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Background The genus Trypanosoma Gruby, 1843 is constituted by terrestrial and aquatic phylogenetic lineages both harboring understudied trypanosomes from reptiles including an increasing diversity of crocodilian trypanosomes. Trypanosoma clandestinus Teixeira & Camargo, 2016 of the aquatic lineage is transmitted by leeches to caimans. Trypanosoma grayi Novy, 1906 of the terrestrial lineage is transmitted by tsetse flies to crocodiles in Africa, but the vectors of Neotropical caiman trypanosomes nested in this lineage remain unknown. Results Our phylogenetic analyses uncovered crocodilian trypanosomes in tabanids from South America and Africa, and trypanosomes other than T. grayi in tsetse flies. All trypanosomes found in tabanids clustered in the crocodilian clade (terrestrial lineage) forming six clades: Grayi (African trypanosomes from crocodiles and tsetse flies); Ralphi (trypanosomes from caimans, African and Brazilian tabanids and tsetse flies); Terena (caimans); Cay03 (caimans and Brazilian tabanids); and two new clades, Tab01 (Brazilian tabanid and tsetse flies) and Kaiowa. The clade Kaiowa comprises Trypanosoma kaiowa n. sp. and trypanosomes from African and Brazilian tabanids, caimans, tsetse flies and the African dwarf crocodile. Trypanosoma kaiowa n. sp. heavily colonises tabanid guts and differs remarkably in morphology from other caiman trypanosomes. This species multiplied predominantly as promastigotes on log-phase cultures showing scarce epimastigotes and exhibited very long flagellates in old cultures. Analyses of growth behavior revealed that insect cells allow the intracellular development of Trypanosoma kaiowa n. sp. Conclusions Prior to this description of Trypanosoma kaiowa n. sp., no crocodilian trypanosome parasitic in tabanid flies had been cultured, morphologically examined by light, scanning and transmission microscopy, and phylogenetically compared with other crocodilian trypanosomes. Additionally, trypanosomes thought to be restricted to caimans were identified in Brazilian and African tabanids, tsetse flies and the dwarf crocodile. Similar repertoires of trypanosomes found in South American caimans, African crocodiles and tabanids from both continents support the recent diversification of these transcontinental trypanosomes. Our findings are consistent with trypanosome host-switching likely mediated by tabanid flies between caimans and transoceanic migrant crocodiles co-inhabiting South American wetlands at the Miocene.

Background: To confirm presence of Mycobacterium tuberculosis complex, some tuberculosis culture laboratories still rely on para-nitrobenzoic acid (PNB), a traditional technique that requires sub-culturing of clinical isolates and two to three weeks to give results. Rapid identification tests have improved turnaround times for mycobacterial culture results. Considering the challenges of the PNB method, we assessed the performance of the SD Bioline TB Ag MPT64 assay by using PNB as gold standard to detect M. tuberculosis complex from acid-fast bacilli (AFB) positive cultures.Objectives: The aim of this study was to determine the sensitivity, specificity and turnaround time of the SD MPT64 assay for identification of M. tuberculosis complex, in a setting with high prevalence of tuberculosis and HIV.Methods: A convenience sample of 690 patients, with tuberculosis symptoms, was enrolled at Epicentre Mbarara Research Centre between April 2010 and June 2011. The samples were decontaminated using NALC-NaOH and re-suspended sediments inoculated in Mycobacterium Growth Indicator Tubes (MGIT) media, then incubated at 37 °C for a maximum of eight weeks. A random sample of 50 known negative cultures and 50 non-tuberculous mycobacteria isolates were tested for specificity, while sensitivity was based on AFB positivity. The time required from positive culture to reporting of results was also assessed with PNB used as the gold standard.Results: Of the 138 cultures that were AFB-positive, the sensitivity of the SD MPT64 assay was 100.0% [95% CI: 97.3 – 100] and specificity was 100.0% (95% CI, 96.4 – 100). The median time from a specimen receipt to confirmation of strain was 10 days [IQR: 8–12] with SD MPT64 and 24 days [IQR: 22–26] with PNB.Conclusion: The SD MPT64 assay is comparable to PNB for identification of M. tuberculosis complex and reduces the time to detection.

