TB Control in Humans and Animals in South Africa: A Perspective on Problems and Successes

Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing

Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.

Drug discovery in Africa tackles zoonotic and related infections

Zoonotic and related infections pose an enormous health threat to the world's second-most populous continent. Despite the challenges faced by drug discovery scientists in Africa, recent progress toward identifying potential medicines across diverse disease areas is a cause for optimism and an indicator of progress in African-led scientific initiatives.

Challenges to the control of Mycobacterium bovis in livestock and wildlife populations in the South African context

Bovine tuberculosis (bTB) was first diagnosed in cattle in South Africa in 1880 and proclaimed a controlled disease in 1911. Testing of cattle for bTB is voluntary and only outbreaks of disease are reported to the National Department of Agriculture so the prevalence of the disease in cattle is largely unknown. There is a Bovine Tuberculosis Scheme which is aimed at the control of bTB in cattle but the same measures of test and slaughter, and the quarantining of the property apply to wildlife as well. bTB was first diagnosed in wildlife in a greater kudu in the Eastern Cape in 1928 and has to date been found in 24 mammalian wildlife species. The African buffalo has become a maintenance host of the disease, which is considered endemic in the Kruger National Park, the Hluhluwe-iMfolozi Park and the Madikwe Game Park. Control of bTB at the wildlife-livestock interface is difficult because of spill-over and spill-back between species. Only buffalo are required by law to be tested before translocation, but bTB has been introduced to the Madikwe Game Park probably by the translocation of other infected wildlife species. There is no national control strategy for the control of bTB in wildlife. Indirect tests have been developed to test for bTB in eight species, 6 of which can be considered endangered. More research needs to be done to develop an effective and efficient vaccine to combat the transmission of bTB within and between species. New policies need to be developed that are effective, affordable and encompassing to control the spread of bTB in South Africa.

Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals

Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.

Isolation, Characterization, and Drug Sensitivity of Mycobacterium tuberculosis in Captive Sloth Bears (Melursus ursinus): Unnatural Habitat With Human Environment May Predispose Sloth Bears to Tuberculosis

We describe the isolation, molecular characterization, and drug sensitivity of Mycobacterium tuberculosis recovered from lung tissues of four rescued captive sloth bears (Melursus ursinus) at Bannerghatta Biological Park (BBP), Bangalore, India. These bears had lived most of their life with humans in circus companies. They were rescued and housed in the Bear Rescue Center (BRC) of BBP. Upon rescue, they showed signs of unthriftiness, chronic debility, and failed to respond to symptomatic treatments. Over the period of the next 12–14 months, the four sloth bears died and the post-mortem examination revealed nodular lesions in the lungs that showed the presence of acid-fast bacilli. Polymerase chain reaction (PCR), culture, and nucleotide sequencing confirmed the bacilli as Mycobacterium tuberculosis. Histopathology of the lungs revealed characteristic granulomatous reaction with caseation. We determined the sensitivity of these isolates to rifampicin and isoniazid drugs by a WHO approved test, Line Probe Assay (LPA) using Genotype MTBDRplus VER 2.0. We discuss the role of unnatural habitat with the human environment in predisposing captive sloth bears for tuberculosis (TB). In the absence of any other reliable ante-mortem diagnostic test, this study recommends the use of LPA for early detection of TB in captive wild animals, which will help in taking necessary steps to prevent its further spread to animal caretakers and other susceptible animals in captivity.

Bayesian Estimation of Diagnostic Accuracy of Three Diagnostic Tests for Bovine Tuberculosis in Egyptian Dairy Cattle Using Latent Class Models

The aim of the present study was to calculate the sensitivity (Se) and specificity (Sp) of the single cervical tuberculin test (SCT), rapid lateral flow test (RLFT), and real-time polymerase chain reaction (RT-PCR) for the diagnosis of Mycobacterium bovis (M. bovis) infection in Egyptian dairy cattle herds within a Bayesian framework. The true M. bovis infection within-herd prevalence was assessed as a secondary objective. Data on the test results of SCT, RLFT, and RT-PCR for the detection of M. bovis were available from 245 cows in eleven herds in six major governorates in Egypt. A Bayesian latent class model was built for the estimation of the characteristics of the three tests. Our findings showed that Se of SCT (0.93 (95% Posterior credible interval (PCI): 0.89–0.93)) was higher than that of RT-PCR (0.83 (95% PCI: 0.28–0.93)) but was similar to the Se of RLFT (0.93 (95% PCI: 0.31–0.99)). On the contrary, SCT showed the lowest Sp estimate (0.60 (95% PCI: 0.59–0.65)), whereas Sp estimates of RT-PCR (0.99 (95% PCI: 0.95–1.00)) and RLFT (0.99 (95% PCI: 0.95–1.00)) were comparable. The true prevalence of M. bovis ranged between 0.07 and 0.71. In conclusion, overall, RT-PCR and RLFT registered superior performance to SCT, making them good candidates for routine use in the Egyptian bovine tuberculosis control program.

