A new phylodynamic model of Mycobacterium bovis transmission in a multi-host system uncovers the role of the unobserved reservoir

Multi-host pathogens are particularly difficult to control, especially when at least one of the hosts acts as a hidden reservoir. Deep sequencing of densely sampled pathogens has the potential to transform this understanding, but requires analytical approaches that jointly consider epidemiological and genetic data to best address this problem. While there has been considerable success in analyses of single species systems, the hidden reservoir problem is relatively under-studied. A well-known exemplar of this problem is bovine Tuberculosis, a disease found in British and Irish cattle caused by Mycobacterium bovis, where the Eurasian badger has long been believed to act as a reservoir but remains of poorly quantified importance except in very specific locations. As a result, the effort that should be directed at controlling disease in badgers is unclear. Here, we analyse densely collected epidemiological and genetic data from a cattle population but do not explicitly consider any data from badgers. We use a simulation modelling approach to show that, in our system, a model that exploits available cattle demographic and herd-to-herd movement data, but only considers the ability of a hidden reservoir to generate pathogen diversity, can be used to choose between different epidemiological scenarios. In our analysis, a model where the reservoir does not generate any diversity but contributes to new infections at a local farm scale are significantly preferred over models which generate diversity and/or spread disease at broader spatial scales. While we cannot directly attribute the role of the reservoir to badgers based on this analysis alone, the result supports the hypothesis that under current cattle control regimes, infected cattle alone cannot sustain M. bovis circulation. Given the observed close phylogenetic relationship for the bacteria taken from cattle and badgers sampled near to each other, the most parsimonious hypothesis is that the reservoir is the infected badger population. More broadly, our approach demonstrates that carefully constructed bespoke models can exploit the combination of genetic and epidemiological data to overcome issues of extreme data bias, and uncover important general characteristics of transmission in multi-host pathogen systems

Grazing cattle exposure to neighbouring herds and badgers in relation to bovine tuberculosis risk

Publication history: Accepted - 28 September 2020; Published online - 30 September 2020.Bovine tuberculosis (bTB) can be spread between and among cattle and wildlife hosts e.g. European badger (Meles meles). The majority of cattle in the UK and Ireland are grazed during the summer, potentially exposing them to Mycobacterium bovis. 18 farms were surveyed (39% dairy, 61% beef; fields n = 697) for one grazing season (May-November 2016, n = 148,461 field days) to quantify the co-occurrence of cattle with badger setts and latrines and adjacency to neighbouring cattle herds. 3% (n = 24) of the fields had a badger sett or latrine recorded, dairy cattle were significantly more likely to co-occur with badger setts and latrines than beef cattle. Most farms (89%) grazed cattle adjacent to a neighbouring herd, which accounted for 18% of the grazing season. Potential exposure to neighbouring herds did not differ between production systems but did vary between life stages. A significant positive association between the proportion of time cattle spent grazing fields with setts present and the historic 1-, 3- and 5- year bTB status (p = 0.007, p = 0.013 and p = 0.013 respectively) was found. However, when cattle were grazed in fields with latrines, a significant negative association was found between the proportion of time cattle spent grazing fields with latrines present and the historic 3- and 5- year bTB status (p = 0.033 and p = 0.012 respectively). Historic bTB status and percentage of days spent beside a neighbouring herd was unrelated. Idiosyncrasies at farm-level and between risk factors indicated that individual farm assessments would be beneficial to understand potential exposure risk.This research was funded as part of a PhD studentship by the Department of Agriculture, Environment and Rural Affair

Relative abundance of Mycobacterium bovis molecular types in cattle:a simulation study of potential epidemiological drivers

Background: The patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. In this study, we use ecological approaches and simulation modelling to investigate the distribution of relative abundances of MVLA-types and its potential drivers. We explore four biologically plausible hypotheses regarding the processes driving molecular type relative abundances: sampling and speciation; structuring of the pathogen population; historical changes in population size; and transmission heterogeneity (superspreading). Results: Northern Irish herd-level MVLA-type surveillance shows a right-skewed distribution of MVLA-types, with a small number of types present at very high frequencies and the majority of types very rare. We demonstrate that this skew is too extreme to be accounted for by simple neutral ecological processes. Simulation results indicate that the process of MVLA-type speciation and the manner in which the MVLA-typing loci were chosen in Northern Ireland cannot account for the observed skew. Similarly, we find that pathogen population structure, assuming for example a reservoir of infection in a separate host, would drive the relative abundance distribution in the opposite direction to that observed, generating more even abundances of molecular types. However, we find that historical increases in bovine tuberculosis prevalence and/or transmission heterogeneity (superspreading) are both capable of generating the skewed MVLA-type distribution, consistent with findings of previous work examining the distribution of molecular types in human tuberculosis. Conclusion: Although the distribution of MVLA-type abundances does not fit classical neutral predictions, our simulations show that increases in pathogen population size and/or superspreading are consistent with the pattern observed, even in the absence of selective pressures acting on the system

The impact of BCG strains and repeat vaccinations on immunodiagnostic tests in Eurasian badgers (Meles meles)

