Recent Submissions

  • Stressors and coping mechanisms of family care-givers of older relatives living with long-term conditions in mainland China: A scoping review of the evidence

    Bífárìn, Oládayò, O.; Quinn, Catherine; Breen, Liz; Wu, C.; Ke, M.; Yu, L.; Oyebode, Jan R. (Cambridge University Press, 2021)
    As the ageing population in China continues to grow, more people will be living with long-term health conditions and require support from family care-givers. This scoping review therefore aims to explore sources of stress and coping mechanisms adopted by care-givers of older relatives living with long-term conditions in mainland China. Literature searches were conducted in English (CINAHL, EMBASE, MEDLINE, PsycINFO and SCOPUS) and Chinese (CNKI, WANFANG DATA, CQVIP and CBM) databases between October and November 2019. The searches focused on the stressors and coping mechanisms utilised by family care-givers residing in the community. Narrative synthesis was used to identify themes within the data. Forty-six papers were included: 20 papers from English and 26 from Chinese databases. Six themes captured stressors: care-giving time (N = 22), financial resources (N = 17), role and personal strains (N = 42), preparedness (N = 4), social roles (N = 10) and lack of adequate formal support (N = 22); and one theme captured coping (N = 14). Unmet needs of care-givers of older relatives in mainland China were found to be extensive. Only a few studies had attempted to explore the causal link between stressors, coping and the influence of culture. Findings underscore the significance of adequately capturing intricacies around care-givers’ unmet needs, rather than generalising on the basis of culture. Qualitative studies are critical to providing a better understanding of the relationship between stressors, coping and resources afforded to care-givers by their cultural environment. Having such understanding is crucial to inform the development of competent care, which promotes self-efficacy and self-actualisation in care-givers in mainland China.
  • An exploration of the impact of SARS-CoV-2 (COVID-19) restrictions on marginalised groups in the UK

    Eshareturi, Cyril; Wareham, C.; Rattray, Marcus; Haith-Cooper, Melanie; McCarthy, R. (2021-08)
    Background: To contain the spread of COVID-19 within the UK over the past year, there have been a series of local and national lockdowns. These restrictions are likely to have impacted upon the health and well-being of marginalised groups who rely on now closed social and community support services to stay healthy. An understanding of the experiences of marginalised people is important; therefore, this study aimed to explore the impact of the COVID-19 restrictions on the health and well-being of marginalised groups in the UK. Methods: In summer 2020, a rapid telephone survey was conducted by trained, trusted volunteers with 76 participants who were from marginalised groups. As part of this survey, 64 participants consented to describe their experience of lockdown. These case studies were thematically analysed to identify patterns of meaning. Results: Findings indicate that lockdown led to the deterioration of health of participants, impacted adversely on their socio-economic positions and affected access to food and essential supplies. In addition, government public health messaging was considered confusing and inadequate. Conclusions: This study highlights the need for pathways into services which support marginalised groups to remain accessible during periods of restrictions and essential supplies and food to be mapped and protected for marginalised individuals within our local communities.
  • Digest of Evidence 9, The Human Bone

    Clark, J.; Garner-Lahire, J.; Spall, C.; Toop, N.; Curtis-Summers, Shirley (2021-06)
  • Patient Perspectives on Factors Affecting Direct Oral Anticoagulant Use for Stroke Prevention in Atrial Fibrillation

