National Health Laboratory Service Research Articles

Incidence and distribution of human leptospirosis in the Western Cape Province, South Africa (2010-2019): a retrospective study.

leptospirosis is an emerging zoonosis of global importance. In South Africa, the infection is an underreported public health concern, with limited information on its incidence and distribution. This study investigated the incidence of human leptospirosis in Western Cape Province (WCP) between 2010 and 2019, and compared the incidence based on seasonal and demographic factors. a retrospective study was conducted with data on leptospirosis diagnoses in WCP obtained from the National Health Laboratory Services. With the provincial population sizes as the denominator, incidence of leptospirosis was estimated and expressed as cases per 100,000 population. Negative binomial regression was used to estimate the effect of sex, season, and year on the incidence of leptospirosis. two hundred and fifty-four (254) cases of leptospirosis were reported between 2010 and 2019, with the highest number of cases being in 2015 and the annual incidence ranged between 0.15 and 0.66/100,000 population. Males had a higher incidence compared to females (0.55 vs. 0.25/ 100,000 population; incidence rate ratio (IRR) 2.2, 95% CI: 1.66,3.03). The 18-44 age cohort had the highest average incidence (0.56/100,000 population), while the ≤17 age cohort had the lowest incidence (0.07/100,000 population). The 18-44 (IRR 8.0, 95% CI: 4.65,15.15) and ≥45 (IRR 7.4, 95% CI: 4.17,14.17) age cohorts were more at risk of infection compared to ≤17 age cohort. leptospirosis is an important zoonosis in WCP disproportionately affecting males and the productive age demographic groups. These findings should enhance targeted prevention and provoke further investigation on the importance of environmental and socioeconomic factors on leptospirosis burden.

Retraction of a ‘hot-headed resignation’ caused by depression: Lessons from Cairncross/Legal and Tax (Pty) Ltd 2019 (2) BALR 137 (CCMA)

Unlike its celebrated siblings, Metropolitan Health Risk Management v Majatladi 2015 (36) ILJ 958 (LAC) (‘Majatladi’), National Health Laboratory Service v Yona (2015) 36 ILJ 2259 (LAC) (‘Yona’) and HC Heat Exchangers (Pty) Ltd v Araujo 2020 (3) BLLR 280 (LC) (‘HC Heat Exchangers’), Cairncross/Legal and Tax (Pty) Ltd 2019 (2) BALR 137 (CCMA) (‘Cairncross’) is the black sheep of the constructive dismissal family. The arbitration award in Cairncross brings into sharp focus emotional distress in the context of constructive dismissal. Cairncross provides a platform to isolate some of the critical issues that have arisen in recent times concerning constructive dismissal. First, there is a troublesome jurisdictional puzzle: Has the employee resigned or was he or she dismissed? Secondly, the case deals with the vexed question of what would constitute intolerable circumstances to continue the employment relationship, and in particular, whether work-related stress could form the basis of a constructive dismissal claim. In the case under scrutiny, the employee had claimed that her depression was attributable to the unbearable working environment. The basis of her claim of intolerability of continued employment was that an employer has a common-law and statutory duty to provide a safe working environment, which it had failed to deliver. Lastly, Cairncross also brings to the fore a consideration of the effect of tendering a resignation and the aggrieved employee’s subsequent attempt to withdraw it. The question that is answered is whether an employer’s failure to accept the withdrawal of resignation by an employee suffering from work-related stress constitutes a type of constructive dismissal.

The impact of lockdown measures during the SARS-CoV-2 pandemic on the management of diabetes in a Northern Gauteng Region of South Africa.

coronavirus disease 2019 (SARS-CoV-2), a global pandemic, popularised the term "lockdown" due to its rapid spread around the world. "Lockdown" was used as an emergency measure to temporarily prevent people from entering or leaving their communities in an effort to reduce the spread of the virus. The effects of the "lockdown" measures on the management of chronic medical conditions in African populations have been inconsistent. This study aimed to assess the effects of the lockdown on glycaemic control in patients with diabetes. retrospective study that examined metadata from 1st January 2019 to 31st December 2021, to assess the impact of the national SARS-CoV-2 response on the quantity and average level of haemoglobin A1c and random glucose in patients with diabetes at Dr. George Mukhari Academic Hospital. The data was retrieved from the National Health Laboratory Services corporate data warehouse. from 2019 to 2021, a total of 9,039 tests were performed, with females accounting for 63.21% (n = 5,714) and males for 36.08% (n = 3,261), while 0.7% (n = 70) did not have an assigned gender. Mean age was 49, with a standard deviation (SD) of 21.71. The testing rate (TR) in 2019 was 10.74 per day, 2020 had a TR of 6.07, and 2021 had a TR of 7.95. During the pandemic phase, all other age groups had TRs below 1.85, except the 50-59, 60-69, and 70+ year-old groups. the study revealed that SARS-CoV-2 lockdown measures were linked to poor diabetes control in patients. As a result, the consequences of managing SARS-CoV-2 had a direct influence on diabetes management.

