Assessing very advanced HIV disease in adolescent girls and young women.

Background: South Africa has the largest HIV epidemic globally, with ~7.5 million people living with HIV in 2021. Adolescent girls (AG) and young women (YW), aged 15-19 years and 20-24 years, are twice as likely to be living with HIV as their male counterparts. The national HIV prevalence for young women was 9.1% (2021), with limited data on disease severity. Objectives: This study assessed very advanced HIV disease (CD4 < 100 cells/µL) in adolescent girls and young women (AGYW) in South Africa. Method: A retrospective descriptive study analysed data collated from the National Health Laboratory Service database for 2017 to 2021 calendar years for AGYW. National and provincial specimen volumes, the percentage of tests with a CD4 < 100 cells/µL and ≥ 100 cells/µL, and the median and interquartile ranges, were calculated. Logistic regression determined the odds ratio for a CD4 < 100 cells/µL, controlling for age category. Results: Data for 1 199 010 CD4 specimens indicated a significant decrease in volumes of 34% from 287 410 (2017) to 189 533 (2021). The percentage of samples with a count < 100 cells/µL ranged from 4.9% to 5.2% for YW versus 5.6% to 6.1% for AG. Provincial data for a CD4 count < 100 cells/µL ranged between 4.5% and 8.3% in AG and 3.6% to 6.3% for YW. Logistic regression indicated a 24% higher likelihood for AG having a CD4 count < 100 cells/µL. Conclusion: The study reported a higher proportion of very advanced HIV disease for AG versus YW nationally, with provincial disparity needing further analysis.

More Than a Decade of GeneXpert®Mycobacterium tuberculosis/Rifampicin (Ultra) Testing in South Africa: Laboratory Insights from Twenty-Three Million Tests.

This study seeks to describe the rollout and current state of South Africa's GeneXpert molecular diagnostic program for tuberculosis (TB). Xpert MTB/RIF was introduced in 2011 with a subsequent expansion to include extra-pulmonary and paediatric testing, followed by Xpert MTB/RIF Ultra in 2017. Through a centralised laboratory information system and the use of a standardised platform for more than a decade, over 23 million tests were analysed, describing the numbers tested, Mycobacterium tuberculosis complex detection, rifampin resistance, and the unsuccessful test rates. The stratification by province, specimen type, age, and sex identified significant heterogeneity across the program and highlighted testing gaps for men, low detection yield for paediatric pulmonary TB, and the effects of inadequate specimen quality on the detection rate. The insights gained from these data can aid in the monitoring of interventions in support of the national TB program beyond laboratory operational aspects.

HIV Viral Load Testing in the South African Public Health Setting in the Context of Evolving ART Guidelines and Advances in Technology, 2013-2022.

HIV viral load (VL) testing plays a key role in the clinical management of HIV as a marker of adherence and antiretroviral efficacy. To date, national and international antiretroviral treatment recommendations have evolved to endorse routine VL testing. South Africa (SA) has recommended routine VL testing since 2004. Progressively, the centralised HIV VL program managed by its National Health Laboratory Service (NHLS) has undergone expansive growth. Retrospective de-identified VL data from 2013 to 2022 were evaluated to review program performance. Test volumes increased from 1,961,720 performed in 2013 to 45,334,864 in 2022. The median total in-laboratory turnaround time (TAT) ranged from 94 h (2015) to 51 h (2022). Implementation of two new assays improved median TATs in all laboratories. Samples of VL greater than 1000 copies/mL declined steadily. Despite initial increases, samples of fewer than 50 copies/mL stagnated at about 70% from 2019 and declined to 68% in 2022. Some variations between assays were observed. Overall, the SA VL program is successful. The scale of the VL program, the largest of its kind in the world by some margin, provides lessons for future public health programs dependent on laboratories for patient outcome and program performance monitoring.

Using laboratory data to assess the impact of coronavirus (COVID-19) on reflex cryptococcal antigenaemia (CrAg) testing in South Africa.

