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Background Accurate diagnosis of malaria infection is essential for successful control and management of the disease. Both microscopy and rapid diagnostic tests (RDTs) are recommended for malaria diagnosis, however, RDTs are more commonly used. The aim of the current study was to assess the performance of microscopy and RDTs in the diagnosis of Plasmodium falciparum infection using a nested polymerase chain reaction (PCR) assay as the gold standard. Methods A cross-sectional study was carried out in Kassala Hospital, eastern Sudan. A total of 341 febrile participants of all ages were recruited. Blood specimens were collected and malaria testing was performed using an RDT (SD Bioline Malaria Ag Pf), microscopy and nested PCR. The sensitivity, specificity, positive and negative predictive values (PPV and NPV, respectively) of microscopy and the RDT were investigated. Results The prevalence of P. falciparum malaria infections in this study was 22.9%, 24.3% and 26.7% by PCR, microscopy and RDT, respectively. Compared with microscopy, the RDT had slightly higher sensitivity (80.7% vs 74.3%; p=0.442), equivalent specificity (89.3% vs 90.4%), a similar PPV (69.2% vs 69.8%) and a higher NPV (94.0% vs 92.2%). Conclusions The diagnostic performance of the RDT was better than that of microscopy in the diagnosis of P. falciparum malaria when nested PCR was used as the gold standard.

Arboviruses (dengue, Zika, and chikungunya) have recently emerged as an important public health issue and can lead to adverse obstetrics outcomes. The current study was conducted to assess maternal and perinatal outcomes following chikungunya fever/infection and to compare adverse pregnancy outcomes with data from the community collected in a previous study.This study was performed during a chikungunya infection epidemic in Kassala, Sudan by recruiting all pregnant women with a confirmed chikungunya fever diagnosis by using antibodies/detection viral RNA using reverse transcriptase-polymerase chain reaction.Ninety-three pregnant women with confirmed chikungunya infection were enrolled. Their mean (standard deviation) age and parity were 31.6 (3.4) years and 3.5 (1.4), respectively. Of the 93 women, 58 (62.4%) delivered a live infant at term and 18 (19.4%), 13 (13.9%), and 4 (4.3%) women experienced miscarriage, preterm birth, and stillbirth, respectively. In the logistic regression model, severe thrombocytopenia (platelets 50,000 cells/mmChikungunya infections during pregnancy were associated with miscarriage and preterm birth. Women with severe thrombocytopenia and leukopenia were at higher risk of poor obstetric outcomes. Women with severe thrombocytopenia and leukopenia were at higher risk of poor obstetric outcomes.

Background The public health impact of Chikungunya virus (CHIKV) is often underestimated. Usually considered a mild condition of short duration, recent outbreaks have reported greater incidence of severe illness, fatality, and longer-term disability. In 2018/19, Eastern Sudan experienced the largest epidemic of CHIKV in Africa to date, affecting an estimated 487,600 people. Known locally as Kankasha, this study examines clinical characteristics, risk factors, and phylogenetics of the epidemic in Kassala City. Methodology/Principal findings A prospective cohort of 102 adults and 40 children presenting with chikungunya-like illness were enrolled at Kassala Teaching Hospital in October 2018. Clinical information, socio-demographic data, and sera samples were analysed to confirm diagnosis, characterise illness, and identify viral strain. CHIKV infection was confirmed by real-time reverse transcription-PCR in 84.5% (120/142) of participants. Nine (7.5%) CHIKV-positive participants had concurrent Dengue virus (DENV) infection; 34/118 participants (28.8%) had a positive Rapid Diagnostic Test for Plasmodium falciparum; six (5.0%) had haemorrhagic symptoms including two children with life-threatening bleeding. One CHIKV-positive participant died with acute renal injury. Age was not associated with severity of illness although CHIKV-infected participants were younger (p = 0.003). Two to four months post-illness, 63% of adults available for follow-up (30) were still experiencing arthralgia in one or more joints, and 11% remained moderately disabled on Rapid3 assessment. Phylogenetic analysis showed all CHIKV sequences from this study belonged to a single clade within the Indian Ocean Lineage (IOL) of the East/Central/South African (ECSA) genotype. History of contact with an infected person was the only factor associated with infection (p = 0.01), and likely related to being in the same vector environment. Conclusions/Significance Vulnerability to CHIKV remains in Kassala and elsewhere in Sudan due to widespread Aedes aegypti presence and mosquito-fostering household water storage methods. This study highlights the importance of increasing awareness of the severity and impact of CHIKV outbreaks, and the need for urgent actions to reduce transmission risk in households., Author summary Chikungunya is an arboviral disease transmitted to humans by infected mosquitoes and characterised by fever and arthralgia. Although it is generally considered a short self-limiting infection, long term sequelae and severe disease are increasingly recognised. In 2018/19, Eastern Sudan experienced the largest epidemic of Chikungunya in Africa to date, affecting approximately 500,000 people. We undertook a prospective hospital-based cohort study of patients presenting with undifferentiated febrile illness in Kassala city, Sudan, supported by next-generation sequencing. We confirmed that CHIKV was the dominant pathogen, with positive CHIKV RT-PCR in 85% of patients presenting during the 7-day study period. Dengue virus was also circulating with nine CHIKV RT-PCR-positive patients co-infected, and we identified high rates of Plasmodium falciparum infection and CHIKV/P.falciparum co-infection. Genetic sequencing confirmed Indian Ocean Lineage of the East/Central/South African CHIKV genotype. A quarter of participants available for follow-up (16/60, 26.6%) reported being admitted to hospital including two children with haemorrhage, reflecting the severe phenotype linked to this genotype. Increased understanding of the health and economic burden of Chikungunya is needed, and recognition that severe and occasionally fatal infection exists. With widespread presence of Ae. aegypti and household water storage practices that encourage mosquito breeding, timely actions will be essential to prevent further large outbreaks.