    Medlinskiene, Kristina; Richardson, S.; Fylan, Beth; Stirling, K.; Rattray, Marcus; Petty, Duncan (2021-05-10)
    Introduction: Oral anticoagulant therapy choices for patients with atrial fibrillation (AF) expanded in the last decade with the introduction of direct oral anticoagulants (DOAC). However, the implementation of DOACs was slow and varied across different health economies in England. There is limited evidence on the patient role in the uptake of new medicines, including DOACs, apart from considering their demographic and clinical characteristics. Hence, this study aimed to address the gap by exploring the view of patients with AF on factors affecting DOAC use. Methods: A qualitative study using semi-structured interviews was conducted in three health economies in the North of England. Adult patients (>18 years) diagnosed with non-valvular AF, prescribed an oral anticoagulant (vitamin K antagonist or DOAC), and able to give written consent were recruited. Data were collected between August 2018 and April 2019. Audio recorded interviews were transcribed verbatim and analyzed using the framework method. Results: Four themes with eleven subthemes discussed identified factors affecting the use of DOACs. They were linked to limited healthcare financial and workforce resources, patient involvement in decision-making, patient knowledge about DOACs, safety concerns about oral anticoagulants, and oral anticoagulant therapy impact on patients' daily lives. Lack of a) opportunities to voice patient preferences and b) information on available therapy options resulted in some patients experiencing difficulties with the prescribed therapy. This was reported to cause negative impact on their daily lives, adherence, and overall satisfaction with the therapy. Conclusion: Greater patient involvement in decision-making could prevent and resolve difficulties encountered by some patients and potentially improve outcomes plus increase the uptake of DOACs.
  • Probing cytochrome P450 (CYP) bioactivation with chloromethylindoline bioprecursors derived from the duocarmycin family of compounds

    Ortuzar, N.; Karu, K.; Presa, Daniela; Morais, Goreti R.; Sheldrake, Helen M.; Shnyder, Steve D.; Barnieh, Francis M.; Loadman, Paul M.; Patterson, Laurence H.; Pors, Klaus; et al. (2021-06-15)
    The duocarmycins belong to a class of agent which has great potential for use in cancer therapy. Their exquisite potency means they are too toxic for systemic use, and targeted approaches are required to unlock their clinical potential. In this study, we have explored seco-OH-chloromethylindoline (CI) duocarmycin-based bioprecursors for their potential for cytochrome P450 (CYP)-mediated cancer cell kill. We report on synthetic and biological explorations of racemic seco-CI-MI, where MI is a 5-methoxy indole motif, and dehydroxylated analogues. We show up to a 10-fold bioactivation of de-OH CI-MI and a fluoro bioprecursor analogue in CYP1A1-transfected cells. Using CYP bactosomes, we also demonstrate that CYP1A2 but not CYP1B1 or CYP3A4 has propensity for potentiating these compounds, indicating preference for CYP1A bioactivation.
  • How can the potential of the duocarmycins be unlocked for cancer therapy?

    Jukes, Zoë; Morais, Goreti R.; Loadman, Paul M.; Pors, Klaus (2021-02)
    The duocarmycins belong to a class of agent that has fascinated scientists for over four decades. Their exquisite potency, unique mechanism of action, and efficacy in multidrug-resistant tumour models makes them attractive to medicinal chemists and drug hunters. However, despite great advances in fine-tuning biological activity through structure-activity relationship studies (SARS), no duocarmycin-based therapeutic has reached clinical approval. In this review, we provide an overview of the most promising strategies currently used and include both tumour-targeted prodrug approaches and antibody-directed technologies.
  • Luminal Bioavailability of Orally Administered ω-3 PUFAs in the Distal Small Intestine, and Associated Changes to the Ileal Microbiome, in Humans with a Temporary Ileostomy

