Optimizing HIV case identification: investigating client characteristics predictive of HIV positivity from provider-initiated testing (PITC) in central Kenya.

BACKGROUND: Routine program data indicates positivity rates under 2% from HIV testing services (HTS) at sites supported by Centre for Health Solutions-Kenya in Central Kenya. Achieving the UNAIDS 95:95:95 goals requires continuous identification of people living with HIV in an environment of diminishing resources. We assessed non-clinical and clinical characteristics of persons who tested HIV-positive aimed at improving the process of HTS through Provider-Initiated HIV Testing & Counseling (PITC). METHODS: We conducted a retrospective analysis of routine PITC program data collected between October 2018 and September 2019 from six health facilities located in three counties in central Kenya. Stratification was based on county and facility volume. A multivariable logistic regression model, clustered adjusted for facility using robust standard errors, was used to determine predictors of a positive HIV result. RESULTS: The total sample was 80,693 with an overall positivity rate of 1.2%. Most, (65.5%), were female and 6.1% were < 15 years. Most clients, 55,464 (68.7%), had previously tested for HIV. Client characteristics associated with a higher odds of positivity on multivariable analysis included: being female (adjusted odds ratio [aOR] 1.27, 95% confidence interval [CI] (1.03-1.57); adults 15 years and above compared to children < 15 years, divorced and married polygamous compared to married monogamous [aOR 3.98, 95% CI (2.12-7.29) and aOR 2.41 95% CI (1.48-3.94) respectively]; clients testing for the first time compared to repeat testers in less than 12 months [aOR 1.39, 95% CI (1.27-1.51)]. Similarly, repeat testers in more than 12 months compared to repeat testers in less than 12 months [aOR 1.90, 95% CI (1.55-2.32)]; presumptive TB clients compared to those without signs of TB [aOR 16.25, 95% CI (10.63-24.84)]. Clients tested at inpatient departments (IPD) were more likely to get a positive HIV result compared to those tested at outpatient departments (OPD), and other departments. CONCLUSIONS: The study findings highlight client characteristics such as age, marital status, HIV test entry point, first-time test, repeat test after 12 months, and TB status as factors that could influence PITC results and could be used to develop a screening tool to target eligible clients for HTS in low HIV prevalence settings.

The effect of an interactive weekly text-messaging intervention on retention in prevention of mother-to-child transmission of HIV care: a randomised controlled trial (WelTel PMTCT).

Retention in prevention of mother-to-child transmission (PMTCT) care is critical to prevent vertical HIV transmission and reduce morbidity and mortality of mother-infant pairs. We investigated whether weekly, interactive text-messaging improved 18-month postpartum retention in PMTCT care. This randomised, two-armed, parallel trial was conducted at six PMTCT clinics in western Kenya. Pregnant women with HIV at least 18 years of age with access to a mobile phone, able to text-message, or had somebody who could text on their behalf, were eligible. Participants were randomly assigned at a 1:1 ratio in block sizes of four to the intervention or control group. The intervention group received weekly text messages asking "How are you?" ("Mambo?" in Swahili) and were requested to respond within 48 h. Healthcare workers called women who indicated a problem or did not respond. The intervention was administered up to 24 months after delivery. Both groups received standard care. The primary outcome was retention in care at 18 months postpartum (i.e., clinic attendance 16-24 months after delivery based on data from patient files, patient registers and Kenya's National AIDS and STI Control Programme database), which was analysed by intention-to-treat. Researchers and data collectors were masked to group assignment, while healthcare workers were not. Between June 25th, 2015, and July 5th, 2016, we randomly assigned 299 women to the intervention and 301 to standard care only. Follow-up concluded on July 26th, 2019. The proportion of women retained in PMTCT care at 18 months postpartum was not significantly different between the intervention (n = 210/299) and control groups (n = 207/301) (risk ratio 1.02, 95% confidence interval 0.92-1.14, p = 0.697). No adverse events related to the mobile phone intervention were reported. Weekly, interactive text-messaging was not associated with improved retention in PMTCT care at 18 months postpartum or linkage to care up to 30 months postpartum in this setting. (ISRCTN No. 98818734).

