Bio

Publications


2017

Okoth, S.  2017.  Genetic characterisation of Plasmodium falciparum isolates with deletion of the pfhrp2 and/or pfhrp3 genes in Colombia: the Amazon region, a challenge for malaria diagnosis and control. PloS one. :1-17. Abstractjournal.pone_.0163137.pdfWebsite

Most Plasmodium falciparum-detecting rapid diagnostic tests (RDTs) target histidine-rich
protein 2 (PfHRP2). However, P. falciparumisolates with deletion of the pfhrp2 gene and its
homolog gene, pfhrp3, have been detected. We carried out an extensive investigation on
365 P. falciparumdried blood samples collected from seven P. falciparumendemic sites in
Colombia between 2003 and 2012 to genetically characterise and geographically map
pfhrp2- and/or pfhrp3-negative P. falciparumparasites in the country. We found a high proportion
of pfhrp2-negative parasites only in Amazonas (15/39; 38.5%), and these parasites
were also pfhrp3-negative. These parasites were collected between 2008 and 2009 in
Amazonas, while pfhrp3-negative parasites (157/365, 43%) were found in all the sites and
from each of the sample collection years evaluated (2003 to 2012). We also found that all
pfhrp2- and/or pfhrp3-negative parasites were also negative for one or both flanking genes.
Six sub-population clusters were established with 93.3% (14/15) of the pfhrp2-negative
parasites grouped in the same cluster and sharing the same haplotype. This haplotype
corresponded with the genetic lineage BV1, a multidrug resistant strain that caused two outbreaks
reportedin Peru between 2010 and 2013. We found this BV1 lineage in the Colombian
Amazon as early as 2006. Two new clonal lineages were identified in these parasites
from Colombia: the genetic lineages EV1 and F. PfHRP2 sequence analysis revealed high
genetic diversity at the amino acid level, with 17 unique sequences identified among 53
PfHRP2 sequences analysed. The use of PfHRP2-based RDTs is not recommended in
Amazonas because of the high proportionof parasites with pfhrp2 deletion (38.5%), and
implementation of new strategies for malaria diagnosis and control in Amazonas must be
prioritised.Moreover, studies to monitor and genetically characterise pfhrp2-negative P. falciparumparasites in the Americas are warranted, given the extensive human migration
occurring in the region.

Okoth, S.  2017.  Sex-Related Differences in Hematological Parameters and Organosomatic Indices of Oreochromis niloticus Exposed to Aflatoxin B1 Diet. Scientifica. :1-7. Abstract4268926.pdfWebsite

A 24-week feeding experiment was conducted to assess whether males and females of Oreochromis niloticus exhibit differences in
their hematological responses and organosomatic indices to dietary AFB1 contamination. Triplicate groups of O. niloticus (initial
body weight: 24.1 ± 0.6 g) were fed with four diets (Diets 1 to 4) containing 0, 20, 200, and 2,000

Okoth, S.  2017.  Histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in Plasmodium falciparum isolates from select sites in Brazil and Bolivia. PLOS One. :1-13. Abstractjournal.pone_.0171150.pdfWebsite

More than 80% of available malaria rapid diagnostic tests (RDTs) are based on the detection of histidine-rich protein-2 (PfHRP2) for diagnosis of Plasmodium falciparum malaria. Recent studies have shown the genes that code for this protein and its paralog, histidine-rich protein-3 (PfHRP3), are absent in parasites from the Peruvian Amazon Basin. Lack of PfHRP2 protein through deletion of the pfhrp2 gene leads to false-negative RDT results for P. falciparum. We have evaluated the extent of pfhrp2 and pfhrp3 gene deletions in a convenience sample of 198 isolates from six sites in three states across the Brazilian Amazon Basin (Acre, Rondonia and Para) and 25 isolates from two sites in Bolivia collected at different times between 2010 and 2012. Pfhrp2 and pfhrp3 gene and their flanking genes on chromosomes 7 and 13, respectively, were amplified from 198 blood specimens collected in Brazil. In Brazil, the isolates collected in Acre state, located in the western part of the Brazilian Amazon, had the highest percentage of deletions for pfhrp2 25 (31.2%) of 79, while among those collected in Rondonia, the prevalence of pfhrp2 gene deletion was only 3.3% (2 out of 60 patients). In isolates from Para state, all parasites were pfhrp2-positive. In contrast, we detected high proportions of isolates from all 3 states that were pfhrp3-negative ranging from 18.3% (11 out of 60 samples) to 50.9% (30 out of 59 samples). In Bolivia, only one of 25 samples (4%) tested had deleted pfhrp2 gene, while 68% (17 out of 25 samples) were pfhrp3-negative. Among the isolates tested, P. falciparum pfhrp2 gene deletions were present mainly in those from Acre State in the Brazilian Amazon. These results indicate it is important to reconsider the use of PfHRP2-based RDTs in the western region of the Brazilian Amazon and to implement appropriate surveillance systems to monitor pfhrp2 gene deletions in this and other parts of the Amazon region.

Okoth, S.  2017.  Determining resistance to Fusarium verticillioides and fumonisin accumulation in African maize inbred lines resistant to Aspergillus flavus and aflatoxins. Euphytica. 213(4):93. Abstract10.10072fs10681-017-1883-7.pdfWebsite

Fusarium verticillioides and Aspergillus
flavus cause Fusarium ear rot (FER) and Aspergillus
ear rot (AER) of maize, respectively. Both pathogens
are of concern to producers as they reduce grain yield
and affect quality. F. verticillioides and A. flavus also
contaminate maize grain with the mycotoxins fumonisins
and aflatoxins, respectively, which has been
associated with mycotoxicosis in humans and animals.
The occurrence of common resistance mechanisms to
FER and AER has been reported. Hence, ten Kenyan
inbred lines resistant to AER and aflatoxin accumulation
were evaluated for resistance to FER, F.
verticillioides colonisation and fumonisin accumulation;
and compared to nine South African lines
resistant to FER and fumonisin accumulation. Field
trials were conducted at three localities in South Africa
and two localities in Kenya. FER severity was
determined by visual assessment, while F. verticillioides
colonisation and fumonisin content were
quantified by real-time PCR and liquid chromatography
tandem mass spectrometry, respectively. Significant
genotype x environment interactions was
determined at each location (P B 0.05). Kenyan
inbred CML495 was most resistant to FER and F.
verticillioides colonisation, and accumulated the lowest
concentration of fumonisins across localities. It
was, however, not significantly more resistant than
Kenyan lines CML264 and CKL05015, and the South
African line RO549 W, which also exhibited low FER
severity (B5%), fungal target DNA (B0.025 ng lL-1
)
and fumonisin levels (B2.5 mg kg-1
). Inbred lines
resistant to AER and aflatoxin accumulation appear to
be promising sources of resistance to F. verticillioides
and fumonisin contamination.
Keywords Fusarium ear rot Aspergillus ear rot
Resistance Mycotoxins Maize inbred lines
In

Okoth, S.  2017.  Molecular profile of malaria drug resistance markers of Plasmodium falciparum in Suriname. Antimicrobial Agents and Chemotherapy. :02655-16. Abstractantimicrob._agents_chemother.-2017-chenet-aac.02655-16.pdfWebsite

In Suriname, an artesunate monotherapy therapeutic efficacy trial was recently conducted to evaluate partial artemisinin resistance emerging in Plasmodium falciparum. We genotyped the PfK13 propeller domain of P. falciparum in forty samples as well as other mutations proposed to be associated with artemisinin resistant mutants. We did not find any mutations previously associated with artemisinin resistance in Southeast Asia but we found fixed resistance mutations for chloroquine and sulfadoxine-pyrimethamine. Additionally, the Pfcrt C350R mutation, associated with reversal of CQ resistance and piperaquine selective pressure was present in 62% of the samples. Our results from neutral microsatellite data also confirmed a high parasite gene flow in the Guiana Shield. Although recruiting participants for therapeutic efficacy studies in very low malaria endemic areas is challenging due to the low number of malaria cases reported, conducting these studies along with molecular surveillance remains essential to monitor artemisinin resistant alleles and to characterize the population structure P. falciparum in areas targeting malaria elimination.

