Transforming Parkinson's Care in Africa (TraPCAf): protocol for a multimethodology National Institute for Health and Care Research Global Health Research Group project.

BACKGROUND: Parkinson's disease (PD) is the second most common neurodegenerative disorder and, according to the Global Burden of Disease estimates in 2015, was the fastest growing neurological disorder globally with respect to associated prevalence, disability, and deaths. Information regarding the awareness, diagnosis, phenotypic characteristics, epidemiology, prevalence, risk factors, treatment, economic impact and lived experiences of people with PD from the African perspective is relatively sparse in contrast to the developed world, and much remains to be learned from, and about, the continent. METHODS: Transforming Parkinson's Care in Africa (TraPCAf) is a multi-faceted, mixed-methods, multi-national research grant. The study design includes multiple sub-studies, combining observational (qualitative and quantitative) approaches for the epidemiological, clinical, risk factor and lived experience components, as appropriate, and interventional methods (clinical trial component). The aim of TraPCAf is to describe and gain a better understanding of the current situation of PD in Africa. The countries included in this National Institute for Health and Care Research (NIHR) Global Health Research Group (Egypt, Ethiopia, Ghana, Kenya, Nigeria, South Africa and Tanzania) represent diverse African geographies and genetic profiles, with differing resources, healthcare systems, health and social protection schemes, and policies. The research team is composed of experts in the field with vast experience in PD, jointly led by a UK-based and Africa-based investigator. DISCUSSION: Despite the increasing prevalence of PD globally, robust data on the disease from Africa are lacking. Existing data point towards the poor awareness of PD and other neurological disorders on the continent and subsequent challenges with stigma, and limited access to affordable services and medication. This multi-site study will be the first of its kind in Africa. The data collected across the proposed sub-studies will provide novel and conclusive insights into the situation of PD. The selected country sites will allow for useful comparisons and make results relevant to other low- and middle-income countries. This grant is timely, as global recognition of PD and the public health challenge it poses builds. The work will contribute to broader initiatives, including the World Health Organization's Intersectoral global action plan on epilepsy and other neurological disorders. TRIAL REGISTRATION: https://doi.org/10.1186/ISRCTN77014546 .

The impact of malaria-protective red blood cell polymorphisms on parasite biomass in children with severe Plasmodium falciparum malaria.

Severe falciparum malaria is a major cause of preventable child mortality in sub-Saharan Africa. Plasma concentrations of P. falciparum Histidine-Rich Protein 2 (PfHRP2) have diagnostic and prognostic value in severe malaria. We investigate the potential use of plasma PfHRP2 and the sequestration index (the ratio of PfHRP2 to parasite density) as quantitative traits for case-only genetic association studies of severe malaria. Data from 2198 Kenyan children diagnosed with severe malaria, genotyped for 14 major candidate genes, show that polymorphisms in four major red cell genes that lead to hemoglobin S, O blood group, α-thalassemia, and the Dantu blood group, are associated with substantially lower admission plasma PfHRP2 concentrations, consistent with protective effects against extensive parasitized erythrocyte sequestration. In contrast the known protective ATP2B4 polymorphism is associated with higher plasma PfHRP2 concentrations, lower parasite densities and a higher sequestration index. We provide testable hypotheses for the mechanism of protection of ATP2B4.

Development of a new peptide-bead coupling method for an all peptide-based Luminex multiplexing assay for detection of Plasmodium falciparum antibody responses.

