The gram-negative bacterium Campylobacter jejuni has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in seven housekeeping loci to determine the genetic relationships among isolates. The MLST system was established using 194 C. jejuni isolates of diverse origins, from humans, animals, and the environment. The allelic profiles, or sequence types (STs), of these isolates were deposited on the Internet (http://mlst.zoo.ox.ac.uk), forming a virtual isolate collection which could be continually expanded. These data indicated that C. jejuni is genetically diverse, with a weakly clonal population structure, and that intra-and interspecies horizontal genetic exchange was common. Of the 155 STs observed, 51 (26% of the isolate collection) were unique, with the remainder of the collection being categorized into 11 lineages or clonal complexes of related STs with between 2 and 56 members. In some cases membership in a given lineage or ST correlated with the possession of a particular Penner HS serotype. Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism.

We analyze the physical conditions of the cool, photoionized (T ∼ 10 4 K) circumgalactic medium (CGM) using the COS-Halos suite of gas column density measurements for 44 gaseous halos within 160 kpc of L ∼ L * galaxies at z ∼ 0.2. These data are well described by simple photoionization models, with the gas highly ionized (n HII /n H 99%) by the extragalactic ultraviolet background (EUVB). Scaling by estimates for the virial radius, R vir , we show that the ionization state (tracked by the dimensionless ionization parameter, U) increases with distance from the host galaxy. The ionization parameters imply a decreasing volume density profile n H = (10 −4.2±0.25 )(R/R vir ) −0.8±0.3 . Our derived gas volume densities are several orders of magnitude lower than predictions from standard two-phase models with a cool medium in pressure equilibrium with a hot, coronal medium expected in virialized halos at this mass scale. Applying the ionization corrections to the H I column densities, we estimate a lower limit to the cool gas mass M cool CGM > 6.5 × 10 10 M ⊙ for the volume within R < R vir . Allowing for an additional warm-hot, OVI-traced phase, the CGM accounts for at least half of the baryons purported to be missing from dark matter halos at the 10 12 M ⊙ scale.

We assess the metal content of the cool (∼10 4 K) circumgalactic medium (CGM) about galaxies at z 1 using an H I-selected sample of 28 Lyman limit systems (LLS, defined here as absorbers with 16.2 log N H I 18.5) observed in absorption against background QSOs by the Cosmic Origins Spectrograph on-board the Hubble Space Telescope. The N H I selection avoids metallicity biases inherent in many previous studies of the low-redshift CGM. We compare the column densities of weakly ionized metal species (e.g., O II, Si II, Mg II) to N H I in the strongest H I component of each absorber. We find that the metallicity distribution of the LLS (and hence the cool CGM) is bimodal with metal-poor and metal-rich branches peaking at [X/H] −1.6 and −0.3 (or about 2.5% and 50% solar metallicities). The cool CGM probed by these LLS is predominantly ionized. The metal-rich branch of the population likely traces winds, recycled outflows, and tidally stripped gas; the metal-poor branch has properties consistent with cold accretion streams thought to be a major source of fresh gas for star forming galaxies. Both branches have a nearly equal number of absorbers. Our results thus demonstrate there is a significant mass of previously-undiscovered cold metal-poor gas and confirm the presence of metal enriched gas in the CGM of z 1 galaxies.

Citation for published item:rohskD tF vier nd erkD tessi uF nd orsekD q¡ or nd rippD odd wF nd umlinsonD tson nd furhettD toseph xF nd poxD endrew tF nd pumglliD wihele nd vehnerD xiols nd eeplesD wolly F nd ejosD xiols @PHIUA 9he gyErlos survey X metlliities in the lowEredshift irumglti mediumF9D estrophysil journlFD VQU @PAF pF ITWF Further information on publisher's website: Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractWe analyze new far-ultraviolet spectra of 13quasars from thez 0.2 COS-Halos survey that cover the H I Lyman limit of 14circumgalactic medium (CGM) systems. These data yield precise estimates or more constraining limits than previous COS-Halos measurements on the H I column densities N H I . We then apply a Monte-Carlo Markov chain approach on 32systems from COS-Halos to estimate the metallicity of the cool (T 10 4 K) CGM gas that gives rise to low-ionization state metal lines, under the assumption of photoionization equilibrium with the extragalactic UV background. The principle results are: (1) the CGM of field L * galaxies exhibits a declining H I surface density with impact parameterR (at >99.5% confidence), (2) the transmission of ionizing radiation through CGM gas alone is 70±7%; (3) the metallicity distribution function of the cool CGM is unimodal with a median of - to >  Z 3 ; the incidence of metal-poor (<  Z 1 100 ) gas is low, implying any such gas discovered along quasar sightlines is typically unrelated to L * galaxies; (4) we find an unexpected increase in gas metallicity with declining N H I (at >99.9% confidence) and, therefore, also with increasingR ; the high metallicity at large radii implies early enrichment; and (5) a non-parametric estimate of the cool CGM gas mass is = ´ ( ) M M 9.2 4.3 10 CGM cool 10, which together with new mass estimates for the hot CGM may resolve the galactic missing baryons problem. Future analyses of halo gas should focus on the underlying astrophysics governing the CGM, rather than processes that simply expel the medium from the halo.

A single-tube 5 nuclease multiplex PCR assay was developed on the ABI 7700 Sequence Detection System (TaqMan) for the detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae from clinical samples of cerebrospinal fluid (CSF), plasma, serum, and whole blood. Capsular transport (ctrA), capsulation (bexA), and pneumolysin (ply) gene targets specific for N. meningitidis, H. influenzae, and S. pneumoniae, respectively, were selected. Using sequence-specific fluorescent-dye-labeled probes and continuous real-time monitoring, accumulation of amplified product was measured. Sensitivity was assessed using clinical samples (CSF, serum, plasma, and whole blood) from culture-confirmed cases for the three organisms. The respective sensitivities (as percentages) for N. meningitidis, H. influenzae, and S. pneumoniae were 88.4, 100, and 91.8. The primer sets were 100% specific for the selected culture isolates. The ctrA primers amplified meningococcal serogroups A, B, C, 29E, W135, X, Y, and Z; the ply primers amplified pneumococcal serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10A, 11A, 12, 14, 15B, 17F, 18C, 19, 20, 22, 23, 24, 31, and 33; and the bexA primers amplified H. influenzae types b and c. Coamplification of two target genes without a loss of sensitivity was demonstrated. The multiplex assay was then used to test a large number (n ‫؍‬ 4,113) of culture-negative samples for the three pathogens. Cases of meningococcal, H. influenzae, and pneumococcal disease that had not previously been confirmed by culture were identified with this assay. The ctrA primer set used in the multiplex PCR was found to be more sensitive (P < 0.0001) than the ctrA primers that had been used for meningococcal PCR testing at that time.