National Health Laboratory Research Articles

Experiences, Lessons, and Challenges With Adapting REDCap for COVID-19 Laboratory Data Management in a Resource-Limited Country: Descriptive Study.

The COVID-19 pandemic brought challenges requiring timely health data sharing to inform accurate decision-making at national levels. In Botswana, we adapted and integrated the Research Electronic Data Capture (REDCap) and the District Health Information System version 2 (DHIS2) platforms to support timely collection and reporting of COVID-19 cases. We focused on establishing an effective COVID-19 data flow at the national public health laboratory, being guided by the needs of health care professionals at the National Health Laboratory (NHL). This integration contributed to automated centralized reporting of COVID-19 results at the Ministry of Health (MOH). This paper reports the experiences, challenges, and lessons learned while designing, adapting, and implementing the REDCap and DHIS2 platforms to support COVID-19 data management at the NHL in Botswana. A participatory design approach was adopted to guide the design, customization, and implementation of the REDCap platform in support of COVID-19 data management at the NHL. Study participants included 29 NHL and 4 MOH personnel, and the study was conducted from March 2, 2020, to June 30, 2020. Participants' requirements for an ideal COVID-19 data management system were established. NVivo 11 software supported thematic analysis of the challenges and resolutions identified during this study. These were categorized according to the 4 themes of infrastructure, capacity development, platform constraints, and interoperability. Overall, REDCap supported the majority of perceived technical and nontechnical requirements for an ideal COVID-19 data management system at the NHL. Although some implementation challenges were identified, each had mitigation strategies such as procurement of mobile Internet routers, engagement of senior management to resolve conflicting policies, continuous REDCap training, and the development of a third-party web application to enhance REDCap's capabilities. Lessons learned informed next steps and further refinement of the REDCap platform. Implementation of REDCap at the NHL to streamline COVID-19 data collection and integration with the DHIS2 platform was feasible despite the urgency of implementation during the pandemic. By implementing the REDCap platform at the NHL, we demonstrated the possibility of achieving a centralized reporting system of COVID-19 cases, hence enabling timely and informed decision-making at a national level. Challenges faced presented lessons learned to inform sustainable implementation of digital health innovations in Botswana and similar resource-limited countries.

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.

Antimicrobial Resistance Patterns in Patients with Vaginal Discharge: A 2019-2022 Analysis at the National Health Laboratory in Eritrea.

Antimicrobial resistance poses a significant global threat to the treatment of bacterial infections, particularly in low- and middle-income regions such as Africa. This study is aimed at analyzing antimicrobial resistance patterns in vaginal swab samples from patients at the National Health Laboratory from 2019 to 2022. This retrospective study examined patient records from vaginal swab analyses performed at the National Health Laboratory between January 1, 2019, and December 31, 2022. Ethical approval was obtained from the Ministry of Health Research Ethical Approval and Clearance Committee on 15/02/2023. Of the 622 samples, 83% underwent microbial isolation and identification. Citrobacter spp. exhibited high resistance (>43%) to antibiotics such as cephalexin, ceftazidime, nalidixic acid, ampicillin, gentamicin, and tetracycline. E. coli showed resistance rates of more than 50% to ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. Klebsiella spp. and Proteus spp. exhibited resistance rates that exceeded 47% to specific antibiotics. Gram-positive bacteria have resistance rates of more than 49% with ampicillin, trimethoprim-sulfamethoxazole, tetracycline, oxacillin, vancomycin, and penicillin G. In particular, S. aureus demonstrated no resistance to rifampicin or clindamycin, while Streptococcus spp. showed 100% resistance to rifampicin and vancomycin. Several species, including Proteus species, Streptococcus spp., S. aureus, and Klebsiella spp. exhibited multidrug resistance. Most gram-negative bacteria displayed higher resistance of >45% to ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. Among gram-positive bacteria, a higher resistance rate with ampicillin, trimethoprim-sulfamethoxazole, tetracycline, oxacillin, vancomycin, and penicillin G was recorded. S. aureus showed no resistance to rifampicin and clindamycin, and Strep. spp. indicated 100% resistance to rifampicin and vancomycin. This study highlights critical gaps and areas for further exploration. Expanding the spectrum of antibiotics tested and investigating underlying multidrug resistance mechanisms would provide a more comprehensive understanding of resistance patterns.

