National Health Laboratory Service Research Articles

Assessing compliance with national guidelines in diabetes care: A study leveraging data from south Africa's National Health Laboratory Service (NHLS).

Diabetes is a major global health issue. We evaluated compliance to laboratory-based management guidelines for diabetes (type 1 and 2), essential for effective treatment and reducing diabetes-related morbidity and mortality. Our study utilized South Africa's National Health Laboratory Services (NHLS) data, focusing on patients from birth to age 80 years who underwent initial diabetes laboratory testing between January 1, 2012-January 1, 2016. Patients were categorized into type 1 (<30 years) or type 2 (≥30-80 years) diabetes based on age at first diabetes test. National diabetes guidelines recommend blood glucose to be checked every three-six months post laboratory-diagnosis. We employed a sharp regression discontinuity design to estimate the effect of a laboratory-diagnosis of diabetes on the likelihood of having a follow-up laboratory test 24 months post-diagnosis. Among patients with type 2 diabetes, the probability of a diabetes follow-up laboratory test within 24 months was 52.4% for patients presenting above the diabetes diagnosis threshold vs 31.1% for those presenting below. Although the likelihood of repeat testing rose with higher HbA1c and glucose levels, at the diagnostic threshold there was no clinically meaningful difference (risk difference: -2.2%, 95% CI: -3.3%, -1.2%). These results were consistent among patients with type 1 diabetes, those living with and without HIV, and healthcare setting. In a national laboratory cohort, diabetes laboratory-diagnosis did not lead to increased monitoring as recommended in national guidelines. Strategies to improve patient education, healthcare provider communication, and healthcare system support are essential to enhance guideline compliance and overall diabetes management.

Long-term effect of pneumococcal conjugate vaccines on invasive pneumococcal disease incidence among people of all ages from national, active, laboratory-based surveillance in South Africa, 2005–19: a cohort observational study

In South Africa, 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2009 and 13-valent PCV (PCV13) was introduced in 2011, both in a two plus one schedule. We evaluated the ongoing effects of PCV on the prevention of invasive pneumococcal disease (IPD) over 15 years of sustained surveillance in South Africa before the COVID-19 pandemic. We conducted national, active, laboratory-based surveillance for IPD among all ages in South Africa, including isolate serotyping and susceptibility testing. We fitted linear regression models with vaccine covariates to imputed IPD case counts each year by serotype and age to compare expected and actual IPD cases in 2019, which was the main outcome. Vaccine effects were set to zero to identify expected incidence after the introduction of PCV7 and PCV13. From Jan 1, 2005, to Dec 31, 2019, surveillance identified 52 957 IPD cases. Among the 50 705 individuals with age data available, 9398 (18·5%) were infants aged younger than 2 years. Compared with expected case numbers (no vaccination) predicted using all available data, overall IPD rates among children younger than 2 years declined by 76·0% (percentage risk difference; 95% CI -79·0 to -72·8%) in 2019; notably, PCV7 and additional PCV13 serotype IPD rates declined by 95·5% (-97·0 to -93·4%) and 93·8% (-96·2 to-90·5%), respectively, whereas non-vaccine serotypes (NVTs) did not change significantly. Among adults aged 25-44 years, overall IPD declined by 50·4% (-54·2 to -46·3%), and PCV7 and additional PCV13 serotype IPD rates declined by 86·1% (-88·7 to -83·1%) and 77·2% (-80·9 to -73·0%), respectively, whereas NVTs increased by 78·5% (56·8 to 103·4%). Individuals aged older than 64 years also benefited from declines in IPD (-30·2%; -41·9 to -16·2%), but NVTs increased (234·9%; 138·1 to 379·4%). We documented sustained direct and indirect benefits of PCV across age groups, and NVT increases in adults older than 24 years. Higher valency PCVs would have the added benefit of preventing this residual disease. National Institute for Communicable Diseases of the National Health Laboratory Service (South Africa) and US Agency for International Development Antimicrobial Resistance Initiative, US Centers for Disease Control and Prevention.

Prevalence and progression of chronic kidney disease among adults undergoing creatinine testing in South African public healthcare facilities: a study leveraging data from South Africa’s National Health Laboratory Service (NHLS)

BackgroundChronic kidney disease (CKD) has emerged as a substantial global health challenge, with a marked rise in associated mortality. However, it often goes undetected until advanced stages, particularly in low-income...

Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.

The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information. We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This offers us with a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach. The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data. The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective tool for deterministic linking in health data, and may provide a method of creating large, linked data sets without compromising patient confidentiality.

Breast cancer in women by HIV status: A report from the South African National Cancer Registry.

Breast cancer (BC) is the leading cause of cancer-related morbidity and mortality in women living in South Africa, a country with a high HIV burden. However, characteristics of the double burden of HIV and BC in South Africa have not been properly investigated. We described characteristics of BC cases by HIV status in South Africa. In this nationwide South African study, we obtained BC records for women aged ≥15 years diagnosed in the public health sector between January 2004 and December 2014. We included records from the National Cancer Registry that had been linked to HIV-related laboratory records from the National Health Laboratory Service. We assessed the odds of being HIV positive versus HIV negative in relation to patient-, cancer-, and municipality-related characteristics. From 2004-2014, 40 520 BC cases were diagnosed in women aged ≥15 years. Of these, 73.5% had unknown HIV status, 18.7% were HIV negative, and 7.7% were HIV positive. The median age at BC diagnosis was 43 years (interquartile range [IQR]: 37-52) in HIV positive and 57 years (IQR: 46-68) in HIV negative women, respectively. The odds of being HIV positive was higher for women who were aged 30-34 years compared to women aged 35-39 years at cancer diagnosis (odds ratio [OR] 1.38, 95% confidence interval [CI] 1.10-1.71), Black versus non-Black (OR 6.41, 95% CI 5.68-7.23), diagnosed with cancer in rural versus urban areas (OR 1.59, 95% CI 1.40-1.82) and diagnosed in municipalities with low and middle (OR 3.46, 95% CI 2.48-4.82) versus high socioeconomic position (OR 2.69, 95% CI 2.11-3.42). HIV status was unknown for the majority of BC patients. Among those with known HIV status, being HIV positive was associated with a younger age at cancer diagnosis, being Black and receiving care in municipalities of poor socioeconomic position. Future studies should examine opportunities to integrate HIV and BC control programs.

Determinants of sub-optimal glycemic control among patients enrolled in a medicine dispensing programme in KwaZulu-Natal: A cohort study, 2018-2021.

The Central Chronic Medicines Dispensing and Distribution (CCMDD) programme facilitates clinically stable patients to collect their chronic medication from community-based pick-up points. We determined baseline glycaemic control and rates and predictors of becoming sub-optimally controlled for type 2 diabetes mellitus (T2DM) CCMDD-enrolled patients. The setting of the study was eThekwini, KwaZulu-Natal, South Africa. We performed a cohort study (April 2018- December 2021). We linked T2DM CCMDD-enrolled patients to glycated haemoglobin (HbA1c) data from the National Health Laboratory Service. We selected patients optimally controlled at their baseline HbA1c, with ≥ 1 repeat-test available. We used Kaplan-Meier analysis to assess survival rates and extended Cox regression to determine associations between time to sub-optimal control (HbA1c 7%) and predictors. Adjusted hazard ratios (aHRs), 95% confidence interval (CI), andp-values are reported. Of the 41145 T2DM patients enrolled in the CCMDD programme, 7960 (19%) had a HbA1c result available. Twenty-seven percent (2147/7960) were optimally controlled at their baseline HbA1c. Of those controlled at baseline, 695 (32%) patients had a repeat test available, with 35% (242/695) changing to sub-optimal status. The HbA1c testing frequency as per national guidelines was associated with a lower hazard of sub-optimal glycaemic control (aHR: 0.46; 95% CI: 0.24-0.91;p-value = 0.024). Patients prescribed dual-therapy had a higher hazard of sub-optimal glycaemic control (aHR: 1.50; 95% CI: 1.16-1.95;p-value = 0.002) versus monotherapy. The HbA1c monitoring, in-line with testing frequency guidelines, is needed to alert the CCMDD programme of patients who become ineligible for enrolment. Patients receiving dual-therapy require special consideration.Contribution:Addressing identified shortfalls can assist programme implementation.

