Host adaptation of aquatic Streptococcus agalactiae

Streptococcus agalactiae is a pathogen of multiple hosts. The bacterium, an aetiological agent of septicaemia and meningo-encephalitis in freshwater and saltwater fish species, is considered a major threat to the aquaculture industry, particularly for tilapia. Cattle and humans are however the main known reservoirs for S. agalactiae. In humans, the bacterium (commonly referred to as Group B Streptococcus or GBS) is a member of the commensal microflora of the intestinal and genito-urinary tracts, but it is also a major cause of neonatal invasive disease and an emerging pathogen in adults. In cattle, S. agalactiae is a well-recognized causative agent of mastitis. Numerous studies focusing on S. agalactiae from human and bovine origins have provided insight into the population structure of the bacterium, as well as the genome content and pathogenic mechanisms through identification of virulence determinants. Concerning S. agalactiae from aquatic origins, scientific information mainly focused on case reporting and/or experimental challenges, with a limited or absence of information in terms of pathogenesis, virulence determinants and genotypes of the strains involved. The objective of this study was to enhance our understanding of the molecular epidemiology, host-adaptation and pathogenicity of S. agalactiae in aquatic species, with particular emphasis on tilapia. Firstly, a collection of 33 piscine, amphibian and sea mammal isolates originating from several countries and continents was assembled, with the aim of exploring the population structure and potential host specificity of aquatic S. agalactiae. Isolates were characterised using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and a standardised 3-set genotyping system comprising molecular serotypes, surface protein gene profiles and mobile genetic element profiles. Two major subpopulations were identified in fish. The first subpopulation consisted of non-haemolytic isolates that belonged to sequence type (ST) 260 or 261, which are STs that have been reported only from teleosts. These isolates exhibited a low level of genetic diversity by PFGE and clustered with other STs that have been reported only in fish. Another common feature was the absence of all surface protein genes or mobile genetic elements targeted as part of the 3-set genotyping and that are usually found in human or bovine isolates. The second subpopulation consisted of β-haemolytic isolates recovered from fish, frogs and sea mammals, and that exhibited medium to high genetic diversity by PFGE. STs identified among these isolates have previously been identified from strains associated with asymptomatic carriage and invasive disease in humans. The human pathogenic strain ST7 serotype Ia was detected in fish from Asia. Moreover, ST283 serotype III-4 and its novel single locus variant ST491 detected in fish from Southeast Asia shared a 3-set genotype identical to that of an emerging ST283 clone associated with invasive disease of adult humans in Asia. These observations suggested that some strains of aquatic S. agalactiae may present a zoonotic or anthroponotic hazard. STs found among the seal isolates (ST23) have also been reported from humans and numerous other host species, but never from teleosts. This work provided an excellent basis for exploration of the virulence of selected strains in experimental challenges. The virulence of two strains of S. agalactiae was experimentally investigated by intra-peritoneal infection of Nile tilapia (Oreochromis niloticus), using an isolate originally recovered from fish and belonging to ST260, and an isolate originating from a grey seal and belonging to ST23. The clinical signs, the in vivo distribution of viable bacteria and bacterial antigens, and the gross and histopathological lesions that developed during the time course of the infection were investigated. The ST260 strain was highly virulent, whereas no major clinical sign or mortalities occurred in the fish challenged with the ST23 strain. After injection, both strains however gained access to the bloodstream and viable bacteria were recovered from all organs under investigation. During the early stages of infection, bacteria were mostly found within the reticulo-endothelial system of the spleen and kidney. Thereafter, the ST260 demonstrated a particular tropism for the brain and the heart, but granulomatous inflammation and associated necrotic lesions were observed in all organs. ST23 was responsible for a mixed inflammatory response associated with the presence of bacteria in the choroid rete and in the pancreatic tissue only. After 7 days post-challenge and for both strain, the formation or containment of bacteria within granulomata or other encapsulated structures appeared to be a major component of the fish response. However, the load of viable bacteria remained high within organs of fish infected with ST260, suggesting that, unlike ST23, this strain is able to survive within macrophages and/or to evade the immune system of the fish. This work demonstrates that the lack of report of ST23 strains in fish is possibly not due to a lack of exposure but to a lack of virulence in this host. The two strains, which differ in prevalence and virulence in fish, provide an excellent basis to investigate genomic differences underlying the host-association of distinct S. agalactiae subpopulations. The genome of the ST260 strain used in challenge studies was sequenced. We therefore provided the first description for the genome sequence of a non-haemolytic S. agalactiae isolated from tilapia (strain STIR-CD-17) and that belongs by multi-locus sequence typing (MLST) to clonal complex (CC) 552, which corresponds to a presumptive fish-adapted subgroup of S. agalactiae. The genome was compared to 13 S. agalactiae genomes of human (n=7), bovine (n=2), fish (n=3) and unknown (n=1) origins. Phylogenetic analysis based on the core genome identified isolates of CC552 as the most diverged of all S. agalactiae studied. Conversely, genomes from β-haemolytic isolates of CC7 recovered from fish were found to cluster with human isolates of CC7, further supporting the possibility that some strains may represent a zoonotic or anthroponotic hazard. Comparative analysis of the accessory genome enabled the identification of a cluster of genes uniquely shared between CC7 and CC552, which encode proteins that may provide enhanced fitness in specific niches. Other genes identified were specific to STIR-CD-17 or to CC552 based on genomic comparisons; however the extension of this analysis through the PCR screening of a larger population of S. agalactiae suggested that some of these genes may occasionally be present in isolates belonging to CC7. Some of these genes, occurring in clusters, exhibited typical signatures of mobile genetic elements, suggesting their acquisition through horizontal gene transfer. It is not possible to date to determine whether these genes were acquired through intraspecies transfer or through interspecies transfer from the aquatic environment. Finally, general features of STIR-CD-17 highlighted a distinctive genome characterised by an absence of well conserved insertion sequences, an abundance of pseudogenes, a smaller genomic size than normally observed among human or bovine S. agalactiae, and an apparent loss of metabolic functions considered conserved within the bacterial species, indicating that the fish-adapted subgroup of isolates (CC552) has undergone niche restriction. Finally, genes encoding recognised virulence factors in human S. agalactiae were selected and their presence and structural conservation was evaluated within the genome of STIR-CD-17. Numerous genes were absent in STIR-CD-17, while the cyl operon responsible for the β-haemolysin production was found to be only partially present, indicating that their encoded proteins are not important contributors to pathogenecity of S. agalactiae in fish. The gene encoding an immunogenic bacterial adhesin in certain human S. agalactiae (gbs2018) was identified as a distinct variant, unique to fish isolates of CC552, which possibly reflects differences or adaptations in the function of the protein. Finally, a limited set of genes were found to be well-conserved in STIR-CD-17 and included fbsA, pavA, srr1, cfb, hylB, ponA and sodA. The cspA gene was also found to be well conserved, but a deletion responsible for a frameshift suggested that, if the gene is expressed, the protein would be secreted and not cell-wall anchored. The cps genes were also found to be well-conserved, with the exception of cpsK, but whether the variations in cpsK affect the biosynthesis of the capsule is unknown. In conclusion this study used a multidisciplinary and sequential approach in order to enhance our understanding of the molecular epidemiology, host-adaptation and virulence of S. agalactiae in tilapia. This thesis has laid a firm foundation for further studies that should address the questions of epidemio-surveillance for assessment of transmission of S. agalactiae between humans and fish and the evaluation of the role of putative virulence determinants, with a view to effective control of the disease in fish through prevention or vaccine development

