Spatial epidemiology of Foot and Mouth Disease in Great Britain

During 2007 the UK experienced outbreaks of three notifiable exotic livestock diseases; Foot and Mouth Disease (FMD), Highly Pathogenic Avian Influenza (HPAI) and bluetongue. Large epidemics of any of these diseases would have a serious impact on animal welfare, farming, food production and the economy. In light of this, understanding holdings which are most likely to acquire and spread infection and being able to identify areas at higher risk of an epidemic is valuable when preparing for and managing an epidemic. This thesis uses a spatial epidemiological framework and the detailed disease and demographic data from the 2001 Great Britain (GB) FMD epidemic to develop static models of the risk of FMD susceptibility and transmission. These models are used to develop maps of FMD risk. These methods are then applied to the outbreak of FMD in 2007. The inputs for this analysis comprised a set of data relating to the farms diagnosed with FMD and farms culled as part of the disease control measures. The cleaning of these data is described and data which were estimated relating to dates of infection and putative sources of infection are evaluated. The distribution of farm holdings and animals is taken from the June 2000 GB agricultural census, off-fields of farms in the agricultural census are recorded in other datasets and these have been identified and linked to census holdings. A model of holding level susceptibility is developed using both farm level variables and measures of animal numbers in the locality of the holding as well as the distance to the nearest farm infected before the ban on animal movements (seeds). The overall fit of the model was very good with an area under the Receiver Operator Characteristic (ROC) curve of 0.91. A further model was developed to describe the risk of FMD transmission. However, due to incompleteness of transmission data, this was a model of the risk of finding a subsequent Infected Premises (IP) within 3km of an IP. Risk factors were a combination of holding level variables and locality measures as well as data relevant to the infection, such as infectious period and the species initially infected. The area under the ROC curve for this model was 0.71, which is regarded as an acceptable fit. Geographical barriers to FMD transmission were investigated using a case-control methodology, linear barriers comprising rivers and railways had a significant protective effect with respect to disease transmission (odds ratio = 0.54, 95% CIs = 0.30,0.96, p=0.038). Modelled values for the transmission and susceptibility models were transformed to a raster surface in ESRI ArcMap for both the disease as it was seeded in the 2001 epidemic and a non-specific background risk surface independent of the distribution of seeds. A risk map generated for the outbreak of FMD in Surrey in August 2007 suggested that there was little risk of a large outbreak in Surrey. Potential disease introductions through livestock movements from Surrey into Scotland were identified and these suggested that if the disease were introduced into Scotland there was great danger of substantial local spread. These methods described in this thesis have been used to map risk of FMD and subsequently applied to inform the risk presented by a different outbreak of FMD. The study underlines the value of detailed data both disease and demographic, for epidemic management. Similar methods could and should be applied to other infectious diseases threats of livestock such as HPAI and bluetongue

Risk factors for bovine Tuberculosis at the national level in Great Britain

<p><b>Background:</b> The continuing expansion of high incidence areas of bovine Tuberculosis (bTB) in Great Britain (GB) raises a number of questions concerning the determinants of infection at the herd level that are driving spread of the disease. Here, we develop risk factor models to quantify the importance of herd sizes, cattle imports from Ireland, history of bTB, badgers and cattle restocking in determining bTB incidence. We compare the significance of these different risk factors in high and low incidence areas (as determined by parish testing intervals).</p> <p><b>Results:</b> Large herds and fattening herds are more likely to breakdown in all areas. In areas with lower perceived risk (longer testing intervals), the risk of breaking down is largely determined by the number of animals that a herd buys in from high incidence areas. In contrast, in higher perceived risk areas (shorter testing intervals), the risk of breakdown is defined by the history of disease and the probability of badger occurrence. Despite differences in the management of bTB across different countries of GB (England, Wales and Scotland), we found no significant differences in bTB risk at the national level after these other factors had been taken into account.</p> <p><b>Conclusions:</b> This paper demonstrates that different types of farm are at risk of breakdown and that the most important risk factors vary according to bTB incidence in an area. The results suggest that significant gains in bTB control could be made by targeting herds in low incidence areas that import the greatest number of cattle from high incidence areas.</p&gt

Risk of Foot-and-Mouth Disease Spread Due to Sole Occupancy Authorities and Linked Cattle Holdings