Geospatial and temporal mapping of detectable HIV-1 viral loads amid dolutegravir rollout in KwaZulu-Natal, South Africa.

South Africa rolled out dolutegravir (DTG) as first-line antiretroviral therapy (ART) in December 2019 to overcome high rates of pretreatment non-nucleoside reverse transcriptase inhibitor drug resistance. In the context of transition to DTG-based ART, this study spatiotemporally analysed detectable HIV viral loads (VLs) prior to- and following DTG rollout in public-sector healthcare facilities in KwaZulu-Natal (KZN) province, the epicentre of the HIV epidemic in South Africa. We retrospectively curated a HIV VL database using de-identified routine VL data obtained from the National Health Laboratory Service for the period January 2018 to June 2022. We analysed trends in HIV viraemia and mapped median log10 HIV VLs per facility on inverse distance weighted interpolation maps. We used Getis-Ord Gi* hotspot analysis to identify geospatial HIV hotspots. We obtained 7,639,978 HIV VL records from 736 healthcare facilities across KZN, of which 1,031,171 (13.5%) had detectable VLs (i.e., VLs ≥400 copies/millilitre (mL)). Of those with detectable VLs, we observed an overall decrease in HIV VLs between 2018 and 2022 (median 4.093 log10 copies/mL; 95% confidence interval (CI) 4.087-4.100 to median 3.563 log10 copies/mL; CI 3.553-3.572), p<0.01 (median test). The downward trend in proportion of HIV VLs ≥1000 copies/mL over time was accompanied by an inverse upward trend in the proportion of HIV VLs between 400 and 999 copies/mL. Moreover, specific coastal and northern districts of KZN had persistently higher VLs, with emergent hotspots demonstrating spatial clustering of high median log10 HIV VLs. The overall decrease in HIV VLs over time shows good progress towards achieving UNAIDS 95-95-95 targets in KZN, South Africa. The DTG-transition has been associated with a reduction in VLs, however, there is a need for pre-emptive monitoring of low-level viraemia. Furthermore, our findings highlight that specific districts will need intensified HIV care despite DTG rollout.

Hypervirulent Klebsiella pneumoniae in a South African tertiary hospital—Clinical profile, genetic determinants, and virulence in Caenorhabditis elegans

IntroductionA distinct strain of Klebsiella pneumoniae (K. pneumoniae) referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in K. pneumoniae isolates from one of the largest tertiary hospitals in a South African province.MethodsA total of 74 K. pneumoniae isolates were received from Pelonomi Tertiary Hospital National Health Laboratory Service (NHLS), Bloemfontein. Virulence-associated genes (rmpA, capsule serotype K1/K2, iroB and irp2) were screened using Polymerase Chain Reaction (PCR). The iutA (aerobactin transporter) gene was used as a primary biomarker of hvKp. The extracted DNAs were sequenced using the next-generation sequencing pipeline and the curated sequences were used for phylogeny analyses using appropriate bioinformatic tools. The virulence of hvKp vs. classical Klebsiella pneumoniae (cKp) was investigated using the Caenorhabditis elegans nematode model.ResultsNine (12.2%) isolates were identified as hvKp. Moreover, hvKp was significantly (p &amp;lt; 0.05) more virulent in vivo in Caenorhabditis elegans relative to cKp. The virulence-associated genes [rmpA, iroB, hypermucoviscous phenotype (hmv) phenotype and capsule K1/K2] were significantly (p &amp;lt; 0.05) associated with hvKp. A homology search of the curated sequences revealed a high percentage of identity between 99.8 and 100% with other homologous iutA gene sequences of other hvKp in the GenBank.ConclusionFindings from this study confirm the presence of hvKp in a large tertiary hospital in central South Africa. However, the low prevalence and mild to moderate clinical presentation of infected patients suggest a marginal threat to public health. Further studies in different settings are required to establish the true potential impact of hvKp in developing countries.

Attrition Rates in HIV Viral Load Monitoring and Factors Associated With Overdue Testing Among Children Within South Africa's Antiretroviral Treatment Program: Retrospective Descriptive Analysis.

