Xpert MTB/XDR implementation in South Africa: cost outcomes of centralised vs. decentralised approaches.

INTRODUCTION: In South Africa, Xpert® MTB/RIF Ultra (Ultra) is the recommended diagnostic assay for TB with line-probe assays for first- (LPAfl) and second-line drugs (LPAsl) providing additional drug susceptibility testing (DST) for samples that were rifampicin-resistant (RR-TB). To guide implementation of the recently launched Xpert® MTB/XDR (MTB/XDR) assay, a cost-outcomes analysis was conducted comparing total costs for genotypic DST (gDST) for persons diagnosed with RR-TB considering three strategies: replacing LPAfl/LPAsl (centralised level) with MTB/XDR vs. Ultra reflex testing (decentralised level). Further, DST was performed using residual specimen following RR-TB diagnosis. METHODS: The total cost of gDST was determined for three strategies, considering loss to follow-up (LTFU), unsuccessful test rates, and specimen volume. RESULTS: For 2019, 9,415 persons were diagnosed with RR-TB. A 35% LTFU rate between RR-TB diagnosis and LPAfl/LPAsl-DST was estimated. Unsuccessful test rates of 37% and 23.3% were reported for LPAfl and LPAsl, respectively. The estimated total costs were $191,472 for the conventional strategy, $122,352 for the centralised strategy, and $126,838 for the decentralised strategy. However, it was found that sufficient residual volume for reflex MTB/XDR testing is a limiting factor at the decentralised level. CONCLUSION: Centralising the implementation of XDR testing, as compared to LPAfl/LPAsl, leads to significant cost savings.

INTRODUCTION: En Afrique du Sud, Xpert® MTB/RIF Ultra (Ultra) est le test de diagnostic recommandé pour la TB avec des tests par sonde de ligne pour les médicaments de première (LPAfl) et de deuxième ligne (LPAsl) fournissant des tests de sensibilité aux médicaments (DST) supplémentaires pour les échantillons résistants à la rifampicine (RR-TB). Afin d'orienter la mise en œuvre du test Xpert® MTB/XDR (MTB/XDR) récemment lancé, une analyse coûts-résultats a été réalisée en comparant les coûts totaux de la DST génotypique (gDST) pour les personnes diagnostiquées avec une RR-TB en tenant compte de trois stratégies : remplacer le LPAfl/LPAsl (niveau centralisé) par le MTB/XDR par rapport au test Ultra reflex (niveau décentralisé). De plus, l'heure d'été a été réalisée à l'aide d'un échantillon résiduel après le diagnostic de RR-TB. MÉTHODES: Le coût total de la gDST a été déterminé pour trois stratégies, en tenant compte de la perte de suivi (LTFU), des taux d'échec des tests et du volume d'échantillons. RÉSULTATS: En 2019, 9 415 personnes ont reçu un diagnostic de RR-TB. Un taux de LTFU de 35% entre le diagnostic de RR-TB et le diagnostic de LPAfl/LPAsl-DST a été estimé. Des taux d'échec de 37% et de 23,3% ont été signalés pour LPAfl et LPAsl, respectivement. Les coûts totaux estimés étaient de 191 472 dollars pour la stratégie conventionnelle, de 122 352 dollars pour la stratégie centralisée et de 126 838 dollars pour la stratégie décentralisée. Cependant, il a été constaté qu'un volume résiduel suffisant pour les tests réflexes MTB/XDR est un facteur limitant au niveau décentralisé. CONCLUSION: La centralisation de la mise en œuvre des tests XDR, par rapport à LPAfl/LPAsl, permet de réaliser d'importantes économies.

Sentinel seroprevalence of SARS-CoV-2 in Gauteng Province, South Africa, August - October 2020.

