Using laboratory data to categorise CD4 laboratory turn-around-time performance across a national programme

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

Background

The Northern Cape is South Africa’s largest province with an HIV prevalence of 7.1% versus a 13.5% national prevalence. CD4 testing is provided at three of five National Health Laboratory Service district laboratories, each covering a 250 km precinct radius. Districts without a local service report prolonged CD4 turn-around times (TAT).

Objective

This study documented the impact of a new CD4 laboratory in Tshwaragano in the remote John Taolo Gaetsewe district of the Northern Cape, South Africa.

Methods

CD4 test volumes and TAT (total, pre-analytical, analytical, and post-analytical) data for the Northern Cape province were extracted for June 2018 to October 2019. The percentage of CD4 results within the stipulated 40-h TAT cut-off and the median and 75th percentiles of all TAT parameters were calculated. Pre-implementation, samples collected at Tshwaragano were referred to Kimberley or Upington, Northern Cape, South Africa.

Results

Pre-implementation, 95.4% of samples at Tshwaragano were referred to Kimberley for CD4 testing (36.3% of Kimberley’s test volumes). Only 7.5% of Tshwaragano’s total samples were referred post-implementation. The Tshwaragano laboratory’s CD4 median total TAT decreased from 24.7 h pre-implementation to 12 h post-implementation (p = 0.003), with > 95.0% of results reported within 40 h. The Kimberley laboratory workload decreased by 29.0%, and testing time significantly decreased from 10 h to 4.3 h.

Conclusion

The new Tshwaragano CD4 service significantly decreased local TAT. Upgrading existing community laboratories to include CD4 testing can alleviate provincial service load and improve local access, TAT and efficiency in the centralised reference laboratory.

Categorising specimen referral delays for CD4 testing: How inter-laboratory distances and travel times impact turn-around time across a national laboratory service in South Africa

Background

The South African National Health Laboratory Service provides laboratory services for public sector health facilities, utilising a tiered laboratory model to refer samples for CD4 testing from 255 source laboratories into 43 testing laboratories.

Objective

The aim of this study was to determine the impact of distance on inter-laboratory referral time for public sector testing in South Africa in 2018.

Methods

A retrospective cross-sectional study design analysed CD4 testing inter-laboratory turn-around time (TAT) data for 2018, that is laboratory-to-laboratory TAT from registration at the source to referral receipt at the testing laboratory. Google Maps was used to calculate inter-laboratory distances and travel times. Distances were categorised into four buckets, with the median and 75th percentile reported. Wilcoxon scores were used to assess significant differences in laboratory-to-laboratory TAT across the four distance categories.

Results

CD4 referrals from off-site source laboratories comprised 49% (n = 1 390 510) of national reporting. A positively skewed distribution of laboratory-to-laboratory TAT was noted, with a median travel time of 11 h (interquartile range: 7–17), within the stipulated 12 h target. Inter-laboratory distance categories of less than 100 km, 101–200 km, 201–300 km and more than 300 km (p < 0.0001) had 75th percentiles of 8 h, 17 h, 14 h and 27 h.

Conclusion

Variability in inter-laboratory TAT was noted for all inter-laboratory distances, especially those exceeding 300 km. The correlation between distance and laboratory-to-laboratory TAT suggests that interventions are required for distant laboratories.

Weekly laboratory turn-around time identifies poor performance masked by aggregated reporting

Background

High-level monthly, quarterly and annual turn-around time (TAT) reports are used to assess laboratory performance across the National Health Laboratory Service in South Africa. Individual laboratory performances are masked by aggregate TAT reporting across network of testing facilities.

Objective

This study investigated weekly TAT reporting to identify laboratory inefficiencies for intervention.

Methods

CD4 TAT data were extracted for 46 laboratories from the corporate data warehouse for the 2016/2017 financial period. The total TAT median, 75th percentile and percentage of samples meeting organisational TAT cut-off (90% within 40 hours) were calculated. Total TAT was reported at national, provincial and laboratory levels. Provincial TAT performance was classified as markedly or moderately poor, satisfactory and good based on the percentage of samples that met the cut-off. The pre-analytical, testing and result review TAT component times were calculated.

