The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus: the role of competition and interactions with host's immune response

<p>Abstract</p> <p>Background</p> <p>The first step in invasive disease caused by the normally commensal bacteria <it>Streptococcus pneumoniae</it>, <it>Staphylococcus aureus </it>and <it>Haemophilus influenzae </it>is their colonization of the nasal passages. For any population to colonize a new habitat it is necessary for it to be able to compete with the existing organisms and evade predation. In the case of colonization of these species the competition is between strains of the same and different species of bacteria and the predation is mediated by the host's immune response. Here, we use a neonatal rat model to explore these elements of the ecology of nasal colonization by these occasionally invasive bacteria.</p> <p>Results</p> <p>When neonatal rats are colonized by any one of these species the density of bacteria in the nasal passage rapidly reaches a steady-state density that is species-specific but independent of inoculum size. When novel populations of <it>H. influenzae </it>and <it>S. pneumoniae </it>are introduced into the nasal passages of neonatal rats with established populations of the same species, residents and invaders coexisted. However, this was not the case for <it>S. aureus </it>- the established population inhibited invasion of new <it>S. aureus </it>populations. In mixed-species introductions, <it>S. aureus </it>or <it>S. pneumoniae </it>facilitated the invasion of another <it>H. influenzae </it>population; for other pairs the interaction was antagonistic and immune-mediated. For example, under some conditions <it>H. influenzae </it>promoted an immune response which limited the invasion of <it>S. pneumoniae</it>.</p> <p>Conclusions</p> <p>Nasal colonization is a dynamic process with turnover of new strains and new species. These results suggest that multiple strains of either <it>H. influenzae </it>or <it>S. pneumoniae </it>can coexist; in contrast, <it>S. aureus </it>strains require a host to have no other <it>S. aureus </it>present to colonize. Levels of colonization (and hence the possible risk of invasive disease) by <it>H. influenzae </it>are increased in hosts pre-colonized with either <it>S. aureus </it>or <it>S. pneumoniae</it>.</p

Association of active and passive smoking with risk of breast cancer among postmenopausal women: a prospective cohort study

Objective To examine the association between smoking and risk of invasive breast cancer using quantitative measures of lifetime passive and active smoking exposure among postmenopausal women

Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru.

BACKGROUND: The southern Amazon Basin in the Madre de Dios region of Peru has undergone rapid deforestation and habitat disruption, leading to an unknown zoonotic risk to the growing communities in the area. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed the prevalence of rodent-borne Leptospira and Bartonella, as well as potential environmental sources of human exposure to Leptospira, in 4 communities along the Inter-Oceanic Highway in Madre de Dios. During the rainy and dry seasons of 2014-2015, we captured a total of 97 rodents representing 8 genera in areas that had experienced different degrees of habitat disturbance. Primarily by using 16S metagenomic sequencing, we found that most of the rodents (78%) tested positive for Bartonella, whereas 24% were positive for Leptospira; however, the patterns differed across seasons and the extent of habitat disruption. A high prevalence of Bartonella was identified in animals captured across both trapping seasons (72%-83%) and the relative abundance was correlated with increasing level of land disturbance. Leptospira-positive animals were more than twice as prevalent during the rainy season (37%) as during the dry season (14%). A seasonal fluctuation across the rainy, dry, and mid seasons was also apparent in environmental samples tested for Leptospira (range, 55%-89% of samples testing positive), and there was a high prevalence of this bacteria across all sites that were sampled in the communities. CONCLUSIONS/SIGNIFICANCE: These data indicate the need for increased awareness of rodent-borne disease and the potential for environmental spread along the communities in areas undergoing significant land-use change

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Hydrogen Peroxide-Mediated Interference Competition by Streptococcus pneumoniae Has No Significant Effect on Staphylococcus aureus Nasal Colonization of Neonatal Rats▿

It has been proposed that the relative scarcity of Staphylococcus aureus and Streptococcus pneumoniae cocolonization in the nasopharynxes of humans can be attributed to hydrogen peroxide-mediated interference competition. Previously it has been shown in vitro that H2O2 produced by S. pneumoniae is bactericidal to S. aureus. To ascertain whether H2O2 has this inhibitory effect in the nasal passages of neonatal rats, colonization experiments were performed with S. aureus and S. pneumoniae. The results of these experiments with neonatal rats are inconsistent with the hypothesis that hydrogen peroxide-mediated killing of S. aureus by S. pneumoniae is responsible for the relative scarcity of cocolonization by these bacteria. In mixed-inoculum colonization experiments and experiments where S. aureus invaded the nasopharynxes of rats with established S. pneumoniae populations, the density of S. aureus did not differ whether the S. pneumoniae strain was H2O2 secreting or non-H2O2 secreting (SpxB). Moreover, the advantage of catalase production by S. aureus in competition with a non-catalase-producing strain (KatA) during nasal colonization was no greater in the presence of H2O2-producing S. pneumoniae than in the presence of non-H2O2-producing S. pneumoniae

Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities

Abstract Background Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we evaluate the accuracy of operational taxonomic unit (OTU) generation, taxonomic classification, alpha- and beta-diversity measures for different settings in QIIME, MOTHUR and a pplacer-based classification pipeline, using a novel software package: DECARD. Results In-silico we generated 100 synthetic bacterial communities approximating human stool microbiomes to be used as a gold-standard for evaluating the colligative performance of microbiome analysis software. Our synthetic data closely matched the composition and complexity of actual healthy human stool microbiomes. Genus-level taxonomic classification was correctly done for only 50.4–74.8% of the source organisms. Miscall rates varied from 11.9 to 23.5%. Species-level classification was less successful, (6.9–18.9% correct); miscall rates were comparable to those of genus-level targets (12.5–26.2%). The degree of miscall varied by clade of organism, pipeline and specific settings used. OTU generation accuracy varied by strategy (closed, de novo or subsampling), reference database, algorithm and software implementation. Shannon diversity estimation accuracy correlated generally with OTU-generation accuracy. Beta-diversity estimates with Double Principle Coordinate Analysis (DPCoA) were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in all outcomes tested. Conclusions Even when using the same classification pipeline, the specific OTU-generation strategy, reference database and downstream analysis methods selection can have a dramatic effect on the accuracy of taxonomic classification, and alpha- and beta-diversity estimation. Even minor changes in settings adversely affected the accuracy of the results, bringing them far from the best-observed result. Thus, specific details of how a pipeline is used (including OTU generation strategy, reference sets, clustering algorithm and specific software implementation) should be specified in the methods section of all microbiome studies. Researchers should evaluate their chosen pipeline and settings to confirm it can adequately answer the research question rather than assuming the tutorial or standard-operating-procedure settings will be adequate or optimal

Additional file 2: Figure S1. of Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities

True versus Estimated Relative Abundance for Three Synthetic Communities. Each band represents one organism. The height of each band of color is proportional to the relative abundance of sequence types. Taxonomically similar organisms are closer in color. Colors are by phylum (inspired by a gram stain): Blue and purple for Firmucutes; orange for Bacteroides; Tan and pinks for Proteobacteria. The left-most column for each community is the true composition of the community. The second column is as estimated by Mothur, the second as by our internal pplacer-based classifier, the third as by QIIME with Uclust-based de novo OTU generation and then classification against Silva, the fourth QIIME with closed OTU generation and classification against the GreenGenes reference. (EPS 615 kb

Additional file 1: Table S1–S4. of Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities

Community composition definitions. (ZIP 11 kb

Additional file 3: Figure S2. of Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities

Possible Classification Outcomes. (EPS 1039 kb