BACKGROUND: Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China. Due to the rapid spread globally, it was declared a pandemic in March 2020. Social distancing and lockdown measures were introduced to limit transmission. These strategies could potentially impact the diagnosis and treatment of patients with advanced HIV who are susceptible to secondary infections like cryptococcal disease. In South Africa, reflexed cryptococcal antigenaemia (CrAg) testing and pre-emptive antifungal treatment are recommended preceding antiretroviral therapy initiation for patients with a CD4<100 cells/µl. This study aimed to assess the impact of COVID-19 on CrAg testing in South Africa. METHODS: Specimen-level data was extracted for individuals ≥15 years from the National Health Laboratory Services repository for calendar years 2018 to 2021. Test volumes and CrAg positivity were assessed at national and provincial levels, by age category and gender. The percentage change in annual and monthly CrAg test volumes for 2020 and 2021 (during lockdown levels) are compared to data reported for 2018. The monthly median CD4 and the percentage of samples with a count <25, 25-50, 51-75 and >75-<100 cells/µl were assessed. RESULTS: Specimen data of 11 944 929 CD4 results included 1 306 456 CrAg tests. Annual CD4 and CrAg test volumes declined by 22.4% and 27.8% for 2020 and 2021 respectively (relative to 2018). There were 23 670 CrAg positive outcomes in 2018 compared to 21 399 (-9.6%) and 17 847 (-24.6%) in 2020 and 2021 respectively. A monthly test volume reduction of up to 36.6%, 35.5%, 36.1% and 13.3% was reported for infection waves one to four. CrAg detection increased from 6.3% in 2018 to 7.5% in 2020. More testing was offered to males (>56%) with a higher detection rate of 8.1% in 2020. Between 81.0% and 81.8% of testing was for patients aged 20 to 49 years. The monthly percentage of specimens <25 cells/µl ranged from 30.2% (June 2019) to 35.3% (August 2020). Overall, the monthly median CD4 ranged from 39 (IQR: 15-70)(August 2020) to 45 (IQR: 19-72)(March 2019) cells/µl. In 2020, the provincial percentage change in CrAg test volumes ranged from 2.9% to -33.7%. CONCLUSION: Our findings confirmed the impact of lockdown measures on both the absolute number of CrAg tests performed and detection (increase in 2020). A smaller impact on the median CD4 was noted. The long-term impact on patient management in immune- compromised individuals needs further investigation.

National Impact of SARS-CoV-2 Infection on HIV Virological Suppression in South Africa.

BACKGROUND: Coronavirus disease (COVID-19) severely disrupted routine health care globally. This study assessed the impact of successive COVID-19 waves on HIV viral load (VL) suppression in South Africa, using the national public sector laboratory database. Guidelines recommend VL monitoring at 6 months after treatment initiation, annually once if suppressed, or more frequently if unsuppressed. METHODS: Specimen-level VL data were extracted for the period January 2019-December 2021. We assessed the national percentage of samples with a VL <50 (virological suppression), 50-999 (low-level viremia), and ≥1000 (viremia) copies/mL. Data were analyzed by calendar year and month. Data for 2019 (pre-COVID-19) were compared with the 2020 and 2021 calendar years (lockdowns imposed). The national number of COVID-19 cases was reported to indicate the wave periods as follows: 1 (ancestral)-June-August 2020; 2 (Beta)-December 2020-January 2021; 3 (Delta)-June-August 2021, and 4 (Omicron)-December 2021. RESULTS: Data are reported for 17,460,264 samples, with 5,608,733, 5,840,056, and 6,011,475 tests performed in 2019, 2020, and 2021 respectively. Overall, a VL of <50, 50-999, and ≥1000 copies/mL were reported for 69.4%, 17.3%, and 13.4% of samples, respectively. A VL <50 copies/mL was reported for 67.7%, 70.3%, and 70.0% of patients in 2019, 2020, and 2021, respectively. For the 2020 and 2021 calendar years, the monthly percentage of patients with a VL <50 copies/mL ranged between 64.6% and 72.7%. CONCLUSION: Our findings indicate that COVID-19 has not had a substantial impact on the percentage of samples with virological suppression at the national level.

