Articles: Department of Biological Sciences

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Exploring Genetic Diversity: Optimizing Simple Sequence Repeat (SSR) Markers in Crotalaria for Enhanced Precision in Biodiversity Research
(University of Embu, 2025-05-14) Odhoch Phenny Sharon; Budambula Nancy L. M.; Felix Kiprotich; Muli Joshua Kiilu
Crotalaria is a plant genus with more than 700 species of shrubs and herbs. Despite its potential economic importance, Crotalaria has received limited research attention; hence, there is limited information on its genetic diversity. Hence, there is need to establish its genetic diversity as a foundation for its conservation and breeding. The current study aimed to optimize and validate simple sequence repeat (SSR) markers polymerase chain reaction—conditions for the assessment of genetic diversity in Crotalaria. The genomic DNA of 31 Crotalaria accessions was extracted from 2-week-old leaves using a modified CTAB protocol and Quick-DNA Plant/Seed Kits (Zymo Research Corp) were used for recalcitrant samples. The samples were then amplified using the 29 SSR markers under the optimized conditions. The polymorphism information content (PIC) of the polymorphic markers was calculated to determine their effectiveness. This study determined that the optimal concentrations of dNTPs, MgCl2, and primers as 2.5, 2, and 5 mM, respectively, and the quantity of the DNA template was 1 μL, and the quantity of Taq was 0.125 μL in a 25 μL reaction mixture. The mean PIC value was 0.233, which shows that the markers were slightly informative. The marker PC004 was the most informative marker with the highest PIC value (0.605) and it detected the largest number of alleles despite being a hexanucleotide motif repeat. Its uniqueness augments its potential use in the assessment of genetic diversity. This study implies that the SSR markers designed and optimized for the study are significant for genetic diversity and population structure analysis of Crotalaria species and molecular verification of Crotalaria genotypes as well as other related genera. Besides, the results of the study form a basis for genetic improvement of Crotalaria.
Field Evaluation of Local and Improved Cassava Varieties for Cassava Mosaic Begomoviruses in Lower Eastern Kenya Region
(University of Embu, 2025) Onyango, Ephine Awuor; Kituyi, Sarah Naulikha; Huja, Carol Wangui; Kimatu, Josphert Ngui; Nyaboga, Evans Nyaega
Cassava is a drought-tolerant crop that can help ensure long-term food security in Kenya. However, various diseases and climatic variations pose significant challenges to its production. One of the most detrimental diseases affecting cassava is cassava mosaic disease (CMD), primarily caused in East Africa by two viral species: East Africa Cassava Mosaic Virus (EACMV) and African Cassava Mosaic Virus (ACMV). This study focused on agronomically screening different cassava varieties for diseases and examining their prevalence across Makueni, Machakos, and Kitui Counties in Kenya, using an experimental design. The aim was to determine the cause of abnormal morphological changes observed in some cassava varieties in the field. The investigation revealed that all cassava varieties grown in Kitui, Makueni, and Machakos counties were affected by CMD, except for the bitter cassava variety grown in Kitui County. Morphological confirmation of CMD was conducted by carefully examining the disease characteristics in the field, supported by literature on cassava leaf diseases. Statistical analysis showed no significant difference in the prevalence of ACMV and EACMV among the locations (p = 0.3141 > 0.05) and (p = 0.1394 > 0.05) or between the cultivars (p = 0.3141 > 0.05) and (p = 0.1394 > 0.05), respectively. Additionally, molecular analysis performed on randomly selected leaves confirmed the presence of ACMV and EACMV in the three counties. For improved management of cassava, further research should focus on bitter cassava to better understand the genetic traits that make it less susceptible to CMD and to inform future breeding programs.
