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author:("eshu, Norbert")
1.  An Integrated Approach for Antiretroviral Adherence and Secondary HIV Transmission Risk-Reduction Support by Nurses in Kenya 
Ongoing antiretroviral therapy (ART) adherence and secondary HIV transmission risk reduction (positive prevention) support are needed in resource-limited settings. We evaluated a nurse-delivered counseling intervention in Kenya. We trained 90 nurses on a brief counseling algorithm that comprised ART and sexual risk assessment, risk reduction messages, and health promotion planning. Self-reported measures were assessed before, immediately after, and 2 months post-training. Consistent ART adherence assessment was reported by 29% of nurses at baseline and 66% at 2 months post-training (p < 0.001). Assessment of patient sexual behaviors was 25% at baseline and 60% at 2 months post-training (p < 0.001). Nurse practice behaviors recommended in the counseling algorithm improved significantly at 2 months post-training compared with baseline, odds ratios 4.30–10.50. We found that training nurses in clinical counseling for ART adherence and positive prevention is feasible. Future studies should test impact of nurse counseling on patient outcomes in resource-limited settings.
doi:10.1016/j.jana.2011.05.001
PMCID: PMC4018811  PMID: 21803605
antiretrovirals; HIV counseling; prevention with positives; resource-limited settings; treatment adherence
2.  High HIV-1 incidence, correlates of HIV-1 acquisition, and high viral loads following seroconversion among men who have sex with men in Coastal Kenya 
AIDS (London, England)  2013;27(3):437-446.
Background
HIV-1 incidence estimates and correlates of HIV-1 acquisition in African men who have sex with men are largely unknown.
Methods
Since 2005, HIV-1-uninfected men who reported sex with men and women (MSMW) or sex with men exclusively (MSME) were followed at scheduled visits for collection of behavioural and clinical examination data and plasma for HIV-1 testing. Urethral or rectal secretions were collected from symptomatic men to screen for gonorrhoea. Poisson regression methods were used to estimate adjusted incidence rate ratios (aIRR) to explore associations between risk factors and incident HIV-1 infection. Plasma viral loads (PVL) were assessed over two years following seroconversion.
Results
Overall HIV-1 incidence in 449 men was 8.6 (95% confidence interval [CI]: 6.7–11.0) per 100 person-years (py). Incidence was 5.8 (95% CI: 4.2–7.9) per 100 py among MSMW, and 35.2 (95% CI: 23.8–52.1) per 100 py among MSME. Unprotected sex, receptive anal intercourse, exclusive sex with men, group sex, and gonorrhoea in the past 6 months were strongly associated with HIV-1 acquisition, adjusted for confounders. PVL in seroconverters was >4 log10 copies/mL at 230 (73.4%) of 313 visits in MSMW and 153 (75.0%) of 204 visits in MSME.
Conclusions
HIV-1 incidence is very high among MSM in coastal Kenya, and many seroconverters maintain high PVL for up to two years after infection. Effective HIV-1 prevention interventions, including treatment as prevention, are urgently needed in this population.
doi:10.1097/QAD.0b013e32835b0f81
PMCID: PMC3929859  PMID: 23079811
HIV-1 incidence; MSM; gonorrhoea; anal intercourse; viral load; sexually transmitted infection; group sex; Africa
3.  Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya 
Scientific Reports  2013;3:3318.
Early identification of causal genetic variants underlying antimalarial drug resistance could provide robust epidemiological tools for timely public health interventions. Using a novel natural genetics strategy for mapping novel candidate genes we analyzed >75,000 high quality single nucleotide polymorphisms selected from high-resolution whole-genome sequencing data in 27 isolates of Plasmodium falciparum. We identified genetic variants associated with susceptibility to dihydroartemisinin that implicate one region on chromosome 13, a candidate gene on chromosome 1 (PFA0220w, a UBP1 ortholog) and others (PFB0560w, PFB0630c, PFF0445w) with putative roles in protein homeostasis and stress response. There was a strong signal for positive selection on PFA0220w, but not the other candidate loci. Our results demonstrate the power of full-genome sequencing-based association studies for uncovering candidate genes that determine parasite sensitivity to artemisinins. Our study provides a unique reference for the interpretation of results from resistant infections.
doi:10.1038/srep03318
PMCID: PMC3839035  PMID: 24270944
4.  Human SNP Links Differential Outcomes in Inflammatory and Infectious Disease to a FOXO3-Regulated Pathway 
Cell  2013;155(1):57-69.
Summary
The clinical course and eventual outcome, or prognosis, of complex diseases varies enormously between affected individuals. This variability critically determines the impact a disease has on a patient’s life but is very poorly understood. Here, we exploit existing genome-wide association study data to gain insight into the role of genetics in prognosis. We identify a noncoding polymorphism in FOXO3A (rs12212067: T > G) at which the minor (G) allele, despite not being associated with disease susceptibility, is associated with a milder course of Crohn’s disease and rheumatoid arthritis and with increased risk of severe malaria. Minor allele carriage is shown to limit inflammatory responses in monocytes via a FOXO3-driven pathway, which through TGFβ1 reduces production of proinflammatory cytokines, including TNFα, and increases production of anti-inflammatory cytokines, including IL-10. Thus, we uncover a shared genetic contribution to prognosis in distinct diseases that operates via a FOXO3-driven pathway modulating inflammatory responses.
