Evidence of Transfer by Conjugation of Type IV Secretion System Genes between Bartonella Species and Rhizobium radiobacter in Amoeba

Background: Bartonella species cospeciate with mammals and live within erythrocytes. Even in these specific niches, it has been recently suggested by bioinformatic analysis of full genome sequences that Lateral Gene Transfer (LGT) may occur but this has never been demonstrated biologically. Here we describe the sequence of the B. rattaustraliani (AUST/NH4 T) circular plasmid (pNH4) that encodes the tra cluster of the Type IV secretion system (T4SS) and we eventually provide evidence that Bartonella species may conjugate and exchange this plasmid inside amoeba. Principal Findings: The T4SS of pNH4 is critical for intracellular viability of bacterial pathogens, exhibits bioinformatic evidence of LGT among bacteria living in phagocytic protists. For instance, 3 out of 4 T4SS encoding genes from pNH4 appear to be closely related to Rhizobiales, suggesting that gene exchange occurs between intracellular bacteria from mammals (bartonellae) and plants (Rhizobiales). We show that B. rattaustraliani and Rhizobium radiobacter both survived within the amoeba Acanthamoeba polyphaga and can conjugate together. Our findings further support the hypothesis that tra genes might also move into and out of bacterial communities by conjugation, which might be the primary means of genomic evolution for intracellular adaptation by cross-talk of interchangeable genes between Bartonella species and plant pathogens. Conclusions: Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows fo

Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics

The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals

The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

Outbreaks of hospital infections caused by multidrug resistant Acinetobacter baumannii strains are of increasing concern worldwide. Although it has been reported that particular outbreak strains are geographically widespread, little is known about the diversity and phylogenetic relatedness of A. baumannii clonal groups. Sequencing of internal portions of seven housekeeping genes (total 2,976 nt) was performed in 154 A. baumannii strains covering the breadth of known diversity and including representatives of previously recognized international clones, and in 19 representatives of other Acinetobacter species. Restricted amounts of diversity and a star-like phylogeny reveal that A. baumannii is a genetically compact species that suffered a severe bottleneck in the recent past, possibly linked to a restricted ecological niche. A. baumannii is neatly demarcated from its closest relative (genomic species 13TU) and other Acinetobacter species. Multilocus sequence typing analysis demonstrated that the previously recognized international clones I to III correspond to three clonal complexes, each made of a central, predominant genotype and few single locus variants, a hallmark of recent clonal expansion. Whereas antimicrobial resistance was almost universal among isolates of these and a novel international clone (ST15), isolates of the other genotypes were mostly susceptible. This dichotomy indicates that antimicrobial resistance is a major selective advantage that drives the ongoing rapid clonal expansion of these highly problematic agents of nosocomial infections

Environmental risk assessments for transgenic crops producing output trait enzymes

The environmental risks from cultivating crops producing output trait enzymes can be rigorously assessed by testing conservative risk hypotheses of no harm to endpoints such as the abundance of wildlife, crop yield and the rate of degradation of crop residues in soil. These hypotheses can be tested with data from many sources, including evaluations of the agronomic performance and nutritional quality of the crop made during product development, and information from the scientific literature on the mode-of-action, taxonomic distribution and environmental fate of the enzyme. Few, if any, specific ecotoxicology or environmental fate studies are needed. The effective use of existing data means that regulatory decision-making, to which an environmental risk assessment provides essential information, is not unnecessarily complicated by evaluation of large amounts of new data that provide negligible improvement in the characterization of risk, and that may delay environmental benefits offered by transgenic crops containing output trait enzymes

Ethnic diversity in the UK: new opportunities and changing constraints

The study of ethnicity and migration is a fast evolving field. Much remains to be understood about economic, social, demographic and health outcomes across ethnic groups and generations, and the extent of integration and exclusion of different immigrant-origin groups in countries of destination. While cross-national studies are increasingly shedding light on issues of differential migrant selection and institutional influences, detailed single-country studies, based on high quality nationally representative data have much to offer in enhancing our understanding of diversity within and between groups. The introduction to this special issue on ‘ethnic diversity in the UK: new opportunities and changing constraints’ provides a background to the contributions in the issue by outlining key research agendas relating to immigrant and ethnic minority groups in Western Europe. It then elaborates why the UK represents a good case for exploring ethnic diversity and change; and outlines the contributions made by the papers in the issue. We highlight the distinctive features of the data source used in the papers, Understanding Society, the UK Household Longitudinal Study. We also consider limitations in the data and in the applications in the issue. We conclude by briefly outlining the policy-relevant contributions of the papers in the issue

Phenotyping asthma in the elderly: Allergic sensitization profile and upper airways comorbidity in patients older than 65 years

BACKGROUND: Data about allergic rhinitis in elderly patients with asthma are lacking. OBJECTIVE: To investigate the presence of rhinitis and the role of sensitization of airborne allergens in elderly patients with asthma. METHODS: This was a multicenter cross-sectional study involving subjects at least 65 years old with asthma. Demographic features, comorbidities, and the presence of allergic respiratory disease were retrieved through interview. Skin prick tests for common allergens were performed. Associations of demographic and clinical features were evaluated in relation to asthma control and forced expiratory volume in the first second less than 80% in the total population and in the subgroup with features resembling chronic obstructive pulmonary disease. RESULTS: Of 368 elderly subjects with asthma, 101 had features resembling chronic obstructive pulmonary disease. Rhinitis was present in 59.0% of subjects (allergic rhinitis in 47.6%), with an age of onset significantly different from that of asthma (49 ± 18 vs 57 ± 18 years). At least 1 sensitization was observed in 52.4% of subjects, more frequently for house dust mite (HDM; 31.8%). The prevalence of poorly and partially controlled asthma was higher in patients sensitized to airborne allergens (odds ratio 1.64, 95% confidence interval 1.03-2.61), in particular to HDM (odds ratio 1.73, 95% confidence interval 1.05-2.85). CONCLUSION: Approximately 60% of elderly subjects with asthma had rhinitis, mainly allergic and often untreated, whose onset preceded asthma symptoms by a mean of approximately 10 years. Nonallergic asthma was better controlled than allergic asthma. However, HDM sensitization was greater in subjects with asthma with features resembling chronic obstructive pulmonary disease (39% vs 28%). When restricting analysis to this group, the negative role of HDM in overall asthma control (forced expiratory volume in first second and Asthma Control Test) was significant