Population analysis of bacterial pathogens on distinct temporal and spatial scales

Bacteria have been the causative agents of major infectious disease pandemics throughout human history. Over the past 4 decades, a combination of changing medical practices, industrialization, and globalisation have led to a number of emergences and re-emergences of bacterial pathogens. The design of rational control programs and bespoke therapies will require an enhanced understanding of the dynamics underpinning the emergence and transmission of pathogenic clones. The recent development of new technologies for sequencing bacterial genomes rapidly and economically has led to a greatly enhanced understanding of the diversity of bacterial populations. This thesis describes the application of whole genome sequencing of 2 bacterial pathogens, Staphylococcus aureus and Legionella pneumophila, in order to understand the dynamics of bacterial infections on different temporal and spatial scales. The first study involves the examination of S. aureus evolution during a chronic infection of a single patient over a period of 26 months revealing differences in antibiotic resistance profiles and virulence factor expression over time. The genetic variation identified correlated with differences in growth rate, haemolytic activity, and antibiotic sensitivity, implying a profound effect on the ecology of S. aureus. Importantly, polymorphisms were identified in global regulators of virulence, with a high frequency of polymorphisms within the SigB locus identified, suggesting this region may be under selection in this patient. The identification of genes under diversifying selection during long-term infection may inform the design of novel therapeutics for the control of refractory chronic infections. Secondly, the emergence and transmission of 3 pandemic lineages derived from S. aureus clonal complex 30 (CC30) were investigated. Independent origins for each pandemic lineage were identified, with striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements, such as bacteriophage and Staphylococcal pathogenicity islands, and non-synonymous mutations affecting antibiotic resistance and virulence. Hospitals in large cities were identified as hubs for the transmission of MRSA to regional health care centres. In addition, comparison of whole genome sequences revealed that at least 3 independent acquisitions of TSST-1 have occurred in CC30, but a single distinct clade of diverse community-associated CC30 strains was responsible for the TSS epidemic of the late 1970s, and for subsequent cases of TSS in the UK and USA. Finally, whole genome sequencing was used as a tool for investigating a recent outbreak of legionellosis in Edinburgh. An unexpectedly high level of genomic diversity was identified among the outbreak strains, with respect to core genome polymorphisms, and accessory genome content. The data indicate that affected individuals may be infected with heterogeneous strains. The findings highlight the complexities in identifying environmental sources and suggest possible differences in pathogenic potential among isolates from a single outbreak. Taken together, the findings demonstrate applications of bacterial genome sequencing leading to enhanced understanding of bacterial pathogen evolution, emergence, and transmission, which may ultimately inform appropriate infection control measures

Aqueous Processes and Microbial Habitability of Gale Crater Sediments from the Blunts Point to the Glenn Torridon Clay Unit

A driving factor for sending the Mars Science Laboratory, Curiosity rover to Gale Crater was the orbital detection of clay minerals in the Glen Torridon (GT) clay unit. Clay mineral detections in GT suggested a past aqueous environment that was habitable, and could contain organic evidence of past microbiology. The mission of the Sample Analysis at Mars (SAM) instrument onboard Curiosity was to detect organic evidence of past microbiology and to detect volatile bearing mineralogy that can inform on whether past geochemical conditions would have supported microbiological activity. The objective of this work was to 1) evaluate the depositional/alteration conditions of Blunts Point (BP) to GT sediments 2) search for evidence of organics, and 3) evaluate microbial habitability in the BP, Vera Rubin Ridge (VRR), and GT sedimentary rock

Evidence for Smectite Clays from MSL SAM Analyses of Mudstone at Yellowknife Bay, Gale Crater, Mars

Drilled samples of mudstone from the Sheepbed unit at Yellowknife Bay were analyzed by MSL instruments including the Sample Analysis at Mars (SAM) and Chemistry and Mineralogy (CheMin) instruments in MSL's Analytical Laboratory. CheMin analyses revealed the first in situ X-ray diffraction based evidence of clay minerals on Mars, which are likely trioctahedral smectites (e.g., saponite) and comprise approx 20% of the mudstone sample (e.g., Bristow et al., this meeting). SAM analyses, which heated the mudstone samples to 1000 C and monitored volatiles evolved to perform in situ evolved gas analysis mass spectrometry (EGA-MS), resulted in a H2O trace exhibiting a wide evolution at temperatures < 500 C, and an evolution peak at higher temperatures near approx 750 C. The low temperature H2O evolution has many potential contributors, including adsorbed H2O, smectite interlayer H2O, and structural H2O/OH from bassanite and akaganeite (identified by CheMin) and H2O/OH from amorphous phases in the sample. The high temperature H2O is consistent with the evolution of H2O from the dehydroxylation of the smectite clay mineral. Comparison to EGA-MS data collected under SAM-like conditions on a variety of clay mineral reference materials indicate that a trioctahedral smectite, such as saponite, is most consistent with the high temperature H2O evolution observed. There may also be SAM EGA-MS evidence for a small high temperature H2O evolution from scoop samples from the Yellowknife Bay Rocknest sand shadow bedform. As in the mudstone samples, this evolution may indicate the detection of smectite clays, and the idea that minor clays may be present in Rocknest materials that could be expected to be at least partially derived from local sources is reasonable. But, because smectite clays were not definitively observed in CheMin analyses of Rocknest materials, they must be present at much lower abundances than the approx 20% observed in the mudstone samples. This potential detection underscores the complementary nature of the MSL CheMin and SAM instruments for investigations of martian sample mineralogy. Information on the nature of Yellowknife Bay clay minerals may also be available from the detection of H2 evolved during SAM EGA-MS at high temperature. A likely source of at least some of this H2 is H2O evolved from the smectite clays at high temperature, and it is possible these evolutions can be used in a similar fashion to high temperature H2O releases to provide constraints on the clay minerals in a sample. In addition, the D/H of this high temperature H2, as well as the H2O, can be derived from SAM MS and Tunable Laser Spectrometer (TLS) data, respectively. These D/H values may help to inform the provenance of high and low temperature water evolved from martian sample