Improved detection of Mycobacterium tuberculosis and M. bovis in African wildlife samples using cationic peptide decontamination and mycobacterial culture supplementation

In South Africa, mycobacterial culture is regarded as the gold standard for the detection of Mycobacterium tuberculosis complex (MTBC) infection in wildlife even though it is regarded as “imperfect.” We compared a novel decontamination and mycobacterial culture technique (TiKa) to the conventional mycobacterium growth indicator tube (MGIT) system using known amounts of bacilli and clinical samples from MTBC-infected African buffaloes (Syncerus caffer), white rhinoceros (Ceratotherium simum), and African elephants (Loxodonta africana). Use of the TiKa-KiC decontamination agent on samples spiked with 10,000 to 10 colony forming units (cfu) of M. bovis (SB0121) and M. tuberculosis (H37Rv) had no effect on isolate recovery in culture. In contrast, decontamination with MGIT MycoPrep resulted in no growth of M. bovis samples at concentrations < 1,000 cfu and M. tuberculosis samples < 100 cfu. Subsequently, we used the TiKa system with stored clinical samples (various lymphatic tissues) collected from wildlife and paucibacillary bronchoalveolar lavage fluid, trunk washes, and endotracheal tube washes from 3 species with known MTBC infections. Overall, MTBC recovery by culture was improved significantly (p < 0.01) by using TiKa compared to conventional MGIT, with 54 of 57 positive specimens versus 25 of 57 positive specimens, respectively. The TiKa mycobacterial growth system appears to significantly enhance the recovery of MTBC members from tissue and paucibacillary respiratory samples collected from African buffaloes, African elephants, and white rhinoceros. Moreover, the TiKa system may improve success of MTBC culture from various sample types previously deemed unculturable from other species.

Occupational exposure and challenges in tackling M. bovis at human-animal interface: a narrative review

Zoonotic tuberculosis caused by Mycobacterium bovis (M. bovis), a member of Mycobacterium tuberculosis complex (MTBC) has increasingly gathered attention as a public health risk, particularly in developing countries with higher disease prevalence. M. bovis is capable of infecting multiple hosts encompassing a number of domestic animals, in particular cattle as well as a broad range of wildlife reservoirs. Humans are the incidental hosts of M. bovis whereby its transmission to humans is primarily through the consumption of cattle products such as unpasteurized milk or raw meat products that have been contaminated with M. bovis or the transmission could be due to close contact with infected cattle. Also, the transmission could occur through aerosol inhalation of infective droplets or infected body fluids or tissues in the presence of wound from infected animals. The zoonotic risk of M. bovis in humans exemplified by miscellaneous studies across different countries suggested the risk of occupational exposure towards M. bovis infection, especially those animal handlers that have close and unreserved contact with cattle and wildlife populations These animal handlers comprising of livestock farmers, abattoir workers, veterinarians and their assistants, hunters, wildlife workers as well as other animal handlers are at different risk of contracting M. bovis infection, depending on the nature of their jobs and how close is their interaction with infected animals. It is crucial to identify the underlying transmission risk factors and probable transmission pathways involved in the zoonotic transmission of M. bovis from animals to humans for better designation and development of specific preventive measures and guidelines that could reduce the risk of transmission and to protect these different occupational-related/populations at risk. Effective control and disease management of zoonotic tuberculosis caused by M. bovis in humans are also hindered by various challenges and factors involved at animal–human interface. A closer look into factors affecting proper disease control and management of M. bovis are therefore warranted. Hence, in this narrative review, we have gathered a number of different studies to highlight the risk of occupational exposure to M. bovis infection and addressed the limitations and challenges underlying this context. This review also shed lights on various components and approaches in tackling M. bovis infection at animal–human interface.