Results

Median annual TAT was 18.8 h, 75th percentile was 25 h and percentage within cut-off was 92% (n = 3 332 599). Corresponding 75th percentiles of component TAT were 10 h (pre-analytical), 22 h testing and 1.6 h review. Provincial 75th percentile TAT varied from 17.6 h to 34.1 h, with three good (n = 13 laboratories), four satisfactory (n = 24 laboratories) and two poor performers (n = 9 laboratories) provinces. Weekly TAT analysis showed 12/46 laboratories (28.6%) without outlier weeks, 31/46 (73.8%) with 1-10 outlier weeks and 3/46 (6.5%) with more than 10 (highest of 20/52 weeks) outlier weeks.

Conclusion

Masked TAT under-performances were revealed by weekly TAT analyses, identifying poorly performing laboratories needing immediate intervention; TAT component analyses identified specific areas for improvement.

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

Background

Prostate cancer (PCa) is a leading male neoplasm in South Africa.

Objective

The aim of our study was to describe PCa using Systemized Nomenclature of Medicine (SNOMED) clinical terms codes, which have the potential to generate more timely data.

Methods

The retrospective study design was used to analyse prostate biopsy data from our laboratories using SNOMED morphology (M) and topography (T) codes where the term ’prostate’ was captured in the narrative report. Using M code descriptions, the diagnosis, sub-diagnosis, sub-result and International Classification of Diseases for Oncology (ICD-O-3) codes were assigned using a lookup table. Topography code descriptions identified biopsies of prostatic origin. Lookup tables were prepared using Microsoft Excel and combined with the data extracts using Access. Contingency tables reported M and T codes, diagnosis and sub-diagnosis frequencies.

Results

An M and T code was reported for 88% (n = 22 009) of biopsies. Of these, 20 551 (93.37%) were of prostatic origin. A benign diagnosis (ICD-O-3:8000/0) was reported for 10 441 biopsies (50.81%) and 45.26% had a malignant diagnosis (n = 9302). An adenocarcinoma (8140/3) sub-diagnosis was reported for 88.16% of malignant biopsies (n = 8201). An atypia diagnosis was reported for 760 biopsies (3.7%). Inflammation (39.03%) and hyperplasia (20.82%) were the predominant benign sub-diagnoses.

Conclusion

Our study demonstrated the feasibility of generating PCa data using SNOMED codes from national laboratory data. This highlights the need for extending the results of our study to a national level to deliver timeous monitoring of PCa trends.

Cryptococcal meningitis: a review of cryptococcal antigen screening programs in Africa

INTRODUCTION

Cryptococcal meningitis remains a significant contributor to AIDS-related mortality despite widened access to antiretroviral therapy. Cryptococcal antigen (CrAg) can be detected in the blood prior to development of meningitis. Development of highly sensitive and specific rapid diagnostic CrAg tests has helped facilitate the adoption of CrAg screening programs in 19 African countries.

AREAS COVERED

The biological rationale for CrAg screening and the programmatic strategies for its implementation are reviewed. We describe the approach to the investigation of patients with cryptococcal antigenemia and the importance of lumbar puncture to identify individuals who may have cryptococcal meningitis in the absence of symptoms. The limitations of current treatment recommendations and the potential role of newly defined combination antifungal therapies are discussed. A literature review was conducted using a broad database search for cryptococcal antigen screening and related terms in published journal articles dating up to December 2019. Conference abstracts, publicly available guidelines, and project descriptions were also incorporated.

EXPERT OPINION

As we learn more about the risks of cryptococcal antigenemia, it has become clear that the current management paradigm is inadequate. More intensive investigation and management are required to prevent the development of cryptococcal meningitis and reduce mortality associated with cryptococcal antigenemia.

Timely delivery of laboratory efficiency information, Part I: Developing an interactive turnaround time dashboard at a high-volume laboratory

BACKGROUND

Mean turn-around time (TAT) reporting for testing laboratories in a national network is typically static and not immediately available for meaningful corrective action and does not allow for test-by-test or site-by-site interrogation of individual laboratory performance.

OBJECTIVE

The aim of this study was to develop an easy-to-use, visual dashboard to report interactive graphical TAT data to provide a weekly snapshot of TAT efficiency.

