Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

In the HTML version of this Letter, the affiliations for authors Andrew S. Azman, Dhirendra Kumar and Thandavarayan Ramamurthy were inverted (the PDF and print versions of the Letter were correct); the affiliations have been corrected online.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

Community perception of epilepsy and its treatment in onchocerciasis-endemic villages of Maridi county, western equatoria state, South Sudan.

OBJECTIVE: To assess the community's perception of epilepsy and its treatment in onchocerciasis-endemic villages of Maridi County, Western Equatoria State, South Sudan. The study was conducted prior to the setting up of a community-based intervention to manage the important disease burden caused by onchocerciasis-associated epilepsy in these villages. METHOD: Five focus group discussions (FGD) were conducted with community leaders and with persons with epilepsy (PWE) and their families between November and December 2019. RESULTS: Villages close to the Maridi dam were considered to be most affected by epilepsy. Misconceptions about the cause and treatment of epilepsy were identified. Most people believed that epilepsy is caused by bad spirits and is contagious, transmitted through saliva, air, and contact with PWE. Very few participants were aware of the link between onchocerciasis and epilepsy. Persons with epilepsy are restricted in their day-to-day activities and children with epilepsy are often denied going to school. Persons with epilepsy are stigmatized and seen as unfit for marriage. Most participants considered both traditional and medical treatment as ineffective. Uninterrupted anti-seizure treatment continuously was unaffordable for most families with one or more PWE. CONCLUSION: There is a need to establish a comprehensive epilepsy treatment program which addresses misconceptions about epilepsy and reduces epilepsy-related stigma. Explaining the link between onchocerciasis and epilepsy could lead to a reduction in epilepsy-related stigma.

Performance of a fully-automated system on a WHO malaria microscopy evaluation slide set.

BACKGROUND: Manual microscopy remains a widely-used tool for malaria diagnosis and clinical studies, but it has inconsistent quality in the field due to variability in training and field practices. Automated diagnostic systems based on machine learning hold promise to improve quality and reproducibility of field microscopy. The World Health Organization (WHO) has designed a 55-slide set (WHO 55) for their External Competence Assessment of Malaria Microscopists (ECAMM) programme, which can also serve as a valuable benchmark for automated systems. The performance of a fully-automated malaria diagnostic system, EasyScan GO, on a WHO 55 slide set was evaluated. METHODS: The WHO 55 slide set is designed to evaluate microscopist competence in three areas of malaria diagnosis using Giemsa-stained blood films, focused on crucial field needs: malaria parasite detection, malaria parasite species identification (ID), and malaria parasite quantitation. The EasyScan GO is a fully-automated system that combines scanning of Giemsa-stained blood films with assessment algorithms to deliver malaria diagnoses. This system was tested on a WHO 55 slide set. RESULTS: The EasyScan GO achieved 94.3 % detection accuracy, 82.9 % species ID accuracy, and 50 % quantitation accuracy, corresponding to WHO microscopy competence Levels 1, 2, and 1, respectively. This is, to our knowledge, the best performance of a fully-automated system on a WHO 55 set. CONCLUSIONS: EasyScan GO's expert ratings in detection and quantitation on the WHO 55 slide set point towards its potential value in drug efficacy use-cases, as well as in some case management situations with less stringent species ID needs. Improved runtime may enable use in general case management settings.

Towards harmonization of microscopy methods for malaria clinical research studies.

Microscopy performed on stained films of peripheral blood for detection, identification and quantification of malaria parasites is an essential reference standard for clinical trials of drugs, vaccines and diagnostic tests for malaria. The value of data from such research is greatly enhanced if this reference standard is consistent across time and geography. Adherence to common standards and practices is a prerequisite to achieve this. The rationale for proposed research standards and procedures for the preparation, staining and microscopic examination of blood films for malaria parasites is presented here with the aim of improving the consistency and reliability of malaria microscopy performed in such studies. These standards constitute the core of a quality management system for clinical research studies employing microscopy as a reference standard. They can be used as the basis for the design of training and proficiency testing programmes as well as for procedures and quality assurance of malaria microscopy in clinical research.