A Retrospective Analysis of Culture-Confirmed Enterococci Bloodstream Infections in South Africa, 2016-2020: A Cross-Sectional Study.

(1) Background: The emergence of multidrug resistance enterococci is a major public health concern. This study aimed to determine the prevalence and antimicrobial resistance of enterococci isolated from blood cultures over a five-year period (2016−2020) at public hospitals in South Africa. (2): Methods: A retrospective analysis of clinical enterococci isolated from bloodstream infection samples at the South African public hospitals was conducted. The ESKAPE dataset from January 2016 to December 2020 was obtained from the central data warehouse (CDW) at the National Health Laboratory Service (NHLS). (3): Results: Following de-duplication, a total of 130,352/306,592 organisms isolated from blood cultures were identified as ESKAPE pathogens. In this study, K. pneumoniae (25%; 33,082/130,352), was the most frequently isolated pathogen from blood cultures, followed by S. aureus (23%; 29,922/130,352) and enterococci (16%; 21,339/130,352). Of the enterococci cases, about 43% (9132/21,339) of cases were from the infants aged (<1-year old) and 32% (6745/21,339) from the adult patients. No changes observed in vancomycin, teicoplanin, and linezolid susceptibility; however, E. faecium and E. faecalis blood culture isolates remained highly susceptible (>97%) to these antibiotics. (4): Conclusions: The current study revealed a significant increase of E. faecalis and E. faecium blood culture isolates as compared to the previous national ESKAPE data. Low vancomycin resistance was observed. Continuous monitoring of antimicrobial resistant Enterococcus species is warranted in South Africa.

Age and Cancer Incidence in 5.2 Million People With Human Immunodeficiency Virus (HIV): The South African HIV Cancer Match Study.

Old age is an important risk factor for developing cancer, but few data exist on this association in people with human immunodeficiency virus (HIV, PWH) in sub-Saharan Africa. The South African HIV Cancer Match study is a nationwide cohort of PWH based on a linkage between HIV-related laboratory records from the National Health Laboratory Service and cancer diagnoses from the National Cancer Registry for 2004-2014. We included PWH who had HIV-related tests on separate days. Using natural splines, we modeled cancer incidence rates as a function of age. We included 5 222 827 PWH with 29 580 incident cancer diagnoses-most commonly cervical cancer (n = 7418), Kaposi sarcoma (n = 6380), and breast cancer (n = 2748). In young PWH, the incidence rates for infection-related cancers were substantially higher than for infection-unrelated cancers. At age 40 years, the most frequent cancer was cervical cancer in female and Kaposi sarcoma in male PWH. Thereafter, the rates of infection-unrelated cancers increased steeply, particularly among male PWH, where prostate cancer became the most frequent cancer type at older age. Whereas Kaposi sarcoma rates peaked at 34 years (101/100 000 person-years) in male PWH, cervical cancer remained the most frequent cancer among older female PWH. Infection-related cancers are common in PWH in South Africa, but rates of infection-unrelated cancers overtook those of infection-related cancers after age 54 years in the overall study population. As PWH in South Africa live longer, prevention and early detection of infection-unrelated cancers becomes increasingly important. Meanwhile, control strategies for infection-related cancers, especially cervical cancer, remain essential.