METHODS

An interactive dashboard was developed by staff from the National Priority Programme and Central Data Warehouse of the National Health Laboratory Service, Johannesburg, South Africa, during 2018. Steps required to develop the dashboard were summarised in a flowchart. To illustrate the dashboard, one week of data from a busy laboratory for a specific set of tests was analysed using annual performance plan TAT cut-offs. Data were extracted and prepared to deliver an aggregate extract, with statistical measures provided, including test volumes, global percentage of tests that were within TAT cut-offs and percentile statistics.

RESULTS

Nine steps were used to develop the dashboard iteratively with continuous feedback for each step. The data warehouse environment conformed and stored laboratory information system data in two formats: (1) fact and (2) dimension. Queries were developed to generate an aggregate TAT data extract to create the dashboard. The dashboard successfully delivered weekly TAT reports.

CONCLUSION

Implementation of a TAT dashboard can successfully enable the delivery of near real-time information and provide a weekly snapshot of efficiency in the form of TAT performance to identify and quantitate bottlenecks in service delivery.

Timely delivery of laboratory efficiency information, Part II: Assessing the impact of a turn-around time dashboard at a high-volume laboratory

Background

In South Africa’s National Health Laboratory Service, ad hoc mean turn-around time (TAT) reporting is an important indicator of performance. However, historic static TAT reporting did not assess very long or very short times. An interactive TAT dashboard was developed using the following TAT measures; (1) median, (2) 75th percentile and (3) percentage of within cut-off TAT to allow for improved differentiation of TAT performance.

Objectives

The objective of our study was to demonstrate increased efficiency achieved by using an interactive TAT dashboard.

Methods

A retrospective descriptive study design was used. Creatinine TAT outcomes were reported over 122 weeks from a high-volume laboratory in Gauteng, South Africa. The percentage of within cut-off and 75th percentile TAT were analysed and reported using Microsoft Excel. A focus group session was used to populate a cause and effect diagram.

Results

The percentage of within cut-off TAT increased from 10% in week 4 to 90% and higher from week 81. The 75th percentile decreased from 10 hours in week 4 to under 5 h from week 71. Component TAT analysis revealed that the 75th percentile testing was 5 h or longer for weeks 4, 5 and 48. The 75th percentile review TAT ranged from 1 h to 15 h. From week 41, the review TAT was under 1 h.

Conclusion

Our study demonstrated that the use of an interactive TAT dashboard coupled with good management can dramatically improve TAT and efficiency in a high-volume laboratory.

Magnitude of delayed turnaround time of laboratory results in Amhara Public Health Institute, Bahir Dar, Ethiopia

BACKGROUND

Clinical decisions depend on timely laboratory result reporting. The timeliness is commonly expressed in turnaround time and serves as a quality improvement tool to assess the effectiveness and efficiency of the laboratory. According to the International Organization for Standardization (ISO) guidelines, each laboratory shall establish turnaround times for each of its examinations that reflect clinical needs, and shall periodically evaluate whether or not it is meeting the established turnaround times. Therefore, this study aimed to assess the TAT of laboratory results done in the reference laboratories of the Amhara Public Health Institute, Bahir Dar, Ethiopia.

METHODS

A retrospective cross sectional study was carried out from 01 January to 31 September 2018. Each patient sample was considered as a study unit. Nine months data were extracted from the sample tracking log and from the Laboratory Information System (LIS) database. Descriptive and summary statistics were calculated using SPSS version 20.0 statistical software.

RESULTS

A total of 34,233 patients samples were tested during the study period. Monthly average TAT ranged from 38.6 to 51.3 days for tuberculosis (TB) culture, 5.3 to 42.4 days for exposed infant diagnosis (EID) for HIV, 8.4 to 26 days for HIV 1 viral load, and 1.9 to 3.5 days for TB genexpert tests. Compared with the standard, 76.5% of the viral load, 68.1% of the EID for HIV and 53.8% of the TB genexpert tests had delayed TAT. Repeated reagent stock out, high workload, activities overlapping, and staff turnover were major reasons for the result delays.

CONCLUSIONS

There was a delayed turnaround time of laboratory results in APHI. HIV viral load, EID and TB genexpert results were the most affected tests. Workload reduction plan, proper stock management, specific work assignment and trained staff retention are important approaches to minimize the delayed TAT in the setting.