Using a recombinant protein antigen for antibody testing shows a sum of antibody responses to multiple different immune epitopes existing in the protein antigen. In contrast, the antibody testing to an immunogenic peptide epitope reflects a singular antibody response to the individual peptide epitope. Therefore, using a panel of peptide epitopes provides an advantage for profiling multiple singular antibody responses with potential to estimate recent malaria exposure in human infections. However, transitioning from malaria immune epitope peptide-based ELISA to an all peptide bead-based multiplex Luminex assay presents some challenges including variation in the ability of different peptides to bind beads. The aim of this study was to develop a peptide coupling method while demonstrating the utility of these peptide epitopes from multiple stage antigens of Plasmodium falciparum for measuring antibodies. Successful coupling of peptide epitopes to beads followed three steps: 1) development of a peptide tag appended to the C-terminus of each peptide epitope consisting of beta-alanine-lysine (x 4)--cysteine, 2) bead modification with a high concentration of adipic acid dihydrazide, and 3) use of the peptide epitope as a blocker in place of the traditional choice, bovine serum albumin (BSA). This new method was used to couple 12 peptide epitopes from multiple stage specific antigens of P. falciparum, 1 Anopheles mosquito salivary gland peptide, and 1 Epstein-Barr virus peptide as an assay control. The new method was applied to testing of IgG in pooled samples from 30 individuals with previously repeated malaria exposure in western Kenya and IgM and IgG in samples from 37 U.S. travelers with recent exposure to malaria. The new peptide-bead coupling method and subsequent multiplex Luminex assay showed reliable detection of IgG to all 14 peptides in Kenyan samples. Among 37 samples from U.S. travelers recently diagnosed with malaria, IgM and IgG to the peptide epitopes were detected with high sensitivity and variation. Overall, the U.S. travelers had a much lower positivity rates of IgM than IgG to different peptide epitopes, ranging from a high of 62.2% positive for one epitope to a low of only 5.4% positive for another epitope. In contrast, the travelers had IgG positive rates from 97.3% to 91.9% to various peptide epitopes. Based on the different distribution in IgM and IgG positivity to overall number of peptide epitopes and to the number of pre-erythrocytic, erythrocytic, gametocytic, and salivary stage epitopes at the individual level, four distinct patterns of IgM and IgG responses among the 37 samples from US travelers were observed. Independent peptide-bead coupling and antibody level readout between two different instruments also showed comparable results. Overall, this new coupling method resolves the peptide-bead coupling challenge, is reproducible, and can be applied to any other immunogenic peptide epitopes. The resulting all peptide bead-based multiplex Luminex assay can be expanded to include other peptide epitopes of P. falciparum, different malaria species, or other diseases for surveillance, either in US travelers or endemic areas.

Feasibility of direct venous inoculation of the radiation-attenuated Plasmodium falciparum whole sporozoite vaccine in children and infants in Siaya, western Kenya.

PfSPZ Vaccine, composed of radiation-attenuated, aseptic, purified, cryopreserved Plasmodium falciparum sporozoites, is administered by direct venous inoculation (DVI) for maximal efficacy against malaria. A critical issue for advancing vaccines that are administered intravenously is the ability to efficiently administer them across multiple age groups. As part of a pediatric safety, immunogenicity, and efficacy trial in western Kenya, we evaluated the feasibility and tolerability of DVI, including ease of venous access, injection time, and crying during the procedure across age groups. Part 1 was an age de-escalation, dose escalation trial in children aged 13 months-5 years and infants aged 5-12 months; part 2 was a vaccine efficacy trial including only infants, using the most skilled injectors from part 1. Injectors could use a vein viewer, if needed. A total of 1222 injections (target 0.5 mL) were initiated by DVI in 511 participants (36 were 5-9-year-olds, 65 were 13-59-month-olds, and 410 infants). The complete volume was injected in 1185/1222 (97.0%) vaccinations, 1083/1185 (91.4%) achieved with the first DVI. 474/511 (92.8%) participants received only complete injections, 27/511 (5.3%) received at least one partial injection (<0.5 mL), and in 10/511 (2.0%) venous access was not obtained. The rate of complete injections by single DVI for infants improved from 77.1% in part 1 to 92.8% in part 2. No crying occurred in 51/59 (86.4%) vaccinations in 5-9-year-olds, 25/86 (29.1%) vaccinations in 13-59-month-olds and 172/1067 (16.1%) vaccinations in infants. Mean administration time ranged from 2.6 to 4.6 minutes and was longer for younger age groups. These data show that vaccination by DVI was feasible and well tolerated in infants and children in this rural hospital in western Kenya, when performed by skilled injectors. We also report that shipping and storage in liquid nitrogen vapor phase was simple and efficient. (Clinicaltrials.gov NCT02687373).