Diabetic control and compliance using glycated haemoglobin (HbA1C) testing guidelines in public healthcare facilities of Gauteng province, South Africa.

OBJECTIVE: This study aimed at evaluating diabetic control and compliance with testing guidelines, across healthcare facilities of Gauteng Province, South Africa, as well as factors associated with time to achieve control. South Africa's estimated total unmet need for care for patients with type 2 diabetes mellitus is 80%. RESEARCH DESIGN, METHODS AND FINDINGS: The data of 511 781 patients were longitudinally evaluated. Results were reported by year, age category, race, sex, facility and test types. HbA1C of ≤7% was reported as normal, >7 - ≤9% as poor control and >9% as very poor control. The chi-squared test was used to assess the association between a first-ever HbA1C status and variables listed above. The Kaplan-Meier analysis was used to assess probability of attaining control among those who started with out-of-control HbA1C. The extended Cox regression model assessed the association between time to attaining HbA1C control from date of treatment initiation and several covariates. We reported hazard ratios, 95% confidence intervals and p-values. Data is reported for 511 781 patients with 705 597 laboratory results. Poorly controlled patients constituted 51.5%, with 29.6% classified as very poor control. Most poorly controlled patients had only one test over the entire study period. Amongst those who started with poor control status and had at least two follow-up measurements, the likelihood of achieving good control was higher in males (adjusted Hazard Ratio (aHR) = 1.16; 95% CI:1.12-1.20; p<0.001) and in those attending care at hospitals (aHR = 1.99; 95% CI:1.92-2.06; p<0.001). CONCLUSION: This study highlights poor adherence to guidelines for diabetes monitoring.

Appropriateness of laboratory expenditure for primary health care facilities across South Africa.

BACKGROUND: Primary health care (PHC) services have been prioritised from a cost-containment perspective. To manage expenditure, facility managers use the Laboratory Handbook that indicates the Essential Laboratory List (ELL) tests. AIM: The aim of this study was to analyse PHC laboratory expenditure to assess the impact of the ELL in South Africa. SETTING: We reported ELL compliance at the national, provincial and health district levels. METHODS: A retrospective cross-sectional study was used to analyse data for the 2019 calendar year. The unique tariff code descriptions were used to develop a lookup table to identify ELL compliant testing. Researchers analysed data for the human immunodeficiency virus (HIV) conditional grant tests and by facility for the bottom two districts. RESULTS: There were 356 497 tests (1.3%) that were not ELL compliant that equated to an expenditure of $2.4 million. Essential Laboratory List compliance ranged from 97.9% to 99.2% for clinics, community healthcare centres and community day centres. The provincial ELL compliance ranged from 97.6% for the Western Cape to 99.9% for the Mpumalanga province. The average cost per ELL test was $7.92. At the district level, ELL compliance ranged from 93.4% for Central Karoo to 100% for Ehlanzeni. CONCLUSIONS: High levels of ELL compliance have been demonstrated from the national to the health district level, demonstrating the value of the ELL.Contribution: This study provides data for quality improvement initiatives at primary care facilities.

Modelling CD4 reagent usage across a national hierarchal network of laboratories in South Africa.

