Country adoption of WHO 2019 guidance on HIV testing strategies and algorithms: a policy review across the WHO African region.

OBJECTIVES: In 2019, the WHO released guidelines on HIV testing service (HTS). We aim to assess the adoption of six of these recommendations on HIV testing strategies among African countries. DESIGN: Policy review. SETTING: 47 countries within the WHO African region. PARTICIPANTS: National HTS policies from the WHO African region as of December 2021. PRIMARY AND SECONDARY OUTCOME MEASURES: Uptake of WHO recommendations across national HTS policies including the standard three-test strategy; discontinuation of a tiebreaker test to rule in HIV infection; discontinuation of western blotting (WB) for HIV diagnosis; retesting prior to antiretroviral treatment (ART) initiation and the use of dual HIV/syphilis rapid diagnostic tests (RDTs) in antenatal care. Country policy adoption was assessed on a continuum, based on varying levels of complete adoption. RESULTS: National policies were reviewed for 96% (n=45/47) of countries in the WHO African region, 38% (n=18) were published before 2019 and 60% (n=28) adopted WHO guidance. Among countries that had not fully adopted WHO guidance, not yet adopting a three-test strategy was the most common reason for misalignment (45%, 21/47); of which 31% and 22% were in low-prevalence (<5%) and high-prevalence (≥5%) countries, respectively. Ten policies (21%) recommended the use of WB and 49% (n=23) recommended retesting before ART initiation. Dual HIV/syphilis RDTs were recommended in 45% (n=21/47) of policies. CONCLUSIONS: Many countries in the African region have adopted WHO-recommended HIV testing strategies; however, efforts are still needed to fully adopt WHO guidance. Countries should accelerate their efforts to adopt and implement a three-test strategy, retesting prior to ART initiation and the use of dual HIV/syphilis RDTs.

Surveillance for variants of SARS-CoV-2 to inform risk assessments.

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, some leading to large increases in infections, hospitalizations and deaths globally. The virus's impact on public health depends on many factors, including the emergence of new viral variants and their global spread. Consequently, the early detection and surveillance of variants and characterization of their clinical effects are vital for assessing their health risk. The unprecedented capacity for viral genomic sequencing and data sharing built globally during the pandemic has enabled new variants to be rapidly detected and assessed. This article describes the main variants circulating globally between January 2020 and June 2023, the genetic features driving variant evolution, and the epidemiological impact of these variants across countries and regions. Second, we report how integrating genetic variant surveillance with epidemiological data and event-based surveillance, through a network of World Health Organization partners, supported risk assessment and helped provide guidance on pandemic responses. In addition, given the evolutionary characteristics of circulating variants and the immune status of populations, we propose future directions for the sustainable genomic surveillance of SARS-CoV-2 variants, both nationally and internationally: (i) optimizing variant surveillance by including environmental monitoring; (ii) coordinating laboratory assessment of variant evolution and phenotype; (iii) linking data on circulating variants with clinical data; and (iv) expanding genomic surveillance to additional pathogens. Experience during the COVID-19 pandemic has shown that genomic surveillance of pathogens can provide essential, timely and evidence-based information for public health decision-making.

Depuis le début de la pandémie de coronavirus survenue en 2019 (COVID-19), de nombreux variants du coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2) sont apparus, certains entraînant une forte augmentation du nombre d'infections, d'hospitalisations et de décès dans le monde. L'impact du virus sur la santé publique dépend de nombreux facteurs, notamment l'émergence de nouveaux variants viraux et leur propagation à l'échelle mondiale. Par conséquent, la détection précoce et la surveillance des variants ainsi que la caractérisation de leurs effets cliniques sont essentielles pour évaluer leur risque pour la santé. La capacité sans précédent de séquençage du génome viral et de partage des données, capacité mise en place à l'échelle mondiale pendant la pandémie, a permis de détecter et d'évaluer rapidement de nouveaux variants. Le présent article décrit les principaux variants circulant dans le monde entre janvier 2020 et juin 2023, les caractéristiques génétiques à l'origine de leur évolution et leur impact épidémiologique dans les différents pays et régions. Ensuite, nous expliquerons comment l'intégration de la surveillance des variants génétiques aux données épidémiologiques et à la surveillance fondée sur les événements, par l'intermédiaire d'un réseau de partenaires de l'Organisation mondiale de la santé, a permis de faciliter l'évaluation des risques et de fournir des orientations sur les mesures à prendre en période de pandémie. En outre, compte tenu des caractéristiques évolutives des variants en circulation et de l'état immunitaire des populations, nous proposons des orientations futures pour une surveillance génomique durable des variants du SARS-CoV-2, au niveau tant national qu'international: (i) optimiser la surveillance des variants en incluant le suivi environnemental; (ii) coordonner l'évaluation en laboratoire de l'évolution des variants et du phénotype; (iii) établir un lien entre les données sur les variants en circulation et les données cliniques; et (iv) étendre la surveillance génomique à d'autres agents pathogènes. L'expérience de la pandémie de COVID-19 a mis en évidence que la surveillance génomique des agents pathogènes peut fournir en temps utile des informations essentielles fondées sur des preuves en vue de la prise de décisions en matière de santé publique.

