Transcriptome profiles of Trypanosoma brucei rhodesiense in Malawi reveal focus specific gene expression profiles associated with pathology.

BACKGROUND: Sleeping sickness caused by Trypanosoma brucei rhodesiense is a fatal disease and endemic in Southern and Eastern Africa. There is an urgent need to develop novel diagnostic and control tools to achieve elimination of rhodesiense sleeping sickness which might be achieved through a better understanding of trypanosome gene expression and genetics using endemic isolates. Here, we describe transcriptome profiles and population structure of endemic T. b. rhodesiense isolates in human blood in Malawi. METHODOLOGY: Blood samples of r-HAT cases from Nkhotakota and Rumphi foci were collected in PaxGene tubes for RNA extraction before initiation of r-HAT treatment. 100 million reads were obtained per sample, reads were initially mapped to the human genome reference GRCh38 using HiSat2 and then the unmapped reads were mapped against Trypanosoma brucei reference transcriptome (TriTrypDB54_TbruceiTREU927) using HiSat2. Differential gene expression analysis was done using the DeSeq2 package in R. SNP calling from reads that were mapped to the T. brucei genome was done using GATK in order to identify T.b. rhodesiense population structure. RESULTS: 24 samples were collected from r-HAT cases of which 8 were from Rumphi and 16 from Nkhotakota foci. The isolates from Nkhotakota were enriched with transcripts for cell cycle arrest and stumpy form markers, whereas isolates in Rumphi focus were enriched with transcripts for folate biosynthesis and antigenic variation pathways. These parasite focus-specific transcriptome profiles are consistent with the more virulent disease observed in Rumphi and a less symptomatic disease in Nkhotakota associated with the non-dividing stumpy form. Interestingly, the Malawi T.b. rhodesiense isolates expressed genes enriched for reduced cell proliferation compared to the Uganda T.b. rhodesiense isolates. PCA analysis using SNPs called from the RNAseq data showed that T. b. rhodesiense parasites from Nkhotakota are genetically distinct from those collected in Rumphi. CONCLUSION: Our results suggest that the differences in disease presentation in the two foci is mainly driven by genetic differences in the parasites in the two major endemic foci of Rumphi and Nkhotakota rather than differences in the environment or host response.

Development, validation, and pilot application of a high throughput molecular xenomonitoring assay to detect Schistosoma mansoni and other trematode species within Biomphalaria freshwater snail hosts.

Schistosomiasis is a neglected tropical disease (NTD) caused by infection with parasitic trematodes of the genus Schistosoma that can lead to debilitating morbidity and mortality. The World Health Organization recommend molecular xenomonitoring of Biomphalaria spp. freshwater snail intermediate hosts of Schistosoma mansoni to identify highly focal intestinal schistosomiasis transmission sites and monitor disease transmission, particularly in low-endemicity areas. A standardised protocol to do this, however, is needed. Here, two previously published primer sets were selected to develop and validate a multiplex molecular xenomonitoring end-point PCR assay capable of detecting S. mansoni infections within individual Biomphalaria spp. missed by cercarial shedding. The assay proved highly sensitive and highly specific in detecting and amplifying S. mansoni DNA and also proved highly sensitive in detecting and amplifying non-S. mansoni trematode DNA. The optimised assay was then used to screen Biomphalaria spp. collected from a S. mansoni-endemic area for infection and successfully detected S. mansoni infections missed by cercarial shedding as well as infections with non-S. mansoni trematodes. The continued development and use of molecular xenomonitoring assays such as this will aid in improving disease control efforts, significantly reducing disease-related morbidities experienced by those in schistosomiasis-endemic areas.

Prevalence, risk factors, and antimicrobial resistance of endemic healthcare-associated infections in Africa: a systematic review and meta-analysis.

