; Jacobson, A.L.; Wambugu, Mary; Mware, Benard; Hanley-Bowdoin, L.
Cassava mosaic disease is caused by a complex of whitefly-transmitted begomoviruses, which often occur in co-infections. These viruses have bipartite genomes consisting of DNA-A and DNA-B that are encapsidated into separate virions. Individual viruses exist in plants and whitefly vectors as populations comprising both genome segments, which can occur at different frequencies. Both segments are required for infection, and must be transmitted for virus spread to occur. Cassava plants infected with African cassava mosaic virus (ACMV) and/or East African cassava mosaic Cameroon virus (EACMCV), in which the ratios of DNA-A:DNA-B titers differed between plants, were used to examine how titers of the segments in a plant relate to their respective probabilities of acquisition by whiteflies and to the titers of each segment acquired and subsequently transmitted by whiteflies. The probabilities of acquiring each segment of ACMV did not reflect their relative titers in the source plant but they did for EACMCV. However, for both viruses, DNA-A:DNA-B ratios acquired by whiteflies differed from those in the source plant and the ratios transmitted by the whitefly did not differ from one – the ratio at which the highest probability of transmitting both segments is expected.
Analysis of local cassava landraces and improved genotypes in response to infections by cassava mosaic begomoviruses under field conditions in Kenya
(Journal Article, 2023-02-14) Orek, Charles; Kyallo, Martina M.; Yao, Nasser
Characterization of blast resistance in a diverse rice panel from sub-Saharan Africa
(Journal Article, 2023-07) Mutiga, Samuel Kilonzo; Orwa, Philemon; Ng'ang'a, Everlyne M.; Kyallo, Martina M.; Rotich, Felix; Gichuhi, Emily W.; Kimani, John M.; Mwongera, David T.; Were, Vincent M.; Yanoria, Mary Jeanie; Murori, Rosemary; Mgonja, Emmanuel M.; Ziyomo, Cathrine; Wasilwa, Lusike; Bachabi, Famata; Ndjiondjop, Marie-Noëlle; Ouedraogo, Ibrahima; Correll, James C.; Talbot, Nicholas J.
There is a recent unparalleled increase in demand for rice in sub-Saharan Africa, yet its production is affected by blast disease. Characterization of blast resistance in adapted African rice cultivars can provide important information to guide growers and rice breeders. We used molecular markers for known blast resistance genes ( Pi genes; n = 21) to group African rice genotypes ( n = 240) into similarity clusters. We then used greenhouse-based assays to challenge representative rice genotypes ( n = 56) with African isolates ( n = 8) of Magnaporthe oryzae which varied in virulence and genetic lineage. The markers grouped rice cultivars into five blast resistance clusters (BRC) which differed in foliar disease severity. Using stepwise regression, we found that the Pi genes associated with reduced blast severity were Pi50 and Pi65, whereas Pik-p, Piz-t, and Pik were associated with increased susceptibility. All rice genotypes in the most resistant cluster, BRC 4, possessed Pi50 and Pi65, the only genes that were significantly associated with reduced foliar blast severity. Cultivar IRAT109, which contains Piz-t, was resistant against seven African M. oryzae isolates, whereas ARICA 17 was susceptible to eight isolates. The popular Basmati 217 and Basmati 370 were among the most susceptible genotypes. These findings indicate that most tested genes were not effective against African blast pathogen collections. Pyramiding genes in the Pi2/9 multifamily blast resistance cluster on chromosome 6 and Pi65 on chromosome 11 could confer broad-spectrum resistance capabilities. To gain further insights into genomic regions associated with blast resistance, gene mapping could be conducted with resident blast pathogen collections.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle
(Journal Article, 2023-01-13) Kibegwa, F.M.; Bett, R.C.; Gachuiri, C.K.; Machuka, Eunice M.; Stomeo, Francesca; Mujibi, F.D.
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
African suid genomes provide insights into the local adaptation to diverse African environments
(Journal Article, 2022-12-05) Hai-Bing Xie; Chen Yan; Adeola, A.C.; Kun Wang; Cui-Ping Huang; Ming-Min Xu; Qiang Qiu; Xue Yin; Chen-Yu Fan; Yun-Fei Ma; Ting-Ting Yin; Yun Gao; Jia-Kun Deng; Okeyoyin, A.O.; Oluwole, O.O.; Omotosho, O.; Okoro, V.M.O.; Omitogun, O.G.; Dawuda, P.M.; Olaogun, S.C.; Nneji, L.M.; Ayoola, A.O.; Sanke, O.J.; Luka, P.D.; Okoth, Edward A.; Lekolool, I.; Mijele, D.; Bishop, Richard P.; Jianlin Han; Wen Wang; Min-Sheng Peng; Ya-Ping Zhang
African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.