Okoth, S.  2017.  Effects of Medicinal Plant Extracts and Photosensitization on Aflatoxin Producing Aspergillus flavus (Raper and Fennell). International journal of microbiology. :1-9. Abstract5273893.pdfWebsite

This study was undertaken with an aim of exploring the effectiveness of medicinal plant extracts in the control of aflatoxin
production. Antifungal properties, photosensitization, and phytochemical composition of aqueous and organic extracts of fruits
fromSolanumaculeastrum, bark fromSyzygium cordatum, and leaves from Prunus africana, Ocimum lamiifolium, Lippia kituiensis,
and Spinacia oleracea were tested. Spores from four-day-old cultures of previously identified toxigenic fungi, UONV017 and
UONV003, were used. Disc diffusion and broth dilution methods were used to test the antifungal activity. The spores were
suspended in 2ml of each extract separately and treated with visible light (420 nm) for varying periods. Organic extracts displayed
species and concentration dependent antifungal activity. Solanum aculeastrum had the highest zones of inhibition diameters in
both strains: UONV017 (mean = 18.50 ± 0.71 mm) and UONV003 (mean = 11.92 ± 0.94 mm) at 600mg/ml. Aqueous extracts
had no antifungal activity because all diameters were below 8 mm. Solanum aculeastrum had the lowest minimum inhibitory
concentration at 25mg/ml against A. flavusUONV017.All the plant extracts in combinationwith light reduced the viability of fungal
conidia compared with the controls without light, without extracts, and without both extracts and light. Six bioactive compounds
were analyzed in the plant extracts. Medicinal plant extracts in this study can control conidia viability and hence with further
development can control toxigenic fungal spread.

Okoth, S.  2017.  Mycoflora and mycotoxins in finished fish feed and feed ingredients from smallholder farms in East Africa. Egyptian Journal of Aquatic Research. 43:169-176. Abstract1-s2.0-s1687428517300298-main.pdfWebsite

A total of 52 samples of finished fish feeds and ingredients were collected from smallholder farmers in
Kenya, Tanzania, Rwanda and Uganda, and analyzed. Culture and molecular techniques were used to
identify fungal isolates from the feedstock, and mycotoxin profiles were determined using liquid chromatography–tandem
mass spectrometry. The most prevalent fungal species recovered in the samples
was Asperigillus flavus (54.5%). Other fungal species recovered from the samples were Aspergillus tamarii
(9.1%), Mucor velutinosus (9%), Phoma sp. (6.1%), Aspergillus niger (6%), Eurotium rubrum (3%) and
Penicillium chrysogenum (3%). Fourteen mycotoxins were identified: aflatoxins B1, B2, G1 and G2, fumonisin
B1 and B3, deoxynivalenol (DON) and acetyldeoxynivalenol (sum of 3-ADONand 15-ADON), ochratoxin
A, roquefortine C, alternariol, T-2 toxin, and nivalenol. DON (92.9%), aflatoxins (64.3%) and
fumonisins (57.1%) were the most prevalent within locally manufactured feeds, while no contamination
was found in imported feed. Samples from Kenya were the most contaminated with aflatoxin (maximum
806.9 lgkg1
). The high levels of aflatoxin and trichothecene type A and B contamination found in this
study point to potential risks to fish performance and to the health of consumers of the fish and derived
products.

Okoth, S.  2017.  Susceptibility of locally cultivated groundnut (Arachis hypogaea) varieties to aflatoxin accumulation in Homa Bay County, Kenya. African Journal of Microbiology Research. 11(33):1329-1337. Abstract69593d265885.pdf69593d265885.pdfWebsite

Groundnut is one of the staple foods in many parts of the world. Due to its high nutrient content, the nuts are liable to colonization by aflatoxigenic fungi and subsequent aflatoxin accumulation. This study was aimed at determining susceptibility of locally grown groundnut varieties to Aspergillus flavus in Homa Bay County, Western Kenya. A pretested questionnaire was used to survey agronomic practices on groundnut cultivation in 75 randomly selected households in the study site. From each household farm, 100 g soil samples and 500 g of groundnuts were collected at harvest and A. flavus isolated on Modified Rose-Bengal Agar and identified. Aflatoxin was then extracted from each of the groundnut samples and quantified using direct competitive enzyme linked immunosorbent assay (ELISA). Red Valencia was the most cultivated among the 8 varieties identified. Farmers (66%) obtained the planting seeds from the local market and most (92%) did not use fertilizers with majority (94%) having no knowledge of aflatoxins. There was no significant inter-variety difference in aflatoxin accumulation (p=0.744, F=0.581, Df=6, 61). A highly significant association (t = 2.652; P = 0.010) was found between storage state of the groundnuts and aflatoxin levels, with 94% of the samples stored unshelled having aflatoxin levels below 10 ppb. Overall, only 6.7% of kernels sampled from all the divisions did not meet the EC aflatoxin limit of ≤4 ppb while 4% did not meet the KEBS limit of ≤10 ppb. Though the agronomic practices were poor, aflatoxin levels were predominantly low in the region suggesting that the aflatoxin accumulation is likely influenced by agro-ecological zoning as other studies have also been indicated.

Key words: Groundnuts, Aflatoxins, Aspergillus flavus.

Okoth, S.  2017.  Field evaluation of resistance to aflatoxin accumulation in maize inbred lines in Kenya and South Africa. Journal of Crop Improvement. 31(6):862-878. AbstractWebsite

ABSTRACT
Aflatoxin, a carcinogenic toxin, is produced mainly by Aspergillus flavus and Aspergillus parasiticus. Contamination of maize (Zea mays L.) grain by these fungi occurs before harvest, and the easiest strategy to prevent this is to develop/use maize varieties resistant to Aspergillus spp. and aflatoxin accumulation. The objective of this investigation was to identify potential sources of resistance among 23 maize inbred lines (13 obtained from the MAIZE Competitive Grants Initiative, International Maize and Wheat Improvement Centre and 10 from Agricultural Research Council, South Africa). The inbred lines were planted in a randomized complete-block design at two locations each in Kenya and South Africa. Maize ears were inoculated at silking with three toxigenic strains of A. flavus. The inoculated ears in each plot were harvested at 12–18% moisture, dried, and visually assessed for Aspergillus ear rot (AER). Aflatoxin concentration in the kernels was determined using liquid chromatography–tandem mass spectrometry. Significant variation for both AER and aflatoxin concentration existed among the inbred lines at both locations in Kenya and one location in South Africa. Combined analysis revealed a significant (p < 0.001) lines × locations interaction for both AER and aflatoxin concentration. Higher incidences of AER (0–86.0%) and aflatoxin concentration (0.21–6.51 µg/kg) were recorded at Kiboko in Kenya than at the other three locations. A stronger genetic correlation (rG = 0.936, p < 0.0001) between the AER and aflatoxin concentration was recorded in Potchefstroom than at the other three locations. Repeatability of aflatoxin concentration was high at Kiboko (0.87) and Potchefstroom in South Africa (0.74). Three inbred lines, CML247, CML444, and CML495, emerged as potentially useful sources of resistance to AER and aflatoxin accumulation as they showed low levels of aflatoxin contamination in both localities in Kenya and in South Africa.