BACKGROUND: Healthcare-associated infections (HCAI) place a significant burden on healthcare systems globally. This systematic review and meta-analysis aimed to investigate the prevalence, risk factors, and aetiologic agents of endemic HCAI in Africa. METHODS: MEDLINE/PubMed, CINAHL, and Global Health databases (EBSCOhost interface) were searched for studies published in English and French describing HCAI in Africa from 2010 to 2022. We extracted data on prevalence of HCAI, risk factors, aetiologic agents, and associated antimicrobial resistance patterns. We used random-effects models to estimate parameter values with 95% confidence intervals for risk factors associated with HCAI. This study was registered in PROSPERO (CRD42022374559) and followed PRISMA 2020 guidelines. RESULTS: Of 2541 records screened, 92 were included, comprising data from 81,968 patients. Prevalence of HCAI varied between 1.6 and 90.2% with a median of 15% across studies. Heterogeneity (I2) varied from 93 to 99%. Contaminated wound (OR: 1.75, 95% CI: 1.31-2.19), long hospital stay (OR: 1.39, 95% CI: 0.92-1.80), urinary catheter (OR: 1.57, 95% CI: 0.35-2.78), intubation and ventilation (OR: 1.53, 95% CI: 0.85-2.22), vascular catheters (OR: 1.49, 95% CI: 0.52-2.45) were among risk factors associated with HCAI. Bacteria reported from included studies comprised 6463 isolates, with E. coli (18.3%, n = 1182), S. aureus (17.3%, n = 1118), Klebsiella spp. (17.2%, n = 1115), Pseudomonas spp. (10.3%, n = 671), and Acinetobacter spp. (6.8%, n = 438) being most common. Resistance to multiple antibiotics was common; 70.3% (IQR: 50-100) of Enterobacterales were 3rd -generation cephalosporin resistant, 70.5% (IQR: 58.8-80.3) of S. aureus were methicillin resistant and 55% (IQR: 27.3-81.3) Pseudomonas spp. were resistant to all agents tested. CONCLUSIONS: HCAI is a greater problem in Africa than other regions, however, there remains a paucity of data to guide local action. There is a clear need to develop and validate sustainable HCAI definitions in Africa to support the implementation of routine HCAI surveillance and inform implementation of context appropriate infection prevention and control strategies.

Mass drug administration campaigns: comparing two approaches for schistosomiasis and soil-transmitted helminths prevention and control in selected Southern Malawi districts.

BACKGROUND: Mass drug administration is one of the key interventions recommended by WHO to control certain NTDs. With most support from donors, health workers distribute antihelminthic drugs annually in Malawi. Mean community coverage of MDA from 2018 to 2020 was high at 87% for praziquantel and 82% for albendazole. However, once donor support diminishes sustaining these levels will be challenging. This study intended to compare the use of the community-directed intervention approach with the standard practice of using health workers in delivery of MDA campaigns. METHODS: This was a controlled implementation study carried out in three districts, where four health centres and 16 villages in each district were selected and randomly assigned to intervention and control arms which implemented MDA campaigns using the CDI approach and the standard practice, respectively. Cross-sectional and mixed methods approach to data collection was used focusing on quantitative data for coverage and knowledge levels and qualitative data to assess perceptions of health providers and beneficiaries at baseline and follow-up assessments. Quantitative and qualitative data were analyzed using IBM SPSS software version 26 and NVivo 12 for Windows, respectively. RESULTS: At follow-up, knowledge levels increased, majority of the respondents were more knowledgeable about what schistosomiasis was (41%-44%), its causes (41%-44%) and what STH were (48%-64%), while knowledge on intermediate host for schistosomiasis (19%-22%), its types (9%-13%) and what causes STH (15%-16%) were less known both in intervention and control arm communities. High coverage rates for praziquantel were registered in intervention (83%-89%) and control (86%-89%) communities, intervention (59%-79) and control (53%-86%) schools. Costs for implementation of the study indicated that the intervention arm used more resources than the control arm. Health workers and community members perceived the use of the CDI approach as a good initiative and more favorable over the standard practice. CONCLUSIONS: The use of the CDI in delivery of MDA campaigns against schistosomiasis and STH appears feasible, retains high coverages and is acceptable in intervention communities. Despite the initial high costs incurred, embedding into community delivery platforms could be considered as a possible way forward addressing the sustainability concern when current donor support wanes. TRIAL REGISTRATION: Pan-African Clinical Trials Registry PACTR202102477794401, date: 25/02/2021.

Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi.

