The potential distribution of Bacillus anthracis suitability across Uganda using INLA.

To reduce the veterinary, public health, environmental, and economic burden associated with anthrax outbreaks, it is vital to identify the spatial distribution of areas suitable for Bacillus anthracis, the causative agent of the disease. Bayesian approaches have previously been applied to estimate uncertainty around detected areas of B. anthracis suitability. However, conventional simulation-based techniques are often computationally demanding. To solve this computational problem, we use Integrated Nested Laplace Approximation (INLA) which can adjust for spatially structured random effects, to predict the suitability of B. anthracis across Uganda. We apply a Generalized Additive Model (GAM) within the INLA Bayesian framework to quantify the relationships between B. anthracis occurrence and the environment. We consolidate a national database of wildlife, livestock, and human anthrax case records across Uganda built across multiple sectors bridging human and animal partners using a One Health approach. The INLA framework successfully identified known areas of species suitability in Uganda, as well as suggested unknown hotspots across Northern, Eastern, and Central Uganda, which have not been previously identified by other niche models. The major risk factors for B. anthracis suitability were proximity to water bodies (0-0.3 km), increasing soil calcium (between 10 and 25 cmolc/kg), and elevation of 140-190 m. The sensitivity of the final model against the withheld evaluation dataset was 90% (181 out of 202 = 89.6%; rounded up to 90%). The prediction maps generated using this model can guide future anthrax prevention and surveillance plans by the relevant stakeholders in Uganda.

From laboratory tests to field trials: a review of cathodic protection and microbially influenced corrosion.

Cathodic protection (CP), an electrochemical method for managing corrosion, is widely used in many industries in both marine and buried environments. However, literature surrounding cathodic protection and its ability to prevent microbially influenced corrosion (MIC) is mixed. This review describes the mechanics of CP, how CP may influence MIC, and collates and summarises tests on CP and MIC reported in literature. The aim of the review is to identify any trends and knowledge gaps requiring further study. While the outcomes of CP testing are generally mixed, some trends can be seen and, overall, MIC is detrimental to the protective effects of CP, with CP being less effective when used according to current international standards. Tests conducted in the field or with mix communities of microbes showed that CP could be effective at preventing MIC, while tests with sulfate-reducing bacteria generally proved CP to be highly ineffective. It was commonly seen that the effectiveness of CP can be improved by increasing polarization, to potentials as low as -1000 mV (Ag/AgCl). However, a balance does need to be met via careful monitoring to ensure negative side effects of over protection do not become a major problem.

High Taxonomic Diversity in Ship Bilges Presents Challenges for Monitoring Microbial Corrosion and Opportunity To Utilize Community Functional Profiling.

One of the key areas in which microbially influenced corrosion (MIC) has been found to be a problem is in the bilges of maritime vessels. To establish effective biological monitoring protocols, baseline knowledge of the temporal and spatial biological variation within bilges, as well as the effectiveness of different sampling methodologies, is critical. We used 16S rRNA gene metabarcoding of pelagic and sessile bacterial communities from ship bilges to assess the variation in bilge bacterial communities to determine how the inherent bilge diversity could guide or constrain biological monitoring. Bilge communities exhibited high levels of spatial and temporal variation, with >80% of the community able to be turned over in the space of 3 months, likely due to disturbance events such as cleaning and maintenance. Sessile and pelagic communities within a given bilge were also inherently distinct, with dominant exact sequence variants (ESVs) rarely shared between the two. Taxa containing KEGG orthologies (KOs) associated with dissimilatory sulfate reduction and biofilm production, functions typically associated with MIC, were generally more prevalent in sessile communities. Collectively, our findings indicate that neither bilge water nor an unaffected bilge from within the same vessel would constitute an appropriate reference community for MIC diagnosis. Optimal sampling locations and strategies that could be incorporated into a standardized method for monitoring bilge biology in relation to MIC were identified. Finally, taxonomic and functional comparisons of bilge diversity highlight the potential of functional approaches in future biological monitoring of MIC and MIC mitigation strategies in general. IMPORTANCE Microbially influenced corrosion (MIC) has been estimated to contribute 20 to 50% of the costs associated with corrosion globally. Diagnosis and monitoring of MIC are complex problems requiring knowledge of corrosion rates, corrosion morphology, and the associated microbiology to distinguish MIC from abiotic corrosion processes. Historically, biological monitoring of MIC utilized a priori knowledge to monitor sulfate-reducing bacteria; however, it is becoming widely accepted that a holistic or community-level understanding of corrosion-associated microbiology is needed for MIC diagnosis and monitoring. Before biology associated with MIC attack can be identified, standardized protocols for sampling and monitoring must be developed. The significance of our research is in contributing to the development of robust and repeatable sampling strategies of bilges, which are required for the development of standardized biological monitoring methods for MIC. We achieve this via a biodiversity survey of bilge communities and by comparing taxonomic and functional variation.