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

Assessment of the yellow fever outbreak in Angola from December 2015 through December 2016: A retrospective study.

The acute tropical infectious disease known as yellow fever (YF) is caused by an arbovirus and is characterized by fever, jaundice, hemorrhage, headache, muscle pain, nausea, vomiting, and fatigue. Angola experienced a yellow fever virus (YFV) outbreak that was documented in December 2015. However, little is known about the outcome of this outbreak. We aimed to demonstrate epidemic features and lessons learned during the YF epidemic in Angola. A total of 4618 blood samples from suspected YF cases were sent to the Instituto Nacional de Investigação em Saúde (INIS), a national referral and public health laboratory, between December 5, 2015, and December 23, 2016. Sample analyses were conducted using enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR) assays. Blood samples were sent from 16 out of the 18 provinces of Angola. We detected 884 (19.1%) cases that were positive for ELISA, which were confirmed by RT-PCR assay. Considering the positive cases, the incidence among male patients was around three times higher (n = 223; 10.9%) than in female patients (n = 59; 2.6%) in the 20-29 age group, followed by the age group 10-19 with n = 211 (6.8%) in males versus n = 108 (3.3%) in females; and the age group 30-39 had n = 68 (4.8%) in males versus n = 28 (1.8%) in females. The other groups had an incidence below 3.0%. The case fatality ratio for YF was in young adults in the age group 20-29 with n = 39 cases, followed by the age group 10-19 with n = 16 cases, and finally the age group 0-9 with n = 13 cases. The other age groups had several deaths by YF below 10 cases. This study demonstrates features of the YF epidemic that occurred in Angola. Also, it demonstrates that YF causes deaths in young people but is preventable by high vaccine coverage. Thus, public health laboratory surveillance must be strengthened to reduce the possibility of emerging and re-emerging human infections.

National Health Laboratory Service (NHLS) changes the method of LDL-cholesterol calculation in South Africa

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Gaps in the type 2 diabetes care cascade: a national perspective using South Africa’s National Health Laboratory Service (NHLS) database

BackgroundResearch out of South Africa estimates the total unmet need for care for those with type 2 diabetes mellitus (diabetes) at 80%. We evaluated the care cascade using South Africa’s National Health Laboratory Service (NHLS) database and assessed if HIV infection impacts progression through its stages.MethodsThe cohort includes patients from government facilities with their first glycated hemoglobin A1c (HbA1c) or plasma glucose (fasting (FPG); random (RPG)) measured between January 2012 to March 2015 in the NHLS. Lab-diagnosed diabetes was defined as HbA1c ≥ 6.5%, FPG ≥ 7.0mmol/l, or RPG ≥ 11.1mmol/l. Cascade stages post diagnosis were retention-in-care and glycaemic control (defined as an HbA1c < 7.0% or FPG < 8.0mmol/l or RPG < 10.0mmol/l) over 24-months. We estimated gaps at each stage nationally and by people living with HIV (PLWH) and without (PLWOH).ResultsOf the 373,889 patients tested for diabetes, 43.2% had an HbA1c or blood glucose measure indicating a diabetes diagnosis. Amongst those with lab-diagnosed diabetes, 30.9% were retained-in-care (based on diabetes labs) and 8.7% reached glycaemic control by 24-months. Prevalence of lab-diagnosed diabetes in PLWH was 28.6% versus 47.3% in PLWOH. Among those with lab-diagnosed diabetes, 34.3% of PLWH were retained-in-care versus 30.3% PLWOH. Among people retained-in-care, 33.8% of PLWH reached glycaemic control over 24-months versus 28.6% of PLWOH.ConclusionsIn our analysis of South Africa's NHLS database, we observed that 70% of patients diagnosed with diabetes did not maintain in consistent diabetes care, with fewer than 10% reaching glycemic control within 24 months. We noted a disparity in diabetes prevalence between PLWH and PLWOH, potentially linked to different screening methods. These differences underscore the intricacies in care but also emphasize how HIV care practices could guide better management of chronic diseases like diabetes. Our results underscore the imperative for specialized strategies to bolster diabetes care in South Africa.

