Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model

Human challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designed Mycobacterium tuberculosis (Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10 -10 per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.

Attenuated Mycobacterium tuberculosis vaccine protection in a low-dose murine challenge model

Bacillus Calmette-Guérin (BCG) remains the only approved tuberculosis (TB) vaccine despite limited efficacy. Preclinical studies of next-generation TB vaccines typically use a murine aerosol model with a supraphysiologic challenge dose. Here, we show that the protective efficacy of a live attenuated Mycobacterium tuberculosis (Mtb) vaccine ΔLprG markedly exceeds that of BCG in a low-dose murine aerosol challenge model. BCG reduced bacterial loads but did not prevent establishment or dissemination of infection in this model. In contrast, ΔLprG prevented detectable infection in 61% of mice and resulted in anatomic containment of 100% breakthrough infections to a single lung. Protection was partially abrogated in a repeated low-dose challenge model, which showed serum IL-17A, IL-6, CXCL2, CCL2, IFN-γ, and CXCL1 as correlates of protection. These data demonstrate that ΔLprG provides increased protection compared to BCG, including reduced detectable infection and anatomic containment, in a low-dose murine challenge model.

Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis

Despite the existence of well-characterized, canonical mutations that confer high-level drug resistance to Mycobacterium tuberculosis (Mtb), there is evidence that drug resistance mechanisms are more complex than simple acquisition of such mutations. Recent studies have shown that Mtb can acquire non-canonical resistance-associated mutations that confer survival advantages in the presence of certain drugs, likely acting as stepping-stones for acquisition of high-level resistance. Rv2752c/rnj, encoding RNase J, is disproportionately mutated in drug-resistant clinical Mtb isolates. Here we show that deletion of rnj confers increased tolerance to lethal concentrations of several drugs. RNAseq revealed that RNase J affects expression of a subset of genes enriched for PE/PPE genes and stable RNAs and is key for proper 23S rRNA maturation. Gene expression differences implicated two sRNAs and ppe50-ppe51 as important contributors to the drug tolerance phenotype. In addition, we found that in the absence of RNase J, many short RNA fragments accumulate because they are degraded at slower rates. We show that the accumulated transcript fragments are targets of RNase J and are characterized by strong secondary structure and high G+C content, indicating that RNase J has a rate-limiting role in degradation of highly structured RNAs. Taken together, our results demonstrate that RNase J indirectly affects drug tolerance, as well as reveal the endogenous roles of RNase J in mycobacterial RNA metabolism.

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis

Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics-even below this breakpoint-is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic.

Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates

OBJECTIVES

Drug-resistant TB remains a public health challenge. Rifamycins are among the most potent anti-TB drugs. They are known to target the RpoB subunit of RNA polymerase; however, our understanding of how rifamycin resistance is genetically encoded remains incomplete. Here we investigated rpoB genetic diversity and cross-resistance between the two rifamycin drugs rifampicin and rifabutin.

METHODS

We performed WGS of 1003 Mycobacterium tuberculosis clinical isolates and determined MICs of both rifamycin agents on 7H10 agar using the indirect proportion method. We generated rpoB mutants in a laboratory strain and measured their antibiotic susceptibility using the alamarBlue reduction assay.

RESULTS

Of the 1003 isolates, 766 were rifampicin resistant and 210 (27%) of these were rifabutin susceptible; 102/210 isolates had the rpoB mutation D435V (Escherichia coli D516V). Isolates with discordant resistance were 17.2 times more likely to harbour a D435V mutation than those resistant to both agents (OR 17.2, 95% CI 10.5-27.9, P value <10-40). Compared with WT, the D435V in vitro mutant had an increased IC50 of both rifamycins; however, in both cases to a lesser degree than the S450L (E. coli S531L) mutation.

CONCLUSIONS

The observation that the rpoB D435V mutation produces an increase in the IC50 of both drugs contrasts with findings from previous smaller studies that suggested that isolates with the D435V mutation remain rifabutin susceptible despite being rifampicin resistant. Our finding thus suggests that the recommended critical testing concentration for rifabutin should be revised.

Defining and evaluating transdisciplinary research: implications for aging and technology

Purpose: Transdisciplinary research has the potential to enhance the real-world impact of the field of aging and technology. This is a context-driven and problem-focused approach to knowledge production that involves collaboration across scientific disciplines and academic and nonacademic sectors. To sustain broader implementation of this approach, a scoping review was conducted on the impact of this approach on research processes, outcomes and uptake. Materials and Methods: A systematic search was conducted of aging, health/medicine, and technology literatures indexed in three electronic data bases (Medline/OVID, EBSCO, ProQuest) from 1 January 2005 to 31 December 2015. Search terms included three themes: (1) transdisciplinarity; (2) research outcomes and (3) social change. Results: Twenty articles met the inclusion criteria. We found that a transdisciplinary approach to research enhances integration of diverse knowledge, scientific and extra-scientific outcomes, capacity to engage in translational research and the uptake of research knowledge. We also identified a number of facilitators and barriers to successful implementation of this approach. No articles evaluating transdisciplinary research specifically in the context of aging and technology were found. Conclusions: Adoption of transdisciplinary research in aging and technology may foster greater uptake of technological innovation in the real-world by supporting integration of diverse knowledge and enhancing engagement of experiential and nonacademic stakeholders in the research and development process. However, supporting successful implementation of this approach requires investment of personal and structural resources. More research is needed to better understand the evidence base on the adoption of this approach in aging and technology projects. IMPLICATIONS FOR REHABILITATION Transdisciplinary research is context-driven and problem-focused and involves collaboration between academic and non-academic sectors. A transdisciplinary approach can enhance knowledge integration, scientific productivity and capacity and public involvement in research. Future research is needed to determine the effectiveness of transdisciplinarity for optimizing the development and uptake of assistive technologies.

