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BACKGROUND: Farming has been associated with respiratory symptoms and with protection against atopy. To date, effects of organic farming on respiratory health have not been studied. AIMS: To (1) compare hay fever and asthma-like symptoms in organic and conventional farmers and (2) assess associations between current and childhood farm exposures and respiratory health effects by conducting a survey. METHODS: Questionnaire data from 1205 conventional and 593 organic farmers were evaluated. Associations between health effects and farm exposures were assessed by logistic regression analyses. RESULTS: Organic farmers reported less wheezing with shortness of breath and slightly more hay fever than conventional farmers. However, organic farming was not an independent determinant of hay fever when adjusted for farming practices and potential confounders. Livestock farmers who grew up on a farm had a threefold lower prevalence of hay fever than crop farmers without a farm childhood (odds ratio (OR) 0.3, 95% confidence interval (CI) 0.1 to 0.5). Both crop farmers who grew up on a farm and livestock farmers who did not grow up on a farm had a reduced prevalence, although less pronounced and not statistically significant. Use of disinfectants containing quaternary ammonium compounds was positively related to hay fever (OR 2.1, 95% CI 1 to 4.4). No effects of farming practices were found for asthma. CONCLUSIONS: Our study adds to the evidence that a farm childhood in combination with current livestock farming protects against allergic disorders. This effect was found for both organic and conventional farmers. [ABSTRACT FROM AUTHOR]

Background: Livestock-related emissions have been associated with aggravations of respiratory symptoms in patients with chronic obstructive pulmonary disease (COPD), potentially by altering the respiratory resistome., Objectives: This study investigates the structure of the acquired oropharyngeal (OP) resistome of patients with COPD and controls, its interplay with the respiratory microbiome and associations with residential livestock exposure., Methods: In a matched case-control study in the rural Netherlands, we analysed OP swabs from 35 patients with COPD and 34 controls, none of whom had used antibiotics in the preceding 4 weeks. Resistome profiling was performed using ResCap, complemented by prior characterization of the microbiome via 16S rRNA-based sequencing. Residential livestock farm exposure was defined using distance-based variables alongside modelled concentrations of livestock-emitted microbial pollutants. We compared resistome profiles between patients with COPD and controls, examining alpha and beta diversity as well as differential abundance. Additionally, we assessed the interplay between the resistome and microbiome using co-occurrence networks and Procrustes analysis. Variations in resistome profiles were also analysed based on residential livestock exposures., Results: Patients with COPD exhibited higher resistome diversity than controls (Shannon diversity, P = 0.047), though resistome composition remained similar between groups (PERMANOVA, P = 0.19). Significant correlations were observed between the OP resistome and microbiome compositions, with distinct patterns in co-occurrence networks. Residential exposure to livestock farms was not associated with resistome alterations., Conclusions: Our findings reveal the COPD airway as a hospitable environment for antimicrobial resistance genes, irrespective of recent antimicrobial usage. Demonstrating the interplay between the resistome and microbiome, our study underscores the importance of a deeper understanding of the resistome in respiratory health., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Our understanding of the normal variation in the upper respiratory tract (URT) microbiota across the human lifespan and how these relate to host, environment, and health is limited. We studied the microbiota of 3,104 saliva (<10 year-olds)/oropharynx (≥10 year-olds) and 2,485 nasopharynx samples of 3,160 Dutch individuals 0-87 years of age, participating in a cross-sectional population-wide study (PIENTER-3) using 16S-rRNA sequencing. The microbiota composition was strongly related to age, especially in the nasopharynx, with maturation occurring throughout childhood and adolescence. Clear niche- and age-specific associations were found between the microbiota composition and host/environmental factors and health outcomes. Among others, social interaction, sex, and season were associated with the nasopharyngeal microbial community. By contrast, the oral microbiota was more related to antibiotics, tobacco, and alcohol use. We present an atlas of the URT microbiota across the lifespan in association with environment and health, establishing a baseline for future research., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Total bacterial count (TBC) and SCC are important quality parameters in goat milk. Exceeding the bulk milk TBC (BMTBC) thresholds leads to price penalties for Dutch dairy goat farmers. Controlling these milk quality parameters can be challenging, especially around kidding. First, we describe the variation and the peaks around kidding of TBC and SCC in census data on Dutch bulk milk over the last 22 yr. Second, to explore causes of these elevations, we studied the variation of TBC and SCC in individual goat milk from 3 wk before to 5 wk after kidding and their association with systemic response markers IFN-γ, calprotectin, BHB, BCS, and fecal consistency. We visited 4 Dutch dairy goat farms weekly for 10 to 16 wk around kidding. Some of the goats had been dried off; other goats were milked continuously throughout pregnancy. A total of 1,886 milk samples from 141 goats were collected for automated flow cytometric quantification of TBC and SCC measurement. IFN-γ, calprotectin, and BHB were determined twice in blood of the same goats; most samples were collected after kidding. The BCS and fecal consistency were scored visually before and after kidding. We found a strong correlation between TBC and SCC (Spearman's rho = 0.87) around kidding. Furthermore, in the third week before kidding, the average TBC (5.67 log 10 cfu/mL) and SCC (6.70 log 10 cells/mL) were significantly higher compared with the fifth week after kidding, where the average TBC decreased to 4.20 log 10 cfu/mL, and the average SCC decreased to 5.92 log 10 cells/mL. In multivariable linear regression models, farm and stage of lactation were significantly associated with TBC and SCC, but none of the systemic response markers correlated with TBC or SCC. In conclusion, TBC and SCC in dairy goats were high in late lactation and decreased shortly after parturition. For SCC, the dilution effect might have caused the decrease, but this was not plausible for TBC. Moreover, the excretion of bacteria and cells in goat milk was not associated with the selected systemic response markers that were chosen as a readout for general immunity status, intestinal health, and metabolic diseases. Therefore, we assume that the TBC increase before kidding and the decrease after parturition are caused by other systemic, possibly hormonal, processes. To reduce BMTBC and bulk milk SCC, it would be advisable to keep milk of goats with highest numbers of bacteria and cells in their milk out of the bulk milk during end lactation. Further studies are needed to investigate the effects of withholding this end-lactation milk from the bulk tank., (© 2024, The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Several studies have linked air pollution to COVID-19 morbidity and severity. However, these studies do not account for exposure levels to SARS-CoV-2, nor for different sources of air pollution. We analyzed individual-level data for 8.3 million adults in the Netherlands to assess associations between long-term exposure to ambient air pollution and SARS-CoV-2 infection (i.e., positive test) and COVID-19 hospitalisation risks, accounting for spatiotemporal variation in SARS-CoV-2 exposure levels during the first two major epidemic waves (February 2020-February 2021). We estimated average annual concentrations of PM 10 , PM 2.5 and NO 2 at residential addresses, overall and by PM source (road traffic, industry, livestock, other agricultural sources, foreign sources, other Dutch sources), at 1 × 1 km resolution, and weekly SARS-CoV-2 exposure at municipal level. Using generalized additive models, we performed interval-censored survival analyses to assess associations between individuals' average exposure to PM 10 , PM 2.5 and NO 2 in the three years before the pandemic (2017-2019) and COVID-19-outcomes, adjusting for SARS-CoV-2 exposure, individual and area-specific confounders. In single-pollutant models, per interquartile (IQR) increase in exposure, PM 10 was associated with 7% increased infection risk and 16% increased hospitalisation risk, PM 2.5 with 8% increased infection risk and 18% increased hospitalisation risk, and NO 2 with 3% increased infection risk and 11% increased hospitalisation risk. Bi-pollutant models suggested that effects were mainly driven by PM. Associations for PM were confirmed when stratifying by urbanization degree, epidemic wave and testing policy. All emission sources of PM, except industry, showed adverse effects on both outcomes. Livestock showed the most detrimental effects per unit exposure, whereas road traffic affected severity (hospitalisation) more than infection risk. This study shows that long-term exposure to air pollution increases both SARS-CoV-2 infection and COVID-19 hospitalisation risks, even after controlling for SARS-CoV-2 exposure levels, and that PM may have differential effects on these COVID-19 outcomes depending on the emission source., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Air pollution is a known risk factor for several diseases, but the extent to which it influences COVID-19 compared to other respiratory diseases remains unclear. We performed a test-negative case-control study among people with COVID-19-compatible symptoms who were tested for SARS-CoV-2 infection, to assess whether their long- and short-term exposure to ambient air pollution (AAP) was associated with testing positive (vs. negative) for SARS-CoV-2. We used individual-level data for all adult residents in the Netherlands who were tested for SARS-CoV-2 between June and November 2020, when only symptomatic people were tested, and modeled ambient concentrations of PM10, PM2.5, NO 2 and O 3 at geocoded residential addresses. In long-term exposure analysis, we selected individuals who did not change residential address in 2017-2019 (1.7 million tests) and considered the average concentrations of PM10, PM2.5 and NO 2 in that period, and different sources of PM (industry, livestock, other agricultural activities, road traffic, other Dutch sources, foreign sources). In short-term exposure analysis, individuals not changing residential address in the two weeks before testing day (2.7 million tests) were included in the analyses, thus considering 1- and 2-week average concentrations of PM10, PM2.5, NO 2 and O 3 before testing day as exposure. Mixed-effects logistic regression analysis with adjustment for several confounders, including municipality and testing week to account for spatiotemporal variation in viral circulation, was used. Overall, there was no statistically significant effect of long-term exposure to the studied pollutants on the odds of testing positive vs. negative for SARS-CoV-2. However, significant positive associations of long-term exposure to PM10 and PM2.5 from specifically foreign and livestock sources, and to PM10 from other agricultural sources, were observed. Short-term exposure to PM10 (adjusting for NO 2 ) and PM2.5 were also positively associated with increased odds of testing positive for SARS-CoV-2. While these exposures seemed to increase COVID-19 risk relative to other respiratory diseases, the underlying biological mechanisms remain unclear. This study reinforces the need to continue to strive for better air quality to support public health., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors., Competing Interests: The authors declare no conflict of interest.

