Pharmaceutical, Biomedical and Veterinary Sciences

Margot Merlot 

• 22 January 2026, 4pm - 6pm
• Auditorium O1 (CDE)
• Promoters: Guy Caljon, Louis Maes

Abstract

Coccidiosis in chickens and turkeys is caused by various closely related Eimeria species. The infection is transmitted through the fecal-oral route and may lead to large outbreaks that are difficult to mitigate, hence leading to considerable economic losses. The current standard in-feed use of anticoccidials suffers from disadvantages such as increasing drug-resistance, residues in food for human consumption, and legislative pressure to reduce antimicrobial use. The alternative control method is based on the use of multivalent (attenuated) vaccines for which the EU-regulatory authorities require stringent quality criteria for species composition and viability, overall immunogenicity, and vaccine stability. Unfortunately, these data are currently only obtained in expensive and time-consuming in vivo immunization and challenge experiments. In an attempt to overcome the need for these in vivo experiments, this thesis focused on the development of novel in vitro laboratory methodologies by using a combination of flow cytometry and molecular methods for oocyst speciation and viability assessment to better define vaccine composition and batch release characteristics.

To enable quantitation of species-specific viability of oocysts in a multivalent vaccine, permeabilization of the notoriously impermeable oocyst wall was required, which was achieved by developing a detergent-enhanced oocyst viability staining technique. As oocysts of poultry Eimeria species are genetically and morphologically very similar, hereby complicating straightforward species identification, flow cytometric sorting in combination with innovative digital PCR technology using Sequence Characterized Amplified Region (SCAR) primers was implemented. Species quantitation was further refined by applying correction factors that account for DNA extraction efficiency, PCR efficiency and SCAR copy numbers in chicken and turkey Eimeria species. The resulting assay was extensively validated for its intended use as a batch release test and was shown to be applicable across multiple stages of vaccine production, including shelf-life determination and vaccine formulation optimization.

In summary, the PhD thesis describes the development and validation of a novel in vitro laboratory method to quickly determine the species-specific volumetric viability during vaccine development and in the final multivalent coccidiosis vaccine product, providing a novel way to perform batch release testing without the need of animal testing. A provisional patent application of the developed technique has been filed (No. PCT/US2025/032408).

Elizabeth Tabitha Abbew 

• 8 January 2026, 4pm - 6pm
• Aula Janssens (ITG)
• Promoters: Leen Rigouts, Lut Lynen, Dorcas Obiry-Yeboah 

Abstract

Nontuberculous mycobacteria (NTM) are increasingly detected in tuberculosis (TB)-endemic regions, yet their clinical significance remains poorly defined. In sub-Saharan Africa (SSA), limited diagnostic capacity and absence of guidelines contribute to uncertainty in patient management.

This PhD research combined (i) a systematic scoping review of NTM in SSA, (ii) a retrospective laboratory analysis of 2,492 sputum samples in Ghana (2012–2021), (iii) a retrospective cohort of 380 MDR/RR-TB patients in Ghana (2018–2021), and (iv) three prospective cohort studies involving 9,981 symptomatic individuals in Ghana, Nigeria, and Niger. Standard mycobacterial culture, MPT64 antigen testing, line probe assays, and sequencing were used for species identification. Clinical and radiological data were analysed against international ATS/IDSA/ERS/ESCMID criteria for NTM pulmonary disease (NTM-PD).

The scoping review highlighted major gaps: most SSA studies did not apply international diagnostic criteria, species-level identification was rare, and MPT64 antigen misclassified Mycobacterium tuberculosis complex (MTBc) as NTM.

In Ghana, retrospective laboratory analysis showed 33.7% culture positivity. Initially, 30.6% were presumed NTM, but only 53 isolates (23.6%) were confirmed after molecular speciation, reducing the prevalence to 2%. M. intracellulare (66%) predominated, while 18 MTBc isolates, including M. africanum, were misclassified as NTM by MPT64. Four patients fulfilled NTM-PD criteria, all previously treated as RR-TB.

Among 380 MDR/RR-TB patients, 7.1% had NTM isolated, mainly M. intracellulare and M. fortuitum. Treatment success was 67.9%, higher with all-oral bedaquiline regimens (71.4%) compared to injectable-containing regimens (60.3%). HIV was associated with unfavourable outcomes (aOR 1.80, 95% CI 1.05–3.11), while NTM isolation itself was not. Geographic variation showed higher odds of NTM isolation in Eastern (aOR 15.68) and Brong Ahafo regions (aOR 4.74).

In the prospective cohorts, 99/938 (10.6%) had NTM isolated. Predominant species were M. intracellulare (34.3%), M. fortuitum (16.2%), and M. abscessus (10.1%). Among patients with ≥2 sputum samples, 15 (30.6%) met NTM-PD criteria, with 20% mortality. Unique isolates such as M. palustre were detected only by sequencing, reflecting diagnostic limitations of commercial assays.

This thesis demonstrates that although NTM are frequently isolated among presumed TB patients in West Africa, their presence did not adversely affect MDR/RR-TB treatment outcomes in Ghana, while their clinical significance remains challenging to determine due to limited repeated culture data from SSA. These findings underscore the need to strengthen laboratory capacity for species-level identification, integrate molecular diagnostics into routine algorithms, and develop regional clinical guidelines for the diagnosis and management of NTM-PD, while systematically excluding TB