The prevalence and spectrum of thyroid dysfunction among children with Down syndrome attending the paediatric services at two tertiary hospitals in Pretoria, South Africa

Background. Down syndrome (DS) is the most common chromosomal abnormality in the paediatric setting, and thyroid dysfunction is more commonly encountered in this population than among the general population. The literature shows that the most common type of thyroid dysfunction seen in these children is subclinical hypothyroidism.Objective. The purpose of this study was to establish the prevalence and spectrum of thyroid disease in this population with the aim of establishing easy-to-follow protocols. Method. A retrospective study was conducted in children with DS who were seen at the paediatric genetic clinic at two academic hospitals. Data were collected from the hospital files and the results were extracted from the National Health Laboratory Service database system. Results. A total of 158 children were recruited; 25 children were excluded as they had had no thyroid function tests done. From the total of 133 included children, 70 (52.6%) were male. Babies born in one of the two hospitals numbered 60 (45.1%), whereas 54.9% were born in the other hospital. A total of 77 (57.9%) were found to have thyroid dysfunction; 55.8% of these patients were male. The most common thyroid abnormality was subclinical hypothyroidism in n=66/133 (49.6%), accounting for 85.7% of the causes of the thyroid dysfunction. Most children (n=45/133 (33.8%)) had their first thyroid function test done before the age of 2 months, followed by the age group of 1 - 5 years (n=34/133 (25.56%)). The total number of children started on treatment for their thyroid dysfunction was n=5/77 (6.49%). Conclusion. Thyroid dysfunction is seen more commonly in children with DS compared with the general population, which was very evident in the present study. A standardised protocol will have a significant impact on the early management of these children, to prevent further cognitive impairment, especially in developing countries and at any level of healthcare. The recommendations for thyroid dysfunction screening by the American Academy of Pediatrics can be adjusted and tailored for the South African population. Early diagnosis and referral of children with DS to a secondary- or tertiary-level facility is of utmost benefit for these children for screening and treatment of comorbidities and complications.

Tuberculosis testing patterns in South Africa to identify groups that would benefit from increased investigation

The National Health Laboratory Service (NHLS) collects all public health laboratory test results in South Africa, providing a cohort from which to identify groups, by age, sex, HIV, and viral suppression status, that would benefit from increased tuberculosis (TB) testing. Using NHLS data (2012–2016), we assessed levels and trends over time in TB diagnostic tests performed (count and per capita) and TB test positivity. Estimates were stratified by HIV status, viral suppression, age, sex, and province. We used logistic regression to estimate the odds of testing positive for TB by viral suppression status. Nineteen million TB diagnostic tests were conducted during period 2012–2016. Testing per capita was lower among PLHIV with viral suppression than those with unsuppressed HIV (0.08 vs 0.32) but lowest among people without HIV (0.03). Test positivity was highest among young adults (aged 15–35 years), males of all age groups, and people with unsuppressed HIV. Test positivity was higher for males without laboratory evidence of HIV than those with HIV viral suppression, despite similar individual odds of TB. Our results are an important national baseline characterizing who received TB testing in South Africa. People without evidence of HIV, young adults, and males would benefit from increased TB screening given their lower testing rates and higher test positivity. These high-test positivity groups can be used to guide future expansions of TB screening.