Cost effectiveness of Electronic Gate Keeping (EGK) system on laboratory tests demand at a rural academic hospital in Eastern Cape, South Africa: a cross sectional study

Background: Monitoring laboratory expenditure is crucial to ensure that laboratory services remain sustainable and affordable. In South Africa, the National Department of Health (NDoH) and its partner, the National Health Laboratory Services (NHLS) collaborated to introduce Electronic Gate Keeping (EGK) systems across the country. This study estimated the cost-effectiveness of EGK on laboratory tests requested at a rural academic hospital in the Eastern Cape province of South Africa. Methods: The methodological approach involved the use of a cross-sectional study design. For 24 months (June 2015 to May 2017), data on the number and types of laboratory tests initially requested along with those rejected because there were unnecessary was obtained. Data management and cost effectiveness analysis to estimate cost savings due to EGK on laboratory test demands were carried out using MS Excel and Stata software. There were 28 types of tests requested, of which 22 were chemical tests, two were haematological tests, and four were serological tests. Results: Out of 448 028 tests requested, 17,480 (3.9%) were rejected after being identified as unnecessary through the EGK system. This rejection rate of 3.9% generated cost savings of USD 51,967.07. The top three tests that generated the most savings were the c-reactive protein (USD 6,077.68), free thyroxine (USD 5,199.92) and hepatitis A IgM (USD 3,813.61). Conclusions: The study demonstrates that the introduction of EGK has positive spinoffs; it reduced costs, strengthened the dialogue between clinicians and pathologists allowing a platform for continuous education, teaching and learning.

Recognition of infants at high risk for vertical HIV transmission at delivery in rural Western Cape Province, South Africa.

Despite South Africa’s substantial reduction in vertical HIV transmission (VHT), national paediatric HIV elimination is not yet attained. National and Western Cape Province (WC) HIV guidelines recommend enhanced postnatal prophylaxis for infants at high risk for VHT, identified in the WC 2015/2016 guidelines by any single high-risk criterion (maternal antiretroviral therapy (ART) <12 weeks, absent/ unsuppressed maternal HIV viral load (HIV-VL) <12 weeks before/including delivery, spontaneous preterm labour, prolonged rupture of membranes, chorioamnionitis). Accuracy of high-risk infant identification is unknown. Primarily, to determine the proportion of infants at high risk for VHT, the accuracy of labour-ward risk classification, the criteria determining high-risk statuses and the criteria missed among unrecognised high-risk infants; secondarily, to determine maternal factors associated with high-risk infants. Infants born to women living with HIV at a rural regional hospital (May 2016 - April 2017) were retrospectively evaluated using data from the labour ward VHT register, standardised maternity case records, National Health Laboratory Service database and WC Provincial Health Data Centre. The study-derived risk status for each infant was determined using documented presence/absence of risk criteria and compared with labour ward assigned risk to determine accuracy. Proportions of high-risk and unrecognised high-risk infants with each high-risk criterion were determined. Maternal characteristics associated with having a high-risk infant were evaluated using multivariable logistic regression. For liveborn infants, labour ward assigned risk classifications were 40% (n=75/188) high risk, 50% (n=94/188) low risk and 10% (n=19/188) unclassified. Study-derived risk was high risk for 69% (n=129/188) and low risk for 31% (n=59/188), yielding a high-risk classification sensitivity of 51% (95% confidence interval (CI) 42 - 60) and specificity of 69% (95% CI 56 - 80). Absent/unsuppressed HIVVL <12 weeks before delivery accounted for 83% (n=119/143) of study-derived high-risk exposures and 81% (n=60/74) of missed high-risk exposures. Fewer mothers of high-risk infants had >4 antenatal visits (38% v. 81%, p<0.01) and first antenatal visit <20 weeks’ gestation (57% v. 77%, p=0.01). Only the number of antenatal visits remained associated with having a high-risk infant after adjusting for gestation at first visit and timing of HIV diagnosis and ART initiation: each additional antenatal visit conferred a 39% (95% CI 25 - 50) reduction in the odds of having a high-risk infant. Labour ward risk classification failed to recognise half of high-risk infants. Infant high-risk status as well as non-detection thereof were driven by suboptimal maternal HIV-VL monitoring. Reinforcing visit frequency later in pregnancy may improve antenatal HIV-VL monitoring, and point-of-care HIV-VL monitoring at delivery could improve recognition of virally unsuppressed mothers and their high-risk infants.

Cohort profile: CareConekta: a pilot study of a smartphone application to improve engagement in postpartum HIV care in South Africa

PurposePregnant and postpartum women living with HIV in South Africa are at high risk of dropping out of care, particularly after delivery. Population mobility may contribute to disruptions in HIV...

Characterisation of RSV Fusion Proteins from South African Patients with RSV Disease, 2019 to 2020.