Numerous studies in South Africa have reported low HIV viral load (VL) suppression and high attrition rates within the pediatric HIV treatment program. Using routine laboratory data, we evaluated HIV VL monitoring, including mobility and overdue VL (OVL) testing, within 5 priority districts in South Africa. We performed a retrospective descriptive analysis of National Health Laboratory Service (NHLS) data for children and adolescents aged 1-15 years having undergone HIV VL testing between May 1, 2019, and April 30, 2020, from 152 facilities within the City of Johannesburg, City of Tshwane, eThekwini, uMgungundlovu, and Zululand. HIV VL test-level data were deduplicated to patient-level data using the NHLS CDW (Corporate Data Warehouse) probabilistic record-linking algorithm and then further manually deduplicated. An OVL was defined as no subsequent VL determined within 18 months of the last test. Variables associated with the last VL test, including age, sex, VL findings, district type, and facility type, are described. A multivariate logistic regression analysis was performed to identify variables associated with an OVL test. Among 21,338 children and adolescents aged 1-15 years who had an HIV VL test, 72.70% (n=15,512) had a follow-up VL test within 18 months. Furthermore, 13.33% (n=2194) of them were followed up at a different facility, of whom 3.79% (n=624) were in a different district and 1.71% (n=281) were in a different province. Among patients with a VL of ≥1000 RNA copies/mL of plasma, the median time to subsequent testing was 6 (IQR 4-10) months. The younger the age of the patient, the greater the proportion with an OVL, ranging from a peak of 52% among 1-year-olds to a trough of 21% among 14-year-olds. On multivariate analysis, 2 consecutive HIV VL findings of ≥1000 RNA copies/mL of plasma were associated with an increased adjusted odds ratio (AOR) of having an OVL (AOR 2.07, 95% CI 1.71-2.51). Conversely, patients examined at a hospital (AOR 0.86, 95% CI 0.77-0.96), those with ≥2 previous tests (AOR 0.78, 95% CI 0.70-0.86), those examined in a rural district (AOR 0.63, 95% CI 0.54-0.73), and older age groups of 5-9 years (AOR 0.56, 95% CI 0.47-0.65) and 10-14 years (AOR 0.51, 95% CI 0.44-0.59) compared to 1-4 years were associated with a significantly decreased odds of having an OVL test. Considerable attrition occurs within South Africa's pediatric HIV treatment program, with over one-fourth of children having an OVL test 18 months subsequent to their previous test. In particular, younger children and those with virological failure were found to be at increased risk of having an OVL test. Improved HIV VL monitoring is essential for improving outcomes within South Africa's pediatric antiretroviral treatment program.

The prevalence of human papillomavirus in ocular surface squamous neoplasia in HIV positive and negative patients in a South African population.

To assess the prevalence and subtypes of Human Papillomavirus (HPV) in Ocular Surface Squamous Neoplasia (OSSN) in Human Immunodeficiency Virus (HIV) positive and negative patients in South Africa. This study was a single center retrospective cross-sectional study, conducted at Tygerberg Hospital, Western Cape, South Africa. We assessed 63 histopathologically confirmed OSSN formalin-fixed paraffin-embedded (FFPE) tissue blocks from 2015-2023. The presence of HPV was determined using the Hybrispot Direct Flow Chip Kit. Corresponding clinical data was retrieved from the National Health Laboratory Service (NHLS) central data warehouse. Of the confirmed OSSN samples, 66.7% tested positive for HPV (95% confidence interval [CI] 54-77.3%). Of the 42 HPV positive samples, 38 (90.5%) had one or more known genotypes detected and 4 had unknown genotypes. The most prevalent subtypes were HPV 11, 16 and 18 (found in 61.9%, 52.4% and 33.3% of HPV positive samples respectively). 88.9% of the lesions biopsied were from HIV positive patients, of whom 56.4% had a CD4 + count of < 200 cells/µL. A lower median CD4 + count was detected among HIV positive patients with invasive squamous cell carcinoma compared to those with moderate dysplasia (p < 0.0198). There is a high prevalence of HPV in OSSN in South Africa. Certain subtypes namely, 11, 16, 18, 31, 33 and 35 may be more carcinogenic. HIV with HPV co-infection may be linked as a causative factor in the development of OSSN.

The prevalence of malaria in the five districts of Limpopo Province, South Africa, 2015 - 2017.