Okoth, S.  2017.  Awareness and Prevalence of Mycotoxin Contamination in Selected Nigerian Fermented Foods. Toxins. 9(11):363. Abstracttoxins-09-00363.pdfWebsite

Fermented food samples (n = 191) including maize gruel (ogi), sorghum gruel (ogi-baba), melon seed (ogiri), locust bean (iru) and African oil bean seed (ugba) from Southwest Nigeria were quantified for 23 mycotoxins, including aflatoxin B1 (AFB1), fumonisin B1 (FB1), and sterigmatocystin (STE) using liquid chromatography-tandem mass spectrometry. The practices, perceived understanding and health risks related to fungal and mycotoxin contamination amongst fermented food sellers was also established. Data obtained revealed that 82% of the samples had mycotoxins occurring singly or in combination. FB1 was present in 83% of ogi-baba samples, whereas 20% of ugba samples contained AFB1 (range: 3 to 36 µg/kg) and STE was present in 29% of the ogi samples. In terms of multi-mycotoxin contamination, FB1 + FB2 + FB3 + STE + AFB1 + alternariol + HT-2 co-occurred within one sample. The awareness study revealed that 98% of respondents were unaware of mycotoxin contamination, and their education level slightly correlated with their level of awareness (p < 0.01, r = 0.308). The extent to which the analyzed mycotoxins contaminated these food commodities, coupled with the poor perception of the population under study on fungi and mycotoxins, justifies the need to enact fungal and mycotoxin mitigation strategies along the food chain.

2016

Okoth, S.  2016.  Co-occurrence and Diversity of Soil Trichoderma and Fusarium species from Different Land Use Intensities in Machakos County, Kenya. Arch. Curr. Res. Int. 4(1):1-13. Abstractmaina412016acri24894.pdfWebsite

Soil fungi are important components of the soil biota and their diversity is a good indicator of soil
health. Soil fungi respond differently to land use practices and to their relative populations. The cooccurrence
and diversity of Trichoderma and Fusarium species against various land use types
(LUTs) was investigated. The genus Trichoderma contains many important species with potential
for biocontrol of soil-borne plant pathogens as well as high saprophytic capacity while the genus
Fusarium has many species that are highly pathogenic to plants and with potential for mycotoxin
production. This research adopted a cross-sectional study design. Soil samples were collected
from 3 land-use types (LUTs) in Kabaa irrigation scheme in Machakos County, Kenya, that is,
intensive land-uses under irrigation and rain-fed agriculture and undisturbed lands. From the top
soil layer, 100 soil samples were collected. The samples were processed and 369 Trichoderma and 1,546 Fusarium isolates recovered. Fusarium had a higher abundance than Trichoderma in
the highly disturbed lands. In the undisturbed lands, Trichoderma had a higher abundance than
Fusarium. There was a clear negative correlation between Trichoderma and Fusarium occurrence
and diversity. The study further revealed that disturbance had a positive effect on Fusarium but a
negative one on Trichoderma.

Okoth, S.  2016.  Molecular investigation into a malaria outbreak in Cusco, Peru: Plasmodium falciparum BV1 lineage is linked to a second outbreak in recent times. The American journal of tropical medicine and hygiene. 94(1):128-131. Abstract128.pdfWebsite

n November 2013, a Plasmodium falciparum malaria outbreak of 11 cases occurred in Cusco, southern Peru, where falciparum malaria had not been reported since 1946. Although initial microscopic diagnosis reported only Plasmodium vivax infection in each of the specimens, subsequent examination by the national reference laboratory confirmed P. falciparum infection in all samples. Molecular typing of four available isolates revealed identity as the B-variant (BV1) strain that was responsible for a malaria outbreak in Tumbes, northern Peru, between 2010 and 2012. The P. falciparum BV1 strain is multidrug resistant, can escape detection by PfHRP2-based rapid diagnostic tests, and has contributed to two malaria outbreaks in Peru. This investigation highlights the importance of accurate species diagnosis given the potential for P. falciparum to be reintroduced to regions where it may have been absent. Similar molecular epidemiological investigations can track the probable source(s) of outbreak parasite strains for malaria surveillance and control purposes.

Okoth, S.  2016.  Sclerotia Formation and Toxin Production in Large Sclerotial Aspergillus flavus Isolates from Kenya. Advances in Microbiology. 6(01):47-56. Abstractsclerotia_formation.pdfWebsite

We studied the relationship between sclerotia formation and aflatoxin production by Aspergillusflavus
strains isolated from maize kernels from Nandi County. Isolates recovered from maize kernels
were tested for their ability to form sclerotia on different growth media. PCR analysis was
done on the isolates to detect 2 structural genes, aflD and aflQ, involved in aflatoxin biosynthesis
pathway. Positive A. flavus isolates for one or both genes were grown on Yeast Extract Sucrose
Agar medium and aflatoxins quantified using LCMSMS. All the isolates formed large sclerotia and
their formation was influenced by media type but could not be related to amount of aflatoxins
produced both in vivo and in vitro. Though sclerotia are perennating structures and so contribute
to survival index of a fungus, their initiation is regulated by external factors though ability to form
is genetic. This brings ambiguity of their presence or abundance as a measure of toxicity.

Okoth, S.  2016.  Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya. Infection, Genetics and Evolution. 39:372-380. Abstractingasia2016.pdfingasia2016.pdfWebsite

Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p = 0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p < 0.0001) whereas Kisii had the least significant index of association values (0.03; p < 0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether–lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.

Okoth, S.  2016.  Prospective Study of Plasmodium vivax Malaria Recurrence after Radical Treatment with a Chloroquine-Primaquine Standard Regimen in Turbo, Colombia. Antimicrobial agents and chemotherapy. 60(8):4610-4619. Abstractantimicrob._agents_chemother.-2016-zuluaga-idarraga-4610-9.pdfWebsite

Plasmodium vivax recurrences help maintain malaria transmission. They are caused by recrudescence, reinfection, or relapse, which are not easily differentiated. A longitudinal observational study took place in Turbo municipality, Colombia. Participants with uncomplicated P. vivax infection received supervised treatment concomitantly with 25 mg/kg chloroquine and 0.25 mg/kg/day primaquine for 14 days. Incidence of recurrence was assessed over 180 days. Samples were genotyped, and origins of recurrences were established. A total of 134 participants were enrolled between February 2012 and July 2013, and 87 were followed for 180 days, during which 29 recurrences were detected. The cumulative incidence of first recurrence was 24.1% (21/87) (95% confidence interval [CI], 14.6 to 33.7%), and 86% (18/21) of these events occurred between days 51 and 110. High genetic diversity of P. vivax strains was found, and 12.5% (16/128) of the infections were polyclonal. Among detected recurrences, 93.1% (27/29) of strains were genotyped as genetically identical to the strain from the previous infection episode, and 65.5% (19/29) of infections were classified as relapses. Our results indicate that there is a high incidence of P. vivax malaria recurrence after treatment in Turbo municipality, Colombia, and that a large majority of these episodes are likely relapses from the previous infection. We attribute this to the primaquine regimen currently used in Colombia, which may be insufficient to eliminate hypnozoites.