Genomic characterization and antimicrobial susceptibility of dromedary-associated Staphylococcaceae from the Horn of Africa
(Journal Article, 2022-11-08) Akarsu, H.; Liljander, Anne M.; Younan, M.; Brodard, I.; Overesch, G.; Glücks, Ilona; Labroussaa, F.; Kuhnert, P.; Perreten, V.; Monecke, S.; Drexler, J.F.; Corman, V.M.; Laurent, L.; Jores, Joerg
Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to Staphylococcaceae infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks.
Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
(Journal Article, 2022-10-03) Makombu, J.G.; Cheruiyot, E.K.; Stomeo, Francesca; Thuo, D.N.; Oben, P.M.; Oben, Benedicta O.; Zango, P.; Mialhe, E.; Ngueguim, J.R.; Mujibi, F.D.N.
Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright’s Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.
A single exon-encoded Theileria parva strain Muguga cysteine protease (ThpCP): Molecular modelling and characterization
(Journal Article, 2023-03) Chauke, E.; Pelle, Roger; Coetzer, T.H.T.
Assessment of aflatoxin and fumonisin contamination and associated risk factors in feed and feed ingredients in Rwanda
(Journal Article, 2019-05-15) Nishimwe, K.; Bowers, E.; Ayabagabo, Jd.D.; Habimana, R.; Mutiga, Samuel K.; Maier, D.
Mycotoxins are fungal metabolites that contaminate crops, food, and animal feeds. Aflatoxins and fumonisins are among the mycotoxins that have been increasingly reported to affect health and productivity of livestock globally. Given that the health and productivity of livestock can directly influence human food safety and security, a study was conducted to assess the levels and factors for aflatoxin and fumonisin contamination in feed and feed ingredients in Rwanda. Aflatoxins and fumonisins were analyzed in 3328 feed and feed ingredient samples collected at six time points between March and October 2017 in all 30 districts of Rwanda. Of the 612 participants providing samples, there were 10 feed processors, 68 feed vendors, 225 dairy farmers, and 309 poultry farmers. Enzyme-Linked Immunosorbent Assay (ELISA) was used for aflatoxin and fumonisin analyses. Mean aflatoxin levels of 108.83 µg/kg (Median (MD): 43.65 µg/kg), 103.81µg/kg (MD: 48.4 µg/kg), 88.64 µg/kg (MD: 30.90 µg/kg), and 94.95 µg/kg (MD: 70.45 µg/kg) were determined for dairy farmers, poultry farmers, feed vendors, and feed processors, respectively. Mean fumonisin levels were 1.52 mg/kg (MD: 0.71 mg/kg), 1.21 mg/kg (MD: 0.56 mg/kg), 1.48 mg/kg (MD: 0.76 mg/kg), and 1.03 mg/kg (MD: 0.47 mg/kg) for dairy farmers, poultry farmers, feed vendors, and feed processors, respectively. Aflatoxin contamination was significantly affected by time of sampling and district from which feed samples originated (p < 0.05). Fumonisins did not show any correlation trends. Ninety-two percent of survey participants were unaware of aflatoxins and fumonisins and their adverse effects. This study has provided the basic understanding of the extent of feed contamination across the country and has established a baseline for future interventions in Rwanda. Further studies are needed to explore strategies for mitigating mycotoxins in the feed value chain in Rwanda.
A bounds analysis of world food futures: Global agriculture through to 2050
(Journal Article, 2014-10) Pardey, Philip G.; Beddow, J.M.; Hurley, T.M.; Beatty, T.K.M.; Eidman, V.R.
The notion that global agricultural output needs to double by 2050 is oft repeated. Using a new International Agricultural Prospects (iAP) Model, to project global agricultural consumption and production, we find in favour of a future where aggregate agricultural consumption (in tonnes) increases more modestly, by around 69 per cent (1.3 per cent per year) from 2010 to 2050. The principal driver of this result is a deceleration in population growth in the decades ahead. Per capita income growth and changing demographics (generally ageing population) have significant but secondary roles in spurring growth in agricultural consumption, as does our projected growth in the use of agricultural feedstocks to meet the growth we envisage in biofuel demand. Worldwide (but not equally everywhere), crop yield growth has generally slowed over the past decade or so. Notwithstanding a projected continuance of this slowdown, the prospective improvements in crop productivity are still sufficient to reduce per capita cropland use, such that land devoted to crops would need to increase by less than 10 per cent. Even in our upper‐bound (high‐consumption) scenario, we estimate that there remains sufficient productive agricultural land to more than meet the demand without ploughing‐in additional forest‐dominated lands.
