In Vitro Confirmation of Artemisinin Resistance in Plasmodium falciparum from Patient Isolates, Southern Rwanda, 2019.

Artemisinin resistance in Plasmodium falciparum is conferred by mutations in the kelch 13 (K13) gene. In Rwanda, K13 mutations have increased over the past decade, including mutations associated with delayed parasite clearance. We document artemisinin resistance in P. falciparum patient isolates from Rwanda carrying K13 R561H, A675V, and C469F mutations.

Increase in Kelch 13 Polymorphisms in Plasmodium falciparum, Southern Rwanda.

Artemisinin resistance in Plasmodium falciparum is associated with nonsynonymous mutations in the Kelch 13 (K13) propeller domain. We found that 12.1% (8/66) of clinical P. falciparum isolates from Huye district, Rwanda, exhibited K13 mutations, including R561H, a validated resistance marker. K13 mutations appear to be increasing in this region.

Changing Pattern of Plasmodium falciparum pfmdr1 Gene Polymorphisms in Southern Rwanda.

Plasmodium falciparum multidrug resistance-1 gene (pfmdr1) polymorphisms associate with altered antimalarial susceptibility. Between 2010 and 2018/2019, we observed that the prevalence of the wild-type allele N86 and the wild-type combination NYD increased 10-fold (4% versus 40%) and more than 2-fold (18% versus 44%), respectively. Haplotypes other than NYD or NFD declined by up to >90%. Our molecular data suggest the pfmdr1 pattern shifted toward one associated with artemether-lumefantrine resistance.

Co-infections with Plasmodium, Ascaris and Giardia among Rwandan schoolchildren.

OBJECTIVES: Co-infections with Plasmodium, Ascaris and Giardia are common in sub-Saharan Africa but epidemiological and clinical data are rare. We examined factors associated with co-infections and their clinical manifestation among Rwandan schoolchildren. METHODS: Schoolchildren aged 6-10 years attending 12 schools in Huye district, Rwanda, were recruited preceding routine deworming. Data on socioeconomic status (SES) and children's histories were obtained, and children were clinically and anthropometrically examined. Blood and stool samples were collected, and infections with Plasmodium, Ascaris and Giardia were determined by microscopy and PCR assays. RESULTS: Among 878 schoolchildren, Plasmodium, Ascaris and Giardia were present in 22%, 35% and 36%, respectively. Co-infections with two or more parasites were found in 24%; only one-third of the children did not harbour any of the parasites examined. Factors associated with parasite (co-)infections largely overlapped and reflected low SES, in addition to a few specific risk factors. Clinically, most children were asymptomatic but anaemia (38%), underweight (17%), and reported signs and symptoms in the preceding 2 weeks (46%) were common. Many of the reported and assessed signs and symptoms were associated with Plasmodium infection, and co-infection with Ascaris and/or Giardia did basically not modify the clinical picture. One exception was malnutrition, which was pronounced in Ascaris-Giardia co-infection vs. individual mono-infections. CONCLUSIONS: Parasitic co-infections are common in Rwandan schoolchildren, and are associated with a rather silent clinical manifestation that nevertheless may affect school performance and long-term development. School-based health interventions should target such co-infections in an integrated manner.