Okoth, S.  2016.  Genetic Characterisation of Plasmodium falciparum Isolates with Deletion of the pfhrp2 and/or pfhrp3 Genes in Colombia: The Amazon Region, a Challenge for Malaria Diagnosis and Control. PLOS One. :1-17. Abstractjournal.pone_.0163137.pdfWebsite

Most Plasmodium falciparum-detecting rapid diagnostic tests (RDTs) target histidine-rich
protein 2 (PfHRP2). However, P. falciparumisolates with deletion of the pfhrp2 gene and its
homolog gene, pfhrp3, have been detected. We carried out an extensive investigation on
365 P. falciparumdried blood samples collected from seven P. falciparumendemic sites in
Colombia between 2003 and 2012 to genetically characterise and geographically map
pfhrp2- and/or pfhrp3-negative P. falciparumparasites in the country. We found a high proportion
of pfhrp2-negative parasites only in Amazonas (15/39; 38.5%), and these parasites
were also pfhrp3-negative. These parasites were collected between 2008 and 2009 in
Amazonas, while pfhrp3-negative parasites (157/365, 43%) were found in all the sites and
from each of the sample collection years evaluated (2003 to 2012). We also found that all
pfhrp2- and/or pfhrp3-negative parasites were also negative for one or both flanking genes.
Six sub-population clusters were established with 93.3% (14/15) of the pfhrp2-negative
parasites grouped in the same cluster and sharing the same haplotype. This haplotype
corresponded with the genetic lineage BV1, a multidrug resistant strain that caused two outbreaks
reportedin Peru between 2010 and 2013. We found this BV1 lineage in the Colombian
Amazon as early as 2006. Two new clonal lineages were identified in these parasites
from Colombia: the genetic lineages EV1 and F. PfHRP2 sequence analysis revealed high
genetic diversity at the amino acid level, with 17 unique sequences identified among 53
PfHRP2 sequences analysed. The use of PfHRP2-based RDTs is not recommended in
Amazonas because of the high proportionof parasites with pfhrp2 deletion (38.5%), and
implementation of new strategies for malaria diagnosis and control in Amazonas must be
prioritised.Moreover, studies to monitor and genetically characterise pfhrp2-negative P. falciparumparasites in the Americas are warranted, given the extensive human migration
occurring in the region.

Okoth, S.  2016.  Efficacy of Chloroquine and Primaquine for the Treatment of Uncomplicated Plasmodium vivax Malaria in Cruzeiro do Sul, Brazil. Am. J. Trop. Med. Hyg.. 95(5):1061–1068. Abstract811.pdfWebsite

We evaluated the efficacy of chloroquine and primaquine on uncomplicated Plasmodium vivax malaria
in Cruzeiro do Sul, Brazil, in 2014. Patients ≥ 5 years of age with either fever or history of fever, and laboratoryconfirmed
P. vivax monoinfection received chloroquine (total dose = 25 mg/kg) and primaquine (total dose = 3.5 mg/kg),
and were followed up for 168 days (24 weeks). We used microsatellite genotyping to differentiate recurrent infections
caused by heterologous parasites from those caused by homologous ones. No new P. vivax episode occurred by Day 28
among 119 enrolled patients, leading to Day 28, with adequate clinical and parasitological response (ACPR) of 100%
(95% confidence interval [CI] = 96.7–100%). Twenty-eight P. vivax episodes occurred by Day 168, with uncorrected
ACPR of 69.9% (95% CI = 59.5–79.0%). Fifteen of these episodes were caused by either homologous haplotypes
or haplotypes that could not be determined. Excluding the 13 recurrent episodes caused by heterologous parasites,
Day 168 microsatellite-corrected ACPR was estimated at 81.2% (95% CI = 71.0–89.1%). Chloroquine and primaquine
remain efficacious to tr

2015

Okoth, S.  2015.  Distribution and Diversity of Indigenous Trichoderma species in Machakos County, Kenya. British Microbiology Research Journal. 9(4):1-15. Abstractmaina_et_al_distribution_and_diversity_of_indigenous_trichoderma_species.pdfWebsite

Aim: This study was undertaken in order to determine the effect of land-use intensification on
occurrence, distribution, and diversity of Trichoderma fungus.
Study Design: Cross-sectional study.
Place and Distribution of Study: Mycology Laboratory, University of Nairobi between March and
September, 2014.
Methodology: Soil samples were collected from both Mwala and Kauti irrigation blocks in Kabaa
irrigation scheme of Machakos County, in Kenya under three land use types (LUTs): intensively
cultivated farmlands under irrigation, rainfed intensively cultivated farmlands and undisturbed lands.
A total of 100 soil samples were obtained from the top 0- 20 cm depth. Trichoderma species were
isolated using the dilution plate technique using Trichoderma-selective media (TSM).
Results: A total of 369 Trichoderma isolates were recovered from the three LUTs. These were
identified and classified into eleven species. The species identified were: T. harzianum, T. koningii, T. viride, T. asperellum, T. atroviride, T. spirale, T. virens, T. tomentosum, T. brevicompactum, T.
crassum and T. hamatum. The most abundant Trichoderma species was T. harzianum with a
frequency of isolation of 38.87%, followed by T. koningii and T. viride at 18.03 and 15.49%,
respectively. Trichoderma hamatum had the least isolation frequency at 0.41%. T. harzianum also
had the widest distribution. The difference in abundance of Trichoderma in the three LUTs was
significant (P=0.05). The undisturbed lands had a higher abundance of Trichoderma compared to
the disturbed areas. Mwala irrigation block A had the least abundance while block D which is more
recent in cultivation had highest mean abundance of Trichoderma. Difference in Trichoderma
species mean richness between LUTs was not significant (P=0.203). Undisturbed lands had the
highest richness. Undisturbed lands also had the highest diversity while irrigated lands were the
least diverse
Conclusion: Enhanced land-use intensification lowers the abundance and diversity of Trichoderma
in the soil.

Okoth, S.  2015.   Authors. Journal of Biology, Agriculture and Healthcare. :16-21. Abstractkiamabudambulaetal2015.pdf

Application of Fungi for effective removal of hydrocarbon contamination from soil is being considered as the better option when it comes to biodegradation. Other method like physical and chemical bioremediation leads to production of toxic compounds and these methods are not cost effective. In the present study, soil samples from four different oil contaminated soils were assessed for any recovery of fungi present. Cultural characterization was used as preliminary identification using keys. Initial isolation from the oil contaminated soil was done using potato dextrose agar. Colonies were observed and characterized morphologically. The isolates were grown at varied temperatures and pH. Eight fungal isolates were recovered from polluted soils namely, Trichoderma viride, Trichoderma spirale, Neosartorya pseudofischeri, Neosartorya aureola, Aspergillus flavus, Aspergillus terreus, Penicillium griseofulvum and Trichoderma longibrachiatum. The optimum growth temperature range for the eight fungi was 30 o C and 40 o C. There was no growth at 50 o C for all isolates except some slight growth by Aspergillus flavus. Optimum growth at pH 7 and pH 9 and poor growth at pH 5 was noted. This study will contribute to the database on locally available fungal diversity and their ecology.

Okoth, S.  2015.  Effects of land-use intensification on distribution and diversity of Fusarium species in Machakos County, Kenya. Journal of Agricultural Science. 7(4):48. Abstract41855-159169-1-pb.pdfWebsite

Land-use intensification has a significant influence on occurrence of soil microorganisms. The effect of this phenomenon on Fusarium species is poorly characterized. One hundred soil samples were obtained from 3 replicated land- use types (LUT) in Mwala and Kauti irrigation regions in Machakos County. These included two intensive land-uses under irrigation and rain-fed agriculture and undisturbed lands. Mwala irrigated lands were divided into four blocks based on history of cultivation. Using soil dilution plate technique, 1,546 isolates of Fusarium were recovered and identified into twelve species namely; F. oxysporum, F. solani, F. nygamai, F. equiseti, F. chlamydosporum, F. beomiforme, F. verticillioides, F. proliferatum, F. acuminatum, F. compactum, F. semitectum, and F. merismoides. Fusarium oxysporum was the most abundant and diverse Fusarium species. Fusarium semitectum, F. compactum and F .merismoides had the least distribution being isolated from only one LUT. Fusarium beomiforme and F. acuminatum were recovered from irrigated farmlands only while F. verticillioides, F. proliferatum and F. acuminatum were restricted to disturbed lands only. The difference in abundance of Fusarium between the three LUTs was significant (P = 0.047) with irrigated lands having the highest abundance. Mwala block A had the highest abundance, richness and diversity of Fusarium. Lands with a higher intensity of disturbance had a higher abundance and richness of Fusarium than the less undisturbed lands. This may have severe implication on crop production as most species of Fusarium isolated are pathogenic. Sustainable ways of controlling these potential crop pathogens should be sought.

