To Test or Not? Xpert MTB/RIF as an Alternative to Smear Microscopy to Guide Line Probe Assay Testing for Drug-Resistant Tuberculosis.

Xpert MTB/RIF (Xpert) revolutionized tuberculosis (TB) diagnosis. Laboratory decision making on whether widely-used reflex drug susceptibility assays (MTBDRplus, first-line resistance; MTBDRsl, second-line) are conducted is based on smear status, with smear-negative specimens often excluded. We performed receiver operator characteristic (ROC) curve analyses using bacterial load information (smear microscopy grade, Xpert-generated semi-quantitation categories and minimum cycle threshold [CTmin] values) from Xpert rifampicin-resistant sputum for the prediction of downstream line probe assay results as "likely non-actionable" (no resistance or susceptible results generated). We evaluated actionable-to-non-actionable result ratios and pay-offs with missed resistance versus LPAs done universally. Smear-negatives were more likely than smear-positive specimens to generate a non-actionable MTBDRplus (23% [133/559] versus 4% [15/381]) or MTBDRsl (39% [220/559] versus 12% [47/381]) result. However, excluding smear-negatives would result in missed rapid diagnoses (e.g., only 49% [264/537] of LPA-diagnosable isoniazid resistance would be detected if smear-negatives were omitted). Testing smear-negatives with a semi-quantitation category ≥ "medium" had a high ratio of actionable-to-non-actionable results (12.8 or a 4-fold improvement versus testing all using MTBDRplus, 4.5 or 3-fold improvement for MTBDRsl), which would still capture 64% (168/264) and 77% (34/44) of LPA-detectable smear-negative resistance, respectively. Use of CTmins permitted optimization of this ratio with higher specificity for non-actionable results but decreased resistance detected. Xpert quantitative information permits identification of a smear-negative subset in whom the payoffs of the ratio of actionable-to-non-actionable LPA results with missed resistance may prove acceptable to laboratories, depending on context. Our findings permit the rational expansion of direct DST to certain smear-negative sputum specimens.

Comparison of isothermal microcalorimetry and BACTEC MGIT960 for the detection of the metabolic activity of Mycobacterium tuberculosis in sputum samples.

INTRODUCTION: This study explores the uses of microcalorimetry to detect Mycobacterium tuberculosis (TB) in sputum. Microcalorimetry measures metabolic heat evolution during cellular proliferation of tuberculosis (TB) and is considered as a possible alternative to conventional diagnostic tools. OBJECTIVES: To compare the time to detection (TTD) from the BACTEC™ MGIT™ 960 and the calScreener™ calorimetric system. METHODS: Sixty-four sputa samples were selected from patients with confirmed pulmonary tuberculosis. Those sample were then decontaminated and analysed using calorimetry and BACTEC MGIT 960 system. RESULTS: The incubation period until detection of M. tuberculosis in the sample was 8·5 ± 3·7 days for the MGIT system and 10·1 ± 4·1 days (mean ± SD) for calorimetry. CONCLUSIONS: The microincubations in the 48-well format calScreener offers potential for rapid and accurate diagnostic of TB in different samples. Although TTD from calorimetry is still longer than with the MGIT, our findings suggest that several improvements are possible. Still, the instrument is ideal for continuous, real-time analysis of net metabolic heat release of limited sample numbers. SIGNIFICANCE AND IMPACT OF THE STUDY: Our result emphasizes that with further optimization, calorimetry can become an alternative detection method for tuberculosis.

Slow Acceptance of Universal Antiretroviral Therapy (ART) Among Mothers Enrolled in IMPAACT PROMISE Studies Across the Globe.

The PROMISE trial enrolled asymptomatic HIV-infected pregnant and postpartum women not eligible for antiretroviral treatment (ART) per local guidelines and randomly assigned proven antiretroviral strategies to assess relative efficacy for perinatal prevention plus maternal/infant safety and maternal health. The START study subsequently demonstrated clear benefit in initiating ART regardless of CD4 count. Active PROMISE participants were informed of results and women not receiving ART were strongly recommended to immediately initiate treatment to optimize their own health. We recorded their decision and the primary reason given for accepting or rejecting the universal ART offer after receiving the START information. One-third of participants did not initiate ART after the initial session, wanting more time to consider. Six sessions were required to attain 95% uptake. The slow uptake of universal ART highlights the need to prepare individuals and sensitize communities regarding the personal and population benefits of the "Treat All" strategy.

