Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the... more Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf 4.1 sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand. Positively significant departures from neutral expectations were detected on the surf 4.1 region encoding C-terminus of the variable region 2 (Var2) by 3 population-based tests in the western Kenyan population as similar in the Thai population, which was not covered by the previous analysis for eastern Kenyan population. Significant excess of non-synonymous substitutions per nonsynonymous site over synonymous substitutions per synonymous site was also detected in the Var2 region. Negatively si...
Characterising the genomic variation and population dynamics of Plasmodium falciparum parasites i... more Characterising the genomic variation and population dynamics of Plasmodium falciparum parasites in high transmission regions of Sub-Saharan Africa is crucial to the long-term efficacy of regional malaria elimination campaigns and eradication. Whole-genome sequencing (WGS) technologies can contribute towards understanding the epidemiology and structural variation landscape of P. falciparum populations, including those within the Lake Victoria basin, a region of intense transmission. Here we provide a baseline assessment of the genomic diversity of P. falciparum isolates in the Lake region of Kenya, which has sparse genetic data. Lake region isolates are placed within the context of African-wide populations using Illumina WGS data and population genomic analyses. Our analysis revealed that P. falciparum isolates from Lake Victoria form a cluster within the East African parasite population. These isolates also appear to have distinct ancestral origins, containing genome-wide signatures...
Background In Plasmodium falciparum infection, clinical conditions such as anaemia, thrombocytope... more Background In Plasmodium falciparum infection, clinical conditions such as anaemia, thrombocytopenia and leukocytosis are common. Mutation in haemoglobin sub-unit beta gene (HBB) may be a genetic factor responsible for these haematological changes during infection. However, the contributions of the carriage of different HBB genotypes on these changes remain largely unknown. Methodology In this cross-sectional study, we evaluated haematological abnormalities in P. falciparum-infected children (n = 217, aged 1–192 months) with different haemoglobin sub-unit beta (HBB) genotypes (HbAA, HbAS and HbSS). Children with acute febrile conditions were recruited at Jaramogi Oginga Odinga Teaching and Referral Hospital at the outpatient clinic. Haematological parameters were determined using Beckman Coulter counter ACTdiff2™ while HBB genotyping was done using TaqMan® SNP genotyping assay. Chi-square (χ2) was used to determine differences between proportions. Differences in haematological param...
ABSTRACTBackgroundUnderstanding the perceptions of quality of care given to sick young infants in... more ABSTRACTBackgroundUnderstanding the perceptions of quality of care given to sick young infants in primary health care settings is key for developing strategies for effective uptake and utilization of PSBI guidelines. The purpose of this study is to assess families’ and providers’ perceptions of care given to sick young infants at primary healthcare facilities in four diverse counties in Kenya.MethodsA cross-sectional qualitative design involving in-depth interviews (23) and focus group discussions (25) with very young (15-18 years), young (19-24 years) and older (25-45 years) caregivers of young infants 0-59 days; and key informant interviews with community- and facility-based frontline health providers (14) in primary health care facilities. Qualitative data were captured using audio tapes and field notes, transcribed, translated, and exported into QSR NVivo 12 for analysis. A thematic framework approach was adopted to classify and analyze data.ResultsPerceived care given to SYIs w...
Background Antimicrobial resistance is a significant public health concern with the establishment... more Background Antimicrobial resistance is a significant public health concern with the establishment of antimicrobial stewardship in hospitals being increasingly obligatory. Perspectives and insights of health managers on antimicrobial stewardship (AMS), complementary health services and building blocks are imperative towards implementation of robust AMS programs. This study aimed to understand perspectives of hospital managers on AMS and identify areas of management engagement while addressing potential blockades to change. Methods A cross-sectional, qualitative, multicenter study was conducted in three hospitals in Kenya. Key-informant interviews on perspectives on AMS were administered to hospital managers. Qualitative data was captured using audio tapes and field notes, transcribed and managed using NVivo 12 software. An iterative process was used to develop the thematic framework and updated in two rounds of iteration analysis. Analysis charts for each emergent theme were develope...