T. b. rhodesiense is the causative agent of Rhodesian human African trypanosomiasis (r-HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between foci and differs from East African HAT clinical phenotypes. The purpose of this study was to gain more insights into the transcriptomic profiles of patients with early stage 1 and late stage 2 HAT disease in Malawi. Whole blood from individuals infected with T. b. rhodesiense was used for RNA-Seq. Control samples were from healthy trypanosome negative individuals matched on sex, age range, and disease foci. Illumina sequence FASTQ reads were aligned to the GRCh38 release 84 human genome sequence using HiSat2 and differential analysis was done in R Studio using the DESeq2 package. XGR, ExpressAnalyst and InnateDB algorithms were used for functional annotation and gene enrichment analysis of significant differentially expressed genes. RNA-seq was done on 23 r-HAT case samples and 28 healthy controls with 7 controls excluded for downstream analysis as outliers. A total of 4519 genes were significant differentially expressed (p adjusted <0.05) in individuals with early stage 1 r-HAT disease (n = 12) and 1824 genes in individuals with late stage 2 r-HAT disease (n = 11) compared to controls. Enrichment of innate immune response genes through neutrophil activation was identified in individuals with both early and late stages of the disease. Additionally, lipid metabolism genes were enriched in late stage 2 disease. We further identified uniquely upregulated genes (log2 Fold Change 1.4-2.0) in stage 1 (ZNF354C) and stage 2 (TCN1 and MAGI3) blood. Our data add to the current understanding of the human transcriptome profiles during T. b. rhodesiense infection. We further identified biological pathways and transcripts enriched than were enriched during stage 1 and stage 2 r-HAT. Lastly, we have identified transcripts which should be explored in future research whether they have potential of being used in combination with other markers for staging or r-HAT.

Molecular Epidemiology and Assemblage Typing of Giardia duodenalis in School-Age Children Situated along the Southern Shoreline of Lake Malawi, Malawi.

Almost all human giardiasis infections are caused by Giardia duodenalis assemblages A and B. Differentiation between human infections with these assemblages, as well as between single-assemblage (A or B) and mixed-assemblage (A and B) infections, is therefore needed to better understand the pathological impact of infection with either, or both, assemblages. We assessed the prevalence of G. duodenalis assemblages A and B using 305 fecal samples provided by school-age children situated along the southern shoreline of Lake Malawi. Concurrently, intestinal pathology data were also collected to test for association(s) between assemblage infection status and intestinal health. Prevalence of G. duodenalis infection was 39.3% by real-time polymerase chain reaction. Of all identified infections, 32% were single G. duodenalis assemblage A and 32% were single G. duodenalis assemblage B, whereas 33% were mixed-assemblage infections. Fifteen unique G. duodenalis assemblage A and 13 unique G. duodenalis assemblage B ß-giardin haplotypes were identified. There was a positive association between single infection with G. duodenalis assemblage B and both self-reporting of abdominal pain (odds ratio [OR]: 3.05, P = 0.004) and self-reporting of diarrhea (OR: 3.1, P = 0.003). No association between single infection with assemblage A and any form of intestinal pathology was found. Additionally, there was a positive association between mixed-assemblage infections and self-reporting of abdominal pain (OR: 3.1, P = 0.002). Our study highlights the importance G. duodenalis assemblage typing and reaffirms the need for improved access to water, sanitation and hygiene infrastructure in rural areas of low- and middle-income countries.

Differential Effects of Antimalarial Drugs on Parasite Clearance Rates Are Reflected by Plasmodium falciparum Ring Ratio.

Background: The location of Plasmodium falciparum within the body is determined by the life cycle of the parasite; young rings are in the peripheral blood, whereas mature parasites are sequestered in deep tissues. We can calculate a "ring ratio," the proportion of parasites in the periphery to the total number of parasites in the body. Artesunate acts on all parasite life stages, whereas quinine is effective only on sequestered parasites. Children with cerebral malaria (CM) treated with artesunate clear parasites faster than those treated with quinine. In this study, we established the relationship between ring ratio and parasite clearance rate and used the ring ratio to determine if the benefit derived from artesunate treatment could be attributed to its broader effect on life cycle stages. Methods: Ring ratios were calculated for 400 hospitalized children with CM in Blantyre, Malawi between 2010 and 2019 (quinine: 2010-2013, artesunate: 2014-2019). Results: In both treatment groups, parasite clearance rates were positively associated with the ring ratios, with a stronger association in the artesunate era than the quinine era. In the quinine era, an increase of 1-unit log10 difference between parasitemia and plasma P falciparum histidine-rich protein 2 (a proxy for ring ratio) resulted in a 0.27-unit increase in the parasite clearance rate, whereas in the artesunate era an equal increase resulted in a 0.41-unit increase (P = .04 for the difference). Conclusions: This analysis provides in vivo evidence supporting the hypothesis that more rapid parasite clearance rates in artesunate recipients are due to its superiority over quinine in killing ring-stage parasites.

Biomphalaria pfeifferi (Gastropoda: Planorbidae) in Lake Malawi and Upper Shire River, Mangochi District, Malawi: Distribution, Genetic Diversity and Pre-Patent Schistosome Infections.