Okoth, S.  2015.  Identification Key for Aspergillus Species Isolated from Maize and Soil of Nandi County, Kenya. Advances in Microbiology. 5(04):205. AbstractWebsite

The aim of this study was to identify Aspergillus species isolated from maize kernels and soils of
maize fields of Nandi County using macro and micro morphological characteristics. A cross sectional
research design was used in the study and purposive sampling was employed to determine
districts of Nandi County and sub locations where sampling was done. This study was part of a
larger project whose aim was to survey aflatoxin exposure in the maize value chain. Aspergillus
species were isolated from maize and soil samples using quarter strength potato dextrose agar
and modified Rose Bengal agar respectively. Pure cultures of the isolates were sub cultured and
transferred onto differential media; malt extract agar, czapek yeast extract agar and czapek dox
agar for species identification using macro morphological characteristics. Fungal slides were prepared
from pure cultures on potato dextrose agar media after three days to identify micro morphological
characteristics. Based on morphological characteristics, seven sections of Aspergillus
namely: Flavi, Fumigati, Nigri, Circumdati, Clavati, Nidulantes and Candidi were identified. Aspergillus
section Flavi was the most predominant with 57% followed by section Nigri with 27% from
maize and 58% of section Flavi followed by 26% of section Nigri from the soil across the three locations.
Aspergillus sections Nidulantes and Candidi were rare and only recovered from the soil
samples of Kaptumo location. All the Aspergillius flavus that formed sclerotia both from the soils
or maize kernels were of the L strains. In conclusion Aspergillus section Flavi was most frequent
during the isolation process and dominated with Aspergillus flavus from both the maize and soil.
Morphological characteristics remain the primary tool for detection and identification of Aspergillus
species. The significance for high incidence of Aspergillus section Flavi is in regard to their
aflatoxin production profiles that poses a health threat to the community and it is of public health
concern. Morphological characteristics as a primary tool for Aspergillus identification should be
embraced and more personnel with the knowledge are required since modern and faster techniques
are scarce and expensive.

Okoth, S.  2015.  Occurrence of arbuscular mycorrhizal fungi and Fusarium in TC banana rhizosphere inoculated with microbiological products in different soils in Kenya. International Journal of Soil Science. 10(2):45. Abstractmukhongoetal.2015a.pdfWebsite

The impact of microbiological commercial products (PHC Biopak, Rhizatech and ECO-T) on
the occurrence of mycorrhizae and Fusarium in the rhizosphere of tissue culture banana
(Gros Mitchel cv.) was assessed. Tissue cultured banana plantlets were inoculated with PHC
Biopak (Bacillus), Rhizatech (mycorrhiza) and ECO-T (T. harzianum) under greenhouse conditions
using a completely randomized design in a Vertisol, Rhodic Ferralsol and Humic Nitisol sampled
from the major banana growing regions in Kenya. Potted plants were later established under field
conditions in the three agro ecological zones. Roots and soils sampled at end of potting and at
flowering were assessed for AM fungi colonization and Fusarium populations. The effect of product
inoculation on AM fungi colonization varied and only significant (p<0.05) in Rhodic Ferralsol with
Rhizatech increasing intensity of colonization by 31.9% and PHC Biopak increasing the frequency
of colonization by 38.6% compared to the non-inoculated control (12.9%). F. oxysporum, fsp. cubense,
F. proliferatum and F. incarnatum were recovered from the experimental soils. Foc was the most
abundant in the three soils (prior to inoculation) accounting for 60.6% of all Fusarium colony
forming units. After inoculation, at the end of potting stage and at flowering, F. proliferatum was
mostly isolated from the three zones accounting for 35.2% of the total fungal population. Foc was
isolated from Humic Nitisol and Vertisol accounting for 11.5% of the total fungal population. PHC
Biopak, ECO-T and Rhizatech suppressed Foc colony forming units per gram of soil by 47, 68 and
55%, respectively in the Humic Nitisol. ECO-T reduced Fusarium colony forming units per gram
of soil by 6% in Rhodic Ferralsol and PHC Biopak by 50% in Vertisol compared to the
non-inoculated soils. There is potential in use of commercial microbiological products to suppress
Foc and the efficacy of the products depends on soil physico-chemical properties.
Key words: Tissue culture banana, Trichoderma

Okoth, S.  2015.  Selection and spread of artemisinin-resistant alleles in Thailand prior to the global artemisinin resistance containment campaign. PLoS pathogens. 11(4):e1004789. Abstractjournal.ppat_.1004789.pdfWebsite

The recent emergence of artemisinin resistance in the Greater Mekong Subregion poses a major threat to the global effort to control malaria. Tracking the spread and evolution of artemisinin-resistant parasites is critical in aiding efforts to contain the spread of resistance. A total of 417 patient samples from the year 2007, collected during malaria surveillance studies across ten provinces in Thailand, were genotyped for the candidate Plasmodium falciparum molecular marker of artemisinin resistance K13. Parasite genotypes were examined for K13 propeller mutations associated with artemisinin resistance, signatures of positive selection, and for evidence of whether artemisinin-resistant alleles arose independently across Thailand. A total of seven K13 mutant alleles were found (N458Y, R539T, E556D, P574L, R575K, C580Y, S621F). Notably, the R575K and S621F mutations have previously not been reported in Thailand. The most prevalent artemisinin resistance-associated K13 mutation, C580Y, carried two distinct haplotype profiles that were separated based on geography, along the Thai-Cambodia and Thai-Myanmar borders. It appears these two haplotypes may have independent evolutionary origins. In summary, parasites with K13 propeller mutations associated with artemisinin resistance were widely present along the Thai-Cambodia and Thai-Myanmar borders prior to the implementation of the artemisinin resistance containment project in the region.

Okoth, S.  2015.  Molecular epidemiology of Plasmodium falciparum malaria outbreak, Tumbes, Peru, 2010–2012. Emerging infectious diseases. 21(5):797. AbstractWebsite

During 2010–2012, an outbreak of 210 cases of malaria occurred in Tumbes, in the northern coast of Peru, where no Plasmodium falciparum malaria case had been reported since 2006. To identify the source of the parasite causing this outbreak, we conducted a molecular epidemiology investigation. Microsatellite typing showed an identical genotype in all 54 available isolates. This genotype was also identical to that of parasites isolated in 2010 in the Loreto region of the Peruvian Amazon and closely related to clonet B, a parasite lineage previously reported in the Amazon during 1998–2000. These findings are consistent with travel history of index case-patients. DNA sequencing revealed mutations in the Pfdhfr, Pfdhps, Pfcrt, and Pfmdr1 loci, which are strongly associated with resistance to chloroquine and sulfadoxine/pyrimethamine, and deletion of the Pfhrp2 gene. These results highlight the need for timely molecular epidemiology investigations to trace the parasite source during malaria reintroduction events.