PaperClip
Graphical Abstract
Highlights
•Reanalysis of GWAS data identifies a SNP associated with outcome in Crohn’s disease•This SNP modulates inflammatory responses in monocytes via a FOXO3-driven pathway•The mild disease-associated allele reduces TNFα and increases IL-10 production•Prognosis in RA and malaria (also TNFα-related diseases) is also linked to this SNP
An analysis of GWAS data of patients with Crohn’s disease distinguishes SNPs associated with disease risk from those associated with outcome. Functional studies indicate that a noncoding SNP associated with FOXO3A influences a cytokine inflammatory pathway that impacts outcome, not only in Crohn’s but also other diseases such as rheumatoid arthritis and malaria.
doi:10.1016/j.cell.2013.08.034
PMCID: PMC3790457  PMID: 24035192
5.  Antiretroviral Treatment Interruptions Predict Female Genital Shedding of Genotypically Resistant HIV-1 RNA 
Objectives
Resistant viruses may emerge in the female genital tract during antiretroviral therapy (ART). Our objective was to identify predictors of drug-resistant HIV-1 RNA in genital secretions after initiation of non-nucleoside reverse transcriptase inhibitor (NNRTI)-based therapy.
Design
We conducted a prospective cohort study with periodic evaluation of plasma and genital swab samples for HIV-1 RNA levels and antiretroviral resistance mutations.
Methods
First-line ART was initiated in 102 women. Plasma and genital HIV-1 RNA levels were measured at months 0, 3, 6, and 12. Genotypic resistance testing was performed for samples from all participants with RNA >1,000 copies/mL at month 6 or 12. Cox regression analysis was used to identify factors associated with incident genital tract resistance.
Results
Detectable genital tract resistance developed in 5 women, all with detectable plasma resistance (estimated incidence, 5.5/100 person-years of observation). Treatment interruption >48 hours, adherence by pill count, adherence by visual analog scale, and baseline plasma viral load were associated with incident genital tract resistance. In multivariate analysis, only treatment interruption was associated with risk of detectable genital tract resistance (adjusted hazard ratio 14.2, 95% CI 1.3–158.4).
Conclusions
Treatment interruption >48 hours during NNRTI-based therapy led to a significantly increased risk of detecting genotypically resistant HIV-1 RNA in female genital tract secretions. Patient- and program-level interventions to prevent treatment interruptions could reduce the risk of shedding resistant HIV-1 during ART.
doi:10.1097/QAI.0b013e31825bd703
PMCID: PMC3404237  PMID: 22592588
HIV drug resistance; virus shedding; female; antiretroviral therapy; adherence
7.  Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations 
PLoS Genetics  2013;9(5):e1003509.
Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles.
Author Summary
Malaria kills nearly a million people every year, most of whom are young children in Africa. The risk of developing severe malaria is known to be affected by genetics, but so far only a handful of genetic risk factors for malaria have been identified. We studied over a million DNA variants in over 5,000 individuals with severe malaria from the Gambia, Malawi, and Kenya, and about 7,000 healthy individuals from the same countries. Because the populations of Africa are far more genetically diverse than those in Europe, it is necessary to use statistical models that can account for both broad differences between countries and subtler differences between ethnic groups within the same community. We identified known associations at the genes ABO (which affects blood type) and HBB (which causes sickle cell disease), and showed that the latter is heterogeneous across populations. We used these findings to guide the development of statistical tests for association that take this heterogeneity into account, by modelling differences in the strength and genomic location of effect across and within African populations.
doi:10.1371/journal.pgen.1003509
PMCID: PMC3662650  PMID: 23717212
8.  HIV-1 RNA May Decline More Slowly in Semen than in Blood following Initiation of Efavirenz-Based Antiretroviral Therapy 
PLoS ONE  2012;7(8):e43086.
Objectives
Antiretroviral therapy (ART) decreases HIV-1 RNA levels in semen and reduces sexual transmission from HIV-1-infected men. Our objective was to study the time course and magnitude of seminal HIV-1 RNA decay after initiation of efavirenz-based ART among 13 antiretroviral-naïve Kenyan men.
Methods
HIV-1 RNA was quantified (lower limit of detection, 120 copies/mL) in blood and semen at baseline and over the first month of ART. Median log10 HIV-1 RNA was compared at each time-point using Wilcoxon Signed Rank tests. Perelson’s two-phase viral decay model and nonlinear random effects were used to compare decay rates in blood and semen.
Results
Median baseline HIV-1 RNA was 4.40 log10 copies/mL in blood (range, 3.20–5.08 log10 copies/mL) and 3.69 log10 copies/mL in semen (range, <2.08–4.90 log10 copies/mL). The median reduction in HIV-1 RNA by day 28 was 1.90 log10 copies/mL in blood (range, 0.56–2.68 log10 copies/mL) and 1.36 log10 copies/mL in semen (range, 0–2.66 log10 copies/mL). ART led to a decrease from baseline by day 7 in blood and day 14 in semen (p = 0.005 and p = 0.006, respectively). The initial modeled decay rate was slower in semen than in blood (p = 0.06). There was no difference in second-phase decay rates between blood and semen.