Respiratory syncytial virus (RSV) is classified into RSV-A and RSV-B, which are further classified into genotypes based on variability in the G gene. The fusion (F) protein is highly conserved; however, variability within antigenic sites has been reported. This study aimed to characterise F proteins from RSV strains detected in South Africa from 2019 to 2020. Patients of all ages, from whom respiratory samples were submitted to the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic Hospital, South Africa during 2019 to 2020, were included. Complete RSV F genes were amplified for next-generation sequencing. MEGA X software was used for phylogenetic analysis. The overall prevalence of RSV was 5.8% (101/1734). Among 101 RSV positive samples only 69.3% (70/101) were available for characterization of the RSV F protein gene. Among cases included for F gene characterisation, viral co-infections were observed in 50% (35/70) and 25.7% (18/70) were admitted to intensive care units (ICU). About 74.2% (23/31) of F gene sequences cluster with other African NA1/ON1 genotypes. At antigenic site I, the V384I mutation was replaced by V384T in South African strains. The S275F mutation was seen in a single South African strain. The N120 N-linked glycosylation site was present in 25.8% (8/31) of RSV-A F proteins described in this study. For the first time, we detected the rare S275F mutation that is associated with palivizumab resistance.

Infant HIV Testing Amid the COVID-19 Pandemic and Evolving PMTCT Guidelines in Johannesburg, South Africa.

Background: The COVID-19 pandemic impacted HIV programmes with the diversion of resources and lockdown measures. We assessed the impact of COVID-19 on infant HIV diagnosis in the context of updated 2019 prevention of mother-to-child transmission of HIV (PMTCT) guidelines in Johannesburg, South Africa. Methods: HIV PCR data for children <2 years were extracted from the National Health Laboratory Service database from October 2018 to September 2021, inclusive. Trends in the total number of tests performed and the total number of children with HIV diagnosed, stratified by age, were determined to assess the effect of different COVID-19 lockdown levels and updated guidelines. Results: When comparing three 12-month periods ending September 2019–2021, respectively, the total number of HIV PCR tests performed increased (from 41 879 to 47 265 to 56 813), and the total number of children with HIV decreased (from 659 to 640 to 620), year-on-year. There was a substantial increase in 6-month testing in response to updated guidelines. Excluding 6-month testing, the year-on-year increase in total tests was maintained with birth and 10-week testing closely approximating total live births to women living with HIV. A decrease in the total number of children with HIV diagnosed was noted in Q2 2020, coinciding with the most restrictive lockdown, followed by a rebound in cases. Conclusions: Despite the restrictions and diversion of resources associated with COVID-19, there was a successful implementation of PMTCT guideline updates and minimal disruption to infant HIV testing. However, much work remains in order to achieve the elimination of mother-to-child transmission of HIV.

Cohort profile: the South African National Health Laboratory Service (NHLS) National HIV Cohort

PurposeSouth Africa’s National Health Laboratory Service (NHLS) National HIV Cohort was established in 2015 to facilitate monitoring, evaluation and research on South Africa’s National HIV Treatment Programme. In South Africa,...

Comparison of commercial assays and two-step approach to detect Clostridioides difficile in South Africa.

BackgroundClostridioides difficile is the number one cause of hospital-acquired diarrhoea. Accurate diagnosis of C. difficile is of utmost importance as it guides patient management and infection control practices. Studies evaluating the performance of commercially available nucleic acid amplification tests (NAATs) versus algorithms are lacking in resource-limited settings.ObjectiveThis study assessed the performance of three commercially available tests and a two-step approach for the diagnosis of C. difficile infection using toxigenic culture (TC) as the gold standard.MethodsTwo hundred and twenty-three non-duplicate loose stool samples were submitted to the National Health Laboratory Service Microbiology Laboratory at Tygerberg Hospital, Cape Town, South Africa, from October 2017 to October 2018. The samples were tested in parallel using the C. DIFF QUIK CHEK COMPLETE enzyme immunoassay (EIA) and two NAATs (Xpert C. difficile and BD MAX Cdiff), and the results were compared to TC. The performance of a two-step approach consisting of the C. DIFF QUIK CHEK COMPLETE followed by the Xpert C. difficile was also determined.ResultsOf 223 faecal specimens tested, 37 (16.6%) were TC-positive. The sensitivity and specificity of the C. DIFF QUIK CHEK COMPLETE were 54.1% and 98.9%; Xpert C. difficile, 86.4% and 96.8%; BD MAX Cdiff, 89.2% and 96.8%; and two-step approach, 89.2% and 96.2%.ConclusionThe C. DIFF QUIK CHEK COMPLETE, in a two-step approach with the Xpert C. difficile, performed similarly to the NAATs on their own and offer advantages in terms of cost and workflow in low-resource settings.