Keywords: Falciparum malaria, Plasmodium, Peru, microsatellite markers, parasites, malaria, Peru

Okoth, S.  2015.  Variation in Plasmodium falciparum histidine-rich protein 2 (Pfhrp2) and Plasmodium falciparum histidine-rich protein 3 (Pfhrp3) gene deletions in Guyana and Suriname. PLOS One. 10(5):e0126805. Abstractjournal.pone_.0126805.pdfWebsite

Guyana and Suriname have made important progress in reducing the burden of malaria. While both countries use microscopy as the primary tool for clinical diagnosis, malaria rapid diagnostic tests (RDTs) are useful in remote areas of the interior where laboratory support may be limited or unavailable. Recent reports indicate that histidine-rich protein 2 (PfHRP2)-based diagnostic tests specific for detection of P. falciparum may provide false negative results in some parts of South America due to the emergence of P. falciparum parasites that lack the pfhrp2 gene, and thus produce no PfHRP2 antigen. Pfhrp2 and pfhrp3 genes were amplified in parasite isolates collected from Guyana and Suriname to determine if there were circulating isolates with deletions in these genes. Pfhrp3 deletions were monitored because some monoclonal antibodies utilized in PfHRP2-based RDTs cross-react with the PfHRP3 protein. We found that all 97 isolates from Guyana that met the inclusion criteria were both pfhrp2- and pfhrp3-positive. In Suriname (N = 78), 14% of the samples tested were pfhrp2-negative while 4% were pfhrp3-negative. Furthermore, analysis of the genomic region proximal to pfhrp2 and pfhrp3 revealed that genomic deletions extended to the flanking genes. We also investigated the population substructure of the isolates collected to determine if the parasites that had deletions of pfhrp2 and pfhrp3 belonged to any genetic subtypes. Cluster analysis revealed that there was no predominant P. falciparum population substructure among the isolates from either country, an indication of genetic admixture among the parasite populations. Furthermore, the pfhrp2-deleted parasites from Suriname did not appear to share a single, unique genetic background.

Okoth, S.  2015.  Survey of nematode-destroying fungi from selected vegetable-growing areas in Kenya. JOURNAL OF HORTICULTURAL SCIENCES. 10(1):64-69. Abstractjhs101june2015.pdfWebsite

Plant-parasitic nematodes cause severe damage to a wide range of economic crops, causing upto 5% yield losses
globally. In Kenya, vegetables are affected, among other pests, by parasitic nematodes, causing upto 80% loss in yield.
Nematode control is very difficult and relies heavily on use of chemical nematicides. Use of these chemical nematicides
leads to biological magnification, and elimination of natural enemies of other pathogens, thus creating a need for
greater application of pesticides, increased production costs, and development of insecticide-resistance. These factors
have led to a growing interest in search for alternate management strategies. The objective of this study was, therefore,
to document nematode-destroying fungi in selected, major vegetable-growing areas in Kenya as a step towards
developing a self-sustaining system for management of plant-parasitic nematodes. Soil samples were collected from
five vegetable-production zones, viz., Kinare, Kabete, Athi-river, Machakos and Kibwezi, and transported to the laboratory
for extraction of nematode-destroying fungi. The soil-sprinkle technique described by Jaffee et al (1996) was used for
isolating the nematode-destroying fungi from soil, while, their identification was done using identification keys
described by Soto Barrientos et al (2001). From this study, a total of 171 fungal isolates were identified as nematodedestroying.
The highest population was recorded in Kabete, at 33.9% of the total, followed by Machakos, Kibwezi,
Athi-river, with the least in Kinare, at 24.6, 22.2, 11.7 and 7.6% of the total population, in that order. Arthrobotrys was
the most frequent genus, with mean occurrence of 7.3, followed by Monacrosporium with 6 and Stylophage with 5.2.
A. dactyloides was significantly (P=0.002) affected by the agro-ecological zone, with the highest occurrence recorded
in Kabete, and the least in Athi-river. Kibwezi recorded highest diversity index, with a mean of 1.017, while, Athi-river
recorded the least, with a mean of 0.333. Kibwezi had the highest species richness, recording a mean of 3.4, while, the
least mean of 1.6 was recorded in Athi-river. Mean species richness of 2.2 was recorded for both Kabete and Machakos,
and 1.8 for Kinare. From the three genera recorded, Arthrobotrys was more effective at trapping nematodes compared
to Monocrosporium and Stylopage. The genus Arthrobotrys had the highest number of trapped nematodes, with a
total population of 57, followed by Monacrosporium, the least being Stylopage, with 45 and 36, respectively, in a period
of 104 hours. From the study, it is evident that agricultural practices affect occurrence and diversity of nematodedestroying
fungi, and, Arthrobotrys can be used as a bio-control agent for managing plant-parasitic nematodes.
Key words: Artabotrys, biological control, plant-parasitic nematodes

Okoth, S.  2015.  EFFICACY OF CHLOROQUINE TO PRIMAQUINE IN THE TREATMENT OF UNCOMPLICATED PLASMODIUM VIVAX MALARIA, CRUZEIRO DO SUL, ACRE, BRAZIL, 2014. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE. 93(4):574-575.
Okoth, S.  2015.  Arbuscular mycorrhizal fungi with different soil fertility amendment practices in agricultural landscapes of Kenyan highlands. Nutrient Cycling in Agroecosystems. 103(2):229-240. Abstract10.10072fs10705-015-9744-z.pdfWebsite

Several interrelated and site-specific agronomic factors ranging from agroecological conditions to systems management practices have been shown to variably affect arbuscular mycorrhizal fungi (AMF) diversity in the soil. Also, there have been various attempts in the past to evaluate the potential of AMF field inoculation but a majority focussed on the use of exotic strains, disregarding the potential of the existing naturally occurring strains. In an attempt to address these problems, our study aimed to develop ‘best-bet practice’ based on soil fertility amendment practice (SFAP) that encourages occurrence and diversity of AMF in the soil. Control treatment (no application) was compared with three (3) SFAP used singly or in combination with AMF or two other soil nutrients enhancing organisms (Bacillus and Trichoderma) which included the following: (1) Mavuno (macro- and micronutrients and secondary nutrients) fertilizer, (2) calcium ammonium nitrate (CAN) plus triple super phosphate (TSP) and (3) cattle manure. Maize (Zea mays L.) and common bean (Phaseoli vulgaris L.) were planted at on-station and on-farm plots for two consecutive cropping seasons with the experiment replicated in two benchmark sites of Embu and Taita-Taveta Districts. Embu site recorded a lower soil pH and also very low phosphorus levels compared to Taita site. The number of AMF spores per kg of soil was very low, ranging from 30 to 100, at Embu in the first season and application of SFAP resulted in no significant difference. However, in the second season, use of Trichoderma + CAN plus TSP was shown to significantly stimulate AMF species in the soil, with a 250 % increase in species density compared to use of Bacillus + Manure. At Taita, after the first cropping season, significant change in spore density was only recorded from AMF applied singly with a 66.1 % increase in spore density compared to Control treatment. In comparison, after the second cropping season, use of AMF applied singly, AMF + CAN plus TSP and AMF + Manure increased spore density by 135.4, 109.6 and 100 % respectively compared to Control treatment. Use of AMF applied singly increased species density in the soil by 100 and 81.1 % compared to CAN plus TSP and Trichoderma treatments respectively after first season at Taita site: while after the second cropping season, application of AMF + CAN plus TSP, AMF + Manure and AMF + Mavuno increased AMF species density in the soil by 60.3, 51.5 and 55.9 % respectively compared to Control treatment. These findings provide evidence that it is possible to increase the number of AMF spores in the soil through inoculation with native species and also possibly stimulate dormant species through other SFAP treatments.

