The role of Escherichia coli in the etiology of piglet diarrhea in selected pig producing districts of central Uganda

Background: Pig production in Uganda is highly constrained by rampant piglet mortalities with diarrhea being a key feature. The present study was conducted to determine possible involvement of Escherichia coli (E. coli) as agents of diarrhea in piglets and elucidate the factors for their spread and virulence, towards development of mitigation strategies in the smallholder pig value chains in Uganda. Methodology: This was a cross-sectional study carried out from January to August 2020 on pre- and post-weaned piglets from households in Kayunga and Mityana districts of Central Uganda, selected by snowballing method to redundancy. Data about herd management and risk factors for colibacillosis were collected from selected farmers in the two districts. A total of 179 faecal samples were collected from randomly selected neonatal and pre-weaning piglets for bacteriological isolation of Escherichia coli. Virulence (enterotoxin and fimbrial) genes from the isolates were detected by multiplex polymerase chain reaction (PCR) assay. Results: From the 179 faecal samples, a total of 158 (88.3%) E. coli isolates were obtained. Virulence gene markers were detected in 18.4% (29/158) of the isolates. Among the investigated genes encoding for enterotoxin production, STb was the most prevalent (16/158, 10.13%), followed by STa (12/158, 7.59%), while gene for LT was not detected. The gene coding for F4 adhesin was the only one detected while F18 adhesin was not detected from the isolates. On multiple logistic regression analysis, only tertiary educational level (OR=0.141; 95% CI=0.30-0.666; p=0.013) and infrequent use of antibiotics (OR=0.231, 95% CI=0.062-0.859; p=0.029) among the farmers, were the two factors significantly protective of the piglets from diarrhoea. Conclusion: This study reports a high prevalence of enterotoxin gene markers among E. coli isolates in piglets and revealed the potential role of these bacteria in the aetiology of piglet diarrhoea and mortalities in Uganda. Additionally, this study identified risk factors that can be useful in formulating treatment and control strategies of infection caused by these bacteria. Further studies are needed to identify more adhesins these E. coli isolates employ for intestinal colonization, a step that will help inform vaccine development.   French title: Le rôle d'Escherichia coli dans l'étiologie de la diarrhée des porcelets dans certains districts producteurs de porcs du centre de l'Ouganda   Contexte: La production porcine en Ouganda est fortement limitée par la mortalité généralisée des porcelets, la diarrhée étant une caractéristique clé. La présente étude a été menée pour déterminer l'implication possible Escherichia coli piglet diarrhea in Uganda  d'Escherichia coli (E. coli) en tant qu'agents de diarrhée chez les porcelets et élucider les facteurs de leur propagation et de leur virulence, vers le développement de stratégies d'atténuation dans les chaînes de valeur des petits producteurs de porcs en Ouganda. Méthodologie: Il s'agit d'une étude transversale réalisée de janvier à août 2020 sur des porcelets pré- et post-sevrés issus de ménages des districts de Kayunga et Mityana du centre de l'Ouganda, sélectionnés par la méthode boule de neige jusqu'à la redondance. Les données sur la gestion du troupeau et les facteurs de risque de colibacillose ont été recueillies auprès d'éleveurs sélectionnés dans les deux districts. Au total, 179 échantillons de matières fécales ont été prélevés sur des porcelets néonatals et en pré-sevrage sélectionnés au hasard pour l'isolement bactériologique d'Escherichia coli. Les gènes de virulence (entérotoxine et fimbrial) des isolats ont été détectés par une amplification en chaîne par polymérase (PCR) multiplex. Résultats: À partir des 179 échantillons de matières fécales, un total de 158 (88,3%) isolats d'E. coli ont été obtenus. Des marqueurs du gène de virulence ont été détectés dans 18,4% (29/158) des isolats. Parmi les gènes étudiés codant pour la production d'entérotoxines, STb était le plus répandu (16/158, 10,13%), suivi de STa (12/158, 7,59%), tandis que le gène de la LT n'a pas été détecté. Le gène codant pour l'adhésine F4 était le seul détecté alors que l'adhésine F18 n'a pas été détectée dans les isolats. Sur l'analyse de régression logistique multiple, seul le niveau d'enseignement supérieur (OR=0,141; IC à 95%=0,30-0,666; p=0,013) et l'utilisation peu fréquente d'antibiotiques (OR=0,231, IC à 95 %=0,062-0,859; p=0,029) parmi les éleveurs, étaient les deux facteurs de protection significative des porcelets contre la diarrhée. Conclusion: Cette étude rapporte une prévalence élevée de marqueurs génétiques d'entérotoxines parmi les isolats d'E. coli chez les porcelets et a révélé le rôle potentiel de ces bactéries dans l'étiologie de la diarrhée et de la mortalité des porcelets en Ouganda. De plus, cette étude a identifié des facteurs de risque qui peuvent être utiles dans la formulation de stratégies de traitement et de contrôle de l'infection causée par ces bactéries. D'autres études sont nécessaires pour identifier plus d'adhésines que ces isolats d'E. coli utilisent pour la colonisation intestinale, une étape qui aidera à éclairer le développement de vaccins