BACKGROUND: Estimates of prevalence of anti-SARS-CoV-2 antibody positivity (seroprevalence) for tracking the COVID-19 epidemic are lacking for most African countries. OBJECTIVES: To determine the prevalence of antibodies against SARS-CoV-2 in a sentinel cohort of patient samples received for routine testing at tertiary laboratories in Johannesburg, South Africa. METHODS: This sentinel study was conducted using remnant serum samples received at three National Health Laboratory Service laboratories in the City of Johannesburg (CoJ) district. Collection was from 1 August to 31 October 2020. We extracted accompanying laboratory results for glycated haemoglobin (HbA1c), creatinine, HIV, viral load and CD4 T-cell count. An anti-SARS-CoV-2 targeting the nucleocapsid (N) protein of the coronavirus with higher affinity for IgM and IgG antibodies was used. We reported crude as well as population-weighted and test-adjusted seroprevalence. Multivariate logistic regression analysis was used to determine whether age, sex, HIV and diabetic status were associated with increased risk for seropositivity. RESULTS: A total of 6 477 samples were analysed, the majority (n=5 290) from the CoJ region. After excluding samples with no age or sex stated, the model population-weighted and test-adjusted seroprevalence for the CoJ (n=4 393) was 27.0% (95% confidence interval (CI) 25.4 - 28.6). Seroprevalence was highest in those aged 45 - 49 years (29.8%; 95% CI 25.5 - 35.0) and in those from the most densely populated areas of the CoJ. Risk for seropositivity was highest in those aged 18 - 49 years (adjusted odds ratio (aOR) 1.52; 95% CI 1.13 - 2.13; p=0.0005) and in samples from diabetics (aOR 1.36; 95% CI 1.13 - 1.63; p=0.001). CONCLUSIONS: Our study conducted between the first and second waves of the pandemic shows high levels of current infection among patients attending public health facilities in Gauteng Province.

Documented higher burden of advanced and very advanced HIV disease among patients, especially men, accessing healthcare in a rapidly growing economic and industrial hub in South Africa: A call to action.

BACKGROUND: Lephalale Municipality in Limpopo Province, South Africa, has seen significant economic and industrial development owing to expansion of the coal mining and power generation sectors. This development has coincided with substantial population growth of 65% between 2001 and 2016, attributable to largely (migrant) males living in the area who, overall, outnumbered females by ~121:100. The local HIV prevalence is reported to be higher than national rates. OBJECTIVES: Anonymised National Health Laboratory Service CD4+ data were used to document increasing laboratory services workload and to establish the burden of advanced (CD4+ count <200 cells/µL) and very advanced (<100 cells/µL) HIV disease among adult patients accessing public healthcare in Lephalale between 2006 and 2015. METHODS: A cross-sectional design was used to analyse CD4+ laboratory data. CD4+ outcomes were categorised by volumes of tests, year, health facility type, age categories (15 - 19, 20 - 24, 25 - 29, 30 - 34, 35 - 39, 40 - 44, 45 - 49 and >49 years), CD4+ test range (≤50, 51 - 100, 101 - 200, 201 - 350, 351 - 500 and ≥501 cells/µL) and gender. Median CD4+ counts were calculated. RESULTS: Extracted Lephalale data comprised 57 490 CD4+ results, with a mean patient age of 34 years. Considerably fewer male than female patients had CD4+ counts reported (male/female ratio 0.45:1). CD4+ test volumes showed a five-fold escalation over the study period, increasing from 1 458 tests in 2006 to 8 239 in 2015. A considerable burden of advanced and very advanced HIV disease (exceeding 50% of all cases) was noted in 2006/2007; by 2015 the proportion had fallen, but was still high at 27%. The overall median CD4+ count in 2006 (192 cells/µL) confirmed a high burden of advanced disease, with modest improvement to 289 cells/µL by 2015. Between 2006 and 2015, the median CD4+ count for females increased from 204 to 405 cells/µL, while that for males increased from 126 to 285 cells/µL. Age analysis further revealed that men aged <20 years or >25 years, and specifically those aged 30 - 45 years, had up to 44% more advanced HIV disease. CONCLUSIONS: Lower median CD4+ counts and a dramatic increase in volumes of CD4+ tests performed from 2007 onwards revealed a high burden of advanced and very advanced HIV disease in patients accessing care in Lephalale. Viewed together with Statistics South Africa census documentation of a disproportionately high number of males compared with females living in the area, these figures suggest that improved systems are urgently needed to encourage and accommodate access to HIV care for male (migrant worker) patients living and working in emerging industrial centres.