In November 2017, Biomphalaria pfeifferi, the key intermediate host for Schistosoma mansoni in Africa, was first reported in Lake Malawi, Mangochi District. Two subsequent malacological surveys in 2018 and 2019 confirmed its lacustrine presence, as well as its presence along the Upper Shire River. These surveys provided sufficient specimens for analyses of the genetic structure and a transmission assessment for intestinal schistosomiasis. A total of 76 collected snails were characterized by a DNA sequence analysis of a 650 bp fragment of the mitochondrial cytochrome oxidase subunit 1 (cox1); by size fractionation of six fluorescently labelled microsatellite loci (Bgµl16, Bgµl, Bpf8, rg6, U-7, and rg9);by denaturing PAGE; and by detection of pre-patent Schistosoma infection by real-time PCR with a TaqMan® probe. Five closely related cox1 haplotypes were identified, all present within a single location, with only one haplotype common across all the other locations sampled. No allelic size variation was detected with the microsatellites and all loci were monomorphic. Overall, the pre-patent prevalence of Schistosoma spp. was 31%, with infected snails found at several sampling locations. In this part of Lake Malawi, Bi. pfeifferi exhibits low genetic diversity and is clearly being exposed to the miracidia of S. mansoni, which is likely facilitating the autochthonous transmission of this parasite.

An assessment of implementation and effectiveness of mass drug administration for prevention and control of schistosomiasis and soil-transmitted helminths in selected southern Malawi districts.

BACKGROUND: Mass drug administration (MDA) is one of the key interventions recommended by WHO for prevention and control of neglected tropical diseases (NTD). In Malawi, MDA is widely carried out annually since 2009 for prevention and control of schistosomiasis and soil-transmitted helminths (STH). No study has been carried out to assess effectiveness of the MDA approach and to document perceptions of health providers and beneficiaries regarding use of MDA. This study was done to understand how well MDA is being implemented and to identify opportunities for improvement in MDA delivery in Malawi. METHODS: Designed as a cross-sectional and multi-methods research, the study was carried out in three southern Malawi districts of Chiradzulu, Mangochi and Zomba. In each district, four health centres and 16 villages were randomly selected to participate. A mixed-methods approach to data collection focusing on quantitative data for coverage and knowledge, attitudes and practices assessments; and qualitative data for assessing perceptions of health providers and beneficiaries regarding MDA was used. Quantitative data were processed and analyzed using IBM SPSS software version 26 while qualitative data were analysed using NVivo 12 for Windows. RESULTS: Knowledge levels about schistosomiasis and STH in the districts varied according to disease aspects asked about. Majority are more knowledgeable about what schistosomiasis is (78%) and whether STH are treatable with drugs (97%); with least knowledgeable about the organism that transmits schistosomiasis (18%), types of schistosomiasis (11%) and what causes STH (20%). In 2018 and 2019 the districts registered high coverage rates for praziquantel and albendazole using community-based MDA (73-100%) and using school-based MDA (75-91%). Both the health authorities and community members perceived the MDA approach as good because it brings treatment closer to people. CONCLUSION: With the high MDA coverage obtained in communities and schools, the effectiveness of MDA in the target districts is satisfactory. There are, however, several challenges including disproportionate knowledge levels, which are hampering progress towards attainment of the 2030 global NTD goals. There is a need for promotion of community participation and partnerships as well as implementation of other recommended interventions for sustainable prevention and control of schistosomiasis and STH.

Virulence factors and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from urinary tract infections: a systematic review and meta-analysis.

BACKGROUND: Uropathogenic Escherichia coli (UPEC) are amongst the most frequent causes of urinary tract infections. We report a systematic review and meta-analysis of virulence factors and antimicrobial resistance of UPEC isolated from urinary tract infections. METHODS: A systematic review and meta-analysis were performed using PRISMA guidelines (Research Registry ref. 5874). Data were extracted from PubMed/MEDLINE and ScienceDirect databases for studies published from January 1, 2000 to December 31, 2019. Studies reporting antimicrobial resistance and virulence factors of UPEC isolated in confirmed urinary tract infections (≥105CFU/ml) were eligible. Prevalence of antimicrobial resistance and virulence factors of UPEC were estimated using random-effects meta-analysis model. Estimates with 95% confidence intervals, I-square (I2) statistic, and Cochran's Q test were computed using the score statistic and the exact binomial method by incorporating the Freeman-Tukey double arcsine transformation of proportions. RESULTS: Our search returned 2504 hits, of which 13 studies were included in the meta-analysis, totalling 1888 UPEC isolates. Highest antimicrobial resistance rates were observed among the antibiotic class of tetracycline in 69.1% (498/721), followed by sulphonamides in 59.3% (1119/1888), quinolones in 49.4% (1956/3956), and beta-lactams in 36.9% (4410/11964). Among beta-lactams, high resistance was observed in aminopenicillins in 74.3% (1157/1557) and first generation cephalosporins in 38.8% (370/953). Meanwhile, virulence factors with highest prevalence were immune suppressors (54.1%) followed by adhesins (45.9%). Taken individually, the most observed virulence genes were shiA (92.1%), CSH (80.0%), fimH/MSHA (75.3%), traT (75.1%), sisA (72.2%), iucD (65.7%), iutA (61.8%), kpsMTII (60.6%), and PAI (55.2%). CONCLUSIONS: The increased antibiotic resistance of UPEC isolates was demonstrated and suggested a need for reassessment of empirical therapies in urinary tract infections treatment caused by this pathogen. In addition, this pathotype exhibited diverse surface and secreted virulence factors.

