Molecular technology revolutionized the diagnosis of tuberculosis (TB) with a paradigm shift to faster, more sensitive, clinically relevant patient care. The most recent molecular leader is the GeneXpert MTB/RIF assay (Xpert) (Cepheid, Sunnyvale, CA), which was endorsed by the World Health Organization with unprecedented speed in December 2010 as the initial diagnostic for detection of HIV-associated TB and for where high rates of drug resistance are suspected. South Africa elected to take an aggressive smear replacement approach to facilitate earlier diagnosis and treatment through the decision to implement the Xpert assay nationally in March 2011, against the backdrop of approximately 6.3 million HIV-infected individuals, one of highest global TB and HIV coinfection rates, no available implementation models, uncertainties around field performance and program costs, and lack of guidance on how to operationalize the assay into existing complex clinical algorithms. South Africa’s national implementation was conducted as a phased, forecasted, and managed approach (March 2011 to September 2013), through political will and both treasury-funded and donor-funded support. Today there are 314 GeneXperts across 207 microscopy centers; over 8 million assays have been conducted, and South Africa accounts for over half the global test cartridge usage. As with any implementation of new technology, challenges were encountered, both predicted and unexpected. This chapter discusses the challenges and consequences of such large-scale implementation efforts, the opportunities for new innovations, and the need to strengthen health systems, as well as the impact of the Xpert assay on rifampin-sensitive and multidrug-resistant TB patient care that translated into global TB control as we move toward the sustainable development goals.

The implementation of antiretroviral therapy demands the need for increased access to viral load (VL) monitoring. Newer real-time VL testing technologies are faster and have larger dynamic ranges and fully automated extraction to benefit higher throughputs in resource-poor environments. The Abbott RealTi m e human immunodeficiency virus type 1 (HIV-1) assay was evaluated as a new option for testing for HIV-1 subtype C in South Africa, and its performance was compared to the performance of existing assays (the Cobas AmpliPrep-Cobas TaqMan HIV-1, version 1, assay; the AmpliPrep-Cobas Monitor standard HIV-1 assay; and the NucliSENS EasyQ-EasyMag HIV-1 assay) in a high-throughput laboratory. The total precision of the RealTi m e HIV-1 assay was acceptable over all viral load ranges. This assay compared most favorably with the Cobas AmpliPrep-Cobas TaqMan HIV-1 assay ( R ² = 0.904), with a low standard deviation of difference being detected (0.323 copies/ml). The bias against comparator assays ranged from −0.001 copies/ml to −0.228 copies/ml. Variability in the reporting of VLs for a 20-member subtype panel compared to the variability of other assays was noted with subtypes G and CRF02-AG. The RealTi m e HIV-1 assay can test 93 samples per day with minimal manual preparation, less staff, and the minimization of contamination through automation. This assay is suitable for HIV-1 subtype C VL quantification in South Africa.

Background: Routine plasma viral load (VL) testing is recommended for monitoring human immunodeficiency virus–infected patients on antiretroviral therapy. In Zambia, VL scale-up is limited due to logistical obstacles around plasma specimen collection, storage, and transport to centralized laboratories. Dried blood spots (DBSs) could circumvent many logistical challenges at the cost of increased misclassification. Recently, plasma separation cards (PSCs) have become available and, though more expensive, have lower total misclassification than DBSs. Methods: Using a geospatial model created for optimizing VL utilization in Zambia, we estimated the short-term cost of uptake/correct VL result using either DBSs or PSCs to increase VL access on equipment available in-country. Five scenarios were modeled: (1) plasma only (status quo); (2) plasma at high-volume sites, DBS at low-volume sites; (3) plasma at high-volume sites, PSC at low-volume sites; (4) PSC only; (5) DBS only. Results: Scenario 1 resulted in 795 342 correct results due to limited patient access. When allowing for full and partial adoption of dried specimens, access increases by 19%, with scenario 3 producing the greatest number of correct results expected (929 857). The average cost per correct VL result was lowest in the plasma + DBS scenario at $30.90 compared to $31.62 in our plasma + PSC scenario. The cost per correct result of using dried specimens only was dominated in the incremental analysis, due primarily to fewer correct results. Conclusions: Adopting the partial use of dried specimens will help achieve improved VL access for patients at the lowest cost per correct result.

