Dihydroartemisinin-piperaquine (DP) has demonstrated excellent efficacy for the treatment and prevention of malaria in Uganda. However, resistance to both components of this regimen has emerged in Southeast Asia. The efficacy of artemether-lumefantrine, the first-line regimen to treat malaria in Uganda, has also been excellent, but continued pressure may select for parasites with decreased sensitivity to lumefantrine. To gain insight into current drug sensitivity patterns, ex vivo sensitivities were assessed and genotypes previously associated with altered drug sensitivity were characterized for 58 isolates collected in Tororo, Uganda, from subjects presenting in 2016 with malaria from the community or as part of a clinical trial comparing DP chemoprevention regimens. Compared to community isolates, those from trial subjects had lower sensitivities to the aminoquinolines chloroquine, monodesethyl amodiaquine, and piperaquine and greater sensitivities to lumefantrine and mefloquine, an observation consistent with DP selection pressure. Compared to results for isolates from 2010 to 2013, the sensitivities of 2016 community isolates to chloroquine, amodiaquine, and piperaquine improved (geometric mean 50% inhibitory concentrations [IC ₅₀ ] = 248, 76.9, and 19.1 nM in 2010 to 2013 and 33.4, 14.9, and 7.5 nM in 2016, respectively [ P < 0.001 for all comparisons]), the sensitivity to lumefantrine decreased (IC ₅₀ = 3.0 nM in 2010 to 2013 and 5.4 nM in 2016 [ P < 0.001]), and the sensitivity to dihydroartemisinin was unchanged (IC ₅₀ = 1.4 nM). These changes were accompanied by decreased prevalence of transporter mutations associated with aminoquinoline resistance and low prevalence of polymorphisms recently associated with resistance to artemisinins or piperaquine. Antimalarial drug sensitivities are changing in Uganda, but novel genotypes associated with DP treatment failure in Asia are not prevalent.

Treatment and control of malaria depends on artemisinin-based combination therapies (ACTs) and is challenged by drug resistance, but thus far resistance to artemisinins and partner drugs has primarily occurred in southeast Asia. The aim of this study was to characterise antimalarial drug susceptibility of Plasmodium falciparum isolates from Tororo and Busia districts in Uganda. In this prospective longitudinal study, P falciparum isolates were collected from patients aged 6 months or older presenting at the Tororo District Hospital (Tororo district, a site with relatively low malaria incidence) or Masafu General Hospital (Busia district, a high-incidence site) in eastern Uganda with clinical symptoms of malaria, a positive Giemsa-stained blood film for P falciparum, and no signs of severe disease. Ex-vivo susceptibilities to ten antimalarial drugs were measured using a 72-h microplate growth inhibition assay with SYBR Green detection. Relevant P falciparum genetic polymorphisms were characterised by molecular methods. We compared results with those from earlier studies in this region and searched for associations between drug susceptibility and parasite genotypes. From June 10, 2016, to July 29, 2019, 361 P falciparum isolates were collected in the Busia district and 79 in the Tororo district from 440 participants. Of 440 total isolates, 392 (89%) successfully grew in culture and showed excellent drug susceptibility for chloroquine (median half-maximal inhibitory concentration [IC₅₀] 20·0 nM [IQR 12·0–26·0]), monodesethylamodiaquine (7·1 nM [4·3–8·9]), pyronaridine (1·1 nM [0·7–2·3]), piperaquine (5·6 nM [3·3–8·6]), ferroquine (1·8 nM [1·5–3·3]), AQ-13 (24·0 nM [17·0–32·0]), lumefantrine (5·1 nM [3·2–7·7]), mefloquine (9·5 nM [6·6–13·0]), dihydroartemisinin (1·5 nM [1·0–2·0]), and atovaquone (0·3 nM [0·2–0·4]). Compared with results from our study in 2010–13, significant improvements in susceptibility were seen for chloroquine (median IC₅₀ 288·0 nM [IQR 122·0–607·0]; p<0·0001), monodesethylamodiaquine (76·0 nM [44·0–137]; p<0·0001), and piperaquine (21·0 nM [7·6–43·0]; p<0·0001), a small but significant decrease in susceptibility was seen for lumefantrine (3·0 nM [1·1–7·6]; p100 nM) was more common in isolates from the Tororo district (11 [15%] of 71), compared with those from the Busia district (12 [4%] of 320; p=0·0017). We showed significant increases between 2010–12 and 2016–19 in the prevalences of wild-type P falciparum multidrug resistance protein 1 (PfMDR1) Asn86Tyr from 60% (391 of 653) to 99% (418 of 422; p<0·0001), PfMDR1 Asp1246Tyr from 60% (390 of 650) to 90% (371 of 419; p<0·0001), and P falciparum chloroquine resistance transporter (PfCRT) Lys76Thr from 7% (44 of 675) to 87% (364 of 417; p<0·0001). Our results show marked changes in P falciparum drug susceptibility phenotypes and genotypes in Uganda during the past decade. These results suggest that additional changes will be seen over time and continued surveillance of susceptibility to key ACT components is warranted. National Institutes of Health and Medicines for Malaria Venture.