Impact of annual community-directed treatment with ivermectin on the incidence of epilepsy in Mvolo, a two-year prospective study.

OBJECTIVES: The potential impact of cumulative community-directed treatment with ivermectin (CDTI) on epilepsy epidemiology in Mvolo County, South Sudan, an onchocerciasis-endemic area with high epilepsy prevalence, was investigated. Annual CDTI was introduced in 2002 in Mvolo, with interruptions in 2016 and 2020. METHODS: Comprehensive house-to-house surveys in Mvolo (June 2020 and 2022) identified cases of epilepsy, including probable nodding syndrome (pNS). Community workers screened households in selected sites for suspected epilepsy, and medical doctors confirmed the diagnosis and determined the year of seizure onset. The incidence of epilepsy, including pNS, was analysed using 95% confidence intervals (CIs). Data on ivermectin intake and onchocerciasis-associated manifestations (itching and blindness) were collected. RESULTS: The surveys covered 15,755 (2020) and 15,092 (2022) individuals, identifying 809 (5.2%, 95% CI: 4.8-5.5%) and 672 (4.5%, 95% CI: 4.1-4.8%) epilepsy cases, respectively. Each survey reported that a third of the surveyed population experienced skin itching, and 3% were blind. Epilepsy incidence per 100,000 person-years gradually declined, from 326.5 (95% CI: 266.8-399.1) in 2013-2015 to 96.6 (95% CI: 65.5-141.7) in 2019-2021. Similarly, pNS incidence per 100,000 person-years decreased from 151.7 (95% CI: 112.7-203.4) to 27.0 (95% CI: 12.5-55.5). Coverage of CDTI was suboptimal, reaching only 64.0% of participants in 2019 and falling to 24.1% in 2021 following an interruption in 2020 due to COVID-19 restrictions. Additionally, while 99.4% of cases had active epilepsy in 2022, less than a quarter of these had access to antiseizure medication. CONCLUSIONS: The observed decrease in epilepsy incidence despite suboptimal CDTI coverage highlights the potential impact of onchocerciasis control efforts and underscores the need to strengthen these efforts in Mvolo County and across South Sudan. As a proactive measure, Mvolo and neighbouring counties are transitioning to biannual CDTI. Furthermore, the substantial epilepsy treatment gap in Mvolo should be addressed.

Effect of onchocerciasis elimination measures on the incidence of epilepsy in Maridi, South Sudan: a 3-year longitudinal, prospective, population-based study.

BACKGROUND: High onchocerciasis transmission predisposes endemic communities to a high epilepsy burden. The 4·4% epilepsy prevalence documented in 2018 in Maridi, South Sudan, prompted the strengthening of onchocerciasis elimination measures. Community-directed treatment with ivermectin was implemented annually in 2017, 2018, and 2019, interrupted in 2020, and re-implemented biannually in 2021. We aimed to assess the effect of these interventions, along with slash and clear vector control on the incidence of epilepsy, including nodding syndrome. METHODS: In this longitudinal, prospective, population-based study, we did a two-stage house-to-house epilepsy survey before (May 10-30, 2018) and after (March 9-19, 2022) the strengthening of onchocerciasis elimination interventions in South Sudan. Strengthening also included the implementation of a community-based slash and clear vector control method that we initiated in 2019 at the Maridi dam (the main blackfly breeding site). Eight sites were surveyed near the Maridi dam and inclusion required residence in one of these sites. All household residents were first screened by community workers, followed by confirmation of the epilepsy diagnosis by trained clinicians. The primary outcome was epilepsy incidence, including nodding syndrome, which was assessed via self-reported new-onset epilepsy in the previous 4 years of each survey, confirmed by clinician assessment. FINDINGS: The preintervention survey included 17 652 people of whom 736 had epilepsy (315 female and 421 male), and the post-intervention survey included 14 402 people of whom 586 had epilepsy (275 female and 311 male). When biannual community-directed treatment with ivermectin was initiated in 2021, the intervention's coverage rose by 15·7% (95% CI 14·6-16·8); although only 56·6% of the population took ivermectin in 2021. Between 2018 and 2022, epilepsy incidence decreased from 348·8 (307·2-395·8) to 41·7 (22·6-75·0) per 100 000 person-years. Similarly, the incidence of nodding syndrome decreased from 154·7 (127·6-187·3) to 10·4 (2·7-33·2) per 100 000 person-years. The identified risk factors for epilepsy were: living closer to the Maridi dam, being aged between 6 and 40 years, not taking ivermectin, and being male. INTERPRETATION: In onchocerciasis-endemic areas with high epilepsy prevalence, strengthening onchocerciasis elimination interventions can decrease the incidence of epilepsy, including nodding syndrome. Additional efforts are needed to increase community-directed treatment with ivermectin coverage and sustain blackfly control in Maridi. FUNDING: Research for Health in Humanitarian Crisis, European Research Council, Research Foundation-Flanders, Research Foundation-Flanders, the Italian Agency for Development Cooperation, and La Caixa Foundation.