Scale-up of HIV index testing in an urban population: Experiences and achievements from Nairobi County, Kenya.

OBJECTIVE: To describe the implementation strategies of the index testing program across Nairobi County in Kenya, assess outcomes along the HIV index testing cascade (acceptance, elicitation ratio, HIV positivity and linkage to treatment), and assess annual changes along the HIV index testing cascade during the first 2 years of implementation. METHODS: Retrospective analysis of programmatic aggregate data collected from October 2017 to September 2019 after the roll-out of index testing services in 48 health facilities in Nairobi County. Proportions and ratios were calculated for acceptance, elicitation ratio, testing uptake and HIV positivity. We compared these outcomes between years using a chi-squared test, Fisher's exact test or Wilcoxon sign test, and we assessed trends using the Mann-Kendall test. RESULTS: Testing among eligible partners increased from 42.4% (1471/3470) to 74.9% (6114/8159) in the general population, and the positivity yield remained high across both years (25.2% in year 1 and 24.1% in year 2). Index testing positivity yield remained significantly higher than other testing modalities (24.3% vs. 1.3%, p < 0.001). The contribution of index testing services to the total number of HIV-positive individuals identified increased from 7.5% in the first year to 28.6% in the second year (p < 0.001). More men were tested, but the positivity yield was higher among women (30.0%) and those aged 50 years or older (32.4%). Testing eligible partners in key populations (KPs) decreased from 52.4% (183/349) to 40.7% (109/268) (p = 0.674); however, the HIV positivity yield increased from 8.6% to 23.9% (p < 0.001) by the second year of implementation. The HIV positivity yield from index testing remained higher than other testing modalities (14% vs. 0.9%, p < 0.001) for KPs. CONCLUSION: Index testing was well-accepted and effective in identifying individuals living with HIV in a Kenyan urban setting across both general populations and KPs. Ongoing adaptations to the strategies deployed as part of index testing services helped improve most of the outcomes along the index testing cascade.

Characteristics of users of HIV self-testing in Kenya, outcomes, and factors associated with use: results from a population-based HIV impact assessment, 2018.

BACKGROUND AND SETTING: About 20% of persons living with HIV aged 15-64 years did not know their HIV status in Kenya, by 2018. Kenya adopted HIV self-testing (HIVST) to help close this gap. We examined the sociodemographic characteristics and outcomes of self-reported users of HIVST as our primary outcome. METHODS: We used data from a 2018 population-based cross-sectional household survey in which we included self-reported sociodemographic and behavioral characteristics and HIV test results. To compare weighted proportions, we used the Rao-Scott χ-square test and Jackknife variance estimation. In addition, we used logistic regression to identify associations of sociodemographic, behavioral, and HIVST utilization. RESULTS: Of the 23,673 adults who reported having ever tested for HIV, 937 (4.1%) had ever self-tested for HIV. There were regional differences in HIVST, with Nyanza region having the highest prevalence (6.4%), p < 0.001. Factors independently associated with having ever self-tested for HIV were secondary education (adjusted odds ratio [aOR], 3.5 [95% (CI): 2.1-5.9]) compared to no primary education, being in the third (aOR, 1.7 [95% CI: 1.2-2.3]), fourth (aOR, 1.6 [95% CI: 1.1-2.2]), or fifth (aOR, 1.8 [95% CI: 1.2-2.7]) wealth quintiles compared to the poorest quintile and having one lifetime sexual partner (aOR, 1.8 [95% CI: 1.0-3.2]) or having ≥ 2 partners (aOR, 2.1 [95% CI: 1.2-3.7]) compared to none. Participants aged ≥ 50 years had lower odds of self-testing (aOR, 0.6 [95% CI: 0.4-1.0]) than those aged 15-19 years. CONCLUSION: Kenya has made progress in rolling out HIVST. However, geographic differences and social demographic factors could influence HIVST use. Therefore, more still needs to be done to scale up the use of HIVST among various subpopulations. Using multiple access models could help ensure equity in access to HIVST. In addition, there is need to determine how HIVST use may influence behavior change towardsaccess to prevention and HIV treatment services.

Health related quality of life among pregnant women living with HIV in Kenya, results from comparing a patient generated index and the Euroqol 5 dimension 3 level.