Although there is scientific evidence for an increased prevalence of sleep disorders during the coronavirus disease 2019 (COVID-19) pandemic, there is still limited information on how lifestyle factors might have affected sleep patterns. Therefore, we followed a large cohort of participants in the Netherlands (n = 5,420) for up to 1 year (September 2020-2021) via monthly Web-based questionnaires to identify lifestyle changes (physical activity, cigarette smoking, alcohol consumption, electronic device use, and social media use) driven by anti-COVID-19 measures and their potential associations with self-reported sleep (latency, duration, and quality). We used the Containment and Health Index (CHI) to assess the stringency of anti-COVID-19 measures and analyzed associations through multilevel ordinal response models. We found that more stringent anti-COVID-19 measures were associated with higher use of electronic devices (per interquartile-range increase in CHI, odds ratio (OR) = 1.47, 95% confidence interval (CI): 1.40, 1.53), less physical activity (OR = 0.94, 95% CI: 0.90, 0.98), lower frequency of alcohol consumption (OR = 0.63, 95% CI: 0.60, 0.66), and longer sleep duration (OR = 1.11, 95% CI: 1.05, 1.16). Lower alcohol consumption frequency and higher use of electronic devices and social media were associated with longer sleep latency. Lower physical activity levels and higher social media and electronic device use were related to poorer sleep quality and shorter sleep duration., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.)

Adverse health effects have been linked with exposure to livestock farms, likely due to airborne microbial agents. Accurate exposure assessment is crucial in epidemiological studies, however limited studies have modelled bioaerosols. This study used measured concentrations in air of livestock commensals (Escherichia coli (E. coli) and Staphylococcus species (spp.)), and antimicrobial resistance genes (tetW and mecA) at 61 residential sites in a livestock-dense region in the Netherlands. For each microbial agent, land use regression (LUR) and random forest (RF) models were developed using Geographic Information System (GIS)-derived livestock-related characteristics as predictors. The mean and standard deviation of annual average concentrations (gene copies/m 3 ) of E. coli, Staphylococcus spp., tetW and mecA were as follows: 38.9 (±1.98), 2574 (±3.29), 20991 (±2.11), and 15.9 (±2.58). Validated through 10-fold cross-validation (CV), the models moderately explained spatial variation of all microbial agents. The best performing model per agent explained respectively 38.4%, 20.9%, 33.3% and 27.4% of the spatial variation of E. coli, Staphylococcus spp., tetW and mecA. RF models had somewhat better performance than LUR models. Livestock predictors related to poultry and pig farms dominated all models. To conclude, the models developed enable enhanced estimates of airborne livestock-related microbial exposure in future epidemiological studies. Consequently, this will provide valuable insights into the public health implications of exposure to specific microbial agents., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Evidence on the public health relevance of exposure to livestock farm emissions is increasing. Research mostly focused on chemical air pollution, less on microbial exposure, while endotoxins are suggested relevant bacterial components in farm emissions. Acute respiratory health effects of short-term exposure to livestock-related air pollution has been shown for NH 3 and PM 10 , but has not yet been studied for endotoxin. We aimed to assess associations between lung function and short-term exposure to livestock farming emitted endotoxin in co-pollutant models with NH 3 and PM 10 ., Methods: In 2014/2015, spirometry was conducted in 2308 non-farming residents living in a rural area in the Netherlands. Residential exposure to livestock farming emitted endotoxin during the week prior to spirometry was estimated by dispersion modelling. The model was applied to geo-located individual barns within 10 km of each home address using provincial farm data and local hourly meteorological conditions. Regional week-average measured concentrations of NH 3 and PM 10 were obtained through monitoring stations. Lung function parameters (FEV 1 , FVC, FEV 1 /FVC, MMEF) were expressed in %-predicted value based on GLI-2012. Exposure-response analyses were performed by linear regression modelling., Results: Week-average endotoxin exposure was negatively associated with FVC, independently from regional NH 3 and PM 10 exposure. A 1.1% decline in FVC was estimated for an increase of endotoxin exposure from 10th to 90th percentile. Stratified analyses showed a larger decline (3.2%) for participants with current asthma and/or COPD. FEV 1 was negatively associated with week-average endotoxin exposure, but less consistent after co-pollutant adjustment. FEV 1 /FVC and MMEF were not associated with week-average endotoxin exposure., Conclusions: Lower lung function in non-farming residents was observed in relation to short-term residential exposure to livestock farming emitted endotoxin. This study indicates the probable relevance of exposure to microbial emissions from livestock farms considering public health besides chemical air pollution, necessitating future research incorporating both., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: All authors reports financial support was provided by Netherlands Ministry of Infrastructure and Water Management. All authors reports financial support was provided by Province of Noord-Brabant. All authors reports financial support was provided by Netherlands Ministry of Health Welfare and Sport. All authors reports financial support was provided by Netherlands Ministry of Economic Affairs. All authors reports financial support was provided by Lung Foundation Netherlands. Co-author Gerard Hoek is associate editor at Environmental Research., (Copyright © 2023 Utrecht University. Published by Elsevier Inc. All rights reserved.)