The Deuterium to Hydrogen Ratio in the Water that Formed the Yellowknife Bay Mudstones in Gale Crater

A suite of isotope ratios of light elements in the present martian atmosphere (13C/12C, 15N/14N, 18O/16O, 38Ar/36Ar, and D/H) are all substantially enriched in the heavy element suggesting atmospheric loss to space over the past billions of years with preferential loss of the lighter isotope from each pair. In situ measurements from MSL's Sample Analysis at Mars (SAM) instrument [e.g. 1,2,3] have considerably refined previous measurements from the Viking mass spectrometers [e.g. 4], from remote spectroscopic observations [e.g. 5,6], and from martian meteorite studies [e.g. 7,8]. The persistence of habitable environments such as the ancient Yellowknife Bay lake recently revealed by measurements from the Curiosity rover [9] depends on the surface temperatures and the duration of an atmosphere thicker than that at present. Current and planned measurements from orbit with the Mars Express and MAVEN missions respectively intend to study the processes of atmospheric escape including solar wind interaction, sputtering, thermal escape, and dissociative recombination, and determine or refine the current rate of atmospheric loss caused by these and other mechanisms. The goal of these programs is to understand the physical processes sufficiently well so that robust extrapolations over the past billions of years can be made D/H is measured by both the Tunable Laser Spectrometer (TLS) and the Quadrupole Mass Spectrometer (QMS) of the SAM suite. to predict the atmospheric and surface conditions on early Mars. However, the study of the history of martian atmospheric evolution will be greatly facilitated if we are able to also directly measure the isotopic composition of volatiles captured in rocks that are representative of the ancient atmosphere. To date, D/H is one of the most promising candidates for this study since water is the most abundant volatile thermally released from the Yellowknife Bay phylosilicates discovered by the SAM and CheMin experiments of MSL and it

Political mobilisation by minorities in Britain: negative feedback of ‘race relations'?

This article uses a political opportunity approach to study the relationship of minority groups to the political community in Britain. The main argument is that the British race relations approach established in the 1960s had an important effect that still shapes the patterns of political contention by different minority groups today. Original data on political claims-making by minorities demonstrate that British 'racialised' cultural pluralism has structured an inequality of opportunities for the two main groups, African-Caribbeans and Indian subcontinent minorities. African-Caribbeans mobilise along racial lines, use a strongly assimilative 'black' identity, conventional action forms, and target state institutions with demands for justice that are framed within the recognised framework of race relations. Conversely, a high proportion of the Indian subcontinent minority mobilisation is by Muslim groups, a non-assimilative religious identity. These are autonomously organised, but largely make public demands for extending the principle of racial equality to their non-racial group. Within the Indian subcontinent minorities, the relative absence of mobilisation by Indian, Sikh and Hindu minorities, who have achieved much better levels of socio-economic success than Pakistani and Bangladeshi Muslims, suggests that there is also a strong socioeconomic basis for shared experiences and grievances as Muslims in Britain. This relativises the notion that Muslim mobilisation is Britain is purely an expression of the right for cultural difference per se, and sees it as a product of the paradoxes of British race relations

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone

BACKGROUND New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype. AIM To investigate the role of clonal variants of MRSA in an outbreak of MRSA bacteraemia at a hospital in England. METHODS Bacteraemia isolates of the major UK lineages (EMRSA-15 and -16) from before and after the outbreak were analysed by whole-genome sequencing in the context of epidemiological and clinical data. For comparison, EMRSA-15 and -16 isolates from another hospital in England were sequenced. A clonal variant of EMRSA-16 was identified at the outbreak hospital and a molecular signature test designed to distinguish variant isolates among further EMRSA-16 strains. FINDINGS By whole-genome sequencing, EMRSA-16 isolates during the outbreak showed strikingly low genetic diversity (P < 1 × 10(-6), Monte Carlo test), compared with EMRSA-15 and EMRSA-16 isolates from before the outbreak or the comparator hospital, demonstrating the emergence of a clonal variant. The variant was indistinguishable from the ancestral strain by conventional typing. This clonal variant accounted for 64/72 (89%) of EMRSA-16 bacteraemia isolates at the outbreak hospital from 2006. CONCLUSIONS Evolutionary changes in epidemic MRSA strains not detected by conventional typing may be associated with changes in disease epidemiology. Rapid and affordable technologies for whole-genome sequencing are becoming available with the potential to identify and track the emergence of variants of highly clonal organisms