OBJECTIFS: Les coinfections par Plasmodium, Ascaris et Giardia sont courantes en Afrique subsaharienne, mais les données épidémiologiques et cliniques sont rares. Nous avons examiné les facteurs associés aux coinfections et leurs manifestations cliniques chez les écoliers rwandais. MÉTHODES: Des écoliers âgés de 6 à 10 ans fréquentant 12 écoles du district de Huye au Rwanda ont été recrutés avant le déparasitage de routine. Les données sur le statut socioéconomique (SSE) et les antécédents des enfants ont été obtenues et les enfants ont été examinés cliniquement et anthropométriquement. Des échantillons de sang et de selles ont été recueillis et les infections à Plasmodium, Ascaris et Giardia ont été déterminées par microscopie et par PCR. RÉSULTATS: sur 878 écoliers, Plasmodium, Ascaris et Giardia étaient présents chez 22%, 35% et 36%, respectivement. Des coinfections avec deux parasites ou plus ont été trouvées chez 24%; seul un tiers des enfants n'hébergeait aucun des parasites examinés. Les facteurs associés aux (co)infections parasitaires se chevauchaient largement et reflétaient un faible statut SSE, en plus de quelques facteurs de risque spécifiques. Sur le plan clinique, la plupart des enfants étaient asymptomatiques mais l'anémie (38%), l'insuffisance pondérale (17%) et les signes et symptômes rapportés au cours des deux semaines précédentes (46%) étaient fréquents. De nombreux signes et symptômes rapportés et évalués étaient associés à l'infection au Plasmodium et la coinfection par Ascaris et/ou Giardia n'a fondamentalement pas modifié le tableau clinique. Une exception était la malnutrition, qui était prononcée dans la coinfection Ascaris-Giardia par rapport aux mono-infections individuelles. CONCLUSIONS: Les coinfections parasitaires sont courantes chez les écoliers rwandais et sont associées à une manifestation clinique plutôt silencieuse qui peut néanmoins affecter les performances scolaires et le développement à long terme. Les interventions de santé en milieu scolaire devraient cibler ces coinfections de manière intégrée.

Efficacy of Helicobacter pylori eradication regimens in Rwanda: a randomized controlled trial.

BACKGROUND: Successful H. pylori treatment requires the knowledge of local antimicrobial resistance. Data on the efficacy of H. pylori eradication regimens available in sub-Saharan Africa are scant, hence the optimal treatment is unknown. Our goals were to determine the efficacy of available regimens in Rwanda as well as evaluate the effect of treatment on health-related quality of life (HRQoL) in patients undergoing esophagogastroduodenoscopy. METHODS: This is a randomized controlled trial conducted from November 2015 to October 2016 at a tertiary hospital in Rwanda. Enrollees were 299 patients (35% male, age 42 ± 16 years (mean ± SD)) who had a positive modified rapid urease test on endoscopic biopsies. After a fecal antigen test (FAT) and HRQoL assessment by the Short Form Nepean Dyspepsia Index (SF-NDI) questionnaire, patients were randomized 1:1:1:1 to either a triple therapy combining omeprazole, amoxicillin and one of clarithromycin/ciprofloxacin/metronidazole or a quadruple therapy combining omeprazole, amoxicillin, ciprofloxacin and doxycycline. All therapies were given for a duration of 10 days. The outcome measures were the persistence of positive FAT (treatment failure) 4 to 6 weeks after treatment and change in HRQoL scores. RESULTS: The treatment success rate was 80% in the total population and 78% in patients with a history of prior triple therapy. Significant improvement in HRQoL in the total group (HRQoL mean scores before and after treatment respectively: 76 ± 11 and 32 ± 11, p < 0.001) and the group with functional dyspepsia (HRQoL mean scores before and after treatment respectively: 73 ± 11 and 30 ± 9, P < 0.001) was observed across all treatment groups. Using clarithromycin based triple therapy (standard of care) as a reference, the group treated with metronidazole had worse HRQoL (p = 0.012) and had a trend towards worse treatment outcome (p = 0.086) compared to the ciprofloxacin based combination therapies. CONCLUSION: Clarithromycin and ciprofloxacin based combination therapies are effective and safe to use alternatively for H. pylori eradication and improve HRQoL. Among the regimens studied, metronidazole based triple therapy is likely to be clinically inferior. TRIAL REGISTRATION: The clinical trial was retrospectively registered ( PACTR201804003257400 ) with the Pan African Clinical Trial Registry database, on April 6th, 2018 in South Africa.

Intense pre-admission carriage and further acquisition of ESBL-producing Enterobacteriaceae among patients and their caregivers in a tertiary hospital in Rwanda.

