Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms. High number of farm infections (68/126) in minks and farm workers (>50% of farms) were detected, with limited community spread. Three of five initial introductions of SARS-CoV-2 led to subsequent spread between mink farms until November 2020. Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combining genetic information with epidemiological information when investigating outbreaks at the animal-human interface

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and related humans in the Netherlands

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combing genetic information with epidemiological information at the animal-human interface

Temporal dynamics of cloacal microbiota in adult laying chickens with and without access to an outdoor range

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition

Response to a Salmonella Enteritidis challenge in old laying hens with different vaccination histories

Extending the laying period of laying hens is beneficial for economic and sustainability purposes. Because vaccines were designed with a shorter laying period envisaged, it is unclear whether current Salmonella vaccines can provide sufficient levels of protection against infection at an older age. The purpose of this experiment was to determine the efficacy of early rearing vaccination schemes against Salmonella challenge late in the laying period. There were four treatment groups: birds that had not been vaccinated (Group 1), birds vaccinated with live Salmonella En-teritidis (SE) (Group 2), with live and inactivated SE (Group 3), or with live SE and live Salmonella Ty-phimurium (Group 4). At the end of the laying period , the birds were transported from the laying farm to the research facility where they were orally challenged with 2.06 × 10 9 colony-forming units SE at around 82 wk of age. Hens were euthanized and bacteriology was performed on cecum, liver, spleen, and follicular fluid samples to determine SE colonization 7 and 14 d after challenge. Clinical and bacteriological findings of hens vaccinated with different vaccination schemes and the non-vaccinated control group were compared. No significant differences in SE colonization were found for vaccinated groups compared to the non-vaccinated control group. This may be a result of waning immunity due to the long time between vaccination and challenge. Also, as vaccination took place in the rearing period in the field, initial levels of immunity may not have been optimal due to shortcomings in the vaccination technique. Furthermore, the results of this study may have been affected by differences in age, breed, and origin between the groups. Therefore, controlled studies from early age onwards are necessary for more accurate comparisons between vaccines

Response to a Salmonella Enteritidis challenge in old laying hens with different vaccination histories

Extending the laying period of laying hens is beneficial for economic and sustainability purposes. Because vaccines were designed with a shorter laying period envisaged, it is unclear whether current Salmonella vaccines can provide sufficient levels of protection against infection at an older age. The purpose of this experiment was to determine the efficacy of early rearing vaccination schemes against Salmonella challenge late in the laying period. There were four treatment groups: birds that had not been vaccinated (Group 1), birds vaccinated with live Salmonella En-teritidis (SE) (Group 2), with live and inactivated SE (Group 3), or with live SE and live Salmonella Ty-phimurium (Group 4). At the end of the laying period , the birds were transported from the laying farm to the research facility where they were orally challenged with 2.06 × 10 9 colony-forming units SE at around 82 wk of age. Hens were euthanized and bacteriology was performed on cecum, liver, spleen, and follicular fluid samples to determine SE colonization 7 and 14 d after challenge. Clinical and bacteriological findings of hens vaccinated with different vaccination schemes and the non-vaccinated control group were compared. No significant differences in SE colonization were found for vaccinated groups compared to the non-vaccinated control group. This may be a result of waning immunity due to the long time between vaccination and challenge. Also, as vaccination took place in the rearing period in the field, initial levels of immunity may not have been optimal due to shortcomings in the vaccination technique. Furthermore, the results of this study may have been affected by differences in age, breed, and origin between the groups. Therefore, controlled studies from early age onwards are necessary for more accurate comparisons between vaccines

Enterococcus hirae-associated endocarditis outbreaks in broiler flocks : clinical and pathological characteristics and molecular epidemiology