This longitudinal study aimed to assess the impact of COVID-19 containment measures on perceived health, health protective behavior and risk perception, and investigate whether chronic disease status and urbanicity of the residential area modify these effects. Participants (n = 5420) were followed for up to 14 months (September 2020-October 2021) by monthly questionnaires. Chronic disease status was obtained at baseline. Urbanicity of residential areas was assessed based on postal codes or neighborhoods. Exposure to containment measures was assessed using the Containment and Health Index (CHI). Bayesian multilevel-models were used to assess effect modification of chronic disease status and urbanicity by CHI. CHI was associated with higher odds for worse physical health in people with chronic disease (OR = 1.09, 95% credibility interval (CrI) = 1.01, 1.17), but not in those without (OR = 1.01, Crl = 0.95, 1.06). Similarly, the association of CHI with higher odds for worse mental health in urban dwellers (OR = 1.31, Crl = 1.23, 1.40) was less pronounced in rural residents (OR = 1.20, Crl = 1.13, 1.28). Associations with behavior and risk perception also differed between groups. Our study suggests that individuals with chronic disease and those living in urban areas are differentially affected by government measures put in place to manage the COVID-19 pandemic. This highlights the importance of considering vulnerable subgroups in decision making regarding containment measures., (© 2024. The Author(s).)

Methicillin-resistant strains of Staphylococcus aureus (MRSA) are resistant to most β-lactam antibiotics. Pigs are an important reservoir of livestock-associated MRSA (LA-MRSA), which is genetically distinct from both hospital and community-acquired MRSA. Occupational exposure to pigs on farms can lead to LA-MRSA carriage by workers. There is a growing body of research on MRSA found in the farm environment, the airborne route of transmission, and its implication on human health. This study aims to directly compare two sampling methods used to measure airborne MRSA in the farm environment; passive dust sampling with electrostatic dust fall collectors (EDCs), and active inhalable dust sampling using stationary air pumps with Gesamtstaubprobenahme (GSP) sampling heads containing Teflon filters. Paired dust samples using EDCs and GSP samplers, totaling 87 samples, were taken from 7 Dutch pig farms, in multiple compartments housing pigs of varying ages. Total nucleic acids of both types of dust samples were extracted and targets indicating MRSA (femA, nuc, mecA) and total bacterial count (16S rRNA) were quantified using quantitative real-time PCRs. MRSA could be measured from all GSP samples and in 94% of the EDCs, additionally MRSA was present on every farm sampled. There was a strong positive relationship between the paired MRSA levels found in EDCs and those measured on filters (Normalized by 16S rRNA; Pearson's correlation coefficient r = 0.94, Not Normalized; Pearson's correlation coefficient r = 0.84). This study suggests that EDCs can be used as an affordable and easily standardized method for quantifying airborne MRSA levels in the pig farm setting., (© The Author(s) 2023. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.)

Background: Although the association between living in the vicinity of a goat farm and the occurrence of pneumonia is well-documented, it is unclear whether the higher risk of pneumonia in livestock dense areas is season-specific or not. This study explored the temporal variation of the association between exposure to goat farms and the occurrence of pneumonia., Methods: A large population-based study was conducted in the Netherlands, based on electronic health records from 49 general practices, collected for a period of six consecutive years (2014-2019). Monthly incidence rates of pneumonia in a livestock dense area were compared with those of a control group (areas with low livestock density) both per individual year and cumulatively for the entire six-year period. Using individual estimates of livestock exposure, it was also examined whether incidence of pneumonia differed per month if someone lived within a certain radius from a goat farm, compared to residents who lived further away., Results: Pneumonia was consistently more common in the livestock dense area throughout the year, compared to the control area. Analyses on the association between the individual livestock exposure estimates and monthly pneumonia incidence for the whole six-year period, yielded a generally higher risk for pneumonia among people living within 500 m from a goat farm, compared to those living further away. Significant associations were observed for March (IRR 1.68, 95% CI 1.02-2.78), August (IRR 2.67, 95% CI 1.45-4.90) and September (IRR 2.52, 95% CI 1.47-4.32)., Conclusions: The increased occurrence of pneumonia in the vicinity of goat farms is not season-specific. Instead, pneumonia is more common in livestock dense areas throughout the year, including summer months., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Residential microbial composition likely contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor airborne dust bacterial and fungal microbiota and childhood LRTI in Ibadan, Nigeria. Ninety-eight children under the age of five years hospitalized with LRTI were recruited and matched by age (±3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants' homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a meta-barcoding approach using amplicons targeting simultaneously the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi in association with the SILVA and UNITE database respectively. A 100-unit change in house dust bacterial, but not fungal, richness (OR 1.06; 95%CI 1.03-1.10) and a 1-unit change in Shannon diversity (OR 1.92; 95%CI 1.28-3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p < 0.001, R 2  = 0.036) and fungal (PERMANOVA p < 0.001, R 2  = 0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001) was negatively associated with LRTI. Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Background: Occupational exposure to soluble chlorinated platinum (Pt) salts, commonly called chloroplatinates, is a known cause of Pt salt sensitisation (PSS) and occupational asthma. We aimed to model inhalable soluble Pt salts exposure levels based on measurements in precious metal refineries for use in a retrospective cohort study on PSS., Methods: Five platinum refineries located in the United Kingdom (3 sites), United States, and South Africa provided time weighted average inhalable soluble Pt salts exposure data, measured in 2,982 personal air samples over a 17-year period (2000-2016). We used a Bayesian hierarchical model to estimate geometric mean (GM) exposure levels for each refinery and job title over time., Results: The GM of measured exposure levels over all facilities was 92 ng/m3 with a geometric standard deviation (GSD) of 9.07. Facility-specific GMs ranged from 48 ng/m3 (GSD 15.3) to 242 ng/m3 (GSD 5.99). Exposure modelling showed that soluble Pt salts exposure levels declined approximately 10% per year in two of the five facilities, but there were no clear time trends in the other facilities. A priori specified exposure groups captured most of the between-jobs differences, which helps to accurately predict exposures for jobs with no measurement data available., Conclusions: We applied exposure modelling to estimate time, refinery, and job-specific soluble Pt salts exposures. A significant annual decline in exposure levels was observed in two of the five participating facilities. Modelled exposure levels can be linked to individual workers' job history for exposure-response analysis of PSS in an epidemiological study., (© The Author(s) 2023. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.)

Background: Previous studies, performed between 2009-2019, in the Netherlands observed an until now still unexplained increased risk for pneumonia among residents living close to goat farms. Since data were collected in the provinces Noord-Brabant and Limburg (NB-L), an area with relatively high air pollution levels and proximity to large industrial areas in Europe, the question remains whether the results are generalizable to other regions. In this study, a different region, covering the provinces Utrecht, Gelderland, and Overijssel (UGO) with a similar density of goat farms, was included to assess whether the association between goat farm proximity and pneumonia is consistently observed across the Netherlands., Methods: Data for this study were derived from the Electronic Health Records (EHR) of 21 rural general practices (GPs) in UGO, for 2014-2017. Multi-level analyses were used to compare annual pneumonia prevalence between UGO and data derived from rural reference practices ('control area'). Random-effects meta-analysis (per GP practice) and kernel analyses were performed to study associations of pneumonia with the distance between goat farms and patients' home addresses., Results: GP diagnoses of pneumonia occurred 40% more often in UGO compared to the control area. Meta-analysis showed an association at a distance of less than 500m (~70% more pneumonia compared to >500m) and 1000m (~20% more pneumonia compared to >1000m). The kernel-analysis for three of the four individual years showed an increased risk up to a distance of one or two kilometers (2-36% more pneumonia; 10-50 avoidable cases per 100,000 inhabitants per year)., Conclusions: The positive association between living in the proximity of goat farms and pneumonia in UGO is similar to the previously found association in NB-L. Therefore, we concluded that the observed associations are relevant for regions with goat farms in the entire country., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Lotterman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Objective: We aimed to assess SARS-CoV-2 contamination of air and surfaces to gain insight into potential occupational exposure in a large meat processing plant experiencing COVID-19 clusters. Methods: Oro-nasopharyngeal SARS-CoV-2 screening was performed in 76 workers. Environmental samples ( n = 275) including air, ventilation systems, sewage, and swabs of high-touch surfaces and workers' hands were tested for SARS-CoV-2 RNA by real-time quantitative polymerase chain reaction. Results: Twenty-seven (35.5%) of the (predominantly asymptomatic) workers tested positive with modest to low viral loads (cycle threshold ≥ 29.7). Six of 203 surface swabs, 1 of 12 personal air samples, and one of four sewage samples tested positive; other samples tested negative. Conclusions: Although one third of workers tested positive, environmental contamination was limited. Widespread SARS-CoV-2 transmission via air and surfaces was considered unlikely within this plant at the time of investigation while strict COVID-19 control measures were already implemented., Competing Interests: Conflict of interest: The authors are employed by the respective affiliations mentioned. The authors declare no conflicts of interest., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American College of Occupational and Environmental Medicine.)