Keywords

Arbuscular mycorrhizae fungi Soil fertility amendment practices Native species Spore density Species density AMF inoculation

Okoth, S.  2015.  Prevalence of pfhrp2 and pfhrp3 gene deletions in Puerto Lempira, Honduras. Malaria journal. 14(1):19. Abstracts12936-014-0537-7.pdfWebsite

Background: Recent studies have demonstrated the deletion of the histidine-rich protein 2 (PfHRP2) gene (pfhrp2)
in field isolates of Plasmodium falciparum, which could result in false negative test results when PfHRP2-based rapid
diagnostic tests (RDTs) are used for malaria diagnosis. Although primary diagnosis of malaria in Honduras is
determined based on microscopy, RDTs may be useful in remote areas. In this study, it was investigated whether
there are deletions of the pfhrp2, pfhrp3 and their respective flanking genes in 68 P. falciparum parasite isolates
collected from the city of Puerto Lempira, Honduras. In addition, further investigation considered the possible
correlation between parasite population structure and the distribution of these gene deletions by genotyping
seven neutral microsatellites.
Methods: Sixty-eight samples used in this study, which were obtained from a previous chloroquine efficacy
study, were utilized in the analysis. All samples were genotyped for pfhrp2, pfhrp3 and flanking genes by PCR.
The samples were then genotyped for seven neutral microsatellites in order to determine the parasite
population structure in Puerto Lempira at the time of sample collection.
Results: It was found that all samples were positive for pfhrp2 and its flanking genes on chromosome 8.
However, only 50% of the samples were positive for pfhrp3 and its neighboring genes while the rest were either
pfhrp3-negative only or had deleted a combination of pfhrp3 and its neighbouring genes on chromosome 13.
Population structure analysis predicted that there are at least two distinct parasite population clusters in this
sample population. It was also determined that a greater proportion of parasites with pfhrp3-(and flanking gene)
deletions belonged to one cluster compared to the other.
Conclusion: The findings indicate that the P. falciparum parasite population in the municipality of Puerto Lempira
maintains the pfhrp2 gene and that PfHRP2-based RDTs could be considered for use in this region; however continued
monitoring of parasite population will be useful to detect any parasites with deletions of pfhrp2.
Keywords: Plasmodium falciparum, Histidine-rich protein, Rapid diagnostic tests, Microsatellites, Honduras

Okoth, S.  2015.  In vitro and molecular surveillance for antimalarial drug resistance in Plasmodium falciparum parasites in Western Kenya reveals sustained artemisinin sensitivity and increased chloroquine sensitivity. Antimicrobial agents and chemotherapy. 59(12):7540-7547. AbstractWebsite

Malaria control is hindered by the evolution and spread of resistance to antimalarials, necessitating multiple changes to drug
policies over time. A comprehensive antimalarial drug resistance surveillance program is vital for detecting the potential emergence
of resistance to antimalarials, including current artemisinin-based combination therapies. An antimalarial drug resistance
surveillance study involving 203 Plasmodium falciparum malaria-positive children was conducted in western Kenya between
2010 and 2013. Specimens from enrolled children were analyzed in vitro for sensitivity to chloroquine (CQ), amodiaquine (AQ),
mefloquine (MQ), lumefantrine, and artemisinin derivatives (artesunate and dihydroartemisinin) and for drug resistance allele
polymorphisms in P. falciparum crt (Pfcrt), Pfmdr-1, and the K13 propeller domain (K13). We observed a significant increase in
the proportion of samples with the Pfcrt wild-type (CVMNK) genotype, from 61.2% in 2010 to 93.0% in 2013 (P<0.0001), and
higher proportions of parasites with elevated sensitivity to CQ in vitro. The majority of isolates harbored the wild-type N allele
in Pfmdr-1 codon 86 (93.5%), with only 7 (3.50%) samples with the N86Y mutant allele (the mutant nucleotide is underlined).
Likewise, most isolates harbored the wild-type Pfmdr-1 D1246 allele (79.8%), with only 12 (6.38%) specimens with the D1246Y
mutant allele and 26 (13.8%) with mixed alleles. All the samples had a single copy of the Pfmdr-1 gene (mean of 0.9070.141
copies). None of the sequenced parasites had mutations in K13. Our results suggest that artemisinin is likely to remain highly
efficacious and that CQ sensitivity appears to be on the rise in western Kenya.

Okoth, S.  2015.  Clonal population expansion in an outbreak of Plasmodium falciparum on the northwest coast of Ecuador. Malaria journal. 14(1):497. Abstracts12936-015-1019-2.pdfWebsite

Abstract
Background: Determining the source of malaria outbreaks in Ecuador and identifying remaining transmission
foci will help in malaria elimination efforts. In this study, the genetic signatures of Plasmodium falciparum isolates,
obtained from an outbreak that occurred in northwest Ecuador from 2012 to 2013, were characterized.
Methods: Molecular investigation of the outbreak was performed using neutral microsatellites, drug resistance markers
and pfhrp2 and pfhrp3 genotyping.
Results: A majority of parasite isolates (31/32) from this outbreak were of a single clonal type that matched a clonal
lineage previously described on the northern coast of Peru and a historical isolate from Ecuador. All but one isolate
carried a chloroquine-resistant pfcrt genotype and sulfadoxine- and pyrimethamine-sensitive pfdhps and pfdhfr genotypes.
Pfmdr1 mutations were identified in codons 184 and 1042. In addition, most samples (97 %) showed presence
of pfhrp2 gene.
Conclusions: This study indicates that parasites from a single clonal lineage largely contributed to this outbreak and
this lineage was found to be genetically related to a lineage previously reported in the Peruvian coast and historical
Ecuadorian parasites.
Keywords: Plasmodium falciparum, Malaria, Ecuador, Outbreak, Microsatellite markers

Okoth, S.  2015.  Independent emergence of the Plasmodium falciparum kelch propeller domain mutant allele C580Y in Guyana. The Journal of infectious diseases. 213(9):1472-1475. Abstractjiv752.pdfWebsite

Suspected artemisinin resistance in Plasmodium falciparum can be explored by examining polymorphisms in the Kelch (PfK13) propeller domain. Sequencing of PfK13 and other gene resistance markers was performed on 98 samples from Guyana. Five of these samples carried the C580Y allele in the PfK13 propeller domain, with flanking microsatellite profiles different from those observed in Southeast Asia. These molecular data demonstrate independent emergence of the C580Y K13 mutant allele in Guyana, where resistance alleles to previously used drugs are fixed. Therefore, in Guyana and neighboring countries, continued molecular surveillance and periodic assessment of the therapeutic efficacy of artemisinin-based combination therapy are warranted.

2014

Okoth, S.  2014.  Influence of soil fertility amendment practices on ex-situ utilisation of indigenous arbuscular mycorrhizal fungi and performance of maize and common bean in Kenyan highlands. Tropical and Subtropical Agroecosystems. 17:129-141. AbstractWebsite

Arbuscular Mycorrhizal Fungi (AMF) are important
in agriculture and have received attention as they are
considered a part of an active and diverse soil
biological community essential for increasing the
sustainability of agricultural systems. However, most
of agricultural practices have a negative impact on
AMF association and agricultural soils are AMF
impoverished. Interventions to replenish AMF
include re-introduction through inoculation or
manipulation of existing AMF to increase density. A
major problem with inoculation is that there is
possible competition with native (indigenous) AMF
species. Indigenous AMF will be more adapted to the
soil environment than introduced strains but with
conflicting results on the effects of AMF inoculation
on crop yield, more field studies for different
ecological areas are required. The objective of the
study was to compare the effect of inoculating crops
with indigenous AMF applied applied singly or
combined with other Soil Fertility Amendment
Practices (SFAP) on root colonisation and subsequent
performance of maize (Zea mays L.) and common
bean (Phaseolus vulgaris L.). Analysis was also done
on the best soil amendment practice that encourages
crop colonisation by AMF. This was tested under
field experiment and compared with control treatment
(no soil amendment practice) and three other soil
fertility amendment practices used singly or in
combination with AMF; (1) MAVUNO (macro- and
micronutrients and secondary nutrients) fertilizer, and
(2) Calcium Ammonium Nitrate (CAN) and Triple
Super Phosphate (TSP) (3) cattle manure. Maize and
bean performances were determined and compared
between the treatments for a period of two
consecutive seasons with the experiment replicated in
two benchmark sites of Embu district (highlands of
central Kenya) and Taita-Taveta district (coastal
highlands). Soils at Embu have high soil pH than at
Taita which results in low phosphorus levels and
possible micronutrients deficiencies. Even though no
significant differences were observed from root
colonisation by AMF with application of SFAP,
significant differences were observed at the crop
yield. Bean crop was more responsive to AMF
inoculation than maize in terms of yield. Combination
of AMF inoculant with other organic and inorganic
fertilizers resulted in higher crop yield compared to
AMF applied singly. Thus, utilisation of indigenous
AMF species has potential to constitute an
environmentally friendly method of soil fertility
amendment over time to improve maize and bean
production potential of small-scale holders but
consideration should be done on the local soil
nutrients conditions, other soil fertility amendment
practices in use and the targeted crop.
Keywords: Arbuscular Mycorrhizae Fungi; Soil
fertility amendment practices; indigenous species;
inoculation; crop yield; colonisation intensity.