BACKGROUND: Enterococcus hirae-associated endocarditis, characterized by a peak in mortality during the second week of the grow-out, and occasionally lameness, was diagnosed at Dutch broiler farms. OBJECTIVES: Field cases were studied to increase knowledge on clinical and pathological characteristics, pathogenesis and epidemiology of these infections. ANIMALS AND METHODS: In total, 1266 birds of 25 flocks from 12 farms were examined. Post-mortem examinations, bacteriology, histopathology, PCR and DNA fingerprinting was carried out. Six flocks were followed longitudinally (n = 1017 birds). RESULTS: Average mortality was 4.1% for the entire grow-out, of which 36% was attributed to endocarditis. Fibrinous thromboendocarditis of the right atrioventricular (AV) valve was found in 24% of hearts, compared to 7% and 4% with lesions of left and both AV valves, respectively. Thrombotic lesions were found in 24% (n = 432) of lungs, but only in larger branches of the Arteria pulmonalis. Occasionally, thrombi were found in the Arteria ischiadica externa and in liver and brain vessels. Enterococcus was cultured from 54% (n = 176) of heart and in 75% (n = 28), 62% (n = 106) and 31% (n = 16) of liver, bone marrow and lung samples, respectively. Further identification, using the Rapid ID Strep 32 API system and a PCR targeting mur-2 and mur-2(ed) genes was carried out on a subset of Enterococcus positive isolates (n = 65): both techniques identified the isolates as Enterococcus hirae. Pulsed-field gel electrophoresis did not indicate evidence of clonality between farms and flocks. CONCLUSIONS: The relevance of these findings for pathogenesis and epidemiology of E. hirae infections is discussed. CLINICAL IMPORTANCE. This study may facilitate diagnosis of field cases and may contribute to the design of further research and development of control measures

Wild Bird Densities and Landscape Variables Predict Spatial Patterns in HPAI Outbreak Risk across The Netherlands

Highly pathogenic avian influenza viruses' (HPAIVs) transmission from wild birds to poultry occurs globally, threatening animal and public health. To predict the HPAI outbreak risk in relation to wild bird densities and land cover variables, we performed a case-control study of 26 HPAI outbreaks (cases) on Dutch poultry farms, each matched with four comparable controls. We trained machine learning classifiers to predict outbreak risk with predictors analyzed at different spatial scales. Of the 20 best explaining predictors, 17 consisted of densities of water-associated bird species, 2 of birds of prey, and 1 represented the surrounding landscape, i.e., agricultural cover. The spatial distribution of mallard ( Anas platyrhynchos) contributed most to risk prediction, followed by mute swan ( Cygnus olor), common kestrel ( Falco tinnunculus) and brant goose ( Branta bernicla). The model successfully distinguished cases from controls, with an area under the receiver operating characteristic curve of 0.92, indicating accurate prediction of HPAI outbreak risk despite the limited numbers of cases. Different classification algorithms led to similar predictions, demonstrating robustness of the risk maps. These analyses and risk maps facilitate insights into the role of wild bird species and support prioritization of areas for surveillance, biosecurity measures and establishments of new poultry farms to reduce HPAI outbreak risks

The ADKAR (R) change management model for farmer profiling with regard to antimicrobial stewardship in livestock production = Het ADKAR®-verandermodel voor typering van veehouders met betrekking tot verantwoord antibioticagebruik bij landbouwhuisdieren

Antimicrobial stewardship in veterinary practice and animal production is important from a One Health perspective. The ADKAR (R) change management model is a well-known strategy to implement behavioral change in people and small businesses. The objective of this study was to adapt the existing ADKAR (R) change management model to enable herd veterinarians to profile farmers with regard to antimicrobial stewardship. Therefore, an antimicrobial stewardship related scoring scale was defined. Subsequently, ADKAR (R) profiles of 26 poultry and 28 pig farmers from Belgium and the Netherlands were determined. For 57% of the farmers, perception and/or motivation were expected to limit successful change. For 70% of the farmers, knowledge and for 52% of the farmers, a lack of ability were the limiting factor. The ADKAR (R) model proved useful for identifying the key elements that prevent successful behavioral change in farmers to reduce the use of antibiotics in farm animals