Spread of Coxiella burnetii between dairy cattle herds in an enzootic region: modelling contributions of airborne transmission and trade

Screening for Coxiella Burnetii in Dairy Cattle Herds in Poland

Introduction

The intracellular bacterium Coxiella burnetii is the aetiological agent of Q fever, a zoonosis affecting many animal species worldwide. Cattle and small ruminants are considered the major reservoirs of the bacteria and they shed it through multiple routes.

Material and Methods

A total of 2,180 sera samples from 801 cattle herds in all Polish voivodeships were tested by ELISA for the presence of specific antibodies. Milk samples were obtained from seropositive cows in 133 herds as part of a separate study. The milk samples were examined by ELISA and real-time PCR tests.

Results

Seroprevalence at the animal level was 7.06% and true positive seroprevalence was 6.0% (95% confidence interval (CI) 1.1-9.4). Seroprevalence at the herd level was estimated at 11.1% and true positive seroprevalence was 10.5% (95% CI 3.2-15.8). Shedding of the pathogen in milk was detected by real-time PCR in 33 out of 133 tested herds (24.81%, 95% CI 17.74-33.04%) and the presence of C. burnetii antibodies was confirmed in 85 of them (63.9%, 95% CI 55.13-72.05%). The highest level of conformity between ELISA and real-time PCR results was obtained for bulk tank milk samples.

Conclusion

Coxiella burnetii infections are quite common in cattle herds across the country, which emphasises the crucial roles of surveillance and adequate biosecurity measures in the prevention and limitation of Q fever spread in Poland.

Molecular detection of Coxiella burnetii in small ruminants and genotyping of specimens collected from goats in Poland

Background

Coxiella burnetii is the etiological agent of Q fever, a zoonosis affecting many animal species including sheep and goats. The aims of this study were to evaluate the shedding of Coxiella burnetii in small ruminant herds and to identify the pathogen’s genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods.

Results

Overall, 165 samples from 43 herds of goats and 9 flocks of sheep were collected including bulk tank milk (BTM), individual milk samples, vaginal swabs, tissue sections from stillborn kids, feces and placentas. These were tested by real-time PCR targeting the IS1111 element. C. burnetii infection was confirmed in 51.16% of the herds of goats and 22.2% of the flocks of sheep. Six out of nine samples originating from goats were successfully genotyped using the MLVA method. The presence was confirmed of two widely distributed MLVA genotypes (I and J) and genotype PL1 previously reported only in cattle. Only one sequence type (ST61) was identified; however, the majority of specimens represented partial STs and some of them may belong to ST61. Other partial STs could possibly be ST74.

Conclusion

This study confirmed the relatively common occurrence of Coxiella burnetii in small ruminant herds in Poland. Interestingly, all genotyped samples represent cattle-associated MLVA genotypes.

Multi-Scale Airborne Infectious Disease Transmission

Airborne disease transmission is central to many scientific disciplines including agriculture, veterinary biosafety, medicine, and public health. Legal and regulatory standards are in place to prevent agricultural, nosocomial, and community airborne disease transmission. However, the overall importance of the airborne pathway is underappreciated, e.g.,, US National Library of Medicine's Medical Subjects Headings (MESH) thesaurus lacks an airborne disease transmission indexing term. This has practical consequences as airborne precautions to control epidemic disease spread may not be taken when airborne transmission is important, but unrecognized. Publishing clearer practical methodological guidelines for surveillance studies and disease outbreak evaluations could help address this situation.To inform future work, this paper highlights selected, well-established airborne transmission events - largely cases replicated in multiple, independently conducted scientific studies. Methodologies include field experiments, modeling, epidemiology studies, disease outbreak investigations and mitigation studies. Collectively, this literature demonstrates that airborne viruses, bacteria, and fungal pathogens have the capability to cause disease in plants, animals, and humans over multiple distances - from near range (< 5 m) to continental (> 500 km) in scale. The plausibility and implications of undetected airborne disease transmission are discussed, including the notable underreporting of disease burden for several airborne transmitted diseases.