    Nana, G.; Mitra, S.; Watson, H.; Young, C.; Wood, H.M.; Perry, S.L.; Race, Amanda D.; Quirke, P.; Toogood, G.J.; Loadman, Paul M.; et al. (2021-05)
    Background: Oral administration of purified omega-3 (ω-3) PUFAs is associated with changes to the fecal microbiome. However, it is not known whether this effect is associated with increased PUFA concentrations in the gut. Objectives: We investigated the luminal bioavailability of oral ω-3 PUFAs (daily dose 1 g EPA and 1g DHA free fatty acid equivalents as triglycerides in soft-gel capsules, twice daily) and changes to the gut microbiome, in the ileum. Methods: Ileostomy fluid (IF) and blood were obtained at baseline, after first capsule dosing (median 2 h), and at a similar time after final dosing on day 28, in 11 individuals (median age 63 y) with a temporary ileostomy. Fatty acids were measured by LC–tandem MS. The ileal microbiome was characterized by 16S rRNA PCR and Illumina sequencing. Results: There was a mean 6.0 ± 9.8-fold and 6.6 ± 9.6-fold increase in ileal EPA and DHA concentrations (primary outcome), respectively, at 28 d, which was associated with increased RBC ω-3 PUFA content (P ≤ 0.05). The first oral dose did not increase the ileal ω-3 PUFA concentration except in 4 individuals, who displayed high luminal EPA and DHA concentrations, which reduced to concentrations similar to the overall study population at day 28, suggesting physiological adaptation. Bacteroides, Clostridium, and Streptococcus were abundant bacterial genera in the ileum. Ileal microbiome variability over time and between individuals was large, with no consistent change associated with acute ω-3 PUFA dosing. However, high concentrations of EPA and DHA in IF on day 28 were associated with higher abundance of Bacteroides (r2 > 0.86, P < 0.05) and reduced abundance of other genera, including Actinomyces (r2 > 0.94, P < 0.05). Conclusions: Oral administration of ω-3 PUFAs leads to increased luminal ω-3 PUFA concentrations and changes to the microbiome, in the ileum of individuals with a temporary ileostomy.
  • The effect of photoperiod and high fat diet on the cognitive response in photoperiod-sensitive F344 rats

    McLean, Samantha L.; Yun, Haesung; Tedder, Andrew; Helfer, Gisela (2021)
    In many species, seasonal changes in day length (photoperiod) have profound effects on physiology and behavior. In humans, these include cognitive function and mood. Here we investigated the effect of photoperiod and high fat diets on cognitive deficits, as measured by novel object recognition, in the photoperiod-sensitive F344 rat, which exhibits marked natural changes in growth, body weight and food intake in response to photoperiod. 32 male juvenile F344 rats were housed in either long or short photoperiod and fed either a high fat or nutrient-matched chow diet. Rats were tested in the novel object recognition test before photoperiod and diet intervention and re-tested 28 days after intervention. In both tests during the acquisition trials there was no significant difference in exploration levels of the left and right objects in the groups. Before intervention, all groups showed a significant increase in exploration of the novel object compared to the familiar object. However, following the photoperiod and diet interventions the retention trial revealed that only rats in the long photoperiod-chow group explored the novel object significantly more than the familiar object, whereas all other groups showed no significant preference. These results suggest that changing rats to short photoperiod impairs their memory regardless of diet. The cognitive performance of rats on long photoperiod-chow remained intact, whereas the high fat diet in the long photoperiod group induced a memory impairment. These findings suggest that rats exposed to long photoperiod have different cognitive responses to rats exposed to short photoperiod and high fat diet.
  • A Simple Subjective Evaluation of Enface OCT Reflectance Images Distinguishes Glaucoma From Healthy Eyes

    Cheloni, Riccardo; Dewsbery, S.D.; Denniss, Jonathan (2021-05-25)
    Purpose: We present a subjective approach to detecting glaucomatous defects in enface images and assess its diagnostic performance. We also test the hypothesis that if reflectivity changes precede thickness changes in glaucoma there should be reduced correlation between the modalities in glaucoma compared to controls. Methods: Twenty glaucoma participants and 20 age-matched controls underwent high-resolution OCT scans of one eye. 4 μm-thick enface slabs were constructed through the retina. Enface indices were depths of first gap in visible retinal nerve fiber bundles (RNFBs) and last visible bundle, subjectively evaluated in six sectors of a 3.5 mm circle around the optic disc. Retinal nerve fiber layer thickness (RNFLT) along the same circle was extracted at angles corresponding to enface indices. Between-group differences were tested by linear mixed models. Diagnostic performance was measured by partial receiver operating characteristic area (pAUC). Results: First gap and last visible bundle were closer to the inner limiting membrane in glaucoma eyes (both P < 0.0001). Enface indices showed excellent diagnostic perfor mance (pAUCs 0.63–1.00), similar to RNFLT (pAUCs 0.63–0.95). Correlation between enface and RNFLT parameters was strong in healthy (r = 0.81–0.92) and glaucoma eyes (r = 0.73–0.80). Conclusions: This simple subjective method reliably identifies glaucomatous defects in enface images with diagnostic performance at least as good as existing thickness indices. Thickness and reflectivity were similarly related in healthy and glaucoma eyes, providing no strong evidence of reflectivity loss preceding thinning. Objective analyses may realize further potential of enface OCT images in glaucoma. Translational Relevance: Novel enface OCT indices may aid glaucoma diagnosis.
  • Effects of Chemical and Radiation Sterilisation on the Biological and Biomechanical Properties of Decellularised Porcine Peripheral Nerves