Associations of antenatal maternal psychological distress with infant birth and development outcomes: Results from a South African birth cohort.

BACKGROUND: Antenatal maternal psychological distress is common in low and middle-income countries (LMIC), but there is a dearth of research on its effect on birth and developmental outcomes in these settings, particularly in Sub-Saharan Africa. This study set out to identify risk factors for antenatal maternal psychological distress and determine whether antenatal maternal psychological distress was associated with infant birth and developmental outcomes, using data from the Drakenstein Child Health Study (DCHS), a birth cohort study in South Africa. METHODS: Pregnant women were enrolled in the DCHS from primary care antenatal clinics. Antenatal maternal psychological distress was measured using the Self-Reporting Questionnaire 20-item (SRQ-20). A range of psychosocial measures, including maternal childhood trauma, depression, and posttraumatic stress disorder (PTSD) were administered. Birth outcomes, including premature birth, weight-for-age z-score and head circumference-for-age z-score, were measured using revised Fenton growth charts. The Bayley III Scales of Infant and Toddler Development was administered at 6 months of age to assess infant development outcomes, including cognitive, language, and motor domains in a subset of n=231. Associations of maternal antenatal psychological distress with psychosocial measures, and with infant birth and developmental outcomes were examined using linear regression models. RESULTS: 961 women were included in this analysis, with 197 (21%) reporting scores indicating the presence of psychological distress. Antenatal psychological distress was associated with maternal childhood trauma, antenatal depression, and PTSD, and inversely associated with partner support. No association was observed between antenatal maternal psychological distress and preterm birth or early developmental outcomes, but antenatal maternal psychological distress was associated with a smaller head circumference at birth (coefficient=-0.30, 95% CI: -0.49; -0.10). CONCLUSION: Antenatal maternal psychological distress is common in LMIC settings and was found to be associated with key psychosocial measures during pregnancy, as well as with adverse birth outcomes, in our study population. These associations highlight the potential value of screening for antenatal maternal psychological distress as well as of developing targeted interventions.

Deterministic processes structure bacterial genetic communities across an urban landscape.

Land-use change is predicted to act as a driver of zoonotic disease emergence through human exposure to novel microbial diversity, but evidence for the effects of environmental change on microbial communities in vertebrates is lacking. We sample wild birds at 99 wildlife-livestock-human interfaces across Nairobi, Kenya, and use whole genome sequencing to characterise bacterial genes known to be carried on mobile genetic elements (MGEs) within avian-borne Escherichia coli (n = 241). By modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance (AMR) against ecological and anthropogenic forms of urban environmental change, we demonstrate that communities of avian-borne bacterial genes are shaped by the assemblage of co-existing avian, livestock and human communities, and the habitat within which they exist. In showing that non-random processes structure bacterial genetic communities in urban wildlife, these findings suggest that it should be possible to forecast the effects of urban land-use change on microbial diversity.

Household socio-economic position and individual infectious disease risk in rural Kenya.

The importance of household socio-economic position (SEP) in shaping individual infectious disease risk is increasingly recognised, particularly in low income settings. However, few studies have measured the extent to which this association is consistent for the range of pathogens that are typically endemic among the rural poor in the tropics. This cross-sectional study assessed the relationship between SEP and human infection within a single community in western Kenya using a set of pathogens with diverse transmission routes. The relationships between household SEP and individual infection with Plasmodium falciparum, hookworm (Ancylostoma duodenale and/or Necator americanus), Entamoeba histolytica/dispar, Mycobacterium tuberculosis, and HIV, and co-infections between hookworm, P. falciparum and E. histolytica/dispar, were assessed using multivariable logistic and multinomial regression. Individuals in households with the lowest SEP were at greatest risk of infection with P. falciparum, hookworm and E. histolytica/dispar, as well as co-infection with each pathogen. Infection with M. tuberculosis, by contrast, was most likely in individuals living in households with the highest SEP. There was no evidence of a relationship between individual HIV infection and household SEP. We demonstrate the existence of a household socio-economic gradient within a rural farming community in Kenya which impacts upon individual infectious disease risk. Structural adjustments that seek to reduce poverty, and therefore the socio-economic inequalities that exist in this community, would be expected to substantially reduce overall infectious disease burden. However, policy makers and researchers should be aware that heterogeneous relationships can exist between household SEP and infection risk for different pathogens in low income settings.