Flower orientation and corolla length as reproductive barriers in the pollinator-driven divergence of Erica shannonea and Erica ampullacea.

A variety of reproductive barriers can enable reproductive isolation and stable coexistence of plant species. Differing floral traits might play an important role in reproductive isolation imposed by pollinators. Such shifts in pollinator use have been hypothesized to contribute to the radiation of Erica (Ericaceae) in the Cape Floristic Region, South Africa. The sister species Erica shannonea and Erica ampullacea co-occur and overlap in flowering phenology. Both have unscented long-tubed flowers consistent with adaptations for pollination by long-proboscid flies (LPFs), but differences in flower orientation and corolla tube length are indicative of a shift in pollinator species. We conducted controlled pollination experiments and pollinator observations to determine the breeding system and pollinators of the two species. Both species are self-incompatible and require pollinator visits for seed production, suggesting that pollinators could strongly influence flower evolution. The horizontally orientated flowers of E. shannonea were found to be pollinated by Philoliche rostrata (Tabanidae), which has a long, fixed forward-pointing proboscis, while the vertically upright orientated flowers of E. ampullacea were found to be pollinated by Prosoeca westermanni (Nemestrinidae), which has a shorter proboscis that can swivel downwards. The nemestrinid fly's proboscis is too short to access the nectar in the relative long-tubed flowers of E. shannonea and the tabanid fly's proboscis cannot swivel down to access the upright flowers of E. ampullacea. Consequently, these traits are likely to act as reproductive barriers between the two Erica species and thereby might have contributed to speciation and enable stable coexistence.

Every maternal near-miss counts: Need for a national audit in South Africa? A mixed-methods study.

BACKGROUND: To improve maternal health, studies of maternal morbidity are increasingly being used to evaluate the quality of maternity care, in addition to studies of mortality. While South Africa (SA) has a well-established confidential enquiry into maternal deaths, there is currently no structure in place to systematically collect and analyse maternal near-misses (MNMs) at national level. OBJECTIVES: To synthesise MNM indicators and causes in SA by performing a systematic literature search, and to investigate perceived needs for data collection related to MNMs and determine whether the MNM tool from the World Health Organization (WHO-MNM) would require adaptations in order to be implemented. METHODS: The study used a mixed-methods approach. A systematic literature search was conducted to find all published data on MNM audits in SA. Semi-structured interviews were conducted virtually with maternal health experts throughout the country who had been involved in studies of MNMs, and main themes arising in the interviews were synthesised. A method for MNM data collection for SA use was discussed with these experts. RESULTS: The literature search yielded 797 articles, 15 of which met the WHO-MNM or Mantel et al. severe acute maternal morbidity criteria. The median (interquartile range) MNM incidence ratio in SA was 8.4/1 000 (5.6 - 8.7) live births, the median maternal mortality ratio was 130/100 000 (71.4 - 226) live births, and the median mortality index was 16.6% (11.7 - 18.8). The main causes of MNMs were hypertensive disorders of pregnancy and obstetric haemorrhage. Eight maternal health experts were interviewed from May 2020 to February 2021. All participants focused on the challenges of implementing a national MNM audit, yet noted the urgent need for one. Recognition of MNMs as an indicator of quality of maternity care was considered to lead to improved management earlier in the chain of events, thereby possibly preventing mortality. Obtaining qualitative information from women with MNMs was perceived as an important opportunity to improve the maternity care system. Participants suggested that the WHO-MNM tool would have to be adapted into a simplified tool with more clearly defined criteria and a number of specific diagnoses relevant to the SA setting. This 'Maternal near-miss: Inclusion criteria and data collection form' is provided as a supplementary file. CONCLUSION: Adding MNMs to the existing confidential maternal death enquiry could potentially contribute to a more robust audit with data that may inform health systems planning. This was perceived by SA experts to be valuable, but would require context-specific adaptations to the WHO-MNM tool. The available body of evidence is sufficient to justify moving to implementation.

Immunologic and imaging signatures in post tuberculosis lung disease.