OBJECTIVES: To assess the presence and risk factors of intestinal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) among patients admitted to the University Teaching Hospital of Butare and among their attending caregivers, and to analyse the acquisition of ESBL-PE carriage during hospital stay and associated factors. METHODS: We screened 392 patients and their attending caregivers at admission and discharge for ESBL-PE carriage. Bacterial species were determined using the API-20E system, and antimicrobial susceptibility testing was performed by agar disc diffusion. Data on socio-economic status, diet, behaviour, household assets, livestock and hospital procedures were collected. RESULTS: At admission, 50% of the patients showed intestinal ESBL-PE carriage (Escherichia coli, 51%; Klebsiella pneumoniae, 39%; Enterobacter cloacae, 19%) as did 37% of their caregivers. Co-resistance was common but no carbapenem resistance was detected. At discharge, the proportion of ESBL-PE-colonised patients increased to 65% (caregivers, 47%) with almost complete carriage in paediatric patients (93%). The acquisition rate among initially non-colonised patients was 55% (or, 71/1000 patient days). Independent predictors of admission carriage included a colonised caregiver, prior antibiotic intake, egg consumption and neglecting to boil drinking water, whereas being a paediatric patient, undergoing surgery and male gender predicted acquisition during hospitalisation. CONCLUSIONS: Abundant admission carriage of ESBL-PE and a high acquisition rate in a Rwandan university hospital point to potential intrahospital transmission and community dissemination. Caregivers are an additional source of possible spread. Risk factors of colonisation such as diet and water source need to be tackled to prevent the further emergence and spread of ESBL-PE.

Asymptomatic only at first sight: malaria infection among schoolchildren in highland Rwanda.

BACKGROUND: Plasmodium infection and malaria in school children are increasingly recognized as a relevant public health problem, but data on actual prevalence and health consequences are insufficient. The present study from highland southern Rwanda aimed at estimating infection prevalence among children attending school, at identifying associated factors and at assessing the clinical consequences of these infections. METHODS: In a survey including 12 schools in the Huye district of Rwanda, 1089 children aged 6-10 years were clinically and anthropometrically examined, malaria parasites were diagnosed by microscopy and PCR, haemoglobin concentrations were measured, and socio-economic and behavioural parameters as well as medical histories were obtained. RESULTS: Upon examination, the vast majority of children was asymptomatic (fever 2.7%). Plasmodium infection was detected in 22.4% (Plasmodium falciparum, 18.8%); 41% of these were submicroscopic. Independent predictors of infection included low altitude, higher age, preceding antimalarial treatment, and absence of electricity or a bicycle in the household. Plasmodium infection was associated with anaemia (mean haemoglobin difference of -1.2 g/dL; 95% CI, -0.8 to -1.5 g/dL), fever, underweight, clinically assessed malnutrition and histories of fever, tiredness, weakness, poor appetite, abdominal pain, and vomiting. With the exception of underweight, these conditions were also increased at submicroscopic infection. CONCLUSION: Malaria infection is frequent among children attending school in southern highland Rwanda. Although seemingly asymptomatic in the vast majority of cases, infection is associated with a number of non-specific symptoms in the children´s histories, in addition to the impact on anaemia. This argues for improved malaria surveillance and control activities among school children.

Plasmodium vivax Malaria in Duffy-Positive Patients in Rwanda.

Plasmodium vivax is the second-most common malaria pathogen globally, but is considered very rare in the predominantly Duffy-negative sub-Saharan African population. In 259 malaria patients from highland southern Rwanda, we assessed Plasmodium species and Duffy blood group status by polymerase chain reaction (PCR). Plasmodium falciparum, P. vivax, Plasmodium malariae, and Plasmodium ovale were seen in 90.7%, 8.1%, 11.6%, and 5.0%, respectively. Plasmodium vivax occurred more frequently as a monoinfection than in combination with P. falciparum. All P. vivax-infected individuals showed heterozygous Duffy positivity, whereas this was the case for only 3.1% of patients with P. falciparum monoinfection and malaria-negative control subjects (P < 0.01). Based on PCR diagnosis, P. vivax is not rare in southern Rwanda. All episodes of P. vivax were observed in heterozygous Duffy-positive patients, whereas elsewhere in Africa, P. vivax is also reported in Duffy-negative individuals. Refined mapping of Plasmodium species is required to establish control and elimination strategies including all malaria species.

Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda.

Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes bla CTX-M-15 , tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.

Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131.

Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics to study MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance of different MRGN including E. coli pathogenic lineage ST131 suggesting the important role of flies in disseminating highly virulent pathogens in clinical settings and beyond.