Okoth, S.  2014.  Conservation and Sustainable Management of Soil Biodiversity for Agricultural Productivity. Sustainable Living with Environmental Risks. : Springer Link Abstract

Soil biodiversity represents the variety of life belowground whose interaction with plants and small animals forms a web of biological activity. It improves the entry and storage of water, resistance to soil erosion, and plant nutrition, while also controlling soil pests and disease, and facilitating recycling of organic matter in the soil. Soil biodiversity is therefore the driver of healthy soil for sustainable crop production.

However, intensive agricultural activities are reported to lead to loss of soil biodiversity. This has been attributed to environmental degradation, and consequently to climate change. This paper highlights the importance of soil biodiversity and some factors associated with its loss, and presents a case study on selected soil organisms in Kenya. Results from this study indicated that land use changes affect soil biodiversity, and soil biodiversity determines the distribution of the aboveground biodiversity.

Keywords

Biological control Crop productivity Soil biodiversity Soil health Sustainable utilization of soil

Okoth, S.  2014.  Compatibility of Rhizobium inoculant and water hyacinth compost formulations in Rosecoco bean and consequences on Aphis fabae and Colletotrichum lindemuthianum infestations.. Applied Soil Ecology. 76:68–77. AbstractWebsite

The common bean, Phaseolus vulgaris is an important crop for food security and nitrogen fixation through Rhizobium symbiosis. Commercial Rhizobium inoculants are being promoted to fix nitrogen and enhance bean production in the Lake Victoria basin. Rhizobium symbiosis depends on nutrients, especially phosphorus, which is widely applied as diammonium phosphate (DAP) in the Lake Victoria basin. Water hyacinth, Eichornia crassipes (Mart.) Solms-Laubach (Pontederiaceae) is being developed into compost, with perceived benefits of improving crop production and limiting its disastrous spread in Lake Victoria. High nutrient content in water hyacinth compost can stimulate Rhizobium nodulation and nitrogen fixation, consequently improving plant growth and pest resistance. However, it is not yet established whether Rhizobium inoculants and water hyacinth composts are compatible options for plant growth promotion and pest suppression in beans. A field experiment with two trials was conducted to assess the compatibility of commercial Rhizobium inoculant, DAP, cattle farmyard manure (FYM), and four formulations of water hyacinth compost i.e., water hyacinth only (H), with molasses (H+Mol), cattle manure culture (H+CMC) or effective microbes (H+EM). Rhizobium inoculated plants had high number of root nodules when grown with H+CMC and H+EM. Plants were large in size with short development period when grown with the composts, especially H+CMC and H+EM. Those grown with H+EM produced high number of flowers. Rhizobium inoculated plants had high anthracnose incidence than non-inoculated ones when grown with H+CMC. Those grown with H+EM had low anthracnose incidence, but was high in FYM. During flowering, Rhizobium inoculated plants had higher Aphis fabae population than non-inoculated ones when grown in FYM or without fertilizer. Those grown with H+EM had the lowest A. fabae population. Yields in water hyacinth compost were improved, especially for H+CMC in the second trial. DAP treated plants had more flowers and pods having heavy seeds, with low anthracnose and A. fabae infestations; but had low germination rates that reduced the yields. In conclusion, the commercial Rhizobium inoculant is predominantly compatible with water hyacinth compost formulations containing effective microbes and cattle manure culture, which could enhance tolerance of bean plants to aphids and possibly to anthracnose disease. These two water hyacinth compost formulations need further investigation for their potential in enhancing food production and alleviating the water hyacinth problem in the Lake Victoria basin.

Okoth, S.  2014.  Effects of Soil Chemical Characteristics on the Occurrence of Entomopathogenic Nematodes. British Journal of Applied Science & Technology. 4(16):2333-2343. AbstractWebsite

This study was conducted to determine the effect of selected soil chemical characteristics on the occurrence of entomopathogenic nematodes (EPNs) under different land uses in Embu and Taita Districts in Kenya.
Study Design: The sampling points were systematically marked in a grid-mesh construction using GPS marking.
Place and Duration of Study: Soil sampling was done between January 2008 and May 2008 in Embu district in the highlands of Central and Taita-Taveta district in the Coastal highlands of Kenya.
Methodology: EPNs were baited from soil using Galleria mellonella larvae and infective juveniles identified using morphological- biometric characteristics. The nematode occurrence was evaluated through relative abundance and recovery frequency expressed as percentage from the soils.
Results: EPNs were detected in 43.3% of the samples with Steinernema spp being the dominant species. The occurrence of EPNs is affected by selected soil chemical properties, land use systems and heavy metals.
Conclusion: Soil fertility management practices and heavy metals influence the occurrence of EPNs and should be considered for their effective use as biological control agents.

Okoth, S.  2014.  Effect of Land Use on Abundance and Diversity of Nematode Destroying Fungi and Soil Nematodes in Embu County, Kenya. Journal of Agricultural Science. 6(5):132. Abstract33586-122272-2-pb.pdfWebsite

Belowground biodiversity is one of the key indicators of the sustainability of a land use. This study sought to document the occurrence and diversity of nematode destroying fungi in an area characterized by small scale agriculture in Embu County, Kenya. The study area was divided into six main land use types namely; coffee, fallow, forest, maize/bean intercrop, napier and tea. Nematode destroying fungi were extracted from five soil samples from each of the land uses. A total of 161 isolates of nematode destroying fungi belonging to nine genera and 19 species were isolated and identified. The genera represented were Arthrobotrys, Dactyllela, Dactylaria, Harposporium, Monacrosporium, Myzocytium, Nematoctonous, Paecilomyces and Stylophage. The occurrence of nematode destroying fungi was significantly (P=0.02519) affected by the land use types in the study area. With the exception of Arthrobotrys superb, Dactyllela haptospora, Dactyllela reticulate, Harposporium anguillulae and Monacrosporium ellipsoporum all the other 19 isolated species were not affected by land use types. The highest total mean occurrence of nematode destroying fungi was recorded in maize/bean, followed by nappier, coffee, forest, fallow and tea , in that order. The respective frequency of detection of the fungal species was 7.6, 7.2, 5.0, 4.0 and 3.6. The Shannon index of diversity was highest and lowest at 1.971and 1.177 in the land under maize/bean intercrop and tea, respectively. The species richness was higher in napier, followed by maize bean, coffee, forest and least in tea. Out of the fungi that were isolated, the highest proportion of 23% was from the maize/bean intercrop, while the least 11% was from land under ea. Arthrobotrys oligospora was the most frequently isolated species with a frequency of 24% while Nematoctonus pachysporus had the least frequency of occurrence of 1%. It can be concluded that land use influences the diversity of nematode destroying fungi and nematodes in the soil. More work is needed to determine the efficacy of these indigenous isolates on plant parasitic nematodes.

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