Laboratories play a significant role in the diagnosis, monitoring and treatment of diseases.¹ Multiple factors affect specimen losses in the pathology value chain (PVC), such as the capacity of the laboratory workforce, laboratory infrastructure, availability of equipment and specimen collection materials and pre- and post-analytical factors.^1,2 The total testing process (TTP) in the PVC comprises three phases: (1) pre-analytical, (2) analytical, and (3) post-analytical.^3,4 The pre-analytical phase includes all procedures performed before the specimen reaches the laboratory, that is specimen collection, packaging, storage and transport.^3,4 In contrast, the analytical phase refers to the actual laboratory test analysis (sample preparation, testing and troubleshooting).^3,4 The post-analytical phase includes test result review and release to the health care worker (HCW).^3,4 It has been estimated that most errors are because of pre-analytical factors (46% – 68.2%) followed by post-analytical factors (18.5% – 47%).² Errors in the analytical phase, which include sample preparation errors, equipment malfunction and instrument downtime, have been significantly reduced because of state-of-the-art technology (closed, fully automated systems) and a focus on quality through both internal and external quality control measures.^2,5

Losses in the PVC are defined as specimens collected from patients attending a health facility for laboratory testing that have been registered in the paper-based register but are not found in the laboratory information system (LIS) or that have been subsequently rejected.^2,5,6,7 This is confirmed by the primary health care (PHC) laboratory handbook that states that specimens should be collected, packaged, stored and prepared for transportation, and the laboratory results should be received.⁶ Where this has not taken place, it can be defined as a PVC loss.⁶ This implies that specimens were collected for which no clinical decision could be made for patient management. These PVC specimen losses may occur at multiple points of the TTP and result in missed diagnostic opportunities (MDO) that potentially affect patient clinical management.^8,9 In addition, PVC losses also result in the patient having to return to the PHC facility for an additional visit for a repeat specimen to be collected. A local study indicated that patients accessing antiretroviral therapy (ART) incurred expenses that consisted of transportation as well as payment for medical care.¹⁰ Therefore, PVC losses should be minimised to reduce MDO and retain patients in care.

The reasons for specimen losses in the PVC may include: incomplete request forms (such as the failure to provide mandatory data variables), specimen collection errors, specimens lost in transit, data capturing errors, haemolysed or clotted specimens, as well as analytical challenges.^4,11 There are many pre-analytical challenges between the health facility and the laboratory that cannot be assessed because of the paper-based recording systems and the absence of specimen tracking outside the LIS.^4,11 The paper-based systems make it difficult to assess PVC losses outside of electronic data generated by the laboratory.

The LIS belongs to the class of application software intended for the storage and management of information obtained in the course of the work of the laboratory service.¹² The systems are used to control and manage specimens, standards, test results, reports, laboratory staff and instruments, as well as workflow automation.¹² Within the LIS, electronic dates and times are allocated when specimens are registered, tested and reviewed. In addition, when specimens are referred within the national laboratory network, electronic dates and times are allocated when the specimens are referred and received at the testing laboratory. Furthermore, when a test is rejected, the date of rejection is also captured on the LIS. The electronic date/time information is vital in the laboratory network to assess turnaround time performance.^13,14 Furthermore, the outstanding testing can be identified using the LIS.

There have been platforms such as eLABS that are used to track specimens across the PVC.¹⁵ eLABS is a mobile workflow solution where HCWs are able to request tests and capture a sample barcode as well as the patient details.^15,16 The specimens are tracked from acquisition by the HCW and at each step of the laboratory workflow.^15,16

Once results are available, HCWs are notified on the mobile application.^15,16 Through use of ‘Results for Action’, facilities become aware of results that require triaging quicker than traditional methods of result delivery.^15,16 In addition, the eLABS patient support module (PSM) sends test results, relevant educational messages and appointment reminders directly to patients.^15,16 However, these systems have only been implemented for selected tests and facilities in health districts supported by both the Centers for Disease Control and Prevention (CDC) and the President’s Emergency Plan for AIDS Relief (PEPFAR).^15,17 There are also initiatives to develop a Health Patient Registration System (HPRS) in South Africa for use by PHC facilities.⁶ Despite the existence of these systems, the clinic-laboratory interface (CLI) is still paper based.^18,19 Order entry is an application that enables HCWs to create electronic orders within the facility. This will replace traditional pen-and-paper request forms and registers for ordering laboratory investigations.^20,21,22 With order entry, the HCW can select the tests required, with the patient and HCW information populated by a system such as the HPRS.²¹ The order is electronically transmitted to the LIS and the patient result outcomes are returned electronically – removing the need for paper-based systems.^21,23 The absence of order entry systems in a South African health setting makes it difficult to objectively assess PVC specimen losses as data are only captured electronically once registered in the LIS.

