The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

BACKGROUND

Anopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. The current study sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well as describe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzii populations.

METHODS

Mosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing (WGS) data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS. Comparisons were made with An. coluzzii cohorts from West and Central Africa.

RESULTS

This study reports the detection of An. coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points from which samples were analyzed and its presence confirmed through taxonomic analysis. Additionally, there was a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies up to 64%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.

CONCLUSIONS

These findings emphasize the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

The Anopheles coluzzii range extends into Kenya: Detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

Background

Anopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. In the current study, we sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well asdescribe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzi populations.

Methods

Mosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS.

Results

This study reports the detection of Anopheles coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points sampled and its presence confirmed through taxonomic analysis. Additionally, we found a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies of ~60%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.

Conclusions

These findings emphasise the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

Comparison of quantitative polymerase chain reaction, Kato-Katz and circulating cathodic antigen rapid test for the diagnosis of Schistosoma mansoni infection: A cross-sectional study in Kirinyaga County, Kenya

The current standard diagnostic tests for Schistosoma mansoni are the Kato-Katz and circulating cathodic antigen (CCA) techniques. However, these techniques have been documented to have several limitations that have a direct impact on schistosomiasis control programmes. Therefore, there is a need for more sensitive and specific tests for diagnosing schistosomiasis. This study compared the performance of quantitative polymerase chain reaction (qPCR), Kato-Katz, and point-of-care circulating cathodic antigen (POC-CCA) techniques in the diagnosis of S. mansoni infection in the Mwea irrigation scheme, Kirinyaga County in Central Kenya. We carried out a cross-sectional study on 357 individuals residing in four villages in the Mwea irrigation scheme. The participants provided urine and stool samples which were screened for S. mansoni infections using the three techniques. The prevalence of S. mansoni by each technique was calculated and 95% confidence intervals estimated using binomial regression model. Sensitivity and specificity were determined using 2 × 2 contingency tables and compared using the McNemar’s chi-square test. Positive and negative predictive values were also determined using the weighted generalized score chi-square test for paired data. The study showed that the prevalence of S. mansoni was 32.8%, 62.5% and 72.8% using Kato-Katz, POC-CCA and qPCR techniques, respectively. Further, when using Kato-Katz as a gold standard, POC-CCA sensitivity was 78.6% and specificity was 45.4%, while qPCR sensitivity was 97.4% and specificity was 39.2%. When using qPCR as the gold standard, Kato-Katz sensitivity was 43.8% and specificity was 96.9%, while POC-CCA sensitivity was 78.1% and specificity was 79.4%. Finally, when using the averaged results from the three techniques as the gold standard, the sensitivity was 41.6%, 79.4% and 92.5% for Kato-Katz, POC-CCA and qPCR, respectively, with a specificity of 100% for all techniques. Kato-Katz technique showed low sensitivity compared to the POC-CCA and qPCR despite it being the most commonly preferred method of choice to diagnose S. mansoni infections. qPCR showed superior sensitivity followed by POC-CCA, hence it can be used as an alternative or to confirm the results obtained by the Kato-Katz technique.

•

Comparison of the performance of Kato-Katz, POC-CCA and qPCR for diagnosis of S. mansoni in Kirinyaga County, Kenya.

•

A total of 357 urine and stool samples were tested for S. mansoni infection.

•

qPCR estimated the highest prevalence followed by POC-CCA and Kato-Katz.

•

qPCR showed a generally high sensitivity and specificity.

Improved Sample Selection and Preparation Methods for Sampling Plans Used to Facilitate Rapid and Reliable Estimation of Aflatoxin in Chicken Feed

Aflatoxin B1 (AFB1), a toxic fungal metabolite associated with human and animal diseases, is a natural contaminant encountered in agricultural commodities, food and feed. Heterogeneity of AFB1 makes risk estimation a challenge. To overcome this, novel sample selection, preparation and extraction steps were designed for representative sampling of chicken feed. Accuracy, precision, limits of detection and quantification, linearity, robustness and ruggedness were used as performance criteria to validate this modification and Horwitz function for evaluating precision. A modified sampling protocol that ensured representativeness is documented, including sample selection, sampling tools, random procedures, minimum size of field-collected aggregate samples (primary sampling), procedures for mass reduction to 2 kg laboratory (secondary sampling), 25 g test portion (tertiary sampling) and 1.3 g analytical samples (quaternary sampling). The improved coning and quartering procedure described herein (for secondary and tertiary sampling) has acceptable precision, with a Horwitz ratio (HorRat = 0.3) suitable for splitting of 25 g feed aliquots from laboratory samples (tertiary sampling). The water slurring innovation (quaternary sampling) increased aflatoxin extraction efficiency to 95.1% through reduction of both bias (-4.95) and variability of recovery (1.2-1.4) and improved both intra-laboratory precision (HorRat = 1.2-1.5) and within-laboratory reproducibility (HorRat = 0.9-1.3). Optimal extraction conditions are documented. The improved procedure showed satisfactory performance, good field applicability and reduced sample analysis turnaround time.

