Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

Despite significant advances in treatment strategies targeting the underlying defect in cystic fibrosis (CF), airway infection remains an important cause of lung disease. In this two-part series, we review recent evidence related to the complexity of CF airway infection, explore data suggesting the relevance of individual microbial species, and discuss current and future treatment options. In Part I, the evidence with respect to the spectrum of bacteria present in the CF airway, known as the lung microbiome is discussed. Subsequently, the current approach to treat methicillin-resistant Staphylococcus aureus, gram-negative bacteria, as well as multiple coinfections is reviewed. Newer molecular techniques have demonstrated that the airway microbiome consists of a large number of microbes, and the balance between microbes, rather than the mere presence of a single species, may be relevant for disease pathophysiology. A better understanding of this complex environment could help define optimal treatment regimens that target pathogens without affecting others. Although relevance of these organisms is unclear, the pathologic consequences of methicillin-resistant S. aureus infection in patients with CF have been recently determined. New strategies for eradication and treatment of both acute and chronic infections are discussed. Pseudomonas aeruginosa plays a prominent role in CF lung disease, butmany other nonfermenting gram-negative bacteria are also found in the CF airway. Many new inhaled antibiotics specifically targeting P. aeruginosa have become available with the hope that they will improve the quality of life for patients. Part I concludes with a discussion of how best to treat patients with multiple coinfections.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

Predatory Bdellovibrio bacteria use gliding motility to scout for prey on surfaces

Bdellovibrio bacteriovorus is a famously fast, flagellate predatory bacterium, preying upon Gram-negative bacteria in liquids; how it interacts with prey on surfaces such as in medical biofilms is unknown. Here we report that Bdellovibrio bacteria "scout" for prey bacteria on solid surfaces, using slow gliding motility that is present in flagellum-negative and pilus-negative strains.

Religion, pragmatic fundamentalism and the transformation of the Northern Ireland conflict

Since 11 September 2001, the religious dimension of conflict has been the focus of increasing attention. In The Clash of Civilizations, Huntington has identified the West in religious-cultural terms, as Christian with a dominant democratic culture emphasizing tolerance, moderation and consensus. The persistence of conflict in Northern Ireland among 'White' Protestant and Catholic Christians undermines this simplistic argument and demands a more subtle understanding of the role of religion and fundamentalism in contemporary conflict. Modernization theory - which is echoed among some theorists of globalization - had predicted the declining importance of religion as the world became industrialized and increasingly interconnected. This is echoed by those who argue that the Northern Ireland conflict is 'ethno-national' and dismiss the role of religion. On the other hand, others have claimed that the conflict is religious and stress the role of Protestant fundamentalism. This article draws on new evidence from Northern Ireland of the complex and subtle ways in which religion impacts on the conflict there, incorporating insights about the pragmatism of fundamentalist Protestants and how religious actors are contributing to conflict transformation. This analysis leads to three broader conclusions about understanding conflicts with religious dimensions. First, the complexity of religion must be understood, and this includes a willingness to recognize the adaptability of fundamentalisms to particular contexts. Second, engaging with fundamentalists and taking their grievances seriously opens up possibilities for conflict transformation. Third, governments and religious actors within civil society can play complementary roles in constructing alternative (religious) ideologies and structures as part of a process of transformation. In a world in which the impact of religion is persistent, engaging with the religious dimension is a vital part of a broader-based strategy for dealing with conflict. © 2008 Journal of Peace Research.

Religion and Transformation in South Africa? Institutional and Discursive Change in a Charismatic Congregation

A number of Christian churches in South Africa have proclaimed their commitment to reconciliation and the elimination of unjust inequalities. This study analyses how these commitments are being worked out at the micro-level of a congregation. Using an ethnographic approach, I explore how a charismatic congregation in Cape Town has changed from being nearly all-white to being more inclusive. I explore links between individual, cognitive identity change and institutional change; and consider the discourses which justify change, including their emphasis on 'unity in diversity' and 'restitution'. I outline the limitations of change, including the persistence of 'racialised' leadership structures and the discursive privileging of unity over restitution. This allows us to understand how micro-level changes take place, to explore their potentialities and limitations, and to apply these insights to other contexts.

Reduced Bacterial Colony Count of Anaerobic Bacteria Is Associated with a Worsening in Lung Clearance Index and Inflammation in Cystic Fibrosis

Anaerobic bacteria have been identified in abundance in the airways of cystic fibrosis (CF) subjects. The impact their presence and abundance has on lung function and inflammation is unclear. The aim of this study was to investigate the relationship between the colony count of aerobic and anaerobic bacteria, lung clearance index (LCI), spirometry and C-Reactive Protein (CRP) in patients with CF. Sputum and blood were collected from CF patients at a single cross-sectional visit when clinically stable. Community composition and bacterial colony counts were analysed using extended aerobic and anaerobic culture. Patients completed spirometry and a multiple breath washout (MBW) test to obtain LCI. An inverse correlation between colony count of aerobic bacteria (n = 41, r = -0.35; p = 0.02), anaerobic bacteria (n = 41, r = -0.44, p = 0.004) and LCI was observed. There was an inverse correlation between colony count of anaerobic bacteria and CRP (n = 25, r = -0.44, p = 0.03) only. The results of this study demonstrate that a lower colony count of aerobic and anaerobic bacteria correlated with a worse LCI. A lower colony count of anaerobic bacteria also correlated with higher CRP levels. These results indicate that lower abundance of aerobic and anaerobic bacteria may reflect microbiota disruption and disease progression in the CF lung.

