Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan.

Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides (erm(C) and mph(C')), aminoglycosides (aac(6")-aph(2")), tetracyclines (tet(K)), and trimethoprim (dfrG).

Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda.

Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum ß-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.

Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda.

Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.

Genome Sequence Analysis of a Wohlfahrtiimonas chitiniclastica Strain Isolated from a Septic Wound of a Hospitalized Patient in Uganda.

We report a genome sequence of Wohlfahrtiimonas chitiniclastica strain MUWRP0946, isolated from a hospitalized patient in Uganda. The genome size was 2.08 million bases, and the genome completeness was 94.22%. The strain carries tetracycline, folate pathway antagonist, ß-lactam, and aminoglycoside antibiotic resistance genes.

Characterization of Ugandan Endemic Aspergillus Species and Identification of Non-Aflatoxigenic Isolates for Potential Biocontrol of Aflatoxins.

Acute stunting in children, liver cancer, and death often occur due to human exposure to aflatoxins in food. The severity of aflatoxin contamination depends on the type of Aspergillus fungus infecting the crops. In this study, Aspergillus species were isolated from households' staple foods and were characterized for different aflatoxin chemotypes. The non-aflatoxigenic chemotypes were evaluated for their ability to reduce aflatoxin levels produced by aflatoxigenic A. flavus strains on maize grains. Aspergillus flavus (63%), A. tamarii (14%), and A. niger (23%) were the main species present. The A. flavus species included isolates that predominantly produced aflatoxins B1 and B2, with most isolates producing a high amount (>20 ug/µL) of aflatoxin B1 (AFB1), and a marginal proportion of them also producing G aflatoxins with a higher level of aflatoxin G1 (AFG1) than AFB1. Some non-aflatoxigenic A. tamarii demonstrated a strong ability to reduce the level of AFB1 by more than 95% when co-inoculated with aflatoxigenic A. flavus. Therefore, field evaluation of both non-aflatoxigenic A. flavus and A. tamarii would be an important step toward developing biocontrol agents for mitigating field contamination of crops with aflatoxins in Uganda.

Genetic Characterization of Fungal Biodiversity in Storage Grains: Towards Enhancing Food Safety in Northern Uganda.

Worldwide fungal contamination leads to both quantitative and qualitative grain losses during crop growth and/or storage. A greater proportion of grains contamination with toxins often occurs in sub-Saharan Africa, where control measures are limited. We determined fungal diversity and their toxin production ability in household grains meant for human consumption to highlight the risk of mycotoxin exposure among people from northern Uganda. The study underlines the high diversity of fungi that group into 15 genera; many of which are plant pathogens with toxigenic potential. Fusarium verticillioides was the most common fungal species isolated from household grains. The study also indicates that northern Uganda is favored by a high proportion of toxigenic isolates of F. verticillioides, F. andiyazi, and F. proliferatum, which are characterized by a high fumonisins production capability. The fumonisins production ability was not dependent on the species, grain types, and haplotype group to which the isolates belong. The contamination of most household grains with fungi capable of producing a high amount of toxin shows that most people are exposed to an elevated amount of mycotoxins, which shows the frequent problems with mycotoxins that have been reported in most parts of sub-Saharan Africa.

Genomic analysis of Sweet potato feathery mottle virus from East Africa.

Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.

Prevalence of sweetpotato viruses in Acholi sub-region, northern Uganda.

The purpose of the study was to identify different viruses infecting sweetpotato and the level of co-infection and spatial distribution of the viruses within the Acholi sub-region of northern Uganda. Multiplex PCR was used to screen and determine level of co-infection in 380 sweetpotato plants. The PCR scores were computed to give overall frequency of occurrence of different viruses. The spatial distribution of viruses was represented on an ArcGIS map. Of all screened samples, 24% (92/380) were infected with at least one virus. Sweetpotato feathery mottle virus (65/92), sweetpotato chlorotic fleck virus (17/92) and sweetpotato mild mottle virus (8/92) were the most frequent viruses detected. Of sampled fields, 74% (28/38) had at least one virus-infected sweetpotato plant. The four viruses detected are the major viruses causing significant yield losses in major sweetpotato growing regions of Uganda and East Africa. The findings of limited distribution and low prevalence of the viruses in the region indicate it causes less burden to sweetpotato production in the sub-region compared with other parts of Uganda.

Farmers' practices and their knowledge of biotic constraints to sweetpotato production in East Africa.

Sweetpotato (Ipomoea batatas) is a vital crop for overcoming food insecurity in sub-Saharan Africa and its production is highest in East Africa where yields are high and the growing seasons are short. This cross-country study assessed farmers' local practices and their knowledge of the biotic constraints to sweetpotato production in Uganda, Rwanda, Kenya and Tanzania with the aim of providing empirical data that can ultimately be used to enhance sweetpotato production in these four countries. We collected data from 675 households using a standardized questionnaire integrated with a web-based mobile app. Survey results provided strong evidence that sweetpotato is valued as an important subsistence crop among smallholder farmers on pieces of land of less than 0.4 ha, and we observed that females were more involved than males in sweetpotato production. Sweetpotato was ranked as the second most important staple crop after cassava. Farmers noted an increase in sweetpotato production over the past five years in Uganda and Kenya but a decrease in Rwanda and Tanzania; the proportion of farmers who reported a decrease (33%) and an increase (36%) did not significantly differ. The main constraints to production were reported to be pests (32.6%), drought (21.6%), diseases (11.9%) and lack of disease-free planting materials (6.8%). Farmers recognized the signs and symptoms associated with sweetpotato diseases on leaves, root tubers, and whole plants, but most were unable to assign the disease type (bacterial, fungal or viral) correctly. We suggest that regional governments improve education, increase the provision of clean planting materials and strengthen breeding programs to improve disease resistance.

Sweetpotato seed exchange systems and knowledge on sweetpotato viral diseases among local farmers in Acholi Sub Region-Northern Uganda.

Viral infections greatly limit sweetpotato yields. Good farming practices are critical for effective disease management. 383 Ugandan farmers were surveyed to document symptom incidence, crop-management practices, and buyer preferences. Results showed that 89.27% farmers grow sweet potatoes yearly and 62.76% of these farmers were female. A total of 56.83% farmers obtained vine seeds from their previous gardens, 25.85% from neighbours, and 12.20% purchased. Only ~8% of sellers and ~4% of buyers were selected for disease-free materials. None of the farmers who used vine-cutting knives sterilised them. Almost half of farmers (47%) observed whitefly or aphids but most were unaware they are viral vectors. Most farmers (77%) observed viral symptoms, but few (<2%) recognised them as infections. Insufficient knowledge of sweetpotato viruses and their vectors is common and increases the risk of spread. Practices like vine selling, sharing of vines coupled with insufficient knowledge on sweet potato viruses and its vectors among farmers increase the risk of virus spread among different farms.