Background: To confirm presence of Mycobacterium tuberculosis complex, some tuberculosis culture laboratories still rely on para-nitrobenzoic acid (PNB), a traditional technique that requires sub-culturing of clinical isolates and two to three weeks to give results. Rapid identification tests have improved turnaround times for mycobacterial culture results. Considering the challenges of the PNB method, we assessed the performance of the SD Bioline TB Ag MPT64 assay by using PNB as gold standard to detect M. tuberculosis complex from acid-fast bacilli (AFB) positive cultures. Objectives: The aim of this study was to determine the sensitivity, specificity and turnaround time of the SD MPT64 assay for identification of M. tuberculosis complex, in a setting with high prevalence of tuberculosis and HIV. Methods: A convenience sample of 690 patients, with tuberculosis symptoms, was enrolled at Epicentre Mbarara Research Centre between April 2010 and June 2011. The samples were decontaminated using NALC-NaOH and re-suspended sediments inoculated in Mycobacterium Growth Indicator Tubes (MGIT) media, then incubated at 37 °C for a maximum of eight weeks. A random sample of 50 known negative cultures and 50 non-tuberculous mycobacteria isolates were tested for specificity, while sensitivity was based on AFB positivity. The time required from positive culture to reporting of results was also assessed with PNB used as the gold standard. Results: Of the 138 cultures that were AFB-positive, the sensitivity of the SD MPT64 assay was 100.0% [95% CI: 97.3 – 100] and specificity was 100.0% (95% CI, 96.4 – 100). The median time from a specimen receipt to confirmation of strain was 10 days [IQR: 8–12] with SD MPT64 and 24 days [IQR: 22–26] with PNB. Conclusion: The SD MPT64 assay is comparable to PNB for identification of M. tuberculosis complex and reduces the time to detection.

Treatment guidelines for schistosomiasis recommend increasing frequency of preventative chemotherapy (PC) administration of praziquantel to twice per annum in persistent hotspots of transmission, in combination with integrated control strategies. FibroScHot was an individual randomised superiority trial designed to examine twice per annum and four times per annum treatment frequency. It was conducted in two primary schools, Buhirigi and Kaiso, in Hoima District Uganda - a designated Schistosoma mansoni high transmission area in which PC is targeted at children and adults. The baseline parasitology data was assessed against international control programme thresholds of success and the criteria for persistent hotspots. Further, the study also assessed the potential for integrated control strategies within the surrounding communities. The prevalence of infection, heavy infection and the infection intensity were derived for 700 participants from Kato-Katz examination of one stool sample. Neither school met the threshold of morbidity control (<5% with heavy infection). A strong school effect was observed in models of prevalence and prevalence of heavy infection, with these being greater in Kaiso. By prevalence, Kaiso was a high transmission area and Buhirigi a moderate transmission area. Kaiso but not Buhirigi met the definition of a persistent hotspot. Persistent hotspot classification did not change when intensity of infection was used. Intermediate snail hosts were collected at both Kaiso landing site and from the River Hoimo in Buhirigi, though in smaller numbers in the latter. Questionnaire data indicates that reliance on water collection from transmission sites and open defecation occurs more frequently in Kaiso than in Buhirigi. The criteria for persistent hotspots were met in the high transmission but not the moderate transmission community despite neither community meeting the threshold of morbidity control. This disconnect indicates that endemic communities exist in which control has not been achieved but increased frequency of treatment is currently not recommended. FibroScHot will be able to inform on whether widening the current recommendation of increased treatment frequency to these communities will achieve improved control. Evidence provided also indicates scope for the integrated control strategies of vector control and WASH improvements in both the participating communities.

Background Safe, high-quality surgical care in many African countries is a critical need. Challenges include availability of surgical providers, improving quality of care, and building workforce capacity. Despite growing evidence that mentoring is effective in African healthcare settings, less is known about its role in surgery. We examined a multimodal approach to mentorship as part of a safe surgery intervention (Safe Surgery 2020) to improve surgical quality. Our goal was to distill lessons for policy makers, intervention designers, and practitioners on key elements of a successful surgical mentorship program. Methods We used a convergent, mixed-methods design to examine the experiences of mentees, mentors, and facility leaders with mentorship at 10 health facilities in Tanzania’s Lake Zone. A multidisciplinary team of mentors worked with surgical providers over 17 months using in-person mentorship, telementoring, and WhatsApp. We conducted surveys, in-depth interviews, and focus groups to capture data in four categories: (1) satisfaction with mentorship; (2) perceived impact; (3) elements of a successful mentoring program; and (4) challenges to implementing mentorship. We analyzed quantitative data using frequency analysis and qualitative data using the constant comparison method. Recurrent and unifying concepts were identified through merging the qualitative and quantitative data. Results Overall, 96% of mentees experienced the intervention as positive, 88% were satisfied, and 100% supported continuing the intervention in the future. Mentees, mentors, and facility leaders perceived improvements in surgical practice, the surgical ecosystem, and in reducing postsurgical infections. Several themes related to the intervention’s success emerged: (1) the intervention’s design, including its multimodality, side-by-side mentorship, and standardization of practices; (2) the mentee–mentor relationship, including a friendly, safe, non-hierarchical, team relationship, as well as mentors’ understanding of the local context; and (3) mentorship characteristics, including non-judgmental feedback, experience, and accessibility. Challenges included resistance to change, shortage of providers, mentorship dose, and logistics. Conclusions Our study suggests a multimodal mentorship approach is promising in building the capacity of surgical providers. By distilling the experiences of the mentees, mentors, and facility leaders, our lessons provide a foundation for future efforts to establish effective surgical mentorship programs that build provider capacity and ultimately improve surgical quality.