The potential for quality assurance systems to save costs and lives: the case of early infant diagnosis of HIV.

OBJECTIVES: Scaling up of point-of-care testing (POCT) for early infant diagnosis of HIV (EID) could reduce the large gap in infant testing. However, suboptimal POCT EID could have limited impact and potentially high avoidable costs. This study models the cost-effectiveness of a quality assurance system to address testing performance and screening interruptions, due to, for example, supply stockouts, in Kenya, Senegal, South Africa, Uganda and Zimbabwe, with varying HIV epidemics and different health systems. METHODS: We modelled a quality assurance system-raised EID quality from suboptimal levels: that is, from misdiagnosis rates of 5%, 10% and 20% and EID testing interruptions in months, to uninterrupted optimal performance (98.5% sensitivity, 99.9% specificity). For each country, we estimated the 1-year impact and cost-effectiveness (US$/DALY averted) of improved scenarios in averting missed HIV infections and unneeded HIV treatment costs for false-positive diagnoses. RESULTS: The modelled 1-year costs of a national POCT quality assurance system range from US$ 69 359 in South Africa to US$ 334 341 in Zimbabwe. At the country level, quality assurance systems could potentially avert between 36 and 711 missed infections (i.e. false negatives) per year and unneeded treatment costs between US$ 5808 and US$ 739 030. CONCLUSIONS: The model estimates adding effective quality assurance systems are cost-saving in four of the five countries within the first year. Starting EQA requires an initial investment but will provide a positive return on investment within five years by averting the costs of misdiagnoses and would be even more efficient if implemented across multiple applications of POCT.

OBJECTIFS: L'intensification du dépistage au point des soins (DPS) pour le diagnostic précoce du VIH chez le nourrisson (DPVN) pourrait réduire le grand écart dans le dépistage des nourrissons. Cependant, un DPVN DPS sous-optimal pourrait avoir un impact limité et des coûts évitables potentiellement élevés. Cette étude modélise la rentabilité d'un système d'assurance qualité pour traiter les performances des tests et les interruptions de dépistage, dues par exemple à des ruptures de stock, au Kenya, au Sénégal, en Afrique du Sud, en Ouganda et au Zimbabwe, avec des épidémies variables du VIH et des systèmes de santé différents. MÉTHODES: Nous avons modélisé une qualité de DPVN soulevée par le système d'assurance qualité à partir de niveaux sous-optimaux: c'est-à-dire des taux d'erreurs de diagnostic de 5%, 10% et 20% et des interruptions des tests de DPVN en mois, à des performances optimales ininterrompues (sensibilité de 98,5%, spécificité de 99,9%). Pour chaque pays, nous avons estimé l'impact sur un an et la rentabilité (en USD/DALY évitée) de scénarios améliorés pour éviter les infections à VIH manquées et les coûts inutiles de traitement du VIH pour les diagnostics faux positifs. RÉSULTATS: Les coûts modélisés sur un an d'un système national d'assurance qualité DPS vont de 69.359 USD en Afrique du Sud à 334.341 USD au Zimbabwe. Au niveau des pays, les systèmes d'assurance de la qualité pourraient potentiellement éviter entre 36 et 711 infections manquées (c'est-à-dire des faux négatifs) par an et des coûts de traitement inutiles entre 5.808 et 739.030 USD. CONCLUSIONS: Le modèle estime que l'ajout de systèmes d'assurance qualité efficaces permet de réaliser des économies dans quatre des cinq pays au cours de la première année. Le lancement de l'assurance qualité nécessite un investissement initial, mais fournira un retour sur investissement positif dans les cinq ans en évitant les coûts des diagnostics erronés et serait encore plus efficace s'il était mis en œuvre dans plusieurs applications de DPS.

Assessing the fit of 3D printed bolus from CT, optical scanner and photogrammetry methods.

