Malaria is caused by parasites of the genus Plasmodium, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich Plasmodium DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich Plasmodium reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches Plasmodium reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.

HIV patients with recurrent visceral leishmaniasis (VL) could potentially drive Leishmania transmission in areas with anthroponotic transmission such as East-Africa, but studies are lacking. Leishmania parasitemia has been used as proxy for infectiousness. This study is nested within the PreLeish prospective cohort study, following a total of 490 HIV infected individuals free of VL at enrollment for upto 24-37 months in North-West Ethiopia. Blood Leishmania PCR was done systematically. This case series reports on ten HIV-coinfected individuals with chronic VL (≥3 VL episodes during follow-up) for upto 37 months, and three individuals with asymptomatic Leishmania infection for upto 24 months. All ten chronic VL cases were male, on antiretroviral treatment, with 0-11 relapses before enrollment. Median baseline CD4 counts were 82 cells/µL. They displayed three to six VL treatment episodes over a period upto 37 months. Leishmania blood PCR levels were strongly positive for almost the entire follow-up time (median Ct value 26 (IQR 23-30), including during periods between VL treatment. Additionally, we describe three HIV-infected individuals with asymptomatic Leishmania infection and without VL history, with equally strong Leishmania parasitemia over a period of upto 24 months without developing VL. All were on antiretroviral treatment at enrollment, with baseline CD4 counts ranging from 78 to 350 cells/µL. These are the first data on chronic parasitemia in HIV-infected individuals from L donovani endemic areas. HIV patients with asymptomatic and symptomatic Leishmania infection could potentially be highly infectious and constitute Leishmania superspreaders. Xenodiagnosis studies are required to confirm infectiousness.

BackgroundThere is limited data on dolutegravir (DTG)-associated weight gain from settings with a dual burden of HIV and overnutrition.MethodsIn Eswatini (at Matsanjeni), among 156 and 160 adult patients on DTG-based and EFV-based antiretroviral therapy (ART), respectively, we studied excessive weight gain (BMI at 24 months ART greater than baseline and ≥25 kg/m2).ResultsThe median BMI increase in DTG-based patients was 1.09 (IQR:-0.28,3.28) kg/m2 compared to 0.20 (IQR:-0.85,2.18) kg/m2 in EFV-based patients (p value = 0.001). DTG-based ART predicted excessive weight gain (aOR 2.61;95% CI:1.39–4.93).ConclusionPractitioners should consider DTG-based regimens as one of the risk factors for overweight/obesity.

BackgroundAnaemia during pregnancy causes adverse outcomes to the woman and the foetus, including anaemic heart failure, prematurity, and intrauterine growth restriction. Iron deficiency anaemia (IDA) is the leading cause of anaemia and oral iron supplementation during pregnancy is widely recommended. However, little focus is directed to dietary intake. This study estimates the contribution of IDA among pregnant women and examines its risk factors (including dietary) in those with moderate or severe IDA in Lagos and Kano states, Nigeria.MethodsIn this cross-sectional study, 11,582 women were screened for anaemia at 20-32 weeks gestation. The 872 who had moderate or severe anaemia (haemoglobin concentration < 10 g/dL) were included in this study. Iron deficiency was defined as serum ferritin level < 30 ng/mL. We described the sociodemographic and obstetric characteristics of the sample and their self-report of consumption of common food items. We conducted bivariate and multivariable logistic regression analysis to identify risk factors associated with IDA.ResultsIron deficiency was observed among 41% (95%CI: 38 – 45) of women with moderate or severe anaemia and the prevalence increased with gestational age. The odds for IDA reduces from aOR: 0.36 (95%CI: 0.13 – 0.98) among pregnant women who consume green leafy vegetables every 2-3 weeks, to 0.26 (95%CI: 0.09 – 0.73) among daily consumers, compared to those who do not eat it.Daily consumption of edible kaolin clay was associated with increased odds of having IDA compared to non-consumption, aOR 9.13 (95%CI: 3.27 – 25.48). Consumption of soybeans three to four times a week was associated with higher odds of IDA compared to non-consumption, aOR: 1.78 (95%CI: 1.12 – 2.82).ConclusionAbout 4 in 10 women with moderate or severe anaemia during pregnancy had IDA. Our study provides evidence for the protective effect of green leafy vegetables against IDA while self-reported consumption of edible kaolin clay and soybeans appeared to increase the odds of having IDA during pregnancy. Health education on diet during pregnancy needs to be strengthened since this could potentially increase awareness and change behaviours that could reduce IDA among pregnant women with moderate or severe anaemia in Nigeria and other countries.