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa. Here, Ratmann et al. show how viral deep sequencing data can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks.

BackgroundEvidence on heterogeneity in outcomes of surgical quality interventions in low-income and middle-income countries is limited. We explored factors driving performance in the Safe Surgery 2020 intervention in Tanzania’s Lake Zone to distil implementation lessons for low-resource settings.MethodsWe identified higher (n=3) and lower (n=3) performers from quantitative data on improvement from 14 safety and teamwork and communication indicators at 0 and 12 months from 10 intervention facilities, using a positive deviance framework. From 72 key informant interviews with surgical providers across facilities at 1, 6 and 12 months, we used a grounded theory approach to identify practices of higher and lower performers.ResultsPerformance experiences of higher and lower performers differed on the following themes: (1) preintervention context, (2) engagement with Safe Surgery 2020 interventions, (3) teamwork and communication orientation, (4) collective learning orientation, (5) role of leadership, and (6) perceived impact of Safe Surgery 2020 and beyond. Higher performers had a culture of teamwork which helped them capitalise on Safe Surgery 2020 to improve surgical ecosystems holistically on safety practices, teamwork and communication. Lower performers prioritised overhauling safety practices and began considering organisational cultural changes much later. Thus, while also improving, lower performers prioritised different goals and trailed higher performers on the change continuum.ConclusionFuture interventions should be tailored to facility context and invest in strengthening teamwork, communication and collective learning and facilitate leadership engagement to build a receptive climate for successful implementation of safe surgery interventions.

•Country-led cost-effectiveness analyses of rotavirus vaccine introduction.•The analysis were done for Kenya and Uganda and informed by national data.•Rotavirus vaccine introduction is very cost effective in both countries.•Process used helps support evidence based decision making.•Strengthen national capacity to undertake economic evaluations. Rotavirus vaccines have the potential to prevent a substantial amount of life-threatening gastroenteritis in young African children. This paper presents the results of prospective cost-effectiveness analyses for rotavirus vaccine introduction for Kenya and Uganda. In each country, a national consultant worked with a national technical working group to identify appropriate data and validate study results. Secondary data on demographics, disease burden, health utilization, and costs were used to populate the TRIVAC cost-effectiveness model. The baseline analysis assumed an initial vaccine price of $0.20 per dose, corresponding to Gavi, the Vaccine Alliance stipulated copay for low-income countries. The incremental cost-effectiveness of a 2-dose rotavirus vaccination schedule was evaluated for 20 successive birth cohorts from the government perspective in both countries, and from the societal perspective in Uganda. Between 2014 and 2033, rotavirus vaccination can avert approximately 60,935 and 216,454 undiscounted deaths and hospital admissions respectively in children under 5 years in Kenya. In Uganda, the respective number of undiscounted deaths and hospital admission averted is 70,236 and 329,779 between 2016 and 2035. Over the 20-year period, the discounted vaccine program costs are around US$ 80 million in Kenya and US$ 60 million in Uganda. Discounted government health service costs avoided are US$ 30 million in Kenya and US$ 10 million in Uganda (or US$ 18 million including household costs). The cost per disability-adjusted life-year (DALY) averted from a government perspective is US$ 38 in Kenya and US$ 34 in Uganda (US$ 29 from a societal perspective). Rotavirus vaccine introduction is highly cost-effective in both countries in a range of plausible ‘what-if’ scenarios. The involvement of national experts improves the quality of data used, is likely to increase acceptability of the results in decision-making, and can contribute to strengthened national capacity to undertake economic evaluations.