The Prevalence of Onchocerciasis-Associated Epilepsy in Mundri West and East Counties, South Sudan: A Door-to-Door Survey.

A two-phase survey of epilepsy was conducted in selected villages in Mundri West and East Counties (26 June-8 July, 2021), an onchocerciasis-endemic area in Western Equatoria State in South Sudan. In the first phase, households were visited by a trained research team to identify persons suspected to have epilepsy. In the second phase, persons suspected to have epilepsy were interviewed and examined by a clinician to confirm the diagnosis. A total of 364 households agreed to participate in the survey, amounting to 2588 individuals. The epilepsy screening questionnaire identified 91 (3.5%) persons with suspected epilepsy, of whom the diagnosis of epilepsy was confirmed by a clinician in 86 (94.5%). The overall prevalence of confirmed epilepsy was 3.3% (95% CI: 2.7-4.1%), and of nodding syndrome was 0.9% (95% CI: 0.6-1.4%). In 61 (16.8%) households there was at least one person with epilepsy. Only 1212 (46.9%) of 2583 people took ivermectin during the last distribution round in 2021. The annual epilepsy incidence was 77.3/100,000 (95% CI: 9.4-278.9/100,000) and the annual epilepsy mortality was 251.2/100,000 (95% CI: 133.8-428.7/100,000). In conclusion, a high prevalence and incidence of epilepsy was observed in villages in Mundri. Urgent action is needed to prevent children from developing onchocerciasis-associated epilepsy by strengthening the local onchocerciasis-elimination programme.

"Slash and Clear", a Community-Based Vector Control Method to Reduce Onchocerciasis Transmission by Simulium sirbanum in Maridi, South Sudan: A Prospective Study.

BACKGROUND: High ongoing Onchocerca volvulus transmission was recently documented in Maridi County, South Sudan. To complement community-directed treatment with ivermectin (CDTI) as the main onchocerciasis control strategy, we initiated a community-based vector control method "slash and clear" at the Maridi dam, a Simulium damnosum s.l. breeding site, to reduce O. volvulus transmission. METHODS: Simulium damnosum s.l. biting rates were collected before and during the twenty months following the "slash and clear" intervention using the human landing catches. Black flies were dissected to measure parity rates before and twelve months after the intervention. Larvae and pupae of S. damnosum s.l. were collected from the dam for morphological and chromosomal characterization to identify the cytospecies involved. RESULTS: Biting rates of S. damnosum s.l. close to the Maridi dam spillway decreased by >90% post-"slash and clear" for more than six months. Twelve months after the "slash and clear" intervention, the reduction in biting rates was still at <50% (p = 0.0007). Parity rates reduced from 13% pre-"slash and clear" (November 2019) to 5.6% post-"slash and clear" (November 2020). Larvae collected from the dam were identified as Simulium sirbanum. CONCLUSION: The "slash and clear" method was found to be an effective and cheap community-based method to reduce black fly biting rates caused by S. sirbanum. When repeated at least annually together with a high CDTI coverage, this intervention has the potential to considerably accelerate onchocerciasis elimination.