Dynamics and risk of transmission of bovine tuberculosis in the emerging dairy regions of Ethiopia.

The Ethiopian government has several initiatives to expand and intensify the dairy industry; however, the risk of bovine tuberculosis (bTB) spread is a challenge. To assess the rate of expansion and risk factors for transmission of bTB within-herds, we carried out a repeated cross-sectional survey at two time points, 2016/17 and 2018, in three regional cities, namely, Gondar, Hawassa and Mekelle, representing the emerging dairy belts of Ethiopia. The total number of herds involved was 128, comprising an average of 2303 cattle in each round. The Single Intradermal Comparative Cervical Tuberculin (SICCT) test was used to identify reactor status and data on herd-level risk factors were collected using a structured questionnaire. In the first survey, the apparent prevalence of bTB, as measured by the SICCT test, was 4.5% (95% CI 3.7-5.4%) at the individual animal-level and 24% (95% CI 17.5-32%) at the herd-level. There was no statistically significant change in the overall apparent prevalence or regional distribution at the second survey, consistent with the infection being endemic. The incidence rate was estimated at 3.6 (95% CI 2.8-4.5) and 6.6 (95% CI 3.0-12.6) cases/100 cattle (or herd)-years at the animal- and herd-levels, respectively. Risk factors significantly associated with the within-herd transmission of bTB were age group and within-herd apparent prevalence at the start of the observation period. We noted that farmers voluntarily took steps to remove reactor cattle from their herds as a consequence of the information shared after the first survey. Removal of reactors between surveys was associated with a reduced risk of transmission within these herds. However, with no regulatory barriers to the sale of reactor animals, such actions could potentially lead to further spread between herds. We therefore advocate the importance of setting up regulations and then establishing a systematic bTB surveillance programme to monitor the impact prior to implementing any control measures in Ethiopia.

Physics of Nuclei: Key Role of an Emergent Symmetry.

We show through first-principles nuclear structure calculations that the special nature of the strong nuclear force determines highly regular patterns heretofore unrecognized in nuclei that can be tied to an emergent approximate symmetry. This symmetry is ubiquitous and mathematically tracks with a symplectic symmetry group. This, in turn, has important implications for understanding the physics of nuclei: we find that nuclei are made of only a few equilibrium shapes, deformed or not, with associated vibrations and rotations. It also opens the path for ab initio large-scale modeling of open-shell intermediate-mass nuclei without the need for renormalized interactions and effective charges.

Long-term follow-up of owned, free-roaming dogs in South Africa naturally exposed to Babesia rossi.