Reconstitution des principaux stades glaciaires du Chablais : base scientifique pour la valorisation d'un patrimoine glaciaire régional

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Human streptococcus agalactiae strains in aquatic mammals and fish

<p>Background: In humans, Streptococcus agalactiae or group B streptococcus (GBS) is a frequent coloniser of the rectovaginal tract, a major cause of neonatal infectious disease and an emerging cause of disease in non-pregnant adults. In addition, Streptococcus agalactiae causes invasive disease in fish, compromising food security and posing a zoonotic hazard. We studied the molecular epidemiology of S. agalactiae in fish and other aquatic species to assess potential for pathogen transmission between aquatic species and humans.</p> <p>Methods: Isolates from fish (n = 26), seals (n = 6), a dolphin and a frog were characterized by pulsed-field gel electrophoresis, multilocus sequence typing and standardized 3-set genotyping, i.e. molecular serotyping and profiling of surface protein genes and mobile genetic elements.</p> <p>Results: Four subpopulations of S. agalactiae were identified among aquatic isolates. Sequence type (ST) 283 serotype III-4 and its novel single locus variant ST491 were detected in fish from Southeast Asia and shared a 3-set genotype identical to that of an emerging ST283 clone associated with invasive disease of adult humans in Asia. The human pathogenic strain ST7 serotype Ia was also detected in fish from Asia. ST23 serotype Ia, a subpopulation that is normally associated with human carriage, was found in all grey seals, suggesting that human effluent may contribute to microbial pollution of surface water and exposure of sea mammals to human pathogens. The final subpopulation consisted of non-haemolytic ST260 and ST261 serotype Ib isolates, which belong to a fish-associated clonal complex that has never been reported from humans.</p> <p>Conclusions: The apparent association of the four subpopulations of S. agalactiae with specific groups of host species suggests that some strains of aquatic S. agalactiae may present a zoonotic or anthroponotic hazard. Furthermore, it provides a rational framework for exploration of pathogenesis and host-associated genome content of S. agalactiae strains.</p&gt