Livestock movements in Great Britain are well recorded, have been extensively analysed with respect to their role in disease spread, and have been used in real time to advise governments on the control of infectious diseases. Typically, livestock holdings are treated as distinct entities that must observe movement standstills upon receipt of livestock, and must report livestock movements. However, there are currently two dispensations that can exempt holdings from either observing standstills or reporting movements, namely the Sole Occupancy Authority (SOA) and Cattle Tracing System (CTS) Links, respectively. In this report we have used a combination of data analyses and computational modelling to investigate the usage and potential impact of such linked holdings on the size of a Foot-and-Mouth Disease (FMD) epidemic. Our analyses show that although SOAs are abundant, their dynamics appear relatively stagnant. The number of CTS Links is also abundant, and increasing rapidly. Although most linked holdings are only involved in a single CTS Link, some holdings are involved in numerous links that can be amalgamated to form "CTS Chains" which can be both large and geographically dispersed. Our model predicts that under a worst case scenario of "one infected - all infected", SOAs do pose a risk of increasing the size (in terms of number of infected holdings) of a FMD epidemic, but this increase is mainly due to intra-SOA infection spread events. Furthermore, although SOAs do increase the geographic spread of an epidemic, this increase is predominantly local. Whereas, CTS Chains pose a risk of increasing both the size and the geographical spread of the disease substantially, under a worse case scenario. Our results highlight the need for further investigations into whether CTS Chains are transmission chains, and also investigations into intra-SOA movements and livestock distributions due to the lack of current data

Mapping the Galactic Halo I. The `Spaghetti' Survey

We describe a major survey of the Milky Way halo designed to test for kinematic substructure caused by destruction of accreted satellites. We use the Washington photometric system to identify halo stars efficiently for spectroscopic followup. Tracers include halo giants (detectable out to more than 100 kpc), blue horizontal branch stars, halo stars near the main sequence turnoff, and the ``blue metal-poor stars'' of Preston et al (1994). We demonstrate the success of our survey by showing spectra of stars we have identified in all these categories, including giants as distant as 75 kpc. We discuss the problem of identifying the most distant halo giants. In particular, extremely metal-poor halo K dwarfs are present in approximately equal numbers to the distant giants for V fainter than 18, and we show that our method will distinguish reliably between these two groups of metal-poor stars. We plan to survey 100 square degrees at high galactic latitude, and expect to increase the numbers of known halo giants, BHB stars and turnoff stars by more than an order of magnitude. In addition to the strong test that this large sample will provide for the question `was the Milky Way halo accreted from satellite galaxies?', we will improve the accuracy of mass measurements of the Milky Way beyond 50 kpc via the kinematics of the many distant giants and BHB stars we will find. We show that one of our first datasets constrains the halo density law over galactocentric radii of 5-20 kpc and z heights of 2-15 kpc. The data support a flattened power-law halo with b/a of 0.6 and exponent -3.0. More complex models with a varying axial ratio may be needed with a larger dataset.Comment: 55 pages, 22 figures, to appear in the Astronomical Journa

A Survey of Local Group Galaxies Currently Forming Stars. I. UBVRI Photometry of Stars in M31 and M33

We present UBVRI photometry obtained from Mosaic images of M31 and M33 using the KPNO 4-m telescope. The survey covers 2.2 sq degrees of M31, and 0.8 sq degrees of M33, chosen so as to include all of the regions currently active in forming massive stars. The catalog contains 371,781 and 146,622 stars in M31 and M33, respectively, where every star has a counterpart (at least) in B, V, and R. We compare our photometry to previous studies. We provide cross references to the stars confirmed as members by spectroscopy, and compare the location of these to the complete set in color-magnitude diagrams. While follow-up spectroscopy is needed for many projects, we demonstrate the success of our photometry in being able to distinguish M31/M33 members from foreground Galactic stars. We also present the results of newly obtained spectroscopy, which identifies 34 newly confirmed members, including B-A supergiants, the earliest O star known in M31, and two new Luminous Blue Variable candidates whose spectra are similar to that of P Cygni.Comment: Accepted by the Astronomical Journal. A version with higher resolution figures can be found at: http://www.lowell.edu/users/massey/M3133.pdf.g

Strengthening Visceral Leishmaniasis Diagnosis Capacity to Improve Access to Care in Kenya: The Example of Marsabit County