Cytokines and Onchocerciasis-Associated Epilepsy, a Pilot Study and Review of the Literature.

Neuro-inflammation may be associated with onchocerciasis-associated epilepsy (OAE) but thus far very few immunological studies have been performed in children with this form of epilepsy. In a pilot study we measured the cytokine levels in cerebrospinal fluid (CSF) of persons with OAE from Maridi, South Sudan, and from Mosango, Democratic Republic of the Congo (DRC) and compared these results with cytokine levels in CSF of Africans with non-OAE neurological disorders, and Europeans with epilepsy or other neurological conditions. The following cytokines were studied: IL-6, TNF-α, IL1-ß, IL-5, IL-4, IL-13, CCL3 (Mip-1α), VEGF-C, VCAM-1. No cytokine was significantly associated with OAE, although a lower IL-13 level was observed in CSF of persons with OAE compared to African controls. Observed cytokine profiles and neuro-inflammation may be the consequence of long-standing epilepsy, concomitant infections and malnutrition. Ideally cytokine levels should be determined in a prospective study in serum and CSF collected at the time of onset of the first seizures.

High Prevalence of Epilepsy in an Onchocerciasis-Endemic Area in Mvolo County, South Sudan: A Door-To-Door Survey.

In June 2020, a door-to-door household survey was conducted in Mvolo County, an onchocerciasis-endemic area in South Sudan. A total of 2357 households containing 15,699 individuals agreed to participate in the study. Of these, 5046 (32.1%, 95% CI: 31.4-32.9%) had skin itching and 445 (2.8%, 95% CI: 2.6-3.1%) were blind. An epilepsy screening questionnaire identified 813 (5.1%) persons suspected of having epilepsy. Of them, 804 (98.9%) were seen by a medical doctor, and in 798 (98.1%) the diagnosis of epilepsy was confirmed. The overall epilepsy prevalence was 50.8/1000 (95% CI: 47.6-54.4/1000), while the prevalence of nodding syndrome was 22.4/1000 (95% CI: 20.1-24.9/1000). Younger age, being male, skin itching, blindness, and living in a neighbourhood or village close to the Naam River were risk factors for epilepsy. The annual incidence of epilepsy was 82.8/100,000 (95% CI: 44.1-141.6/100,000). Among children 7-9 years old without epilepsy, 34% were Ov16 seropositive, suggesting high ongoing Onchocerca volvulus transmission, but only 41.9% of them took ivermectin during the last mass distribution. In conclusion, a high prevalence and incidence of epilepsy was observed in Mvolo, South Sudan. Strengthening of the onchocerciasis elimination programme is urgently needed in order to prevent epilepsy in this region.

Epilepsy-related stigma and cost in two onchocerciasis-endemic areas in South Sudan: A pilot descriptive study.

INTRODUCTION: Epilepsy is a major public health concern in sub-Saharan Africa, particularly in resource-limited rural villages where persons with epilepsy (PWE) are often confronted with a wide treatment gap, frequent stigma and high cost of epilepsy care. We investigated stigma and economic cost related to epilepsy in the states of Maridi and Amadi in South Sudan, two onchocerciasis endemic areas with high epilepsy prevalence. METHODS: Between November 2019 and February 2020, community-based surveys were conducted in eight villages of Maridi and Amadi States. Consenting PWE were identified via a door-to-door approach, and perceived stigma was assessed using the validated Kilifi stigma scale. Additional data about household income, as well as epilepsy-related direct and indirect costs were collected. RESULTS: 239 PWE were recruited (95 from Maridi, 144 from Amadi). Stigma scores were higher in Maridi compared to Amadi (mean scores: 13.9 vs 6.5, p < 0.001). Mean weighted epilepsy costs per month in Maridi (38.4 USD) were double those observed in Amadi (17.6 USD). The main epilepsy-related expenditure was the purchase of anti-epileptic drugs (AED). Stigma scores correlated with epilepsy cost (Spearman-rho = 0.24, p < 0.001) and were positively associated with traditional medicine use (regression estimate = 1.9; p = 0.027). CONCLUSION: In rural South Sudan, PWE and their families often experienced stigma from the community. Higher perceived stigma was associated with traditional medicine use, which increased the overall cost of epilepsy management. Demystifying epilepsy and making AED more accessible would improve the quality of life of PWE and their families, and reduce the economic burden of epilepsy.