    Holland, J.D.R.; Webster, G.; Rooney, P.; Wilshaw, Stacy-Paul; Jennings, L.M.; Berry, H.E. (2021-06)
    There is a clinical need for novel graft materials for the repair of peripheral nerve defects. A decellularisation process has been developed for porcine peripheral nerves, yielding a material with potentially significant advantages over other devices currently being used clinically (such as autografts and nerve guidance conduits). Grafts derived from xenogeneic tissues should undergo sterilisation prior to clinical use. It has been reported that sterilisation methods may adversely affect the properties of decellularised tissues, and therefore potentially negatively impact on the ability to promote tissue regeneration. In this study, decellularised nerves were produced and sterilised by treatment with 0.1% (v/v) PAA, gamma radiation (25-28 kGy) or E Beam (33-37 kGy). The effect of sterilisation on the decellularised nerves was determined by cytotoxicity testing, histological staining, hydroxyproline assays, uniaxial tensile testing, antibody labelling for collagen type IV, laminin and fibronectin in the basal lamina, and differential scanning calorimetry. This study concluded that decellularised nerves retained biocompatibility following sterilisation. However, sterilisation affected the mechanical properties (PAA, gamma radiation), endoneurial structure and basement membrane composition (PAA) of decellularised nerves. No such alterations were observed following E Beam treatment, suggesting that this method may be preferable for the sterilisation of decellularised porcine peripheral nerves.
  • Using experience-based co-design with patients, carers and healthcare professionals to develop theory-based interventions for safer medicines use

    Fylan, Beth; Tomlinson, Justine; Raynor, D.K.; Silcock, Jonathan (2021)
    Background: Experience-Based Co-Design (EBCD) is a participatory design method which was originally developed and is still primarily used as a healthcare quality improvement tool. Traditionally, EBCD has been sited within single services or settings and has yielded improvements grounded in the experiences of those delivering and receiving care. Method: In this article we present how EBCD can be adapted to develop complex interventions, underpinned by theory, to be tested more widely within the healthcare system as part of a multi-phase, multi-site research study. We begin with an outline of co-design and the stages of EBCD. We then provide an overview of how EBCD can be assimilated into an intervention development and evaluation study, giving examples of the adaptations and research tools and methods that can be deployed. We also suggest how to appraise the resulting intervention so it is realistic and tractable in multiple sites. We describe how EBCD can be combined with different behaviour change theories and methods for intervention development and finally, we make suggestions about the skills needed for successful intervention development using EBCD. Conclusion: EBCD has been recognised as being a collaborative approach to improving healthcare services that puts patients and healthcare staff at the heart of initiatives and potential changes. We have demonstrated how EBCD can be integrated into a research project and how existing research approaches can be assimilated into EBCD stages. We have also suggested where behaviour change theories can be used to better understand intervention change mechanisms.
  • A non-randomised feasibility study of an intervention to optimise medicines at transitions of care for patients with heart failure