The use of Perioscan as a potential screening test for mothers at risk for delivery of pre-term and low birth-weight infants.

Increased levels of oestrogen and progesterone during pregnancy may lead to periodontal disease. The anaerobic Gram-negative bacteria classified as the "red complex" (Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola) are frequently associated with periodontal disease. Periodontopathogens produce toxins and enzymes that can enter the bloodstream and cross the placenta to harm the foetus. The response of the mother's immune system to infection by these periodontopathogens brings about the release of inflammatory mediators which may trigger preterm labour or result in low birth-weight infants. The purpose of this study was to examine the use of Perioscan as a potential screening test for mothers at risk for pre-term delivery of low birth weight infants due to periodontal disease. Subgingival plaque samples were obtained from pregnant women between the ages of 17 to 45 years attending an ante-natal clinic in the Western Cape in South Africa. Plaque samples were analyzed by the enzymatic Perioscan test for detection of the red complex in 372 sites from 66 women. Results were confirmed by polymerase chain reaction (PCR) detection of the three species of the red complex. Seventeen (25.75%) of the population group tested positive with Perioscan but only 27 (7.25%) of the 372 sites were positive. Of the 66 mothers examined, we managed to retrieve 29 records post-delivery. In all the mothers examined, Perioscan results showed an association with the indices used to diagnose periodontal disease, and could also be associated with preterm delivery of low birth-weight infants in two of the 29 maternal records recovered.

Prevalence of Strongyloides stercoralis infection and other soil-transmitted helminths by cross-sectional survey in a rural community in Gisagara District, Southern Province, Rwanda.

Background: Strongyloides stercoralis is one of the most neglected tropical diseases. Sparse, dated central African and Rwandan data on seroprevalence are available to guide public health efforts and clinical care. Methods: In February 2016 we conducted a community-based cross-sectional study among 539 asymptomatic participants in a rural area in the Gisagara District, Southern Province, Rwanda. Direct faecal smear (DFS) and modified Koga agar plate culture (APC) were used to detect S. stercoralis infection in a single stool sample. Data on other soil-transmitted helminths diagnosed by DFS were also recorded. Results: Four intestinal helminth infections were diagnosed, with S. stercoralis (17.4%) and hookworms (8.2%) seen most often. APC, compared with DFS, increased the diagnosis rate for S. stercoralis from 1.9% to 17.4% (p<0.01). The prevalence was higher in farmers and those with lower socio-economic status. Females were less often infected than males (odds ratio 0.6 [95% confidence interval 0.3 to 0.9], p=0.02). Conclusions: S. stercoralis is highly prevalent among the general population in a rural area of Gisagara District, Southern Province, Rwanda. Access to effective diagnosis and treatment is needed for this neglected disease.

Reduced efficacy of albendazole against Ascaris lumbricoides in Rwandan schoolchildren.

Control of human soil-transmitted helminths (STHs) relies on preventive chemotherapy of schoolchildren applying the benzimidazoles (BZ) albendazole or mebendazole. Anthelmintic resistance (AR) is a common problem in nematodes of veterinary importance but for human STHs, information on drug efficacy is limited and routine monitoring is rarely implemented. Herein, the efficacy of single dose albendazole (400 mg) was evaluated in 12 schools in the Huye district of Rwanda where Ascaris is the predominant STH. Ascaris eggs were detected by wet mount microscopy and the Mini-FLOTAC method to assess cure rate (CR) and faecal egg count reduction (FECR). Blood and faecal samples were analysed for co-infections with Plasmodium sp. and Giardia duodenalis, respectively. Ascaris positive samples collected before and after treatment were analysed for putatively BZ-resistance associated ß-tubulin gene single nucleotide polymorphisms. The overall CR was 69.9% by Mini-FLOTAC and 88.6% by wet mount microscopy. The FECR was 75.4% and the 95% calculated confidence intervals were 50.4-87.8% using sample variance, 55.4-88.8% by bootstrapping, and 75.0-75.7% applying a Markov Chain Monte Carlo Bayesian approach. FECR varied widely between 0 and 96.8% for individual schools. No putative BZ-resistance associated polymorphisms were found in the four Ascaris ß-tubulin isotype genes examined. Since FECRs <95% indicate reduced efficacy, these findings raise the suspicion of BZ resistance. In the absence of respective molecular evidence, heritable AR in the local Ascaris populations cannot be formally proven. However, since FECRs <95% indicate reduced efficacy, BZ resistance may be suspected which would be alarming and calls for further analyses and routine monitoring in preventive chemotherapy programs.