NECROTIZING SOFT-TISSUE INFECTIONS: A RETROSPECTIVE CASE SERIES AT A DISTRICT HOSPITAL IN SOUTH AFRICA

Necrotizing soft tissue infection (NSTI) is a rapidly progressive infection that typically starts in the dermis and epidermis and spreads along soft tissue planes, penetrating subdermal layers and can lead to massive tissue necrosis resulting in severe morbidity and mortality. The aim of this case series was to describe the epidemiology and burden of NSTI's at a District Hospital servicing a South African urban settlement.This retrospective case series was performed at a single centre. Consecutive patients were identified following a clinical diagnosis for NSTI. Further laboratory pre-operative work up was standardized including: use of validated Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC scores) and Human Immunodeficiency Virus (HIV) status. All patients who underwent surgical debridement were captured on the Theatre Database (www.medwebtools.org™). All patients received standardized perioperative, intra-operative and post-operative protocols for antibiotics, debridement and soft tissue closure or cover based on the severity of disease. Medical records, theatre notes, National Health Laboratory Service (NHLS) results and radiological results were captured for every patient.28 patients (14 male, 14 female) presented with NSTI over a 3 year period (2021–2023). The mean age was 39.5 years. The most common organisms cultured were Streptococcus pyogenes (10 patients), Staphylococcus aureus (9 patients), Bacillus cereus (3 patients).This retrospective case series is an important study because it demonstrates some of the highest incidence of NSTI globally; however, the cause of this is yet to be determined. Our results show that having a high clinical index of suspicion; using the LRINEC score to assess severity and using a standardized antibiotic and peri-operative protocol with early soft tissue cover that NSTI's can be managed effectively with a reduction in patient morbidity and overall length of hospital stay.

THE IMPACT OF HIV INFECTION ON WOUND HEALING AND FRACTURE UNION IN PATIENTS WITH CLOSED ANKLE FRACTURES TREATED WITH A PLATE OSTEOSYNTHESIS AT A TERTIARY LEVEL HOSPITAL

Fractures of the ankle are common, and they mostly affect young adults. Wound complications are not uncommon following the fixation of these fractures. This study evaluated the impact of HIV on wound healing after plate osteosynthesis in patients with closed ankle fractures.This is an observational retrospective study of patients operated on at a tertiary level hospital. We reviewed hospital records for patients above 18 years of age who presented with wound breakdown following ankle open reduction and internal fixation. The patients’ hospital records were retrieved to identify all the patients treated for closed ankle fractures and those who developed wound breakdown. Patients with Pilon fractures were excluded. The National Health Laboratory System (NHLS) database was accessed to retrieve the CD4 count, viral load, haematology study results, and biochemistry results of these patients at the time of surgery and subsequent follow-up. The x-rays were retrieved from the electronic picture archiving system (PACS) and were assessed for fracture union at a minimum of 3 months follow-up.We reviewed the medical records of 172 patients with closed ankle fractures treated from 2018 to 2022. Thirty-one (18.0%) developed wound breakdown after surgery, and they were all tested for HIV. Most of the patients were male (58.0%), and the average age of the cohort was 43.7 years (range: 21 years to 84 years). Ten of these patients (32.2%) were confirmed HIV positive, with CD4 counts ranging from 155 to 781. Viral load levels were lower than detectable in 40% of these patients. All patients progressed to fracture union at a minimum of 3 months follow-up.We observed no difference between HIV-positive and HIV-negative patients in terms of wound breakdown and bone healing post-plate osteosynthesis for closed ankle fractures.