Serological and Molecular Phylogenetic Detection of Coxiella burnetii in Lactating Cows, Iraq

This study is carried out to investigate the prevalence of Coxiella burnetii (C. burnetii) infections in cattle using an enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) assay targeting IS1111A transposase gene. A total of 130 lactating cows were randomly selected from different areas in Wasit province, Iraq and subjected to blood and milk sampling during the period extended between November 2018 and May 2019. ELISA and PCR tests revealed that 16.15% and 10% of the animals studied were respectively positive. Significant correlations (P<0.05) were detected between the positive results and clinical data. Two positive PCR products were analyzed phylogenetically, named as C. burnetii IQ-No.5 and C. burnetii IQ-No.6; and then recorded in the National Center for Biotechnology Information (NCBI) under an accession numbers of MN473204.1 and MN473205.1. Comparative identity of the local strains with NCBI-BLAST strains/isolates revealed 97% similarity and 0.1-0.6% of total genetic mutations/changes. NCBI-BLAST Homology Sequence reported high significant identity (P<0.05) between the local, C. burnetii IQ-No.5 and C. burnetii IQ-No.6; strains and C. burnetii 3345937 (CP014354.1) Netherlands isolate at 99.10% and 99.06%, respectively. The current study concluded that the percentage of infected cows with coxiellosis is relatively high, and Coxiella should be listed as abortive pathogen. Therefore, additional studies should be performed including different animals, samples, and regions.

Emerging Influenza D virus infection in European livestock as determined in serology studies: Are we underestimating its spread over the continent?

Influenza D virus (IDV) is a novel orthomyxovirus that was first isolated in 2011 in the United States from a swine exhibiting influenza-like disease. To date, its detection is extended to all continents and in a broad host range: IDV is circulating in cattle, swine, feral swine, camelids, small ruminants and horses. Evidence also suggests a possible species jump to humans, underlining the issue of zoonotic potential. In Europe, serological investigations in cattle have partially allowed the understanding of the virus diffusion in different countries such as Italy, France, Luxembourg and Ireland. The infection is widespread in cattle but limited in other investigated species, consolidating the assumption of cattle as IDV primary host. We hypothesize that commercial livestock trade could play a role in the observed differences in IDV seroprevalence among these areas. Indeed, the overall level of exposure in cattle and swine in destination countries (e.g. Italy) is higher than in origin countries (e.g. France), leading to the hypothesis of a viral shedding following the transportation of young cattle abroad and thus contributing to larger diffusion at countries of destination. IDV large geographic circulation in cattle from Northern to more Southern European countries also supports the hypothesis of a viral spread through livestock trade. This review summarizes available data on IDV seroprevalence in Europe collected so far and integrates unpublished data from IDV European surveillance framework of the last decade. In addition, the possible role of livestock trade and biosecurity measures in this pathogen's spread is discussed.

Sero-epidemiology investigation of Coxiella burnetii in domestic ruminants throughout most Greek regions

Q fever is not considered as a public health problem in Greece where most regions are considered as Coxiella burnetii free possibly because of the low interest for this agent. Our objective was to conduct a large‐scale study to investigate the sero‐epidemiology of C. burnetii in domestic ruminants throughout the most of Greek regions. We tested serum samples obtained from goats, sheep and bovines from different regions of Greece. All sera were tested for C. burnetii IgG antibodies by a commercial ELISA according to the manufacturer's recommendations. We tested 1,173 goats and sheep obtained from 177 different herds and totally 194 (17%) animals from 78 (44%) herds were positive for C. burnetii. Positive animals were present in seven (88%) different regions and seropositivity varied widely among these regions. The highest percentage was observed in Peloponnese (44%), where all the tested herds presented animals with C. burnetii antibodies. Ιn all Aegean Islands except the island of Limnos we detected goats and sheep positive for C. burnetii with seroposivity varying between 2% in Kos to 37% in Rhodes. Finally, in 22 (85%) Greek prefectures we found C. burnetii IgG‐positive animals whereas in 14 (54%) prefectures more than 50% of tested herds had seropositive animals. We also tested 28 cows from five different herds in Macedonia and Aegean Islands and six (21%) of them, obtained from two (40%) herds were positive. Considering the importance of C. burnetii for public health, our data reflect the lack of awareness by veterinarians, physicians and competent authorities as we provide evidence of C. burnetii seropositivity in productive animals throughout the most of Greek territories. Due to the increased risk of inhalation of the bacterium by people who entered the affected farms we raise the question of Q fever emergence in Greece.

Monitoring Coxiella burnetii Infection in Naturally Infected Dairy Sheep Flocks Throughout Four Lambing Seasons and Investigation of Viable Bacteria