Background Dengue fever (DF) is an arthropod-borne disease caused by dengue virus (DENV). DENV is a member of the genus Flavivirus in the family Flaviviridae. Recently, DENV has been reported as an important emerging infectious viral pathogen in Sudan. Multiple outbreaks and sporadic cases of DF have been frequently reported in the eastern region of Sudan. The present study was conducted to confirm DENV outbreak in Kassala State, eastern Sudan, 2019, and to provide some information on the molecular characterization of the DENV isolate associated with the disease outbreak. Methods A hundred serum samples were collected during the outbreak from residents of Kassala State, Sudan, 2019. ELISA was used to detect DENV non structural protein NS1 (DENV-NS1) in acute phase sera sampled during the disease outbreak. RT-PCR assays were used to amplify a fragment of the capsid/pre-membrane region (CprM) of the viral polyprotein gene. The PCR products of the amplified CprM region of the viral polyprotein gene were purified and partial sequences were generated and used to confirm the specificity of DENV sequences and to identify the virus serotype. Phylogenetic tree was constructed to determine the genotype of DENV associated with the outbreak. Results Using DENV-NS1 ELISA assay, DENV infection was confirmed in 23% sampled sera. The detection of DENV RNA was made possible using group-specific RT-PCR assay. The virus was serotyped as DENV serotype 3 (DENV-3) using DENV serotype-specific RT-PCR assay. Phylogenetic analysis of the partial CprM sequences of the viral polyprotein gene indicates that the virus belonged to genotype III of DENV-3. Conclusion The scientific data presented in this investigation confirmed that genotype III of DENV-3 was associated with the disease outbreak in eastern Sudan, 2019. The study represents the first report on molecular characterization of DENV-3 in Sudan.

Among patients who were pregnant and had visceral leishmaniasis infections at Gadarif Hospital, Sudan, a case–fatality rate of 18% was recorded. Visceral leishmaniasis is an endemic disease in tropical and subtropical regions [1–3]. The aim of the present cross-sectional, hospital-based study was to calculate the case–fatality rate of visceral leishmaniasis (the number of maternal deaths due to visceral leishmaniasis per 100 patients with visceral leishmaniasis) and to investigate factors associated with visceral leishmaniasis-related maternal death at Gadarif Hospital, Sudan. This article is protected by copyright. All rights reserved.

Objective: To investigate the prevalence of Helicobacter pylori (H. pylori) among patients with dyspepsia and to evaluate the correlation between H. pylori infection and socio-demographic factors. Methods: This cross-sectional hospital-based study, which ran from June to August 2012, determined seroprevalence of H. pylori among adult patients in Eastern Sudan. The presence of H. pylori was determined using ELISA. Results: A total of 225 adult Sudanese patients were enrolled in the study. Of these, 148 (65.8%) tested positive for H. pylori. In logistic regression analysis, rural residency (OR=3.933, CI=1.337- 11.26, P=0.01) was the only socio-demographic factor that was associated with H. pylori infection. The most common symptoms among seropositive patients were heartburn (OR=30.442, CI=9.478- 97.776, P≤0.001) and/or epigastria pain (OR=28.225, CI=4.365-182.508, P≤0.001). Conclusions: Clinical suspicion can facilitate the detection of H. pylori among patients with dyspeptic symptoms in a geographic area with high prevalence of H. pylori infection.