Bacteria microarrays as sensitive tools for exploring pathogen surface epitopes and recognition by host receptors

We describe a protocol for the generation and validation of bacteria microarrays and their application to the study of specific features of the pathogen's surface and interactions with host receptors. Bacteria were directly printed on nitrocellulose-coated glass slides, using either manual or robotic arrayers, and printing quality, immobilization efficiency and stability of the arrays were rigorously controlled by incorporating a fluorescent dye into the bacteria. A panel of wild type and mutant strains of the human pathogen Klebsiella pneumoniae, responsible for nosocomial and community-acquired infections, was selected as model bacteria, and SYTO-13 was used as dye. Fluorescence signals of the printed bacteria were found to exhibit a linear concentration-dependence in the range of 1 x 10(8) to 1 x 10(9) bacteria per ml. Similar results were obtained with Pseudomonas aeruginosa and Acinetobacter baumannii, two other human pathogens. Successful validation of the quality and applicability of the established microarrays was accomplished by testing the capacity of the bacteria array to detect recognition by anti-Klebsiella antibodies and by the complement subcomponent C1q, which binds K. pneumoniae in an antibody-independent manner. The biotin/AlexaFluor-647-streptavidin system was used for monitoring binding, yielding strain-and dose-dependent signals, distinctive for each protein. Furthermore, the potential of the bacteria microarray for investigating specific features, e.g. glycosylation patterns, of the cell surface was confirmed by examining the binding behaviour of a panel of plant lectins with diverse carbohydrate-binding specificities. This and other possible applications of the newly developed arrays, as e.g. screening/evaluation of compounds to identify inhibitors of host-pathogen interactions, make bacteria microarrays a useful and sensitive tool for both basic and applied research in microbiology, biomedicine and biotechnology.

The influence of microbial factors on the susceptibility of bacteria to photocatalytic destruction

The role that bacterial factors play in determining how bacteria respond to photocatalytic degradation is becoming increasingly recognised. Fimbriae which are thin, proteinaceous cell surface structures produced by many enterobacteria are generally considered to be important bacterial virulence determinants in the host. Recent studies, however, suggest that their expression may be increased during times of environmental stress to protect them against factors such as nutrient depletion and oxidation. In this study bacteria were grown under defined culture conditions to promote the expression of type 1 fimbriae and subjected to photocatalytic treatment. Results showed that Escherichia coli grown under conditions to express type 1 fimbriae were more resistant to photocatalytic destruction than control cultures, taking 75 min longer to be destroyed. Curli fimbriae are also known to play a role in environmental protection of bacteria and they are associated with biofilm production. The ability of the E. coli strain to produce curli fimbriae was confirmed and biofilms were grown and subjected to photocatalytic treatment. Biofilm destruction by photocatalysis was assessed using a resazurin viability assay and a loss of cell viability was demonstrated within 30 min treatment time. This study suggests that intrinsic bacterial factors may play a role in determining an organism’s response to photocatalytic treatment and highlights their importance in this disinfection process.

Identification of lactic acid bacteria strains modulating incretin hormone secretion and gene expression in enteroendocrine cells

Glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) are incretin hormones released from intestinal enteroendocrine (EE) cells and have well-established glucose-lowering actions. Lactic acid bacteria (LAB) colonise the human intestine, but it is unknown whether LAB and EE cells interact. Acute co-culture of LAB with EE cells showed that certain LAB strains elicit GLP-1 and GIP secretion (13-194-fold) and upregulate their gene expression. LAB-induced incretin hormone secretion did not appear to involve nutrient mechanisms, nor was there any evidence of cytolysis. Instead PCR array studies implicated signalling agents of the toll-like receptor system, e.g. adaptor protein MyD88 was decreased 23-fold and cell surface antigen CD14 was increased 17-fold. Mechanistic studies found that blockade of MyD88 triggered significant GLP-1 secretion. Furthermore, blocking of CD14 completely attenuated LAB-induced secretion. A recent clinical trial clearly shows that LAB have potential for alleviating type 2 diabetes, and further characterisation of this bioactivity is warranted.