IntroductionAntimicrobial resistance (AMR) is a growing problem globally especially in Sub-Sahara... more IntroductionAntimicrobial resistance (AMR) is a growing problem globally especially in Sub-Saharan Africa including Kenya. Without any intervention, lower/middle-income countries (LMICs) will be most affected due to already higher AMR levels compared with higher income countries and due to the far higher burden of diseases in the LMICs. Studies have consistently shown that inappropriate use of antimicrobials is the major driver of AMR. To address this challenge, hospitals are now implementing antibiotic stewardship programmes (ASPs), which have been shown to achieve reduced antibiotic usage, to decrease the prevalence of resistance and lead to significant economic benefits. However, the implementation of the guideline is highly dependent on the settings in which they are rolled out. This study, employing an implementation science approach, aims to address the knowledge gap in this area and provide critical data as well as practical experiences when using antibiotic guidelines and st...
Background: Sickle cell disease (SCD) is a monogenic disorder due to point mutation in the β-glob... more Background: Sickle cell disease (SCD) is a monogenic disorder due to point mutation in the β-globin gene resulting in substitution of Valine for Glutamic acid. The SCD is prevalent in P. falciparum endemic regions such as western Kenya. Carriage of different sickle cell genotypes may influence haematological parameter during malaria. Children resident in malaria holoendemic regions suffer more from malaria-related complications and this is moderated by the presence of the SCD. In the current study, we determined the association between sickle cell genotypes and haematological parameters in children with P. falciparum malaria resident in Kisumu County in Western Kenya.Methodology: Children (n=217, aged 1-192 months) with acute febrile condition were recruited at Jaramogi Oginga Odinga Teaching and Referral Hospital. Chi-square (2) analysis was used to determine differences between proportions. Differences in haematological parameters were compared across groups using Kruskal Wallis ...
Background: COVID-19 continues to wreak havoc in different countries across the world, claiming t... more Background: COVID-19 continues to wreak havoc in different countries across the world, claiming thousands of lives, increasing morbidity and disrupting lifestyles. The global scientific community is in urgent need of relevant evidence, to understand the challenges and knowledge gaps, as well as the opportunities to contain the spread of the virus. Considering the unique socio-economic, demographic, political, ecological and climatic contexts in Africa, the responses which may prove to be successful in other regions may not be appropriate on the continent. This paper aims to provide insight for scientists, policy makers and international agencies to contain the virus and to mitigate its impact at all levels. Methods: The Affiliates of the African Academy of Sciences (AAS), came together to synthesize the current evidence, identify the challenges and opportunities to enhance the understanding of the disease. We assess the potential impact of this pandemic and the unique challenges of ...
Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19)... more Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19) has rapidly spread worldwide, achieving pandemic status on 11th March, 2020. As of 1st April 2020, COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had infected over 800,000 people and caused over 40,000 deaths in 205 countries and territories. COVID-19 has had its heaviest toll on Europe, United States and China. As of 1st of April 2020, the number of confirmed COVID-19 cases in Africa was relatively low, with the highest number registered by South Africa, which had reported 1,380 confirmed cases. On the same date (also the date of this review), Africa had reported 5,999 confirmed cases, of which 3,838 (almost 65%) occurred in South Africa, Algeria, Egypt, Morocco and Tunisia, with the remaining 2,071 cases distributed unevenly across the other African countries. We speculate that while African nations are currently experiencing much lower rate...
Background: It is projected that by 2030, 70% of all cancer related deaths will occur in low-midd... more Background: It is projected that by 2030, 70% of all cancer related deaths will occur in low-middle income countries. However, data on the state of cancer in most African countries is scanty. Cancer estimates for Kenya are based on the Nairobi and Eldoret cancer registries, leaving most parts of the country unrepresented. Lacking national coverage, these data do not accurately reflect Kenya’s cancer burden. The paucity of reliable data impedes formulation of effective cancer control strategies and cancer research prioritization. Here, we report the findings of a retrospective study of the cancer state in Meru County, Kenya. Methods: A retrospective analysis of patient files at Meru hospice was carried out. 2349 cancer cases seen at the Meru hospice between 2003 and 2018 were analyzed. Data abstracted from the records included patient age, gender and cancer type. The abstracted data was analyzed by descriptive statistics. Results: Our results indicate that cancer is almost evenly dis...