Background: The National Health Laboratory Service is mandated to deliver cost-effective and efficient diagnostic services across South Africa. Their mandate is achieved by a network of laboratories ranging from centralised national laboratories to distant rural facilities. Objective: This study aimed to establish a model of CD4 reagent utilisation as an independent measure of laboratory efficiency. Methods: The efficiency percentage was defined as finished goods (number of reportable results) over raw materials (number of reagents supplied) for 47 laboratories in nine provinces (both anonymised) for 2019. The efficiency percentage at national and provincial levels was calculated and compared to the optimal efficiency percentage derived using pre-set assumptions. Comparative laboratory analysis was conducted for the provinces with the best and worst efficiency percentages. The possible linear relationship between the efficiency percentage and call-outs, days lost, referrals, and turn-around time was assessed. Results: Data are reported for 2 806 799 CD4 tests, with an overall efficiency percentage of 84.5% (optimal of 84.98%). The efficiency percentage varied between 75.7% and 87.7% between provinces, while within the laboratory it ranged from 66.1% to 111.5%. Four laboratories reported an efficiency percentage ranging from 67.8% to 85.7%. No linear correlation was noted between the efficiency percentage, call-outs, days lost, and turn-around time performance. Conclusion: Reagent efficiency percentage distinguished laboratories into different utilisation levels irrespective of their CD4 service level. This parameter is an additional independent indicator of laboratory performance, with no relationship with any contributing factors tested, that can be implemented across pathology disciplines for monitoring reagent utilisation. What this study adds: This study provides an objective methodology to assess reagent utilisation as an independent measure of laboratory efficiency. This model could be applied to all routine pathology services.

Assessing the cost and utilization of SMS printers by primary health care facilities: lessons learned from South Africa.

Background: Historically, paper-based laboratory reports were delivered by couriers to health facilities resulting in post-analytical delays. As a result, short message service (SMS) printers were deployed to fill this gap, with the global data service platform (GDSP) being primarily used to facilitate deployment. In addition, these printers generate binary and quantitative information that can be used to assess utilization. Objective: The objective of this study was to determine the costs and utilization of the SMS printer program in South Africa. Methods: A cost analysis for 2020 was undertaken. We determined annual equivalent costs (AEC) for staffing, printers, fixed costs related to the national coordinator, consumables, travel costs, database support/hosting/dashboard development, printer repairs, and results transmission. The main outcome of interest was the cost per SMS printer result delivered. Data were extracted to assess utilization as follows: i) months active (based on internet protocol data); ii) signal; iii) battery strength. Results: There were 4,450,116 results delivered to printers that were situated at 2232 primary health care facilities. An AEC of $687,727 was reported, with a cost per result delivered of $0.1618. The SMS printers contributed 73.52% to the total AEC. Overall, 90% of the printers were GDSP based, of which only 69.5% were determined to be active. The majority of active printers reported a signal strength of ≥60% and a battery strength of ≥6 volts. Conclusion: Although the SMS printer program has the potential to reduce post-analytical delays, pathology services should migrate to an end-to-end electronic interface to improve patient care.

Optimising courier specimen collection time improves patient access to HIV viral load testing in South Africa.

Background: South Africa uses a courier network for transporting specimens to public laboratories. After the daily collection of specimens from the facility by the courier, patients not yet attended to are unlikely to receive same-day blood draws, potentially inhibiting access to viral load (VL) testing for HIV patients. Objective: We aimed to design an optimised courier network and assess whether this improves VL testing access. Methods: We optimised the specimen transport network in South Africa for 4046 facilities (November 2019). For facilities with current specimen transport times (n = 356), we assessed the relationship between specimen transport time and VL testing access (number of annual VL tests per antiretroviral treatment patient) using regression analysis. We compared our optimised transport times with courier collection times to determine the change in access to same-day blood draws. Results: The number of annual VL tests per antiretroviral treatment patient (1.14, standard deviation: 0.02) was higher at facilities that had courier collection after 13:36 (the average latest collection time) than those that had their last collection before 13:36 (1.06, standard deviation: 0.03), even when adjusted for facility size. Through network optimisation, the average time for specimen transport was delayed to 14:35, resulting in a 6% - 13% increase in patient access to blood draws. Conclusion: Viral load testing access depends on the time of courier collection at healthcare facilities. Simple solutions are frequently overlooked in the quest to improve healthcare. We demonstrate how simply changing specimen transportation timing could markedly improve access to VL testing.

Cost of running a full-service receiving office at a centralised testing laboratory in South Africa.