Publication history: Accepted - 29 June 2022; Published online - 9July 2022.Bacille Calmette-Guerin (BCG) is a potential tool in the control of Mycobacterium bovis in European badgers (Meles meles). A five year Test and Vaccinate or Remove (TVR) research intervention project commenced in 2014 using two BCG strains (BCG Copenhagen 1331 (Years 1–3/ BadgerBCG) and BCG Sofia SL2222 (Years 4–5). Badgers were recaptured around 9 weeks after the Year 5 vaccination and then again a year later. The Dual-Path Platform (DPP) Vet TB assay was used to detect serological evidence of M. bovis infection. Of the 48 badgers, 47 had increased Line 1 readings (MPB83 antigen) between the Year 5 vaccination and subsequent recapture. The number of BCG Sofia vaccinations influenced whether a badger tested positive to the recapture DPP VetTB assay Line 1 (p < 0.001) while the number of BadgerBCG vaccinations did not significantly affect recapture Line 1 results (p = 0.59). Line 1 relative light units (RLU) were more pronounced in tests run with sera than whole blood. The results from an in_house MPB83 ELISA results indicated that the WB DPP VetTB assay may not detect lower MPB83 IgG levels as well as the serum DPP VetTB assay. Changes in interferon gamma assay (IFN-γ) results were seen in 2019 with significantly increased CFP-10 and PPDB readings. Unlike BadgerBCG, BCG Sofia induces an immune response to MPB83 (the immune dominant antigen in M. bovis badger infection) that then affects the use of immunodiagnostic tests. The use of the DPP VetTB assay in recaptured BCG Sofia vaccinated badgers within the same trapping season is precluded and caution should be used in badgers vaccinated with BCG Sofia in previous years. The results suggest that the DPP VetTB assay can be used with confidence in badgers vaccinated with BadgerBCG as a single or repeated doses.This work was funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland (DAERA)

A Bayesian analysis of a Test and Vaccinate or Remove study to control bovine tuberculosis in badgers (Meles meles)

Publication history: Accepted - 13 January 2021; Published - 28 January 2021.A novel five year Test and Vaccinate or Remove (TVR) wildlife research intervention project in badgers (Meles meles) commenced in 2014 in a 100km2 area of Northern Ireland. It aimed to increase the evidence base around badgers and bovine TB and help create well-informed and evidence-based strategies to address the issue of cattle-to-cattle spread and spread between cattle and badgers. It involved real-time trap-side testing of captured badgers and vaccinating those that tested negative for bTB (BadgerBCG–BCG Danish 1331) and removal of those that tested bTB positive using the Dual-Path Platform VetTB test (DPP) for cervids (Chembio Diagnostic Systems, Medford, NY USA). Four diagnostic tests were utilised within the study interferon gamma release assay (IGRA), culture (clinical samples and post mortem), DPP using both whole blood and DPP using serum. BCG Sofia (SL222) was used in the final two years because of supply issues with BadgerBCG. Objectives for this study were to evaluate the performance of the DPP in field conditions and whether any trend was apparent in infection prevalence over the study period. A Bayesian latent class model of diagnostic test evaluation in the absence of a gold standard was applied to the data. Temporal variation in the sensitivity of DPP and interferon gamma release assay (IGRA) due to the impact of control measures was investigated using logistic regression and individual variability was assessed. Bayesian latent class analysis estimated DPP with serum to have a sensitivity of 0.58 (95% CrI: 0.40–0.76) and specificity of 0.97 (95% CrI: 0.95–0.98). The DPP with whole blood showed a higher sensitivity (0.69 (95% CrI: 0.48–0.88)) but similar specificity (0.98 (95% Crl: 0.96–0.99)). The change from BCG Danish to BCG Sofia significantly impacted on DPP serum test characteristics. In addition, there was weak evidence of increasing sensitivity of IGRA over time and differences in DPP test sensitivity between adults and cubs. An exponential decline model was an appropriate representation of the infection prevalence over the 5 years, with a starting prevalence of 14% (95% CrI: 0.10–0.20), and an annual reduction of 39.1% (95% CrI: 26.5–50.9). The resulting estimate of infection prevalence in year 5 of the study was 1.9% (95% CrI: 0.8–3.8). These results provide field evidence of a statistically significant reduction in badger TB prevalence supporting a TVR approach to badger intervention. They give confidence in the reliability and reproducibility in the DPP Whole Blood as a real time trap-side diagnostic test for badgers, and describe the effect of vaccination and reduced infection prevalence on test characteristics.The study was funded by the Department of Agriculture, Environment and Rural Affairs in Northern Ireland (DAERA)

Systemic retention of ingested cantharidin by frogs

Frogs (Rana pipiens) fed on blister beetles (Meloidae) or cantharidin, retain cantharidin systemically. After cessation of feeding, they void the compound relatively quickly. Systemic cantharidin does not protect frogs against ectoparasitic feeding by leeches (Hirudo medicinalis) or predation by snakes (Nerodia sipedon). As suggested by our data, and from reports in the early literature, ingestion of cantharidin-containing frogs can pose a health threat to humans.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43540/1/49_2005_Article_BF01325229.pd