Reducing the number of grazing geese on agricultural fields - Effectiveness of different scaring techniques
(University of Embu, 2023-12-06) Robai Christine I.; Nyaga Justin M.; Hannah Karuri; Johan Elmberg; Johan Månsson
Scaring is a widely used damage mitigation tool to make agricultural fields less attractive to wildlife and by that reduce crop damage. However, few experimental studies exist where the numerical response of different scaring devices has been compared. We tested experimentally the effect of three different scaring devices (kite, scarecrow, inflatable man) on the number of geese in fields with cereals, ley, rapeseed, potatoes, and carrots in Sweden. Geese were counted by camera traps and two approaches were used; in a first (model 1) only geese within 50–150m of the scaring devices were counted, and in a second (model 2) all geese in the field were included. A total of 42,281 geese were counted: Greylag goose Anser anser was the most common species (87%), followed by bean goose Anser fabalis (6%), greater white-fronted goose Anser albifrons (3%), barnacle goose Branta leucopsis (2%), and Canada goose Branta canadensis (2%). During scaring the number of geese significantly decreased for all three devices in model 2. The inflatable man decreased goose numbers by 90.0 %, scarecrow 64.6%, and kite 60.5%. A similar pattern was found in model 1, but the decrease was not significant. Our study shows that the scaring devices studied can reduce goose grazing pressure for some time and locally. However, since geese continue to graze during scaring, we conclude that scaring alone is not a final solution to mitigate crop damage. Future work to develop more effective control measures should address the efficiency of other management tools and scaring techniques in combination.
Multiple pathogens co-exposure and associated risk factors among cattle reared in a wildlife-livestock interface area in Kenya
(University of Embu, 2024-07-25) Sophina Manyenya; Daniel Nthiwa; Lutta Harrison Osundwa; Mathew Muturi; Richard Nyamota; Athman Mwatondo; Grace Watene; James Akoko; Bernard Bett
Introduction: Understanding multi-pathogen infections/exposures in livestock is critical to inform prevention and control measures against infectious diseases. We investigated the co-exposure of foot-and-mouth disease virus (FMDV), Brucella spp., Leptospira spp., and Coxiella burnetii in cattle in three zones stratified by land use change and with different wildlife-livestock interactions in Narok county, Kenya. We also assessed potential risk factors associated with the transmission of these pathogens in cattle. Methods: We identified five villages purposively, two each for areas with intensive (zone 1) and moderate wildlife-livestock interactions (zone 2) and one for locations with low wildlife-livestock interactions (zone 3). We sampled 1,170 cattle from 390 herds through a cross-sectional study and tested the serum samples for antibodies against the focal pathogens using enzyme linked immunosorbent assay (ELISA) kits. A questionnaire was administered to gather epidemiological data on the putative risk factors associated with cattle’s exposure to the investigated pathogens. Data were analyzed using the Bayesian hierarchical models with herd number as a random effect to adjust for the within-herd clustering of the various co-exposures among cattle. Results: Overall, 88.0% (95% CI: 85.0–90.5) of the cattle tested positive for at least one of the targeted pathogens, while 41.7% (95% CI: 37.7–45.8) were seropositive to at least two pathogens. FMDV and Brucella spp. had the highest co-exposure at 33.7% (95% CI: 30.9–36.5), followed by FMDV and Leptospira spp. (21.8%, 95% CI: 19.5–24.4), Leptospira spp. and Brucella spp. (8.8%, 95% CI: 7.2–10.6), FMDV and C. burnetii (1.5%, 95% CI: 0.7–2.8), Brucella spp. and C. burnetii (1.0%, 95% CI: 0.3–2.2), and lowest for Leptospira spp. and C. burnetii (0.3%, 95% CI: 0.0–1.2). Cattle with FMDV and Brucella spp., and Brucella spp. and Leptospira spp. co-exposures and those simultaneously exposed to FMDV, Brucella spp. and Leptospira spp. were significantly higher in zone 1 than in zones 2 and 3. However, FMDV and Leptospira spp. co-exposure was higher in zones 1 and 2 than zone 3. Discussion/conclusion: We recommend the establishment of a One Health surveillance system in the study area to reduce the morbidity of the targeted zoonotic pathogens in cattle and the risks of transmission to humans
Bacterial diversity in honey bee environment: Embu County, Kenya
(2024-03) Njoroge, James K.; Njire, Moses; Maina, Julianna; Mwirichia, Romano; Nyabuga, Franklin N.; Mugweru, Julius
Short Communication: Efficacy of Two Commercial Disinfectants on Paenibacillus larvae Spores
(University of Embu, 2022-05-12) Kiriamburi, Joseph; Muturi, Jamleck; Mugweru, Julius; Forsgren, Eva; Nilsson, Anna
Paenibacillus larvae is a spore-forming bacterium causing American foulbrood (AFB) in honey bee larvae. The remains of a diseased larva contains billions of extremely resilient P. larvae spores viable for decades. Burning clinically symptomatic colonies is widely considered the only workable strategy to prevent further spread of the disease, and the management practices used for decontamination requires high concentrations of chemicals or special equipment. The aim of this study was to test and compare the biocidal effect of two commercially available disinfectants, “Disinfection for beekeeping” and Virkon S on P. larvae. The two products were applied to P. larvae spores in suspension as well as inoculated on two common beehive materials, wood and Styrofoam. “Disinfection for beekeeping” had a 100 % biocidal effect on P. larvae spores in suspension compared to 87.0–88.6% for Virkon S which, however, had a significantly better effect on P. larvae on Styrofoam. The two disinfectants had similar effect on infected wood material.