Background: The National Health Laboratory Service operates a platform of 226 laboratories across South Africa, ranging from highly sophisticated central academic hospitals to distant rural hospitals. The core function of the National Health Laboratory Service is to provide cost-effective and efficient health laboratory services in the public healthcare sector. Objective: This study aimed to assess the comprehensive cost of running a full-service receiving office (RO) at the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) laboratory. Methods: Top-down costing was conducted, with the cost per registration as the main outcome of interest. The annual equivalent costs (AEC) for the following categories were determined: registration materials, collection materials, staffing, laboratory equipment, building and electricity, and other operating costs. Data for the period from 01 April 2019 to 31 March 2020 were included in the analyses. Results: The AEC was $1 657 483.00 United States dollars (USD) and the cost per registration was $0.766 USD. Staff contributed 59.9% of the total cost per registration, while collection materials contributed 21.4%. The RO core staff (data clerks) contributed 50.8% of the total staffing costs, while messengers and drivers contributed 31.2%. The introduction of order entry at the CMJAH and other primary healthcare facilities reduced the total AEC by 20%. A single order entry application would serve both the CMJAH and primary healthcare facilities - hence we would prefer to not refer to order entries. Conclusion: Providing a comprehensive RO service costs approximately $1.00 USD per registration. The implementation of order entry at the CMJAH would reduce AECs substantially and improve efficiency.

Newly implemented community CD4 service in Tshwaragano, Northern Cape province, South Africa, positively impacts result turn-around time.

Background: The Northern Cape is South Africa's largest province with an HIV prevalence of 7.1% versus a 13.5% national prevalence. CD4 testing is provided at three of five National Health Laboratory Service district laboratories, each covering a 250 km precinct radius. Districts without a local service report prolonged CD4 turn-around times (TAT). Objective: This study documented the impact of a new CD4 laboratory in Tshwaragano in the remote John Taolo Gaetsewe district of the Northern Cape, South Africa. Methods: CD4 test volumes and TAT (total, pre-analytical, analytical, and post-analytical) data for the Northern Cape province were extracted for June 2018 to October 2019. The percentage of CD4 results within the stipulated 40-h TAT cut-off and the median and 75th percentiles of all TAT parameters were calculated. Pre-implementation, samples collected at Tshwaragano were referred to Kimberley or Upington, Northern Cape, South Africa. Results: Pre-implementation, 95.4% of samples at Tshwaragano were referred to Kimberley for CD4 testing (36.3% of Kimberley's test volumes). Only 7.5% of Tshwaragano's total samples were referred post-implementation. The Tshwaragano laboratory's CD4 median total TAT decreased from 24.7 h pre-implementation to 12 h post-implementation (p = 0.003), with > 95.0% of results reported within 40 h. The Kimberley laboratory workload decreased by 29.0%, and testing time significantly decreased from 10 h to 4.3 h. Conclusion: The new Tshwaragano CD4 service significantly decreased local TAT. Upgrading existing community laboratories to include CD4 testing can alleviate provincial service load and improve local access, TAT and efficiency in the centralised reference laboratory.

Assessing CD4 rejections across a national laboratory service for 2018 in South Africa: highlighting the importance of adherence to national handbook guidelines.

The National Health Laboratory Service as the preferred pathology service provider for the public health sector in South Africa, developed a national laboratory handbook to improve the clinic-laboratory-interface. A separate primary health care laboratory handbook was developed as part of the ideal clinic initiative by the National Department of Health. This study aimed to assess adherence to these guidelines using CD4 rejections the indicator. The retrospective crosssectional study design was used to analyse national laboratory data for the period from January to December 2019. Data were analysed using SAS 9.4. Lookup tables assigned the origin (health facility/laboratory), rejection reason, and sub-reason based on the populated rejection description that was captured in the laboratory information system. The rejection rate [RR = (rejections/total volume) ´ 100] was reported at the national, provincial and district levels. There were 85,378 rejections reported for 2,844,242 tests (RR 3.0%). Data was reported for 4136 health facilities across nine provinces. The RR was higher for an origin defined as health facility (2.9%) than laboratories (0.1%). The most common rejection reason was unsuitable specimen received (RR=2.3%), representing 75% of all rejections. This rejection criteria included using the incorrect anticoagulant, clotted sample and haemolysis. The provincial RR ranged from 2.2% to 4.0%. Three districts had an elevated RR ≥6% (organisational cut-off set at RR ≤5%). This study demonstrated the value of laboratory data to assess specimen rejections and identify causes to facilitate targeted training.