Summary: Because of the overlapping global incidence of tuberculosis (TB) and human immunodeficiency virus (HIV) infections, collaborative efforts are required for successful TB and HIV control programs. The current study was conducted at Kassala Hospital in Eastern Sudan and investigated the implementation of provider-initiated HIV testing and counseling (PITC) for patients infected with TB.Using a cross-sectional study design, patients who had been recently diagnosed with TB between January and December 2010 were consecutively enrolled. A total of 858 newly infected TB patients were enrolled in the study. Of these patients, 152 patients (17.7%) were given counseling, and 109 patients (12.7%) underwent HIV testing. The overall HIV infection rate among those tested was 18.3%. From a multivariate analysis, female sex (OR = 17.0, 95% CI = 8.7–33.1; P

Introduction: There is a need to investigate the treatment (artesunate and quinine) of severe malaria, as this will influence the outcome of morbidity and the mortality of the disease. Methodology: An open randomized trial conducted at Kassala, Sudan. Patients with severe P. falciparum malaria were randomly assigned to either intravenous artesunate at 2.4 mg/kg at 0, 12, and 24 hours, then daily, or intravenous quinine at a 20 mg/kg loading dose, then 10 mg/kg three times a day. Fever and parasite clearance and coma resolution time were compared between the two groups . Results: The two groups (47 in each group) were well matched in the clinical and biochemical characteristics. Hypotension, convulsions, severe anemia, hypoglycemia, cerebral malaria, and jaundice were the predominant manifestations of severe malaria. The mean (SD) of the fever clearance (10.8 [5.5] vs. 14.0 [8.1] hours, p = 0.028) and the parasite clearance time (16.5 [6.4] vs. 21.7 [11.3] hours, p = 0.007) were significantly shorter in the artesunate-treated patients. In comatose patients, there was no difference between the two groups in coma resolution time. Following quinine infusion, ten patients developed tinnitus (p < 0.001), and four had hypoglycemia (p = 0.033). Tinnitus and hypoglycemia were not detected in the artesunate group. One patient in the artesunate group died. Conclusions: Artesunate is more effective than quinine, in term of parasite and fever clearance time, in the treatment of P. falciparum malaria in eastern Sudan. The study found no difference between artesunate and quinine in coma resolution time.

Background Artemisinin-based combination therapy (ACT) is the treatment of choice for uncomplicated Plasmodium falciparum malaria in most areas of the world, where malaria is endemic, including Sudan. However, few published data are available on the use of ACT for treatment of P. vivax malaria. Methods This study was conducted at a health centre in Kassala, eastern Sudan, from October to December 2011. Patients with uncomplicated P. vivax malaria received artemether-lumefantrine (AL) tablets (containing 20mg artemether and 120 mg lumefantrine) and were monitored for 28 days. Results Out of the 43 cases enrolled in this study, 38 completed the 28-day follow-up. Their mean age was 25.1 years (SD: 1.5). On day 3 following AL treatment, all of the patients were afebrile and aparasitaemic. By day 28, all 38 patients exhibited adequate clinical and parasitological responses to AL treatment. The cure rate was 100% and 88.4% for the per protocol analysis andfor the intention to treat analysis, respectively. Mild adverse effects (nausea, vomiting, abdominal pain, dizziness and/or rash) that resolved spontaneously were observed in four (10.5%) of the patients. Conclusion AL combination therapy was fully effective for treatment of P. vivax malaria in the study in eastern Sudan. Trial registration Trial. Gov: NCT01625871

This was a cross sectional prospective study carried out in Kassala Maternity Hospital, Eastern Sudan (2008-2011) to investigate the incidence rate and factors associated with delayed presentation in ruptured ectopic pregnancy. The total number of deliveries during the study period was 9578. The total number of ectopic pregnancy was 199 yielding an incidence rate of (1 in 48 deliveries or 20.7 per 1000 deliveries). One hundred eighty six (93.5%) out of these were ruptured ectopic reflecting very low rate of diagnosis (6.5%) before rupture occurred. Maternal educations secondary, parity and history of subfertilty were associated with ruptured ectopic pregnancy (P=0.00, 0.003 and 0.00 respectively). The causes of delay reported by the patients include: 64.5 not aware of the pregnancy, 28% have been seen by health provider but reassure and 7.5% regarded the symptoms not serious enough to ask for care.

