National Health Laboratory Service Research Articles

The relationship between seasonality and the diagnosis of acute leukaemia in central South Africa

Background: Leukaemias are haematological malignancies resulting from the abnormal clonal proliferation of haematopoietic precursors. Their incidence is influenced by various environmental and genetic factors.Aim: With this retrospective descriptive study, the authors aimed to explore the possible influence of seasonality on the type and number of acute leukaemia (AL) diagnoses made at the Universitas Academic Hospital (UAH) National Health Laboratory Service (NHLS) from 01 January 2018 to 31 December 2021.Setting: Universitas Academic Hospital, Bloemfontein, South Africa.Methods: Archived laboratory reports of all patients diagnosed with lymphoid and myeloid during the study period were included. Patients’ age, sex, ethnicity, final diagnosis and date of diagnosis were recorded. Information was pseudonymised to maintain confidentiality. A descriptive statistical analysis was performed to explore the possible influence of seasonality on the number of cases and type of leukaemia diagnosed.Results: In all, 249 patients were included. Acute myeloid leukaemia (AML) was the most common AL subtype (n = 117; 47.0%). Over the 4-year study period, all AL subtypes were more frequently diagnosed in summer (n = 131; 52.6%). However, the monthly number of AL diagnoses was relatively consistent over the 4 years for all subtypes (p = 0.7603), with consistent peaks of AML cases during January and February (summer) and May (autumn).Conclusion: No statistically significant association between the different seasons and AL diagnosis was noted.Contribution: Further studies using a larger study population and a wider geographical area, conducted over a more extended period, might affect the observations made in this study

Risk factors for and timing of presumptive recurrent TB.

<sec><title>INTRODUCTION</title>Understanding factors associated with increased risk for tuberculosis (TB) recurrence is essential in lowering the TB burden. We aimed to quantify the burden, risk factors, and timing of TB presumptive recurrence.</sec><sec><title>METHODS</title>We analyzed test results from 2013 to 2017 in the South African National Health Laboratory Service's database. We defined a person's TB episode to start with their first positive TB test. In the absence of treatment outcome data, we assumed the episode concluded 6 months later for rifampicin-susceptible TB (RS-TB) and 18 months later for rifampicin-resistant TB (RR-TB), provided that at least one negative smear or culture test was recorded within this period. We defined a presumptive recurrent TB episode to start with a positive TB test after the completion of a prior episode. We calculated recurrence measures stratified by various demographics and RR-TB status.</sec><sec><title>RESULTS</title>Of 574,316 people with RS-TB, 4.7% experienced at least one presumptive recurrent TB episode. Higher local TB notification rates, HIV coinfection, and males experienced higher recurrence rates. Most (89.4%) of the first RS-TB recurrences occurred within a year of the initial episode.</sec><sec><title>CONCLUSION</title>Our findings of when and among whom recurrent TB is more likely to occur can be used to assist early interventions and inform impact on patient care.</sec>.

Reducing colorectal cancer mortality in South Africa: experiences and progress from the South African National Cancer Prevention Services

Aim The incidence rates of colorectal cancer are rapidly increasing in South Africa. Previous studies have shown that the prevalence of inherited colorectal cancer in South Africa is 3-5 times higher than in high-income countries. Targeted screening and surveillance programmes for individuals with known colorectal cancer-causing mutations have resulted in increased life expectancy. The South African National Cancer Prevention Services (SANCaPS), was established to implement national systems for identifying individuals with inherited cancers, improving their clinical management, and reducing the overall disease burden. Methods Using colorectal cancer as an example, SANCaPS aimed to extend surveillance and management practices from the Western Cape to a national level. The goals included improving the quality of pathology reporting, establishing counselling systems for at-risk individuals, developing cost-effective mutation detection protocols, identifying and counselling at-risk family members, providing mutation testing, organising endoscopic surveillance programmes for high-risk individuals, setting ethical frameworks for research, and extrapolating learnings from the inherited colorectal cancers surveillance programme to other cancers with known hereditary predispositions. Results SANCaPS initiated the standardisation of national pathology reporting for colorectal cancers. Currently, a minimum core pathology dataset collection is being piloted in the National Health Laboratory Service’s TrakCare system. Subsequently, SANCaPS aims for broader adoption through stakeholder engagements. This will help to identify patients with mismatch repair-deficient colorectal cancers, facilitate research, and improve reporting. Conclusions To improve patient outcomes, this consultative process and framework will be replicated to introduce standardised management workflows for other common cancers, including breast, prostate, uterine, and others.