Conclusions
Efavirenz-based ART reduced HIV-1 RNA levels more slowly in semen than in blood. Although this difference was of borderline significance in this small study, our observations suggest that there is suboptimal suppression of seminal HIV-1 RNA for some men in the early weeks of treatment.
doi:10.1371/journal.pone.0043086
PMCID: PMC3418270  PMID: 22912795
9.  Association between Participant Self-Report and Biological Outcomes Used to Measure Sexual Risk Behavior in HIV-1-Seropositive Female Sex Workers in Mombasa, Kenya 
Sexually transmitted diseases  2011;38(5):429-433.
Background
Few studies have examined the association between self-reported sexual risk behaviors and biological outcomes in HIV-1-seropositive African adults.
Methods
We conducted a prospective cohort study in 898 HIV-1-seropositive women who reported engaging in transactional sex in Mombasa, Kenya. Primary outcome measures included detection of sperm in genital secretions, pregnancy, and sexually transmitted infections (STIs). Because three outcomes were evaluated, data are presented with odds ratios [OR] and 96.7% confidence intervals [CI] to reflect that we would reject a null hypothesis if a p-value were ≤0.033 (Simes’ methodology).
Results
During 2,404 person-years of follow-up, self-reported unprotected intercourse was associated with significantly higher likelihood of detecting sperm in genital secretions (OR 2.32, 96.7% CI 1.93, 2.81), and pregnancy (OR 2.78, 96.7% CI 1.57, 4.92), but not with detection of STIs (OR 1.20, 96.7% CI 0.98, 1.48). At visits where women reported being sexually active, having >1 sex partner in the past week was associated with lower likelihood of detecting sperm in genital secretions (OR 0.74, 96.7% CI 0.56, 0.98). This association became non-significant after adjustment for reported condom use (adjusted OR 0.81, 96.7% CI 0.60, 1.08).
Conclusions
Combining behavioral and biological outcomes, which provide complementary information, is advantageous for understanding sexual risk behavior in populations at risk for transmitting HIV-1. The paradoxical relationship between higher numbers of sex partners and less frequent identification of sperm in genital secretions highlights the potential importance of context-specific behavior, such as condom use dependent on partner type, when evaluating sexual risk behavior.
doi:10.1097/OLQ.0b013e31820369f6
PMCID: PMC3155001  PMID: 21217420
HIV-1; sexually transmitted disease; women; Africa; sexual risk behavior
10.  Profile: The Kilifi Health and Demographic Surveillance System (KHDSS) 
Summary The Kilifi Health and Demographic Surveillance System (KHDSS), located on the Indian Ocean coast of Kenya, was established in 2000 as a record of births, pregnancies, migration events and deaths and is maintained by 4-monthly household visits. The study area was selected to capture the majority of patients admitted to Kilifi District Hospital. The KHDSS has 260 000 residents and the hospital admits 4400 paediatric patients and 3400 adult patients per year. At the hospital, morbidity events are linked in real time by a computer search of the population register. Linked surveillance was extended to KHDSS vaccine clinics in 2008.
KHDSS data have been used to define the incidence of hospital presentation with childhood infectious diseases (e.g. rotavirus diarrhoea, pneumococcal disease), to test the association between genetic risk factors (e.g. thalassaemia and sickle cell disease) and infectious diseases, to define the community prevalence of chronic diseases (e.g. epilepsy), to evaluate access to health care and to calculate the operational effectiveness of major public health interventions (e.g. conjugate Haemophilus influenzae type b vaccine). Rapport with residents is maintained through an active programme of community engagement. A system of collaborative engagement exists for sharing data on survival, morbidity, socio-economic status and vaccine coverage.
doi:10.1093/ije/dys062
PMCID: PMC3396317  PMID: 22544844
Disease burden; invasive bacterial diseases; haemoglobinopathies; vaccine effectiveness; child mortality; demography
11.  Seizures in 204 comatose children: incidence and outcome 
Intensive Care Medicine  2012;38(5):853-862.
Purpose
Seizures are common in comatose children, but may be clinically subtle or only manifest on continuous electroencephalographic monitoring (cEEG); any association with outcome remains uncertain.
Methods
cEEG (one to three channels) was performed for a median 42 h (range 2–630 h) in 204 unventilated and ventilated children aged ≤15 years (18 neonates, 61 infants) in coma with different aetiologies. Outcome at 1 month was independently determined and dichotomized for survivors into favourable (normal or moderate neurological handicap) and unfavourable (severe handicap or vegetative state).
Results
Of the 204 patients, 110 had clinical seizures (CS) before cEEG commenced. During cEEG, 74 patients (36 %, 95 % confidence interval, 95 % CI, 32–41 %) had electroencephalographic seizures (ES), the majority without clinical accompaniment (non-convulsive seizures, NCS). CS occurred before NCS in 69 of the 204 patients; 5 ventilated with NCS had no CS observed. Death (93/204; 46 %) was independently predicted by admission Paediatric Index of Mortality (PIM; adjusted odds ratio, aOR, 1.027, 95 % CI 1.012–1.042; p < 0.0005), Adelaide coma score (aOR 0.813, 95 % CI 0.700–0.943; p = 0.006), and EEG grade on admission (excess slow with >3 % fast, aOR 5.43, 95 % CI 1.90–15.6; excess slow with <3 % fast, aOR 8.71, 95 % CI 2.58–29.4; low amplitude, 10th centile <9 µV, aOR 3.78, 95 % CI 1.23–11.7; and burst suppression, aOR 10.68, 95 % CI 2.31–49.4) compared with normal cEEG, as well as absence of CS at any time (aOR 2.38, 95 % CI 1.18–4.81). Unfavourable outcome (29/111 survivors; 26 %) was independently predicted by the presence of ES (aOR 15.4, 95 % CI 4.7–49.7) and PIM (aOR 1.036, 95 % CI 1.013–1.059).