Eighty-one (71.7%) out of 113 patients had confirmed dengue infection (using ELISA IgM serology) at Kassala, Eastern Sudan during the period of August through November 2010. According to the WHO criteria, dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) were observed in 30.9, 58, and 11.1% of these patients, respectively. The mean age of these 81 patients was 25.5 years. Male:female ratio was 1.8:1. Various symptoms including fever (100%), headache (75.3%), vomiting (55.6%), nausea (53.1%), and backache (30.9%) were observed among these patients. Thrombocytopenia (100/10(9) platelets/L), and leucopenia (WBC count4,000 × 10(9) cells/L) and hemoconcentration (hematocrit45) were reported in 86.4, 69.1, and 67.9% of the patients, respectively. High alanine aminotransferase (ALT,65 U/L) and aspartate aminotransferase (AST37 U/L) were seen in 9.9 and 14.8% of the patients, respectively. There were five (6.1%) deaths, three of them had DHF and the other two patients had DSS.

Objective To describe the epidemiology and clinical presentation of female genital tuberculosis (FGTB) among women in eastern Sudan. Methods A cross-sectional survey was conducted at Kassala Maternity Hospital, Sudan, from January 1 to December 31, 2010. Results Of the 2778 women presenting with various gynecologic symptoms, 44 suspected cases of FGTB were identified. Granulomatous tissue reactions were observed in 25 of the suspected FGTB cases, yielding an incidence of 0.9%. The majority (20/25; 80%) of these patients presented with chronic pelvic and lower abdominal pain; however, 68.0% (17/25) presented with pelvic mass, cyst and/or abscess; 48.0% (12/25) had dyspareunia; 40.0% (10/25) were infertile; 28% (7/25) had menstrual dysfunction; 20.0% (5/25) had dysmenorrhea; and 4.0% (1/25) experienced postmenopausal bleeding. Body mass index, residence, and educational level were significantly different between women diagnosed with FGTB and those where FGTB was excluded (P values = 0.02, 0.03, and 0.01, respectively). However, no significant differences were found in age and Bacillus Calmette-Guerin vaccination status. Conclusion Clinical suspicion may facilitate and improve the detection of FGTB, with chronic pelvic pain identified as the predominant clinical presentation among women in eastern Sudan.

The aim of this study was to investigate the seasonal variation and hypertensive disorders of pregnancy in eastern Sudan, in the period between January 2008 and December 2010. The medical files of women attending at Kassala hospital, eastern Sudan with hypertension, with or without proteinuria were retrospectively retrieved. The data of patients with hypertensive disorders of pregnancy were compared with a similar number of controls that were normotensive and non-proteinuric. During the study period, there were 9,578 deliveries; 153 patients had hypertensive disorders of pregnancy, yielding an incidence rate of 1.6%. Of all cases and controls (306), there were 183 (59.8%) deliveries in winter, 84 (27.5%) in summer and 39 (12.7%) in autumn. The highest rate of pre-eclampsia was in winter (1.1%) (CI = 1.1-2.7, OR = 1.7, p = 0.004) and the lowest rate was in autumn (0.2%) (CI = 0.4-1.8, OR = 0.8, p = 0.758.). Our study revealed significant association between the incidence of hypertensive disorders of pregnancy and the winter season (103 (67.3%) vs 80 (52.3%), p = 0.001). Thus, more attention in the winter season might reduce the morbidity and mortality of hypertensive disorders of pregnancy.