Cold tolerance of biological control agents Amblydromalus limonicus and Iphiseius degenerans
(University of Embu, 2024-09-01) Mbaka Samuel Musyoka; Sasha Vasconcelos; Rezai Mohammad Hosein; Karlsson Miriam Frida; Mattias Jonsson
Knowledge about cold tolerance of non-native biological control agents is critical to avoid permanently establishing them in new temperate areas outside of their na tive range. The cold tolerance of the predatory mites, Amblydromalus limonicus and Iphiseius degenerans, was investigated in the laboratory to assess their establishment potential in northern Europe, particularly Sweden. The lethal time of I. degenerans (the number of days until 100% mortality was reached) declined steeply from 5°C to 0°C and was almost zero at −5°C. The lethal time of A. limonicus did not differ between 5°C and 0°C, but was reduced at −5°C. For both species, LTime50 (the number of days until 50% of the mites died) was longer for fed than for unfed mites. The lethal temperature of A. limonicus (the temperature at which 100% mortality was reached) was −17.75°C, whereas most I. degenerans died at −8.5°C. LTemp50 (the temperature at which 50% of the mites died) was lower for A. limonicus (−9.8°C) than for I. degenerans (−0.1°C). Collectively, these findings suggest that I. degenerans is unlikely to establish in Sweden but that A. limonicus is more cold tolerant. This highlights the risk associated with re leasing A. limonicus in Sweden due to concerns about potential establishment.
The Latitudinal Biotic Interaction Hypothesis revisited contrasting latitudinal richness gradients in actively vs. passively accumulated interaction partners of honey bees
(UoEm, 2025) Cirtwill, Alyssa R.; Roslin, Tomas; Peña‑Aguilera, Pablo; Agboto, Agathe; Bercê, William; Bondarchuk, Svetlana N.; Brodschneider, Robert; Heidari, Behzad; Kaizirege, Camara; Nyaga, Justine Muhoro; Ojonugwa, Ekpah; Gomez, Gonzalo Ossa; Paz, Claudia; Pirk, Christian; Salehi‑Najafabadi, Amir; Salonen, Anneli; Soloniaina, Chantal; Wirta, Helena
Contrasting hypotheses suggest that the number of biotic interactions per species couldeither increase towards the equator due to the increasing richness of potential interaction partners (Neutral theory),or decrease in the tropics due to increased biotic competition (Latitudinal Biotic Interaction Hypothesis). Empiricaltesting of these hypotheses remains limited due to practical limitations, differences in methodology, and speciesturnover across latitudes. Here, we focus on a single species with a worldwide distribution, the honey bee (Apis mellif-era L.), to assess how the number of different types of interactions vary across latitudes. Foraging honey bees interactwith many organisms in their local environment, including plants they actively select to visit and microbes that theylargely encounter passively (i.e., unintentionally and more or less randomly). Tissue pieces and spores of these organ‑isms are carried to the hive by foraging honey bees and end up preserved within honey, providing a rich recordof the species honey bees encounter in nature.
Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya
(UoEm, 2024-08-08) Wambugu, Evalyne N.; Kimita, Gathii; Kituyi, Sarah N.; Washington, Michael A.; Masakhwe, Clement; Mutunga, Lucy M.; Jaswant, Gurdeep; Thumbi, S.M.; Schaefer, Brian C.; Waitumbi, John N.