Conclusion
Seizures are common in comatose children, and are associated with an unfavourable outcome in survivors. cEEG allows the detection of subtle CS and NCS and is a prognostic tool.
doi:10.1007/s00134-012-2529-9
PMCID: PMC3338329  PMID: 22491938
Seizures; Status epilepticus; Coma; Child; Outcome; Medicine & Public Health; Pain Medicine; Emergency Medicine; Intensive / Critical Care Medicine; Pneumology/Respiratory System; Pediatrics; Anesthesiology
12.  Post-Prostatic Massage Fluid/Urine (post-PMF/U) as an Alternative to Semen for Studying Male Genitourinary HIV-1 Shedding 
Sexually transmitted infections  2011;87(3):232-237.
Objectives
Genitourinary tract samples are required to investigate male HIV-1 infectivity. Because semen collection is often impractical, we evaluated the acceptability, feasibility, and validity of post-prostatic massage fluid/urine (post-PMF/U) for studying male genitourinary HIV-1 shedding.
Methods
HIV-1-seropositive men were evaluated after 48 hours of sexual abstinence. At each visit, a clinician performed prostatic massage, then post-PMF/U and blood were collected. Participants provided semen specimens one week later. An audio computer-assisted self-interview (ACASI) administered after each specimen collection evaluated acceptability, adherence to instructions, and recent genitourinary symptoms. HIV-1 RNA was quantified using a real-time PCR assay. Detection and quantitation of HIV-1 RNA and stability over visits were compared for semen, post-PMF/U, and blood.
Results
Post-PMF/U was successfully obtained at 106 visits (64%) and semen at 136 visits (81%, p<0.001). In ACASI, discomfort was rated higher for post-PMF/U collection (p=0.003), but there was no significant difference in acceptability. Detection of HIV-1 RNA in post-PMF/U was associated with detection in semen (p=0.02). Semen and post-PMF/U HIV-1 RNA levels were correlated (ρ=0.657, p<0.001). Concordance of results at repeat visits was 78.9% for post-PMF/U (κ = 0.519, p = 0.02), and 89.5% for both blood and semen (κ = 0.774, p = 0.001).
Conclusions
Although semen collections were more successful, both post-PMF/U and semen collections were acceptable to many participants. HIV-1 RNA detection and levels were closely associated in semen and post-PMF/U, and results were relatively stable across visits. To assess male HIV-1 infectivity, post-PMF/U may represent a valid alternative when semen cannot be obtained.
doi:10.1136/sti.2010.047118
PMCID: PMC3075574  PMID: 21278399
HIV-1; semen; prostate; infectivity; validation
13.  Genital Ulceration Does Not Increase HIV-1 Shedding in Cervical or Vaginal Secretions of Women Taking Antiretroviral Therapy 
Sexually transmitted infections  2010;87(2):114-117.
Objectives
Genital ulcer disease (GUD) is associated with increased HIV-1 RNA shedding in antiretroviral therapy (ART)-naïve women. The effect of GUD on HIV-1 shedding among ART-treated women is not known. Our objective was to test the hypothesis that genital ulcerations increase genital HIV-1 RNA shedding in women receiving ART.
Methods
Eligible women initiated ART and attended monthly visits with inspection for genital lesions and collection of genital swabs. GUD cases diagnosed after ≥2 months on ART were included for analysis and served as their own controls. HIV-1 RNA was quantitated in specimens collected before, during, and after GUD for all cases. The lower limit of quantitation was 100 HIV-1 RNA copies/swab. Using the pre-GUD visit as the reference, we compared detection of genital HIV-1 RNA before versus during and after GUD episodes.
Results
Thirty-six women had GUD episodes after ART initiation. HIV-1 RNA was detected before, during, and after GUD in cervical secretions from 4 (11%), 1 (3%), and 6 (17%) women respectively, and in vaginal secretions from 3 (8%), 4 (11%) and 4 (11%) women respectively. After adjustment for time on ART, there was no difference in detection of cervical HIV-1 RNA before versus during GUD (aOR 0.22, 95% CI 0.04–1.23). Likewise, GUD did not increase HIV-1 detection in vaginal secretions (adjusted odds ratio [aOR] 1.32, 95% CI 0.29–5.92).
