Modelling the deactivation of Escherichia coli in Nigerian soils amended with differently treated manures.

AIM: This study aimed to simulate deactivation of Escherichia coli in soils amended with cattle manure after burning, anaerobic digestion, composting, or without treatment. METHOD AND RESULTS: The Weibull survival function was used to describe deactivation of E. coli. Parameters for each treatment were determined using E. coli measurements from manure-amended soils and evaluated against measurements at different application rates. A statistically significant correlation and high coincidence between the simulated and measured values were obtained. The simulations revealed that although anaerobic digestion or burning of cattle manure effectively reduced the E. coli loads to background levels, burning retained very little nitrogen, so the ash residue was ineffective as an organic fertilizer. Anaerobic digestion was most effective at reducing E. coli levels while retaining a high proportion of N in the bioslurry residue, but the persistence of E. coli was higher than in compost. CONCLUSION: The results from this study suggest that the safest method for production of organic fertilizer would involve anaerobic digestion to reduce E. coli, followed by composting to reduce its persistence.

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.

Impacts of different treatment methods for cattle manure on the spread of faecal indicator organisms from soil to lettuce in Nigeria.

AIM: This study investigated impacts of different organic waste treatment methods on reduction and spread of faecal indicator organisms to food crops in a developing country. METHODS AND RESULTS: Fresh cattle manure was subjected to three different treatments; anaerobic digestion, burning and composting. Escherichia coli, coliforms and nitrogen content of cattle manure were measured before and after treatment in the amended soil and harvested lettuce. All treatments significantly reduced E. coli and coliform counts but differed in the ratio of E. coli or coliforms to nitrogen. Application of the recommended nitrogen dose of 120 kg ha-1 as bioslurry resulted in significantly lower E. coli and coliform contamination of soil than the same nitrogen rate applied as compost or ash. The E. coli content of lettuces grown on soil amended with treated wastes at recommended rates did not differ between treatments but was significantly lower than in lettuces grown on soil amended with untreated manure. CONCLUSIONS: Treatment of manure before use as an organic fertilizer significantly reduces potential contamination of both soil and food crops with E. coli and coliforms. To best reduce the spread of E. coli from organic fertilizers, manures should be treated by anaerobic digestion. SIGNIFICANCE AND IMPACT OF THE STUDY: Information from this study quantifies potential risks associated with use of manures in growing food crops by determining the ratio between pathogen content and required nitrogen application rate.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 2: Application to a small agricultural catchment.

The new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is applied to a small (0.42 km2) Scottish agricultural catchment to simulate the dynamics of E. coli arising from sheep and cattle farming, in order to provide a proof-of-concept. The hydrological environment for MAFIO was simulated by the "best" ensemble run of the tracer-aided ecohydrological model EcH2O-iso, obtained through multi-criteria calibration to stream discharge (MAE: 1.37 L s-1) and spatially-distributed stable isotope data (MAE: 1.14-3.02‰) for the period April-December 2017. MAFIO was then applied for the period June-August for which twice-weekly E. coli loads were quantified at up to three sites along the stream. Performance in simulating these data suggested the model has skill in capturing the transfer of faecal indicator organisms (FIOs) from livestock to streams via the processes of direct deposition, transport in overland flow and seepage from areas of degraded soil. Furthermore, its agent-based structure allowed source areas, transfer mechanisms and host animals contributing FIOs to the stream to be quantified. Such information is likely to have substantial value in the context of designing and spatially-targeting mitigation measures against impaired microbial water quality. This study also revealed, however, that avenues exist for improving process conceptualisation in MAFIO (e.g. to include FIO contributions from wildlife) and highlighted the need to quantitatively assess how uncertainty in the spatial extent of surface flow paths in the simulated hydrological environment may affect FIO simulations. Despite the consequent status of MAFIO as a research-level model, its encouraging performance in this proof-of-concept study suggests the model has significant potential for eventual incorporation into decision support frameworks.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 1: Background and model description.

A new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is developed that attempts to overcome limitations in existing faecal indicator organism (FIO) models arising from coarse spatial discretisations and poorly-constrained hydrological processes. MAFIO is a spatially-distributed, process-based model presently designed to simulate the fate and transport of agents representing FIOs shed by livestock at the sub-field scale in small (<10 km2) agricultural catchments. Specifically, FIO loading, die-off, detachment, surface routing, seepage and channel routing are modelled on a regular spatial grid. Central to MAFIO is that hydrological transfer mechanisms are simulated based on a hydrological environment generated by an external model for which it is possible to robustly determine the accuracy of simulated catchment hydrological functioning. The spatially-distributed, tracer-aided ecohydrological model EcH2O-iso is highlighted as a possible hydrological environment generator. The present paper provides a rationale for and description of MAFIO, whilst a companion paper applies the model in a small agricultural catchment in Scotland to provide a proof-of-concept.

Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7.

BACKGROUND: Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown. METHODS: We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread. RESULTS: The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909-1958), to the United States in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States. CONCLUSIONS: Inter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom.

We examined whole-genome-sequenced Campylobacter jejuni and C. coli from 2012-2015 isolated from birds and human stool samples in North East Scotland for the presence of antimicrobial resistance genes. We found that sequence type (ST) 5136 (clonal complex 464) was the most prevalent multidrug-resistant strain of C. jejuni exclusively associated with poultry host reservoirs and recovered from human cases of campylobacteriosis. Tetracycline resistance in ST5136 isolates was due to a tet(O/32/O) mosaic gene, ampicillin resistance was conferred by G → T transversion in the -10 promoter region of blaOXA-193, fluoroquinolone resistance was due to C257T change in gyrA, and aminoglycoside resistance was conferred by aac. Whole-genome analysis showed that the strain ST5136 evolved from ST464. The nationwide emergence of ST5136 was probably due to stepwise acquisition of antimicrobial resistance genes selected by high use of ß-lactam, tetracycline, fluoroquinolone, and aminoglycoside classes of drugs in the poultry industry.

Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden.

BACKGROUND: With over 800 million cases globally, campylobacteriosis is a major cause of food borne disease. In temperate climates incidence is highly seasonal but the underlying mechanisms are poorly understood, making human disease control difficult. We hypothesised that observed disease patterns reflect complex interactions between weather, patterns of human risk behaviour, immune status and level of food contamination. Only by understanding these can we find effective interventions. METHODS: We analysed trends in human Campylobacter cases in NE England from 2004 to 2009, investigating the associations between different risk factors and disease using time-series models. We then developed an individual-based (IB) model of risk behaviour, human immunological responses to infection and environmental contamination driven by weather and land use. We parameterised the IB model for NE England and compared outputs to observed numbers of reported cases each month in the population in 2004-2009. Finally, we used it to investigate different community level disease reduction strategies. RESULTS: Risk behaviours like countryside visits (t = 3.665, P < 0.001 and t = - 2.187, P = 0.029 for temperature and rainfall respectively), and consumption of barbecued food were strongly associated with weather, (t = 3.219, P = 0.002 and t = 2.015, P = 0.045 for weekly average temperature and average maximum temperature respectively) and also rain (t = 2.254, P = 0.02527). This suggests that the effect of weather was indirect, acting through changes in risk behaviour. The seasonal pattern of cases predicted by the IB model was significantly related to observed patterns (r = 0.72, P < 0.001) indicating that simulating risk behaviour could produce the observed seasonal patterns of cases. A vaccination strategy providing short-term immunity was more effective than educational interventions to modify human risk behaviour. Extending immunity to 1 year from 20 days reduced disease burden by an order of magnitude (from 2412-2414 to 203-309 cases per 50,000 person-years). CONCLUSIONS: This is the first interdisciplinary study to integrate environment, risk behaviour, socio-demographics and immunology to model Campylobacter infection, including pathways to mitigation. We conclude that vaccination is likely to be the best route for intervening against campylobacteriosis despite the technical problems associated with understanding both the underlying human immunology and genetic variation in the pathogen, and the likely cost of vaccine development.

Influence of Plant Species, Tissue Type, and Temperature on the Capacity of Shiga-Toxigenic Escherichia coli To Colonize, Grow, and Be Internalized by Plants.

Contamination of fresh produce with pathogenic Escherichia coli, including Shiga-toxigenic E. coli (STEC), represents a serious risk to human health. Colonization is governed by multiple bacterial and plant factors that can impact the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species) is predictive of the colonization of living plants, as assessed from growth kinetics and biofilm formation in plant extracts. The fitness of STEC isolates was compared to that of environmental E. coli isolates at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the highest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified to be the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonization occurred on alfalfa sprouts, though internalization was 10 times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that the growth potential of STEC could be inferred only for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonization. Overall, the capacity of E. coli to colonize, grow, and be internalized within plants or plant-derived matrices was influenced by the isolate type, plant species, plant tissue type, and temperature, complicating any straightforward relationship between in vitro and in planta behaviors.IMPORTANCE Fresh produce is an important vehicle for STEC transmission, and experimental evidence shows that STEC can colonize plants as secondary hosts, but differences in the capacity to colonize occur between different plant species and tissues. Therefore, an understanding of the impact that these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plant extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonize living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) but not those for leafy vegetables (lettuce and spinach) exhibited a positive relationship between plant extracts and living plants. Therefore, the detailed variations at the level of the bacterial isolate, plant species, and tissue type all need to be considered in risk assessment.