In vitro antiplasmodial, antitrypanosomal and antileishmanial activities of selected medicinal plants from Ugandan flora: Refocusing into multi-component potentials.

ETHNOPHARMACOLOGICAL RELEVANCE: Seven medicinal plants from Ugandan flora, namely Entada abyssinica, Khaya anthotheca, Vernonia amygdalina, Baccharoides adoensis, Schkuhria pinnata, Entandropragma utile and Momordica foetida, were selected in this study. They are used to treat conditions and infections ranging from inflammations, pains and fevers to viruses, bacteria, protozoans and parasites. Two of the plants, V. amygdalina and M. foetida, are also used as human food or relish, while others are important in ethnoveterinary practices and in zoopharmacognosy in the wild. The aim of this study was to evaluate the in vitro antiplasmodial, antitrypanosomal and antileishmanial activities, along with cytotoxicity of the multi-component extracts of these plants. MATERIALS AND METHODS: Different parts of the plants were prepared and serially extracted with hexane, petroleum ether, dichloromethane, ethyl acetate, methanol and double distilled water. Solvent free extracts were assayed for in vitro inhibition against four reference parasite strains, Plasmodium falciparum (K1), Trypanosoma brucei rhodesiense (STIB 900), Trypanosoma cruzi (Talahuen C2C4) and Leishmania donovani (MHOM-ET-67/L82) using standard methods. Toxicity was assessed against L6 skeletal fibroblast and mouse peritoneal macrophage (J774) cells and selectivity indices (SIs) calculated for the most active extracts. RESULTS: The strongest activities, demonstrating median inhibitory concentration (IC50) values ≤ 2 µg/ml, were observed for the dichloromethane and petroleum ether extracts of K. anthotheca, B. adoensis and S. pinnata. Overall, IC50 values ranged from < 1 µg/ml to > 90 µg/ml. Out of 22 extracts demonstrating IC50s < 20 µg/ml, seven were against T. b. rhodesiense (IC50: 1.6-16.2 µg/ml), six against T. cruzi (IC50: 2.1-18.57 µg/ml), none against L. donovani (IC50: falling > 3.3 and >10 µg/ml), and nine against P. falciparum (IC50: 0.96 µg/ml to 4.69 µg/ml). Selectivity indices (SI) calculated for the most active extracts ranged from <1.00 to 94.24. However, the B. adoensis leaf dichloromethane extract (a) was equipotent (IC50 = 3.3 µg/ml) against L. donovani and L6 cells respectively, indicating non-specific selection. Trypanosome and Plasmodium parasites were comparatively more sensitive to the test extracts. CONCLUSIONS: The benefits achieved from the seven tested plant species as traditional ethnomedicinal and ethnoveterinary therapies or in zoopharmacognosy against infections and conditions of animals in the wild are strongly supported by results of this study. The synergy of plant extracts, so achieved by concerted actions of the ligands, produces adequate perturbation of targets in the four parasite genera, resulting in the strong potencies exhibited by low IC50 values. The total inhibitory effect, achieved as a sum of perturbations contributed by each participating compound in the extract, minimises toxic effects of the compounds as seen in the high SI's obtained with some extracts. Those extracts demonstrating SI ≥ 4 form promising candidates for further cell-based and system pharmacology studies.