Retrospective analysis to describe trends in first-ever prostate-specific antigen (PSA) testing for primary healthcare facilities in the Gauteng Province, South Africa, between 2006 and 2016.

OBJECTIVES: The objective of our study was to use laboratory data to describe prostate-specific antigen (PSA) testing trends for primary healthcare (PHC) services from a single province. PHC is a basic package of services offered to local communities, serving as the first point of contact within the health system. These services are offered at clinics and community health centres (CHC), the latter providing additional maternity, accident and emergency services. DESIGN: The retrospective descriptive study design was used. METHODS: We analysed national laboratory data between 2006 and 2016 for men ≥30 years in the Gauteng Province. We used the probabilistic matching algorithm to create first-ever PSA cohort. We used the hot-deck imputation to assign missing race group values and the district health information system facility descriptors to identify PHC testing. We reported patient numbers by calendar year, age category and race group as well as descriptive statistics. We used multivariable logistic regression to assess any association for race group and age with a PSA ≥4 µg/L. RESULTS: Between 2006 and 2016, numbers of men tested increased from 1782 to 67 025, respectively, with 186 984/239 506 (78.1%) tests were from clinics. The majority of testing was for men in the 50-59 age category (31.5%) and Black Africans (86.4%). We reported a median of 0.9 µg/L that increased with age. A PSA ≥4 µg/L was reported for 11.7% of men, increasing to 35.5% for the ≥70 age category. The logistic regression reported that the adjusted odds of having a PSA ≥4 µg/L was significantly lower for Indian/Asians, multiracials and whites than for Black Africans (p value<0.0001). CONCLUSIONS: Our study has shown a marked increase in PSA testing from clinics and CHC suggestive of screening for prostate cancer. The approaches reported in this study can be extended for national data.

Factors influencing the high rejection rates of HIV 1/2 serology samples at Charlotte Maxeke Johannesburg Academic Hospital and the cost implications.

BACKGROUND: HIV enzyme-linked immunosorbent assay (ELISA) is one of the most requested test sets within Virology and forms an essential part of patient management. Assessment of the rejection criteria is a key quality indicator, crucial for improving laboratory services and efficiency to ensure accurate and reliable results. OBJECTIVES: The aim of this study was to identify the factors that influence the HIV 1/2 serology rejection rates (RR) at Charlotte Maxeke Johannesburg Academic Hospital and to evaluate the associated costs. METHODS: A retrospective study was conducted (June to December 2019) to identify the RR and rejection criteria of HIV serology samples throughout the total testing process. Descriptive analysis using percentages and frequencies was used to analyse the RR by phase, health establishment, ward and healthcare professional. A cost analysis incorporating minor and major costs was modelled in each phase of testing, and the total cost of rejections was calculated. RESULTS: A total of 6678 tests were received, and 738 were rejected (RR = 11.1%). The pre-analytical phase contributed significantly to the overall RR, with the requirement of a separate sample (57.44%) the most common reason for rejection. The total cost per rejected test was $2.47, which amounted to a total rejection cost of $197.55, of which $158.18 was caused by the pre-analytical rejection criteria. CONCLUSION: High RR of HIV tests were noted, resulting in significant cost wastage. Identification and analysis of rejections must be implemented across all laboratories to improve the efficiency of testing, provide a cost-saving benefit and maintain high laboratory standards.

Establishing the cost of Xpert MTB/RIF mobile testing in high-burden peri-mining communities in South Africa.