Assessing PVC specimen losses using only LIS data may be an underestimate as it does not account for losses prior to registration at the local laboratory. Therefore, the facility register that records the request form barcode for every patient offers an objective mechanism to assess PVC specimen losses outside the LIS. An objective audit of PVC losses is needed for all tests included as part of the PHC package of services in a local setting, given the limited data available.²⁴

In all, 34 PHC facilities were selected for the study from 117 PHC facilities in Gauteng province (Table 1). These included: 5 (Bophelong Ivory Park, Diepsloot South clinic, Ebony Park CHC, Hikhensile and OR Tambo CHC), 5 (Bosmont clinic, Randburg clinic, Riverlea Major clinic, Sophiatown clinic and Westbury CHC), 4 (Davidonsville clinic, Discoverers CHC, Florida clinic and Rex Street Clinic), 3 (Chiawelo CHC, Lillian Ngoyi CHC and Mofolo CHC), 5 (Alexandria 8th Avenue clinic, Alexandria CHC, East bank clinic, Orchards clinic and Thokomngoma clinic), 5 (Esselen clinic, Hillbrow CHC, Jeppe clinic, Kibler park clinic and Yeoville clinic) and 7 (Cosmo clinic, Ennerdale Extension 8, Freedom Park clinic, Lenasia Extension 13, Lenasia South Civic Centre, Stretford CHC and Thulamntwana) facilities for sub-districts A to G, respectively. There were 34 494 barcodes scanned for this study. Of these, 582/34 494 (1.69%) were excluded because of barcode length. Four barcodes (4/34 494) were excluded as the ‘P’ suffix was missing (0.01%). Test codes associated with surveillance were also excluded (n = 41/34 494; 0.12%) (Figure 1). An example of surveillance testing would include measles testing during an outbreak. The final study dataset analysed included 33 867/34 494 (98.18%) barcodes that had 121 697 associated test codes. On average, there were 3.59 test codes per barcode. Matching registered dates from the laboratory repository were detected for 33 526/33 867 (98.99%) barcodes. Of these, a tested and reviewed date was not found for 419/33 526 barcodes (1.24%). A rejection for one or more test codes was detected for 1961/33 867 barcodes (5.79%).

This is one of the first studies to assess losses in the PVC for a large sample size. Most of the studies that have analysed losses in the PVC outside South Africa have been described for surgical specimens.^7,30,31 The study findings revealed that PVC losses where barcodes were scanned in the facility register but not found in the laboratory repository was 1.01%. However, there was a further 1.24% that did not have a corresponding tested/reviewed data. In addition, 5.79% of barcodes had one or more test codes that were rejected. At the sub-district level, barcodes without a corresponding tested/reviewed date increased to 4.11%. Similarly, the RR increased to 10.9% when analysed at the sub-district level. Carmack et al. conducted a systematic review, which highlighted the limited research in this area, with an average of two articles per year discussing lost specimens.³¹ It is, therefore, difficult to interpret PVC losses for this study comparatively.

It has been reported that the RR for CD4 testing (excluding electronic gatekeeping) ranged from 2.2% to 4.4% at the provincial level in 2019.³² Similarly, a local study at an academic hospital reported that for HIV 1/2 serology, the RR was as high as 11.1%.³³ In contrast, an analysis of rejections at the Green Point complex tuberculosis laboratory reported a rate of 2.3% over a 2-year period.³⁴ The National Priority Programme (NPP) internal report for April 2024 reported a RR of 4.5%, 4.7%, 2.7% and 2.7% for Xpert MTB/RIF, CD4, HIV viral load and HIV DNA PCR testing, respectively.³⁵ The RR is test dependent and our findings are within the range reported locally.^32,33,34,35 However, at the sub-district level, higher RR was reported for Region D, which warrants further investigation. Clearly, the interpretation of RR is context and test specific, with a host of other factors that may play a role.