Equine Histoplasmosis in Ethiopia: Phylogenetic analysis by sequencing of the internal transcribed spacer region of rRNA genes
(Journal Article, 2022-07-08) Ameni, G.; Messele, A.; Zewude, A.; Girma, M.; Asfa, R.; Mamo, M.; Kyallo, Martina M.; Stomeo, Francesca; Gumi, B.; Sori, T.
Equine histoplasmosis commonly known as epizootic lymphangitis (EL) is a neglected granulomatous disease of equine that is endemic to Ethiopia. It is caused by Histoplasma capsulatum variety farciminosum, a dimorphic fungus that is closely related to H. capsulatum variety capsulatum. The objective of this study was to undertake a phylogenetic analysis of H. capsulatum isolated from EL cases of horses in central Ethiopia and evaluate their relationship with H. capsulatum isolates in other countries and/or clades using the internal transcribed spacer (ITS) region of rRNA genes. Clinical and mycological examinations, DNA extraction, polymerase chain reaction (PCR), Sanger sequencing, and phylogenetic analysis were used for undertaking this study. Additionally, sequence data of Histoplasma isolates were retrieved from GenBank and included for a comprehensive phylogenetic analysis. A total of 390 horses were screened for EL and 97 were positive clinically while H. capsulatum was isolated from 60 horses and further confirmed with PCR, of which 54 were sequenced. BLAST analysis of these 54 isolates identified 29 H. capsulatum isolates and 14 isolates from other fungal genera while the remaining 11 samples were deemed insufficient for further downstream analysis. The phylogenetic analysis identified five clades, namely, African, Eurasian, North American 1 and 2, and Latin American A and B. The Ethiopian isolates were closely aggregated with isolates of the Latin American A and Eurasian clades, whereas being distantly related to isolates from North American 1 and 2 clades as well as Latin American B clade. This study highlights the possible origins and transmission routes of Histoplasmosis in Ethiopia.
Incidence of RNA viruses infecting taro and tannia in East Africa and molecular characterisation of dasheen mosaic virusisolates
(Journal Article, 2022-03) Kidanemariam, Dawit B.; Sukal, A.C.; Abraham, Adane D.; Njuguna, Joyce N.; Stomeo, Francesca; Dale, J.L.; James, A.P.; Harding, R.M.
Taro (Colocasia esculenta) and tannia (Xanthosoma sp.) plants growing in 25 districts across Ethiopia, Kenya, Tanzania and Uganda were surveyed for four RNA viruses. Leaf samples from 392 plants were tested for cucumber mosaic virus (CMV), dasheen mosaic virus (DsMV), taro vein chlorosis virus (TaVCV) and Colocasia bobone disease‐associated virus (CBDaV) by RT‐PCR. No samples tested positive for TaVCV or CBDaV, while CMV was only detected in three tannia samples with mosaic symptoms from Uganda. DsMV was detected in 40 samples, including 36 out of 171 from Ethiopia, one out of 94 from Uganda and three out of 41 from Tanzania, while none of the 86 samples from Kenya tested positive for any of the four viruses. The complete genomes of nine DsMV isolates from East Africa were cloned and sequenced. Phylogenetic analyses based on the amino acid sequence of the DsMV CP‐coding region revealed two distinct clades. Isolates from Ethiopia were distributed in both clades, while samples from Uganda and Tanzania belong to different clades. Seven possible recombination events were identified from the analysis carried out on the available 15 full‐length DsMV isolates. Nucleotide substitution ratio analysis revealed that all the DsMV genes are under strong negative selection pressure.
Foliar diseases and the associated fungi in rice cultivated in Kenya
(Journal Article, 2022-05-01) Ng'ang'a, Everlyne M.; Kyallo, Martina M.; Orwa, P.; Rotich, F.; Gichuhi, E.; Kimani, J.M.; Mwongera, D.; Waweru, Bernice; Sikuku, P.; Musyimi, D.M.; Mutiga, Samuel K.; Ziyomo, Cathrine; Murori, R.; Wasilwa, L.; Correl, J.C.; Talbot, N.J.
We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.
Detection of antimicrobial resistance, pathogenicity, and virulence potentials of non-typhoidal Salmonella isolates at the Yaounde abattoir using whole-genome sequencing technique
(Journal Article, 2022-04-23) Matchawe, C.; Machuka, Eunice M.; Kyallo, Martina M.; Bonny, P.; Nkeunen, G.; Njaci, Isaac; Esemu, S.N.; Githae, Dedan; Juma, John; Nfor, B.M.; Nsawir, B.J.; Piasentier, E.; Ndip, L.M.; Pelle, Roger
One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.

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