Healthcare-associated infections and antimicrobial use in surgical wards of a large urban central hospital in Blantyre, Malawi: a point prevalence survey.

BACKGROUND: There are limited data on healthcare-associated infections (HAI) from African countries like Malawi. AIM: We undertook a point prevalence survey of HAI and antimicrobial use in the surgery department of Queen Elizabeth Central Hospital (QECH) in Malawi and ascertained the associated risk factors for HAI. METHODS: A cross-sectional point prevalence survey (PPS) was carried out in the surgery department of QECH. The European Centre for Disease Prevention and Control PPS protocol version 5.3 was adapted to our setting and used as a data collection tool. FINDINGS: 105 patients were included in the analysis; median age was 34 (IQR: 24-47) years and 55.2% patients were male. Point prevalence of HAI was 11.4% (n=12/105) (95% CI: 6.0%-19.1%), including four surgical site infections, four urinary tract infections, three bloodstream infections and one bone/joint infection. We identified the following risk factors for HAI; length-of-stay between 8 and 14 days (OR=14.4, 95% CI: 1.65-124.7, p=0.0143), presence of indwelling urinary catheter (OR=8.3, 95% CI: 2.24-30.70, p=0.003) and history of surgery in the past 30 days (OR=5.11, 95% CI: 1.46-17.83, p=0.011). 29/105 patients (27.6%) were prescribed antimicrobials, most commonly the 3rd-generation cephalosporin, ceftriaxone (n=15). CONCLUSION: The prevalence rates of HAI and antimicrobial use in surgery wards at QECH are relatively high. Hospital infection prevention and control measures need to be strengthened to reduce the burden of HAI at QECH.

Plasma cytokines quantification among Trypanosoma brucei rhodesiense sleeping sickness cases and controls in Rumphi, Malawi.

Introduction: Trypanosoma brucei (T.b.) rhodesiense is the cause of the acute form of human African trypanosomiasis (HAT) in eastern and southern African countries, including Malawi. For a long time, untreated HAT infections were believed to be 100% fatal. However, recent studies show that infection by T.b. rhodesiense can result in a wide range of clinical outcomes in its human host. Apart from other factors such as parasite diversity, cytokines have been strongly implicated to play a major role in the outcome of T.b. rhodesiense infections.In this study, we quantify the levels of three cytokines Interleukin-8 (IL-8), Tumor Necrotic Factor alpha (TNF-α) and Interleukin -10 (IL-10) in plasma amongst HAT cases (treated and untreated) and controls recruited during medical survey. Methods: Two-hundred and thirty-three plasma samples (HAT cases and controls) from Rumphi, one of the endemic areas in Malawi were used. Blood collected was centrifuged, plasma extracted and stored in cryovials at -80°C until processing. Plasma cytokine concentration was measured using ELISA. Results: Plasma samples for 233 individuals, 76 HAT cases and 157 controls were quantified. Among the cases, nine had their plasma collected before treatment (untreated) and the rest were treated before blood for plasma analysis was collected. Controls had significantly higher mean plasmatic levels of TNF-α (94.5 ±474.12 pg/ml) and IL-8 (2258.6 ±5227.4 pg/ml) than cases TNF-α (29.35±181.58 pg/ml) and IL-8 (1191.3±4236.09 pg/ml). Controls and cases had similar mean levels of IL-10 in plasma. Only IL-8 had statistically significant higher median levels in the untreated than treated HAT cases P=0.006. Conclusion: Our data suggest that cytokines could be considered as biomarkers of HAT infection and treatment. Further studies with a larger cohort of cases and additional cytokines which are known to be associated with HAT infection outcomes will be required to evaluate these cytokines further.