Post Tuberculosis Lung Disease (PTLD) affects millions of tuberculosis survivors and is a global health burden. The immune mechanisms that drive PTLD are complex and have historically been under investigated. Here, we discuss two immune-mediated paradigms that could drive human PTLD. We review the characteristics of a fibrotic granuloma that favors the development of PTLD via an abundance of T-helper-2 and T-regulatory cells and an upregulation of TGF-ß mediated collagen deposition. Next, we discuss the post-primary tuberculosis paradigm and the complex mixture of caseous pneumonia, cavity formation and fibrosis that can also lead to PTLD. We review the delicate balance between cellular subsets and cytokines of the innate and adaptive immune system in conjunction with host-derived proteases that can perpetuate the parenchymal lung damage seen in PTLD. Next, we discuss the role of novel host directed therapies (HDT) to limit the development of PTLD and in particular, the recent repurposing of established medications such as statins, metformin and doxycycline. Finally, we review the emerging role of novel imaging techniques as a non-invasive modality for the early recognition of PTLD. While access to computed tomography imaging is unlikely to be available widely in countries with a high TB burden, its use in research settings can help phenotype PTLD. Due to a lack of disease-specific biomarkers and controlled clinical trials, there are currently no evidence-based recommendations for the management of PTLD. It is likely that an integrated antifibrotic strategy that could simultaneously target inflammatory and pro-fibrotic pathways will probably emerge as a successful way to treat this complex condition. In a disease spectrum as wide as PTLD, a single immunologic or radiographic marker may not be sufficient and a combination is more likely to be a successful surrogate that could aid in the development of successful HDTs.

Comparative cost and performance of light-emitting diode microscopy in HIV-tuberculosis-co-infected patients.

Light-emitting diode (LED) microscopy has recently been endorsed by the World Health Organization (WHO). However, it is unclear whether LED is as accurate and cost-effective as Ziehl-Neelsen (ZN) microscopy or mercury vapour fluorescence microscopy (MVFM) in tuberculosis (TB)-HIV-co-infected subjects. Direct and concentrated sputum smears from TB suspects were evaluated using combinations of LED microscopy, ZN microscopy and MVFM. Median reading time per slide was recorded and a cost analysis performed. Mycobacterial culture served as the reference standard. 647 sputum samples were obtained from 354 patients (88 (29.8%) were HIV-infected and 161 (26%) were culture-positive for Mycobacterium tuberculosis). Although overall sensitivity of LED compared with ZN microscopy or MVFM was similar, sensitivity of all three modalities was lower in HIV-infected patients. In the HIV-infected group, the sensitivity of LED microscopy was higher than ZN microscopy using samples that were not concentrated (46 versus 39%; p = 0.25), and better than MVFM using concentrated samples (56 versus 44; p = 0.5). A similar trend was seen in the CD4 count <200 cells · mL(-1) subgroup. Median (interquartile range) reading time was quicker with LED compared with ZN microscopy (1.8 (1.7-1.9) versus 2.5 (2.2-2.7) min; p ≤ 0.001). Average cost per slide read was less for LED microscopy (US$1.63) compared with ZN microscopy (US$2.10). Among HIV-TB-co-infected patients, LED microscopy was cheaper and performed as well as ZN microscopy or MVFM independent of the staining (ZN or auramine O) or processing methods used.

Prevalence of genital mycoplasmas, ureaplasmas and chlamydia in pregnancy.

The study was designed to determine the prevalence of genital mycoplasmas, ureaplasmas and Chlamydia on women attending their first prenatal visit, in conjunction with pre-term labour or HIV status. For pre-term labour (2003), 199 women were monitored for pre-term delivery (<37 weeks); for colonisation and HIV (2005), 219 women were screened. Microbial detection was performed on DNA extracted from endocervical swabs employing PCR techniques. Colonisation was seen to be highest in the 14-20 year age group from 2003. In women aged > or = 21 years, co-colonisation was 13%, although there was a shift from co-colonisation with Mycoplasma hominis and Ureaplasma urealyticum in 2003, to other dual/triple combinations in 2005. Overall, major trends from both collection periods were that the prevalence of U. urealyticum tended to be higher in women > or = 26 years, while the prevalence of Chlamydia trachomatis and M. hominis lower. No association was evident between colonisation with M. hominis, U. urealyticum, Ureaplasma parvum and labour outcome. HIV status had no effect on the prevalence/co-colonisation of M. hominis, U. urealyticum or C. trachomatis. The importance of genital mycoplasmas, ureaplasmas and C. trachomatis in long-term aetiologies requires further investigations, certainly in relation to syndromic management regimens that fail to reduce colonisation rates.