Conclusions
GUD did not significantly increase cervical or vaginal HIV-1 shedding. Our results suggest that ART maintains its effectiveness for genital HIV-1 suppression despite GUD episodes.
doi:10.1136/sti.2010.045369
PMCID: PMC3081651  PMID: 20980464
genital ulcer; antiretroviral therapy; HIV infection; women
14.  UNDERSTANDING THE CONTEXT OF HIV RISK BEHAVIOR AMONG HIV-POSITIVE AND HIV-NEGATIVE FEMALE SEX WORKERS AND MALE BAR CLIENTS FOLLOWING ANTIRETROVIRAL THERAPY ROLLOUT IN MOMBASA, KENYA 
This study explored perceptions of HIV following local introduction of antiretroviral therapy (ART), among 30 HIV-positive and -negative female sex workers (FSWs) and 10 male bar patrons in Mombasa, Kenya. Semi-structured interviews were analyzed qualitatively to identify determinants of sexual risk behaviors. ART was not perceived as a barrier to safer sex and in some cases led to decreased high-risk behaviors. Barriers to safer sex included economic pressure and sexual partnership types. Many women reported that negotiating condom use is more difficult in long-term partnerships. These women favored short-term partnerships to minimize risk through consistent condom use. For women living with HIV, concern about maintaining health and avoiding HIV superinfection was a strong motivator of protective behaviors. For HIV-negative women, a negative HIV test was a powerful motivator. Incorporation of context- and serostatus-specific factors (e.g., self-protection for HIV-positive women) into tailored prevention counseling may support high-risk women to reduce risk behaviors.
doi:10.1521/aeap.2011.23.4.299
PMCID: PMC3244816  PMID: 21861605
Antiretroviral therapy; sexual risk behavior; human immunodeficiency virus type 1; multiple and concurrent partnerships; Africa
15.  Antiretroviral Adherence and Development of Drug Resistance Are the Strongest Predictors of Genital HIV-1 Shedding among Women Initiating Treatment 
The Journal of infectious diseases  2010;202(10):1538-1542.
Persistent genital HIV-1 shedding among women taking antiretroviral therapy (ART) may present a transmission risk. We investigated associations between genital HIV-1 suppression after ART initiation and adherence, resistance, pre-treatment CD4 count, and hormonal contraceptive use. First-line ART was initiated in 102 women. Plasma and genital HIV-1 RNA were measured at months 0, 3, and 6. Adherence was a strong and consistent predictor of genital HIV-1 suppression (p<0.001), while genotypic resistance was associated with higher vaginal HIV-1 RNA at 6 months (p=0.04). These results emphasize the importance of adherence to optimize the potential benefits of ART for reducing HIV-1 transmission risk.
doi:10.1086/656790
PMCID: PMC2957525  PMID: 20923373
antiretroviral therapy; HIV infection; women; genital HIV-1 shedding
16.  Effect of Acquisition and Treatment of Cervical Infections on HIV-1 Shedding in Women on Antiretroviral Therapy 
AIDS (London, England)  2010;24(17):2733-2737.
Background
Cervicitis increases the quantity of HIV-1 RNA in cervical secretions when women are not taking antiretroviral therapy (ART), and successful treatment of cervicitis reduces HIV-1 shedding in this setting.
Objective
To determine the effect of acquisition and treatment of cervical infections on genital HIV-1 shedding in women receiving ART.
Design
Prospective cohort study.
Methods
We followed 147 women on ART monthly for incident non-specific cervicitis, gonorrhea, and chlamydia. Cervical swabs for HIV-1 RNA quantitation were collected at every visit. The lower limit for linear quantitation was 100 copies/swab. We compared the prevalence of HIV-1 RNA detection before (baseline) versus during and after treatment of cervical infections.
Results
Thirty women contributed a total of 31 successfully treated episodes of non-specific cervicitis (N=13), gonorrhea (N=17), and chlamydia (N=1). HIV-1 RNA was detected in cervical secretions before, during, and after cervicitis at 1 (3.2%), 5 (16.1%), and 3 (9.7%) visits respectively. Compared to baseline, detection of HIV-1 RNA was increased when cervical infections were present (adjusted odds ratio 5.7, 95% confidence interval 1.0–30.3, P=0.04). However, even in the subset of women with cervical HIV-1 RNA levels above the threshold for quantitation, most had low concentrations during cervical infections (median 115, range 100–820 copies/swab).
Conclusions
While these data show a statistically significant increase in cervical HIV-1 RNA detection when cervical infections are present, most cervical HIV-1 RNA concentrations were near the threshold for detection, suggesting that infectivity remains low. Antiretroviral therapy appears to limit increases in genital HIV-1 shedding caused by cervical infections.
doi:10.1097/QAD.0b013e32833f9f43
PMCID: PMC2978313  PMID: 20871388
Cervical infection; HIV-1 Shedding; Antiretroviral therapy; Women; Africa
17.  Declining Responsiveness of Plasmodium falciparum Infections to Artemisinin-Based Combination Treatments on the Kenyan Coast 
PLoS ONE  2011;6(11):e26005.
Background
The emergence of artemisinin-resistant P. falciparum malaria in South-East Asia highlights the need for continued global surveillance of the efficacy of artemisinin-based combination therapies.
Methods
On the Kenyan coast we studied the treatment responses in 474 children 6–59 months old with uncomplicated P. falciparum malaria in a randomized controlled trial of dihydroartemisinin-piperaquine vs. artemether-lumefantrine from 2005 to 2008. (ISRCTN88705995)
Results
The proportion of patients with residual parasitemia on day 1 rose from 55% in 2005–2006 to 87% in 2007–2008 (odds ratio, 5.4, 95%CI, 2.7–11.1; P<0.001) and from 81% to 95% (OR, 4.1, 95%CI, 1.7–9.9; P = 0.002) in the DHA-PPQ and AM-LM groups, respectively. In parallel, Kaplan-Meier estimated risks of apparent recrudescent infection by day 84 increased from 7% to 14% (P = 0.1) and from 6% to 15% (P = 0.05) with DHA-PPQ and AM-LM, respectively. Coinciding with decreasing transmission in the study area, clinical tolerance to parasitemia (defined as absence of fever) declined between 2005–2006 and 2007–2008 (OR body temperature >37.5°C, 2.8, 1.9–4.1; P<0.001). Neither in vitro sensitivity of parasites to DHA nor levels of antibodies against parasite extract accounted for parasite clearance rates or changes thereof.