Review of Diagnostic Tests for Detection of Mycobacterium bovis Infection in South African Wildlife

Wildlife tuberculosis is a major economic and conservation concern globally. Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is the most common form of wildlife tuberculosis. In South Africa, to date, M. bovis infection has been detected in 24 mammalian wildlife species. The identification of M. bovis infection in wildlife species is essential to limit the spread and to control the disease in these populations, sympatric wildlife species and neighboring livestock. The detection of M. bovis-infected individuals is challenging as only severely diseased animals show clinical disease manifestations and diagnostic tools to identify infection are limited. The emergence of novel reagents and technologies to identify M. bovis infection in wildlife species are instrumental in improving the diagnosis and control of bTB. This review provides an update on the diagnostic tools to detect M. bovis infection in South African wildlife but may be a useful guide for other wildlife species.

Evaluation of the Control Options of Bovine Tuberculosis in Ethiopia Using a Multi-Criteria Decision Analysis

Bovine tuberculosis (BTB) is a zoonotic bacterial infection caused by Mycobacterium bovis and is characterized by the development of granulomatous lesions in the lymph nodes, lungs and other tissues. It poses serious public health impacts and food security challenges to the agricultural sector in terms of dairy and meat productions. In Ethiopia, BTB has been considered as a priority disease because of its high prevalence in urban and peri-urban dairy farms. However, there has not been any national control program in the country. Thus, in order to initiate BTB control program in the country, information on control options is needed to tailor the best option for the Ethiopian situation. The objective of this study was to identify, evaluate and rank various BTB control options in Ethiopia using a multi-criteria decision analysis based on preference ranking organization method for enrichment evaluations (PROMETHEE) approach while accounting for the stakeholders' preferences. Control options were evaluated under two scenarios: with (scenario 1) and without (scenario 2) bacillus Calmette–Guérin (BCG) vaccination. Nine potential control options were identified that include combinations of three control options (1) test and slaughter with or without government support, (2) test and segregation, and (3) BCG vaccination. Under scenario 1, BCG vaccination, BCG vaccination and test and slaughter with partial compensation by government, and BCG vaccination and test and slaughter with full compensation by government were the top three ranked control options. Under scenario 2, test and slaughter with full compensation by government was the preferred control option, followed by test and segregation supported by test and slaughter with full government compensation, and test and slaughter with half compensation by government. Irrespective of the variability in the weighting by the stakeholders, the sensitivity analysis showed the robustness of the ranking method. In conclusion, the study demonstrated that BCG vaccination, and test and slaughter with full compensation by government were the two most preferred control options under scenarios 1 and 2, respectively. National level discussions were strongly recommended for further concretization and implementation of these control measures.

Understanding the gaps in DR-TB care cascade in Nigeria: A sequential mixed-method study

Background

Despite the availability of free drug-resistant tuberculosis (DR-TB) care in Nigeria since 2011, the country continues to tackle low case notification and treatment rates. In 2018, 11% of an estimated 21,000 cases were diagnosed and 9% placed on treatment. These low rates are nevertheless a marked improvement from 2015 when only 3.4% were diagnosed and 2.3% placed on treatment of an estimated 29,000 cases. This study describes the Nigerian DR-TB care cascade from 2013 to 2017 and considers factors influencing gaps in care.

Methods

Our study utilized a mixed-method design. For the quantitative component, we utilized the national diagnosis and treatment databases, as well as the World Health Organization’s estimates for prevalence to construct a 5-year care cascade: numbers of patients at each level of DR-TB care, including incident cases, individuals who accessed testing, were diagnosed, initiated treated and completed treatment in Nigeria between 2013 and 2017. Using retrospective data for patients diagnosed in 2015, we performed the Fisher’s exact test to determine the association between patient (age and gender) and provider/patient (region- north or south) variables, permitting a closer look at the gaps in care revealed across the 5 years. Barriers to care were explored using framework thematic analysis of 57 qualitative interviews and focus group discussions with patients, including 5 cases not initiated on treatment from the 2015 cohort, treatment supporters, community members, healthcare workers and program managers in 2017.