    Fylan, Beth; Ismail, Hanif; Hartley, S.; Gale, C.P.; Farrin, A.J.; Gardner, Peter H.; Silcock, Jonathan; Alldred, D.P. (2021-03)
    Heart failure affects 26 million people globally, and the optimal management of medicines is crucial for patients, particularly when their care is transferred between hospital and the community. Optimising clinical outcomes requires well-calibrated cross-organisational processes with staff and patients responding and adapting to medicines changes. The aim of this study was to assess the feasibility of implementing a complex intervention (the Medicines at Transitions Intervention; MaTI) co-designed by patients and healthcare staff. The purpose of the intervention was to optimise medicines management across the gaps between secondary and primary care when hospitals handover care. The study objectives were to (1) assess feasibility through meeting specified progression criteria to proceed to the trial, (2) assess if the intervention was acceptable to staff and patients, and (3) determine whether amendment or refinement would be needed to enhance the MaTI. The feasibility of the MaTI was tested in three healthcare areas in the North of England between July and October 2017. Feasibility was measured and assessed through four agreed progression to trial criteria: (1) patient recruitment, (2) patient receipt of a medicines toolkit, (3) transfer of discharge information to community pharmacy, and (4) offer of a community pharmacy medicines review/discussion or medicines reconciliation. From the cardiology wards at each of the three NHS Acute Trusts (sites), 10 patients (aged ≥ 18 years) were recruited and introduced to the 'My Medicines Toolkit' (MMT). Patients were asked to identify their usual community pharmacy or nominate a pharmacy. Discharge information was transferred to the community pharmacy; pharmacists were asked to reconcile medicines and invited patients for a medicines use review (MUR) or discussion. At 1 month following discharge, all patients were sent three questionnaire sets: quality-of-life, healthcare utilisation, and a patient experience survey. In a purposive sample, 20 patients were invited to participate in a semi-structured interview about their experiences of the MaTI. Staff from hospital and primary care settings involved in patients' care were invited to participate in a semi-structured interview. Patient and staff interviews were analysed using Framework Analysis. Questionnaire completion rates were recorded and data were descriptively analysed. Thirty-one patients were recruited across three sites. Eighteen staff and 18 patients took part in interviews, and 19 patients returned questionnaire sets. All four progression to trial criteria were met. We identified barriers to patient engagement with the intervention in hospital, which were compounded by patients' focus on returning home. Some patients described not engaging in discussions with staff about medicines and lacking motivation to do so because they were preoccupied with returning home. Some patients were unable or unwilling to attend a community pharmacy in person for a medicines review. Roles and responsibilities for delivering the MaTI were different in the three sites, and staff reported variations in time spent on MaTI activities. Staff reported some work pressures and staff absences that limited the time they could spend talking to patients about their medicines. Clinical teams reported that recording a target dose for heart failure medicines in patient-held documentation was difficult as they did not always know the ideal or tolerable dose. The majority of patients reported receiving the patient-held documentation. More than two-thirds reported being offered a MUR by their community pharmacists. Delivery of the Medicines at Transitions Intervention (MaTI) was feasible at all three sites, and progression to trial criteria were met. Refinements were found to be necessary to overcome identified barriers and strengthen delivery of all steps of the intervention. Necessary changes to the MaTI were identified along with amendments to the implementation plan for the subsequent trial. Future implementation needs to take into account the complexity of medicines management and adaptation to local context.
  • Post-discharge medicines management: the experiences, perceptions and roles of older people and their family carers