Isotopic and Geochemical Investigation of Two Distinct Mars Analog Environments Using Evolved Gas Techniques in Svalbard, Norway

The 2010 Arctic Mars Analog Svalbard Expedition (AMASE) investigated two distinct geologic settings on Svalbard, using methodologies and techniques to be deployed on Mars Science Laboratory (MSL). AMASErelated research comprises both analyses conducted during the expedition and further analyses of collected samples using laboratory facilities at a variety of institutions. The Sample Analysis at Mars (SAM) instrument suite on MSL includes pyrolysis ovens, a gas-processing manifold, a quadrupole mass spectrometer (QMS), several gas chromatography columns, and a Tunable Laser Spectrometer (TLS). An integral part of SAM development is the deployment of SAM-like instrumentation in the field. During AMASE 2010, two parts of SAM participated as stand-alone instruments. A Hiden Evolved Gas Analysis- Mass Spectrometer (EGA-QMS) system represented the EGA-QMS component of SAM, and a Picarro Cavity Ring Down Spectrometer (EGA-CRDS), represented the EGA-TLS component of SAM. A field analog of CheMin, the XRD/XRF on MSL, was also deployed as part of this field campaign. Carbon isotopic measurements of CO2 evolved during thermal decomposition of carbonates were used together with EGA-QMS geochemical data, mineral composition information and contextual observations made during sample collection to distinguish carbonates formation associated with chemosynthetic activity at a fossil methane seep from abiotic processes forming carbonates associated with subglacial basaltic eruptions. Carbon and oxygen isotopes of the basalt-hosted carbonates suggest cryogenic carbonate formation, though more research is necessary to clarify the history of these rocks

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.ISSN:2057-585

Agroforestry for high value tree systems in Europe

Most farm-based agroforestry projects focus on the integration of trees on arable or livestock enterprises. This paper focuses on the integration of understorey crops and/or livestock within high value tree systems (e.g., apple orchards, olive groves, chestnut woodlands, and walnut plantations), and describes the components, structure, ecosystem services and economic value of ten case studies of this type of agroforestry across Europe. Although their ecological and socio-economic contexts vary, the systems share some common characteristics. The primary objective of the farmer is likely to remain the value of tree products like apples, olives, oranges, or nuts, or particularly high value timber. However there can still be production, environmental or economic benefits of integrating agricultural crops such as chickpeas and barley, or grazing an understorey grass crop with livestock. Three of the systems focused on the grazing of apple orchards with sheep in the UK and France. The introduction of sheep to apple orchards can minimise the need for mowing and provide an additional source of revenue. Throughout the Mediterranean, there is a need to improve the financial viability of olive groves. The case studies illustrate the possibility of intercropping traditional olive stands with chickpea in Greece, or the intercropping of wild asparagus in high density olive groves in Italy. Another system studied in Greece involves orange trees intercropped with chickpeas. Stands of chestnut trees in North-west Spain can provide feed for pigs when the fruit falls in November, and provide an excellent habitat for the commercial production of edible mushrooms. In Spain, in the production of high quality walnut trees using rotations of up to 50–60 years, there are options to establish a legume-based mixed pasture understorey and to introduce sheep to provide financial and environmental benefits

Molecular Longitudinal Tracking of Mycobacterium abscessus spp. during Chronic Infection of the Human Lung

<div><p>The <i>Mycobacterium abscessus</i> complex is an emerging cause of chronic pulmonary infection in patients with underlying lung disease. The <i>M. abscessus</i> complex is regarded as an environmental pathogen but its molecular adaptation to the human lung during long-term infection is poorly understood. Here we carried out a longitudinal molecular epidemiological analysis of 178 <i>M. abscessus</i> spp. isolates obtained from 10 cystic fibrosis (CF) and 2 non CF patients over a 13 year period. Multi-locus sequence and molecular typing analysis revealed that 11 of 12 patients were persistently colonized with the same genotype during the course of the infection while replacement of a <i>M. abscessus sensu stricto</i> strain with a <i>Mycobacterium massiliense</i> strain was observed for a single patient. Of note, several patients including a pair of siblings were colonized with closely-related strains consistent with intra-familial transmission or a common infection reservoir. In general, a switch from smooth to rough colony morphology was observed during the course of long-term infection, which in some cases correlated with an increasing severity of clinical symptoms. To examine evolution during long-term infection of the CF lung we compared the genome sequences of 6 sequential isolates of <i>Mycobacterium bolletii</i> obtained from a single patient over an 11 year period, revealing a heterogeneous clonal infecting population with mutations in regulators controlling the expression of virulence factors and complex lipids. Taken together, these data provide new insights into the epidemiology of <i>M. abscessus</i> spp. during long-term infection of the CF lung, and the molecular transition from saprophytic organism to human pathogen.</p></div