Desde el inicio de la pandemia de la enfermedad por coronavirus de 2019 (COVID-19), han aparecido numerosas variantes del coronavirus de tipo 2 causante del síndrome respiratorio agudo severo (SRAS-CoV-2), algunas de las que han provocado un gran aumento de las infecciones, hospitalizaciones y muertes en todo el mundo. El impacto del virus en la salud pública depende de muchos factores, entre ellos la aparición de nuevas variantes víricas y su propagación mundial. En consecuencia, la detección y vigilancia tempranas de las variantes y la caracterización de sus efectos clínicos son vitales para evaluar su riesgo sanitario. La capacidad sin precedentes de secuenciación genómica viral y de intercambio de datos creada a nivel mundial durante la pandemia ha permitido detectar y evaluar rápidamente variantes nuevas. En este artículo se describen las principales variantes que circulan a nivel mundial entre enero de 2020 y junio de 2023, la característica genética que impulsa la evolución de las variantes y el impacto epidemiológico de estas variantes en los diferentes países y regiones. En segundo lugar, se informa de cómo la integración de la vigilancia de variantes genéticas con los datos epidemiológicos y la vigilancia basada en eventos, a través de una red de asociados de la Organización Mundial de la Salud, apoyó la evaluación de riesgos y ayudó a proporcionar orientación sobre las respuestas a la pandemia. Además, dadas las características evolutivas de las variantes circulantes y el estado inmunitario de las poblaciones, se proponen orientaciones futuras para la vigilancia genómica sostenible de las variantes del SRAS-CoV-2, tanto a nivel nacional como internacional: (i) optimizar la vigilancia de las variantes mediante la inclusión de la monitorización ambiental; (ii) coordinar la evaluación de laboratorio de la evolución y el fenotipo de las variantes; (iii) vincular los datos sobre las variantes circulantes con los datos clínicos; y (iv) ampliar la vigilancia genómica a patógenos adicionales. La experiencia durante la pandemia de la COVID-19 ha demostrado que la vigilancia genómica de patógenos puede proporcionar información esencial, oportuna y basada en evidencias para la toma de decisiones en materia de salud pública.

Building Integrated Testing Programs for Infectious Diseases.

In the past 2 decades, testing services for diseases such as human immunodeficiency virus (HIV), tuberculosis, and malaria have expanded dramatically. Investments in testing capacity and supportive health systems have often been disease specific, resulting in siloed testing programs with suboptimal capacity, reduced efficiency, and limited ability to introduce additional tests or respond to new outbreaks. Emergency demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing overcame these silos and demonstrated the feasibility of integrated testing. Moving forward, an integrated public laboratory infrastructure that services multiple diseases, including SARS-CoV-2, influenza, HIV, tuberculosis, hepatitis, malaria, sexually transmitted diseases, and other infections, will help improve universal healthcare delivery and pandemic preparedness. However, integrated testing faces many barriers including poorly aligned health systems, funding, and policies. Strategies to overcome these include greater implementation of policies that support multidisease testing and treatment systems, diagnostic network optimization, bundled test procurement, and more rapid spread of innovation and best practices across disease programs.

Exploring the mechanisms behind HIV drug resistance in sub-Saharan Africa: conceptual mapping of a complex adaptive system based on multi-disciplinary expert insights.