Conclusions
The significant, albeit small, decline through time of parasitological response rates to treatment with ACTs may be due to the emergence of parasites with reduced drug sensitivity, to the coincident reduction in population-level clinical immunity, or both. Maintaining the efficacy of artemisinin-based therapy in Africa would benefit from a better understanding of the mechanisms underlying reduced parasite clearance rates.
Trial Registration
Controlled-Trials.com ISRCTN88705995
doi:10.1371/journal.pone.0026005
PMCID: PMC3213089  PMID: 22102856
18.  Treatment with Antiretroviral Therapy is Not Associated with Increased Sexual Risk Behaviour in Kenyan Female Sex Workers 
AIDS (London, England)  2010;24(6):891-897.
Objective
The objective of this study was to test the hypothesis that sexual risk behaviour would increase following initiation of antiretroviral therapy (ART) in Kenyan female sex workers (FSWs).
Design
Prospective cohort study.
Setting
FSW cohort in Mombasa, Kenya, 1993-2008.
Subjects
898 women contributed HIV-1-seropositive follow-up visits, of whom 129 initiated ART.
Intervention
Beginning in March 2004, ART was provided to women qualifying for treatment according to Kenyan National Guidelines. Participants received sexual risk reduction education and free condoms at every visit.
Main Outcome Measures
Main outcome measures included unprotected intercourse, abstinence, 100% condom use, number of sexual partners, and frequency of sex. Outcomes were evaluated at monthly follow-up visits using a one week recall interval.
Results
Compared to non-ART-exposed follow-up, visits following ART initiation were not associated with an increase in unprotected sex (adjusted odds ratio [AOR] 0.86, 95% confidence interval [CI] 0.62-1.19, P=0.4). There was a non-significant decrease in abstinence (AOR 0.81, 95% CI 0.65-1.01, P=0.07), which was offset by a substantial increase in 100% condom use (AOR 1.54, 95% CI 1.07-2.20, P=0.02). Numbers of sex partners and frequency of sex were similar before versus after starting ART. A trend for decreased sexually transmitted infections following ART initiation provides additional support for the validity of the self-reported behavioural outcomes (AOR 0.67, 95% CI 0.44-1.02, P=0.06).
Conclusions
In the setting of ongoing risk reduction education and provision of free condoms, initiation of ART was not associated with increased sexual risk behaviour in this cohort of Kenyan FSWs.
doi:10.1097/QAD.0b013e32833616c7
PMCID: PMC2853894  PMID: 20179576
Antiretroviral therapy; sexual risk behaviour; human immunodeficiency virus type 1; sexually transmitted infection; Africa
19.  NFKBIZ polymorphisms and susceptibility to pneumococcal disease in European and African populations 
Genes and immunity  2009;11(4):319-325.
The proinflammatory transcription factor nuclear factor-kappaB (NF-κB) plays a central role in host defence against pneumococcal disease. Both rare mutations and common polymorphisms in the NFKBIA gene encoding the NF-κB inhibitor IκB-α associate with susceptibility to bacterial disease, but the possible role of polymorphisms within the related IκB-ζ gene NFKBIZ in the development of invasive pneumococcal disease has not previously been reported. To investigate this further, we examined the frequencies of 22 single-nucleotide polymorphisms spanning NFKBIZ in two case-control studies, comprising UK Caucasian (n=1008) and Kenyan (n=723) individuals. Nine polymorphisms within a single UK linkage disequilibrium block and all four polymorphisms within the equivalent, shorter Kenyan linkage disequilibrium block displayed either significant association with invasive pneumococcal disease or a trend towards association. For each polymorphism, heterozygosity was associated with protection from invasive pneumococcal disease when compared to the combined homozygous states (e.g. for rs600718, Mantel-Haenszel 2×2 χ2=7.576, P=0.006, OR=0.67, 95% CI for OR: 0.51-0.88; for rs616597, Mantel-Haenszel 2×2 χ2=8.715, P=0.003, OR=0.65, 95% CI: 0.49-0.86). We conclude that multiple NFKBIZ polymorphisms associate with susceptibility to invasive pneumococcal disease in humans. The study of multiple populations may aid fine-mapping of associations within extensive regions of strong linkage disequilibrium (‘transethnic mapping’).
doi:10.1038/gene.2009.76
PMCID: PMC3051152  PMID: 19798075
genetic polymorphism; pneumococcal disease; nuclear factor-kappaB; IkappaB-zeta; NFKBIZ
20.  Clearance of Asymptomatic P. falciparum Infections Interacts with the Number of Clones to Predict the Risk of Subsequent Malaria in Kenyan Children 
PLoS ONE  2011;6(2):e16940.
Background
Protective immunity to malaria is acquired after repeated infections in endemic areas. Asymptomatic multiclonal P. falciparum infections are common and may predict host protection. Here, we have investigated the effect of clearing asymptomatic infections on the risk of clinical malaria.