Persons with onchocerciasis-associated epilepsy and nodding seizures have a more severe form of epilepsy with more cognitive impairment and higher levels of Onchocerca volvulus infection.

Following previous reports of very high epilepsy prevalence in the onchocerciasis-endemic villages in Maridi County, South Sudan, a study was conducted to investigate the association between the level of Onchocerca volvulus infection, epilepsy, and related outcomes. In December 2018, persons with epilepsy (PWE) were recruited from villages where an epilepsy prevalence of 4.4% (range: 3.5-11.9%) was documented. We enrolled 318 participants from whom two skin snips were taken for microscopic detection of O. volvulus microfilariae (mf). Seizure history was obtained for all PWE and their degree of disability assessed using the modified Rankin scale. Almost all (84.9%) PWE had detectable mf in their skin snips. Onchocerciasis-infected PWE experienced nodding seizures more often than uninfected PWE (p=0.034). Moreover, persons with nodding seizures had more frequent seizures (p<0.001) and higher disability scores (p<0.001), and were more often cognitively impaired and younger at the time of their first epileptic seizure (nine years vs 12 years, p<0.001) compared to PWE without nodding seizures. Based on multivariate models, nodding seizures were associated with higher mf densities (aOR: 1.022; 95% CI: 1.005-1.041). Epilepsy onset at a younger age was associated with a worse outcome. Higher frequency of seizures, longer duration of epilepsy and younger age were associated with increased disability. Regular antiepileptic drug use was associated with better cognitive and disability outcomes. PWE with nodding seizures have a more severe form of onchocerciasis-associated epilepsy, with earlier seizure onset and higher levels of O. volvulus infection. Younger PWE were prone to worse epilepsy outcomes, which would be prevented with regular antiepileptic treatment.

Onchocerca volvulus is not detected in the cerebrospinal fluid of persons with onchocerciasis-associated epilepsy.

OBJECTIVES: Epidemiological evidence links onchocerciasis with the development of epilepsy. The aim of this study was to detect Onchocerca volvulus microfilariae or its bacterial endosymbiont, Wolbachia, in the cerebrospinal fluid (CSF) of persons with onchocerciasis-associated epilepsy (OAE). METHODS: Thirteen persons with OAE and O. volvulus skin snip densities of >80 microfilariae were recruited in Maridi County (South Sudan) and their CSF obtained. Cytospin centrifuged preparations of CSF were examined by light microscopy for the presence of O. volvulus microfilariae. DNA was extracted from CSF to detect O. volvulus (O-150 repeat) by quantitative real-time PCR, and Wolbachia (FtsZ gene) by standard PCR. To further investigate whether CSF from onchocerciasis-infected participants could induce seizures, 3- and 7-day old zebrafish larvae were injected with the CSF intracardially and intraperitoneally, respectively. For other zebrafish larvae, CSF was added directly to the larval medium. RESULTS: No microfilariae, parasite DNA, or Wolbachia DNA were detected in any of the CSF samples by light microscopy or PCR. All zebrafish survived the procedures and none developed seizures. CONCLUSIONS: The absence of O. volvulus in the CSF suggests that OAE is likely not caused by direct parasite invasion into the central nervous system, but by another phenomenon triggered by O. volvulus infection.

Clinical characteristics of onchocerciasis-associated epilepsy in villages in Maridi County, Republic of South Sudan.