INTERGROWTH-21st v. local South African growth standards (Theron-Thompson) for identification of small-for-gestational-age fetuses in stillbirths: A closer look at variation across pregnancy.

BACKGROUND: Global growth standards for fetuses were recently developed (INTERGROWTH-21st). It has been advocated that professional bodies should adopt these global standards. OBJECTIVES: To compare the ability of INTERGROWTH-21st with local standards (Theron-Thompson) to identify small-for-gestational-age (SGA) fetuses in stillbirths in the South African (SA) setting. METHODS: Stillbirths across SA were investigated (>500 g, 28 - 40 weeks) between October 2013 and December 2016 (N=14 776). The study applied the INTERGROWTH-21st standards to classify stillbirths as <10th centile (SGA) compared with Theron-Thompson growth charts, across pregnancy overall and at specific gestational ages. RESULTS: The prevalence of SGA was estimated at 32.2% and 31.1% by INTERGROWTH-21st and Theron-Thompson, respectively. INTERGROWTH-21st captured 13.8% more stillbirths as SGA in the earlier gestations (28 - 30 weeks, p<0.001), but 4.0% (n=315) fewer between 33 and 38 weeks (p<0.001). Observed agreement and the Kappa coefficient were lower at earlier gestations and at 34 - 36 weeks. CONCLUSIONS: Our findings demonstrated differences in the proportion of stillbirths considered SGA at each gestational age between the INTERGROWTH-21st and the local SA standard, which have not been considered previously by other studies.

Relationship between chest radiographic characteristics, sputum bacterial load, and treatment outcomes in patients with extensively drug-resistant tuberculosis.

BACKGROUND: Data about the relationship between chest radiographs and sputum bacillary load, with treatment outcomes, in patients with extensively drug-resistant tuberculosis (XDR-TB) from HIV/TB endemic settings are limited. METHODS: Available chest radiographs from 97 South African XDR-TB patients, at the time of diagnosis, were evaluated by two independent readers using a validated scoring system. Chest radiograph findings were correlated with baseline sputum bacillary load (smear-grade and culture time-to-positive in MGIT), and prospectively ascertained clinical outcomes (culture conversion and all-cause mortality). RESULTS: Radiographic bilateral lung disease was present in 75/97 (77%). In the multivariate analysis only a higher total radiographic score (95% CI) was associated with higher likelihood of death [1.16 (1.05-1.28) p=0.003], and failure to culture convert [0.85 (0.74-0.97) p=0.02]. However, when restricting analyses to HIV-infected patients, disease extent, cavitation, and total radiographic scores were not associated with mortality or culture-conversion. Finally, cavitary, disease extent, and total radiographic scores all positively correlated with bacterial load (culture time-to-positive). CONCLUSIONS: In endemic settings, XDR-TB radiological disease extent scores are associated with adverse clinical outcomes, including mortality, in HIV uninfected persons. These data may have implications for clinical and programmatic decision-making and for evaluation of new regimens in clinical trials.

Overcoming limitations of tuberculosis information systems: researcher and clinician perspectives.

SETTING: Tuberculosis (TB) diagnosis and treatment requires patients to have multiple encounters with health care systems and the different stakeholders who play a role in curing them to coordinate their efforts. To optimize this process, high-quality, readily available data are required. Data systems to facilitate these linkages are a neglected priority which, if weak, fundamentally undermine TB control interventions. OBJECTIVE: To describe lessons learnt from the use of programmatic data for TB patient care and research. DESIGN: We did a survey of researcher and clinical provider experiences with information systems and developed a tiered approach to addressing frequently reported barriers to high-quality care. RESULTS: Unreliable linkages, incomplete data, lack of a reliable unique patient identifier, and lack of data management expertise were the most important data-related barriers to high-quality patient care and research. We propose the creation of health service delivery environments that facilitate, prioritize, and evaluate high-quality data entry during patient or specimen registration. CONCLUSION: An integrated approach, focused on high-quality data, and centered on unique patient identification will form the foundation for linkages across health systems that reduce patient management errors, bolster surveillance, and enhance the quality of research based on programmatic data.