Malaria “hotspots” within a larger hotspot; what’s the role of behavioural factors in fine scale heterogeneity in western Kenya?

Background: Malaria remains a major public health problem in Kenya accounting for the highest morbidity and mortality especially among children. Previous reports indicate that infectious agents display heterogeneity in both space and time and malaria is no exception. Heterogeneity has been shown to reduce the effectiveness of interventions. Previous studies have implicated genetic (both human and parasite) and environmental factors as mainly responsible for variation in malaria risk. Human behaviour and its potential risk for contributing to variation in malaria risk has not been extensively explored.Objective: To determine if there were behavioural differences between the people living in hotspots (high malaria burden) and coldspots (low malaria burden) within a geographically homogeneous and high malaria transmission region.Design: A prospective closed cohort study.Setting: The study was conducted in the Health and Demographic Surveillance Site in Bungoma East sub-County.Subjects: A total of 400 people in randomly selected households in both the fever hotspots and cold spots were tested for malaria at quarterly intervals using malaria rapid diagnostic tests (RDTs).Results: Significant heterogeneity in malaria incidence and prevalence was observed between villages. Incidence of malaria was significantly higher in the hotspots (high malaria burden areas) compared to the coldspots (low malaria burden) (49 episodes per 1000 person months compared to 26/1000, ttest p < 0.001). The incidence also varied significantly among the individual villages by season (P: 0.0071). Knowledge on malaria therapy was significantly associated with whether one was in the cold spot or hotspot (P: 0.033). Behavioural practices relating to ITN use were significantly associated with region during particular seasons (P: 0.0001 and P: 0.0001 respectively).Conclusion: There is marked and significant variation in the incidence of malaria among the villages creating actual hotspots of malaria within the larger hotspot. There is a significant difference in malaria infections between the hotspots and cold spots. Knowledge on malaria therapy and behavioural factors such as ITN use may contribute to the observed differences during some seasons

Prevalence, heterogeneity of asymptomatic malaria infections and associated factors in a high transmission region

Background: Although current reports have shown a reduction in malaria cases, the disease still remains a major public health problem in Kenya. In most endemic regions, the majority of infections are asymptomatic which means those infected may not even know and yet they remain infectious to the mosquitoes. Asymptomatic infections are a major threat to malaria control programs since they act as silent reservoirs for the malaria parasites.Objective: The study sought to determine the prevalence of asymptomatic malaria infections, whether they show heterogeneity spatially, across age groups and across time as well as their determinants in a high transmission region.Study Design: This was part of a larger prospective cohort study on malaria indices in the HDSS.Study Setting: The study was conducted in the Webuye Health and Demographic Surveillance Site in Bungoma East Sub-County.Study Subjects: Quarterly parasitological surveys were conducted for a cohort of 400 participants from randomly selected households located in known fever “hotspots” and “coldspots”. Follow-up of all the participants continued for a period of one year. Generalized estimating equations were used to model risk factors associated with asymptomatic parasitemia.Results: Of the total 321 malaria infections detected during the five cross-sectional surveys conducted over the period of one year, almost half (46.3%) of these were asymptomatic. Overall, most of the asymptomatic cases (67%) were in households within known fever “hotspots”. The proportion of infections that were asymptomatic in the coldspots were 73.1%, 31.8%, 13.3%, 55.6% and 48.2% during the first, second, third, fourth and fifth visits respectively. In the known fever “hotspots”, the proportion of infections without symptoms was 47.7%, 48.5%, 35%, 41.3% and 47.5% during the first, second, third, fourth and fifth visits respectively. Factors associated with asymptomatic malaria include; the village one lives: people living in village M were twice likely to be asymptomatic (A.O.R: 2.141, C.I: 0.03 - 1.488), age: children aged between 6 to 15 years were more than twice likely to be asymptomatic (A.O.R: 2.67, C.I. 0.434 - 1.533) and the season: infections during the dry season (January) were less likely to be asymptomatic (A.O.R: 0.26, C.I: -2.289 - 0.400).Conclusion: The prevalence of asymptomatic infections in this region is still very high. The highest proportion of asymptomatic infections was registered in a fever coldpspot village which may explain why the village is a fever coldspot in the first place. There is a need for active surveillance to detect the asymptomatic cases as well as treat them in-order to reduce the reservoir. Targeting interventions to the asymptomatic individuals will further reduce the transmission within this region

QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement

Geographically-weighted regression of knowledge and behaviour determinants to anti-malarial recommending and dispensing practice among medicine retailers in western Kenya: capacitating targeted interventions

Background Most patients with malaria seek treatment first in retail drug shops. Myriad studies have examined retailer behaviours and characteristics to understand the determinants to these behaviours. Geospatial methods are helpful in discovering if geographic location plays a role in the relationship between determinants and outcomes. This study aimed to discover if spatial autocorrelation exists in the relationship between determinants and retailer behaviours, and to provide specific geographic locations and target behaviours for tailoring future interventions. Methods Retailer behaviours and characteristics captured from a survey deployed to medicine retailers in the Webuye Demographic and Health Surveillance Site were analysed using geographic weighted regression to create prediction models for three separate outcomes: recommending the first-line anti-malarial therapy to adults, recommending the first-line anti-malarial therapy to children, and selling that therapy more than other anti-malarials. The estimated regression coefficients for each determinant, as well as the pseudo R2 values for each final model, were then mapped to assess spatial variability and local areas of best model fit. Results The relationships explored were found to be non-stationary, indicating that spatial heterogeneity exist in the data. The association between having a pharmacy-related health training and recommending the first-line anti-malarial treatment to adults was strongest around the peri-urban centre: comparing those with training in pharmacy to those without training (ORæ=æ5.75, pæ=æ0.021). The association between knowing the first-line anti-malarial and recommending it to children was strongest in the north of the study area compared to those who did not know the MOH-recommended anti-malarial (ORæ=æ2.34, pæ=æ0.070). This is also the area with the strongest association between attending a malaria workshop and selling the MOH-recommended anti-malarial more than other anti-malarials, compared to retailers who did not attend a workshop (ORæ=æ2.38, pæ=æ0.055). Conclusion Evidence suggests that spatial heterogeneity exists in these data, indicating that the relationship between determinants and behaviours varies across space. This is valuable information for intervention design, allowing efforts to focus on those factors that have the strongest relationship with their targeted behaviour within that geographic space, increasing programme efficiency and cost-effectiveness

Malaria Parasitaemia among Febrile Children Infected with Human Immunodeficiency Virus in the Context of Prophylactic Cotrimoxazole as Standard of Care: A Cross- Sectional Survey in Western Kenya

Objective: To document the prevalence of malaria parasitaemia among the HIV infected febrile children in a malaria endemic area. Design: A cross-sectional study. Setting: An ambulatory paediatric HIV clinic in Western Kenya, between November 2011 and December 2012. Subjects: A total of 245 febrile HIV infected children aged less than 14 years attending the HIV clinic in the Webuye level IV hospital were included in the study. A systematic sampling method was used. Main outcomes: A blood sample was taken for malaria parasite testing. Presence or absence of malaria parasites was documented. Clinical and socio-demographic characteristics of the participants were also recorded. Results: A total of 245 participants were recruited mean age being 5.53 years. Malaria prevalence was 81.9%. Most participants (97%) were on cotrimoxazole prophylaxis. Some of the factors found to be positively associated with malaria parasitaemia were; male sex, care taker category (parent), WHO stage 3 and 4 of HIV disease, and a high absolute CD4 count. However, only the caretaker association was statistically significant. Conclusion: The frequency of malaria parasitaemia among febrile HIV infected children is still high regardless of the high cotrimoxazole prophylaxis uptake. It is also noted that there is a shift in the age group of fever among children toward the older age group. This implies that policies may need to be relooked at to include the older age group in the aggressive malaria prevention measures to avoid losing on the already made gains

