Case Report: HIV test misdiagnosis

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Factors related to attrition in a cohort study of HIV in Malawi

Background: Longitudinal studies face power reduction due to loss to follow up (LTFU). Bias may also arise because of differences between those who stay in the study and those who are LTFU We studied factors associated with LTFU in a cohort of HIV sero-negative and sera-positive mothers in urban Malawi.Objective: To bridge the existing gaps by examining the factors associated with attrition.Design: Longitudinal study.Setting: Queen Elizabeth Central Hospital (QECH) and the Kamuzu Central Hospital in Blantyre, Malawi.Subjects: One thousand three hundred and fifty three women who attended the prenatal clinic, between October 1989 and October 1990 were recruited as part of a study to determine rates and risk factors of sero-prevalence and sera-conversion of HIV -1 among this cohort.Results: In this cohort study, 1353 women were enrolled at delivery and 1188 (88%) returned for the first follow-up visit at three months post-partum. Of those who returned, 177 (15%) were subsequently lost during the remaining months of follow-up. The main predictors of L TFU were younger maternal age, lower educational level of the father, HIV infection of the mother, lower birth weight of the index child and mother not being married.Conclusions: Researchers planning studies in developing countries should consider the impact of lower education and poorer infant health on study retention in developing countries

Reducing child undernutrition through dietary diversification, reduced aflatoxin exposure, and improved hygiene practices: the immediate impacts in central Tanzania

Open Access Article; Published online: 28 Nov 2019The study aimed to quantify the immediate effects of dietary diversification, food safety, and hygiene interventions on child undernutrition in four rural villages in Kongwa district of central Tanzania. One hundred mothers with their children of less than 24 months old were recruited for this study. The difference-in-difference (DID) method was used to assess the effects of intensive intervention through a learning-by-doing process on the topic of aflatoxin free diversified food utilization and improved hygiene practices. Periodic anthropometric measurements were conducted on the 0th, 7th, 14th, and 21st days, and DID estimator showed the significant and positive average marginal effects of the intervention on Z-Scores being 0.459, 0.252, and 0.493 for wasting, stunting, and underweight, respectively. Notably, at the end of the study, the mean aflatoxin M1 level in urine samples decreased by 64% in the intervention group, while it decreased by 11% in the control group. The study provides quantitative evidence on intensive 21-day training for mothers incorporating integrated technologies yielded positive impacts on their children’s nutritional outcomes

Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species

BACKGROUND: Bacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms. RESULTS: Using Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed. CONCLUSION: Global genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.http://www.biomedcentral.com/bmcgenomics/am201

Aflatoxin contamination: Knowledge disparities among agriculture extension officers, frontline health workers and small holder farming households in Malawi

The aims of this study were to assess the state of knowledge and perceptions regarding aflatoxin contamination among frontline workers in direct contact with small holder farming households in Malawi as well as among the households themselves. The study first investigated and documented demographic profiles of agriculture extension workers (n = 22) and frontline health workers (n = 161) both from Ntchisi district and small holder farming households (n = 915) from Dedza, Balaka and Mzimba districts. Structured questionnaires were administered to document knowledge and perceptions. Majority of the respondents in Ntchisi were frontline nutrition and health workers as follows: care group promoters (31.7%), cluster leaders (51.9%) and health surveillance assistants (4.4%). Only 12% of the respondents were agriculture extension officers. Among frontline workers, using factor analyses, factors highly associated with the knowledge on domestic management of aflatoxin contamination and the impact of aflatoxin contamination on child linear growth and health in general were most prominent. Whereas, their knowledge of pre & post-harvest practices that pre-dispose crops to aflatoxin contamination and impact of aflatoxin contamination on trade and income losses was relatively low. On the other hand, among small holder farming households, lowest knowledge was related to occurrence of aflatoxin contamination pre and post-harvest. Highest knowledge was observed on issues around loss of income due to aflatoxin contamination. Across all districts over 50% of surveyed respondents reported that they perceived aflatoxin contamination severity as low. Majority of the households (>50%) did not perceive aflatoxin contamination as a problem that could be controlled. This is the first study to investigate knowledge, attitudes, practices and perceptions on aflatoxin contamination among a combination of agriculture extension officers and frontline health workers in parallel with the households they usually are in contact with. The current investigation is crucial because it elucidates knowledge gaps in aflatoxin critical control across agriculture extension, health workers and the small holder farming households. This is especially crucial among agriculture extension workers and frontline health workers as they have direct contact with households and therefore serve as an important source of information that could influence behavior change

On-farm Assessment of Post-harvest Losses: the Case of Groundnut in Malawi, Series Paper Number 43.

