AAS Open Research

Journal Information
EISSN : 25159321
Current Publisher: F1000 Research, Ltd. (10.12688)
Total articles ≅ 72
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Published: 10 October 2019
AAS Open Research; doi:10.12688/aasopenres

Lucy Wanjiku Macharia, Marianne Wanjiru Mureithi, Omu Anzala
Published: 3 October 2019
AAS Open Research, Volume 1; doi:10.12688/aasopenres.12910.4

Abstract:Background: Cancer in Africa is an emerging health problem. In Kenya it ranks third as a cause of death after infectious and cardiovascular diseases. Nearly 31% of the total cancer burden in sub-Saharan Africa is attributable to infectious agents. Information on cancer burden is scanty in Kenya and this study aimed to provide comprehensive hospital based data to inform policies. Method: A cross-sectional retrospective survey was conducted at Kenyatta National Hospital (KNH) and Moi Teaching and Referral Hospital (MTRH) from January 2008 to December 2012. Data was obtained from the patients files and the study was approved by the KNH/University of Nairobi and MTRH Ethics and Research Committees. Results: In KNH, the top five cancers were: cervical (62, 12.4%), breast (59, 11.8%), colorectal (31, 6.2%), chronic leukemia (27, 5.4%) and stomach cancer 26 (5.2%). Some 154 (30.8%) of these cancers were associated with infectious agents, while an estimated 138 (27.6%) were attributable to infections. Cancers of the cervix (62, 12.4%), stomach (26, 5.2%) and nasopharynx (17, 3.4%) were the commonest infection-associated cancers. In MTRH, the five common types of cancers were Kaposi’s sarcoma (93, 18.6%), breast (77, 15.4%), cervical (41, 8.2%), non-Hodgkin’s lymphoma (37, 7.4%) and colorectal, chronic leukemia and esophageal cancer all with 27 (5.4%). Some 241 (48.2%) of these cancers were associated with infectious agents, while an estimated 222 (44.4%) were attributable to infections. Kaposi’s sarcoma (93, 18.6%), cancer of the cervix (41, 8.2%) and non-Hodgkin’s lymphoma (37, 7.4%) were the commonest infection-associated cancers. Conclusion: Our results suggest that 30.8% and 48.2% of the total cancer cases sampled in KNH and MTRH respectively were associated with infectious agents, while 27.6% and 44.4% were attributable to infections in the two hospitals respectively. Reducing the burden of infection-attributable cancers can translate to a reduction of the overall cancer burden.
Chimwemwe Kwanjo Banda, Belinda T. Gombachika, Moffat J. Nyirenda, Adamson Sinjani Muula
Published: 19 September 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12992.1

Abstract:Background: Self-management is key to the control of glycaemia and prevention of complications in people living with diabetes. Many people living with diabetes in Malawi have poorly controlled glucose and they experience diabetes-related complications. This study aimed to assess diabetes self-management behaviours and to identify factors associated with it among people living with diabetes at Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi. Methods: This cross-sectional study recruited 510 adults attending a diabetes clinic at a teaching referral hospital in southern Malawi. The social cognitive theory was applied to identify factors associated with following all recommended self-management behaviours. Data on participants’ demographics, clinical history, diabetes knowledge, self-efficacy, outcome expectations, social support, environmental barriers and diabetes self-management were collected. Univariate and multivariate logistic regression analyses were conducted to identify factors associated with following all self-management behaviours. Results: The mean age of participants was 53.6 (SD 13.3) years. Self-reported medication adherence within the last seven days was 88.6% (n=494); 77% reported being physically active for at least 30 minutes on more than three days in the previous seven days; 69% reported checking their feet every day and inspecting inside their shoes; 58% reported following a healthy diet regularly. Overall, only 33% reported following all the self-management behaviours regularly. Multiple logistic regression analysis showed that self-efficacy was the only social cognitive factor associated with following all the self-management practices (p < 0.001). Conclusions: Participants in our study were not consistently achieving all self-management practices with dietary practices being the least adhered to behaviour by many. To improve self-management practices of people living with diabetes, current health education programs should not only aim at improving diabetes related knowledge but also self-efficacy. Adopting interventions that promote self-efficacy in diabetes patients such as exposure to role models, peer education, providing positive feedback, and counselling is recommended.
Augustina Angelina Sylverken, Ellis Owusu-Dabo, Alexander Kwarteng, Sampson Twumasi-Ankrah, Michael Owusu, Louis Adu-Amoah, Rexford Mawunyo Dumevi, Rejoice Agyeiwaa Arthur, Nicholas Addofoh, Francisca Dzata, et al.
Published: 18 September 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12920.2