Isolation and characterization of pectolytic bacterial pathogens infecting potatoes in Nakuru County, Kenya.

AIMS: Isolation and characterization of pectolytic bacteria associated with soft rot disease of potatoes in Nakuru, Kenya, to provide the basis for the development of disease control measures. METHODS AND RESULTS: Potato tubers showing symptoms of soft rot were collected from different farms in Molo and Mau Narok regions within Nakuru county. Isolation was done using crystal violet pectate medium (CVPM). Out of the 71 isolates that showed growth on CVPM, pathogenicity tests revealed that 36 of them had the ability to macerate tissues of potato tubers. All the isolates yielded a fragment of approximately 1500 bp after 16S rDNA amplification. Using the BIOLOG microbial identification system, 20 bacterial isolates were identified as Pectobacterium carotovorum subsp. carotovorum, 7 were Pseudomonas fluorescens B while 9 were Ps. fluorescens A. Y1/Y2 primers successfully amplified pectate lyase-encoding (pel) gene, approximately 434 bp, in all the 20 P. carotovorum species. The virulence of the isolated strains to cause disease, according to pectinolytic tests, varied with change in incubation temperature of the test samples. Pectobacterium carotovorum strains were the most virulent at 30°C while disease severity due to infection by Ps. fluorescens A strains was high at 20°C compared to the other isolates. CONCLUSION: This study reveals the identity of pectolytic bacterial species from two genera, Pectobacterium and Pseudomonas, as causative agents of potato soft rot in Nakuru, Kenya. SIGNIFICANCE AND IMPACT OF THE STUDY: Research findings from this study will aid in developing suitable risk mitigation methods for adoption by farmers to prevent losses due to soft rot.

Expressed Centromere Specific Histone 3 (CENH3) Variants in Cultivated Triploid and Wild Diploid Bananas (Musa spp.).

Centromeres are specified by a centromere specific histone 3 (CENH3) protein, which exists in a complex environment, interacting with conserved proteins and rapidly evolving satellite DNA sequences. The interactions may become more challenging if multiple CENH3 versions are introduced into the zygote as this can affect post-zygotic mitosis and ultimately sexual reproduction. Here, we characterize CENH3 variant transcripts expressed in cultivated triploid and wild diploid progenitor bananas. We describe both splice- and allelic-[Single Nucleotide Polymorphisms (SNP)] variants and their effects on the predicted secondary structures of protein. Expressed CENH3 transcripts from six banana genotypes were characterized and clustered into three groups (MusaCENH-1A, MusaCENH-1B, and MusaCENH-2) based on similarity. The CENH3 groups differed with SNPs as well as presence of indels resulting from retained and/or skipped exons. The CENH3 transcripts from different banana genotypes were spliced in either 7/6, 5/4 or 6/5 exons/introns. The 7/6 and the 5/4 exon/intron structures were found in both diploids and triploids, however, 7/6 was most predominant. The 6/5 exon/introns structure was a result of failure of the 7/6 to splice correctly. The various transcripts obtained were predicted to encode highly variable N-terminal tails and a relatively conserved C-terminal histone fold domain (HFD). The SNPs were predicted in some cases to affect the secondary structure of protein by lengthening or shorting the affected domains. Sequencing of banana CENH3 transcripts predicts SNP variations that affect amino acid sequences and alternatively spliced transcripts. Most of these changes affect the N-terminal tail of CENH3.

Serological evidence of Francisella tularensis in febrile patients seeking treatment at remote hospitals, northeastern Kenya, 2014-2015.

Tularaemia is a highly contagious infectious zoonosis caused by the bacterial agent Francisella tularensis. The aim of this study was to investigate the presence of antibodies to F. tularensis in febrile patients in northeastern Kenya. During 2014-2015, 730 patients were screened for anti-F. tularensis antibodies using a combination of ELISA and Western blot. Twenty-seven (3.7%) individuals were positive for F. tularensis. Tularaemia was not suspected by the treating clinicians in any of them. Our results suggest that tularaemia may be present in Kenya but remain unreported, and emphasizes the need for local clinicians to broaden their diagnostic repertoire when evaluating patients with undifferentiated febrile illness.