An on-farm measurement was conducted in 2015 of groundnut post-harvest loss (PHL) in Central Region of Malawi, aiming to assess the PHL in quantity and quality along the post-harvest processes at the farm level. A total of 15 voluntary farmers from Mchinji, Lilongwe, and Kasungu districts participated in the on-farm assessment using the count and weigh method. The assessment began in April and was forced to end in August due to an unexpected change in funding availability. The close monitoring through resident enumerators revealed that during lifting, drying, stripping, and transport to homestead, an average weight loss of 133.6 kg (shelled nuts equivalent) per hectare was incurred, which is equivalent to 13.7 % of the harvest without post-harvest losses, translating into a value loss of USD 189.7 per hectare. In particular, the lifting process suffered an average loss of 57.3 kg per hectare, due to such factors as hoe damage, weed infestation, and theft. For on-field drying after lifting, 13 % of the farmers practiced the Mandela cork, the best-bet drying method for controlling aflatoxin, while the rest of the farmers dried on ridges or in small drying rounds. During the drying and stripping processes, farmers experienced a mean weight loss of 73.9 kg per hectare, due to factors including attacks by rodents, spillage by children, and biting by workers. As a means of transporting nuts from the field to homestead, farmers used ox-carts (47% of farmers), bicycles (33%) and walking (20%). The mean weight loss during this transportation was 2.4 kg per hectare, due to use of torn sacks and direct loading onto ox-carts without use of sacks. Regarding quality loss, aflatoxin diagnosis was conducted on nuts sampled at two points in time: after drying and after one month of storage. The average contamination level was 0.87 ng/g after drying and 0.88 ng/g after one month of storage. Although the overall level seemed stable, the individual-level changes were large, and so were the district-level and individual-level variances. Seven percent of the farmers registered a level greater than 4 ng/g, which would not be accepted by major international markets such as the European Union. Mitigation measures at each stage of post-harvest operations and methodologies for assessing post-harvest losses in groundnut are discussed

Challenges facing young African scientists in their research careers: A qualitative exploratory study

Background: Africa accounts for 14% of world’s population, and the economies of most African countries are considered to be growing, but this is not reflected in the amount of research published by Africans. This study aimed at identifying the challenges that young African scientists face in their career development.Methods: This was a qualitative exploratory study involving young researchers who attended the Teaching and Research in Natural Sciences for Development (TReND) in Africa scientific writing and communication workshop, which was held in Malawi in September 2015. A semi-structured questionnaire was sent to all workshop participants who consented to taking part in the survey. In total, 28 questionnaires were sent via email and 15 were returned, representing a response rate of 53.6%. Data were analysed using thematic analysis.Results: Young Africans develop their research interests various ways. The most common career-promoting factors identified by the study participants included formal classroom learning, aspirations to attain academic qualifications, work satisfaction, and the desire to fulfill parents’ dreams. Challenges cited by survey respondents included a lack of mentorship, funds, and research and writing skills. Lack of interest in research by policymakers, lack of motivation by peers, and heavy workload (leaving little time for research) were also reported as challenges. Respondents suggested that grants specifically targeting young scientists would be beneficial. Participants also urged for the establishment of mentorship programmes, increasing motivation for research, and more frequent training opportunities.Conclusions: There is need for improved funding for institutional and research network strengthening in Africa, with particular attention given to expanding opportunities for young researchers

TB and HIV stigma compounded by threatened masculinity: implications for TB health-care seeking in Malawi.

SETTING: Urban Blantyre, Malawi. OBJECTIVE: To understand why men with tuberculosis (TB) in the community remain undiagnosed. DESIGN: A multi-method qualitative study applying a modified grounded theory approach. Data were gathered from March 2011 to March 2012 from 134 men and women taking part in 1) focus group discussions with community members (n = 6) and health care workers (n = 2), and 2) in-depth interviews with TB patients (n = 20, females n = 14) and chronic coughers (n = 20, women n = 8). Data were analysed inductively to identify, refine and consolidate, and verify emerging concepts and themes. RESULTS: Two emerging themes highlighting compound stigma in this high human immunodeficiency virus (HIV) prevalence, low-income setting are presented. First, cough or any illness that portended a 'serious' condition were accompanied by portrayals of cough, TB and HIV as being interchangeable. Chronic coughers and TB patients described their illness in ways that foregrounded bodily decimation and rupture of social life and masculine identity. Second, 'resistance strategies' entailed resisting classification as (seriously) ill by evading or ambivalently approaching health care, or acknowledging the 'ill' status then actively pursuing health-appropriate behaviours, including changing lifestyle or adopting non-normative gender roles. CONCLUSIONS: Managing patients requires 1) going beyond syndromic management based on vital signs and clinical indicators to recognising and intervening on health care-seeking related tensions to retain individuals in care, and 2) understanding and addressing TB stigma as it manifests and affects men and women differently in specific settings

Emergence of Double- and Triple-Gene Reassortant G1P[8]Rotaviruses Possessing a DS-1-Like Backbone after RotavirusVaccine Introduction in Malawi