Measles during pregnancy is associated with increased risk of maternal morbidity and mortality. It is also associated with fetal loss, prematurity, and fetal infection [1,2]. In Sudan, measles vaccination was introduced into the routine vaccination schedule before 1967; according to the current Expanded Programme of Immunization, infants receive 1 measles dose at the age of 9 months and a booster dose between 18 and 24 months. The program also includes a measles vaccination campaign covering the age group from 9 months to 15 years, and a strong surveillance system to report measles cases. The aim of the present cross-sectional, hospital-based study was to investigate maternal and perinatal outcomes in cases of measles; to calculate the case-fatality rate of measles (number of maternal deaths due to measles per 100 patients with measles); and to compare sociodemographic data (age, residence, parity, education, and prenatal care) between patients with measles who died and those who survived. All pregnant women with a clinical case definition of measles who presented to hospital in Kassala, eastern Sudan, between January 1, 2011, and December 31, 2012, and who provided informed consent were followed for their pregnancy outcome. The study received ethics clearance from the Health Research Board at the Ministry of Health, Kassala. Measles was diagnosed via the clinical case definition set by WHO—that is, any person with fever plus generalized non-vesicular maculopapular rash and at least 1 of the following: cough, coryza (runnynose), or conjunctivitis (red eyes) [3]. In each of the 13 hospitals, there was a specialized ward for the care of patients with measles, all of whomwere treated according to their symptoms (antipyretics, antibiotics, and fluid). Information regarding sociodemographic characteristics (e.g. age, parity, residence, education, prenatal care); state of immunization; and pregnancy outcome (spontaneous abortion, preterm birth, stillbirth, congenital anomalies, maternal mortality) was obtained via researcher-completed questionnaire. For women who survived, the questionnaires were completed in 2 phases: during presentation and after delivery. Means and proportions for the sociodemographic characteristics were compared via χ and t test between pregnant women who died and those who survived. SPSS version 13.0 (IBM, Armonk, NY, USA) was used for analysis; P b 0.05 was considered to be statistically significant. Themean age, parity, and gestational age of the 61 pregnantwomen with measles who presented to hospitals during the study period were 26.4 ± 4.6 years, 2.6 ± 1.7, and 34.9 ± 8.3 weeks, respectively. There were 11 maternal deaths, giving a case-fatality rate of 18.0%. Thirtyfive (57.4%) of the 61 patients were illiterate, 37 (60.7%) were of rural residence, and 46 (75.4%) had received no prenatal care. Overall, 12 (19.7%), 32 (52.5%), and 17 (27.8%) women reported that they had been vaccinated, that they had not been vaccinated, and that they did not know, respectively; 8 (13.1%) women reported a past medical history of suspected measles infection. Eight of the 61 women died during the prenatal period; the other 53 were followed until delivery. Of these 53 women, 40 (75.5%) delivered a live infant at term; 6 (11.3%), 4 (7.5%), and 3 (5.7%) women experienced spontaneous abortion, preterm birth, and stillbirth, respectively. There were no significant differences in age, parity, gestational age, use of prenatal care, and vaccination status between the women who died and those who survived. However illiteracy (P = 0.001) and rural residence (P = 0.002) were associated with maternal deaths among patients with measles (Table 1). The reported causes of death were pneumonia (n = 9 [81.8%]), encephalitis (n = 1 [9.1%]), and bleeding manifestation (intracranial hemorrhage; n = 1 [9.1%]). A limitation of the present study was that diagnosis depended on clinical findings rather than laboratory investigation. Inability to consider socioeconomic factors and the nutritional status of the women was another limitation. The main finding of the present study was a very high case-fatality rate for measles during pregnancy. Nearly one-fifth of the pregnant women with measles during the study period died. The results indicate that, without applying different measures to prevent and treat measles (e.g. expanded program of immunization, early diagnosis, patient isolation), the high mortality rate is unlikely to be reduced. Eastern Sudan has a high maternal mortality ratio, with lack of prenatal care services and illiteracy the main predictors for maternal mortality [4]. Unfortunately, failure to prevent and control preventable communicable diseases such as measles will increase the problem andmake the Millennium Development Goal to reduce maternal mortality unattainable.

Background There have been few published reports on severe Plasmodium falciparum and Plasmodium vivax malaria among adults in Africa. Methods Clinical pattern/manifestations of severe P. falciparum and P. vivax (according to World Health Organization 2000 criteria) were described in adult patients admitted to Kassala Hospital, eastern Sudan. Results A total of 139 adult patients (80 males, 57.6%) with a mean (SD) age of 37.2 (1.5) years presented with severe P. falciparum (113, 81.3%) or P. vivax (26, 18.7%) malaria. Manifestations among the 139 patients included hypotension (38, 27.3%), cerebral malaria (23, 16.5%), repeated convulsions (18, 13.0%), hypoglycaemia (15, 10.8%), hyperparasitaemia (14, 10.1%), jaundice (14, 10.1%), severe anaemia (10, 7.2%), bleeding (six, 4.3%), renal impairment (one, 0.7%) and more than one criteria (27, 19.4%). While the geometric mean of the parasite count was significantly higher in patients with severe P. vivax than with severe P. falciparum malaria (5,934.2 vs 13,906.6 asexual stage parasitaemia per μL, p = 0.013), the different disease manifestations were not significantly different between patients with P. falciparum or P. vivax malaria. Three patients (2.2%) died due to severe P. falciparum malaria. One had cerebral malaria, the second had renal impairment, jaundice and hypoglycaemia, and the third had repeated convulsions and hypotension. Conclusions Severe malaria due to P. falciparum and P. vivax malaria is an existing entity among adults in eastern Sudan. Patients with severe P. falciparum and P. vivax develop similar disease manifestations.