Methods
Malaria episodes were continuously monitored in 405 children (1–6 years) in an area of moderate transmission, coastal Kenya. Blood samples collected on four occasions were assessed by genotyping the polymorphic P. falciparum merozoite surface protein 2 using fluorescent PCR and capillary electrophoresis. Following the second survey, asymptomatic infections were cleared with a full course of dihydroartemisinin.
Results
Children who were parasite negative by PCR had a lower risk of subsequent malaria regardless of whether treatment had been given. Children with ≥2 clones had a reduced risk of febrile malaria compared with 1 clone after clearance of asymptomatic infections, but not if asymptomatic infections were not cleared. Multiclonal infection was associated with an increased risk of re-infection after drug treatment. However, among the children who were re-infected, multiclonal infections were associated with a shift from clinical malaria to asymptomatic parasitaemia.
Conclusion
The number of clones was associated with exposure as well as blood stage immunity. These effects were distinguished by clearing asymptomatic infection with anti-malarials. Exposure to multiple P. falciparum infections is associated with protective immunity, but there appears to be an additional effect in untreated multiclonal infections that offsets this protective effect.
doi:10.1371/journal.pone.0016940
PMCID: PMC3044709  PMID: 21383984
21.  Correction: Interactions between Age and ITN Use Determine the Risk of Febrile Malaria in Children 
PLoS ONE  2011;6(2):10.1371/annotation/73a096b6-934c-4bc7-b0b1-de1f11231350.
doi:10.1371/annotation/73a096b6-934c-4bc7-b0b1-de1f11231350
PMCID: PMC3040358
22.  Efficacy of RTS,S/AS01E malaria vaccine and exploratory analysis on anti-circumsporozoite antibody titres and protection in children aged 5–17 months in Kenya and Tanzania: a randomised controlled trial 
The Lancet Infectious Diseases  2011;11(2):102-109.
Summary
Background
RTS,S/AS01E is the lead candidate malaria vaccine. We recently showed efficacy against clinical falciparum malaria in 5–17 month old children, during an average of 8 months follow-up. We aimed to assess the efficacy of RTS,S/AS01E during 15 months of follow-up.
Methods
Between March, 2007, and October, 2008, we enrolled healthy children aged 5–17 months in Kilifi, Kenya, and Korogwe, Tanzania. Computer-generated block randomisation was used to randomly assign participants (1:1) to receive three doses (at month 0, 1, and 2) of either RTS,S/AS01E or human diploid-cell rabies vaccine. The primary endpoint was time to first clinical malaria episode, defined as the presence of fever (temperature ≥37·5°C) and a Plasmodium falciparum density of 2500/μL or more. Follow-up was 12 months for children from Korogwe and 15 months for children from Kilifi. Primary analysis was per protocol. In a post-hoc modelling analysis we characterised the associations between anti-circumsporozoite antibodies and protection against clinical malaria episodes. This study is registered with ClinicalTrials.gov, number NCT00380393.
Findings
894 children were assigned, 447 in each treatment group. In the per-protocol analysis, 82 of 415 children in the RTS,S/AS01E group and 125 of 420 in the rabies vaccine group had first or only clinical malaria episode by 12 months, vaccine efficacy 39·2% (95% CI 19·5–54·1, p=0·0005). At 15 months follow-up, 58 of 209 children in the RTS,S/AS01E group and 85 of 206 in the rabies vaccine group had first or only clinical malaria episode, vaccine efficacy 45·8% (24·1–61·3, p=0·0004). At 12 months after the third dose, anti-circumsporozoite antibody titre data were available for 390 children in the RTS,S/AS01E group and 391 in the rabies group. A mean of 15 months (range 12–18 months) data were available for 172 children in the RTS,S/AS01E group and 155 in the rabies group. These titres at 1 month after the third dose were not associated with protection, but titres at 6·5 months were. The level of protection increased abruptly over a narrow range of antibody concentrations. The most common adverse events were pneumonia, febrile convulsion, gastroenteritis, and P falciparum malaria.
Interpretation
RTS,S/AS01E confers sustained efficacy for at least 15 months and shows promise as a potential public health intervention against childhood malaria in malaria endemic countries.
Funding
PATH Malaria Vaccine Initiative (MVI), GlaxoSmithKline.
doi:10.1016/S1473-3099(10)70262-0
PMCID: PMC3341451  PMID: 21237715
23.  Common NFKBIL2 polymorphisms and susceptibility to pneumococcal disease: a genetic association study 
Critical Care  2010;14(6):R227.
Introduction
Streptococcus pneumoniae remains a major global health problem and a leading cause of death in children worldwide. The factors that influence development of pneumococcal sepsis remain poorly understood, although increasing evidence points towards a role for genetic variation in the host's immune response. Recent insights from the study of animal models, rare human primary immunodeficiency states, and population-based genetic epidemiology have focused attention on the role of the proinflammatory transcription factor NF-κB in pneumococcal disease pathogenesis. The possible role of genetic variation in the atypical NF-κB inhibitor IκB-R, encoded by NFKBIL2, in susceptibility to invasive pneumococcal disease has not, to our knowledge, previously been reported upon.