Rabies, a viral disease that causes lethal encephalitis, kills ≈59,000 persons worldwide annually, despite availability of effective countermeasures. Rabies is endemic in Kenya and is mainly transmitted to humans through bites from rabid domestic dogs. We analyzed 164 brain stems collected from rabid animals in western and eastern Kenya and evaluated the phylogenetic relationships of rabies virus (RABV) from the 2 regions. We also analyzed RABV genomes for potential amino acid changes in the vaccine antigenic sites of nucleoprotein and glycoprotein compared with RABV vaccine strains commonly used in Kenya. We found that RABV genomes from eastern Kenya overwhelmingly clustered with the Africa-1b subclade and RABV from western Kenya clustered with Africa-1a. We noted minimal amino acid variances between the wild and vaccine virus strains. These data confirm minimal viral migration between the 2 regions and that rabies endemicity is the result of limited vaccine coverage rather than limited efficacy.
Nutritional status of people who inject drugs in Coastal Kenya: a cross-sectional study
(UoeM, 2024) Budambula, Valentine ; Ngari, Moses ; Budambula, Nancy L.M. ; Ahmed, Abid A. ; Were, Tom
Introduction Despite documentation on injection drug use (IDU) in Kenya, the nutritional status of people who inject drugs (PWIDs) is under-explored. Elsewhere studies report under-nutrition among PWIDs which is attributed to food insecurity; competing priorities between drugs and food supply; chaotic lifestyle; reduced food intake; substance use induced malnutrition due to inflammation and comorbidities. Methods This was a cross-sectional study that sought to assess the nutritional status of PWIDs in Coastal Kenya. We recruited 752 participants of whom 371(49%) were on IDUs and 75 non-IDUs and 306 non-drug users using respondent driven sampling, traditional snowball, makeshift outreach and purposive sampling methods. Results More than one half of the participants (56%) had BMI classified as normal while 35% had BMI < 18.5. The proportion with BMI < 18.5 was higher among IDUs (46%) compared to the non-IDUs (33%) and non-drug users (23%) at P < 0.001. Using the mid upper arm circumference (MUAC), 17% were classified as underweight and the proportion was lowest (11%) among non- drugs users compared to 22% among IDUs (P < 0.001). However, the IDUs had lower proportion of overweight (8.1%) compared to 55% among the non- drug users. The proportion with low waist-for-hip ratio was highest among the IDUs (74%) while high waist-for-hip ratio was lowest in the same group of IDUs (11%) at P < 0.001. One half (50%), of the participants had no signs of anaemia, (47%) had mild/moderate anaemia while 21 (2.8%) had severe anaemia. However, IDUs were more likely to be overweight based on waist circumference as a parameter. The IDUs had the highest proportion (54%) of mild to moderate anaemia compared to non-IDUs (37%) and 40% non- drug users (P < 0.001). In the multivariable models, IDUs (aRRR 2.83 (95%CI 1.84‒4.35)) and non-IDUs (aRRR 1.42 (95%CI 1.07‒1.88)) compared to non- drug users were positively associated with BMI < 18.5. Being an IDU was positively associated with mild or moderate anaemia (aRRR 1.65 (95%CI 1.13‒2.41)) while non-IDUs were positively associated with severe anaemia (aRRR 1.69 (95%CI 1.16‒2.48)). Conclusion A significant proportion of the participants were under-nourished with those injecting drugs bearing the heaviest brunt. Being an IDU was positively associated with the low BMI, MUAC, waist for hip ratio and mild or moderate anaemia but high waist circumference. People who inject drugs have high risk for under-nutrition and should be targeted with appropriate interventions. Keywords Under nutrition, Injection drug use, BMI, MUAC and anaemia
Mapping brucellosis risk in Kenya and its implications for control strategies in sub‑Saharan Africa
(UoEm, 2023-11-30) Akoko, James M.; Mwatondo, Athman; Muturi, Mathew; Wambua, Lillian; Abkallo, Hussein M.; Nyamota, Richard; Bosire, Caroline; Oloo, Stephen; Limbaso, Konongoi S.; Gakuya, Francis; Nthiwa, Daniel; Bartlow, Andrew; Middlebrook, Earl; Fair, Jeanne; Ogutu, Joseph O.; Gachohi, John; Njenga, Kariuki; Bett, Bernard
In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2–7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya’s Brucellosis Control Policy.