BACKGROUND: Standardized tools are used to measure health-related quality of life (HRQoL) and they focus on selected physical, emotional, and social functioning. This approach may miss out on the heterogeneity of HRQoL among various sub-populations. The patient-generated index (PGI) is a tool used to measure HRQoL based on patients' expectations. Among patients living with HIV, HRQoL is an important indicator as the world moves beyond the UNAIDS 90-90-90 goals, towards the so-called fourth 90 that aims at good HRQoL. We compared the PGI and the Euroqol 5 Dimension 3-level (EQ-5D-3L) to identify areas of importance to pregnant women living with HIV affecting thier HRQoL. METHODS: Through convenience sampling, we surveyed 100 pregnant women living with HIV attending antenatal and postnatal clinics in Western Kenya, using both the PGI and the EQ-5D-3L questionnaires. A PGI score and EQ-5D-3L index were generated for each participant. Data from the PGI was also summarized into themes. The PGI scores and EQ-5D-3L index scores were correlated using Pearson correlation. RESULTS: From the PGI tool, 64% of the women reported having two to three main priority areas of their lives affected by their HIV status. These areas centered on themes of economic wellbeing (84% of the women), physical health (58%), psychological/emotional health (49%), and relationships (28%). The mean PGI score was 2.01 [SD = 1.10; median 1.10]. The majority of the women reported having no problems in any of the 5 dimensions captured in the EQ-5D-3L. The mean EQ-5D-3L score was 0.94 [SD = 1.10; median 1.00]. Both the EQ-5D-3L and the PGI showed less than perfect HRQoL. There was no correlation between the PGI and the EQ-5D-3L scores. CONCLUSION: The PGI may capture aspects of contextual social and emotional life for Kenyan pregnant women living with HIV that are not identified by generic tools. Highlighting areas of importance to patients' HRQoL is key as focus shifts towards the fourth 90 and may also inform the design of care programs aligned to patient needs.

Factors Associated with Treatment Outcomes Among Children and Adolescents Living with HIV Receiving Antiretroviral Therapy in Central Kenya.

Expanded access to HIV treatment services has improved outcomes for children and adolescents living with HIV in Kenya. Minimal data are available on these outcomes. We describe temporal trends in outcomes for children and adolescents initiating antiretroviral therapy (ART) from 2004 to 2014 at sites supported by Centre for Health Solutions-Kenya, in central Kenya. We retrospectively analyzed data from children 0-9 years of age (n = 3,519) and adolescents 10-19 years of age (n = 1,663) living with HIV, who newly initiated ART at 47 health facilities in central Kenya. Year cohorts were analyzed from the Comprehensive Patient Application Database (CPAD) and International Quality Care (IQCare) electronic medical databases, including temporal trends in outcomes and associated factors using multivariable competing risk regression analysis. There were more girls (2,453 [52.7%]) than boys, with most enrolled at World Health Organization (WHO) stage II (1,813 [37.7%]) or III disease (1,694 [35.1%]). Most of the children and adolescents (4,431 [96.4%]) did not have tuberculosis (TB) symptoms. Cumulative lost to follow-up (LTFU) incidence at 6, 12, 24, and 36 months were 5.0%, 9.9%, 22.9%, and 33.1%, respectively. Cumulative mortality incidence at 6, 12, 24, and 36 months were 0.7%, 1.0%, 1.2%, and 1.5%, respectively. The incidence of LTFU was higher among female children and adolescents, those initiated on tenofovir-based regimens, and those with presumptive TB symptoms. Mortality risk was higher among those with WHO stage III or IV disease, and children and adolescents on TB treatment or who had presumptive TB. Enrollment occurred at a young age and pediatric-friendly ART regimens were initiated at earlier WHO stages implying effective early infant diagnosis and treatment for all strategies, resulting in improved treatment outcomes. The higher retention rates in recent years as well as the lower retention after many years of follow-up underscore the importance of implementing longitudinal follow-up strategies targeting this population.

The effect of weekly interactive text-messaging on early infant HIV testing in Kenya: a randomised controlled trial (WelTel PMTCT).