Development of a bio-inkjet printed LAMP test kit for detecting human African trypanosomiasis.

Human African trypanosomiasis (HAT) is one of the neglected tropical diseases in sub-Saharan Africa. Early diagnosis and treatment prior to disease progression are crucial for the survival of HAT patients. We had previously established a loop-mediated isothermal amplification (LAMP) method for HAT diagnosis in which the reagents were dried for field-use purposes. In this study, we used a semi-automated process to produce the test tubes using a bio-inkjet printer to achieve an accurate production. The performance of the inkjet printer-produced dried LAMP test (CZC-LAMP) was found to be stable after storage for up to 180 days at 30 °C. The diagnostic accuracy of CZC-LAMP HAT was evaluated using DNA samples that were extracted from 116 Trypanosoma brucei gambiense patients and 66 T. b. rhodesiense patients. The sensitivity was 72% for T. b. gambiense (95%CI: 63%-80%) and 80% for T. b. rhodesiense (95%CI: 69%-89%). The specificity determined using DNA from 116 endemic control DNA samples was 95% (95%CI: 89%-98%). The performance of the CZC-LAMP HAT and CZC-LAMP rHAT were also evaluated using 14 crude blood lysate samples obtained from T. b. rhodesiense patients and endemic control samples collected from Rumphi District in Malawi. The sensitivity and specificity were both 100% (95%CI: 77%-100%). As the developed CZC-LAMP test does not require a cold chain or a sophisticated laboratory, it holds promise for use as a routine simple molecular tool for point-of-care HAT diagnosis in endemic areas.

An outbreak of intestinal schistosomiasis, alongside increasing urogenital schistosomiasis prevalence, in primary school children on the shoreline of Lake Malawi, Mangochi District, Malawi.

BACKGROUND: Intestinal schistosomiasis was not considered endemic in Lake Malawi until November 2017 when populations of Biomphalaria pfeifferi were first reported; in May 2018, emergence of intestinal schistosomiasis was confirmed. This emergence was in spite of ongoing control of urogenital schistosomiasis by preventive chemotherapy. Our current study sought to ascertain whether intestinal schistosomiasis is transitioning from emergence to outbreak, to judge if stepped-up control interventions are needed. METHODS: During late-May 2019, three cross-sectional surveys of primary school children for schistosomiasis were conducted using a combination of rapid diagnostic tests, parasitological examinations and applied morbidity-markers; 1) schistosomiasis dynamics were assessed at Samama (n = 80) and Mchoka (n = 80) schools, where Schistosoma mansoni was first reported, 2) occurrence of S. mansoni was investigated at two non-sampled schools, Mangochi Orphan Education and Training (MOET) (n = 60) and Koche (n = 60) schools, where B. pfeifferi was nearby, and 3) rapid mapping of schistosomiasis, and B. pfeifferi, conducted across a further 8 shoreline schools (n = 240). After data collection, univariate analyses and Chi-square testing were performed, followed by binary logistic regression using generalized linear models, to investigate epidemiological associations. RESULTS: In total, 520 children from 12 lakeshore primary schools were examined, mean prevalence of S. mansoni by 'positive' urine circulating cathodic antigen (CCA)-dipsticks was 31.5% (95% confidence interval [CI]: 27.5-35.5). Upon comparisons of infection prevalence in May 2018, significant increases at Samama (relative risk [RR] = 1.7, 95% CI: 1.4-2.2) and Mchoka (RR = 2.7, 95% CI: 1.7-4.3) schools were observed. Intestinal schistosomiasis was confirmed at MOET (18.3%) and Koche (35.0%) schools, and in all rapid mapping schools, ranging from 10.0 to 56.7%. Several populations of B. pfeifferi were confirmed, with two new eastern shoreline locations noted. Mean prevalence of urogenital schistosomiasis was 24.0% (95% CI: 20.3-27.7). CONCLUSIONS: We notify that intestinal schistosomiasis, once considered non-endemic in Lake Malawi, is now transitioning from emergence to outbreak. Once control interventions can resume after coronavirus disease 2019 (COVID-19) suspensions, we recommend stepped-up preventive chemotherapy, with increased community-access to treatments, alongside renewed efforts in appropriate environmental control.

Molecular identification of trypanosomes in cattle in Malawi using PCR methods and nanopore sequencing: epidemiological implications for the control of human and animal trypanosomiases.