Abstract:Background: The widespread use of social media applications on mobile phones indicate that smart phones have become more than just a simple medium for voice calling. Several studies have shown the potential benefit of these social media applications in discussing many health conditions. We report on tracking sample transport by public and private transport providers using WhatsApp during the first nationwide drug resistance tuberculosis (TB) survey in Ghana. Methods: The survey was conducted between February 2016 and June 2017, and involved 33 TB diagnostic sites selected on the basis of a two-stage cluster randomized sampling design on both anticipated yield and probability proportional to size method. We engaged the services of privately and publicly owned vehicles’ union to transport samples to the Bacteriology department at the Kumasi Centre for Collaborative Research in Tropical Medicine laboratories for further laboratory processing. We created a mobile social group platform (‘National TBDRS’) on WhatsApp consisting of two representatives from each site as well as other stakeholders. The purpose was to notify a laboratory team in Kumasi, on the following details of the sample: date and time of dispatch, driver’s name, car number, estimated time of arrival, and bus terminal name. Results: A total 3077 WhatsApp messages were received during the survey period. Of these, 2879 (93.57%) messages were related to the survey. We observed a positive correlation between the total number of messages received and the total number of well-packaged sputum samples sent (r=0.89, p=0.02). There were no major transport delays (11:44±03:50) and all samples arrived within a 3-day window from the survey sites. Conclusions: Using WhatsApp as a platform of communication can aid in improving tracking of samples, enhance accountability of for example drivers handling the samples over at a road crossing and communication across health facilities.
Samuel Yaw Aboagye, Vincent Amarh, Paul A. Lartey, Patrick Kobina Arthur
Published: 27 August 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12957.2

Abstract:Background: Discovery of bioactive natural products are instrumental for development of novel antibiotics. The discovery and development of natural products such as penicillin represented a major milestone in the treatment of bacterial infections. Currently, many antibiotics have lost their relevance in clinics due to the emergence of drug-resistant microbial pathogens. Hence, there is the need for continuous search of new compounds endowed with potent antimicrobial activity. In this study, wood-decaying fungi (WDF) from Southern Ghana were explored for their potential as sources of novel antimicrobial compounds with intent of expanding the effort into a drug discovery programme in the near future. Methods: A total of 54 WDF isolates were fermented in potato dextrose broth and the secondary metabolites obtained were analyzed for the presence of antimicrobial agents using the disc diffusion assay. Chromatography techniques were used for preliminary analysis of the chemical composition of the extracts and for fractionation of the extracts that showed antimicrobial activity. Results: The extracts from 40 out of the 54 WDF isolates exhibited significant antimicrobial activity against either Staphylococcus aureus, Escherichia coli or Candida albicans. Fractionation of these bioactive extracts, followed by bioassay of the organic fractions obtained, indicate that extracts exhibiting antimicrobial activity against more than one of the three test organisms could be attributed to the presence of different bioactive compounds. Analysis of the composition of the extracts revealed that terpenes were predominant. Conclusions: This study suggests that a significant proportion of WDF in Southern Ghana produce antimicrobial compounds which could be potential sources of novel anti-infective agents and support the plans of developing a drug discovery programme in Ghana based on the fermentation of WDF.
Bonnie R. Joubert, Kiros Berhane, Jonathan Chevrier, Gwen Collman, Brenda Eskenazi, Julius Fobil, Cathrine Hoyo, Chandy C. John, Abera Kumie, Mark Nicol, et al.
Published: 27 August 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12983.1

Abstract:Individuals with African ancestry have extensive genomic diversity but have been underrepresented in genomic research. There is also extensive global diversity in the exposome (the totality of human environmental exposures from conception onwards) which should be considered for integrative genomic and environmental health research in Africa. To address current research gaps, we organized a workshop on environmental health research in Africa in conjunction with the H3Africa Consortium and the African Society of Human Genetics meetings in Kigali, Rwanda. The workshop was open to all researchers with an interest in environmental health in Africa and involved presentations from experts within and outside of the Consortium. This workshop highlighted innovative research occurring on the African continent related to environmental health and the interplay between the environment and the human genome. Stories of success, challenges, and collaborative opportunities were discussed through presentations, breakout sessions, poster presentations, and a panel discussion. The workshop informed participants about environmental risk factors that can be incorporated into current or future epidemiology studies and addressed research design considerations, biospecimen collection and storage, biomarkers for measuring chemical exposures, laboratory strategies, and statistical methodologies. Inclusion of environmental exposure measurements with genomic data, including but not limited to H3Africa projects, can offer a strong platform for building gene-environment (G x E) research in Africa. Opportunities to leverage existing resources and add environmental exposure data for ongoing and planned studies were discussed. Future directions include expanding the measurement of both genomic and exposomic risk factors and incorporating sophisticated statistical approaches for analyzing high dimensional G x E data. A better understanding of how environmental and genomic factors interact with nutrition and infection is also needed. Considering that the environment represents many modifiable risk factors, these research findings can inform intervention and prevention efforts towards improving global health.
Jan Pieter Koopman, Moses Egesa, Anne Wajja, Moses Adriko, Jacent Nassuuna, Gyaviira Nkurunungi, Emmanuella Driciru, Gijsbert Van Willigen, Stephen Cose, Maria Yazdanbakhsh, et al.
Published: 13 August 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12972.2