For this study, losses in the PVC were similar for clinics and CHC. Overall, losses were slightly higher for CHC as well as reporting a higher rate of test codes per barcode. This finding is expected as CHC have a broader package of services that includes a 24-h midwife obstetric unit (MOU), emergency unit and the provision of health support services (physical rehabilitation by physical therapist and occupational therapist, speech and hearing therapy, dietetics, social worker support) as well as oral health services.³⁶ The higher RR for CHC could also be linked to the broader package of services as well as a larger health facility servicing a broader catchment area.³⁶

According to the PHC essential laboratory list (ELL) and updated 2020 Standard Treatment Guidelines (STG) and Essential Medicines List (EML), all top 20 test codes reported for the study are compliant with testing recommendations for this level of care.^6,24 Some testing such as Serum Indices were not indicated in the PHC ELL, but were included in the standard of care in the 2020 STG & EML.²⁴ This is consistent with findings by Mahommed et al. that reported that between 98.2% and 99.1% of testing in the COJ was ELL compliant.³⁷ This highlights the need for PHC ELL and laboratory handbooks to be updated to ensure consistency with updated guidelines.^24,37,38 For example, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing should have been included during the coronavirus disease 2019 (COVID-19) pandemic.^39,40 The PHC ELL should become a real-time document that is continually updated based on new outbreaks as well as guideline changes.^24,38 South Africa should follow the example set by Nigeria that is in line with the World Health Organization (WHO) recommendation for the development and implementation of the National Essential Diagnostics List (NEDL) to facilitate the availability of diagnostic services.^41,42

There are multiple reasons why specimens collected at the health facility are not recorded in the laboratory repository. It has been reported that most errors occur during the pre-analytical and post-analytical phases of the CLI.^2,43 Some of these pre-analytical factors contributing specifically to barcodes not being recorded in the LIS could include: barcodes captured in the register without being collected, specimens collected but not given to the courier or specimens lost during courier transport or at the receiving office prior to capture in the LIS. Unfortunately, this study did not attempt to provide clarity on the exact reason for PVC specimen losses, given the absence of a specimen tracking system. As this was a retrospective study, it would be too late to conduct a vertical audit for the barcodes that were registered but not tested or reviewed.

Continuous audits are warranted, given the wider range in PVC losses, which was not statistically significant at the sub-district level, in particular. The routine and continuous audit of PVC losses would facilitate performance of root cause analysis by both the Department of Health and diagnostic service providers. After the investigation, corrective actions should be taken to reduce losses that will ultimately result in both improved patient care and reduced wastage. This could be conducted routinely by using paper-based facility registers to scan barcodes. To avoid the manual analysis of PVC losses, it is proposed that a cloud-based solution be developed by the CDW. Scanned barcode lists could be uploaded on a portal, processed via an extract, transformed and loaded (ETL) in a data warehouse, compared to LIS data, and used to generate PVC loss reports and dashboards for electronic access or email distribution. These dashboards could also be included as part of the overall quality management system. This would make it possible for managers to conduct a more automated audit of PVC losses. The only investment required would be for laboratory coordinators to be provided with handheld barcode scanners and some development within the CDW. This study could also be further enhanced should order entry be implemented, as routine monitoring of PVC losses would be facilitated.^21,44,45 Order entry would potentially extend the capacity to allow for financial reconciliation and better tracking of specimens. This study also demonstrated the value of well-curated laboratory data.⁴⁶

This study demonstrated an objective methodology independent of the LIS, showing that 4.05% of specimens not tested/reviewed, with a further 5.79% with a rejection. These findings indicate the need for implementation of continuous or frequent/periodic audits of PVC specimen losses in the public health sector. It would be possible to use the existing facility registers to routinely scan barcodes to conduct an audit of PVC losses. Automated solutions could be developed to enable audits to be conducted more autonomously and to detect higher levels of PVC losses earlier. This in turn would allow for more rapid and targeted interventions.