Mother-to-child transmission of HIV remains a significant concern in Africa despite earlier progress. Early infant diagnosis (EID) of HIV is crucial to reduce mortality among infected infants through early treatment initiation. However, a large proportion of HIV-exposed infants are still not tested in Kenya. Our objective was to investigate whether weekly interactive text-messages improved prevention of mother-to-child transmission (PMTCT) of HIV care outcomes including EID HIV testing. This multicentre, parallel-group, randomised, open-label trial included six antenatal care clinics across western Kenya. Pregnant women living with HIV, aged 18 years or older, with mobile phone access, were randomised in a 1:1 ratio to weekly text messages that continued until 24 months postpartum, asking "How are you?" ("Mambo?") to which they were asked to respond within 48 h, or a control group. Healthcare workers contacted participants reporting problems and non-responders by phone. Participants in both groups received routine PMTCT care. The prespecified secondary outcome reported in this paper is EID HIV testing by eight weeks of age (blinded outcome assessment). Final 24-months trial results will be published separately. We estimated risk ratios using Poisson regression with robust standard errors. Between June 2015-July 2016, we screened 735 pregnant women, of whom 600 were enrolled: 299 were allocated to the intervention and 301 to the control group. By eight weeks of age, the uptake of EID HIV testing out of recorded live births was 85.5% in the intervention and 84.7% in the control group (71.2% vs. 71.8% of participants randomised, including miscarriages, stillbirths, etc.). The intention-to-treat risk ratio was 0.99; 95% CI: 0.90-1.10; p = 0.89. The proportion of infants diagnosed with HIV was 0.8% in the intervention and 1.2% in the control group. No adverse events were reported. We found no evidence to support that the WelTel intervention improved EID HIV testing. A higher uptake of EID testing than expected in both groups may be a result of lower barriers to EID testing and improved PMTCT care in western Kenya, including the broader standard use of mobile phone communication between healthcare workers and patients. (ISRCTN No. 98818734. Funded by the European-Developing Countries Clinical Trial Partnership and others).

Where Are the Newly Diagnosed HIV Positives in Kenya? Time to Consider Geo-Spatially Guided Targeting at a Finer Scale to Reach the "First 90".

Background: The UNAIDS 90-90-90 Fast-Track targets provide a framework for assessing coverage of HIV testing services (HTS) and awareness of HIV status - the "first 90." In Kenya, the bulk of HIV testing targets are aligned to the five highest HIV-burden counties. However, we do not know if most of the new HIV diagnoses are in these five highest-burden counties or elsewhere. Methods: We analyzed facility-level HTS data in Kenya from 1 October 2015 to 30 September 2016 to assess the spatial distribution of newly diagnosed HIV-positives. We used the Moran's Index (Moran's I) to assess global and local spatial auto-correlation of newly diagnosed HIV-positive tests and Kulldorff spatial scan statistics to detect hotspots of newly diagnosed HIV-positive tests. For aggregated data, we used Kruskal-Wallis equality-of-populations non-parametric rank test to compare absolute numbers across classes. Results: Out of 4,021 HTS sites, 3,969 (98.7%) had geocodes available. Most facilities (3,034, 76.4%), were not spatially autocorrelated for the number of newly diagnosed HIV-positives. For the rest, clustering occurred as follows; 438 (11.0%) were HH, 66 (1.7%) HL, 275 (6.9%) LH, and 156 (3.9%) LL. Of the HH sites, 301 (68.7%) were in high HIV-burden counties. Over half of 123 clusters with a significantly high number of newly diagnosed HIV-infected persons, 73(59.3%) were not in the five highest HIV-burden counties. Clusters with a high number of newly diagnosed persons had twice the number of positives per 1,000,000 tests than clusters with lower numbers (29,856 vs. 14,172). Conclusions: Although high HIV-burden counties contain clusters of sites with a high number of newly diagnosed HIV-infected persons, we detected many such clusters in low-burden counties as well. To expand HTS where most needed and reach the "first 90" targets, geospatial analyses and mapping make it easier to identify and describe localized epidemic patterns in a spatially dispersed epidemic like Kenya's, and consequently, reorient and prioritize HTS strategies.