BACKGROUND: HIV drug resistance (HIVDR) continues to threaten the effectiveness of worldwide antiretroviral therapy (ART). Emergence and transmission of HIVDR are driven by several interconnected factors. Though much has been done to uncover factors influencing HIVDR, overall interconnectedness between these factors remains unclear and African policy makers encounter difficulties setting priorities combating HIVDR. By viewing HIVDR as a complex adaptive system, through the eyes of multi-disciplinary HIVDR experts, we aimed to make a first attempt to linking different influencing factors and gaining a deeper understanding of the complexity of the system. METHODS: We designed a detailed systems map of factors influencing HIVDR based on semi-structured interviews with 15 international HIVDR experts from or with experience in sub-Saharan Africa, from different disciplinary backgrounds and affiliated with different types of institutions. The resulting detailed system map was conceptualized into three main HIVDR feedback loops and further strengthened with literature evidence. RESULTS: Factors influencing HIVDR in sub-Saharan Africa and their interactions were sorted in five categories: biology, individual, social context, healthcare system and 'overarching'. We identified three causal loops cross-cutting these layers, which relate to three interconnected subsystems of mechanisms influencing HIVDR. The 'adherence motivation' subsystem concerns the interplay of factors influencing people living with HIV to alternate between adherence and non-adherence. The 'healthcare burden' subsystem is a reinforcing loop leading to an increase in HIVDR at local population level. The 'ART overreliance' subsystem is a balancing feedback loop leading to complacency among program managers when there is overreliance on ART with a perceived low risk to drug resistance. The three subsystems are interconnected at different levels. CONCLUSIONS: Interconnectedness of the three subsystems underlines the need to act on the entire system of factors surrounding HIVDR in sub-Saharan Africa in order to target interventions and to prevent unwanted effects on other parts of the system. The three theories that emerged while studying HIVDR as a complex adaptive system form a starting point for further qualitative and quantitative investigation.

Identification of Bacillus anthracis, Brucella spp., and Coxiella burnetii DNA signatures from bushmeat.

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.

Evaluation of stool GeneXpert MTB/RIF for the diagnosis of pulmonary tuberculosis among presumptive patients in Tanzania.

BACKGROUND: Diagnosis of pulmonary tuberculosis remains grim, especially in resource-limited settings. Low quality of sputum, particularly among seriously ill, HIV/AIDS, and pediatric patients might result in missing the diagnosis. This study evaluated the performance of GeneXpert MTB/RIF for the detection of pulmonary tuberculosis on stool specimens as an alternative to respiratory specimens. METHODS: A cross-sectional study design was used to evaluate the performance of GeneXpert MTB/RIF to detect TB in stool specimens from presumptive TB patients. Sputum culture on Lowenstein-Jensen media was used as the gold standard. Recruitment of patients into the study was conducted in 12 selected health facilities in Tanzania. Two sputa and a stool specimen were collected from each study participant. Both sputa and stool samples were tested at their respective study sites of collection using GeneXpert, and their respective portions shipped to the Central Tuberculosis Reference Laboratory for testing by stool GeneXpert and sputum culture in the LJ media. Statistical analysis was performed using STATA software version 14.1. RESULTS: A total of 590 presumptive tuberculosis patients were enrolled in this study. Their median age was 35 years (IQR = 21-47 years). More than half (57.5%, n = 339) of the study participants, were males. Children aged below 15 years constituted 17.6% (n = 104) of the study participants. A total of 75 tuberculosis cases were detected by sputum culture. The sensitivity and specificity of Stool GeneXpert conducted at CTRL was 84% (95% CI: 81.0-87.0%), and 93.4% (CI: 98.5-99.9%) respectively. The overall sensitivity and specificity of stool GeneXpert at the peripheral laboratories was 63.0% (95% CI: 47.8-76.1) and 76.7% (95% CI: 72.1-81.4), respectively. CONCLUSION: Findings from this study suggest that stool is a potential alternative to respiratory specimen for use in routine diagnosis of tuberculosis, especially when obtaining a respiratory specimen is challenging.

Clinical/Laboratory Interface Interventions to Improve Impact of Viral Load and Early Infant Diagnosis Testing Scale-Up.