Improvement of resistance to fusarium root rot through gene pyramiding in common bean

Fusarium root rot (FRR), caused by Fusarium solani f.sp. phaseoli , is one of the most serious root rot diseases of common bean ( Phaseolus vulgaris L.) throughout the world. Yield losses of up to 84% have been attributed to the disease. Development and deployment of resistant materials is the most feasible approach to managing the disease. The objective of this study was to estimate the number of pyramided Fusarium root rot resistance genes among the four resistant lines and determine their effectiveness in improving levels of resistance to Fusarium root rot in the susceptible bean cultivars. Crosses among four Fusarium root rot (Fusarium solani f.sp. phaseoli) resistant common bean (Phaseolus vulgaris) were developed. They involved six inbred lines, MLB-48-89A (M48), MLB-49-89A (M49), G2333 (G2) and G685 (G6), and two susceptible cultivars, K20 and Kanyebwa, The resistant lines were used to develop a double cross (DC) population. The DC F1 and each resistant parent were crossed to each of the two susceptible cultivars to form five-parent and single crosses, respectively. Developed populations were subjected to Fusarium solani f. sp. phasoeli isolate-3 under screenhouse conditions. There were segregation ratios of 15:1 (\u3c72 = 1.89, P = 0.17), 61:3 (\u3c72 = 0.18, P = 0.67) and 249:7 (\u3c72 = 1.74, P = 0.19) indicating that two, three and four genes independently condition resistance to F. solani in lines G2 x G6, M49 x M48 and (M49 x M48) x (G2 x G6). A good fit of only four genes in the double cross compared to two in the G2 x G6 , and three genes in the M49 x M48 cross suggests that at least one parent in the G2 x G6 cross have the same or closely linked genes as a parent in the M49 x M48 cross. The F1 means of the five-parent cross (FPC) involving either susceptible parent had lower disease scores, though not significantly (P > 0.05), than the single-crosses from that parent. The F2 of both FPC showed less disease than the single-cross (SC) means (P < 0.05) compared to the single-cross (SC) while the F2 of both FPC had a significant negative deviation (P < 0.05). The F2 frequency distributions also showed that the FPC in both Kanyebwa and K20 populations had higher proportions of resistant plants than any of the single crosses in the respective populations. The superior performance of the FPC over the SC demonstrates that combining resistance genes form different FRR resistance sources can provide a stable source of resistance than using single sources of resistance.Pourriture racinaire caus\ue9e par Fusarium solani f.sp. phaseoli est l\u2019une des plus dang\ue9reuses pourritures racinaires du haricot commun ( Phaseolus vulgaris L.) partout dans le monde. La maladie cause des pertes de rendement jusqu\u2019\ue0 84%. L\u2019objectif de cette \ue9tude \ue9tait d\u2019estimer le nombre de combinaisons de g\ue8nes de r\ue9sistance \ue0 la pourriture racinaire due au Fusarium parmi 4 lign\ue9es r\ue9sistantes et d\ue9terminer leur efficacit\ue9 dans l\u2019am\ue9lioration des niveaux de r\ue9sistance \ue0 la pourriture racinaire dans les vari\ue9t\ue9s sensibles. Les croisements ont \ue9t\ue9 d\ue9velopp\ue9s parmi les 4 vari\ue9t\ue9s de haricot commun r\ue9sistantes au Fusarium. Les croisements impliquaient six lign\ue9es, MLB48-89A, MLB-49-89A, G2333 et G685, et deux vari\ue9t\ue9s sensibles, K20 et Kanyebwa. Les lign\ue9es r\ue9sistantes \ue9taient utilis\ue9es pour d\ue9velopper une population \ue0 double croisement. Les individus de la g\ue9n\ue9ration F1 du double croisement et chaque parent r\ue9sistant \ue9taient crois\ue9s \ue0 chacun des deux cultivars sensibles pour former des croisements \ue0 cinq parents et simples, respectivement. Les populations d\ue9velopp\ue9es \ue9taient soumises \ue0 l\u2019isolat3 du Fusarium solani f.sp. phaseoli en serre. Les rapports de s\ue9gr\ue9gation \ue9taient de 15:1 (\u3c72 = 1.89, P = 0.17), 61:3 (\u3c72 = 0.18, P = 0.67) et 249:7 (\u3c72 = 1.74, P = 0.19), montrant que deux, trois et quatre g\ue8nes conditionnent ind\ue9pendamment la r\ue9sistance au F. solani dans les lign\ue9es G2 x G6, M49 x M48 et (M49 x M48) x (G2 x G6). Une bon adjustement de quatre g\ue8nes seulement dans le double croisement compar\ue9 \ue0 deux dans le croisement G2 x G6, et trois g\ue8nes dans le croisement M49 x M48 indique qu\u2019au moins un parent dans le croisement a les m\ueames g\ue8nes ou les g\ue8nes \ue9troitement li\ue9s pour un parent dans le croisement M49 x M48. Les moyennes des F1 issues des croisements \ue0 cinq parents impliquant le parent Kanyebwa et les populations de K20 avaient des d\ue9viations n\ue9gatives non significatives (P > 0.05) compar\ue9 au croisement simple. D\u2019autre part, les F2 des deux croisements \ue0 cinq parents avaient des d\ue9viations n\ue9gatives significatives (P < 0.05) issues des moyennes de croisements simples, ce qui indique une s\ue9v\ue9rit\ue9 des sympt\uf4mes de la pourriture racinaire plus faible dans les croisements \ue0 cinq parents que dans les simples croisements. La fr\ue9quence des distributions des F2 montrait aussi que les croisements \ue0 cinq parents \ue0 la fois dans les populations de Kanyebwa et celles de K20 avaient des proportions des plants r\ue9sistants plus \ue9lev\ue9es que toutes celles des croisements simples dans les populations respectives