Previous epidemiological studies demonstrated an increased risk of respiratory health effects in children and adults exposed to dampness or mold. This study investigated associations of quantitative indicators of indoor dampness and mold exposure with severe lower respiratory tract infections (LRTI) among children aged 1-59 months in Ibadan, Nigeria., Methods: In-home visits were conducted among 178 children hospitalized with LRTI matched by age (±3 months), sex, and geographical location with 180 community-based children without LRTI. Trained study staff evaluated the indoor environment using a standardized home walkthrough checklist and measured visible dampness and mold damage. Damp-moldy Index (DMI) was also estimated to quantify the level of exposure. Exposure-response relationships of dampness and mold exposure with severe LRTI were assessed using multivariable restricted cubic spline regression models adjusting for relevant child, housing, and environmental characteristics., Results: Severe LRTI cases were more often male than female (61.8%), and the overall mean (SD) age was 7.3 (1.35) months. Children exposed to dampness <0.3 m 2 (odds ratio [OR] = 2.11; 95% confidence interval [CI] = 1.05, 4.36), and between 0.3 and 1.0 m 2 (OR = 2.34; 95% CI = 1.01, 7.32), had a higher odds of severe LRTI compared with children not exposed to dampness. The restricted cubic spline showed a linear exposure-response association between severe LRTI and residential dampness ( P < 0.001) but a nonlinear relationship with DMI ( P = 0.01)., Conclusions: Residential dampness and DMI were exposure-dependently associated with higher odds of severe LRTI among under-five children. If observed relationships were causal, public health intervention strategies targeted at reducing residential dampness are critically important to mitigate the burden of severe LRTI among under-five children., Competing Interests: The authors declare that they have no conflict of interest with regard to the content of this report., (Copyright © 2023 The Authors. Published by Wolters Kluwer Health, Inc. on behalf of The Environmental Epidemiology. All rights reserved.)

Background: There is a growing interest in the impact of air pollution from livestock farming on respiratory health. Studies in adults suggest adverse effects of livestock farm emissions on lung function, but so far, studies involving children and adolescents are lacking., Objectives: To study the association of residential proximity to livestock farms and modelled particulate matter ≤10 μm (PM 10 ) from livestock farms with lung function in adolescence., Methods: We performed a cross-sectional study among 715 participants of the Dutch prospective PIAMA (Prevention and Incidence of Asthma and Mite Allergy) birth cohort study. Relationships of different indicators of residential livestock farming exposure (distance to farms, distance-weighted number of farms, cattle, pigs, poultry, horses and goats within 3 km; modelled atmospheric PM 10 concentrations from livestock farms) with forced expiratory volume in 1 s (FEV 1 ) and forced vital capacity (FVC) at age 16 were assessed by linear regression taking into account potential confounders. Associations were expressed per interquartile range increase in exposure., Results: Higher exposure to livestock farming was consistently associated with a lower FEV 1 , but not with FVC among participants living in less urbanized municipalities (<1500 addresses/km 2 , N = 402). Shorter distances of homes to livestock farms were associated with a 1.4% (0.2%; 2.7%) lower FEV 1 . Larger numbers of farms within 3 km and higher concentrations of PM 10 from livestock farming were associated with a 1.8% (0.8%, 2.9%) and 0.9% (0.4%,1.5%) lower FEV 1 , respectively., Conclusions: Our findings suggest that higher exposure to livestock farming is associated with a lower FEV 1 in adolescents. Replication and more research on the etiologic agents involved in these associations and the underlying mechanisms is needed., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Myrna MT de Rooij reports a relationship with NCOH (Netherlands Center for One Health) that includes: travel reimbursement. Gerard H. Koppelman reports a relationship with Netherlands Lung Foundation that includes: funding grants. Gerard H. Koppelman reports a relationship with ZonMw that includes: funding grants. Gerard H. Koppelman reports a relationship with Teva The Netherlands that includes: funding grants. Gerard H. Koppelman reports a relationship with GSK that includes: consulting or advisory and funding grants. Gerard H. Koppelman reports a relationship with Vertex that includes: funding grants. Gerard H. Koppelman reports a relationship with Ubbo Emmius foundation that includes: funding grants. Gerard H. Koppelman reports a relationship with European Union (H2020) that includes: funding grants. Gerard H. Koppelman reports a relationship with Pure IMS that includes: consulting or advisory. Gerard H. Koppelman reports a relationship with Sanofi that includes: consulting or advisory. Gerard H. Koppelman reports a relationship with Astra Zeneka that includes: consulting or advisory. Lidwien AM Smit reports a relationship with Ministry of Health, Welfare and Sport of the Netherlands that includes: funding grants. Lenny Hogerwerf reports a relationship with Ministry of Health, Welfare and Sport of the Netherlands that includes: funding grants. Lidwien AM Smit reports a relationship with Ministry of Agriculture, Nature and Food Quality of The Netherlands that includes: funding grants., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria., Methods: One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child's health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children., Results: Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44-4.97), TBC (aOR = 2.51, 95% CI 1.36-4.65), TFC (aOR = 2.75, 95% CI 1.54-4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08-3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55-5.79) were independently associated with LRTI risk among under-five children., Conclusions: This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols., (© 2022. The Author(s).)