Neel order, ring exchange and charge fluctuations in the half-filled Hubbard model

We investigate the ground state properties of the two dimensional half-filled one band Hubbard model in the strong (large-U) to intermediate coupling limit ({\it i.e.} away from the strict Heisenberg limit) using an effective spin-only low-energy theory that includes nearest-neighbor exchange, ring exchange, and all other spin interactions to order t(t/U)^3. We show that the operator for the staggered magnetization, transformed for use in the effective theory, differs from that for the order parameter of the spin model by a renormalization factor accounting for the increased charge fluctuations as t/U is increased from the t/U -> 0 Heisenberg limit. These charge fluctuations lead to an increase of the quantum fluctuations over and above those for an S=1/2 antiferromagnet. The renormalization factor ensures that the zero temperature staggered moment for the Hubbard model is a monotonously decreasing function of t/U, despite the fact that the moment of the spin Hamiltonien, which depends on transverse spin fluctuations only, in an increasing function of t/U. We also comment on quantitative aspects of the t/U and 1/S expansions.Comment: 9 pages - 3 figures - References and details to help the reader adde

Uncertainty Quantification of GEOS-5 L-band Radiative Transfer Model Parameters Using Bayesian Inference and SMOS Observations

Uncertainties in L-band (1.4 GHz) radiative transfer modeling (RTM) affect the simulation of brightness temperatures (Tb) over land and the inversion of satellite-observed Tb into soil moisture retrievals. In particular, accurate estimates of the microwave soil roughness, vegetation opacity and scattering albedo for large-scale applications are difficult to obtain from field studies and often lack an uncertainty estimate. Here, a Markov Chain Monte Carlo (MCMC) simulation method is used to determine satellite-scale estimates of RTM parameters and their posterior uncertainty by minimizing the misfit between long-term averages and standard deviations of simulated and observed Tb at a range of incidence angles, at horizontal and vertical polarization, and for morning and evening overpasses. Tb simulations are generated with the Goddard Earth Observing System (GEOS-5) and confronted with Tb observations from the Soil Moisture Ocean Salinity (SMOS) mission. The MCMC algorithm suggests that the relative uncertainty of the RTM parameter estimates is typically less than 25 of the maximum a posteriori density (MAP) parameter value. Furthermore, the actual root-mean-square-differences in long-term Tb averages and standard deviations are found consistent with the respective estimated total simulation and observation error standard deviations of m3.1K and s2.4K. It is also shown that the MAP parameter values estimated through MCMC simulation are in close agreement with those obtained with Particle Swarm Optimization (PSO)

Assimilation of Freeze - Thaw Observations into the NASA Catchment Land Surface Model

The land surface freeze-thaw (F-T) state plays a key role in the hydrological and carbon cycles and thus affects water and energy exchanges and vegetation productivity at the land surface. In this study, we developed an F-T assimilation algorithm for the NASA Goddard Earth Observing System, version 5 (GEOS-5) modeling and assimilation framework. The algorithm includes a newly developed observation operator that diagnoses the landscape F-T state in the GEOS-5 Catchment land surface model. The F-T analysis is a rule-based approach that adjusts Catchment model state variables in response to binary F-T observations, while also considering forecast and observation errors. A regional observing system simulation experiment was conducted using synthetically generated F-T observations. The assimilation of perfect (error-free) F-T observations reduced the root-mean-square errors (RMSE) of surface temperature and soil temperature by 0.206 C and 0.061 C, respectively, when compared to model estimates (equivalent to a relative RMSE reduction of 6.7 percent and 3.1 percent, respectively). For a maximum classification error (CEmax) of 10 percent in the synthetic F-T observations, the F-T assimilation reduced the RMSE of surface temperature and soil temperature by 0.178 C and 0.036 C, respectively. For CEmax=20 percent, the F-T assimilation still reduces the RMSE of model surface temperature estimates by 0.149 C but yields no improvement over the model soil temperature estimates. The F-T assimilation scheme is being developed to exploit planned operational F-T products from the NASA Soil Moisture Active Passive (SMAP) mission