Bolus plays an important role in the radiation therapy of superficial lesions and the application of 3D printing to its design can improve fit and dosimetry. This study quantitatively compares the fits of boluses designed from different imaging modalities. A head phantom was imaged using three systems: a CT simulator, a 3D optical scanner, and an interchangeable lens camera. Nose boluses were designed and 3D printed from each modality. A 3D printed phantom with air gaps of known thicknesses was used to calibrate mean HU to measure air gaps of unknown thickness and assess the fit of each bolus on the head phantom. The bolus created from the optical scanner data resulted in the best fit, with a mean air gap of 0.16 mm. Smoothing of the CT bolus resulted in a more clinically suitable model, comparable to that from the optical scanner method. The bolus produced from the photogrammetry method resulted in air gaps larger than 1 mm in thickness. The use of optical scanner and photogrammetry models have many advantages over the conventional bolus-from-CT method, however workflow should be refined to ensure accuracy if implemented clinically.

Quasi-simultaneous 3D printing of muscle-, lung- and bone-equivalent media: a proof-of-concept study.

3D printing is a promising solution for the production of bespoke phantoms and phantom components, for radiotherapy dosimetry and quality assurance (QA) purposes. This proof-of-concept study investigated the use of a dual-head printer to deposit two different filaments (polylactic acid (PLA) and StoneFil PLA-concrete (Formfutura BV, Nijmegen, Netherlands)) at several different in-fill densities, to achieve quasi-simultaneous 3D printing of muscle-, lung- and bone-equivalent media. A Raise 3D Pro 3D printer (Raise 3D Technologies Inc, Irvine, USA) was used to print one thoracic and one cranial phantom slab. Analysis using in-house 3D print QA software showed that the two humanoid phantom slabs geometrically matched the stereolithography (STL) files on which they were based, within 0.3 mm, except in one area of the thoracic slab that was affected by thermal warping by up to 3.4 mm. The 3D printed muscle, lung and bone materials in the two humanoid phantom slabs were approximately radiologically-equivalent to human muscle, lung and bone. In particular, the use of StoneFil with a nominally constant in-fill density of 100% resulted in regions that were approximately inner-bone-equivalent, at kV and MV energies. These regions were bounded by walls that were substantially denser than inner bone, although generally not dense enough to be truly cortical-bone-equivalent. This proof-of-concept study demonstrated a method by which multiple tissue-equivalent materials (eg. muscle-, lung- and bone-equivalent media) can be deposited within one 3D print, allowing complex phantom components to be fabricated efficiently in a clinical setting.

Prostate cancer age-standardised incidence increase between 2006 and 2016 in Gauteng Province, South Africa: A laboratory data-based analysis.

BACKGROUND: Prostate cancer (PCa) is the leading male neoplasm in South Africa (SA) and is the second most frequently diagnosed cancer among men globally. Age-specific incidence rates (ASIRs) vary by up to 189-fold globally, with an ASIR of 68.0 per 100 000 in 2018 in SA. OBJECTIVES: To describe PCa among men undergoing prostate biopsy in Gauteng Province, SA. METHODS: We undertook a retrospective descriptive study using prostate biopsy data collected from the National Health Laboratory Service (NHLS) database between 2006 and 2016. We extracted the Systematized Nomenclature of Medicine (SNOMED) clinical terms morphology and topography codes to assign histological findings using the International Classification of Diseases for Oncology. PCa was defined as adenocarcinoma with a reported Gleason Score (GS). The new grade group (GG) based on the GS is defined as follows; (i) GG1 for a GS ≤6; (ii) GG2 for a GS of 3 + 4 = 7 ; (iii) GG3 for a GS of 4 + 3 = 7; (iv) GG4 for a GS of 8; and (v) GG5 for a GS ≥9. Higher-grade disease was defined as GG4 and GG5 (GS ≥8), in line with local guidelines. We reported associations of PCa with a GS ≥7 with age and race and used provincial and world standard population data to determine annual ASIRs. RESULTS: We identified 22 937 biopsies referred to the NHLS between 2006 and 2016. Of the 6 448 biopsies (39%) with a PCa finding for black Africans, 46% were diagnosed with high-risk PCa compared with 36 - 40% for other race groups (p<0.0001). Black Africans were more likely than whites to have GG4 or GG5 PCa (odds ratio 1.45; 95% confidence interval 1.27 - 1.67). The ASIR increased from 44.9 per 100 000 in 2006 to 57.3 per 100 000 in 2016. CONCLUSIONS: Black African men were significantly more likely to present with PCa with a GS ≥8 (GG4 and GG5) compared with the other racial groups in Gauteng. The ASIR increased dramatically during the study period, perhaps as a result of increased screening and awareness. There is a need for additional research to better understand why black African men present with higher-grade disease.