Seroprevalence and related risk factors of Brucella spp. in livestock and humans in Garbatula subcounty, Isiolo county, Kenya
(Uoem, 2023-10-16) Mwatondo, Athman; Nthiwa, Daniel; Muturi, Mathew; Akoko, James; Nyamota, Richard; Bett, Bernard; Omolo, Jack; Gichuhi, Stephen; Mureit, Marianne W.
Seroprevalence of Brucella spp. and Rift Valley fever virus among slaughterhouse workers in Isiolo County, northern Kenya
(UoEm, 2023-10-05) Nyamota, Richard; Maina, Josphat; Mwatondo, Athman; Akoko, James; Nthiwa, Daniel; Bartlow, Andrew W.; Muturi, Mathew; Wambua, Lillian; Middlebrook, Earl A.; Bett, Bernard
Brucella spp. and Rift Valley fever virus (RVFV) are classified as priority zoonotic agents in Kenya, based on their public health and socioeconomic impact on the country. Data on the pathogen-specific and co-exposure levels is scarce due to limited active surveillance. This study investigated seroprevalence and co-exposure of Brucella spp. and RVFV and associated risk factors among slaughterhouse workers in Isiolo County, northern Kenya. A crosssectional serosurvey was done in all 19 slaughterhouses in Isiolo County, enrolling 378 participants into the study. The overall seroprevalences for Brucella spp. and RVFV were 40.2% (95% CI: 35.2–45.4) and 18.3% (95% CI: 14.5–22.5), respectively while 10.3% (95% CI 7.4%-13.8%) of individuals were positive for antibodies against both Brucella spp. and RVFV. Virus neutralisation tests (VNT) confirmed anti-RVFV antibodies in 85% of ELISApositive samples. Our seroprevalence results were comparable to community-level seroprevalences previously reported in the area. Since most of the study participants were not from livestock-keeping households, our findings attribute most of the detected infections to occupational exposure. The high exposure levels indicate slaughterhouse workers are the most at-risk population and there is need for infection, prevention, and control programs among this high-risk group. This is the first VNT confirmation of virus-neutralising antibodies among slaughterhouse workers in Isiolo County and corroborates reports of the area being a high-risk RVFV area as occasioned by previously reported outbreaks. This necessitates sensitization campaigns to enhance awareness of the risks involved and appropriate mitigation measures.
Ecological and Subject‐Level Drivers of Interepidemic Rift Valley Fever Virus Exposure in Humans and Livestock in Northern Kenya
(UoEm, 2023) Mathew, Muturi; Athman, Mwatondo; Nijhof, Ard M; Akoko, James; Nyamota, Richard; Makori, Anita; Mutono, Nyamai; Nthiwa, Daniel; Wambua, Lilian; Roesel, Kristina; Thumbi, S. M.; Bett, Bernard
Do afroalpine plants differ from other alpine plants by their leaf functional traits?
(UoEm, 2023-06-16) Onipchenko, Vladimir G.; Kipkeev, Aliy M.; Kopylova, Natalia A.; Nyaga, Justine M.; Elumeeva, Tatiana G.; Dudova, Ksenia V.; Akhmetzhanova, Asem A.; Tiunov, Alexei V.; Karpukhin, Mikhail M.; Makarov, Mikhail I.