Novel Sampling Method for Assessing Human-Pathogen Interactions in the Natural Environment Using Boot Socks and Citizen Scientists, with Application to Campylobacter Seasonality.

This paper introduces a novel method for sampling pathogens in natural environments. It uses fabric boot socks worn over walkers' shoes to allow the collection of composite samples over large areas. Wide-area sampling is better suited to studies focusing on human exposure to pathogens (e.g., recreational walking). This sampling method is implemented using a citizen science approach: groups of three walkers wearing boot socks undertook one of six routes, 40 times over 16 months in the North West (NW) and East Anglian (EA) regions of England. To validate this methodology, we report the successful implementation of this citizen science approach, the observation that Campylobacter bacteria were detected on 47% of boot socks, and the observation that multiple boot socks from individual walks produced consistent results. The findings indicate higher Campylobacter levels in the livestock-dominated NW than in EA (55.8% versus 38.6%). Seasonal differences in the presence of Campylobacter bacteria were found between the regions, with indications of winter peaks in both regions but a spring peak in the NW. The presence of Campylobacter bacteria on boot socks was negatively associated with ambient temperature (P = 0.011) and positively associated with precipitation (P < 0.001), results consistent with our understanding of Campylobacter survival and the probability of material adhering to boot socks. Campylobacter jejuni was the predominant species found; Campylobacter coli was largely restricted to the livestock-dominated NW. Source attribution analysis indicated that the potential source of C. jejuni was predominantly sheep in the NW and wild birds in EA but did not differ between peak and nonpeak periods of human incidence.IMPORTANCE There is debate in the literature on the pathways through which pathogens are transferred from the environment to humans. We report on the success of a novel method for sampling human-pathogen interactions using boot socks and citizen science techniques, which enable us to sample human-pathogen interactions that may occur through visits to natural environments. This contrasts with traditional environmental sampling, which is based on spot sampling techniques and does not sample human-pathogen interactions. Our methods are of practical value to scientists trying to understand the transmission of pathogens from the environment to people. Our findings provide insight into the risk of Campylobacter exposure from recreational visits and an understanding of seasonal differences in risk and the factors behind these patterns. We highlight the Campylobacter species predominantly encountered and the potential sources of C. jejuni.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major generalist lineages of C. jejuni do not show evidence of recombination with each other in nature, despite having a high degree of host niche overlap and recombining extensively with specialist lineages. However, transformation experiments show that the generalist lineages readily recombine with one another in vitro. This suggests ecological rather than essential barriers to recombination, caused by a cryptic niche structure within the hosts.

Evidence for phenotypic plasticity among multihost Campylobacter jejuni and C. coli lineages, obtained using ribosomal multilocus sequence typing and Raman spectroscopy.

Closely related bacterial isolates can display divergent phenotypes. This can limit the usefulness of phylogenetic studies for understanding bacterial ecology and evolution. Here, we compare phenotyping based on Raman spectrometric analysis of cellular composition to phylogenetic classification by ribosomal multilocus sequence typing (rMLST) in 108 isolates of the zoonotic pathogens Campylobacter jejuni and C. coli. Automatic relevance determination (ARD) was used to identify informative peaks in the Raman spectra that could be used to distinguish strains in taxonomic and host source groups (species, clade, clonal complex, and isolate source/host). Phenotypic characterization based on Raman spectra showed a degree of agreement with genotypic classification using rMLST, with segregation accuracy between species (83.95%), clade (in C. coli, 98.41%), and, to some extent, clonal complex (86.89% C. jejuni ST-21 and ST-45 complexes) being achieved. This confirmed the utility of Raman spectroscopy for lineage classification and the correlation between genotypic and phenotypic classification. In parallel analysis, relatively distantly related isolates (different clonal complexes) were assigned the correct host origin irrespective of the clonal origin (74.07 to 96.97% accuracy) based upon different Raman peaks. This suggests that the phenotypic characteristics, from which the phenotypic signal is derived, are not fixed by clonal descent but are influenced by the host environment and change as strains move between hosts.

Progressive genome-wide introgression in agricultural Campylobacter coli.

Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10-11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.

Effects of seasonality and a diet of brassicas on the shedding of Escherichia coli O157 in sheep.