Using Big Data Techniques to Improve Prostate Cancer Reporting in the Gauteng Province, South Africa.

Prostate cancer (PCa) data is of public health importance in South Africa. Biopsy data is recorded as semi-structured narrative text that is not easily analysed. Our study reports a pilot study that applied predictive analytics and text mining techniques to extract prognostic information that guides patient management. In particular, the Gleason score (GS) reported in a number of formats were extracted successfully. Our study reports that predominantly older men were diagnosed with PCa reporting a high-risk GS (8-10). Where cell differentiation was reported, 64% of biopsies reported poor differentiation. The approaches demonstrated in our study should be extended to a larger dataset to assess whether it has the potential to scale up to the national level.

Piloting a national laboratory electronic programme status reporting system in Ekurhuleni health district, South Africa.

BACKGROUND: The National Health Laboratory Service (NHLS) performs ~4 million CD4 tests per annum for the public health sector at 61 CD4 testing laboratories across South Africa. Currently, CD4 laboratory data captured do not differentiate between antiretroviral treatment (ART) and pre-ART care. METHODS: A cross-sectional study was undertaken to evaluate a redesigned Comprehensive Care, Management and Treatment of HIV and AIDS (CCMT) request form, incorporating a two-tick collection procedure linking the CD4 test request to patient CCMT programme status. Field testing was undertaken at three health facilities, where healthcare personnel were required to capture whether the CD4 count requested was a 'first-ever CD4', 'CD4 taken previously, not yet in ART care' or 'in ART care'. All data were extracted from the NHLS Corporate Data Warehouse and analysed using Microsoft Excel and Stata-12. RESULTS: A substantial increase in the number of request forms with a CCMT programme status (28.1% v. 84.4%) was reported pre- and post-implementation. Post-implementation data (N=1 004) revealed that 30.8% patients were ART naive ('first-ever CD4'), with 7.4% 'not yet on ART' (median CD4 counts of 150 and 328 cells/µL, respectively). Patients on ART comprised 61.9% of the study group (median CD4 count ~346 cells/µL). Sixty percent of patients were aged between 30 and 44 years, and females predominated (male/female ratio 0.7:1). CONCLUSIONS: A simple modification to the CCMT request form can successfully facilitate collection of programme status. For national implementation, it would be advantageous to have a unique patient identifier to further enhance laboratory-based programmatic monitoring and evaluation.

Implementation of a new 'community' laboratory CD4 service in a rural health district in South Africa extends laboratory services and substantially improves local reporting turnaround time.

BACKGROUND: The CD4 integrated service delivery model (ITSDM) provides for reasonable access to pathology services across South Africa (SA) by offering three new service tiers that extend services into remote, under-serviced areas. ITSDM identified Pixley ka Seme as such an under-serviced district. OBJECTIVE: To address the poor service delivery in this area, a new ITSDM community (tier 3) laboratory was established in De Aar, SA. Laboratory performance and turnaround time (TAT) were monitored post implementation to assess the impact on local service delivery. METHODS: Using the National Health Laboratory Service Corporate Data Warehouse, CD4 data were extracted for the period April 2012-July 2013 (n=11,964). Total mean TAT (in hours) was calculated and pre-analytical and analytical components assessed. Ongoing testing volumes, as well as external quality assessment performance across ten trials, were used to indicate post-implementation success. Data were analysed using Stata 12. RESULTS: Prior to the implementation of CD4 testing at De Aar, the total mean TAT was 20.5 hours. This fell to 8.2 hours post implementation, predominantly as a result of a lower pre-analytical mean TAT reducing from a mean of 18.9 to 1.8 hours. The analytical testing TAT remained unchanged after implementation and monthly test volumes increased by up to 20%. External quality assessment indicated adequate performance. Although subjective, questionnaires sent to facilities reported improved service delivery. CONCLUSION: Establishing CD4 testing in a remote community laboratory substantially reduces overall TAT. Additional community CD4 laboratories should be established in under-serviced areas, especially where laboratory infrastructure is already in place.