Audit of amylase and lipase requests in suspected acute pancreatitis and cost implications, South Africa.

BackgroundThe internationally accepted criteria for the diagnosis of acute pancreatitis (AP) requires two of the three following features to be present: characteristic abdominal pain, elevated serum amylase and/or lipase enzymes, or consistent imaging results. However, sensitivity and specificity can vary depending on the population and cut-off values used.ObjectiveThis study evaluated the suitability of amylase and lipase as first-line diagnostic biomarkers of suspected AP for the local population served by Tygerberg Hospital, South Africa.MethodsThis retrospective analysis was conducted in June 2019 using all amylase and/or lipase request data from December 2018. Patient clinical data were included in sensitivity and specificity analyses of amylase, lipase or dual requests for diagnosis of AP. Cost per test data were obtained from the National Health Laboratory Service and used to calculate the total cost of the tests and potential savings.ResultsSensitivity for lipase was 90.0% compared to 50.0% for amylase. Specificity was similar for singular measurements of lipase and amylase. Dual measurement of amylase and lipase showed no improvement in sensitivity (83.3%) and only a minor increase in specificity (97.4%) compared with measurement of lipase alone. The estimated savings was R2522.85 ($174.98 USD), with a potential annual cost saving of R84 423.74 ($5855.69 USD).ConclusionLipase was shown to be a more sensitive biomarker compared to amylase for the screening of AP, providing evidence for laboratories to educate local staff and promote improved requesting practices by clinicians. Additionally, preventing unnecessary dual requests may reduce costs.

Piloting and validating the linkage of routine ART and laboratory records in an HIV endemic setting.

ObjectivesIntegrating clinical and laboratory data systems offers opportunities to understand disease aetiology and improve patient outcomes. We developed and piloted a data linkage algorithm to link HIV patient treatment records with routine laboratory service records in an HIV endemic setting in rural South Africa.&#x0D; ApproachWe used data from the South Africa’s National Health Laboratory Service (NHLS) and Three Integrated Electronic Registers (TIER.Net) databases for 17 primary healthcare clinics from uMkhanyakude district, South Africa. The two databases contained data on key demographic variables such as patient first name, surname, date of birth, sex, and health facility, and national ID numbers for a subset of the data. We adapted a probabilistic record linkage algorithm we previously developed for linkage of laboratory results. We trained and validated our algorithm using two approaches: 1) firstly, we constructed a quasi-gold standard based on manual review of potential matches for 1,061 randomly selected patients; 2) secondly, we constructed a quasi-gold standard based on records that contained national ID numbers. We calculated the probabilities that the algorithm could correctly identify a true match (sensitivity) and the probabilities that the match identified by the algorithm was truly a match (positive predictive value) using the two approaches.&#x0D; ResultsBetween 2015 and 2020, 55,077 patients were recorded in the HIV treatment database and 386,577 laboratory tests were recorded in the laboratory service database. The sensitivity and positive predictive value in the manually reviewed data were estimated to be 94.4% and 81.2% respectively. The sensitivity and positive predictive value in the matched individual identifiers were estimated to be 99.6% and 99.7% respectively.&#x0D; ConclusionsRecords can be linked successfully, but estimated performance of record linkage depends on the validation set used. Manually reviewed data contain noise and may underestimate performance, while national ID numbers may overestimate performance due to non-random patterns of missingness.