We report the rapid detection (20 min) of Streptococcus agalactiae, Group B Streptococcus (GBS) e... more We report the rapid detection (20 min) of Streptococcus agalactiae, Group B Streptococcus (GBS) employing on-chip magnetic isolation of GBS based on immiscible filtration assisted by surface tension (IFAST), followed...
Background: The burden of malaria, schistosomiasis and soil transmitted helminthes (STH) in the i... more Background: The burden of malaria, schistosomiasis and soil transmitted helminthes (STH) in the islands of Lake Victoria, Kenya, poses a considerable public health challenge. Although many studies have been conducted on the co-infection arising from these parasites, few have evaluated communities’ knowledge of the same. Increasing the level of knowledge about a disease or preventive chemotherapy is important, but efforts need to be focused on community perception and understanding of the problem so as to encourage engagement with the proposed control measures. This study aimed at understanding a community’s knowledge of malaria, schistosomiasis and STH in Lake Victoria island where an integrated preventive chemotherapy intervention was implemented. Methods: This study was conducted in Ngodhe Island in Lake Victoria in Homa Bay County, western Kenya region between April and May 2016. The study adopted a mixed method approach where both qualitative and quantitative data collection was...
A correction to this article has been published and is linked from the HTML and PDF versions of t... more A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Plasmodium was first identified in a goat in Angola in 1923, and only recently characterized by D... more Plasmodium was first identified in a goat in Angola in 1923, and only recently characterized by DNA isolation from a goat blood sample in Zambia. Goats were first domesticated in the Fertile Crescent approximately 10,000 years ago, and are now globally distributed. It is not known if the Plasmodium identified in African goats originated from parasites circulating in the local ungulates, or if it co-evolved in the goat before its domestication. To address this question, we performed PCR-based surveillance using a total of 1,299 goat blood samples collected from Sudan and Kenya in Africa, Iran in west Asia, and Myanmar and Thailand in southeast Asia. Plasmodium DNA was detected from all locations, suggesting that the parasite is not limited to Africa, but widely distributed. Whole mitochondrial DNA sequences revealed that there was only one nucleotide substitution between Zambian/Kenyan samples and others, supporting the existence of a goat-specific Plasmodium species, presumably Plas...
Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the... more Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf 4.1 sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand. Positively significant departures from neutral expectations were detected on the surf 4.1 region encoding C-terminus of the variable region 2 (Var2) by 3 population-based tests in the western Kenyan population as similar in the Thai population, which was not covered by the previous analysis for eastern Kenyan population. Significant excess of non-synonymous substitutions per nonsynonymous site over synonymous substitutions per synonymous site was also detected in the Var2 region. Negatively si...
Characterising the genomic variation and population dynamics of Plasmodium falciparum parasites i... more Characterising the genomic variation and population dynamics of Plasmodium falciparum parasites in high transmission regions of Sub-Saharan Africa is crucial to the long-term efficacy of regional malaria elimination campaigns and eradication. Whole-genome sequencing (WGS) technologies can contribute towards understanding the epidemiology and structural variation landscape of P. falciparum populations, including those within the Lake Victoria basin, a region of intense transmission. Here we provide a baseline assessment of the genomic diversity of P. falciparum isolates in the Lake region of Kenya, which has sparse genetic data. Lake region isolates are placed within the context of African-wide populations using Illumina WGS data and population genomic analyses. Our analysis revealed that P. falciparum isolates from Lake Victoria form a cluster within the East African parasite population. These isolates also appear to have distinct ancestral origins, containing genome-wide signatures...
Background In Plasmodium falciparum infection, clinical conditions such as anaemia, thrombocytope... more Background In Plasmodium falciparum infection, clinical conditions such as anaemia, thrombocytopenia and leukocytosis are common. Mutation in haemoglobin sub-unit beta gene (HBB) may be a genetic factor responsible for these haematological changes during infection. However, the contributions of the carriage of different HBB genotypes on these changes remain largely unknown. Methodology In this cross-sectional study, we evaluated haematological abnormalities in P. falciparum-infected children (n = 217, aged 1–192 months) with different haemoglobin sub-unit beta (HBB) genotypes (HbAA, HbAS and HbSS). Children with acute febrile conditions were recruited at Jaramogi Oginga Odinga Teaching and Referral Hospital at the outpatient clinic. Haematological parameters were determined using Beckman Coulter counter ACTdiff2™ while HBB genotyping was done using TaqMan® SNP genotyping assay. Chi-square (χ2) was used to determine differences between proportions. Differences in haematological param...