Febrile patients admitted to remote hospitals in Northeastern Kenya: seroprevalence, risk factors and a clinical prediction tool for Q-Fever.

BACKGROUND: Q fever in Kenya is poorly reported and its surveillance is highly neglected. Standard empiric treatment for febrile patients admitted to hospitals is antimalarials or penicillin-based antibiotics, which have no activity against Coxiella burnetii. This study aimed to assess the seroprevalence and the predisposing risk factors for Q fever infection in febrile patients from a pastoralist population, and derive a model for clinical prediction of febrile patients with acute Q fever. METHODS: Epidemiological and clinical data were obtained from 1067 patients from Northeastern Kenya and their sera tested for IgG antibodies against Coxiella burnetii antigens by enzyme-linked-immunosorbent assay (ELISA), indirect immunofluorescence assay (IFA) and quantitative real-time PCR (qPCR). Logit models were built for risk factor analysis, and diagnostic prediction score generated and validated in two separate cohorts of patients. RESULTS: Overall 204 (19.1 %, 95 % CI: 16.8-21.6) sera were positive for IgG antibodies against phase I and/or phase II antigens or Coxiella burnetii IS1111 by qPCR. Acute Q fever was established in 173 (16.2 %, 95 % CI: 14.1-18.7) patients. Q fever was not suspected by the treating clinicians in any of those patients, instead working diagnosis was fever of unknown origin or common tropical fevers. Exposure to cattle (adjusted odds ratio [aOR]: 2.09, 95 % CI: 1.73-5.98), goats (aOR: 3.74, 95 % CI: 2.52-9.40), and animal slaughter (aOR: 1.78, 95 % CI: 1.09-2.91) were significant risk factors. Consumption of unpasteurized cattle milk (aOR: 2.49, 95 % CI: 1.48-4.21) and locally fermented milk products (aOR: 1.66, 95 % CI: 1.19-4.37) were dietary factors associated with seropositivity. Based on regression coefficients, we calculated a diagnostic score with a sensitivity 93.1 % and specificity 76.1 % at cut off value of 2.90: fever >14 days (+3.6), abdominal pain (+0.8), respiratory tract infection (+1.0) and diarrhoea (-1.1). CONCLUSION: Q fever is common in febrile Kenyan patients but underappreciated as a cause of community-acquired febrile illness. The utility of Q fever score and screening patients for the risky social-economic and dietary practices can provide a valuable tool to clinicians in identifying patients to strongly consider for detailed Q fever investigation and follow up on admission, and making therapeutic decisions.

Molecular Characterization of Giardia duodenalis in Children in Kenya.

BACKGROUND: Giardia duodenalis is an important intestinal protozoan in humans worldwide with high infection rates occurring in densely populated and low resource settings. The parasite has been recorded to cause diarrhea in children. This study was carried out to identify G. duodenalis assemblages and sub-assemblages in children presenting with diarrhea in Kenya. METHODS: A total of 2112 faecal samples were collected from children aged ≤ 5 years and screened for the presence of Giardia cysts using microscopy. A total of 96 (4.5%) samples were identified as Giardia positive samples and were genotyped using glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi) and ß-giardin loci. RESULTS: The three markers successfully genotyped 72 isolates and grouped 2 (1.4) isolates as Assemblage A, 64 (88.9) as Assemblage B and 7 (9.7%) consisted of mixed infections with assemblage A and B. A further analysis of 50 isolates using GDH Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) categorized 2 assemblage A isolates as sub-assemblage AII while 6 and 14 assemblage B isolates were categorized into sub-assemblage BIII and BIV respectively. A mixed infection with sub-assemblage BIII and BIV was recorded in 28 isolates. Over half (55.6%) of Giardia infections were recorded among the children between 13 to 48 months old. CONCLUSION: This paper reports the first data on the assemblages and sub-assemblages of Giardia duodenalis in children representing with diarrhea in Kenya.