A RETROSPECTIVE REVIEW OF THE BACTERIOLOGY OF HAND SEPSIS AT A TERTIARY HOSPITAL IN GAUTENG

The aim of this investigation is to firstly quantify the burden of disease, and secondly qualify the organisms being cultured during debridement to establish their sensitivities to available antibiotics. This study will also look at the concomitant burden of Human Immunodeficiency Virus (HIV) and Diabetes Mellitus (DM) in cases of hand sepsis, to establish whether these two disease processes require special consideration and treatment tailoring.The method employed to collect the data will be retrospective collection of patient information, using random sampling. Included patients will be adult patients who undergo debridement and have a sample registered on the National Health Laboratory System (NHLS). The daily intake sheet will be used to collect patients details and these details will then be used to collect results of intra-operative specimens using the NHLS. These patient details will also be used to check patients’ HIV results and HBA1c (Glycated Haemoglobin A1c) results.Majority of the specimens revealed Methicillin Sensitive Staphylococcus Aureus (MSSA), with a reassuringly low rate of Methicillin Resistant Staphylococcus Aureus (MRSA) when compared to international data. The yield of patients tested for HIV or DM was lower than expected, despite this being the standard of care.The projected impact of this study will be assessment of the current burden of disease and then clarification of our current management strategy, in order to assess if it would be possible to change to a more cost-effective antibiotic with a narrower spectrum of bacteria coverage. The potential exists to not only implement cost saving measures, but also promote antibiotic stewardship by decreasing the practice of empiric broad-spectrum antibiotic use.

Nucleated red blood cells in neonates with hypoxic ischaemic encephalopathy treated with hypothermia: A worthwhile prognostic biomarker for clinicians in LMIC?

Background. Neonatal hypoxic ischaemic encephalopathy (HIE) is a leading cause of term neonatal death worldwide, with a higherincidence in low- to middle-income settings.Objective. To investigate whether nucleated red blood cell (nRBC) counts could predict severity of HIE and outcomes in term neonatestreated with therapeutic hypothermia (TH).Methods. We conducted a retrospective sub-study at Tygerberg Hospital in Cape Town, South Africa. The review included all cooledneonates’ clinical records and blood samples from a National Health Laboratory Services database. One experienced neurodevelopmental expert assessed patients over a period of 12 months.Results. Twenty-five files out of a total of 100 were excluded owing to missing data. In accordance with the Thompson HIE score,the cohort was classified as mild (56%), moderate (27%), and severe (17%). All included patients (n=75) had full blood counts within6 hours of delivery. nRBC were detected in 52% of the samples. There was no correlation between nRBC category and HIE severity(p=0.265). Raised nRBCs (≥30 cells/100 white blood cells (WBCs)) were more frequent in infants who died than in those whosurvived (p=0.008). Infants with nRBC counts ≥30 cells/100 WBCs had an increased likelihood of having cerebral palsy or impairedneurodevelopment (p=0.013).Conclusion. The study demonstrated a significant association between an early increase in nRBC counts in HIE infants treated with TH,and both short- and long-term outcomes. A larger multicentre study is required to better understand the relationship between nRBCcounts and HIE in the era of cooling in our local setting.

RSV bronchiolitis in 2018: A descriptive study of children admitted to two Johannesburg tertiary hospitals

Background. Respiratory syncytial virus (RSV) is the most common cause of severe bronchiolitis in children worldwide.Objectives. To describe clinical characteristics and outcomes of children hospitalised with bronchiolitis and to compare those with RSVbronchiolitis with children with other viral causes of bronchiolitis.Methods. A retrospective study of children admitted with virally screened bronchiolitis to Charlotte Maxeke Johannesburg AcademicHospital (CMJAH) and Nelson Mandela Children’s Hospital (NMCH) from 1 February to 31 August 2018 was conducted, where RSVpositive and -negative children were compared. These children were identified by the National Health Laboratory Service as havingundergone respiratory viral multiplex molecular assay analysis and hospital charts were retrospectively reviewed.Results. A total of 131 children admitted with bronchiolitis from CMJAH and NMCH were compared in this study, 58 from CMJAHand 73 from NMCH. In the sample group, 65 (49.6%) children had RSV in comparison with 66 (50.4%) children without RSV. Childrenwith RSV comprised 55 (42%) children with RSV only and 10 (7.6%) children with RSV in combination with another respiratory virus.Rhinovirus was the second most common virus detected in this cohort of children (n=17, 12.9%) followed by adenovirus (n=12, 9.2%)and coronavirus (n=9, 6.9%). A statistically significant risk factor noted in children requiring hospitalisation for RSV bronchiolitis wasage less than six months (p&lt;0.001).Conclusions. Bronchiolitis is a common disease in children. Respiratory syncytial virus is the most common cause of severe bronchiolitis in hospitalised infants less than six months of age.