Clinical review of the clinical necessity of lumbar punctures performed on adults at National District Hospital Emergency Department

BackgroundPrevious studies have found that indications for lumbar punctures (LPs) are managed differently, which raises the question of whether all LPs performed are clinically necessary. This study aimed to determine whether unnecessary (clinically not indicated) LPs were being performed at a district hospital in the Free State, South Africa.MethodThis was a retrospective descriptive study. A list from the National Health Laboratory Service (NHLS) was used to identify all patients on whom an LP was performed in the adult emergency department of National District Hospital (NDH) in Bloemfontein, from 1 January 2018 to 30 June 2018. Data were captured on a data sheet and included demographic information, clinical signs and symptoms the patients presented with and the cerebrospinal fluid results.ResultsA total of 364 patients fit the inclusion criteria. Of these patients, 97 files (26.6%) could not be found, patient gender and LP results could be retrieved from the NHLS barcodes. After reviewing the presenting symptoms and signs captured on the 267 files, the primary researcher considered 150 (56.4%) of the LPs performed to have been carried out unnecessarily. From the total population of 364 patients, 246 (67.6%) of the LP results were normal. Only 118 (32.4%) of the LPs performed showed some form of central nervous system pathology. Of the 150 LPs assessed to have been unnecessarily performed, 124 (84.0%) were normal.ConclusionThis retrospective review indicates that a high percentage of LPs that were clinically not indicated were performed at NDH during the study period.

Establishment of haemoglobin A2 reference intervals in Pretoria, South Africa: A retrospective secondary data analysis.

BackgroundHaemoglobinopathies are one of the most common inherited diseases worldwide. Quantification of haemoglobin A2 is necessary for the diagnosis of the beta thalassaemia trait. In this context, it is important to have a reliable reference interval for haemoglobin A2 and a local reference range for South Africa has not been established.ObjectiveThis study aimed to establish reference intervals for haemoglobin A2 using stored patient laboratory data.MethodsThis descriptive study used retrospective data to evaluate haemoglobin A2 levels determined using high-performance liquid chromatography at the National Health Laboratory Service haematology laboratory in Pretoria, South Africa. All tests performed from 01 October 2012 to 31 December 2020 were screened for inclusion; of these, 144 patients’ data met the selection criteria. The reference interval was calculated using descriptive statistics (mean and standard deviation) with a 95% confidence interval.ResultsAnalysed data from enrolled patients showed a normal distribution. The mean age of the patients was 40 years (range: 3–84 years). The reference interval for haemoglobin A2 calculated from this data was 2.3% – 3.6%. The minimum haemoglobin A2 was 2.3% and the maximum was 3.9% with a mean of 2.95% and a standard deviation of 0.357%.ConclusionA normal reference interval has been established for the population served by the laboratory that will assist with accurate diagnosis of the beta thalassaemia trait. This reference interval may also be useful to other laboratories that employ the same technology, especially smaller laboratories where obtaining a sufficiently large number of normal controls may be challenging.

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

BackgroundThe 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.ObjectiveThis study aimed to assess the comprehensive cost of running a full-service receiving office (RO) at the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) laboratory.MethodsTop-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.ResultsThe 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.ConclusionProviding 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.

Evaluating patient data quality in South Africa’s National Health Laboratory Service Data Warehouse, 2017-2020: implications for monitoring child health programmes

BackgroundSouth Africa’s National Health Laboratory Service (NHLS), the only clinical laboratory service in the country’s public health sector, is an important resource for monitoring public health programmes.ObjectivesWe describe NHLS data quality, particularly patient demographics among infants, and the effect this has on linking multiple test results to a single patient.MethodsRetrospective descriptive analysis of NHLS data from 1st January 2017—1st September 2020 was performed. A validated probabilistic record-linking algorithm linked multiple results to individual patients in lieu of a unique patient identifier. Paediatric HIV PCR data was used to illustrate the effect on monitoring and evaluating a public health programme. Descriptive statistics including medians, proportions and inter quartile ranges are reported, with Chi-square univariate tests for independence used to determine association between variables.ResultsDuring the period analysed, 485 300 007 tests, 98 217 642 encounters and 35 771 846 patients met criteria for analysis. Overall, 15.80% (n = 15 515 380) of all encounters had a registered national identity (ID) number, 2.11% (n = 2 069 785) were registered without a given name, 63.15% (n = 62 020 107) were registered to women and 32.89% (n = 32 304 329) of all folder numbers were listed as either the patient’s date of birth or unknown. For infants tested at < 7 days of age (n = 2 565 329), 0.099% (n = 2 534) had an associated ID number and 48.87% (n = 1 253 620) were registered without a given name. Encounters with a given name were linked to a subsequent encounter 40.78% (n = 14 180 409 of 34 775 617) of the time, significantly more often than the 21.85% (n = 217 660 of 996 229) of encounters registered with a baby-derivative name (p-value < 0.001).ConclusionUnavailability and poor capturing of patient demographics, especially among infants and children, affects the ability to accurately monitor routine health programmes. A unique national patient identifier, other than the national ID number, is urgently required and must be available at birth if South Africa is to accurately monitor programmes such as the Prevention of Mother-to-Child Transmission of HIV.