Background: Visceral leishmaniasis (VL), also known as kala-azar, is a neglected tropical disease (NTD) that is fatal if not treated early. The WHO targets the elimination of VL as a public health problem in its 2030 NTD road map. However, improving access to VL diagnosis and treatment remains a major challenge in many VL-endemic countries. Kenya is endemic for VL and is among the top 6 high-disease burden countries in the world. Methods: FIND, through its activities in improving the diagnosis of VL and supporting the elimination of the disease in Kenya, has worked with various county ministries of health (MOH) and central MOH over the last couple of years. FIND’s activities in Marsabit county started in 2018. In this work, we present the implementation of activities and the impacts in Marsabit county. We reviewed the data for 2017 and 2019 outbreaks (before and after the implementation of FIND’s activities) and assessed the importance of improving access and community sensitization to VL diagnosis. We assessed the contribution of each facility to the total distance traveled from a perspective of location optimization. Results: There was a sharp increase in the number of people tested in the 2017 outbreak compared to the 2019 outbreak. In 2017, 437 people were tested compared to 2,338 in 2019. The county reported 234 and 688 VL cases in 2017 and 2019, respectively. The data revealed a shift in the demographic structures of cases toward the younger population (mean age in 2017 was 17.6 years and 15.3 years in 2019), with more female cases reported in 2019 compared to 2017. In 2017, 44.4% were 10 years of age or under. In 2019, the proportion 10 years or below was 52.2%. The addition of two new diagnosis facilities in 2018 resulted in a decrease in the distance traveled by confirmed VL cases from 28.1 km in 2017 to 10.8 km in 2019. Assessing the impact of facility placement indicated the most optimal facilities to provide VL diagnostic services and minimize the distance traveled by patients. Adding new facilities reduces the travel distance until a point where the addition of a new facility provides no additional impact. Conclusion: The results from this study indicate the need to carefully consider the placement of health facilities in improving access to VL diagnosis and treatment and could serve as an investment case in deciding when to stop adding new facilities in a particular setting. Extending the activities in Kenya to other VL-endemic countries in East Africa will contribute significantly toward the elimination of the disease, addressing the needs of marginalized populations and leaving no one behind.Funding for the VL activities in Kenya presented in this paper was provided by the Swiss Agency for Development and Cooperation (SDC) and the Fundación Probitas.S

Using sequence data to identify alternative routes and risk of infection: a case-study of campylobacter in Scotland

<b>Background:</b> Genetic typing data are a potentially powerful resource for determining how infection is acquired. In this paper MLST typing was used to distinguish the routes and risks of infection of humans with Campylobacter jejuni from poultry and ruminant sources.<p></p> <b>Methods:</b> C. jejuni samples from animal and environmental sources and from reported human cases confirmed between June 2005 and September 2006 were typed using MLST. The STRUCTURE software was used to assign the specific sequence types of the sporadic human cases to a particular source. We then used mixed case-case logistic regression analysis to compare the risk factors for being infected with C. jejuni from different sources.<p></p> <b>Results:</b> A total of 1,599 (46.3%) cases were assigned to poultry, 1,070 (31.0%) to ruminant and 67 (1.9%) to wild bird sources; the remaining 715 (20.7%) did not have a source that could be assigned with a probability of greater than 0.95. Compared to ruminant sources, cases attributed to poultry sources were typically among adults (odds ratio (OR) = 1.497, 95% confidence intervals (CIs) = 1.211, 1.852), not among males (OR = 0.834, 95% CIs = 0.712, 0.977), in areas with population density of greater than 500 people/km(2) (OR = 1.213, 95% CIs = 1.030, 1.431), reported in the winter (OR = 1.272, 95% CIs = 1.067, 1.517) and had undertaken recent overseas travel (OR = 1.618, 95% CIs = 1.056, 2.481). The poultry assigned strains had a similar epidemiology to the unassigned strains, with the exception of a significantly higher likelihood of reporting overseas travel in unassigned strains.<p></p> <b>Conclusions:</b> Rather than estimate relative risks for acquiring infection, our analyses show that individuals acquire C. jejuni infection from different sources have different associated risk factors. By enhancing our ability to identify at-risk groups and the times at which these groups are likely to be at risk, this work allows public health messages to be targeted more effectively. The rapidly increasing capacity to conduct genetic typing of pathogens makes such traced epidemiological analysis more accessible and has the potential to substantially enhance epidemiological risk factor studies