Abstract:Schistosomiasis is a parasitic infection highly prevalent in sub-Saharan Africa, and a significant cause of morbidity; it is a priority for vaccine development. A controlled human infection model for Schistosoma mansoni (CHI-S) with potential to accelerate vaccine development has been developed among naïve volunteers in the Netherlands. Because responses both to infections and candidate vaccines are likely to differ between endemic and non-endemic settings, we propose to establish a CHI-S in Uganda where Schistosoma mansoni is endemic. As part of a “road-map” to this goal, we have undertaken a risk assessment. We identified risks related to importing of laboratory vector snails and schistosome strains from the Netherlands to Uganda; exposure to natural infection in endemic settings concurrently with CHI-S studies, and unfamiliarity of the community with the nature, risks and rationale for CHI. Mitigating strategies are proposed. With careful implementation of the latter, we believe that CHI-S can be implemented safely in Uganda. Our reflections are presented here to promote feedback and discussion.
Azza E. Ahmed, Phelelani T. Mpangase, Sumir Panji, Shakuntala Baichoo, Yassine Souilmi, Faisal M. Fadlelmola, Mustafa Alghali, Shaun Aron, Hocine Bendou, Eugene De Beste, et al.
Published: 7 August 2019
AAS Open Research, Volume 1; doi:10.12688/aasopenres.12847.2

Abstract:The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network’s Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.
Abdul-Hakim Mutala, Kingsley Badu, Christian Owusu, Samuel Kekeli Agordzo, Austine Tweneboah, Abbas Dawood Ackom, Matthew Glover Addo
Published: 29 July 2019
AAS Open Research, Volume 2; doi:10.12688/aasopenres.12979.1

Abstract:Background: This study aimed at investigating haematological changes in malaria patients across different demographic settlements. Malaria parasites trigger changes in certain haematological parameters, which may result in a number of clinical manifestations. Differences in demographic settlements, such as rural, peri-urban and urban settlements, may also influence these changes, but this has rarely been studied. Methods: We conducted a hospital-based, cross-sectional study from January to December 2018 in three different settlements. A total of 598 participants were recruited. Giemsa-stained blood smears were examined to detect and quantify malaria parasitaemia, while haematological parameters were measured using a haematology analyser. Results: The rural settlement had the highest malaria prevalence compared to the other study communities (p=0.009). The difference in parasite densities across the three communities was also significant (p=0.0149). When the malaria-infected population was compared to the uninfected, there were differences in red blood cell count (p=0.0170), haemoglobin levels (p=0.0165), mean corpuscular volume (p=0.0139) and platelet counts (pp=0.0002), plateletcrit (p=0.0041), mean platelet volume (p=0.0009) and platelet large cell ratio (p=0.0046) levels between patients from the urban, peri-urban and rural areas. Conclusions: Patients infected with malaria generally had low red blood cell, haemoglobin and platelets in comparison to uninfected patients. There were also significant differences in several haematological parameters between malaria-infected patients from the three demographic settlements. Atypical results from routine haematological assays, especially findings of anaemia and thrombocytopenia, may be indicative of malaria and, in cases where the infection is asymptomatic, may improve diagnosis by prompting a more thorough search for the parasite in the peripheral circulation.
Puleng Matatiele, Lerato Mochaki, Bianca Southon, Boitumelo Dabula, Poobalan Poongavanum, Boitumelo Kgarebe
Published: 23 July 2019
AAS Open Research, Volume 1; doi:10.12688/aasopenres.12882.2

Abstract:This report is an overview of requests for biological and environmental monitoring of hazardous chemicals, submitted to the National Institute for Occupational Health, Analytical Services Laboratory for testing from the years 2005 to 2015. The report discusses the nature of tests requested and implications for workers’ health and environment, as well as potential impact of the uncertainties associated with monitoring of hazardous chemicals. This is a retrospective, descriptive, qualitative and quantitative audit of all samples received and tests performed retrieved from records of analysis by the laboratory. The study sample consisted of 44,221 samples. The report indicates that throughout the interrogation period the demand for biological monitoring was higher than that for environmental monitoring, with more requests for toxic metals than organic pollutants. Toxic metal testing was highest for mercury, followed by manganese, lead, aluminium and arsenic. The highest number of tests for organic pollutants was conducted for pesticides followed by toluene and xylene. The study has also revealed that the scope of tests requested is rather narrow and does not reflect the broad spectrum of South Africa’s industrial diversity. Having identified possible reasons for underutilization, a number of reforms that could enhance the laboratory’s performance have been addressed.