Babesia rossi is an important, tick-borne intraerythrocytic protozoan parasite; however, its natural history and epidemiology is poorly understood. Babesia rossi is the most virulent Babesia sp. in domestic dogs and is generally considered to cause severe babesiosis, which is fatal if left untreated. However, subclinical infections and mild disease from B. rossi have been reported, although the clinical progression of these cases was not reported. Therefore, to better understand B. rossi under field conditions, we evaluated its clinical progression and seroprevalence in an owned, free-roaming dog population in Zenzele, South Africa, where the parasite is endemic and prevention is not routine. The entire dog population in Zenzele was monitored intensively at the individual level from March 2008 until April 2014, primarily for a longitudinal study on rabies control. Subsequent evaluation of B. rossi comprised analyses of clinical and laboratory data collected from the Zenzele dog population during the 6 year study period. A substantial proportion (31% (n = 34)) of 109 dogs (randomly selected from every available dog in February/March 2010 older than ~6-8 weeks (n = 246)) tested by Indirect Fluorescent Antibody Test had seroconverted strongly to B. rossi. All 34 dogs were generally consistently healthy adults, determined from regular clinical examinations between March 2008 and April 2014. Blood smear examinations at multiple time points between July 2009 and February 2011 were also undertaken for almost all of these (34) seropositive dogs and all those tested were consistently negative for Babesia spp. Subclinical infections and mild disease were also the main findings for a separate group of 18 dogs positive for Babesia spp. on blood smear examination and confirmed to be infected with B. rossi by Polymerase Chain Reaction - Reverse Line Blot. Almost all of these dogs were positive at only one time point from repeat blood smear examinations between July 2009 and February 2011. We suggest that these observations are consistent with immunity acquired from repeated, low-level exposure to the parasite, generating transient subclinical infections or mild disease. Should this be the case, the use of tick control, particularly in adult dogs in free-roaming populations in B. rossi endemic regions, should be carefully considered.

Multiple Shape Coexistence in

From detailed spectroscopy of ^{110}Cd and ^{112}Cd following the ß^{+}/electron-capture decay of ^{110,112}In and the ß^{-} decay of ^{112}Ag, very weak decay branches from nonyrast states are observed. The transition rates determined from the measured branching ratios and level lifetimes obtained with the Doppler-shift attenuation method following inelastic neutron scattering reveal collective enhancements that are suggestive of a series of rotational bands. In ^{110}Cd, a γ band built on the shape-coexisting intruder configuration is suggested. For ^{112}Cd, the 2^{+} and 3^{+} intruder γ-band members are suggested, the 0_{3}^{+} band is extended to spin 4^{+}, and the 0_{4}^{+} band is identified. The results are interpreted using beyond-mean-field calculations employing the symmetry conserving configuration mixing method with the Gogny D1S energy density functional and with the suggestion that the Cd isotopes exhibit multiple shape coexistence.

An efficient, cost-effective method for determining the growth rate of sulfate-reducing bacteria using spectrophotometry.

The use of sulfate reducing bacteria (SRBs) in laboratory studies is a common approach for investigating microbially influenced corrosion (MIC). The characteristic formation of black iron sulfide precipitates during SRB growth, however, preclude the use of traditional spectrophotometric approaches for capturing growth data instead necessitating labour-intensive or technically specialized approaches. As such, an understanding of SRB growth responses to experimental conditions is often missing from MIC studies. Bernardez and de Andrade Lima (2015) have outlined a spectrophotometric approach for estimating SRB cell mass via the addition of HCl. This method has potential for the study SRB growth however its applicability is currently limited by the use of large aliquot volumes (45 mL), which restrict the number of timepoints that can sampled from one culture, and the extensive time devoted to cell preparation prior to OD readings. •We demonstrate an improved method for capturing SRB growth data via spectrophotometry following acidification. We incorporate lower sample volumes and adapt the method described in Bernardez and de Andrade Lima (2015) to a high throughput microtiter plate approach that increases the efficiency of this method and its applicability to growth rate studies.•Our results allay theoretical concerns that acidification may distort growth rate analysis by impacting cells differently depending on their metabolic state.•We further demonstrate that this method (acid-amended OD measurements) is more accurate and far more cost efficient than traditional methods (dilution spread-plate counting) and popular molecular methods (quantitative PCR) currently in use in SRB growth research.

Integrative modelling for One Health: pattern, process and participation.

This paper argues for an integrative modelling approach for understanding zoonoses disease dynamics, combining process, pattern and participatory models. Each type of modelling provides important insights, but all are limited. Combining these in a '3P' approach offers the opportunity for a productive conversation between modelling efforts, contributing to a 'One Health' agenda. The aim is not to come up with a composite model, but seek synergies between perspectives, encouraging cross-disciplinary interactions. We illustrate our argument with cases from Africa, and in particular from our work on Ebola virus and Lassa fever virus. Combining process-based compartmental models with macroecological data offers a spatial perspective on potential disease impacts. However, without insights from the ground, the 'black box' of transmission dynamics, so crucial to model assumptions, may not be fully understood. We show how participatory modelling and ethnographic research of Ebola and Lassa fever can reveal social roles, unsafe practices, mobility and movement and temporal changes in livelihoods. Together with longer-term dynamics of change in societies and ecologies, all can be important in explaining disease transmission, and provide important complementary insights to other modelling efforts. An integrative modelling approach therefore can offer help to improve disease control efforts and public health responses.This article is part of the themed issue 'One Health for a changing world: zoonoses, ecosystems and human well-being'.