South Africa is a country with a high incidence of tuberculosis (TB), complicated by coinfection with human immunodeficiency virus (HIV). The Xpert MTB/RIF (Cepheid, Sunnyvale, CA, USA) is used in South Africa as the test for the initial diagnosis of TB, and other molecular platforms such as the m 2000 (Abbott Molecular, Des Plaines, IL, USA) are widely used for molecular monitoring of HIV load. The latter platform is now also equipped with the RealTi m e (RT) MTB and RealTi m e MTB RIF/INH assays for TB and first-line drug resistance screening but has not been evaluated in settings of HIV and TB coinfection. A prospective clinical validation study was conducted at a community health center in Johannesburg, South Africa, and consenting individuals with presumptive pulmonary TB were enrolled. The performance of the Abbott assays was compared with those of the Xpert MTB/RIF, liquid culture, drug susceptibility testing, and clinical case definitions. A statistical analysis was performed on 206 individuals (73% were HIV positive). The sensitivity and specificity of the RT MTB were 82.5% (confidence interval [CI], 67.2 to 92.7) and 93.1% (CI, 86.2 to 97.2) on raw sputum and 77.5% (CI, 61.5 to 89.2) and 95.1% (CI, 88.9 to 98.4) on concentrated sputum, respectively, compared with those from liquid culture. The RT MTB correctly identified 17/35 more smear-negative culture-positive specimens than the Xpert MTB/RIF. Both the RT MTB and the Xpert MTB/RIF displayed sensitivities >70% and specificities >90% in HIV-positive individuals. The available drug resistance results concurred with MTBDR plus and drug susceptibility profiles. The RT MTB assay has similar diagnostic performance to the Xpert MTB/RIF and is suited to testing presumptive TB patients coinfected with HIV. The existing laboratory information system connectivity, training, and technical support make this a viable polyvalent option to scale up TB alongside HIV laboratory testing services in South Africa.

The early diagnosis of human immunodeficiency virus (HIV) infection in infants is critical to ensure the initiation of treatment before significant immunological compromise. Each year an estimated 300,000 HIV-exposed infants in South Africa require access to tests for the diagnosis of HIV infection. Currently, testing is performed at several facilities by using PCR amplification of HIV DNA at 6 weeks of age by the use of dried blood spots (DBSs) and whole blood (WB). The Gen-Probe Aptima HIV type 1 (HIV-1) screening assay (the Aptima assay) is a qualitative nucleic acid test based on transcription-mediated amplification (TMA), a technology routinely used in blood banks in South Africa. The performance characteristics of Gen-Probe's TMA technology compared well to those of the Roche Amplicor HIV-1 DNA (version 1.5) assay. The sensitivity of the assay with WB and DBS samples was 100%, and the specificities were 99.4% and 99.5% for DBSs and WB, respectively. The detection of HIV by the Aptima assay at greater levels of dilution in samples negative by the comparator assay indicates an improvement in sensitivity by the use of the TMA technology. The ability to process 1,900 samples in a 24-h period on the Tigris instrument makes the Aptima assay an attractive option for high-volume, centralized laboratories.

Blood-based diagnostics are critical for many medical decisions, but mostly rely on venepuncture, which can be inconvenient and painful. The Onflow Serum Gel (Loop Medical SA, Vaud, Lausanne, Switzerland) is a novel blood collection device that utilises needle-free technology to collect capillary blood. In this pilot study, 100 healthy participants were enrolled and provided two Onflow collected specimens and one venous blood specimen. Five chemistry analytes (AST, ALT, LDH, potassium, creatinine) and haemolysis were measured per specimen, and laboratory analyte results were compared. Onflow was found to be more acceptable than venepuncture with lower pain ratings, and 96.5% of participants would use the Onflow method again. All phlebotomists (100%) found Onflow intuitive and user-friendly, with ~1 mL of Onflow blood successfully collected from 99% of participants in <12 min (mean: 6 min, 40 s) and 91% collected on the first attempt. ALT and AST analytes showed no difference in performance, while creatinine generated a negative bias (−5.6 µmol/L), and increased variability was noted with potassium (3.6%CV) and LDH (6.7%CV), although none were clinically relevant. These differences may be due to 35% of Onflow collected specimens having “mild” haemolysis. Onflow is a promising alternative blood collection device that should now be evaluated in participants with expected abnormal chemistries and as an option for self-collection.