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

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. 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. 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%. 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.

Developing an antibiogram for empiric antibiotic prescribing for adult non-spinal orthopaedic infections in a developing world setting

PurposeEmpiric antibiotic strategies in the treatment of fracture-related infections, chronic osteomyelitis, prosthetic joint infection, and septic arthritis should be based on local microbiological antibiograms. This study aims to describe the microbiology and review the antibiogram profiles of bacterial isolates from patients undergoing surgical treatment for non-spinal orthopaedic infections, to identify the most appropriate empiric antibiotic strategy.MethodsA retrospective review was performed of all cases of non-spinal orthopaedic infections treated surgically from 1 January 2018 to 31 December 2018. The National Health Laboratory Service microbiology database was used to identify all intra-operative microbiological specimens obtained from orthopaedic patients, and data were correlated with the orthopaedic surgical database. Cases were divided into fracture-related infections, chronic osteomyelitis, prosthetic joint infection, and septic arthritis. Antibiotic susceptibility data were used to predict the efficacy of different empiric antibiotic regimens.ResultsA total of 107 cases were included in the study; 184 organisms were cultured. Overall, the most common organism cultured was Staphylococcus aureus (25%) followed by Acinetobacter baumannii (9%), Enterococcus faecalis (7%) and Enterobacter cloacae (5%). Across all categories the oral antibiotic combination with the highest effectiveness (81%) would have been a combination of co-trimoxazole, ciprofloxacin and amoxicillin. The most effective intravenous antibiotic combination would have been either piperacillin–tazobactam, amikacin and vancomycin or meropenem and vancomycin; 90% of tested isolates were susceptible to either of these combinations.ConclusionAntibiogram profiles can serve to guide to empiric antibiotic choice in the management of different categories of non-spinal orthopaedic infections.

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.

How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality.

The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays' gene targets. This continuous quality monitoring rapidly identified delayed hybridization of RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® Xpress SARS-CoV-2 due to XBB.1.5. This near "real-time" monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.

Eliminating Vertical Transmission of HIV in South Africa: Establishing a Baseline for the Global Alliance to End AIDS in Children.

To gain a detailed overview of vertical transmission in South Africa, we describe insights from the triangulation of data sources used to monitor the national HIV program. HIV PCR results from the National Health Laboratory Service (NHLS) were analysed from the National Institute of Communicable Diseases (NICD) data warehouse to describe HIV testing coverage and positivity among children <2 years old from 2017-2021. NICD data were compared and triangulated with the District Health Information System (DHIS) and the Thembisa 4.6 model. For 2021, Thembisa estimates a third of children living with HIV go undiagnosed, with NICD and DHIS data indicating low HIV testing coverage at 6 months (49%) and 18 months (33%) of age, respectively. As immunisation coverage is reported at 84% and 66% at these time points, better integration of HIV testing services within the Expanded Programme for Immunization is likely to yield improved case findings. Thembisa projects a gradual decrease in vertical transmission to 450 cases per 100,000 live births by 2030. Unless major advances and strengthening of maternal and child health services, including HIV prevention, diagnosis, and care, can be achieved, the goal to end AIDS in children by 2030 in South Africa is unlikely to be realised.