PURPOSE: To describe the clinical manifestations of persons with epilepsy (PWE) in onchocerciasis endemic villages in South Sudan. METHODS: During a survey in Maridi County in May 2018, PWE were interviewed and examined in their households by a clinical officer or medical doctor. Onchocerciasis-associated epilepsy (OAE) was defined as ≥2 seizures without any obvious cause, starting between the ages of 3-18 years in previously healthy persons who had resided for at least 3 years in the onchocerciasis endemic area. RESULTS: Seven hundred and thirty-six PWE were included in the study; 315 (42.8%) were females; median age was 18 years. A variety of seizure types were reported: generalized tonic-clonic seizures in 511 PWE (69.4%), absences in 15 (2.0%), focal motor seizures with full awareness in 7 (1.0%), focal motor seizures with impaired awareness in 25 (3.4%), brief episodes of hallucinations in 316 (43.9%) and nodding seizures in 335 (45.5%). The median age of onset of all seizures was 10 years, and 8 years for nodding seizures. PWE with nodding seizures presented with more cognitive disabilities. The diagnostic criteria for OAE were met by 414 (85.2%) of the 486 PWE with complete information. Eighty (11.0%) PWE presented with Nakalanga features. Only 378 (51.4%) PWE were taking anti-epileptic treatment. CONCLUSION: PWE presented with a wide spectrum of seizures. The high percentage of PWE who met the diagnostic criteria for OAE suggests that better onchocerciasis control could prevent new cases. Urgent action is needed to close the anti-epileptic treatment gap.

The effect of bi-annual community-directed treatment with ivermectin on the incidence of epilepsy in onchocerciasis endemic villages in South Sudan: a study protocol.

BACKGROUND: Nodding syndrome (NS) is a devastating epileptic illness of unknown aetiology mainly affecting children 5-15 years of age. Head nodding distinguishes NS from other forms of epilepsy. Other manifestations of the illness include mental and physical growth retardation. Many children die as a result of falling in fires or drowning. Recently, it was shown that NS is only one of the phenotypic presentations of onchocerciasis associated epilepsy (OAE). Despite the strong epidemiological association between epilepsy and onchocerciasis, the causal mechanism is unknown. After implementation of bi-annual community directed treatment with ivermectin (CDTi) and larviciding of rivers in northern Uganda, new cases of NS have ceased, while new cases continue to emerge in South Sudanese onchocerciasis-endemic areas with an interrupted CDTi programme. This study is designed to evaluate the potential effects of bi-annual CDTi on reducing the incidence of NS/OAE in onchocerciasis-endemic areas in South Sudan. METHODS: A pre-intervention door-to-door population-based household survey will be conducted in selected onchocerciasis-endemic villages in Mundri and Maridi Counties, which have a high prevalence of epilepsy. Using a validated questionnaire, the entire village will be screened by community research assistants for suspected epilepsy cases. Suspected cases will be interviewed and examined by a trained clinical officer or medical doctor who will confirm or reject the diagnosis of epilepsy. Bi-annual CDTi will be implemented in the villages and a surveillance system for epilepsy set up. By implementing an epilepsy onchocerciasis awareness campaign we expect to obtain > 90% CDTi coverage of eligible individuals. The door-to-door survey will be repeated two years after the baseline survey. The incidence of NS/OAE will be compared before and after bi-annual CDTi. DISCUSSION: Our study is the first population-based study to evaluate the effect of bi-annual CDTi to reduce the incidence of NS/OAE. If the study demonstrates such a reduction, these findings are expected to motivate communities in onchocerciasis-endemic regions to participate in CDTi, and will encourage policy makers, funders and other stakeholders to increase their efforts to eliminate onchocerciasis.

External quality assessment in resource-limited countries.