BACKGROUND: Globally, tuberculosis remains a major cause of mortality, with an estimated 1.3 million deaths per annum. The Xpert MTB/RIF assay is used as the initial diagnostic test in the tuberculosis diagnostic algorithm. To extend the national tuberculosis testing programme in South Africa, mobile units fitted with the GeneXpert equipment were introduced to high-burden peri-mining communities. OBJECTIVE: This study sought to assess the cost of mobile testing compared to traditional laboratory-based testing in a peri-mining community setting. METHODS: Actual cost data for mobile and laboratory-based Xpert MTB/RIF testing from 2018 were analysed using a bottom-up ingredients-based approach to establish the annual equivalent cost and the cost per result. Historical cost data were obtained from supplier quotations and the local enterprise resource planning system. Costs were obtained in rand and reported in United States dollars (USD). RESULTS: The mobile units performed 4866 tests with an overall cost per result of $49.16. Staffing accounted for 30.7% of this cost, while reagents and laboratory equipment accounted for 20.7% and 20.8%. The cost per result of traditional laboratory-based testing was $15.44 US dollars (USD). The cost for identifying a tuberculosis-positive result using mobile testing was $439.58 USD per case, compared to $164.95 USD with laboratory-based testing. CONCLUSION: Mobile testing is substantially more expensive than traditional laboratory services but offers benefits for rapid tuberculosis case detection and same-day antiretroviral therapy initiation. Mobile tuberculosis testing should however be reserved for high-burden communities with limited access to laboratory testing where immediate intervention can benefit patient outcomes.

Using text mining techniques to extract prostate cancer predictive information (Gleason score) from semi-structured narrative laboratory reports in the Gauteng province, South Africa.

BACKGROUND: Prostate cancer (PCa) is the leading male neoplasm in South Africa with an age-standardised incidence rate of 68.0 per 100,000 population in 2018. The Gleason score (GS) is the strongest predictive factor for PCa treatment and is embedded within semi-structured prostate biopsy narrative reports. The manual extraction of the GS is labour-intensive. The objective of our study was to explore the use of text mining techniques to automate the extraction of the GS from irregularly reported text-intensive patient reports. METHODS: We used the associated Systematized Nomenclature of Medicine clinical terms morphology and topography codes to identify prostate biopsies with a PCa diagnosis for men aged > 30 years between 2006 and 2016 in the Gauteng Province, South Africa. We developed a text mining algorithm to extract the GS from 1000 biopsy reports with a PCa diagnosis from the National Health Laboratory Service database and validated the algorithm using 1000 biopsies from the private sector. The logical steps for the algorithm were data acquisition, pre-processing, feature extraction, feature value representation, feature selection, information extraction, classification, and discovered knowledge. We evaluated the algorithm using precision, recall and F-score. The GS was manually coded by two experts for both datasets. The top five GS were reported, with the remaining scores categorised as "Other" for both datasets. The percentage of biopsies with a high-risk GS (≥ 8) was also reported. RESULTS: The first output reported an F-score of 0.99 that improved to 1.00 after the algorithm was amended (the GS reported in clinical history was ignored). For the validation dataset, an F-score of 0.99 was reported. The most commonly reported GS were 5 + 4 = 9 (17.6%), 3 + 3 = 6 (17.5%), 4 + 3 = 7 (16.4%), 3 + 4 = 7 (14.7%) and 4 + 4 = 8 (14.2%). For the validation dataset, the most commonly reported GS were: (i) 3 + 3 = 6 (37.7%), (ii) 3 + 4 = 7 (19.4%), (iii) 4 + 3 = 7 (14.9%), (iv) 4 + 4 = 8 (10.0%) and (v) 4 + 5 = 9 (7.4%). A high-risk GS was reported for 31.8% compared to 17.4% for the validation dataset. CONCLUSIONS: We demonstrated reliable extraction of information about GS from narrative text-based patient reports using an in-house developed text mining algorithm. A secondary outcome was that late presentation could be assessed.

Preparing for the next pandemic: Lessons from rapid scale-up of SARS-CoV-2 testing in a South African high-throughput automated HIV molecular laboratory.