Reconstructing the Social Fabric amid On-going Violence: Attitudes toward Reconciliation and Structural Transformation in Colombia

Given the increase of reconciliation processes initiated amid on-going violence, this study focuses on community reconciliation and its relation to structural transformation, or social reconstruction through reforming unjust institutions and practices that facilitate protracted violent conflict. Drawing lessons from the Caribbean coast of Colombia, mixed method analyses include eight in-depth interviews and 184 surveys. Four key dimensions of reconciliation – truth, justice, mercy, peace – are examined. In the interviews, participants prioritize reconstructing the truth and bringing perpetrators to justice as essential aspects of reconciliation. Notions of mercy and forgiveness are less apparent. For the participants, sustainable peace is dependent on structural transformation to improve livelihoods. These data, however, do not indicate how this understanding of reconciliation may relate to individual participation in reconciliation processes. Complementing the qualitative data, quantitative analyses identify some broad patterns that relate to participation in reconciliation events. Compared to those who did not participate, individuals who engaged in reconciliation initiatives report higher levels of personal experience with violence, live alongside demobilized paramilitaries, are more engaged in civic life, and express greater preference for structural transformation. The paper concludes with policy implications that integrate reconciliation and structural transformation to deepen efforts to rebuild the social fabric amid violence.

Land wars in India: Contestations, social forces and evolving neoliberal urban transformation

Land wars in India: Contestations, social forces and evolving neoliberal urban transformation
The recent incidents of ‘land wars’ in India have highlighted the contradictions and challenges of the neoliberal urban transformation through a range of issues across governance, equity and empowerment in the development agenda. Simply put, a strong top down approach and corporate-political nexus have determined the modality of land acquisition, compensation and ultimately the nature of its consumption leaving out majority urban poor from its benefits. The paper focuses on the concept of neoliberalism as a modality of urban governance and emergence of the grassroots activism as a countermagnate to neoliberalist hegemony by examining the inequity and marginalization that embody these ‘land wars’ in India and the forms of resistance from the grassroots - their capacity, relationship and modus operandi. Emerging lessons suggest the potential for advancing governance from the bottoms up leading to more equitable distribution of resources. It is however argued that there is a need for a stronger conception of the ‘grassroots’ in both epistemological and empirical context. In particular, the preconditions for the ‘grassroots organisations’ to foster and play a more effective role requires a more inclusive notion of ‘institutionality and plurality’ within the current political economic context. The empirical focus of the paper is ‘land wars’ observed in Kolkata, West Bengal, however references to other examples across the country have also been made.

Molecular mechanisms of virulence of Burkholderia cepacia complex bacteria: Survival in Phagocytic Cells

Burkholderia cepacia complex (Bcc) species are a group of Gram-negative opportunistic pathogens that chronically infect the airways of cystic fibrosis patients, but they can also infect patients with various types of immunosuppressive disorders. Bcc members are multidrug resistant bacteria that have the ability to persist in the infected host and also elicit robust inflammatory responses. Studies using macrophages, neutrophils and dendritic cells, combined with dramatic advances in the ability to genetically manipulate these microorganisms have contributed to increase our understanding of the molecular mechanisms of virulence in these pathogens and the molecular details of the cell host responses triggering inflammation. This chapter reviews our understanding of the pathogenic mechanisms used by Bcc to establish an intracellular niche in phagocytic cells and modulate host cell responses that ultimately end up in cell death and a proinflammatory response.

Leukaemic transformation of donor cells in a patient receiving a second allogeneic bone marrow transplant for severe aplastic anaemia

Allogeneic blood or bone marrow transplantation is a successful treatment for leukaemia and severe aplastic anaemia (SAA). Graft rejection following transplantation for leukaemia is a rare event but leukaemic relapse may occur at varying rates, depending upon the stage of leukaemia at which the transplant was undertaken and the type of leukaemia. Relapse is generally assumed to occur in residual host cells, which are refractory to, or escape from the myeloablative conditioning therapy. Rare cases have been described, however, in which the leukaemia recurs in cells of donor origin. Lack of a successful outcome of blood or bone marrow transplantation for severe aplastic anaemia (SAA), however, is due to late graft rejection or graft-versus-host disease. Leukaemia in cells of donor origin has rarely been reported in patients following allogeneic bone marrow transplantation for SAA. This report describes leukaemic transformation in donor cells following a second allogeneic BMT for severe aplastic anaemia. PCR of short tandem repeats in bone marrow aspirates and in colonies derived from BFUE and CFU-GM indicated the donor origin of leukaemia. Donor leukaemia is a rare event following transplantation for severe aplastic anaemia but may represent the persistence or perturbation of a stromal defect in these patients inducing leukaemic change in donor haemopoietic stem cells.

Successful bone marrow transplant for Fanconi anaemia in transformation

We present a patient who was diagnosed as suffering from Fanconi anaemia at the age of 36 years. At the time of diagnosis his bone marrow showed features of pre-leukaemic transformation. He received an allogeneic bone marrow transplant (BMT) from his HLA-identical sibling. The post-transplant course was unremarkable with evidence of trilineage engraftment at day +32 and no acute or chronic GVHD. He is well with sustained engraftment and no haematological evidence of Fanconi anaemia 18 months post-transplant.