Tuberculosis research in South Africa over the past 30 years: From bench to bedside.

The South African Medical Research Council Centre for Tuberculosis Research has a rich history of high-impact research that has influenced our understating of this hyper-epidemic which is further exacerbated by the emergence and spread of drug-resistant forms of the disease. This review aims to summarise the past 30 years of research conducted in the Centre which has influenced the way that tuberculosis (TB) is diagnosed and treated. The review includes the development of new technologies for rapid screening of people with probable TB and the repurposing of human diagnostics for wildlife conservation.

Commercial products to preserve specimens for tuberculosis diagnosis: a systematic review.

SETTING: Eliminating tuberculosis in high-burden settings requires improved diagnostic capacity. Important tests such as Xpert® MTB/RIF and culture are often performed at centralised laboratories that are geographically distant from the point of specimen collection. Preserving specimen integrity during transportation, which could affect test performance, is challenging. OBJECTIVE: To conduct a systematic review of commercial products for specimen preservation for a World Health Organization technical consultation. DESIGN: Databases were searched up to January 2018. Methodological quality was assessed using Quality Assessment of Technical Studies, a new technical study quality-appraisal tool, and Quality Assessment of Diagnostic Accuracy Studies-2. Studies were analysed descriptively in terms of the different products, study designs and diagnostic strategies used. RESULTS: Four products were identified from 16 studies: PrimeStore-Molecular-Transport-Medium (PS-MTM), FTA card, GENO•CARD (all for nucleic acid amplification tests [NAATs]) and OMNIgene•SPUTUM (OMS; culture, NAATs). PS-MTM, but not FTA card or GENO•CARD, rendered Mycobacterium tuberculosis non-culturable. OMS reduced Löwenstein-Jensen but not MGIT™ 960™ contamination, led to delayed MGIT time-to-positivity, resulted in Xpert performance similar to cold chain-transported untreated specimens, and obviated the need for N-acetyl-L-cysteine-sodium hydroxide decontamination. Data from paucibacillary specimens were limited. Evidence that a cold chain improves culture was mixed and absent for Xpert. The effect of the product alone could be discerned in only four studies. CONCLUSION: Limited evidence suggests that transport products result in test performance comparable to that seen in cold chain-transported specimens.

Detection of tuberculosis by automatic cough sound analysis.

OBJECTIVE: Globally, tuberculosis (TB) remains one of the most deadly diseases. Although several effective diagnosis methods exist, in lower income countries clinics may not be in a position to afford expensive equipment and employ the trained experts needed to interpret results. In these situations, symptoms including cough are commonly used to identify patients for testing. However, self-reported cough has suboptimal sensitivity and specificity, which may be improved by digital detection. APPROACH: This study investigates a simple and easily applied method for TB screening based on the automatic analysis of coughing sounds. A database of cough audio recordings was collected and used to develop statistical classifiers. MAIN RESULTS: These classifiers use short-term spectral information to automatically distinguish between the coughs of TB positive patients and healthy controls with an accuracy of 78% and an AUC of 0.95. When a set of five clinical measurements is available in addition to the audio, this accuracy improves to 82%. By choosing an appropriate decision threshold, the system can achieve a sensitivity of 95% at a specificity of approximately 72%. The experiments suggest that the classifiers are using some spectral information that is not perceivable by the human auditory system, and that certain frequencies are more useful for classification than others. SIGNIFICANCE: We conclude that automatic classification of coughing sounds may represent a viable low-cost and low-complexity screening method for TB.

Widespread use of incorrect PCR ramp rate negatively impacts multidrug-resistant tuberculosis diagnosis (MTBDRplus).