Delays in HIV-1 infant polymerase chain reaction testing may leave children without confirmed diagnoses in the Western Cape province, South Africa

BackgroundEarly diagnosis and confirmation of HIV infection in newborns is crucial for expedited initiation of antiretroviral therapy. Confirmatory testing must be done for all children with a reactive HIV PCR result. There is no comprehensive data on confirmatory testing and HIV PCR test request rejections at National Health Laboratory Service laboratories in South Africa.ObjectiveThis study assessed the metrics of routine infant HIV PCR testing at the Tygerberg Hospital Virology Laboratory, Cape Town, Western Cape, South Africa, including the proportion of rejected test requests, turn-around time (TAT), and rate of confirmatory testing.MethodsWe retrospectively reviewed laboratory-based data on all HIV PCR tests performed on children ≤ 24 months old (n = 43 346) and data on rejected HIV PCR requests (n = 1479) at the Tygerberg virology laboratory over two years (2017–2019). Data from sample collection to release of results were analysed to assess the TAT and follow-up patterns.ResultsThe proportion of rejected HIV PCR requests was 3.3%; 83.9% of these were rejected for various pre-analytical reasons. Most of the test results (89.2%) met the required 96-h TAT. Of the reactive initial test results, 53.5% had a follow-up sample tested, of which 93.1% were positive. Of the initial indeterminate results, 74.7% were negative on follow-up testing.ConclusionA high proportion of HIV PCR requests were rejected for pre-analytical reasons. The high number of initial reactive tests without evidence of follow-up suggests that a shorter TAT is required to allow confirmatory testing before children are discharged.

PB2341: MIDAZOLAM AND LOCAL ANAESTHESIA CO-ADMINISTRATION GIVES BETTER PAIN CONTROL DURING THE BONE MARROW ASPIRATION AND BIOPSY PROCEDURE

Background: During the bone marrow aspiration and biopsy (BMAB) procedure, patients report pain of varying intensity ranging from complete absence of pain to severe pain. There is limited literature on the patient and procedure related factors associated with the pain. Furthermore, evidence-based guidelines on the best method of pain management during BMAB are lacking. The use of local anaesthesia(LA) only is still widespread although it does not abolish the pain of BMAB. Conscious sedation, other pharmacological agents and non-pharmacological interventions are used to a variable extent. Midazolam is the most commonly used benzodiazepine for conscious sedation and may be used in conjunction with local anaesthesia, other systemic pharmacological agents or as a single agent. Our centre introduced universal midazolam sedation unless there is a contraindication to its use, 4 years ago. Aims: To assess the impact of the universal use of intravenous midazolam premedication for the BMAB procedure compared to the use of local anaesthesia only and to determine the patient- and procedure-related factors associated with the patient-reported pain. Methods: A retrospective cross-sectional study was performed on adult patients who had a BMAB in a day procedure operating theatre over the period from 1st July 2018 to 30th March 2019. Patient demographics, the body mass index (BMI), indications, diagnosis, the number of times the patient had the BMAB procedure and the experience of the operator were documented. A numerical rating scale pain assessment tool and questionnaire were used in interviews conducted by the principal investigator. Further data were extracted from the National Health Laboratory Service laboratory information system, patients’ hospital files and the operating theatre records. Results: A total of 182 BMAB procedures were included in the study; 155 procedures performed with midazolam premedication and 27 performed using local anaesthesia only. Pain was reported in all procedures performed under local anaesthesia and only in 29.1% of procedures performed with midazolam administration. Our study showed no influence of age, sex, race, level of educations, indication, diagnosis, experience of the operator on pain. Patients who had previous BMAB experienced less pain. Midazolam dose showed negative correlation with pain. Summary/Conclusion: Local anaesthesia only is not enough to abolish pain of BMAB. Midazolam conscious sedation used with local anaesthesia consistently reduces the reported pain to acceptable levels. Patients with previous experience of BMAB under midazolam premedication reported less pain. The universal use of midazolam conscious sedation for BMAB under carefully controlled circumstances is strongly recommended.