Qualitative health research via the Internet: practical and methodological issues

Electronic mail (email) has become a ubiquitous form of global communication. Much of this discourse concerns the experience of health and illness. As it is stored and accessible via the Internet, it is then available for qualitative analysis by health researchers. In particular, researchers can employ document analysis methods using Internet communication such as email posts and archives. This paper outlines ways in which such research could proceed, including locating potential research sites and collecting and analysing data. In addition, the advantages and disadvantages of using documentary analysis of Internet communication in qualitative health research are explored.

Healthy ageing and home: the perspectives of very old people in five European countries

This paper reports on in-depth research, using a grounded theory approach, to examine the ways in which very old people perceive healthy ageing in the context of living alone at home within urban settings in five European countries. This qualitative study was part of a cross-national project entitled ENABLE-AGE which examined the relationship between home and healthy ageing. Interviews explored the notion of healthy ageing, the meaning and importance of home, conceptualisations of independence and autonomy and links between healthy ageing and home. Data analysis identified five ways in which older people constructed healthy ageing: home and keeping active; managing lifestyles, health and illness; balancing social life; and balancing material and financial circumstances. Older people reflected on their everyday lives at home in terms of being engaged in purposeful, meaningful action and evaluated healthy ageing in relation to the symbolic and practical affordances of the home, contextualised within constructions of their national context. The research suggests that older people perceive healthy ageing as an active achievement, created through individual, personal effort and supported through social ties despite the health, financial and social decline associated with growing older. The physicality and spatiality of home provided the context for establishing and evaluating the notion of healthy ageing, whilst the experienced relationship between home, life history and identity created a meaningful space within which healthy ageing was negotiated.

Comparative genomic and bioinformatic approaches for the identification of new adenosine-to-inosine substrates

Adenosine-to-inosine (A-to-I) RNA editing is the enzymatic deamination of A-to-I catalyzed by ADAR (adenosine deaminase acting on RNA). Adenosine is read by ribosomes as guanosine causing a codon change and potentially protein recoding. A-to-I RNA editing can be either promiscuous, where the editing is nonspecific, or site specific, which requires a complex target RNA secondary structure formed by intramolecular base pairings between editing sequences and intronic or exonic editing site complementary sequences (ECSs). The most numerous editing sites have been found in noncoding regions containing Alu repeats, such as 3' untranslated regions, while specific editing sites are mostly found in transcripts involved in the transmission of neuronal signals. Previously A-to-I RNA editing sites were discovered by chance, but recently investigators have used comparative genomic and bioinformatics methods to identify novel sites. In this chapter, we discuss these approaches to identifying new editing sites.

Ethical issues in the documentary data analysis of Internet posts and archives

The documentary analysis of e-mail posts and archives for qualitative research has been outlined elsewhere. Although there is an increase in the number of studies being conducted on listserv and newsgroup material in health research, this has not always been accompanied by a careful, in-depth consideration of the concomitant ethical issues. Therefore, this article outlines the ethical considerations surrounding this form of research, including issues of accessing voices, consent, privacy, anonymity, interpretation, and ownership and authorship of research material.

Smart care technologies: meeting whose needs?

Recent funding programmes supporting research and development in telecare have argued for a shift in perspective from a technology-driven approach to one that is needs-led. While this is in the interests of both users and technologists, achieving this goal is not straightforward. This paper outlines some of the conceptual, methodological and practical problems that potentially constrain a needs-led approach and illustrates the emergent issues with a case study of the development of an intelligent home monitoring system to support the independent living of older people. The research indicates clear differences between users and technologists in the way problems, needs and requirements are understood and defined. This in turn has consequences for the way assistive technologies are developed and implemented.

A community needs assessment for rural mental health promotion

This paper describes the needs assessment phase of a mental health promotion programme for rural communities in Ireland. As part of a larger study encompassing four rural communities, a cross-sectional study of the mental health beliefs and perceptions of 1014 people was carried out. Employing a combination of interviewer-administered questionnaire and the vignette method, the needs assessment explores the levels of awareness, current practices, attitudes and stigma concerning depression and suicide among a randomly selected quota sample of community members. Lower levels of awareness, less confidence in dealing with mental health issues, negative attitudes to help-seeking and social stigma emerge as particular issues for men and the under 40 age group. Women were found to have more positive attitudes generally, were more likely to use informal social support networks and were more open about discussing mental health matters. The predominant interpretation of the depression vignette was to view it as a mental health problem with good prospects for recovery given appropriate help. Social relationships, negative thinking patterns and social stresses were perceived as being particularly important in explaining the origins of depression. The implications of the findings for planning the intervention phase of the project are considered.

Older people, driving and new technology

There are increasing numbers of older car users on the roads today. This paper examines the particular problems that older people experience as drivers and evaluates the role of road transport informatics (RTI) as a means for enhancing driver capabilities and improving road safety. Implications for product design are also discussed.