Africa's readiness to respond to the SARS-COV-2 pandemic was tested due to reliance on rapid turn-around-time of polymerase chain reaction results for clinical management, isolation and quarantine decisions. The NHLS HIV Molecular Laboratory in Johannesburg, South Africa, is one of the largest automated HIV molecular laboratories worldwide. Despite its extensive molecular capacity and experience in managing high volumes acquired from a large HIV program, significant challenges were encountered during its rapid transition to large scale SARS-CoV-2 testing. We describe the strategies employed to manage these challenges that resulted in a 30% improvement in SARS-CoV-2 test turn-around-time during the first wave peak during which approximately 25000 samples were tested per month, and further improvement during the second wave peak, with 81% within targeted turn-around-time.

Using Systematized Nomenclature of Medicine clinical term codes to assign histological findings for prostate biopsies in the Gauteng province, South Africa: Lessons learnt.

BACKGROUND: Prostate cancer (PCa) is a leading male neoplasm in South Africa. OBJECTIVE: The aim of our study was to describe PCa using Systemized Nomenclature of Medicine (SNOMED) clinical terms codes, which have the potential to generate more timely data. METHODS: The retrospective study design was used to analyse prostate biopsy data from our laboratories using SNOMED morphology (M) and topography (T) codes where the term 'prostate' was captured in the narrative report. Using M code descriptions, the diagnosis, sub-diagnosis, sub-result and International Classification of Diseases for Oncology (ICD-O-3) codes were assigned using a lookup table. Topography code descriptions identified biopsies of prostatic origin. Lookup tables were prepared using Microsoft Excel and combined with the data extracts using Access. Contingency tables reported M and T codes, diagnosis and sub-diagnosis frequencies. RESULTS: An M and T code was reported for 88% (n = 22 009) of biopsies. Of these, 20 551 (93.37%) were of prostatic origin. A benign diagnosis (ICD-O-3:8000/0) was reported for 10 441 biopsies (50.81%) and 45.26% had a malignant diagnosis (n = 9302). An adenocarcinoma (8140/3) sub-diagnosis was reported for 88.16% of malignant biopsies (n = 8201). An atypia diagnosis was reported for 760 biopsies (3.7%). Inflammation (39.03%) and hyperplasia (20.82%) were the predominant benign sub-diagnoses. CONCLUSION: Our study demonstrated the feasibility of generating PCa data using SNOMED codes from national laboratory data. This highlights the need for extending the results of our study to a national level to deliver timeous monitoring of PCa trends.

Mining laboratory data to describe prostate specific antigen testing and prostate cancer in Johannesburg, South Africa.

INTRODUCTION: guidelines issued by different organizations worldwide differ on the use of prostate specific antigen (PSA) in prostate cancer. However, no local data is available describing how PSA testing is offered by our healthcare facilities in the country. The objectives of this study were to describe PSA testing and subsequent prostate biopsy uptake in a South African urban population. METHODS: this was a descriptive retrospective study. Data of all PSA tests and prostate biopsies performed at Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) laboratory for 2013 calendar year was extracted from the laboratory information system. RESULTS: a total of 20 365 PSA tests were performed on 17 481 men during the study period. The majority of men were Black African (79%). The mean age for Black Africans (55.5 years, SD 13.3) was significantly lower than other racial groups (62.9 years, SD 12.6, p < 0.0005). PSA level was lower in Black Africans compared to others. Prostate biopsy uptake across all age groups was lower in Black African men compared to others (2% versus 4%, p = 0.01). Of the 423 men who had a prostate biopsy, 50% had prostate cancer. More Black African men were diagnosed with prostate cancer on biopsy compared to men of other racial groups (54% versus 43%, p = 0.03). CONCLUSION: our study confirms that PSA testing is prevalent in healthcare facilities in South Africa. Black African men are tested for PSA levels but have low biopsy uptake and are more likely to be diagnosed with prostate cancer.