Assimilation of Passive and Active Microwave Soil Moisture Retrievals

Root-zone soil moisture is an important control over the partition of land surface energy and moisture, and the assimilation of remotely sensed near-surface soil moisture has been shown to improve model profile soil moisture [1]. To date, efforts to assimilate remotely sensed near-surface soil moisture at large scales have focused on soil moisture derived from the passive microwave Advanced Microwave Scanning Radiometer (AMSR-E) and the active Advanced Scatterometer (ASCAT; together with its predecessor on the European Remote Sensing satellites (ERS. The assimilation of passive and active microwave soil moisture observations has not yet been directly compared, and so this study compares the impact of assimilating ASCAT and AMSR-E soil moisture data, both separately and together. Since the soil moisture retrieval skill from active and passive microwave data is thought to differ according to surface characteristics [2], the impact of each assimilation on the model soil moisture skill is assessed according to land cover type, by comparison to in situ soil moisture observations

Multi frequency evaporative cooling to BEC in a high magnetic field

We demonstrate a way to circumvent the interruption of evaporative cooling observed at high bias field for $^{87}$Rb atoms trapped in the (F=2, m=+2) ground state. Our scheme uses a 3-frequencies-RF-knife achieved by mixing two RF frequencies. This compensates part of the non linearity of the Zeeman effect, allowing us to achieve BEC where standard 1-frequency-RF-knife evaporation method did not work. We are able to get efficient evaporative cooling, provided that the residual detuning between the transition and the RF frequencies in our scheme is smaller than the power broadening of the RF transitions at the end of the evaporation ramp.Comment: 12 pages, 2 figure

Development and validation of high-resolution melting assays for the detection of potentially virulent strains of \u3ci\u3eEscherichia coli\u3c/i\u3e O103 and O121

Virulent strains of Shiga toxin-producing Escherichia coli (STEC) serogroups O103 and O121 are considered adulterants in beef. Two high-resolution melting (HRM) real-time PCR assays were standardized for the specific detection and discrimination of potentially virulent and avirulent strains of E. coli O103 and O121. The O103 HRM assay offered the possibility to distinguish clearly STEC O103:H2 from STEC O103:H25. The two standardized assays were extensively validated using 215 pure culture strains, laboratory inoculated food samples, and naturally contaminated beef (n = 84) and pork (n = 84) enrichments collected from the red meat surveillance program. Both HRM assays showed 100% inclusivity and exclusivity using pure culture strains and enriched spiked food samples. Data from this study shows the ability of the standardized assays to specifically detect the strains of each target serogroup and, most importantly, to differentiate the strains present into potentially virulent or avirulent groups. The assays standardized in this study can be helpful for food surveillance programs and help mitigate product loss due to the presence of avirulent strains lacking crucial virulence genes (stx and eae)

Quantum spin fluctuations in the dipolar Heisenberg-like rare earth pyrochlores

The magnetic pyrochlore oxide materials of general chemical formula R2Ti2O7 and R2Sn2O7 (R = rare earth) display a host of interesting physical behaviours depending on the flavour of rare earth ion. These properties depend on the value of the total magnetic moment, the crystal field interactions at each rare earth site and the complex interplay between magnetic exchange and long-range dipole-dipole interactions. This work focuses on the low temperature physics of the dipolar isotropic frustrated antiferromagnetic pyrochlore materials. Candidate magnetic ground states are numerically determined at zero temperature and the role of quantum spin fluctuations around these states are studied using a Holstein-Primakoff spin wave expansion to order 1/S. The results indicate the strong stability of the proposed classical ground states against quantum fluctuations. The inclusion of long range dipole interactions causes a restoration of symmetry and a suppression of the observed anisotropy gap leading to an increase in quantum fluctuations in the ground state when compared to a model with truncated dipole interactions. The system retains most of its classical character and there is little deviation from the fully ordered moment at zero temperature.Comment: Latex2e, 18 pages, 4 figures, IOP forma