    Tomlinson, Justine; Silcock, Jonathan; Smith, H.; Karban, K.; Fylan, Beth (2020-12)
    Multiple changes are made to older patients' medicines during hospital admission, which can sometimes cause confusion and anxiety. This results in problems with post-discharge medicines management, for example medicines taken incorrectly, which can lead to harm, hospital readmission and reduced quality of life. To explore the experiences of older patients and their family carers as they enacted post-discharge medicines management. Semi-structured interviews took place in participants' homes, approximately two weeks after hospital discharge. Data analysis used the Framework method. Recruitment took place during admission to one of two large teaching hospitals in North England. Twenty-seven participants aged 75 plus who lived with long-term conditions and polypharmacy, and nine family carers, were interviewed. Three core themes emerged: impact of the transition, safety strategies and medicines management role. Conversations between participants and health-care professionals about medicines changes often lacked detail, which disrupted some participants' knowledge and medicines management capabilities. Participants used multiple strategies to support post-discharge medicines management, such as creating administration checklists, seeking advice or supporting primary care through prompts to ensure medicines were supplied on time. The level to which they engaged with these activities varied. Participants experienced gaps in their post-discharge medicines management, which they had to bridge through implementing their own strategies or by enlisting support from others. Areas for improvement were identified, mainly through better communication about medicines changes and wider involvement of patients and family carers in their medicines-related care during the hospital-to-home transition.
  • The role of cultural heritage in visitor narratives of peatlands: analysis of online user-generated reviews from three peatland sites in England

    Flint, Abbi; Jennings, Benjamin R. (Routledge, 2021-06)
    User-generated reviews of visitor attractions, on publicly available websites, such as Tripadvisor, are frequently used in tourism research but feature less often in published cultural heritage research. In this paper, we describe a qualitative analysis of the text from user-generated reviews of three peatland heritage landscapes in the United Kingdom – Ilkley Moor, Thorne and Hatfield Moors, and Shapwick Heath – to better understand the role tangible and intangible cultural heritage play in visitor perceptions and narratives of these sites. Our analysis indicates that visitors tend to emphasise natural over cultural heritage of peatland landscapes and hold plural, highly contextual and sometimes dissonant perceptions; there is no single story of peatlands. This presents both challenges and opportunities for building public appreciation of peatland cultural heritage. User-generated reviews offer, as-yet under-explored, potential data for use by heritage researchers and managers who seek to explore how visitors understand and use sites, and may also contribute to the emerging intangible heritage of heritage landscapes.
  • Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda

    Ngabonziza, J.C.S.; Decroo, T.; Migambi, P.; Habimana, Y.M.; Van Duen, A.; Meehan, Conor J.; Torrea, G.; Massou, F.; de Rijk, W.B.; Ushizimpumu, B.; et al. (2020-06)
    Background: The Xpert MTB/RIF (Xpert) assay is used globally to rapidly diagnose tuberculosis and resistance to rifampicin. We investigated the frequency and predictors of false-positive findings of rifampicin resistance with Xpert. Methods: We did a prospective, observational study of individuals who were enrolled in a Rwandan nationwide diagnostic cohort study (DIAMA trial; NCT03303963). We included patients identified to have rifampicin resistance on initial Xpert testing. We did a repeat Xpert assay and used rpoB Sanger and deep sequencing alongside phenotypic drug susceptibility testing (pDST) to ascertain final rifampicin susceptibility status, with any (hetero)resistant result overriding. We used multivariable logistic regression to assess predictors of false rifampicin resistance on initial Xpert testing, adjusted for HIV status, tuberculosis treatment history, initial Xpert semi-quantitative bacillary load, and initial Xpert probe. Findings: Between May 4, 2017, and April 30, 2019, 175 people were identified with rifampicin resistance at initial Xpert testing, of whom 154 (88%) underwent repeat Xpert assay. 54 (35%) patients were confirmed as rifampicin resistant on repeat testing and 100 (65%) were not confirmed with resistance. After further testing and sequencing, 121 (79%) of 154 patients had a final confirmed status for rifampicin susceptibility. 57 (47%) of 121 patients were confirmed to have a false rifampicin resistance result and 64 (53%) had true rifampicin resistance. A high pretest probability of rifampicin resistance did not decrease the odds of false rifampicin resistance (adjusted odds ratio [aOR] 6·0, 95% CI 1·0–35·0, for new tuberculosis patients vs patients who needed retreatment). Ten (16%) of the 64 patients with true rifampicin resistance did not have confirmed rifampicin resistance on repeat Xpert testing, of whom four had heteroresistance. Of 63 patients with a very low bacillary load on Xpert testing, 54 (86%) were falsely diagnosed with rifampicin-resistant tuberculosis. Having a very low bacillary load on Xpert testing was strongly associated with false rifampicin resistance at the initial Xpert assay (aOR 63·6, 95% CI 9·9–410·4). Interpretation: The Xpert testing algorithm should include an assessment of bacillary load and retesting in case rifampicin resistance is detected on a paucibacillary sputum sample. Only when rifampicin resistance has been confirmed on repeat testing should multidrug-resistant tuberculosis treatment be started. When rifampicin resistance has not been confirmed on repeat testing, we propose that patients should be given first-line anti-tuberculosis drugs and monitored closely during treatment, including by baseline culture, pDST, and further Xpert testing.
  • Characterization of Genomic Variants Associated with Resistance to Bedaquiline and Delamanid in Naive Mycobacterium tuberculosis Clinical Strains