BackgroundColorectal cancer (CRC) is the second most prevalent cancer in Europe, with one-fifth of cases attributable to unhealthy lifestyles. Risk prediction models for quantifying CRC risk and identifying high-risk groups have been developed or validated across European populations, some considering lifestyle as a predictor.PurposeTo identify lifestyle predictors considered in existing risk prediction models applicable for European populations and characterise their corresponding parameter values for an improved understanding of their relative contribution to prediction across different models.MethodsA systematic review was conducted in PubMed and Web of Science from January 2000 to August 2021. Risk prediction models were included if (1) developed and/or validated in an adult asymptomatic European population, (2) based on non-invasively measured predictors and (3) reported mean estimates and uncertainty for predictors included. To facilitate comparison, model-specific lifestyle predictors were visualised using forest plots.ResultsA total of 21 risk prediction models for CRC (reported in 16 studies) were eligible, of which 11 were validated in a European adult population but developed elsewhere, mostly USA. All models but two reported at least one lifestyle factor as predictor. Of the lifestyle factors, the most common predictors were body mass index (BMI) and smoking (each present in 13 models), followed by alcohol (11), and physical activity (7), while diet-related factors were less considered with the most commonly present meat (9), vegetables (5) or dairy (2). The independent predictive contribution was generally greater when they were collected with greater detail, although a noticeable variation in effect size estimates for BMI, smoking and alcohol.ConclusionsEarly identification of high-risk groups based on lifestyle data offers the potential to encourage participation in lifestyle change and screening programmes, hence reduce CRC burden. We propose the commonly shared lifestyle predictors to be further used in public health prediction modelling for improved uptake of the model.

Is it possible to measure wealth and poverty across settings while being faithful to local understandings? The stages of progress method (SoP) attempts to do this by building ladders of wealth in locally relevant terms and using these in comparisons across groups. This approach is potentially useful among pastoralist populations where monetary income and standard asset inventories may be misleading, and where people are discriminated against by the state and neglected by formal systems of accounting. On the basis of fieldwork among Nyangatom agro–pastoralists in Ethiopia, we expose some problematic assumptions of the SoP method. Participants did not endorse ladder-like stages from poverty to wealth distinguished by material assets, nor did they reach consensus on the definition of a poverty line. We caution that the SoP method carries risks of facipulation, and instead we advocate for multidimensional measures of prosperity based on locally relevant forms of wealth.

Abstract We determined a near complete and complete monkeypox virus (Mpox) genome in an elephant shrew (Petrodromus tetradactylus), a squirrel (Funisciurus bayonii), and produced shorter sequencesobtained from two rats (Stochomys longicaudatus, Cricetomys sp. 2) originating from the Democratic Republic of the Congo. We also ran a series of molecular clock analyses that all agree on a recent, clearly post Dahomey gap opening diversification of Mpox. This suggests that, besides squirrels, a number of rodents and elephant shrews are involved in Mpox ecology, whose current genomic diversity and distribution was likely shaped in the last 1,000 years.

Failure of artemisinin-based combination therapy is increasingly reported in patients with Plasmodium falciparum malaria in sub-Saharan Africa. We aimed to describe the clinical and genomic characteristics of recent cases of P. falciparum malaria failing artemether-lumefantrine in Belgium. Travel-related cases of malaria confirmed at the national reference laboratory of the Institute of Tropical Medicine, Antwerp, Belgium, were reviewed. All cases for which attending clinicians reported persistence (beyond Day 3 post-treatment initiation, i.e. early failure) or recrudescence (from Day 7 to 42, i.e. late failure) of P. falciparum parasites despite adequate drug intake were analysed. Both initial and persistent/recurrent samples were submitted to next generation sequencing to investigate resistance-conferring mutations. From July 2022 to June 2023, eight P. falciparum cases of failure with artemether-lumefantrine therapy were reported (early failure = 1; late failure = 7). All travellers were returning from sub-Saharan Africa, most (6/8) after a trip to visit friends and relatives. PfKelch13 (PF3D7_1343700) mutations associated with resistance to artemisinin were found in two travellers returning from East Africa, including the validated marker R561H in the patient with early failure and the candidate marker A675V in a patient with late failure. Additional mutations were detected that could contribute to decreased susceptibility to artemisinin in another three cases, lumefantrine in six cases and proguanil in all eight participants. Various regimens were used to treat the persistent/recrudescent cases, with favourable outcome. Within a 12-month period, we investigated eight travellers returning from sub-Saharan Africa with P. falciparum malaria and in whom artemether-lumefantrine failure was documented. Mutations conferring resistance to antimalarials were found in all analysed blood samples, especially against lumefantrine and proguanil, but also artemisinin. There is a pressing need for systematic genomic surveillance of resistance to antimalarials in international travellers with P. falciparum malaria, especially those experiencing treatment failure.