Air pollution from livestock farms is known to affect respiratory health of patients with chronic obstructive pulmonary disease (COPD). The mechanisms behind this relationship, however, remain poorly understood. We hypothesise that air pollutants could influence respiratory health through modulation of the airway microbiome. Therefore, we studied associations between air pollution exposure and the oropharyngeal microbiota (OPM) composition of COPD patients and controls in a livestock-dense area. Oropharyngeal swabs were collected from 99 community-based (mostly mild) COPD cases and 184 controls (baseline), and after 6 and 12 weeks. Participants were non-smokers or former smokers. Annual average livestock-related outdoor air pollution at the home address was predicted using dispersion modelling. OPM composition was analysed using 16S rRNA-based sequencing in all baseline samples and 6-week and 12-week repeated samples of 20 randomly selected subjects (n = 323 samples). A random selection of negative control swabs, taken every sampling day, were also included in the downstream analysis. Both farm-emitted endotoxin and PM 10 levels were associated with increased OPM richness in COPD patients (p < 0.05) but not in controls. COPD case-control status was not associated with community structure, while correcting for known confounders (multivariate PERMANOVA p > 0.05). However, members of the genus Streptococcus were more abundant in COPD patients (Benjamini-Hochberg adjusted p < 0.01). Moderate correlation was found between ordinations of 20 subjects analysed at 0, 6, and 12 weeks (Procrustes r = 0.52 to 0.66; p < 0.05; Principal coordinate analysis of Bray-Curtis dissimilarity), indicating that the OPM is relatively stable over a 12 week period and that a single sample sufficiently represents the OPM. Air pollution from livestock farms is associated with OPM richness of COPD patients, suggesting that the OPM of COPD patients is susceptible to alterations induced by exposure to air pollutants., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Several domestic and wild animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Reported (sero)prevalence in dogs and cats vary largely depending on the target population, test characteristics, geographical location and time period. This research assessed the prevalence of SARS-CoV-2-positive cats and dogs (PCR- and/or antibody positive) in two different populations. Dogs and cats living in a household with at least one confirmed COVID-19-positive person (household (HH) study; 156 dogs and 152 cats) and dogs and cats visiting a veterinary clinic (VC) (VC study; 183 dogs and 140 cats) were sampled and tested for presence of virus (PCR) and antibodies. Potential risk factors were evaluated and follow-up of PCR-positive animals was performed to determine the duration of virus shedding and to detect potential transmission between pets in the same HH. In the HH study, 18.8% (27 dogs, 31 cats) tested SARS-CoV-2 positive (PCR- and/or antibody positive), whereas in the VC study, SARS-CoV-2 prevalence was much lower (4.6%; six dogs, nine cats). SARS-CoV-2 prevalence amongst dogs and cats was significantly higher in the multi-person HHs with two or more COVID-19-positive persons compared with multi-person HHs with only one COVID-19-positive person. In both study populations, no associations could be identified between SARS-CoV-2 status of the animal and health status, age or sex. During follow-up of PCR-positive animals, no transmission to other pets in the HH was observed despite long-lasting virus shedding in cats (up to 35 days). SARS-CoV-2 infection in dogs and cats appeared to be clearly associated with reported COVID-19-positive status of the HH. Our study supports previous findings and suggests a very low risk of pet-to-human transmission within HHs, no severe clinical signs in pets and a negligible pet-to-pet transmission between HHs., (© 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance., (© 2022. The Author(s).)

Animals like mink, cats and dogs are susceptible to SARS-CoV-2 infection. In the Netherlands, 69 out of 127 mink farms were infected with SARS-CoV-2 between April and November 2020 and all mink on infected farms were culled after SARS-CoV-2 infection to prevent further spread of the virus. On some farms, (feral) cats and dogs were present. This study provides insight into the prevalence of SARS-CoV-2-positive cats and dogs in 10 infected mink farms and their possible role in transmission of the virus. Throat and rectal swabs of 101 cats (12 domestic and 89 feral cats) and 13 dogs of 10 farms were tested for SARS-CoV-2 using PCR. Serological assays were performed on serum samples from 62 adult cats and all 13 dogs. Whole Genome Sequencing was performed on one cat sample. Cat-to-mink transmission parameters were estimated using data from all 10 farms. This study shows evidence of SARS-CoV-2 infection in 12 feral cats and 2 dogs. Eleven cats (18%) and two dogs (15%) tested serologically positive. Three feral cats (3%) and one dog (8%) tested PCR-positive. The sequence generated from the cat throat swab clustered with mink sequences from the same farm. The calculated rate of mink-to-cat transmission showed that cats on average had a chance of 12% (95%CI 10%-18%) of becoming infected by mink, assuming no cat-to-cat transmission. As only feral cats were infected it is most likely that infections in cats were initiated by mink, not by humans. Whether both dogs were infected by mink or humans remains inconclusive. This study presents one of the first reports of interspecies transmission of SARS-CoV-2 that does not involve humans, namely mink-to-cat transmission, which should also be considered as a potential risk for spread of SARS-CoV-2., (© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

SARS-CoV-2 outbreaks on 69 Dutch mink farms in 2020 were studied to identify risk factors for virus introduction and transmission and to improve surveillance and containment measures. Clinical signs, laboratory test results, and epidemiological aspects were investigated, such as the date and reason of suspicion, housing, farm size and distances, human contact structure, biosecurity measures, and presence of wildlife, pets, pests, and manure management. On seven farms, extensive random sampling was performed, and age, coat color, sex, and clinical signs were recorded. Mild to severe respiratory signs and general diseases such as apathy, reduced feed intake, and increased mortality were detected on 62/69 farms. Throat swabs were more likely to result in virus detection than rectal swabs. Clinical signs differed between virus clusters and were more severe for dark-colored mink, males, and animals infected later during the year. Geographical clustering was found for one virus cluster. Shared personnel could explain some cases, but other transmission routes explaining farm-to-farm spread were not elucidated. An early warning surveillance system, strict biosecurity measures, and a (temporary) ban on mink farming and vaccinating animals and humans can contribute to reducing the risks of the virus spreading and acquisition of potential mutations relevant to human and animal health.