The implementation and outcome of a breast cancer genetic counselling service at Potchefstroom Hospital: a model for outreach

Aim Breast cancer is the most prevalent cancer in South African females, making up 27.1% of all histologically diagnosed cancers in 2020. Although genetic technology and awareness of genetic counselling have improved, genetic counselling services in South Africa remain largely inaccessible. Clinical genetic services are only formally available in four South African provinces and few outreach programmes exist for small towns and cities. Until 2019, genetic counselling services were unavailable in the North West province; however, since then, genetic counsellors from the National Health Laboratory Service and the University of the Witwatersrand have provided genetic counselling services to patients at the Breast Clinic at Potchefstroom Hospital regularly each year. Method The aim of this pilot study was to perform a retrospective file review and report on the implementation and outcomes of the genetic counselling service at the Breast Clinic at Potchefstroom Hospital, from its inception in 2019, until November 2022. Fifty-two patients attended a genetic counselling consultation during that period. Results The majority of patients (83.7%) were diagnosed with an invasive ductal carcinoma, and 57.7% of the patients had a family history of cancer. A total of 62.8% of patients had a histologic grade 3 tumour. A total of 25.5% (12/47) of patients tested positive for a pathogenic variant in BRCA1 or BRCA2. A total of 45 at-risk first-degree relatives were identified who could benefit from predictive testing. Conclusions This study highlights the benefit of offering clinical genetics services through outreach clinics. Being able to offer this service is not only beneficial for the management of the affected individuals, but also for their at-risk relatives. The initiative serves as a positive example of how limited resources can be extended to benefit patients.

Are social protection and food security accelerators for adolescents to achieve the Global AIDS targets?

Without effective, scalable interventions, we will fail to achieve the Global AIDS Targets of zero AIDS-related deaths, zero HIV transmission and zero discrimination. This study examines associations of social protection and food security among adolescents living with HIV (ALHIV), with three Global AIDS Targets aligned outcomes: antiretroviral treatment (ART) adherence and viral suppression, HIV transmission risk behaviour and enacted stigma. We conducted three study visits over 2014-2018 with 1046 ALHIV in South Africa's Eastern Cape province. Standardized surveys provided information on receipt of government-provided cash transfers and past-week food security, alongside self-reported ART adherence, sexual debut and condom use, and enacted HIV-related stigma. Viral load (VL) data was obtained through data extraction from patient files and linkage with National Health Laboratory Service test results (2014-2020). We used a multivariable random-effects regression model to estimate associations between receiving government cash transfers and food security and three outcomes: ART adherence and viral suppression, delayed sexual debut or consistent condom use and no enacted stigma. We tested moderation by sex and age and fitted disaggregated models for each outcome. Among the 933 ALHIV completing all three study visits, 55% were female, and the mean age was 13.6 years at baseline. Household receipt of a government cash transfer was associated with improvements on all outcomes: ART adherence and viral suppression (aOR 2.03, 95% CI 1.29-3.19), delayed sexual debut or consistent condom use (aOR 1.62, 95% CI 1.16-2.27) and no enacted stigma(aOR 2.33, 95% CI 1.39-3.89). Food security was associated with improvements on all outcomes: ART adherence and viral suppression (aOR 1.73, 95% CI 1.30-2.30), delayed sexual debut or consistent condom use (aOR 1.30, 95% CI 1.03-1.64) and no enacted stigma (aOR 1.91, 95% CI 1.32-2.76). Receiving both cash transfers and food security increased the probability of ART adherence and VL suppression from 36% to 60%; delayed sexual debut or consistent condom use from 67% to 81%; and no enacted stigma from 84% to 96%. Government-provided cash transfers and food security, individually and in combination, are associated with improved outcomes for ALHIV aligned with Global AIDS Targets. They may be important, and underutilized, accelerators for achieving these targets.

Demographic and pathogen characteristics of incident bacterial meningitis in infants in South Africa: A cohort study.