UV Resistance of bacteria from the Kenyan Marine cyanobacterium Moorea producens

UV resistance of bacteria isolated from the marine cyanobacterium Moorea producens has not been observed previously, findings which highlight how unsafe germicidal UV irradiation for sterilization of air, food, and water could be. Further, UV resistance of Bacillus licheniformis is being observed for the first time. This study focused on bacteria isolated from the marine cyanobacterium M. producens collected off the Kenyan coast at Shimoni, Wasini, Kilifi, and Mida. UV irradiance of isolates (302 nm, 70 W/m2 , 0-1 hr) established B. licheniformis as the most UV resistant strain, with the following order of taxon resistance: Bacilli> γ proteobacteria > Actinobacteria. UV resistance was independent of pigmentation. The maximum likelihood phylogenetic distance determined for both B. licheniformis and Bacillus aerius relative to M. producens CCAP 1446/4 was 2.0. Survival of B. licheniformis upon UV irradiance followed first-order kinetics (k = 0.035/min, R2  = 0.88). Addition of aqueous extracts (2, 10, 20 and 40 mg/ml) of this B. licheniformis strain on the less resistant Marinobacterium stanieri was not significant, however, the commercial sunscreen benzophenone-3 (BP-3) positive control and the time of irradiance were significant. Detection of bacteria on M. producens filaments stained with acridine orange confirmed its nonaxenic nature. Although the chemistry of UV resistance in cyanobacteria has been studied in depth revealing for example the role of mycosporine like amino acids (MAAs) in UV resistance less is known about how bacteria resist UV irradiation. This is of interest since cyanobacteria live in association with bacteria.

Molecular detection and phylogenetic analysis of Kenyan human bocavirus isolates

Introduction: The commonly expected causative agents associated with flu-like symptoms in Kenya are the classical viral pathogens identifiable as influenza virus, adenovirus, parainfluenza virus, enteroviruses, respiratory syncytial virus (RSV) and rhinovirus. However, newer agents have been identified globally that present with illnesses clinically indistinguishable from those caused by the classical pathogens; one of them is human bocavirus. Methodology: A total of 384 specimens were analyzed, primarily to determine if the emerging human bocavirus (HBoV) infections exist in Kenya as coinfections with other respiratory viruses and to describe the genotype of the virus in circulation. In brief, viral nucleic acids were extracted from culture supernatants, amplified by PCR, and sequenced. Results: HBoV DNA was amplified from 1.8% of screened specimens. Coinfection with parainfluenza virus, adenovirus, and enterovirus was 2.5%, 2%, and 1.4%, respectively. Multiple coinfections consisting of HBoV plus two other viruses were found in 3% of specimens. Isolation occurred in the months of January, March, April, August, and November. Retrospective review of clinical parameters indicated that all the individuals complained of non-specific symptoms, mainly fever, coughs, nasal stuffiness, runny noses, and vomiting. Phylogenetically, the GenBank deposited sequences of this study’s isolates cluster closely to the reference strain NC_07455 (HBoV1). Conclusion: Coinfections with human bocavirus (HBoV1) occur in Kenya, and high incidence might primarily be during the early stages of children’s lives.

Linkage disequilibrium between alleles at highly polymorphic mini- and micro-satellite loci of Theileria parva isolated from cattle in three regions of Kenya

Theileria parva schizont-infected lymphocyte culture isolates from western, central and coastal Kenya were analysed for size polymorphism at 30 T. parva-specific variable number tandem repeat (VNTR) loci using a panel of mini- and micro-satellite markers. The mean number of alleles ranged from 3 to 11 at individual loci and 183 distinct alleles were observed in total, indicating high genetic diversity within the T. parva gene pool in Kenyan cattle. The frequency distribution of the length variation of specific alleles among isolates ranged from normal to markedly discontinuous. Genetic relationships between isolates were analysed using standard indices of genetic distance. Genetic distances and dendrograms derived from these using neighbour-joining algorithms did not indicate significant clustering on a geographical basis. Analysis of molecular variance demonstrated that the genetic variation between individual isolates was 72%, but only 2.3% when isolates from different regions were pooled. Both these observations suggest minimal genetic sub-structuring relative to geographical origin. Linkage disequilibrium was observed between pairs of loci within populations, as in certain Ugandan T. parva populations. A novel observation was that disequilibrium was also detected between alleles at three individual pairs of VNTR loci when isolates from the three regional meta-populations were pooled for analysis.