Interventions to Influence Consulting and Antibiotic Use for Acute Respiratory Tract Infections in Children: A Systematic Review and Meta-Analysis

BACKGROUND: Respiratory tract infections (RTIs) are common in children and generally self-limiting, yet often result in consultations to primary care. Frequent consultations divert resources from care for potentially more serious conditions and increase the opportunity for antibiotic overuse. Overuse of antibiotics is associated with adverse effects and antimicrobial resistance, and has been shown to influence how patients seek care in ensuing illness episodes. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a systematic review and meta-analysis to assess the effectiveness of interventions directed towards parents or caregivers which were designed to influence consulting and antibiotic use for respiratory tract infections (RTIs) in children in primary care. Main outcomes were parental consulting rate, parental knowledge, and proportion of children subsequently consuming antibiotics. Of 5,714 references, 23 studies (representing 20 interventions) met inclusion criteria. Materials designed to engage children in addition to parents were effective in modifying parental knowledge and behaviour, resulting in reductions in consulting rates ranging from 13 to 40%. Providing parents with delayed prescriptions significantly decreased reported antibiotic use (Risk Ratio (RR) 0.46 (0.40, 0.54); moreover, a delayed or no prescribing approach did not diminish parental satisfaction. CONCLUSIONS: IN ORDER TO BE MOST EFFECTIVE, INTERVENTIONS TO INFLUENCE PARENTAL CONSULTING AND ANTIBIOTIC USE SHOULD: engage children, occur prior to an illness episode, employ delayed prescribing, and provide guidance on specific symptoms. These results support the wider implementation of interventions to reduce inappropriate antibiotic use in children

Sources of increase in lowermost stratospheric sulphurous and carbonaceous aerosol background concentrations during 1999–2008 derived from CARIBIC flights

This study focuses on sulphurous and carbonaceous aerosol, the major constituents of particulate matter in the lowermost stratosphere (LMS), based on in situ measurements from 1999 to 2008. Aerosol particles in the size range of 0.08–2 µm were collected monthly during intercontinental flights with the CARIBIC passenger aircraft, presenting the first long-term study on carbonaceous aerosol in the LMS. Elemental concentrations were derived via subsequent laboratory-based ion beam analysis. The stoichiometry indicates that the sulphurous fraction is sulphate, while an O/C ratio of 0.2 indicates that the carbonaceous aerosol is organic. The concentration of the carbonaceous component corresponded on average to approximately 25% of that of the sulphurous, and could not be explained by forest fires or biomass burning, since the average mass ratio of Fe to K was 16 times higher than typical ratios in effluents from biomass burning. The data reveal increasing concentrations of particulate sulphur and carbon with a doubling of particulate sulphur from 1999 to 2008 in the northern hemisphere LMS. Periods of elevated concentrations of particulate sulphur in the LMS are linked to downward transport of aerosol from higher altitudes, using ozone as a tracer for stratospheric air. Tropical volcanic eruptions penetrating the tropical tropopause are identified as the likely cause of the particulate sulphur and carbon increase in the LMS, where entrainment of lower tropospheric air into volcanic jets and plumes could be the cause of the carbon increase

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled &lsquo;reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers

Expert Panel Curation of 113 Primary Mitochondrial Disease Genes for the Leigh Syndrome Spectrum

OBJECTIVE: Primary mitochondrial diseases (PMDs) are heterogeneous disorders caused by inherited mitochondrial dysfunction. Classically defined neuropathologically as subacute necrotizing encephalomyelopathy, Leigh syndrome spectrum (LSS) is the most frequent manifestation of PMD in children, but may also present in adults. A major challenge for accurate diagnosis of LSS in the genomic medicine era is establishing gene-disease relationships (GDRs) for this syndrome with >100 monogenic causes across both nuclear and mitochondrial genomes. METHODS: The Clinical Genome Resource (ClinGen) Mitochondrial Disease Gene Curation Expert Panel (GCEP), comprising 40 international PMD experts, met monthly for 4 years to review GDRs for LSS. The GCEP standardized gene curation for LSS by refining the phenotypic definition, modifying the ClinGen Gene-Disease Clinical Validity Curation Framework to improve interpretation for LSS, and establishing a scoring rubric for LSS. RESULTS: The GDR with LSS across the nuclear and mitochondrial genomes was classified as definitive for 31/114 gene-disease relationships curated (27%); moderate for 38 (33%); limited for 43 (38%); and 2 as disputed (2%). Ninety genes were associated with autosomal recessive inheritance, 16 were maternally inherited, 5 autosomal dominant, and 3 X-linked. INTERPRETATION: GDRs for LSS were established for genes across both nuclear and mitochondrial genomes. Establishing these GDRs will allow accurate variant interpretation, expedite genetic diagnosis of LSS, and facilitate precision medicine, multi-system organ surveillance, recurrence risk counselling, reproductive choice, natural history studies and eligibility for interventional clinical trials. This article is protected by copyright. All rights reserved