Despite tremendous improvements in viral load (VL) monitoring and early infant diagnosis (EID) in many countries, low VL and EID testing rates and low VL suppression rates persist in specific regions and among certain subpopulations. The VL/EID cascade includes patient and provider demand creation, sample collection and transportation, laboratory testing, results transmission back to the clinic, and patient management. Gaps in communication and coordination between clinical and laboratory counterparts can lead to suboptimal outcomes, such as delay or inability to collect and transport samples to the laboratory for testing and failure of test results to reach providers and patients in an efficient, timely, and effective manner. To bridge these gaps and optimize the impact of VL/EID scale-up, we reviewed the components of the cascade and their interrelationships to identify barriers and facilitators. As part of this process, people living with HIV must be engaged in creating demand for VL/EID testing. In addition, there should be strong communication and collaboration between the clinical and laboratory teams throughout the cascade, along with joint performance review, site visits, and continuous quality improvement activities. Strengthening the clinical/laboratory interface requires innovative solutions and implementation of best practices, including the use of point-of-care diagnostics, simplified data systems, and an efficient supply chain system to minimize interface gaps.

The COVID-19 pandemic: broad partnerships for the rapid scale up of innovative virtual approaches for capacity building and credible information dissemination in Africa.

The Corona Virus Disease 2019 (COVID-19) pandemic has rapidly spread in Africa, with a total of 474,592 confirmed cases by 11th July 2020. Consequently, all policy makers and health workers urgently need to be trained and to access the most credible information to contain and mitigate its impact. While the need for rapid training and information dissemination has increased, most of Africa is implementing public health social and physical distancing measures. Responding to this context requires broad partnerships and innovative virtual approaches to disseminate new insights, share best practices, and create networked communities of practice for all teach, and all learn. The World Health Organization (WHO)-Africa region, in collaboration with the Extension for Community Health Outcome (ECHO) Institute at the University of New Mexico Health Sciences Center (UNM HSC), the West Africa college of nurses and the East Central and Southern Africa college of physicians, private professional associations, academia and other partners has embarked on a virtual training programme to support the containment of COVID-19. Between 1st April 2020 and 10th July 2020, about 7,500 diverse health professionals from 172 locations in 58 countries were trained in 15 sessions. Participants were from diverse institutions including: central ministries of health, WHO country offices, provincial and district hospitals and private medical practitioners. A range of critical COVID-19 preparedness and response interventions have been reviewed and discussed. There is a high demand for credible information from credible sources about COVID-19. To mitigate the "epidemic of misinformation" partnerships for virtual trainings and information dissemination leveraging existing learning platforms and networks across Africa will augment preparedness and response to COVID-19.

Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania.

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

Onsite healthcare worker acceptability and performance of the point-of-care Pima CD4 assay in Dar es Salaam, Tanzania.

BACKGROUND: Healthcare workers' acceptance of and ability to perform point-of-care testing is important for reliable and accurate results. The Alere Pima™ CD4 assay (Pima CD4) is the CD4 point-of-care test for HIV management in Tanzania. OBJECTIVES: To evaluate healthcare workers' acceptance and performance of Pima CD4 testing. METHODS: The study was implemented in five high volume sites in Dar es Salaam, Tanzania, in 2011. Trained healthcare workers performed Pima testing using three whole-blood specimens collected from each patient: venous blood, fingerstick blood directly applied to a Pima cartridge (capillary-direct), and fingerstick blood collected in a microtube (capillary-microtube). Using a semi-structured interview guide, we interviewed 11 healthcare workers about specimen collection methods and Pima CD4 acceptability. Quantitative responses were analysed using descriptive statistics. Open-ended responses were summarised by thematic areas. Pima CD4 results were analysed to determine variation between cadres. RESULTS: Healthcare workers found Pima CD4 user-friendly and recommended its use in low volume, peripheral facilities. Both venous and capillary-direct blood were considered easy to collect, with venous preferred. Advantages noted with venous and capillary-microtube methods were the ability to retest, perform multiple tests, or delay testing. Pima CD4 results were trusted by the healthcare workers and were in agreement with laboratory Pima testing. CONCLUSION: In this point-of-care testing setting, the Pima CD4 assay was accepted by healthcare workers. Both venous and fingerstick capillary blood specimens can be used with Pima CD4, but fingerstick methods may require more intensive training on technique to minimise variation in results and increase acceptability.