This study aimed to identify trypanosomes infecting cattle in Malawi in order to understand the importance of cattle in the transmission dynamics of Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). A total of 446 DNA samples from cattle blood from three regions of Malawi were screened for African trypanosomes by ITS1 PCR. The obtained amplicons were sequenced using a portable next-generation sequencer, MinION, for validation. Comparison of the results from ITS1 PCR and MinION sequencing showed that combining the two methods provided more accurate species identification than ITS1 PCR alone. Further PCR screening targeting the serum resistance-associated (SRA) gene was conducted to detect Trypanosoma brucei rhodesiense. Trypanosoma congolense was the most prevalent Trypanosoma sp., which was found in Nkhotakota (10.8%; 20 of 185), followed by Kasungu (2.5%; 5 of 199). Of note, the prevalence of T. b. rhodesiense detected by SRA PCR was high in Kasungu and Nkhotakota showing 9.5% (19 of 199) and 2.7% (5 of 185), respectively. We report the presence of animal African trypanosomes and T. b. rhodesiense from cattle at the human-livestock-wildlife interface for the first time in Malawi. Our results confirmed that animal trypanosomes are important causes of anemia in cattle and that cattle are potential reservoirs for human African trypanosomiasis in Malawi.

TITLE: Identification moléculaire des trypanosomes chez les bovins du Malawi, à l'aide de méthodes de PCR et du séquençage par nanopores : implication épidémiologique pour le contrôle des trypanosomiases humaines et animales. ABSTRACT: Cette étude visait à identifier les trypanosomes infectant les bovins au Malawi afin de comprendre l'importance des bovins dans la dynamique de transmission de la trypanosomiase humaine africaine (THA) et de la trypanosomose animale africaine (TAA). Au total, 446 échantillons d'ADN de sang de bovins provenant de trois régions du Malawi ont été soumis à un dépistage des trypanosomes africains par PCR de l'ITS1. Les amplicons obtenus ont été séquencés à l'aide d'un séquenceur portable de nouvelle génération, MinION, pour validation. La comparaison des résultats de la PCR de l'ITS1 et de la séquence MinION a montré que la combinaison des deux méthodes permettait une identification plus précise des espèces que la seule PCR de l'ITS1. Un autre dépistage par PCR ciblant le gène SRA (associé à la résistance du sérum) a été effectué pour détecter Trypanosoma brucei rhodesiense. Trypanosoma congolense était l'espèce de trypanosome la plus répandue, trouvée à Nkhotakota (10,8 % ; 20 sur 185), suivi de Kasungu (2,5 % ; 5 sur 199). Notamment, la prévalence de T. b. rhodesiense détectée par PCR de SRA était élevée à Kasungu et Nkhotakota, avec respectivement 9,5 % (19 sur 199) et 2,7 % (5 sur 185). Nous rapportons la présence de trypanosomes animaux africains et de T. b. rhodesiense de bovins à l'interface homme-bétail-faune sauvage, pour la première fois au Malawi. Nos résultats confirment que les trypanosomes animaux sont des causes importantes d'anémie chez les bovins et que les bovins sont des réservoirs potentiels pour la trypanosomiase humaine africaine au Malawi.

Health Outcomes of an Integrated Behaviour-Centred Water, Sanitation, Hygiene and Food Safety Intervention-A Randomised before and after Trial.

Diarrhoeal disease in children under five in low income settings has been associated with multiple environmental exposure pathways, including complementary foods. Conducted from February to December 2018 in rural Malawi, this before and after trial with a control used diarrhoeal disease as a primary outcome, to measure the impact of a food hygiene intervention (food hygiene + handwashing) relative to a food hygiene and water, sanitation and hygiene (WASH) intervention (food hygiene + handwashing + faeces management + water management). The 31-week intervention was delivered by community-based coordinators through community events (n = 2), cluster group meetings (n = 17) and household visits (n = 14). Diarrhoeal disease was self-reported and measured through an end line survey, and daily diaries completed by caregivers. Difference-in-differences results show a 13-percentage point reduction in self-reported diarrhoea compared to the control group. There were also significant increases in the presence of proxy measures in each of the treatment groups (e.g., the presence of soap). We conclude that food hygiene interventions (including hand washing with soap) can significantly reduce diarrhoeal disease prevalence in children under five years in a low-income setting. Therefore, the promotion of food hygiene practices using a behaviour-centred approach should be embedded in nutrition and WASH policies and programming.

Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi.