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine.

BACKGROUND: The RTS,S/AS01 vaccine targets the circumsporozoite protein of Plasmodium falciparum and has partial protective efficacy against clinical and severe malaria disease in infants and children. We investigated whether the vaccine efficacy was specific to certain parasite genotypes at the circumsporozoite protein locus. METHODS: We used polymerase chain reaction-based next-generation sequencing of DNA extracted from samples from 4985 participants to survey circumsporozoite protein polymorphisms. We evaluated the effect that polymorphic positions and haplotypic regions within the circumsporozoite protein had on vaccine efficacy against first episodes of clinical malaria within 1 year after vaccination. RESULTS: In the per-protocol group of 4577 RTS,S/AS01-vaccinated participants and 2335 control-vaccinated participants who were 5 to 17 months of age, the 1-year cumulative vaccine efficacy was 50.3% (95% confidence interval [CI], 34.6 to 62.3) against clinical malaria in which parasites matched the vaccine in the entire circumsporozoite protein C-terminal (139 infections), as compared with 33.4% (95% CI, 29.3 to 37.2) against mismatched malaria (1951 infections) (P=0.04 for differential vaccine efficacy). The vaccine efficacy based on the hazard ratio was 62.7% (95% CI, 51.6 to 71.3) against matched infections versus 54.2% (95% CI, 49.9 to 58.1) against mismatched infections (P=0.06). In the group of infants 6 to 12 weeks of age, there was no evidence of differential allele-specific vaccine efficacy. CONCLUSIONS: These results suggest that among children 5 to 17 months of age, the RTS,S vaccine has greater activity against malaria parasites with the matched circumsporozoite protein allele than against mismatched malaria. The overall vaccine efficacy in this age category will depend on the proportion of matched alleles in the local parasite population; in this trial, less than 10% of parasites had matched alleles. (Funded by the National Institutes of Health and others.).

Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon-alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. About 40-50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs low IFN-α in over 1550 SLE cases, including genome-wide association study and replication cohorts. In meta-analysis, the top associations in European ancestry were protein kinase, cyclic GMP-dependent, type I (PRKG1) rs7897633 (P(Meta) = 2.75 × 10(-8)) and purine nucleoside phosphorylase (PNP) rs1049564 (P(Meta) = 1.24 × 10(-7)). We also found evidence for cross-ancestral background associations with the ankyrin repeat domain 44 (ANKRD44) and pleckstrin homology domain containing, family F member 2 gene (PLEKHF2) loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic sub-phenotypes becomes an attractive strategy for genetic discovery in complex disease.

Prevalence and Antibiotic Resistance Patterns of Escherichia coli among Hospitalised Patients at Thika District Hospital

Background: Emerging resistance to antimicrobial drugs increases morbidity and mortality by hampering the provision of effective chemotherapy; and makes treatment more costly. The emergence of resistance to antimicrobial agents is a global public health problem; especially in pathogens causing nosocomial infections. Objectives: To determine the carriage of E. coli from wounds and urine in catheterised inpatients at Thika District Hospital (TDH) and to determine antimicrobial resistance patterns to Beta-lactams; aminoglycosides and (fluoro) quinolones. Design: A cross-sectional study. Setting: Thika District Hospital among hospitalised patients. Subjects: A total of 450 specimens were collected and forty two (42) Escherichia coli isolated. Pus swabs were collected from wounds and urine was collected aseptically from the inpatients with catheters. Escherichia coli were identified by culture methods and biochemical tests. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method and interpreted according to Clinical Laboratory Standards Institute recommendations. Results: Susceptibility results in aminoglycosides were; resistance for amikacin; gentamicin and kanamycin was 20; 39 and 51 respectively. Resistance in penicillin was ampicillin 85 and piperacillin 83 . Resistance for sulfamethoxazole was 83; tetracycline 66 ; nalidixic acid 44; nalidixic acid 44 and chloramphenicol 39and chloramphenicol 39. In amoxicillin/clavulanic acid; resistance was 68 . Cephalosporins' resistance was ceftazidime 22 ; cefotaxime 56 . Resistance for imipenem and tazobactam was 7 and 12 respectively. Conclusion: Due to observations on resistance to antimicrobial agents commonly used in Thika District Hospital; this shows that there is need to revise antimicrobial policy in this region in the treatment of E. coli infections

Genetic variation near IRF8 is associated with serologic and cytokine profiles in systemic lupus erythematosus and multiple sclerosis.