Progression of Coxiella burnetii infection in four naturally infected sheep flocks, and in their farm environment, was monitored throughout four lambing seasons. Flocks with an active infection were selected based on the presence of C. burnetii DNA in bulk-tank milk (BTM) and a high seroprevalence in yearlings during the previous milking period (Spring 2015). During four consecutive lambing seasons (2015/16–2018/19), samples were collected within 1 week after each lambing period from animals (vaginal swabs, milk and feces from ewes, and yearlings) and the environment (dust indoor sheep premises). BTM samples and aerosols (outdoors and indoors) were monthly collected between lambing and the end of milking. Real-time PCR analyses showed different trends in C. burnetii shedding in the flocks, with a general progressive decrease in bacterial shedding throughout the years, interrupted in three flocks by peaks of reinfection associated with specific management practices. A significant relationship was found between C. burnetii fecal shedding and the bacterial burden detected in dust, whereas shedding by vaginal route affected the detection of C. burnetii in indoor aerosols. Three genotypes were identified: SNP8 (three flocks, 52.9% of the samples), SNP1 (two flocks, 44.8% samples), and SNP5 (one flock, two environmental samples). Coxiella burnetii viability in dust measured by culture in Vero cells was demonstrated in two of the flocks, even during the fourth lambing season. The results showed that infection can remain active for over 5 years if effective control and biosafety measures are not correctly implemented.

EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology

Stochastic mechanistic epidemiological models largely contribute to better understand pathogen emergence and spread, and assess control strategies at various scales (from within-host to transnational scale). However, developing realistic models which involve multi-disciplinary knowledge integration faces three major challenges in predictive epidemiology: lack of readability once translated into simulation code, low reproducibility and reusability, and long development time compared to outbreak time scale. We introduce here EMULSION, an artificial intelligence-based software intended to address those issues and help modellers focus on model design rather than programming. EMULSION defines a domain-specific language to make all components of an epidemiological model (structure, processes, parameters…) explicit as a structured text file. This file is readable by scientists from other fields (epidemiologists, biologists, economists), who can contribute to validate or revise assumptions at any stage of model development. It is then automatically processed by EMULSION generic simulation engine, preventing any discrepancy between model description and implementation. The modelling language and simulation architecture both rely on the combination of advanced artificial intelligence methods (knowledge representation and multi-level agent-based simulation), allowing several modelling paradigms (from compartment- to individual-based models) at several scales (up to metapopulation). The flexibility of EMULSION and its capability to support iterative modelling are illustrated here through examples of progressive complexity, including late revisions of core model assumptions. EMULSION is also currently used to model the spread of several diseases in real pathosystems. EMULSION provides a command-line tool for checking models, producing model diagrams, running simulations, and plotting outputs. Written in Python 3, EMULSION runs on Linux, MacOS, and Windows. It is released under Apache-2.0 license. A comprehensive documentation with installation instructions, a tutorial and many examples are available from: https://sourcesup.renater.fr/www/emulsion-public.

Neighbourhood contacts and trade movements drive the regional spread of bovine viral diarrhoea virus (BVDV)

To explore the regional spread of endemic pathogens, investigations are required both at within and between population levels. The bovine viral diarrhoea virus (BVDV) is such a pathogen, spreading among cattle herds mainly due to trade movements and neighbourhood contacts, and causing an endemic disease with economic consequences. To assess the contribution of both transmission routes on BVDV regional and local spread, we developed an original epidemiological model combining data-driven and mechanistic approaches, accounting for heterogeneous within-herd dynamics, animal movements and neighbourhood contacts. Extensive simulations were performed over 9 years in an endemic context in a French region with high cattle density. The most uncertain model parameters were calibrated on summary statistics of epidemiological data, highlighting that neighbourhood contacts and within-herd transmission should be high. We showed that neighbourhood contacts and trade movements complementarily contribute to BVDV spread on a regional scale in endemically infected and densely populated areas, leading to intense fade-out/colonization events: neighbourhood contacts generate the vast majority of outbreaks (72%) but mostly in low immunity herds and correlated to a rather short presence of persistently infected animals (P); trade movements generate fewer infections but could affect herds with higher immunity and generate a prolonged presence of P. Both movements and neighbourhood contacts should be considered when designing control or eradication strategies for densely populated region.

Swab cloths as a tool for revealing environmental contamination by Q fever in ruminant farms

Q fever is a zoonotic abortive disease of ruminants mostly transmitted by inhalation of aerosols contaminated by Coxiella burnetii. Clusters of cases or even epidemics regularly occur in humans but, to date, there is no consensus about the best way to carry out outbreak investigations in order to identify potential farms at risk. Although environmental samples might be useful during such investigations, there are few baseline data on the presence of C. burnetii in the environment of ruminant farms. We thus investigated dust samples from cattle, sheep and goat farm buildings in order to (a) estimate C. burnetii detection frequency and bacterial loads in the environment, and (b) determine whether this environmental contamination is associated with series of abortions attributed to Q fever. We considered 113 herds with a recent abortive episode potentially related (n = 60) or not (n = 53) to C. burnetii. Dust was sampled using a swab cloth and tested by a quantitative PCR method targeting the IS1111 gene. Coxiella burnetii DNA was detected on 9 of 50 cattle farms, 13 of 19 goat farms and 30 of 40 sheep farms. On 16 cloths, bacterial loads were higher than 10⁸ genome equivalents, levels as high as in infectious materials such as placentas and aborted foetuses. Overall, the probability of detecting C. burnetii DNA was higher on small ruminant farms than cattle farms, in herds suspected of Q fever and in large herds. We conclude that swab cloths are a putative indicator of contamination of ruminant farms by C. burnetii.