In South Africa (SA), malaria is endemic in three of nine provinces - KwaZulu-Natal, Mpumalanga and Limpopo. During 2010 - 2014, SA reported that ~47.6% of all malaria cases were imported. Contemporary estimates for the prevalence of malaria in the five districts of Limpopo Province are limited, with unknown proportions of imported malaria cases. We estimated the prevalence of malaria, and the proportion of imported malaria cases in the five districts of Limpopo, from January 2015 to December 2017. To measure the prevalence of malaria in Limpopo Province, the proportion of malaria cases that are imported and to determine factors associated with malaria from January 2015 to December 2017. We retrospectively reviewed data routinely collected through the Malaria Information System and Laboratory Information System of the National Health Laboratory Services, and assessed associations with age, sex and district, using a multivariable logistic regression model. From 2015 to 2017, a total of 43 199 malaria cases were reported, of which 3.5% (n=1 532) were imported. The prevalence of malaria in Limpopo Province was the highest in 2017, at 331.0 per 100 000 population. The highest malaria prevalence district was Vhembe, with 647.9 in 2015, 220.3 in 2016 and 659.4 in 2017 per 100 000 population. However, Waterberg had the highest proportion of imported malaria cases 28.5% (437/1 532). In adjusted analyses, ages 15 - 49 years (adjusted odds ratio (aOR) 1.58, 95% confidence interval (CI) 1.48 - 1.68, p<0.001) and <1 year (aOR 1.55, 95% CI 1.37 - 0.74, p<0.001) were at higher odds of having malaria compared with ages ≥65 years. These findings highlight the significant burden of imported malaria in Limpopo Province. There is a need for strengthened surveillance and control programmes in neighboring countries (such as Mozambique, Zimbabwe and Botswana) to reduce the importation and spread of malaria in this region.

The clinical Spectrum of Viridans Group Streptococci infections in paediatric patients at a tertiary hospital.

Viridans Group Streptococci (VGS) are often considered organisms of low virulence; however, infection can result in clinically significant sepsis and life-threatening complications in paediatric patients. This study aimed to describe the spectrum of clinical presentation of VGS bacteraemia in paediatric patients, to analyse risk factors, and to describe the antibiotics resistance patterns of VGS. Cultures of VGS in paediatric patients admitted to Chris Hani Baragwanath Academic Hospital in 2019 were identified through National Health Laboratory Service. Data were extracted from archived clinical records and analysed. Sepsis scores were calculated at the time of bacteraemia. A total of 133 cultures were identified; 64 (48.1%) polymicrobial cultures and no records 4 (0.03%) were excluded; 65 (48.9%) were analysed. The median age was 1.5 months (range 0.03 to 168, interquartile range [IQR]: 0.3-13.25), 27/65 (42%) were neonates. The median duration of hospitalisation was 7 days (IQR: 3-21). The commonest diagnoses were neonatal sepsis 30.8% (n = 20) and pneumonia 28% (n = 18). The systemic inflammatory response syndrome (SIRS) score was ≥ 2 in 57% (16/28) patients; paediatric sequential organ failure assessment (pSOFA) score was > 2 in 10/24 (42%). Fifty-seven (88%) patients were discharged; three (5%) required ICU admission and 8/65 (12.3%) died. Malnutrition was present in 50% of patients who died. Cephalosporins and penicillin had sensitivity of 89% and 55%, respectively. Viridans Group Streptococci bacteraemia was common in neonates, and pneumonia was a common presentation in this cohort. The VGS bacteraemia was associated with morbidity and deaths in this cohort. The VGS should be considered a significant organism when cultured from sterile sites and routine antibiotic susceptibility testing should be performed. Prospective studies are recommended.