Performance of Cepheid Xpert HIV-1 viral load plasma assay to accurately detect treatment failure.

BACKGROUND: Coverage of viral load testing remains low with only half of the patients in need having adequate access. Alternative technologies to high throughput centralized machines can be used to support viral load scale-up; however, clinical performance data are lacking. We conducted a meta-analysis comparing the Cepheid Xpert HIV-1 viral load plasma assay to traditional laboratory-based technologies. METHODS: Cepheid Xpert HIV-1 and comparator laboratory technology plasma viral load results were provided from 13 of the 19 eligible studies, which accounted for a total of 3790 paired data points. We used random effects models to determine the accuracy and misclassification at various treatment failure thresholds (detectable, 200, 400, 500, 600, 800 and 1000 copies/ml). RESULTS: Thirty percent of viral load test results were undetectable, while 45% were between detectable and 10 000 copies/ml and the remaining 25% were above 10 000 copies/ml. The median Xpert viral load was 119 copies/ml and the median comparator viral load was 157 copies/ml, while the log10 bias was 0.04 (0.02-0.07). The sensitivity and specificity to detect treatment failure were above 95% at all treatment failure thresholds, except for detectable, at which the sensitivity was 93.33% (95% confidence interval: 88.2-96.3) and specificity was 80.56% (95% CI: 64.6-90.4). CONCLUSION: The Cepheid Xpert HIV-1 viral load plasma assay results were highly comparable to laboratory-based technologies with limited bias and high sensitivity and specificity to detect treatment failure. Alternative specimen types and technologies that enable decentralized testing services can be considered to expand access to viral load.

Predictors of non adherence to antiretroviral therapy at an urban HIV care and treatment center in Tanzania.

BACKGROUND: Measurement of adherence to antiretroviral therapy (ART) can serve as a proxy for virologic failure in resource-limited settings. The aim of this study was to determine the factors underlying nonadherence measured by three methods. PATIENTS AND METHODS: This is a prospective longitudinal cohort of 220 patients on ART at Amana Hospital in Dar es Salaam, Tanzania. We measured adherence using a structured questionnaire combining a visual analog scale (VAS) and Swiss HIV Cohort Study Adherence Questionnaire (SHCS-AQ), pharmacy refill, and appointment keeping during four periods over 1 year. Overall adherence was calculated as the mean adherence for all time points over the 1 year of follow-up. At each time point, adherence was defined as achieving a validated cutoff for adherence previously defined for each method. RESULTS: The proportion of overall adherence was 86.4% by VAS, 69% by SHCS-AQ, 79.8% by appointment keeping, and 51.8% by pharmacy refill. Forgetfulness was the major reported reason for patients to skip their medications. In multivariate analysis, significant predictors to good adherence were older age, less alcohol consumption, more advanced World Health Organization clinical staging, and having a lower body mass index with odds ratio (CI): 3.11 (1.55-6.93), 0.24 (0.09-0.62), 1.78 (1.14-2.84), and 0.93 (0.88-0.98), respectively. CONCLUSION: We found relatively good adherence to ART in this setting. Barriers to adherence include young age and perception of well-being.

Evaluation of Specimen Types for Pima CD4 Point-of-Care Testing: Advantages of Fingerstick Blood Collection into an EDTA Microtube.

INTRODUCTION: Effective point-of-care testing (POCT) is reliant on optimal specimen collection, quality assured testing, and expedited return of results. Many of the POCT are designed to be used with fingerstick capillary blood to simplify the blood collection burden. However, fingerstick blood collection has inherent errors in sampling. An evaluation of the use of capillary and venous blood with CD4 POCT was conducted. METHODS: Three different specimen collection methods were evaluated for compatibility using the Alere Pima CD4 assay at 5 HIV/AIDS healthcare sites in Dar es Salaam, Tanzania. At each site, whole blood specimens were collected from enrolled patients by venipuncture and fingerstick. Pima CD4 testing was performed at site of collection on venipuncture specimens (Venous) and fingerstick blood directly applied to a Pima CD4 cartridge (Capillary-Direct) and collected into an EDTA microtube (Capillary-Microtube). Venous blood was also tested at the laboratory by the reference CD4 method and Pima for comparison analysis. RESULTS: All three specimen collection methods were successfully collected by healthcare workers for use with the Pima CD4 assay. When compared to the reference CD4 method, Pima CD4 testing with the Capillary-Microtube method performed similarly to Venous, while Pima CD4 counts with the Capillary-Direct method were slightly more biased (-20 cells/µL) and variable (-229 to +189 cells/µL limit of agreement). Even though all three collection methods had similar invalid Pima testing rates (10.5%, 9.8%, and 8.3% for Capillary-Direct, Capillary-Microtube, and Venous respectively), the ability to perform repeat testing with Capillary-Microtube and Venous specimens increased the likelihood of acquiring a valid CD4 result with the Pima assay. CONCLUSIONS: Capillary blood, either directly applied to Pima CD4 cartridges or collected in an EDTA microtube, and venous blood are suitable specimens for Pima CD4 testing. The advantages of capillary blood collection in an EDTA microtube are that it uses fingerstick collection which mimics venous blood and allows extra testing without additional blood collection.