Trypanosoma brucei (T.b.) rhodesiense is the cause of the acute form of human African trypanosomiasis (HAT) in eastern and southern African countries. There is some evidence that there is diversity in the disease progression of T.b. rhodesiense in different countries. HAT in Malawi is associated with a chronic haemo-lymphatic stage infection compared to other countries, such as Uganda, where the disease is acute with more marked neurological impairment. This has raised the question of the role of host genetic factors in infection outcomes. A candidate gene association study was conducted in the northern region of Malawi. This was a case-control study involving 202 subjects, 70 cases and 132 controls. All individuals were from one area; born in the area and had been exposed to the risk of infection since birth. Ninety-six markers were genotyped from 17 genes: IL10, IL8, IL4, HLA-G, TNFA, IL6, IFNG, MIF, APOL, HLA-A, IL1B, IL4R, IL12B, IL12R, HP, HPR, and CFH. There was a strong significant association with APOL1 G2 allele (p = 0.0000105, OR = 0.14, CI95 = [0.05-0.41], BONF = 0.00068) indicating that carriers of the G2 allele were protected against T.b. rhodesiense HAT. SNP rs2069845 in IL6 had raw p < 0.05, but did not remain significant after Bonferroni correction. There were no associations found with the other 15 candidate genes. Our finding confirms results from other studies that the G2 variant of APOL1 is associated with protection against T.b. rhodesiense HAT.

Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi.

The tsetse fly, Glossina morsitans morsitans, is a significant problem in Zambia and Malawi. It is the vector for the human infective parasite Trypanosoma brucei rhodesiense, which causes human African trypanosomiasis, and various Trypanosoma species, which cause African animal trypanosomiasis. Understanding the genetic diversity and population structure of G. m. morsitans is the basis of elucidating the connectivity of the tsetse fly populations, information that is essential in implementing successful tsetse fly control activities. This study conducted a population genetic study using partial mitochondrial cytochrome oxidase gene 1 (CO1) and 10 microsatellite loci to investigate the genetic diversity and population structure of G. m. morsitans captured in the major HAT foci in Zambia and Malawi. We have included 108 and 99 G. m. morsitans samples for CO1 and microsatellite analyses respectively. Our results suggest the presence of two different genetic clusters of G. m. morsitans, existing East and West of the escarpment of the Great Rift Valley. We have also revealed genetic similarity between the G. m. morsitans in Kasungu National Park and those in the Luangwa river basin in Zambia, indicating that this population should also be included in this historical tsetse belt. Although further investigation is necessary to illustrate the whole picture in East and Southern Africa, this study has extended our knowledge of the population structure of G. m. morsitans in Southern Africa.

Strengthening primary health care at district-level in Malawi - determining the coverage, costs and benefits of community-directed interventions.

BACKGROUND: Community-Directed Interventions (CDI) is a participatory approach for delivery of essential healthcare services at community level. It is based on the values and principles of Primary Health Care (PHC). The CDI approach has been used to improve the delivery of services in areas that have previously applied Community-Directed Treatment with ivermectin (CDTi). Limited knowledge is available about its added value for strengthening PHC services in areas without experience in CDTi. This study aimed to assess how best to use the CDI approach to strengthen locally identified PHC services at district level. METHODS: This was a comparative intervention study carried out over a period of 12 months and involving four health centres and 16 villages assigned to 1) a conventional Essential Health Package (EHP)/PHC approach at health centre level or 2) an EHP/PHC/CDI approach at community level in addition to EHP/PHC at health centre level. Communities decided which intervention components to be included in the intervention. These were home management of malaria (HMM), long lasting insecticide treated nets (LLIN), vitamin A and treatment against schistosomiasis. The outcomes of the two strategies were compared quantitatively after the intervention was completed with regard to intervention component coverage and costs. Qualitative in-depth interviews with involved health professionals, implementers and beneficiaries were carried out to determine the benefits and challenges of applied intervention components. RESULTS: Implementation of the EHP/PHC/CDI approach at community level as an add-on to EHP/PHC services is feasible and acceptable to health professionals, implementers and beneficiaries. Statistically significant increases were observed in intervention components coverage for LLIN among children under 5 years of age and pregnant women. Increases were also observed for HMM, vitamin A among children under 5 years of age and treatment against schistosomiasis but these increases were not statistically significant. Implementation was more costly in EHP/PHC/CDI areas than in EHP/PHC areas. Highest costs were accrued at health centre level while transport was the most expensive cost driver. The study identified certain critical factors that need to be considered and adapted to local contexts for successful implementation. CONCLUSION: The CDI approach is an effective means to increase accessibility of certain vital services at community level thereby strengthening delivery of EHP/PHC services. The approach can therefore complement regular EHP/PHC efforts. TRIAL REGISTRATION: The study was retrospectively registered with the Pan African Clinical Trial Registry TRN: PACTR201903883154921 .