Linkage to HIV care and early retention in HIV care among men in the ‘universal test-and-treat’ era in a high HIV-burdened district, KwaZulu-Natal, South Africa

IntroductionDespite the numerous efforts and initiatives, males with HIV are still less likely than women to receive HIV treatment. Across Sub-Saharan Africa, men are tested, linked, and retained in HIV care at lower rates than women, and South Africa is no exception. This is despite the introduction of the universal test-and-treat (UTT) prevention strategy anticipated to improve the uptake of HIV services. The aim of this study was to investigate linkage to and retention in care rates of an HIV-positive cohort of men in a high HIV prevalence rural district in KwaZulu-Natal province, South Africa.MethodsFrom January 2018 to July 2019, we conducted an observational cohort study in 18 primary health care institutions in the uThukela district. Patient-level survey and clinical data were collected at baseline, 4-months and 12-months, using isiZulu and English REDCap-based questionnaires. We verified data through TIER.Net, Rapid mortality survey (RMS), and the National Health Laboratory Service (NHLS) databases. Data were analyzed using STATA version 15.1, with confidence intervals and p-value of ≤0.05 considered statistically significant.ResultsThe study sample consisted of 343 male participants diagnosed with HIV and who reside in uThukela District. The median age was 33 years (interquartile range (IQR): 29–40), and more than half (56%; n = 193) were aged 18–34 years. Almost all participants (99.7%; n = 342) were Black African, with 84.5% (n = 290) being in a romantic relationship. The majority of participants (85%; n = 292) were linked to care within three months of follow-up. Short-term retention in care (≤ 12 months) was 46% (n = 132) among men who were linked to care within three months.ConclusionWhile the implementation of the UTT strategy has had positive influence on improving linkage to care, men’s access of HIV treatment remains inconsistent and may require additional innovative strategies.

45 Evaluation of Drug-Resistant Tuberculosis Guidelines and Outcomes by Treatment Site in South Africa

OBJECTIVES/GOALS: DR-TB care in South Africa includes decentralized treatment with shorter, all-oral regimens. Treatment guidelines direct regular clinical and laboratory evaluation to assess patient improvement. We therefore measured sputum collection frequency and follow-up time to assess fidelity to these guidelines in Gauteng Province, South Africa. METHODS/STUDY POPULATION: We included Rifampicin-resistant (RR) sputum specimens from the South African National Health Laboratory Service, which provides pathology services to 80% of the population, submitted between August 2022-September 2023. Patient data were obtained from a DR-TB registry and additional sputum specimen data were collected from follow-up laboratory worksheets. Follow-up spanned from first sputum collection date (baseline) to patient outcome date (e.g., completion, lost) or study closure date (if still on treatment). Monthly sputum submission rate was measured for those with ≥1 additional sputum submitted. We compared patient data by treatment site: at the specialized hospital vs. any other site, using Wilcoxon ranksum and χ2 tests. RESULTS/ANTICIPATED RESULTS: Baseline RR-TB specimens were available for 142 patients, of whom 28 (20%) had specimens submitted from the specialized hospital. Patients at the specialized hospital were older (median age 41 vs. 35.5 years, p=0.03), had higher baseline fluoroquinolone resistance (10% vs. 1%, p=0.01), and longer follow-up (median 5.2 vs. 3.5 months, p=0.01) compared to patients elsewhere. Further, 43 (30%) patients had ≥1 additional sputum submitted during follow-up. Among these, monthly sputum collection rates did not differ by site (0.3 vs. 0.3 sputum per month, p=0.89). We anticipate that increased sputum frequency will be associated with successful TB treatment outcomes based on preliminary findings. DISCUSSION/SIGNIFICANCE: These findings highlight ongoing challenges with routine laboratory follow-up according to DR-TB guidelines across treatment sites in South Africa. Future research is needed to determine reasons for low sputum collection rates, such as low patient adherence, variation in practice of healthcare workers, loss to follow-up, and clinical challenges.

An Investigation into the Effectiveness of the Current Performance Appraisal System and Its Contribution to Employee Performance for National Health Laboratory Services Employees at Amajuba-Mzinyathi and Umkhanya-Zulu Business Units, Kwazulu-Natal Region

An Investigation into the Effectiveness of the Current Performance Appraisal System and Its Contribution to Employee Performance for National Health Laboratory Services Employees at Amajuba-Mzinyathi and Umkhanya-Zulu Business Units, Kwazulu-Natal Region

Cancer diagnostic service use in people living with HIV in South Africa: A cross-sectional study.