Use of TaqMan Array Cards to Screen Outbreak Specimens for Causes of Febrile Illness in Tanzania.

We describe the deployment of a custom-designed molecular diagnostic TaqMan Array Card (TAC) to screen for 31 bacterial, protozoal, and viral etiologies in blood from outbreaks of acute febrile illness in Tanzania during 2015-2017. On outbreaks notified to the Tanzanian Ministry of Health, epidemiologists were dispatched and specimens were collected, transported to a central national laboratory, and tested by TAC within 2 days. This algorithm streamlined investigation, diagnosed a typhoid outbreak, and excluded dozens of other etiologies. This method is usable in-country and may be incorporated into algorithms for diagnosing outbreaks.

Assessment of GeneXpert GxAlert platform for multi-drug resistant tuberculosis diagnosis and patients' linkage to care in Tanzania.

OBJECTIVE: The gap between patients diagnosed with multi-drug resistant tuberculosis (MDR-TB) and enrolment in treatment is one of the major challenges in tuberculosis control programmes. A 4-year (2013-2016) retrospective review of patients' clinical data and subsequent in-depth interviews with health providers were conducted to assess the effectiveness of the GeneXpert GxAlert platform for MDR-TB diagnosis and its impact on linkage of patients to care in Tanzania. RESULTS: A total of 782 new rifampicin resistant cases were notified, but only 242 (32.3%) were placed in an MDR-TB regimens. The remaining 540 (67.07%) patients were not on treatment, of which 103 patients had complete records on the GxAlert database. Of the 103 patients: 39 were judged as untraceable; 27 died before treatment; 12 were treated with first-line anti-TBs; 9 repeat tests did not show rifampicin resistance; 15 were not on treatment due to communication breakdown, and 1 patient was transferred outside the country. In-depth interviews with health providers suggested that the pre-treatment loss for the MDR-TB patients was primarily attributed to health system and patients themselves. We recommend strengthening the health system by developing and implementing well-defined interventions to ensure all diagnosed MDR-TB patients are accurately reported and timely linked to treatment.

Evaluation of a laboratory capacity strengthening project: a case of the summative assessment of the African Field Epidemiology Network (AFENET) laboratory project 2010 - 2016.