Methods
An association study was performed examining the frequencies of nine common NFKBIL2 polymorphisms in two invasive pneumococcal disease case-control groups: European individuals from hospitals in Oxfordshire, UK (275 patients and 733 controls), and African individuals from Kilifi District Hospital, Kenya (687 patients with bacteraemia, of which 173 patients had pneumococcal disease, together with 550 controls).
Results
Five polymorphisms significantly associated with invasive pneumococcal disease susceptibility in the European study, of which two polymorphisms also associated with disease in African individuals. Heterozygosity at these loci was associated with protection from invasive pneumococcal disease (rs760477, Mantel-Haenszel 2 × 2 χ2 = 11.797, P = 0.0006, odds ratio = 0.67, 95% confidence interval = 0.53 to 0.84; rs4925858, Mantel-Haenszel 2 × 2 χ2 = 9.104, P = 0.003, odds ratio = 0.70, 95% confidence interval = 0.55 to 0.88). Linkage disequilibrium was more extensive in European individuals than in Kenyans.
Conclusions
Common NFKBIL2 polymorphisms are associated with susceptibility to invasive pneumococcal disease in European and African populations. These findings further highlight the importance of control of NF-κB in host defence against pneumococcal disease.
doi:10.1186/cc9377
PMCID: PMC3220025  PMID: 21171993
24.  Increased risk of genital ulcer disease in women during the first month after initiating antiretroviral therapy 
Introduction
Genital ulcer disease (GUD) is common in HIV-1-infected women, and a small number of studies have suggested increased GUD risk after antiretroviral therapy (ART) initiation. To better define this risk, we monitored 134 women at ART initiation and monthly thereafter.
Methods
Women were evaluated monthly for genital ulcers. Syphilis serology was tested quarterly, and chancroid culture performed on ulcers that were felt to be clinically consistent with a diagnosis of chancroid. A logistic model with generalized estimating equations was used to analyze predictors of GUD from baseline until 6 months after ART initiation.
Results
During the study period, GUD occurred in 54 women (40.3%) at 85 visits (10.0%). GUD prevalence was 9.7% at baseline, increased to 16.7% at month 1 (adjusted odds ratio [aOR] 1.9 [1.0 – 3.6], p = 0.04), then decreased to 6.4% by month 6. History of GUD (aOR 3.8 [1.9 – 7.7], p < 0.001) and CD4 count <100 (aOR 1.8 [1.0 – 3.4, p = 0.06) were associated with increased risk of GUD after ART initiation.
Discussion
Women experience increased risk of GUD in the first month after ART initiation, particularly if they have low CD4 counts or a history of GUD.
doi:10.1097/QAI.0b013e3181b065cf
PMCID: PMC2787852  PMID: 19648822
genital ulcer; HIV; antiretroviral therapy; immune reconstitution
25.  An increase in the burden of neonatal admissions to a rural district hospital in Kenya over 19 years 
BMC Public Health  2010;10:591.
Background
Most of the global neonatal deaths occur in developing nations, mostly in rural homes. Many of the newborns who receive formal medical care are treated in rural district hospitals and other peripheral health centres. However there are no published studies demonstrating trends in neonatal admissions and outcome in rural health care facilities in resource poor regions. Such information is critical in planning public health interventions. In this study we therefore aimed at describing the pattern of neonatal admissions to a Kenyan rural district hospital and their outcome over a 19 year period, examining clinical indicators of inpatient neonatal mortality and also trends in utilization of a rural hospital for deliveries.
Methods
Prospectively collected data on neonates is compared to non-neonatal paediatric (≤ 5 years old) admissions and deliveries' in the maternity unit at Kilifi District Hospital from January 1st 1990 up to December 31st 2008, to document the pattern of neonatal admissions, deliveries and changes in inpatient deaths. Trends were examined using time series models with likelihood ratios utilised to identify indicators of inpatient neonatal death.
Results
The proportion of neonatal admissions of the total paediatric ≤ 5 years admissions significantly increased from 11% in 1990 to 20% by 2008 (trend 0.83 (95% confidence interval 0.45 -1.21). Most of the increase in burden was from neonates born in hospital and very young neonates aged < 7days. Hospital deliveries also increased significantly. Clinical diagnoses of neonatal sepsis, prematurity, neonatal jaundice, neonatal encephalopathy, tetanus and neonatal meningitis accounted for over 75% of the inpatient neonatal admissions. Inpatient case fatality for all ≤ 5 years declined significantly over the 19 years. However, neonatal deaths comprised 33% of all inpatient death among children aged ≤ 5 years in 1990, this increased to 55% by 2008. Tetanus 256/390 (67%), prematurity 554/1,280(43%) and neonatal encephalopathy 253/778(33%) had the highest case fatality. A combination of six indicators: irregular respiration, oxygen saturation of <90%, pallor, neck stiffness, weight < 1.5 kg, and abnormally elevated blood glucose > 7 mmol/l predicted inpatient neonatal death with a sensitivity of 81% and a specificity of 68%.
Conclusions
There is clear evidence of increasing burden in neonatal admissions at a rural district hospital in contrast to reducing numbers of non-neonatal paediatrics' admissions aged ≤ 5years. Though the inpatient case fatality for all admissions aged ≤ 5 years declined significantly, neonates now comprise close to 60% of all inpatient deaths. Simple indicators may identify neonates at risk of death.
doi:10.1186/1471-2458-10-591
PMCID: PMC2965720  PMID: 20925939

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