The objective of this study was to map place of cancer diagnosis in relation to Human Immunodeficiency Virus (HIV) care centre among people living with HIV (PLHIV) within South Africa (SA) using national laboratory database. We linked HIV and cancer laboratory data from 2004-2014 using supervised machine-learning algorithms. We performed a cross-sectional analysis comparing province where individuals accessed their HIV care versus where they had their cancer diagnosis. We used laboratory test records related to HIV diagnostics and care, such as CD4 cell counts and percentages, rapid tests, qualitative Polymerase Chain Reaction (PCR), antibody and antigen tests for HIV data that was documented as HIV positive and laboratory diagnosed cancer records from SA. Our study population consisted of HIV records from the National Health Laboratory Service (NHLS) that linked to cancer record at the National Cancer Registry (NCR) between 2004-2014. We linked HIV records from NHLS to cancer records at NCR in order to study the inherent characteristics of the population with both HIV and cancer. The study population was 68,284 individuals with cancer and documented HIV related laboratory test. The median age at cancer diagnosis was 40 [IQR, 33-48] years for the study population with most cancers in PLHIV diagnosed in females 70.9% [n = 46,313]. Of all the PLHIV and cancer, 25% (n = 16,364 p < 0.001) sought treatment outside their province of residence with 60.7% (n = 10,235) travelling to Gauteng. KZN had 46.6% (n = 4,107) of its PLHIV getting cancer diagnosis in Gauteng. Western Cape had 95% (n = 6,200) of PLHIV getting cancer diagnosis within the province. Our results showed health systems inequalities across provinces in SA with respect to cancer diagnosis. KZN for example had nearly half of the PLHIV getting cancer diagnosis outside the province while Western Cape is able to offer cancer diagnostic services to most of the PLHIV in the province. Gauteng is getting over burdened with referral for cancer diagnosis from other provinces. More effort is required to ensure equitable access to cancer diagnostic services within the country.

A Retrospective Review of Neglected Tropical Diseases Diagnosed on Histopathological Specimens in the Free State Province, South Africa, 2015-2020.

Neglected tropical diseases (NTDs) are a heterogeneous group of medical conditions that commonly occur in underprivileged populations. NTDs are primarily diagnosed in tropical areas. Although South Africa is not situated in a tropical region, the high poverty rate makes the country susceptible to some NTDs. Limited data are available on the burden of NTDs in the Free State province of South Africa. This study aimed to determine the number of NTDs diagnosed on histopathological specimens in the public sector of the Free State province over a six-year period and to evaluate the patient demographics. A retrospective, descriptive study was performed. All NTDs diagnosed in histopathological specimens from public sector hospitals in the province submitted to the Department of Anatomical Pathology, National Health Laboratory Service, and University of the Free State between 1 January 2015 and 31 December 2020 were included in the study. The demographic information, biopsy site, and referring hospital were noted for each case identified. A total of 72 NTDs were diagnosed. The five most common diagnoses were echinococcosis (n = 33; 45.8%), bilharzia (n = 13; 18.1%), leprosy (n = 9; 12.5%), mycetoma (n = 8; 11.1%), and intestinal worms (n = 5; 6.9%). Ten (30.3%) patients diagnosed with echinococcosis came from the Free State's neighbouring country, Lesotho. Echinococcosis was the most prevalent NTD diagnosed in central South Africa. We recommend that the South African Department of Health add echinococcosis to the principal NTDs of significance in South Africa, alongside soil-transmitted helminths, schistosomiasis, leprosy, and rabies.

CLINICAL PROFILES AND OUTCOMES OF ADMISSIONS FOLLOWING COVID-19 ADMISSIONS DURING THREE WAVES OF THE PANDEMIC: EXPERIENCE OF A TERTIARY HOSPITAL IN THE EASTERN CAPE PROVINCE OF SOUTH AFRICA.