Afroalpine plants develop under specific climate with great daily fluctuations and weak seasonal dynamics of temperature. Do leaf functional traits of the plants in Mt. Kenya differ from those of temperate plants in NW Caucasus? To answer this question, we conducted a comparative study at the Teleki valley (4000–4500 m a.s.l.), Mt. Kenya, Kenya, and Teberda national park (2600–2900 m a.s.l.), the Caucasus, Russia. We measured leaf area, fresh and dry mass, C, N, P, δ 13 C, δ 15 N and derivative traits (specific leaf area – SLA, leaf dry matter content – LDMC, C:N and N:P ratios) for 48 species at the Teleki valley, and the same traits, except for the δ 13 C and δ 15 N, for 141 species in the Teberda national park. The CSR-stra tegies scores were calculated. We applied the Principal Component Analysis to reveal the main patterns of trait variation. Leaf dry mass of Mt. Kenya alpine plants ranged from 0.27 mg (Sagina afroalpina) to 14.0 g (Dendrosenecio kenio den dron). Leaf area, mass and LDMC of alpine plants in both regions did not differ significantly. The SLA of Mt. Kenya’s plants varied about 20-fold: from 2.6 mm 2 mg -1 (Festuca pilgeri) to 39.8 mm 2 mg -1 (Cineraria deltoidea), and Caucasian plants had higher SLA. N and P leaf concentrations were higher, but C lower in Caucasian plants than in Kenyan. Leaf N:P ratio was similar for both regions, while C:N ratio was higher in Kenyan plants. Species of “rosette” trees (Dendrosenecio spp.) differed from other species by size characteristics (maximal leaf dry mass and area were in Dendrosenecio kenioden dron), as well as correspondingly higher investment to mechanical tissues (high C:N ratio, low SLA). By the other functional traits, “rosette” trees were similar to many other alpine plants. Thus, afroalpine plants of Mt. Kenya are close to temperate alpine plants by some leaf functional traits, but possess higher stress-tolerance.
HIV Virologic Failure among Patients with Persistent Low-Level Viremia in Nairobi, Kenya: It Is Time to Review the >1000 Virologic Failure Threshold
(Hindawi, 2023-04-27) Nzivo, Mirriam M.; Waruhiu, Cecilia N.; Kang’ethe, James M.; Budambula, Nancy L. M.
Persistent low-level viremia (PLLV) of 200-999 copies/ml has been reported as a risk factor for HIV virologic failure (VF). This retrospective study was aimed at characterizing patients with PLLV, determining factors associated with VF, and determining the effect of regimen change. Data were extracted from electronic medical records for HIV care and treatment. Patients’ characteristics (N = 705) were as follows: a mean age of 42 years, majority female (55%), and 51% married. A majority (78.7%) had a history of opportunistic infections in their ART lifetime. To determine factors associated with VF, 187 records on patients who maintained PLLV and 12 on deceased patients at the time of data review were eliminated from the analysis, leaving 506 patient records. Out of the 506, 89% (451/506) suppressed VL to nondetectable levels while 11% (55/506) had VF, and the difference was significant (P = 0:0001). Virologic failure was significantly associated with ages 10-30 years (P < 0:05). Baseline VL ≥ 1000 (OR 3.929; P = 0:002) and 200-999 copies/ml (OR 4.062; P = 0:004) were associated with VF. During PLLV, factors associated with VF included the following: PLLV of 200-999 copies/ml (P < 0:05), viral blips (OR 4.545; P = 0:0001), mean maximum VL (P < 0:05), and age (P = 0:043). Married marital status was inversely associated with VF (OR 0.318; P = 0:026). Regimen change was not significantly associated with virologic outcomes. However, patients who switched regimens to the second line had a high risk of VF (P = 0:028; OR 3.203). Regimen change was significantly high (P < 0:05) among adolescents and patients with a start regimen of 2NRTI+1NNRTI. Most of the PLLV patients (89%) achieved nondetectable VL after their continued ART monitoring for at least 12 months. Therefore, PLLV was not an indicator of VF. However, a consistent VL of ≥200-999 copies/ml at baseline and more than 12 months of ART care and treatment were significantly associated with VF. Patients with VL 200-999 copies/ml, adolescents, and young adults require intensive ART monitoring and support.
Food web structure of nematode communities in irrigated rice fields
(Heliyon, 2023-02) Mokuah, Dorcas; Karuri, Hannah W.; Nyaga, Justine M.