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator.

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

Specificity of the comparative skin test for bovine tuberculosis in Great Britain.

A novel method for estimating specificity of the Single Intradermal Comparative Cervical Tuberculin (SICCT) test for bovine tuberculosis (bTB) using surveillance tests results is reported. The specificity of the SICCT test at three cut-offs was estimated from the dates, locations and skinfold measurements of all routine tests carried out in Officially TB Free (OTF) cattle herds in Great Britain (GB) between 2002 and 2008, according to their separation (by distance and time) from known infected (OTF-withdrawn) herds. The proportion of animals that tested positive was constant (P>0.20) when the distance between tested herds and nearest infected herd exceeded 8 km. For standard cut-off, calculated specificity was 99.98 per cent (95 per cent confidence interval ±0.004 per cent), equating to one false positive result per 5000 uninfected animals tested. For severe cut-off it was 99.91 per cent (±0.013 per cent) and for ultrasevere cut-off (selecting all reactors and inconclusive reactors) it was 99.87 per cent (±0.017 per cent). The estimated positive predictive value of the test averaged 91 per cent and varied by regional prevalence. This study provides further evidence of the high specificity of the SICCT test under GB conditions, suggests that over 90 per cent of cattle currently culled using this test in GB were infected, and endorses slaughter of at least these cattle for bTB control.

Effective vaccination against rabies in puppies in rabies endemic regions.

In rabies endemic regions, a proportionally higher incidence of rabies is often reported in dogs younger than 12 months of age, which includes puppies less than 3 months of age; this presents a serious risk to public health. The higher incidence of rabies in young dogs may be the effect of low vaccination coverage in this age class, partly as a result of the perception that immature immune systems and maternal antibodies inhibit seroconversion to rabies vaccine in puppies less than three months of age. Therefore, to test this perception, the authors report the virus neutralising antibody titres from 27 dogs that were vaccinated with high quality, inactivated rabies vaccine aged three months of age and under as part of larger serological studies undertaken in Gauteng Province, South Africa, and the Serengeti District, Tanzania. All of these dogs seroconverted to a single dose of vaccine with no adverse reactions reported and with postvaccinal peak titres ranging from 2.0 IU/ml to 90.5 IU/ml. In light of these results, and the risk of human beings contracting rabies from close contact with puppies, the authors recommend that all dogs in rabies endemic regions, including those less than three months of age, are vaccinated with high quality, inactivated vaccine.

Eight challenges in modelling infectious livestock diseases.

The transmission of infectious diseases of livestock does not differ in principle from disease transmission in any other animals, apart from that the aim of control is ultimately economic, with the influence of social, political and welfare constraints often poorly defined. Modelling of livestock diseases suffers simultaneously from a wealth and a lack of data. On the one hand, the ability to conduct transmission experiments, detailed within-host studies and track individual animals between geocoded locations make livestock diseases a particularly rich potential source of realistic data for illuminating biological mechanisms of transmission and conducting explicit analyses of contact networks. On the other hand, scarcity of funding, as compared to human diseases, often results in incomplete and partial data for many livestock diseases and regions of the world. In this overview of challenges in livestock disease modelling, we highlight eight areas unique to livestock that, if addressed, would mark major progress in the area.

Participatory methods for the assessment of the ownership status of free-roaming dogs in Bali, Indonesia, for disease control and animal welfare.