To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunisation programmes. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix™) into its immunisation schedule in 2012. Utilising a surveillance platform of hospitalised rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 - 2012) and after (2013 - 2014) vaccine introduction. Analysis of whole genomes obtained through next generation sequencing revealed that all randomly-selected pre-vaccine G1P[8] strains sequenced (n=32) possessed a Wa-like genetic constellation, whereas post-vaccine G1P[8] strains (n=18) had a DS-1-like constellation. Phylodynamic analyses indicated that post-vaccine G1P[8] strains emerged through reassortment events between human Wa- and DS-1-like rotaviruses that circulated in Malawi from the 1990's, hence classified as atypical DS-1-like reassortants. The time to the most recent common ancestor for G1P[8] strains was from 1981-1994; their evolutionary rates ranged from 9.7 x 10(-4)-4.1 x 10(-3) nucleotide/substitutions/site/year. Three distinct G1P[8] lineages chronologically replaced each other between 1998 and 2014. Genetic drift was the likely driver for lineage turnover in 2005, whereas replacement in 2013 was due to reassortment. Amino acid substitution within the outer glycoprotein VP7 of G1P[8] strains had no impact on the structural conformation of the antigenic regions, suggesting that it is unlikely that they would affect recognition by vaccine-induced neutralizing antibodies. While the emergence of DS-1-like G1P[8] rotavirus reassortants in Malawi was therefore likely due to natural genotype variation, vaccine effectiveness against such strains needs careful evaluation.ImportanceThe error-prone RNA-dependent RNA polymerase and the segmented RNA genome predispose rotaviruses to genetic mutation and genome reassortment, respectively. These evolutionary mechanisms generate novel strains and have the potential to lead to the emergence of vaccine-escape mutants. While multiple African countries have introduced rotavirus vaccine, there are few data describing the evolution of rotaviruses that circulated before and after vaccine introduction. We report the emergence of atypical DS-1-like G1P[8] strains during the post-vaccine era in Malawi. Three distinct G1P[8] lineages circulated chronologically from 1998-2014; mutation and reassortment drove lineage turnover in 2005 and 2013, respectively. Amino acid substitutions within the outer capsid VP7 glycoprotein did not affect the structural conformation of mapped antigenic sites, suggesting limited effect in recognition of G1 specific vaccine-derived antibodies. The genes that constitute the remaining genetic backbone may play important roles in immune evasion, and vaccine effectiveness against such atypical strains needs careful evaluation

Three-year outcomes for women newly initiated on lifelong antiretroviral therapy during pregnancy - Malawi option B+

IntroductionAntiretroviral therapy (ART) is very effective in preventing vertical transmission of HIV but some women on ART experience different virologic, immunologic, and safety profiles. While most pregnant women are closely monitored for short-term effects of ART during pregnancy, few women receive similar attention beyond pregnancy. We aimed to assess retention in care and clinical and laboratory-confirmed outcomes over 3 years after starting ART under Malawi's Option B+program.MethodsWe conducted a prospective cohort study of pregnant women newly diagnosed with HIV who started tenofovir disoproxil fumarate/emtricitabine/efavirenz (TDF/3TC/EFV) for the first time at Bwaila Hospital in Lilongwe, Malawi between May 2015 and June 2016. Participants were followed for 3 years. We summarized demographic characteristics, pregnancy outcomes, and clinical and laboratory adverse events findings using proportions. Log-binomial regression models were used to estimate the overall risk ratios (RR) and the corresponding 95% confidence interval (CI) for the association between index pregnancy (i.e. index pregnancy vs. subsequent pregnancy) and preterm birth, and index pregnancy and low birthweight.ResultsOf the 299 pregnant women who were enrolled in the study, 255 (85.3%) were retained in care. There were 340 total pregnancies with known outcomes during the 36-month study period, 280 index pregnancies, and 60 subsequent pregnancies. The risks of delivering preterm (9.5% for index pregnancy and13.5% for subsequent pregnancy: RR=0.70; 95% CI: 0.32-1.54), or low birth weight infant (9.8% for index pregnancy and 4.2% for subsequent pregnancy: RR=2.36; 95% CI: 0.58-9.66) were similar between index and subsequent pregnancies. Perinatally acquired HIV was diagnosed in 6 (2.3%) infants from index pregnancies and none from subsequent pregnancies. A total of 50 (16.7%) women had at least one new clinical adverse event and 109 (36.5%) women had at least one incident abnormal laboratory finding. Twenty-two (7.3%) women switched to second line ART: of these 64.7% (8/17) had suppressed viral load and 54.9% (6/17) had undetectable viral load at 36 months.ConclusionMost of the women who started TDF/3TC/EFV were retained in care and few infants were diagnosed with perinatally acquired HIV. Despite switching, women who switched to second line therapy continued to have higher viral loads suggesting that additional factors beyond TDF/3TC/EFV failure may have contributed to the switch. Ongoing support during the postpartum period is necessary to ensure retention in care and prevention of vertical transmission