INTRODUCTION: Health laboratory services are a critical component of national health systems but face major operational challenges in resource-limited (RL) settings. New funding for health systems strengthening in RL countries has increased the demand for diagnostics and provided opportunities to address these constraints. An approach to sustainably strengthen national laboratory systems in sub-Saharan African countries is the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme. External Quality Assessment (EQA) is a requirement for laboratory accreditation. EQA comprises proficiency testing (PT), rechecking of samples and on-site evaluation. MATERIALS AND METHODS: A systematic literature search was conducted to identify studies addressing laboratory EQA and quality monitoring in RL countries. Unpublished reports were also sought from national laboratory authorities and personnel. RESULTS: PT schemes in RL countries are provided by commercial companies, institutions in developed countries and national programmes. Most government-supported PT schemes address single diseases using a vertical approach. Regional approaches to delivering PT have also been implemented across RL countries. Rechecking schemes address mainly tuberculosis (TB), malaria and human immunodeficiency virus (HIV); integrated rechecking programmes have been piloted. Constraints include sample transportation, communication of results, unknown proficiency of referee staff and limited resources for corrective action. Global competency assessment standards for malaria microscopists have been established. CONCLUSIONS: EQA is vital for monitoring laboratory performance and maintaining quality of laboratory services, and is a valuable tool for identifying and assessing technology in use, identifying gaps in laboratory performance and targeting training needs. Accreditation of PT providers and competency of EQA personnel must be ensured.

HIV type 1 subtypes in circulation in northern Kenya.

The genetic subtypes of HIV-1 circulating in northern Kenya have not been characterized. Here we report the partial sequencing and analysis of samples collected in the years 2003 and 2004 from 72 HIV-1-positive patients in northern Kenya, which borders Ethiopia, Somalia, and Sudan. From the analysis of partial env sequences, it was determined that 50% were subtype A, 39% subtype C, and 11% subtype D. This shows that in the northern border region of Kenya subtypes A and C are the dominant HIV-1 subtypes in circulation. Ethiopia is dominated mainly by HIV-1 subtype C, which incidentally is the dominant subtype in the town of Moyale, which borders Ethiopia. These results show that cross-border movements play an important role in the circulation of subtypes in Northern Kenya.

Reduction of the efficacy of antifolate antimalarial therapy by folic acid supplementation.

Malaria and anemia are common conditions in patients presenting to outpatient clinics in Kenya. Anemia is usually due to malaria infection with underlying micronutrient deficiency. Iron therapy has been shown to enhance recovery from anemia in children with malaria, without affecting malaria treatment. Iron and folic acid are often prescribed together for anemic individuals. Until recently in Kenya, the drug of first choice for non-severe malaria was sulfadoxine-pyrimethamine (SP), an antifolate antimalarial drug. In this study, 303 patients of all ages with anemia and uncomplicated Plasmodium falciparum malaria attending an outpatient clinic in an area of seasonal malaria were treated with SP and iron, and were randomized to receive folic acid. Parasite clearance rates were measured using a survival analysis plot for both parasitologic and clinical failure. There was a significant reduction in the efficacy of SP in patients taking standard therapeutic doses of folic acid using the survival curve for parasitologic failure (P < 0.0001), but no difference for clinical failure (P = 0.7008). Folic acid supplementation did not enhance recovery from anemia.

Interaction between climatic, environmental, and demographic factors on cholera outbreaks in Kenya.

BACKGROUND: Cholera remains an important public health concern in developing countries including Kenya where 11,769 cases and 274 deaths were reported in 2009 according to the World Health Organization (WHO). This ecological study investigates the impact of various climatic, environmental, and demographic variables on the spatial distribution of cholera cases in Kenya. METHODS: District-level data was gathered from Kenya's Division of Disease Surveillance and Response, the Meteorological Department, and the National Bureau of Statistics. The data included the entire population of Kenya from 1999 to 2009. RESULTS: Multivariate analyses showed that districts had an increased risk of cholera outbreaks when a greater proportion of the population lived more than five kilometers from a health facility (RR: 1.025 per 1% increase; 95% CI: 1.010, 1.039), bordered a body of water (RR: 5.5; 95% CI: 2.472, 12.404), experienced increased rainfall from October to December (RR: 1.003 per 1 mm increase; 95% CI: 1.001, 1.005), and experienced decreased rainfall from April to June (RR: 0.996 per 1 mm increase; 95% CI: 0.992, 0.999). There was no detectable association between cholera and population density, poverty, availability of piped water, waste disposal methods, rainfall from January to March, or rainfall from July to September. CONCLUSION: Bordering a large body of water, lack of health facilities nearby, and changes in rainfall were significantly associated with an increased risk of cholera in Kenya.