Sheep flocks were tested for Escherichia coli O157 from pooled fecal samples while they grazed on pasture in winter, brassicas in spring, and on pasture during the summer. The winter pasture study reported an average individual prevalence of 3.1% (95% confidence interval [CI]: 0.6-5.6%) and an average farm-level prevalence of 10.4% (95% CI: 2.1-18.8%) over the 3-year study period. The spring brassica study reported a prevalence of 0% and the summer pasture study had an individual prevalence of 6.3% (95% CI: 2.1-12.1%) and a farm prevalence of 36.8% (95% CI: 15.8-57.8%). Analysis showed significant differences between the shedding of E. coli O157 in sheep grazing on brassicas in spring when compared to sheep grazing on pasture in the summer (p<0.01) and in winter (p=0.044; odds ratio [OR]=0.106). Furthermore, sheep excreted a lower prevalence of E. coli O157 in winter while grazing on pasture (p=0.017; OR=0.199). E. coli O157 isolates were characterized using polymerase chain reaction for the presence of known virulence factors; all carried the eae and stx2 gene and 10/11 positive flocks possessed the stx2c gene, suggesting that sheep are a potential source of human infection.

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

BACKGROUND: 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 METHODS: 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. RESULTS: 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/km2 (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. CONCLUSIONS: 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.

The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni.

Campylobacter jejuni is a bacterial pathogen recognised as a major cause of foodborne illness worldwide. While Campylobacter jejuni generally does not grow outside its host, it can survive outside of the host long enough to pose a health concern. This review presents an up-to-date description and evaluation of biological, mathematical, and statistical approaches used to understand the behaviour of this foodborne pathogen and suggests future avenues which can be explored. Specifically, the incorporation of mathematical modelling may aid the understanding of C. jejuni biofilm formation both outside and inside the host. Predictive studies may be improved by the introduction of more standardised protocols for assessments of disinfection methods and by assessment of novel physical disinfection strategies as well as assessment of the efficiency of plant extracts on C. jejuni eradication. A full description of the metabolic pathways of C. jejuni, which is needed for the successful application of metabolic models, is yet to be achieved. Finally, a shift from animal models (except for those that are a source of human campylobacteriosis) to human-specific data may be made possible due to recent technological advancements, and this may lead to more accurate predictions of human infections.

Temporal variation and host association in the Campylobacter population in a longitudinal ruminant farm study.

Campylobacter jejuni and C. coli were quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the average Campylobacter concentrations shed by cattle (600 CFU g(-1)) and sheep (820 CFU g(-1)), although sheep did show a significant temporal reduction in the number of Campylobacter organisms shed in their feces. A total of 21 different sequence types (STs) (97.7% C. jejuni, 2.3% C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6% C. jejuni, 59.4% C. coli). The Campylobacter population in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage of Campylobacter species, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of a Campylobacter population on a ruminant farm by identifying the existence of both temporal and between-host variations.

Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species.

Bacterial populations can display high levels of genetic structuring but the forces that influence this are incompletely understood. Here, by combining modelling approaches with multilocus sequence data for the zoonotic pathogen Campylobacter, we investigated how ecological factors such as niche (host) separation relate to population structure. We analysed seven housekeeping genes from published C. jejuni and C. coli isolate collections from a range of food and wild animal sources as well as abiotic environments. By reconstructing genetic structure and the patterns of ancestry, we quantified C. jejuni host association, inferred ancestral populations, investigated genetic admixture in different hosts and determined the host origin of recombinant C. jejuni alleles found in hybrid C. coli lineages. Phylogenetically distinct C. jejuni lineages were associated with phylogenetically distinct wild birds. However, in the farm environment, phylogenetically distant host animals shared several C. jejuni lineages that could not be segregated according to host origin using these analyses. Furthermore, of the introgressed C. jejuni alleles found in C. coli lineages, 73% were attributed to genotypes associated with food animals. Our results are consistent with an evolutionary scenario where distinct Campylobacter lineages are associated with different host species but the ecological factors that maintain this are different in domestic animals such that phylogenetically distant animals can harbour closely related strains.

Importance of untested infectious individuals for interventions to suppress COVID-19.

The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 60-80% of all infected individuals during the early stages of the outbreaks. We propose that reducing the underlying transmission from untested cases is crucial to suppress the virus. This can be achieved through enhanced testing in combination with social distancing and other interventions that reduce transmission such as wearing face masks. Once transmission from silent carriers is kept under control by these means, the virus could have been fully suppressed through fast isolation and contact tracing of tested cases.

Estimated Dissemination Ratio-A Practical Alternative to the Reproduction Number for Infectious Diseases.

Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust measure of the trajectory of an outbreak that has been used for many years in the control of infectious disease in livestock. It is simple to calculate and explain. Its calculation and use are discussed below together with examples from the current COVID-19 outbreak in the UK. These applications illustrate that EDR can demonstrate changes in transmission rate before they may be clear from the epidemic curve. Thus, EDR can provide an early warning that an epidemic is resuming growth, allowing earlier intervention. A conceptual comparison between EDR and the commonly used reproduction number is also provided.