Evaluation of different adjuvants for foot-and-mouth disease vaccine containing all the SAT serotypes.

Foot-and-mouth disease (FMD) is an economically important disease of cloven-hoofed animals that is primarily controlled by vaccination of susceptible animals and movement restrictions for animals and animal-derived products in South Africa. Vaccination using aluminium hydroxide gel-saponin (AS) adjuvanted vaccines containing the South African Territories (SAT) serotypes has been shown to be effective both in ensuring that disease does not spread from the endemic to the free zone and in controlling outbreaks in the free zone. Various vaccine formulations containing antigens derived from the SAT serotypes were tested in cattle that were challenged 1 year later. Both the AS and ISA 206B vaccines adjuvanted with saponin protected cattle against virulent virus challenge. The oil-based ISA 206B-adjuvanted vaccine with and without stimulators was evaluated in a field trial and both elicited antibody responses that lasted for 1 year. Furthermore, the ISA 206 adjuvanted FMD vaccine protected groups of cattle against homologous virus challenge at very low payloads, while pigs vaccinated with an emergency ISA 206B-based FMD vaccine containing the SAT 1 vaccine strains were protected against the heterologous SAT 1 outbreak strain.

Very fast (and safe) inactivation of foot-and-mouth disease virus and enteroviruses by a combination of binary ethyleneimine and formaldehyde.

For FMD vaccine production, inactivation of the FMD virus is the most critical step. Formerly, from 1940 onwards, the virus was inactivated with formaldehyde. This inactivation was relatively slow, about 0.2 - 0.3 log 10 per hour. Because formaldehyde not only reacts with the virus produced but with many other components in the medium, such as proteins and amino acids, its concentration can become rate-limiting and inactivation plots may show tailing-off, resulting in residual infectivity. Many of the bad stories of post-vaccination outbreaks date back to the use of formaldehyde-inactivated vaccines (e.g. the outbreaks in France in 1981 and in Eastern Germany causing the Danish outbreak in 1982). Much faster and safer inactivation was obtained with aziridines and in the 1980s binary ethyleneimine (BEI) was introduced in practically all vaccine production laboratories. If inactivation plots are made of every production batch, as is now required by the European Pharmacopoeia, and these plots show proper inactivation rates, vaccines can considered to be completely safe. Under optimal conditions, inactivation rates are in the range of 0.5 - 1.0 log 10 per hour. In general, the inactivation takes 40-48 hours,which will guarantee complete inactivation of all virus particles in a batch. Since formaldehyde (FA), the 'classical' inactivating agent, inactivates at a rate of 0.3 logs per hour only, a significant contribution of FA to the inactivation of BEI can hardly be expected. However, here it is shown that FA added during the BEI-inactivation process strongly augments inactivation rates with a hundred to thousand-times (to 2.5-3.5 logs per hour). This will enable inactivation during a working day or just overnight with even higher safety levels of the vaccines. Also, it is known that formaldehyde cross-links viral proteins which will stabilise the antigen. The short inactivation times will limit proteolytic destruction of 146 S antigen and increase antigen yields. It is expected that by the cross-linking activity of FA the stability of the antigen (and of vaccines) and the endurance of the immune response will be favourably influenced.

Inhibition of the uncoating of bovine enterovirus by short chain fatty acids.

Short chain fatty acids inhibit the replication of bovine enterovirus but are almost ineffective against poliovirus type 1, coxsackievirus B5, encephalomyocarditis virus and human rhinovirus 1B. Lauric acid binds to bovine enterovirus, thereby stabilizing the virus particle to heat degradation. Fatty acid-bound virions attach to susceptible cells but fail to undergo cell-mediated uncoating. The inhibitory effect is reversible with chloroform and may result from a hydrophobic interaction between the fatty acid and a specific site on the virus particle.