Molecular Detection of Panton Valentine Leukocidin Toxin in Clinical Isolates of Staphylococcus aureus from Kiambu County, Kenya.

Panton-Valentine leukocidin gene is produced by Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus isolates as a pore-forming toxin is largely responsible for skin and soft tissue illnesses. MRSA produces PVL toxins through lukS and lukF proteins causing tissue necrosis by damaging membrane of the defense cells. Presence of PVL toxin was tested from the 54 S. aureus clinical isolates obtained from Thika and Kiambu Level 5 Hospitals, in Kiambu County, Kenya, by Geno Type® MRSA assay (Hain Life Science, Nehren, Germany). DNA was isolated from freshly harvested bacterial cultures by spin column using Geno Type DNA isolation kit. The detection of PVL toxins was performed by amplification of genomic DNA and by reverse hybridization that identifies PVL genes using Geno Type MRSA kit. Out of 138 samples that were collected from patients in Kiambu County, 54 S. aureus isolates were obtained, of which 14 (25.9%; 95% CI = 11.9-38.9) samples had PVL toxins. The isolates that were obtained from the female patients had a higher PVL toxin prevalence of 35.7%, while the isolates collected from the male patients had a lower prevalence of 15.4% (P = 0.09). The pediatrics department had the highest PVL gene prevalence compared to outpatient department and surgical units (P = 0.08). However, the age groups of patients and the hospital attended by patients showed no significant difference in terms of PVL gene prevalence (P = 0.26). Therefore, the patients' gender and hospital units were not significantly associated with PVL gene prevalence (P = 0.08). This study shows that PVL positive isolates occur in the sampled hospitals in the county and female as well as children must be taken into consideration among patients with wound infections when isolating S. aureus.

Phenotypic analysis and antibiotic susceptibility of methicillin-resistant Staphylococcus aureus in Kiambu County, Kenya.

INTRODUCTION: Methicillin resistant Staphylococcus aureus (MRSA) causes illness to people and can be picked up from both healthcare facilities and the environment leading to high morbidity and mortality. The study was aimed at identifying phenotypic characteristics of Methicillin-Resistant Staphylococcus aureus and determine the antibiotic susceptibility pattern of clinical samples isolated from patients attending or admitted in two health facilities in Kiambu County, Kenya. METHODOLOGY: One hundred and thirty-eight (138) clinical samples were collected from patients attending Thika and Kiambu Level-5 Hospitals. The isolates were obtained using standard bacteriological techniques. Methicillin resistance of Staphylococcus aureus was determined using the cefoxitin disk diffusion test. RESULTS: Out of 138 samples, 54 (39.1%) were found to have Staphylococcus aureus of which 22 (40.7%) were shown to be MRSA using the cefoxitin- based susceptibility test. Antibiotic susceptibility testing using Kirby-Bauer technique was performed on all 54 isolates. The highest sensitivity was found in chloramphenicol 46 (85.2%) and lowest in penicillin-G 8 (14.8%). Multi-Drug Resistance (MDR) was reported in 35 (64.8%) of the 54 isolates of Staphylococcus aureus. All 22 MRSA strains were found to be MDR. CONCLUSIONS: the data obtained revealed that there is presence of MRSA in healthcare settings in Kiambu County, Kenya with varying antibiotic sensitivity patterns as well as multidrug resistance. The findings will help healthcare workers in the county to develop preventive strategy as well as institute policy for antibiotic usage, infection control and surveillance.

Factors associated with 36-month loss to follow-up and mortality outcomes among HIV-infected adults on antiretroviral therapy in Central Kenya.