Bacterial meningitis is a major cause of death, with an approximate case fatality rate of 37% across all age groups in South Africa. This study aimed to describe the demographic and pathogen characteristics of incident meningitis in children aged <1 year in South Africa from 2014 through 2018, during a period when Haemophilus influenzae type b vaccine and pneumococcal conjugate vaccines (PCV) were both included in the expanded program on immunization (EPI). We conducted a cohort study of routine laboratory data in the National Health Laboratory Service Corporate Data Warehouse, which covers approximately 80% of the South African population. We defined a case of laboratory-confirmed bacterial meningitis as any person aged <1 year with meningitis diagnosed by culture and identification of a pathogen documented as being a common cause of meningitis in CSF. The cause-specific incidence risks were calculated by dividing the number of positive specimens in each age group and year by the corresponding mid-year population for children under 1 year old and those in the post-neonatal period (≥ 28 days to 365 days old). For children under 28 days old, the annual numbers of registered livebirths were used. We used Poisson regression to compare the incidence of meningitis by year. We identified 3575 (1.5%) cases of culture-confirmed bacterial meningitis from the 232,016 cerebrospinal fluid (CSF) specimens tested from 2014-2018. The highest number of cases were recorded in children aged <28 days (1873, 52.4%), male children (1800, 50.4%) as well as in the Gauteng Province (2014, 56.3%). Acinetobacter baumannii (14.9%), followed by Klebsiella pneumoniae (13.5%), and group B streptococcus (GBS) (10.7%), were the most common pathogens detected. Overall, A. baumannii had the highest incidence risk, occurring at 9.8 per 100,000 persons in children aged <1 year in 2018. Among neonates, A. baumannii peaked at 14.9 per 100,000 livebirths in 2018, while Streptococcus pneumoniae was most common in the post-neonatal period (≥ 28 days to 365 days old), peaking at 9.8 per 100,000 persons in 2014. There was an increase in the annual incidence of most pathogens over the study period. There was an increasing trend in the annual incidence of bacterial meningitis in infants caused by most pathogens, particularly A. baumannii, K. pneumoniae and GBS. In addition to increased uptake of vaccination, prevention measures to reduce nosocomial and mother-to-child transmission of bacteria could include antenatal screening for GBS in pregnant women, rigorous hygiene in the hospital environment as well as rational antibiotic use.

Cohort profile: Rahima Moosa Mother and Child Hospital maternal HIV cohort, Johannesburg, South Africa

PurposeThe Rahima Moosa Mother and Child Hospital (RMMCH) maternal HIV cohort originated from data systems that were developed to support HIV-related birth care and track outcomes of a complete birth...

Performance of an in-house multiplex PCR assay for HIV-1 drug resistance testing – A cheaper alternative

BackgroundCurrently, most HIV drug resistance PCR assays amplify the protease-reverse transcriptase (PR-RT) fragment separately from the integrase (IN) fragment. The aim of this study was to develop a multiplex PCR assay that simultaneously amplifies PR-RT and IN fragments for HIV-1 drug-resistance testing. MethodsThe in-house multiplex PCR assay was evaluated on extracted total nucleic acids obtained from the National Health Laboratory Service (NHLS) and Lancet laboratories. Sanger sequencing was performed on amplicons, and HIV-1 drug-resistance mutations (DRMs) were assessed using HIV Stanford drug resistance database. ResultsThis study tested 59 patient samples with known HIV-1 viral load and DRM results; 41 from Lancet and 18 from NHLS. In-house multiplex PCR assay detected one or both fragments in most samples but had higher sensitivity for detection of IN fragment (93.2 %) compared to PR-RT fragment (83.1 %). There was 100 % concordance between Lancet assay versus in-house assay sequence data for IN DRMs, but lower concordance with PR-RT (87.0 %). The in-house multiplex PCR assay’s precision and reproducibility analysis showed ≥99.9 % sequence similarity and yielded similar DRM results for both PR-RT and IN fragments. ConclusionsThe in-house multiplex PCR assay demonstrated satisfactory performance and higher sensitivity for IN fragment amplification. This could be a cost-effective method for HIV-1 drug resistance testing as both PR-RT and IN fragments are successfully amplified in one reaction in most samples.

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.