Rectal dihydroartemisinin versus intravenous quinine in the treatment of severe malaria: A randomised clinical trial

Objective: To compare the clinical efficacy and safety of rectal dihydroartemisinin (DATM- Cotecxin) and intravenous quinine in the treatment of severe malaria in children and adults.Setting: Moi Teaching and Referral Hospital, Eldoret, Kenya between July and November1998.Patients: A total of sixty seven patients aged two to sixty years with severe malaria were studied.Design: This was an open randomised comparative clinical trial.Outcome measures: These were parasite clearance time, fever clearance time, efficacy and the side effect profile of the two drugs.Results: The two groups were comparable on admission on the clinical and laboratory parameters. The parasite clearance time was shorter in the rectal DATM group than quinine group. There was no statistical difference on the fever clearance time and cure rates in thetwo groups. The adverse reaction profile was better with rectal DATM than with quinine, tinnitus observed more in the quinine group.Conclusion: Rectal DATM is faster in parasite clearance than quinine and is a safe and convenient alternative to quinine in the treatment of severe malaria

Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs

The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits

Characterization and mapping of Dt1 locus which co-segregates with CcTFL1 for growth habit in pigeonpea

Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait. In the present study, identification of mutations affecting growth habit accompanied by a precise analysis of phenotype has been done which will shed more light upon developmental regulation in pigeonpea. A genetic study was conducted to examine the inheritance of growth habit and a genotyping by sequencing (GBS)-based genetic map constructed using F2 mapping population derived from crossing parents ICP 5529 and ICP 11605. Inheritance studies clearly demonstrated the dominance of indeterminate (IDT) growth habit over determinate (DT) growth habit in F2 and F2:3 progenies. A total of 787 SNP markers were mapped in the genetic map of 1454 cM map length. Growth habit locus (Dt1) was mapped on the CcLG03 contributing more than 61% of total phenotypic variations. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with the Dt1 locus. Ability of this Indel-derived marker to differentiate DT/IDT lines was also validated on 262 pigeonpea lines. This study clearly demonstrated that CcTFL1 is a candidate gene for growth habit in pigeonpea and a user-friendly marker was developed in the present study which will allow low-cost genotyping without need of automation