ABSTRACTBackgroundUnderstanding the perceptions of quality of care given to sick young infants in... more ABSTRACTBackgroundUnderstanding the perceptions of quality of care given to sick young infants in primary health care settings is key for developing strategies for effective uptake and utilization of PSBI guidelines. The purpose of this study is to assess families’ and providers’ perceptions of care given to sick young infants at primary healthcare facilities in four diverse counties in Kenya.MethodsA cross-sectional qualitative design involving in-depth interviews (23) and focus group discussions (25) with very young (15-18 years), young (19-24 years) and older (25-45 years) caregivers of young infants 0-59 days; and key informant interviews with community- and facility-based frontline health providers (14) in primary health care facilities. Qualitative data were captured using audio tapes and field notes, transcribed, translated, and exported into QSR NVivo 12 for analysis. A thematic framework approach was adopted to classify and analyze data.ResultsPerceived care given to SYIs w...
Background Antimicrobial resistance is a significant public health concern with the establishment... more Background Antimicrobial resistance is a significant public health concern with the establishment of antimicrobial stewardship in hospitals being increasingly obligatory. Perspectives and insights of health managers on antimicrobial stewardship (AMS), complementary health services and building blocks are imperative towards implementation of robust AMS programs. This study aimed to understand perspectives of hospital managers on AMS and identify areas of management engagement while addressing potential blockades to change. Methods A cross-sectional, qualitative, multicenter study was conducted in three hospitals in Kenya. Key-informant interviews on perspectives on AMS were administered to hospital managers. Qualitative data was captured using audio tapes and field notes, transcribed and managed using NVivo 12 software. An iterative process was used to develop the thematic framework and updated in two rounds of iteration analysis. Analysis charts for each emergent theme were develope...
IntroductionAntimicrobial resistance (AMR) is a growing problem globally especially in Sub-Sahara... more IntroductionAntimicrobial resistance (AMR) is a growing problem globally especially in Sub-Saharan Africa including Kenya. Without any intervention, lower/middle-income countries (LMICs) will be most affected due to already higher AMR levels compared with higher income countries and due to the far higher burden of diseases in the LMICs. Studies have consistently shown that inappropriate use of antimicrobials is the major driver of AMR. To address this challenge, hospitals are now implementing antibiotic stewardship programmes (ASPs), which have been shown to achieve reduced antibiotic usage, to decrease the prevalence of resistance and lead to significant economic benefits. However, the implementation of the guideline is highly dependent on the settings in which they are rolled out. This study, employing an implementation science approach, aims to address the knowledge gap in this area and provide critical data as well as practical experiences when using antibiotic guidelines and st...
Background: Sickle cell disease (SCD) is a monogenic disorder due to point mutation in the β-glob... more Background: Sickle cell disease (SCD) is a monogenic disorder due to point mutation in the β-globin gene resulting in substitution of Valine for Glutamic acid. The SCD is prevalent in P. falciparum endemic regions such as western Kenya. Carriage of different sickle cell genotypes may influence haematological parameter during malaria. Children resident in malaria holoendemic regions suffer more from malaria-related complications and this is moderated by the presence of the SCD. In the current study, we determined the association between sickle cell genotypes and haematological parameters in children with P. falciparum malaria resident in Kisumu County in Western Kenya.Methodology: Children (n=217, aged 1-192 months) with acute febrile condition were recruited at Jaramogi Oginga Odinga Teaching and Referral Hospital. Chi-square (2) analysis was used to determine differences between proportions. Differences in haematological parameters were compared across groups using Kruskal Wallis ...
Background: COVID-19 continues to wreak havoc in different countries across the world, claiming t... more Background: COVID-19 continues to wreak havoc in different countries across the world, claiming thousands of lives, increasing morbidity and disrupting lifestyles. The global scientific community is in urgent need of relevant evidence, to understand the challenges and knowledge gaps, as well as the opportunities to contain the spread of the virus. Considering the unique socio-economic, demographic, political, ecological and climatic contexts in Africa, the responses which may prove to be successful in other regions may not be appropriate on the continent. This paper aims to provide insight for scientists, policy makers and international agencies to contain the virus and to mitigate its impact at all levels. Methods: The Affiliates of the African Academy of Sciences (AAS), came together to synthesize the current evidence, identify the challenges and opportunities to enhance the understanding of the disease. We assess the potential impact of this pandemic and the unique challenges of ...
Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19)... more Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19) has rapidly spread worldwide, achieving pandemic status on 11th March, 2020. As of 1st April 2020, COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had infected over 800,000 people and caused over 40,000 deaths in 205 countries and territories. COVID-19 has had its heaviest toll on Europe, United States and China. As of 1st of April 2020, the number of confirmed COVID-19 cases in Africa was relatively low, with the highest number registered by South Africa, which had reported 1,380 confirmed cases. On the same date (also the date of this review), Africa had reported 5,999 confirmed cases, of which 3,838 (almost 65%) occurred in South Africa, Algeria, Egypt, Morocco and Tunisia, with the remaining 2,071 cases distributed unevenly across the other African countries. We speculate that while African nations are currently experiencing much lower rate...
Background: It is projected that by 2030, 70% of all cancer related deaths will occur in low-midd... more Background: It is projected that by 2030, 70% of all cancer related deaths will occur in low-middle income countries. However, data on the state of cancer in most African countries is scanty. Cancer estimates for Kenya are based on the Nairobi and Eldoret cancer registries, leaving most parts of the country unrepresented. Lacking national coverage, these data do not accurately reflect Kenya’s cancer burden. The paucity of reliable data impedes formulation of effective cancer control strategies and cancer research prioritization. Here, we report the findings of a retrospective study of the cancer state in Meru County, Kenya. Methods: A retrospective analysis of patient files at Meru hospice was carried out. 2349 cancer cases seen at the Meru hospice between 2003 and 2018 were analyzed. Data abstracted from the records included patient age, gender and cancer type. The abstracted data was analyzed by descriptive statistics. Results: Our results indicate that cancer is almost evenly dis...
We report the rapid detection (20 min) of Streptococcus agalactiae, Group B Streptococcus (GBS) e... more We report the rapid detection (20 min) of Streptococcus agalactiae, Group B Streptococcus (GBS) employing on-chip magnetic isolation of GBS based on immiscible filtration assisted by surface tension (IFAST), followed...
Background: The burden of malaria, schistosomiasis and soil transmitted helminthes (STH) in the i... more Background: The burden of malaria, schistosomiasis and soil transmitted helminthes (STH) in the islands of Lake Victoria, Kenya, poses a considerable public health challenge. Although many studies have been conducted on the co-infection arising from these parasites, few have evaluated communities’ knowledge of the same. Increasing the level of knowledge about a disease or preventive chemotherapy is important, but efforts need to be focused on community perception and understanding of the problem so as to encourage engagement with the proposed control measures. This study aimed at understanding a community’s knowledge of malaria, schistosomiasis and STH in Lake Victoria island where an integrated preventive chemotherapy intervention was implemented. Methods: This study was conducted in Ngodhe Island in Lake Victoria in Homa Bay County, western Kenya region between April and May 2016. The study adopted a mixed method approach where both qualitative and quantitative data collection was...
A correction to this article has been published and is linked from the HTML and PDF versions of t... more A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Plasmodium was first identified in a goat in Angola in 1923, and only recently characterized by D... more Plasmodium was first identified in a goat in Angola in 1923, and only recently characterized by DNA isolation from a goat blood sample in Zambia. Goats were first domesticated in the Fertile Crescent approximately 10,000 years ago, and are now globally distributed. It is not known if the Plasmodium identified in African goats originated from parasites circulating in the local ungulates, or if it co-evolved in the goat before its domestication. To address this question, we performed PCR-based surveillance using a total of 1,299 goat blood samples collected from Sudan and Kenya in Africa, Iran in west Asia, and Myanmar and Thailand in southeast Asia. Plasmodium DNA was detected from all locations, suggesting that the parasite is not limited to Africa, but widely distributed. Whole mitochondrial DNA sequences revealed that there was only one nucleotide substitution between Zambian/Kenyan samples and others, supporting the existence of a goat-specific Plasmodium species, presumably Plas...
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