BACKGROUND: The scale-up of HIV treatment programs has resulted in a reduction in HIV-related morbidity and mortality. However, retention of patients in these programs remains a challenge in sub-Saharan Africa. Understanding factors associated with loss to follow-up (LTFU) and mortality outcomes is therefore important to inform targeted program interventions. METHODS: A retrospective multi-cohort analysis of 23,890 adult patients on ART over 36 months of follow-up in Kenya was done. Multivariate logistic regression analysis was done to assess for factors associated with LTFU and mortality at 6, 12, 24, and 36 months of follow-up. RESULTS: Majority, 67.7%, were female. At 36 months, 27.2% were LTFU and 13.5% had died. Factors associated with mortality at 36 months included older age (51 years and above) using 20-35 years as reference [(adjusted odds ratio [aOR], 1.51, 95% confidence interval (CI) 1.23-1.86, p < 0.001], being male (aOR, 1.59, 95% CI 1.39-1.83, p < 0.001), divorced using married as reference (aOR, 1.86, 95% CI 1.56-2.22, p < 0.001), having a body mass index (BMI) score of less than 18.5 kg/m2 using 18.5-24.9 kg/m2 as reference (aOR = 1.79, 95% CI 1.52-2.11, p < 0.001), and, World Health Organization stage III and IV using stage I as the reference (aOR, 1.94, 95% CI 1.43-2.63 and aOR, 4.24, 95% CI 3.06-5.87, p < 0.001 respectively). Factors associated with LTFU at 36 months included being young between 20 and 35 years (aOR, 1.49, 95% CI 1.40-1.59, p < 0.001) using 36-50 years as reference, being male (aOR, 1.19, 95% CI 1.12-1.27, p < 0.001), and being single or divorced using married as reference (aOR, 1.34, 95% CI 1.23-1.45 and aOR, 1.25, 95% CI 1.15-1.36, p < 0.001 respectively). Patients with baseline BMI of less than 18.5 kg/m2 using normal BMI as reference (aOR, 1.68, 95% CI 1.39-2.02, p < 0.001) were also likely to be LTFU. CONCLUSIONS: Factors associated with LTFU and mortality were generally similar over time. Implementation of programs in similar settings should be tailored to gender, age profiles, nutritional, and, marital status of patients to address LTFU. In addition, programs should focus on the care of older patients to reduce the risk of mortality.

Scaling Up Testing for Human Immunodeficiency Virus Infection Among Contacts of Index Patients - 20 Countries, 2016-2018.

In 2017, the Joint United Nations Programme on HIV/AIDS (UNAIDS) estimated that worldwide, 36.9 million persons were living with human immunodeficiency virus (HIV) infection, the virus infection that causes acquired immunodeficiency syndrome (AIDS). Among persons with HIV infection, approximately 75% were aware of their HIV status, leaving 9.4 million persons with undiagnosed infection (1). Index testing, also known as partner notification or contact tracing, is an effective case-finding strategy that targets the exposed contacts of HIV-positive persons for HIV testing services. This report summarizes data from HIV tests using index testing in 20 countries supported by CDC through the U.S. President's Emergency Plan for AIDS Relief (PEPFAR) during October 1, 2016-March 31, 2018. During this 18-month period, 1,700,998 HIV tests with 99,201 (5.8%) positive results were reported using index testing. The positivity rate for index testing was 9.8% among persons aged ≥15 years and 1.5% among persons aged <15 years. During the reporting period, HIV positivity increased 64% among persons aged ≥15 years (from 7.6% to 12.5%) and 67% among persons aged <15 years (from 1.2% to 2.0%). Expanding index testing services could help increase the number of persons with HIV infection who know their status, are initiated onto antiretroviral treatment, and consequently reduce the number of persons who can transmit the virus.

Characterisation of Species and Diversity of Anopheles gambiae Keele Colony.

Anopheles gambiae sensu stricto was recently reclassified as two species, An. coluzzii and An. gambiae s.s., in wild-caught mosquitoes, on the basis of the molecular form, denoted M or S, of a marker on the X chromosome. The An. gambiae Keele line is an outbred laboratory colony strain that was developed around 12 years ago by crosses between mosquitoes from 4 existing An. gambiae colonies. Laboratory colonies of mosquitoes often have limited genetic diversity because of small starting populations (founder effect) and subsequent fluctuations in colony size. Here we describe the characterisation of the chromosomal form(s) present in the Keele line, and investigate the diversity present in the colony using microsatellite markers on chromosome 3. We also characterise the large 2La inversion on chromosome 2. The results indicate that only the M-form of the chromosome X marker is present in the Keele colony, which was unexpected given that 3 of the 4 parent colonies were probably S-form. Levels of diversity were relatively high, as indicated by a mean number of microsatellite alleles of 6.25 across 4 microsatellites, in at least 25 mosquitoes. Both karyotypes of the inversion on chromosome 2 (2La/2L+a) were found to be present at approximately equal proportions. The Keele colony has a mixed M- and S-form origin, and in common with the PEST strain, we propose continuing to denote it as an An. gambiae s.s. line.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.