South Africa was the country worst affected by the Covid-19 pandemic in Africa. There is a paucity of data on the clinical characteristics and mortality of Covid-19 from the Eastern Cape province of South Africa. We report on the demographic and clinical characteristics as well as the mortality of patients admitted to the Covid-19 ward of Nelson Mandela Academic Hospital (NMAH), Mthatha, during three waves of the Covid-19 pandemic in South Africa. We conducted a single centre retrospective observational study of patients admitted for Covid-19 in a tertiary hospital in the rural Eastern Cape of South Africa. Data were collected from patient files, electronic databases and the National Health Laboratory Services (NHLS) database. The outcomes were duration of admission and in-hospital mortality. There were 371 patients admitted across all three waves with a mean age of 52.2 ± 16.3 years. The proportion of females across the three waves is 61.2%. The commonly associated comorbidities, irrespective of the wave, were hypertension, diabetes and HIV infection. The median duration of admission was six days, with an overall mortality of 31%. The mortality for first, second and third wave were 29.3%, 31.5% and 37.9% respectively. Admissions for Covid-19 were predominantly in females and middle-aged. One third of the admitted patients died. Diabetes, hypertension and HIV infection were the most commonly associated comorbidities.

Kidney function in healthcare clients in Khayelitsha, South Africa: Routine laboratory testing and results reflect distinct healthcare experiences by age for healthcare clients with and without HIV.

In South Africa, PLHIV are eligible for free ART and kidney function screening. Serum creatinine (SCr) laboratory test data from the National Health Laboratory Service are collated at the Provincial Health Data Centre and linked with other routine health data. We analysed SCr and estimated glomerular filtration rate (eGFR) results for PLHIV and HIV-negative healthcare clients aged 18-80 years accessing healthcare in Khayelitsha, South Africa and comorbidity profiles at SCr and eGFR testing. 45 640 individuals aged 18-80 years with at least one renal test accessed Khayelitsha public health facilities in 2016/2017. 22 961 (50.3%) were PLHIV. Median age at first SCr and eGFR test for PLHIV was 33yrs (IQR: 27,41) to 36yrs (IQR: 30,43) compared to 49yrs (IQR: 37,57) and 52yrs (IQR: 44,59) for those without HIV. PLHIV first median SCr results were 66 (IQR: 55,78) μmol/l compared to 69 (IQR: 58,82) μmol/l for HIV-negative individuals. Hypertension, diabetes, and CKD at testing were more common in HIV-negative people than PLHIV. HIV, diabetes and tuberculosis (TB) are associated with higher eGFR results; whilst hypertension, being male and older are associated with lower eGFR results. These data reflect testing practices in the Western Cape: younger people without HIV have generally worse kidney function test results; younger PLHIV have generally good test results, and older people with/without HIV have generally similar test results, reflecting regular screening for kidney function in asymptomatic PLHIV whereas young HIV-negative people are tested only when presenting with renal symptoms. Our analysis suggests we cannot infer the future healthcare requirements of younger PLHIV based on the current ageing population, due to changing ART availability for different generations of PLHIV. Instead, routine health data may be used in an agile way to assess ongoing healthcare requirements of ageing PLHIV, and to reflect implementation of treatment guidelines.

Brain tumours in the Western Cape Province of South Africa: A plea for a dedicated brain tumour registry in Africa

Abstract Background: Epidemiological data on brain tumours provides valuable insight into risk factors, treatment modalities and prognoses of these tumours. Despite abundant epidemiological data from brain tumour registries in high-income countries, a critical data gap persists in low- and middle-income countries. Aim: The aim of this study was to report on the epidemiology of brain tumours in South Africa's Western Cape province. Methods: This retrospective study collected data from the National Health Laboratory Services database housed in the public healthcare sector in the Western Cape Province of South Africa. All pathology reports over 2 years (January 2018 to December 2019) that included the term “brain” or equivalent terms were analyzed to compile the epidemiological dataset. Results: The dataset yielded 505 patients with brain tumours, with a mean age at diagnosis of 44 years (range: 0–82 years). A noteworthy subset (16%) of primary tumours occurred in individuals under 20 years of age. The top three primary tumour diagnoses in the study were gliomas, glioneuronal and neuronal tumours, meningiomas and pituitary tumours. Secondary brain tumours (18%) constituted a significant proportion of brain tumours, with lung and breast being the most common primary sites. Comparison with registries and audits from both high- and low-income countries revealed South Africa's unique landscape; ependymal tumours exhibited a substantial proportion, while nerve sheath tumours displayed a reduced proportion. Conclusion: This study offers a unique perspective on brain tumour epidemiology in South Africa's Western Cape Province. It reports on unique trends and emphasizes the feasibility and necessity of establishing a dedicated brain tumour registry.