Background Since 1900s, visceral leishmaniasis (VL) has been among the most important health problems in Sudan, particularly in the endemic areas such as eastern and central regions. Methods This was a cross sectional, hospital-based study conducted from 1st January 2015 to 31st December 2015 to investigate the epidemiological factors of VL in Gadarif hospital, eastern Sudan. Results During the study period there were 47 identified children with VL among 145 suspected cases. The most common clinical presentations were fever (47, 100%), pallor (47, 100%), weight loss (40, 85.1%), splenomegaly (37, 78.7%), lymphadenopathy (33, 70.2%), vomiting (32, 68%) cough (28, 59%), loss of appetite (22, 46.8%), diarrhoea (17, 36.1%) and jaundice (5, 10.6%). With regard to the outcome after short term follow up 37 patients (78.8%) improved without complications, while 3 (6.4%, 2 (4.3%), 2 (4.3%), 1 (2.1%), 1 (2.1%) and 1 (2.1%) developed pneumonia, otitis media, septicaemia, urinary tract infection, parasitic infestation and PKDL respectively. Lower mean of haemoglobin level was observed among the VL cases in comparison with the suspected cases (in whom VL was excluded) haemoglobin level {8.9 (3.1) Vs 11 (6.3), P = 0.021}. Again more proportion of anaemic (47 (100%) Vs 14 (14.2%), P = 0.000) and severely anaemic (23 (48.9%) Vs 2 (2%), P = 0.006) patients was detected among the infected children. Using logistic regression analyses there was significant association between rural residence (CI = 1.5–24, OR = 19.1, P = 0.023), male gender (CI = 6.6–18.7, OR = 6.4, P = 0.001) and VL among children. Conclusions While there is an advance in prevention and management of visceral leishmaniasis our results indicate that VL is still a public health problem with its severe complications among children in eastern Sudan.

BACKGROUND: Artesunate/sulphadoxine-pyrimethamine (AS/SP) has been the first-line treatment for falciparum malaria in Sudan since 2004. The impact of this combination on anti-malarial resistance-associated molecular markers has not been investigated. In this study, an evaluation of the efficacy and prevalence of drug resistance alleles (pfcrt, pfmdr1, pfdhfr and pfdhps) eight years after the adoption of AS/SP in eastern Sudan is reported. METHODS: A 28-day follow-up efficacy trial of AS/SP was conducted in eastern Sudan during the 2012 transmission season. Blood smears were collected from patients on days 0, 1, 2, 3, 7, 14, 21 and 28. Blood spots on filter paper were obtained pre-treatment and on the day the patient was parasite positive by microscopy. Genotyping of alleles was performed by qPCR (pfcrt 72-76 and pfmdr1 copy number) and direct sequencing of pfmdr1, pfdhfr and pfdhps. RESULTS: Sixty-three patients out of 68 (93%) completed the 28-day follow-up, adequate clinical, and parasitological response occurred in 90.5% and 85.3% of the patients in the per-protocol and intent-to-treat analyses, respectively. PCR corrected per-protocol efficacy was 93.7%. The enrolment prevalence of pfcrt-CVMNK was 30.2% and pfmdr1-N86 was 40.3%. The pfmdr1 haplotype NFD occurred in 32.8% of pre-treatment samples and was significantly higher than previous reports (Fisher's exact p = 0.0001). The pfdhfr-51I/108N combination occurred in all sequenced isolates and 59R was observed in a single individual. pfdhps substitutions 436A, 437G, 540E, 581G and 613S were observed at 7.8, 77.3, 76.9%, 33.8% and 0.0%, respectively. Treatment failures were associated with the pfdhps haplotype SGEGA at these five codons (OR 7.3; 95% CI 0.65 - 368; p = 0.048). CONCLUSION: The decrease of CQR associated genotypes reflects the formal policy of complete removal of CQ in Sudan. However, the frequency of markers associated with SP failure is increasing in this study area and may be contributing to the treatment efficacy falling below 90%. Further monitoring of AS/SP efficacy and of post-treatment selection of pfdhfr and pfdhps alleles in vivo is required to inform future treatment guidelines.