The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.

The effect of an interactive weekly mobile phone messaging on retention in prevention of mother to child transmission (PMTCT) of HIV program: study protocol for a randomized controlled trial (WELTEL PMTCT).

BACKGROUND: Improving retention in prevention of mother to child transmission (PMTCT) of HIV programs is critical to optimize maternal and infant health outcomes, especially now that lifelong treatment is immediate regardless of CD4 cell count). The WelTel strategy of using weekly short message service (SMS) to engage patients in care in Kenya, where mobile coverage even in poor areas is widespread has been shown to improve adherence to antiretroviral therapy (ART) and viral load suppression among those on ART. The aim of this study is to determine the effect of the WelTel SMS intervention compared to standard care on retention in PMTCT program in Kenya. METHODS: WelTel PMTCT is a four to seven-centers, two-arm open randomized controlled trial (RCT) that will be conducted in urban and rural Kenya. Over 36 months, we plan to recruit 600 pregnant women at their first antenatal care visit and follow the mother-infant pair until they are discharged from the PMTCT program (when infant is aged 24 months). Participants will be randomly allocated to the intervention or control arm (standard care) at a 1:1 ratio. Intervention arm participants will receive an interactive weekly SMS 'How are you?' to which they are supposed to respond within 24 h. Depending on the response (ok, problem or no answer), a PMTCT nurse will follow-up and triage any problems that are identified. The primary outcome will be retention in care defined as the proportion of mother-infant pairs coming for infant HIV testing at 24 months from delivery. Secondary outcomes include a) adherence to WelTel; (b) adherence to antiretroviral medicine; (c) acceptance of WelTel and (d) cost-effectiveness of the WelTel intervention. DISCUSSION: This trial will provide evidence on the effectiveness of mHealth for PMTCT retention. Trial results and the cost-effectiveness evaluation will be used to inform policy and potential scale-up of mHealth among mothers living with HIV. TRIAL REGISTRATION: ISRCTN98818734 ; registered on 9th December 2014.

Chronic diseases among the elderly in a rural Vietnam: prevalence, associated socio-demographic factors and healthcare expenditures.

BACKGROUND: Globally, the population of elderly persons is increasing as well as the prevalence of chronic diseases. This change is causing increased healthcare costs to health care systems threatening to push many households into poverty. Low and middle income countries are projected to experience the greatest impact from this change. This study aims to describe the prevalence of common chronic diseases (CCDs) among the elderly in Vietnam, the associated socio-demographic factors and healthcare expenditures. METHODS: This is a cross-sectional study in the FilaBavi demographic surveillance site in Vietnam. 2873 persons over 60 years were randomly sampled. Prevalence of CCDs was reported from study subjects who previously were informed by physicians. Healthcare expenditures were determined from recall of expenses during the last hospital visit. Binomial logistic regression was done to determine the socio demographic predictors of having a CCD or multiple CCDs. Mean healthcare expenditures for the elderly with CCDs and those without CCDs were summarised and compared. RESULTS: Forty two percent of the elderly were found to have at least one CCD. Joint problems were the most common CCD at 35 %, followed by hypertension at 15 % and chronic bronchitis at 11 %. Being female (OR = 1.51, 95 % CI = 1.03-2.21, p-value = 0.036), higher education (OR = 2.54, 95 % CI = 1.13-5.74, p-value = 0.025) and having advanced age (OR = 1.92, 95 % CI = 1.22-3.00, p-value = 0.005), were associated with common chronic diseases in the elderly. Outpatient healthcare expenditures were found to be significantly higher for the elderly with CCDs than those without CCDs. CONCLUSIONS: Higher education and being female are important key predictors of having a CCD, while wealth quintile is a predictor of multimorbidity, in the elderly. Healthcare expenditures for outpatient health services are higher for elderly persons with CCDs and these costs should be targeted when planning for financial protection.