Results

A 5-year analysis of cascade of care data shows significant, but inadequate, increases in overall numbers of cases accessing care. On average, between 2013 and 2017, 80% of estimated cases did not access testing; 75% of those who tested were not diagnosed; 36% of those diagnosed were not initiated on treatment and 23% of these did not finish treatment. In 2015, children and patients in Northern Nigeria had odds of 0.3 [95% CI 0.1–0.7] and 0.4 [0.3–0.5] of completing treatment once diagnosed; while males were shown to have a 1.34 [95% CI 1.0–1.7] times greater chance of completing treatment after diagnosis. The main themes from qualitative data identified barriers to care along the care cascade at individual, family and community, as well as health systems levels. At the individual level, a lack of awareness of the true cause of disease and the availability of ‘free’ care was a recurring theme. Family interference was found to be a particular challenge for children and women. At the health system level, low index of suspicion, lack of rapid diagnostic tools and human resource shortages appeared to limit patients’ access.

Conclusions

Any gains in diagnostic technology and shorter regimens are lost with inadequate access to DR-TB services. The biggest losses in the Nigerian cascade happen before treatment initiation. There is a need for urgent action on identified gaps in the DR-TB cascade in order to improve care continuity at multiple stages, improve health service delivery and facilitate TB control in Nigeria.

Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis

Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, which affects various domestic animals, wildlife, and humans. Some wild animals serve as reservoir hosts in the transmission and epidemiology of the disease. Therefore, the monitoring and surveillance of both wild and domestic hosts are critical for prevention and control strategies. For TB diagnosis, the single intradermal tuberculin test or the single comparative intradermal tuberculin test, and the gamma-interferon test, which is regarded as an ancillary test, are used. Postmortem examination can identify granulomatous lesions compatible with a diagnosis of TB. In contrast, smears of the lesions can be stained for acid-fast bacilli, and samples of the affected organs can be subjected to histopathological analyses. Culture is the gold standard test for isolating mycobacterial bacilli because it has high sensitivity and specificity compared with other methods. Serology for antibody detection allows the testing of many samples simply, rapidly, and inexpensively, and the protocol can be standardized in different laboratories. Molecular biological analyses are also applicable to trace the epidemiology of the disease. In conclusion, reviewing the various techniques used in MTBC diagnosis can help establish guidelines for researchers when choosing a particular diagnostic method depending on the situation at hand, be it disease outbreaks in wildlife or for epidemiological studies. This is because a good understanding of various diagnostic techniques will aid in monitoring and managing emerging pandemic threats of infectious diseases from wildlife and also preventing the potential spread of zoonotic TB to livestock and humans. This review aimed to provide up-to-date information on different techniques used for diagnosing TB at the interfaces between wildlife, livestock, and humans.

Bovine tuberculosis at the human-livestock-wildlife interface and its control through one health approach in the Ethiopian Somali Pastoralists: A review

Pastoralism is a way of life in which food supply is produced from animals by using a variety of herding practices based on constant or partial herd mobility in the low land areas of Ethiopia. It covers 12% of the total livestock population and 61% of the total area of land in the country. As a result of their mobile lifestyle, pastoralists are almost completely excluded from the available health services. This review article focuses on bovine tuberculosis in the Ethiopian Somali Pastoralist. It describes Mycobacterium bovis in humans, livestock, and wildlife, and how the disease can be controlled by using One Health approach. Bovine tuberculosis is a chronic bacterial disease caused by Mycobacterium bovis. A study done from 2006 to 2008 on the prevalence of BTB in Ethiopian wildlife showed that sera from 20 of 87 animals (23%) were positive for BTB. In Ethiopia there is no comprehensive report about the status of M. bovis in wildlife populations that often share habitat with livestock. A study done on bovine tuberculosis in Somali pastoral livestock showed low prevalence of the disease. An individual animal prevalence of 2.0%, 0.4%, and 0.2% was reported in cattle, camels, and goats, respectively. In a simultaneous human and cattle study in a pastoralist areas of south-eastern Ethiopia, out of 163 human Mycobacterium tuberculosis complex isolates three were M. bovis. Due to the moderate resistance of the etiological agent to the environmental conditions in one hand and the capacity of its survival in acid milk for not less than 15 days on the other and the habitual consumption of unpasteurized milk by humans make this disease a vital zoonosis in Somali pastoralists in Ethiopia. M. bovis is a pathogen at the human-livestock-wildlife interface. Diseases transmitted between humans, livestock, and wildlife are increasingly challenging public and veterinary health systems. Therefore, studies concerning the burden of the diseases in wildlife, livestock and human beings in Somali Pastoralists should be undertaken. A One Health approach that takes the wellbeing of the pastoralists, the health of their livestock and environment into consideration is also necessary for the control of BTB.