The existence of unowned, free-roaming dogs capable of maintaining adequate body condition without direct human oversight has serious implications for disease control and animal welfare, including reducing effective vaccination coverage against rabies through limiting access for vaccination, and absolving humans from the responsibility of providing adequate care for a domesticated species. Mark-recapture methods previously used to estimate the fraction of unowned dogs in free-roaming populations have limitations, particularly when most of the dogs are owned. We used participatory methods, described as Participatory Rural Appraisal (PRA), as a novel alternative to mark-recapture methods in two villages in Bali, Indonesia. PRA was implemented at the banjar (or sub-village)-level to obtain consensus on the food sources of the free-roaming dogs. Specific methods included semi-structured discussion, visualisation tools and ranking. The PRA results agreed with the preceding household surveys and direct observations, designed to evaluate the same variables, and confirmed that a population of unowned, free-roaming dogs in sufficiently good condition to be sustained independently of direct human support was unlikely to exist.

The effect of seasonal birth pulses on pathogen persistence in wild mammal populations.

The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction.

Antigenic variation of foot-and-mouth disease virus serotype A.

The current measures to control foot-and-mouth disease (FMD) include vaccination, movement control and slaughter of infected or susceptible animals. One of the difficulties in controlling FMD by vaccination arises due to the substantial diversity found among the seven serotypes of FMD virus (FMDV) and the strains within these serotypes. Therefore, vaccination using a single vaccine strain may not fully cross-protect against all strains within that serotype, and therefore selection of appropriate vaccines requires serological comparison of the field virus and potential vaccine viruses using relationship coefficients (r1 values). Limitations of this approach are that antigenic relationships among field viruses are not addressed, as comparisons are only with potential vaccine virus. Furthermore, inherent variation among vaccine sera may impair reproducibility of one-way relationship scores. Here, we used antigenic cartography to quantify and visualize the antigenic relationships among FMD serotype A viruses, aiming to improve the understanding of FMDV antigenic evolution and the scope and reliability of vaccine matching. Our results suggest that predicting antigenic difference using genetic sequence alone or by geographical location is not currently reliable. We found co-circulating lineages in one region that were genetically similar but antigenically distinct. Nevertheless, by comparing antigenic distances measured from the antigenic maps with the full capsid (P1) sequence, we identified a specific amino acid substitution associated with an antigenic mismatch among field viruses and a commonly used prototype vaccine strain, A22/IRQ/24/64.

Infectious risk factors and clinical indicators for tracheal mucus in British National Hunt racehorses.

REASONS FOR PERFORMING STUDY: Many studies of respiratory disease in racehorses have focused on a combination of increased tracheal mucus and airway neutrophilia. Examination of each component separately should provide further insight into this condition. OBJECTIVES: To identify infectious risk factors for endoscopically visible tracheal mucus in National Hunt racehorses. STUDY DESIGN: A 2 year prospective longitudinal study. METHODS: Monthly quantitative bacteriological examinations of tracheal wash samples and viral serological examinations were conducted. Risk factors for 'small amounts of mucus' (mucus score = 1/3) and 'increased mucus' (score ≥2/3) were identified. RESULTS: There were increased odds of small amounts of mucus when both Streptococcus zooepidemicus and nonhaemolytic streptococci (NHS) were isolated (odds ratio [OR] 2.6; 95% confidence interval [CI] 1.5-4.6; P<0.001) but not when either species was isolated in the absence of the other. Increased odds of increased mucus were associated with the isolation of either S. zooepidemicus (OR 5.6; 95% CI 1.2-25.9; P = 0.03) or NHS (OR 3.7; 95% CI 1.2-11.6; P = 0.02), with an increased effect when both were isolated together (OR 12.5; 95% CI 3.7-41.6; P<0.001). Approximately 6-fold increased odds of small amounts of mucus were associated with the first 3 months in training (OR 6.3; 95% CI 2.0-19.4; P<0.001) and 3-fold increased odds of increased mucus associated with the first 6 months in training (OR 2.9; 95% CI 1.3-6.4; P = 0.01). Coughing at exercise and increased serous nasal discharge were specific but insensitive indicators of increased mucus. CONCLUSIONS: Associations with S. zooepidemicus corroborate previous research, but an independent effect of NHS has not previously been reported. The possibility that there are individual pathogenic species within this group should be considered. Further work is required to identify S. zooepidemicus subtypes and NHS species associated with disease. Closer monitoring of the respiratory health of horses entering training for the first time is likely to be valuable.