Nematodes are a key component of the soil food web and they play an important role in the provision of ecosystem services. Rice cultivation in Mwea, Kenya involves the intensive use of fertilizers and pesticides which may affect the complexity of the nematode-based soil food web. This study examined the nematode diversity and food web structure in irrigated rice fields in Nyangati and Tebere in Mwea, Kirinyaga County, Kenya. Nematodes were identified up to the genus level and soil physico-chemical properties were also determined. Aphelenchoides and Longidorus occurred in significantly greater proportions in Tebere, while in Nyangati there was a high abundance of Helicotylenchus. Aphelenchoides was positively correlated to soil electrical conductivity. From additive diversity partitioning of genus richness, the α and β components contributed 33.7% and 66.3% of the γ diversity, respectively. For Shannon and Simpson diversity indices, the largest contribution to overall diversity was from α component. Soil food web indices were similar across the two regions. Channel and basal indices were below 30% while Enrichment (EI) and Structure (SI) indices were above 50%. There was no variation in metabolic footprints except for the fungivore footprint which was significantly higher in Tebere. Based on the EI and SI, the soil food web in paddy rice fields in Mwea was structured and enriched with moderate disturbance. Due to the high prevalence of economically damaging parasitic nematodes in the rice fields, appropriate management schemes that enhance specific components of the soil food web and increase the suppressive ability of soil against plant-parasitic nematodes should be implemented.
Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya
(Heliyon, 2022-11) Kenya, Eucharia U.; Kinyanjui, Grace; Kipnyargis, Alex C.; Kinyua, Franklin; Mwangi, Mary; Khamis, Fathiya; Mwirichia, Romano K.
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was ampliﬁed using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also signiﬁcantly differentiated (R ¼ 0.559, p ¼ 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community proﬁle. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed signiﬁcantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
Poly-drug use among female and male commercial sex workers visiting a drop in centre in Mombasa County, Kenya
(PLOS GLOBAL PUBLIC HEALTH, 2022-11-11) Budambula, Nancy L. M.; Kemunto, Phyllys; Ziro, Onesmus Wanje; Kissinger, George; Ngari, Moses; Budambula, Valentine
The relationship between commercial sex work and drug use is complex and the two exacerbate each other. In Kenya, Mombasa County has one of the highest populations of drug users and commercial sex workers. Despite documentation of drug use among sex workers, most of the studies are based on self-reported history which is prone to social desirability and memory recall biases. It is in this context that we sought to establish actual drug use is this sub-population. A cross-sectional study was conducted to determine self-reported and confirmed drug use among 224 commercial sex workers accessing services at Mvita Dropin. Actual drug use was determined qualitatively using 6 panel plus alcohol Saliva Test kit. The overall prevalence of self-reported and confirmed current use for at least one drug was 98% and 99% respectively. Regardless of the technique used, alcohol and tobacco products were the most consumed substances. Alcohol use increased significantly with age (P = 0.03). Risk of cigarette use and testing positive for cotinine was higher among those age 18 to 35 years compared to >35years at P = 0.001 and P = 0.002 respectively. Poly-drug use was common with 98% testing positive for more than one drug. The reason for drug use was sex work related pressure (88%) with 60% of the respondents reporting they cannot transact this business without drugs. Almost every commercial sex worker is a poly-drug user. We recommend targeted interventions for commercial sex workers.
Vertical Distribution of Plant-Parasitic Nematodes in Sweet Potato
(Sciendo., 2022) Kemboi, Bernard; Karuri, Hannah; Nyaga, Justine M.; Kingsbury, Aaron J.
Plant-parasitic nematodes (PPN) are harmful pests that have become a severe threat to crop production worldwide. Diversity of PPN at horizontal and spatial scales influence the effectiveness of control strategies. This study evaluated the vertical distribution of PPN genera at 0 cm to 30 cm and 30 cm to 60 cm in sweet potato fields in Central, Manyatta, and Nembure regions of Embu County, Kenya. A significant region × depth interaction was observed for Tylenchus. For all the other nematode genera, there were no significant variations in the abundance at 0 cm to 30 cm and 30 cm to 60 cm depths. However, Helicotylenchus, Meloidogyne, and Scutellonema occurred in greater numbers at both depths in all regions. Shannon and Simpson diversity indices were higher at 0 cm to 30 cm depth while Pielou’s evenness was similar at both depths in the three regions. Diversity partitioning of genus richness, Shannon, and Simpson diversities across all regions at 0 cm to 30 cm, indicated that β component contributed 61.9%, 35.6%, and 22.6% of γ diversity, respectively. Coinertia analysis indicated a significant covariation between nematode genera and soil properties. The results show that management of PPN in sweet potato fields should be targeted at soil depths that are not less than 60 cm.

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