Alleles of interferon (IFN) regulatory factor 8 (IRF8) are associated with susceptibility to both systemic lupus erythematosus (SLE) and multiple sclerosis (MS). Although high-type I IFN is thought to be causal in SLE, type I IFN is used as a therapy in MS. We investigated whether IRF8 alleles were associated with type I IFN levels or serologic profiles in SLE and MS. Alleles that have been previously associated with SLE or MS were genotyped in SLE and MS patients. The MS-associated rs17445836G allele was associated with anti-double-stranded DNA (dsDNA) autoantibodies in SLE patients (meta-analysis odds ratio=1.92). The same allele was associated with decreased serum IFN activity in SLE patients with anti-dsDNA antibodies, and with decreased type I IFN-induced gene expression in peripheral blood mononuclear cell from anti-dsDNA-negative SLE patients. In secondary progressive MS patients, rs17445836G was associated with decreased serum type I IFN. Rs17445836G was associated with increased IRF8 expression in SLE patient B cells. In summary, IRF8 rs17445836G is associated with human autoimmune disease characterized by low-type I IFN levels, and this may have pharmacogenetic relevance as type I IFN is modulated in SLE and MS. The association with autoantibodies and increased IRF8 expression in B cells supports a role for rs17445836G in humoral tolerance.

Characterization of methicillin-resistant Staphylococcus aureus from skin and soft tissue infections in patients in Nairobi, Kenya.

BACKGROUND: Skin and soft tissue infections (SSTIs) are among the most common infectious diseases and a frequent cause of hospital visits. In this study we sought to assess the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and antibiotic susceptibility patterns in SSTIs in patients attending hospitals in Kenya. METHODS: Eighty-two S. aureus isolates recovered from SSTIs from both inpatients and outpatients were screened for antibiotic susceptibility, possession of staphylococcal cassette chromosome mec (SCCmec) gene type, and the Panton-Valentine leukocidin (PVL) toxin gene. The prevalence of MRSA was investigated in relation to the type of patient and infection type, as well as the type of health care facility. RESULTS: Of 60 boil cultures, 39 (65%) grew S. aureus, of out of which 34 (87.2%) were MRSA. Of the 60 abscess cultures, 14 (23.3%) grew S. aureus, of which 10 (71.4%) were MRSA. Of 34 cellulitis cultures, 18 (52.9%) grew S. aureus, of which 16 (88.8%) were MRSA. Of 25 ulcer cultures, 11 (44%) grew S. aureus, of which nine (81.8%) were MRSA. Sixty-nine of 82 S. aureus (84.1%) were MRSA, with 52 (75.4%) possessing SCCmec II type and 14 (20.3%) being positive for the PVL gene. Based on hospitals, it was noted that most MRSA were isolated at publicly funded health care facilities serving an economically disadvantaged segment of Nairobi's population, such as those living in urban informal settlements. All 82 S. aureus were susceptible to vancomycin and resistant in high numbers to macrolides, aminoglycosides, and quinolones. Bacterial isolates were mostly susceptible to vancomycin, ciprofloxacin and co-trimoxazole, and none was resistant to vancomycin. However, most organisms showed decreased susceptibility to erythromycin and clindamycin. CONCLUSIONS: These findings suggest that SCCmec II MRSA and a PVL strain of MRSA are significant pathogens in patients with SSTIs presenting to hospitals in Kenya, and that MRSA cases are prevalent at publicly funded health care facilities.