INTRODUCTION: Between September 2010 and September 2016, the African Field Epidemiology Network (AFENET) implemented laboratory strengthening initiatives through a cooperative agreement with the International Laboratory Branch of the US Centers for Disease Control and Prevention (CDC). This project aimed at improving laboratory Quality Management Systems (QMS) towards accreditation in Africa and the Caribbean region and was implemented in 11 countries in the Caribbean and seven African countries. This paper describes the results of a summative evaluation that was commissioned at the end of the project. METHODS: The evaluation team comprised an external consultant who led the evaluation design and implementation and AFENET project staff. The evaluation was done in all 11 Caribbean and seven African countries where the project was implemented. We formulated three evaluation questions to focus and guide the exercise: 1) Were project activities implemented as originally intended? 2) Did the project achieve the objectives it was intended to accomplish over its life? 3) Are the impacts of project interventions likely to survive in the long run? We developed 14 sub-questions from the three evaluation questions and obtained data using a set of online questionnaires. We conducted validation visits to six participating countries; four in Africa and two in the Caribbean. RESULTS: Out of 14 sub-questions that were used to evaluate the project, six (43%) were fully achieved, six (43%) were partially achieved, and two (14%) were not achieved. In effect, > 80% of the sub-questions were either fully achieved or partially achieved. The most frequently mentioned success was the introduction of QMS in participating laboratories, which led to quality improvement in laboratory processes, participation in SLMTA (Strengthening Laboratory Management Towards Accreditation)/SLIPTA (Stepwise Laboratory Quality Improvement Process Towards Accreditation) and attainment of accreditation by some of the project laboratories. However, there were neither clear plans nor budget lines to mainstream activities that were supported under the project into regular activities of the ministries of health of participating countries. CONCLUSION: The evaluation team concluded that there were adequate numbers of laboratorians trained in the FELTP laboratory track but only in Kenya. The DTS testing and biosafety programs were implemented and expanded in participating countries. HIV laboratory networks were strengthened in all participating countries and laboratory information systems were implemented in the Caribbean countries, but the basic laboratory information systems in the African countries were not implemented beyond pilot stages. There were no clear plans and budget lines provided by respective ministries of health to mainstream the activities that were supported under the project. The evaluation team recommended that AFENET develops a new laboratory strategic plan that could leverage the activities that were funded and implemented in the project.

Increased utilisation of PEPFAR-supported laboratory services by non-HIV patents in Tanzania.

BACKGROUND: It is unknown to what extent the non-HIV population utilises laboratories supported by the President's Emergency Plan for AIDS Relief (PEPFAR). OBJECTIVES: We aimed to describe the number and proportion of laboratory tests performed in 2009 and 2011 for patients referred from HIV and non-HIV services (NHSs) in a convenience sample collected from 127 laboratories supported by PEPFAR in Tanzania. We then compared changes in the proportions of tests performed for patients referred from NHSs in 2009 vs 2011. METHODS: Haematology, chemistry, tuberculosis and syphilis test data were collected from available laboratory registers. Referral sources, including HIV services, NHSs, or lack of a documented referral source, were recorded. A generalised linear mixed model reported the odds that a test was from a NHS. RESULTS: A total of 94 132 tests from 94 laboratories in 2009 and 157 343 tests from 101 laboratories in 2011 were recorded. Half of all tests lacked a documented referral source. Tests from NHSs constituted 42% (66 084) of all tests in 2011, compared with 31% (29 181) in 2009. A test in 2011 was twice as likely to have been referred from a NHS as in 2009 (adjusted odds ratio: 2.0 [95% confidence interval: 2.0-2.1]). CONCLUSION: Between 2009 and 2011, the number and proportion of tests from NHSs increased across all types of test. This finding may reflect increased documentation of NHS referrals or that the laboratory scale-up originally intended to service the HIV-positive population in Tanzania may be associated with a 'spillover effect' amongst the general population.

Increased utilisation of PEPFAR-supported laboratory services by non-HIV patients in Tanzania

Background: It is unknown to what extent the non-HIV population utilises laboratories supported by the President's Emergency Plan for AIDS Relief (PEPFAR).Objectives: We aimed to describe the number and proportion of laboratory tests performed in 2009 and 2011 for patients referred from HIV and non-HIV services (NHSs )in a convenience sample collected from 127 laboratories supported by PEPFAR in Tanzania. We then compared changes in the proportions of tests performed for patients referred from NHSs in 2009 vs 2011.Methods: Haematology; chemistry; tuberculosis and syphilis test data were collected from available laboratory registers. Referral sources; including HIV services; NHSs; or lack of a documented referral source; were recorded. A generalised linear mixed model reported the odds that a test was from a NHS.Results: A total of 94 132 tests from 94 laboratories in 2009 and 157 343 tests from 101 laboratories in 2011 were recorded. Half of all tests lacked a documented referral source. Tests from NHSs constituted 42% (66 084) of all tests in 2011; compared with 31% (29 181) in 2009. A test in 2011 was twice as likely to have been referred from a NHS as in 2009 (adjusted odds ratio: 2.0 [95% confidence interval: 2.0-2.1]).Conclusion: Between 2009 and 2011; the number and proportion of tests from NHSs increased across all types of test. This finding may reflect increased documentation of NHS referrals or that the laboratory scale-up originally intended to service the HIV-positive population in Tanzania may be associated with a 'spillover effect' amongst the general population