The scale-up of rapid drug resistance testing for TB is a global priority. MTBDRplus is a WHO-endorsed multidrug-resistant (MDR)-TB PCR assay with suboptimal sensitivities and high indeterminate rates on smear-negative specimens. We hypothesised that widespread use of incorrect thermocycler ramp rate (speed of temperature change between cycles) impacts performance. A global sample of 72 laboratories was surveyed. We tested 107 sputa from Xpert MTB/RIF-positive patients and, separately, dilution series of bacilli, both at the manufacturer-recommended ramp rate (2.2 °C/s) and the most frequently reported incorrect ramp rate (4.0 °C/s). Mycobacterium tuberculosis-complex DNA (TUB-band)-detection, indeterminate results, accuracy, and inter-reader variability (dilution series only) were compared. 32 respondents did a median (IQR) of 41 (20-150) assays monthly. 78% used an incorrect ramp rate. On smear-negative sputa, 2.2 °C/s vs. 4.0 °C/s improved TUB-band positivity (42/55 vs. 32/55; p = 0.042) and indeterminate rates (1/42 vs. 5/32; p = 0.039). The actionable results (not TUB-negative or indeterminate; 41/55 vs. 28/55) hence improved by 21% (95% CI: 9-35%). Widespread use of incorrect ramp rate contributes to suboptimal MTBDRplus performance on smear-negative specimens and hence limits clinical utility. The number of diagnoses (and thus the number of smear-negative patients in whom DST is possible) will improve substantially after ramp rate correction.

Point of care diagnostics for tuberculosis.

The goals of the End TB strategy, which aims to achieve a 90% reduction in tuberculosis (TB) incidence and a 95% reduction in TB mortality by 2035, will not be achieved without new tools to fight TB. These include improved point of care (POC) diagnostic tests that are meant to be delivered at the most decentralised levels of care where the patients make the initial contact with the health system, as well as within the community. These tests should be able to be performed on an easily accessible sample and provide results in a timely manner, allowing a quick treatment turnaround time of a few minutes or hours (in a single clinical encounter), hence avoiding patient loss-to-follow-up. There have been exciting developments in recent years, including the WHO endorsement of Xpert MTB/RIF, Xpert MTB/RIF Ultra, loop-mediated isothermal amplification (TB-LAMP) and lateral flow lipoarabinomannan (LAM). However, these tests have limitations that must be overcome before they can be optimally applied at the POC. Furthermore, worrying short- to medium-term gaps exist in the POC diagnostic test development pipeline. Thus, not only is better implementation of existing tools and algorithms needed, but new research is required to develop new POC tests that allow the TB community to truly make an impact and find the "missed TB cases".

An outbreak of perirenal oedema syndrome in cattle associated with ingestion of pigweed (Amaranthus hybridus L.).

Forty seven of 150, 15-month-old long weaners died of an acute renal disease syndrome following introduction into an old maize field with a heavy stand of Amaranthus spp. The clinical syndrome was characterised by sudden onset neurological disease with ataxia and recumbency. Subcutaneous oedema, ascites and perirenal oedema with urine odour were the major gross necropsy findings. Renal histopathology revealed marked coagulative renal tubular necrosis of the proximal and distal straight tubules with intertubular haemorrhage. Acute renal failure and perirenal oedema has been described in cattle, pigs, horses and sheep associated with the ingestion of A. hybridus L. and A. retroflexus L. This perirenal oedema syndrome has been widely reported in the Americas, while in South Africa intoxication with the amaranths has only previously been associated with nitrate and possibly oxalate poisoning in cattle.

Drug-resistant tuberculosis in patients with minimal symptoms: favourable outcomes in the absence of treatment.

SETTING: Referral hospital for drug-resistant tuberculosis (DR-TB) in KwaZulu-Natal Province, South Africa. OBJECTIVE: To review the clinical outcomes of patients (age  14 years) with a laboratory-confirmed diagnosis of DR-TB who had minimal symptoms and/or did not have chest radiographic evidence of active disease at referral. These patients were not started on treatment, but were enrolled in an observation programme with follow-up at 2, 6 and 12 months. RESULTS: Of 3345 referred patients diagnosed with DR-TB, 192 (6%) were enrolled in the observation programme. The median duration from initial sputum collection in primary care to examination at our hospital was 92 days (IQR 64-124). After 12 months, 120 (62%) patients were well, 36 (19%) were lost to follow-up, 30 (16%) had deteriorated and were started on second-line anti-tuberculosis treatment and 6 (3%) had died. Bilateral disease (OR 4.25, 95%CI 1.14-15.77, P = 0.030) and previous TB (OR 2.14, 95%CI 1.10-4.19, P = 0.026) were independent predictors of an unfavourable end result in a multivariate model. CONCLUSION: In our high-burden setting, most patients diagnosed with DR-TB who had minimal symptoms at referral remained well without treatment. Longitudinal observation, coupled with symptom checking and chest radiograph, is a viable strategy.