Genetic and genomic approaches for the discovery of parasite genes involved in antimalarial drug resistance.

The biggest threat to the war on malaria is the continued evolution of drug resistance by the parasite. Resistance to almost all currently available antimalarials now exists in Plasmodium falciparum which causes the most suffering among all human malaria parasites. Monitoring of antimalarial efficacy and the development and subsequent spread of resistance has become an important part in the treatment and control of malaria. With recent reports of reduced efficacy of artemisinin, the current recommended treatment for uncomplicated malaria, there is urgent need for better methods to recognize and monitor drug resistance for effective treatment. Molecular markers have become a welcome addition to complement the more laborious and costly in vitro and in vivo methods that have traditionally been used to monitor drug resistance. However, there are currently no molecular markers for resistance to some antimalarials. This review highlights the role of the various genetic and genomic approaches that have been used in identifying the molecular markers that underlie drug resistance in P. falciparum. These approaches include; candidate genes, genetic linkage and genome-wide association studies. We discuss the requirements and limitations of each approach and use various examples to illustrate their contributions in identifying genomic regions of the parasite associated with antimalarial drug responses.

Analysis of malaria parasite phenotypes using experimental genetic crosses of Plasmodium falciparum.

We review the principles of linkage analysis of experimental genetic crosses and their application to Plasmodium falciparum. Three experimental genetic crosses have been performed using the human malaria parasite P. falciparum. Linkage analysis of the progeny of these crosses has been used to identify parasite genes important in phenotypes such as drug resistance, parasite growth and virulence, and transmission to mosquitoes. The construction and analysis of genetic maps has been used to characterise recombination rates across the parasite genome and to identify hotspots of recombination.

Alternative splicing of the Anopheles gambiae Dscam gene in diverse Plasmodium falciparum infections.

BACKGROUND: In insects, including Anopheles mosquitoes, Dscam (Down syndrome cell adhesion molecule) appears to be involved in phagocytosis of pathogens, and shows pathogen-specific splice-form expression between divergent pathogen (or parasite) types (e.g. between bacteria and Plasmodium or between Plasmodium berghei and Plasmodium falciparum). Here, data are presented from the first study of Dscam expression in response to genetic diversity within a parasite species. METHODS: In independent field and laboratory studies, a measure of Dscam splice-form diversity was compared between mosquitoes fed on blood that was free of P. falciparum to mosquitoes exposed to either single or mixed genotype infections of P. falciparum. RESULTS: Significant increases in Anopheles gambiae Dscam (AgDscam) receptor diversity were observed in parasite-exposed mosquitoes, but only weak evidence that AgDscam diversity rises further upon exposure to mixed genotype parasite infections was found. Finally, a cluster of AgDscam exon 4 variants that become especially common during Plasmodium invasion was identified. CONCLUSIONS: While the data clearly indicate that AgDscam diversity increases with P. falciparum exposure, they do not suggest that AgDscam diversity rises further in response to increased parasite diversity.

New synchronization method for Plasmodium falciparum.

BACKGROUND: Plasmodium falciparum is usually asynchronous during in vitro culture. Although various synchronization methods are available, they are not able to narrow the range of ages of parasites. A newly developed method is described that allows synchronization of parasites to produce cultures with an age range as low as 30 minutes. METHODS: Trophozoites and schizonts are enriched using Plasmion. The enriched late stage parasites are immobilized as a monolayer onto plastic Petri dishes using concanavalin A. Uninfected erythrocytes are placed onto the monolayer for a limited time period, during which time schizonts on the monolayer rupture and the released merozoites invade the fresh erythrocytes. The overlay is then taken off into a culture flask, resulting in a highly synchronized population of parasites. RESULTS: Plasmion treatment results in a 10- to 13-fold enrichment of late stage parasites. The monolayer method results in highly synchronized cultures of parasites where invasion has occurred within a very limited time window, which can be as low as 30 minutes. The method is simple, requiring no specialized equipment and relatively cheap reagents. CONCLUSIONS: The new method for parasite synchronization results in highly synchronized populations of parasites, which will be useful for studies of the parasite asexual cell cycle.