Artemisinin Resistance-Associated K13 Polymorphisms of Plasmodium falciparum in Southern Rwanda, 2010-2015.

Emerging artemisinin resistance is a threat to global malaria control. Mutations in the Plasmodium falciparum Kelch 13 (K13) propeller domain confer artemisinin resistance and constitute molecular markers for its detection and monitoring. We sequenced 222 P. falciparum isolates obtained from community children in the Huye District of southern Rwanda in 2010, 2014, and 2015 to investigate the presence of K13 polymorphisms. No polymorphisms were observed in 2010 but they were present in 2.5% and 4.5% in 2014 and 2015, respectively. In 2015, two isolates showed candidate K13 resistance mutations (P574L and A675V), which are common in southeast Asia and associated with delayed parasite clearance. K13 polymorphisms in southern Rwanda are infrequent but include variants associated with artemisinin resistance. Establishing correlations with local treatment response and in vitro resistance assays are needed in addition to further monitoring K13 polymorphisms in the study area.

Decreased susceptibility to commonly used antimicrobial agents in bacterial pathogens isolated from urinary tract infections in Rwanda: need for new antimicrobial guidelines.

The aim of this study was to obtain data on susceptibility patterns of pathogens responsible for both community and hospital urinary tract infections (UTIs); and analyzed risk factors for infection caused by ciprofloxacin-resistant Escherichia coli and extended-spectrum ß-lactamase (ESBL)-producing strains in Rwanda. Of 1,012 urine cultures prospectively studied, a total of 196 (19.3%) yielded significant growth of a single organism. The most common isolate (60.7%) was Escherichia coli. The antibiotics commonly used in UTIs are less effective except Fosfomycin-trometamol and imipinem. The use of ciprofloxacin in the previous 6 months (odds ratio [OR] = 7.59 [1.75-32.74]), use of other antibiotics in the previous 6 months (OR = 1.02 [1.02-2.34]), and production of ESBL (OR = 19.32 [2.62-142.16]) were found to be associated with ciprofloxacin resistance among the E. coli isolates. Risk factors for ESBL positivity were the use of ciprofloxacin and third-generation cephalosporin in the preceding 6 months (OR = 3.05 [1.42-6.58] and OR = 9.78 [2.71-35.25], respectively); and being an inpatient (OR = 2.27 [1.79-2.89]). Fosfomycin-trometamol could be included as a reasonable alternative for the therapy of uncomplicated UTI in Rwanda.

Examination of maternal gingival crevicular fluid for the presence of selected periodontopathogens implicated in the pre-term delivery of low birthweight infants.

BACKGROUND: Reports show that more than 20 million infants world-wide are born prematurely with 95% of all pre-term births occurring in developing countries. Oral colonization of gram-negative anaerobes has been implicated as a risk factor for preterm delivery of low birth weight infants. MATERIALS AND METHODS: This study comprised 200 women admitted to the department of obstetrics and gynecology of the teaching hospital of Butare in Rwanda. Gingival crevicular fluid was collected from each quadrant of the mother's mouth (using paper points) within 24 hours of delivery. A dichotomous score of presence or absence of gingival inflammation was recorded for each patient along with demographic data such as age, marital status etc. Samples were examined by PCR for the presence of Aggregatibacter actinomycetemcomitans and selected members of the red and orange complexes described by Socransky et al., (1998), and their presence associated with age, gingival inflammation and pregnancy outcomes. RESULTS: Association of bacterial species with the risk of periodontal disease and thus the risk of preterm delivery was only observed when they occurred in pairs or groups of three or more. Aa appeared to be a necessary co-factor for significant associations of bacterial groups with the variables recorded.