A systematic knowledge synthesis on the spatial dimensions of Q fever epidemics

From 2007 through 2010, the Netherlands experienced the largest Q fever epidemic ever reported. This study integrates the outcomes of a multidisciplinary research programme on spatial airborne transmission of Coxiella burnetii and reflects these outcomes in relation to other scientific Q fever studies worldwide. We have identified lessons learned and remaining knowledge gaps. This synthesis was structured according to the four steps of quantitative microbial risk assessment (QMRA): (a) Rapid source identification was improved by newly developed techniques using mathematical disease modelling; (b) source characterization efforts improved knowledge but did not provide accurate C. burnetii emission patterns; (c) ambient air sampling, dispersion and spatial modelling promoted exposure assessment; and (d) risk characterization was enabled by applying refined dose–response analyses. The results may support proper and timely risk assessment and risk management during future outbreaks, provided that accurate and structured data are available and exchanged readily between responsible actors.

A modelling framework based on MDP to coordinate farmers' disease control decisions at a regional scale

The effectiveness of infectious disease control depends on the ability of health managers to act in a coordinated way. However, with regards to non-notifiable animal diseases, farmers individually decide whether or not to implement control measures, leading to positive and negative externalities for connected farms and possibly impairing disease control at a regional scale. Our objective was to facilitate the identification of optimal incentive schemes at a collective level, adaptive to the epidemiological situation, and minimizing the economic costs due to a disease and its control. We proposed a modelling framework based on Markov Decision Processes (MDP) to identify effective strategies to control PorcineReproductive andRespiratorySyndrome (PRRS), a worldwide endemicinfectiousdisease thatsignificantly impactspig farmproductivity. Using a stochastic discrete-time compartmental model representing PRRS virus spread and control within a group of pig herds, we defined the associated MDP. Using a decision-tree framework, we translated the optimal policy into a limited number of rules providing actions to be performed per 6-month time-step according to the observed system state. We evaluated the effect of varying costs and transition probabilities on optimal policy and epidemiological results. We finally identifiedan adaptive policy that gave the best net financial benefit. The proposed framework is a tool for decision support as it allows decision-makers to identify the optimal policy and to assess its robustness to variations in the values of parameters representing an impact of incentives on farmers' decisions.

Farming, Q fever and public health: agricultural practices and beyond

Since the Neolithic period, humans have domesticated herbivores to have food readily at hand. The cohabitation with animals brought various advantages that drastically changed the human lifestyle but simultaneously led to the emergence of new epidemics. The majority of human pathogens known so far are zoonotic diseases and the development of both agricultural practices and human activities have provided new dynamics for transmission. This article provides a general overview of some factors that influence the epidemic potential of a zoonotic disease, Q fever. As an example of a disease where the interaction between the environment, animal (domestic or wildlife) and human populations determines the likelihood of the epidemic potential, the management of infection due to the Q fever agent, Coxiella burnetii, provides an interesting model for the application of the holistic One Health approach.

Seroprevalence and Factors Associated with Coxiella burnetii Infection in Small Ruminants in Baringo County, Kenya

To improve estimates of C. burnetii epidemiology in Kenya, a survey was undertaken in small ruminants in Baringo County, where acute cases of Q fever in humans had been reported in 2014. From 140 household herds selected, 508 (60.5%) goats and 332 (39.5%) sheep were included and an indirect ELISA assay for C. burnetii IgG antibodies performed. In addition, epidemiological information at both herd and animal level was collected. Generalized mixed-effects multivariable logistic model using herd as the random effect was used to determine variables correlated to the outcome. Overall seroprevalence was 20.5% (95% CI: 17.8%, 23.3%). Goats had 26.0% (95% CI: 22.2%, 30.0%) compared to sheep 12.2% (95% CI: 8.7%, 16.0%). Nomadic pastoralism, goats and older animals (>1 year) were associated with greater risk of C. burnetii seropositivity (P = ≤0.05). Heterogeneity in C. burnetii seropositivity was observed across the sublocations (P = 0.028). Evidence of C. burnetii exposure in small ruminants revealed poses a potential risk of exposure to the people living in close proximity to the animals. We recommended integrated animal-human surveillance and socio-economic studies for C. burnetii, to aid our understanding of the risk of transmission between the animals and humans, and in the design of prevention and control strategies for the disease in the region.