    Battaglia, S.; Spitaleri, A.; Cabibbe, A.M.; Meehan, Conor J.; Utpatel, C.; Ismail, N.; Tahseen, S.; Skrahina, A.; Alikhanova, N.; Mostofa Kamal, S.M.; et al. (2020-10)
    The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of the genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analyzed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole-genome sequencing (WGS) data set from a collection of 4,795 MTBc clinical isolates from six countries with a high burden of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to these medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structures of Ddn (DLM), Fgd1 (DLM), and Rv0678 (BDQ) and performed MIC assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloguing the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35), only two of which were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance for the development of comprehensive molecular diagnostic tools.
  • A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

    Ngabonziza, J.C.S.; Loiseau, C.; Marceau, M.; Jouet, A.; Menardo, F.; Tzfadia, O.; Antoine, R.; Niyigena, E.B.; Mulders, W.; Fissette, K.; et al. (2020-12)
    The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle.
  • Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries.

    Rivière, E.; Heupink, T.H.; Ismail, N.; Dippenaar, A.; Clarke, C.; Abebe, G.; Heusden van, P.; Warren, R.; Meehan, Conor J.; Van Rie, A. (2020-07)
    Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
  • Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

    Coscolla, M.; Gagneux, S.; Menardo, F.; Loiseau, C.; Ruiz-Rodriguez, P.; Borrell, S.; Otchere, I.D.; Asante-Poku, A.; Asare, P.; Sánchez-Busó, L.; et al. (2021-02)
    Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
  • Whole-genome sequencing for TB source investigations: principles of ethical precision public health.

    van Rie, A.; de Viedma, D.G.; Meehan, Conor J.; Comas, I.; Heupink, T.H.; De Vos, E.; de Onate, W.A.; Mathys, V.; Ceyssens, P-J.; Groenen, G.; et al. (2021-03)
    BACKGROUND: Whole-genome sequencing (WGS) of Mycobacterium tuberculosis allows rapid, accurate inferences about the sources, location and timing of transmission. However, in an era of heightened concern for personal privacy and science distrust, such inferences could result in unintended harm and undermine the public´s trust. METHODS: We held interdisciplinary stakeholder discussions and performed ethical analyses of real-world illustrative cases to identify principles that optimise benefit and mitigate harm of M. tuberculosis WGS-driven TB source investigations.RESULTS: The speed and precision with which real-time WGS can be used to associate M. tuberculosis strains with sensitive information has raised important concerns. While detailed understanding of transmission events could mitigate harm to vulnerable patients and communities when otherwise unfairly blamed for TB outbreaks, the precision of WGS can also identify transmission events resulting in social blame, fear, discrimination, individual or location stigma, and the use of defaming language by the public, politicians and scientists. Public health programmes should balance the need to safeguard privacy with public health goals, transparency and individual rights, including the right to know who infects whom or where.CONCLUSIONS: Ethical challenges raised by real-time WGS-driven TB source investigation requires public health authorities to move beyond their current legal mandate and embrace transparency, privacy and community engagement.

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