Background: Uganda adopted the HIV Test and Treat in 2016. There is paucity of data about its implementation among hospitalized patients. We aimed to determine the proportion of patients initiating anti-retroviral therapy (ART) during hospitalization, barriers and mortality outcome. Methods: In this mixed methods cohort study, we enrolled hospitalized patients with a recent HIV diagnosis from three public hospitals in Uganda. We collected data on clinical characteristics, ART initiation and reasons for failure to initiate ART, as well as 30 day outcomes. Healthcare workers in-depth interviews were also conducted and data analyzed by sub-themes. Results: We enrolled 234 patients; females 140/234 (59.8%), median age 34.5 years (IQR 29–42), 195/234 (83.7%) had WHO HIV stage 3 or 4, and 74/116 (63.8%) had CD4 ≤ 200 cell/μL. The proportion who initiated ART during hospitalization was 123/234 (52.6%) (95% CI 46.0–59.1), of these 35/123 (28.5%) initiated ART on the same day of hospitalization, while 99/123 (80.5%) within a week of hospitalization. By 30 days 34/234 (14.5%) (95% CI 10.3–19.7) died. Patients residing ≥ 35 kilometers from the hospital were more likely not to initiate ART during hospitalization, [aRR = 1.39, (95% CI 1.22–1.59). Inadequate patient preparation for ART initiation and advanced HIV disease were highlighted as barriers of ART initiation during hospitalization. Conclusion: In this high HIV prevalence setting, only half of newly diagnosed HIV patients are initiated on ART during hospitalization. Inadequate pre-ART patient preparation and advanced HIV are barriers to rapid ART initiation among hospitalized patients in public hospitals.

Blood culture (BC) processes are critical to the utility of diagnostic testing, bloodstream infection (BSI) management, and antimicrobial resistance (AMR) surveillance. While Uganda has established BC guidelines, often laboratory practice does not meet the desired standards. This compromises pathogen recovery, reliability of antimicrobial susceptibility testing, and diagnostic test utility. This study assessed laboratory BC process outcomes among non-malarial febrile children below five years of age at five AMR surveillance sites in Uganda between 2017 and 2018. Secondary BC testing data was reviewed against established standards. Overall, 959 BC specimens were processed. Of these, 91% were from female patients, neonates, infants, and young children (1–48 months). A total of 37 AMR priority pathogens were identified; Staphylococcus aureus was predominant (54%), followed by Escherichia coli (19%). The diagnostic yield was low (4.9%). Only 6.3% of isolates were identified. AST was performed on 70% (18/26) of identified AMR priority isolates, and only 40% of these tests adhered to recommended standards. Interventions are needed to improve laboratory BC practices for effective patient management through targeted antimicrobial therapy and AMR surveillance in Uganda. Further research on process documentation, diagnostic yield, and a review of patient outcomes for all hospitalized febrile patients is needed.

The emergence and spread of drug resistance threatens malaria control in Uganda. This study reports new data on key polymorphisms associated with antimalarial drug sensitivity at 32 malaria reference centers in Uganda in 2023 and 2024. Samples were collected from patients aged >6 months presenting with uncomplicated falciparum malaria, sequenced using the MAD ⁴ HatTeR panel and Illumina platforms. Multiple validated or candidate K13 mutations associated with artemisinin partial resistance were detected at ≥20% prevalence at one or more sites across multiple timepoints. The K13 mutations A675V and C469Y predominated in northern Uganda, P441L was most common in western Uganda, and R561H and C469F were confined to southwestern Uganda. After rapid increases in earlier years, prevalences of K13 mutations plateaued at most sites, with A675V, C469Y and P441L reaching maximum site prevalences of 40%, 58%, and 46%, respectively. Prevalence of the chloroquine resistance marker CRT K76T was generally low but increased substantially at three sites in northwestern Uganda, rising to 38% at the last timepoint, with CRT H97L, newly reported in Africa, following a similar trend. The antifolate resistance quintuple mutant haplotype remained highly prevalent nationwide. In addition, DHPS A581G and DHFR I164L, markers of higher-level antifolate resistance, were most common in southwestern Uganda with prevalences up to 64% and 76%, respectively; DHFR I164L also expanded into central and eastern regions. These results highlight continued geographic heterogeneity and underscore the need for continued, nationwide molecular surveillance to guide treatment and chemoprevention policies.