Background: Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains., Objectives: We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed., Methods: A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3')-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman's rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data., Results: ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains ('farm to fork') was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman's ρ > 0.7) between qPCR data and metagenomic data of pooled samples., Conclusions: qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure., (© The Author(s) 2022. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Purpose: Industrial food animal production accounts for most animal-source protein consumed in the USA. These operations rely on an array of external inputs, which can include antimicrobials of medical importance. The use of these drugs in this context has been the subject of public health debate for decades because their widespread use contributes to the selection for and proliferation of drug-resistant bacteria and their genetic determinants. Here, we describe legislative and regulatory efforts, at different levels of governance in the USA, to curtail food animal consumption of medically important antimicrobials., Recent Findings: The features and relative success of the US efforts are examined alongside those of selected member states (Denmark and the Netherlands) of the European Union. Evaluation of efforts at all levels of US governance was complicated by shortcomings in prescribed data collection; nevertheless, available information suggests deficiencies in policy implementation and enforcement compromise the effectiveness of interventions pursued to date. The political will, robust systems for collecting and integrating data on antimicrobial consumption and use, and cross-sectoral collaboration that have been integral to the success of efforts in Denmark and The Netherlands have been notably absent in the USA, especially at the federal level., (© 2022. The Author(s).)

Objectives: The occurrence and zoonotic potential of antimicrobial resistance (AMR) in pigs and broilers has been studied intensively in past decades. Here, we describe AMR levels of European pig and broiler farms and determine the potential risk factors., Methods: We collected faeces from 181 pig farms and 181 broiler farms in nine European countries. Real-time quantitative PCR (qPCR) was used to quantify the relative abundance of four antimicrobial resistance genes (ARGs) [aph(3')-III, erm(B), sul2 and tet(W)] in these faeces samples. Information on antimicrobial use (AMU) and other farm characteristics was collected through a questionnaire. A mixed model using country and farm as random effects was performed to evaluate the relationship of AMR with AMU and other farm characteristics. The correlation between individual qPCR data and previously published pooled metagenomic data was evaluated. Variance component analysis was conducted to assess the variance contribution of all factors., Results: The highest abundance of ARG was for tet(W) in pig faeces and erm(B) in broiler faeces. In addition to the significant positive association between corresponding ARG and AMU levels, we also found on-farm biosecurity measures were associated with relative ARG abundance in both pigs and broilers. Between-country and between-farm variation can partially be explained by AMU. Different ARG targets may have different sample size requirements to represent the overall farm level precisely., Conclusions: qPCR is an efficient tool for targeted assessment of AMR in livestock-related samples. The AMR variation between samples was mainly contributed to by between-country, between-farm and within-farm differences, and then by on-farm AMU., (© The Author(s) 2022. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Background: There is increasing evidence of associations between residential proximity to livestock farms and respiratory morbidity, but less is known about potential effects on respiratory mortality among residents., Objectives: We aimed to assess potential associations between respiratory mortality and residential proximity to (intensive) livestock farming., Methods: In DUELS, a national census-based cohort, we selected all inhabitants from rural and semi-urban areas of the Netherlands, aged ≥30 years and living at the same address for five years up to baseline (2004). We followed these ∼4 million individuals for respiratory mortality (respiratory system diseases, chronic lower respiratory diseases, pneumonia) from 2005 to 2012. We computed the average number of cattle, pigs, chicken, and mink present in 500 m, 1000 m, 1500 m and 2000 m of each individual's residence in the period 1999-2003. Analyses were conducted using Cox proportional hazards regression, adjusting for potential confounders at individual and neighbourhood level., Results: We found evidence that living up to 2000 m of pig farms was associated with respiratory mortality, namely from chronic lower respiratory diseases, with Hazard Ratios ranging from 1.06 (1.02, 1.10) in people living close to low numbers (

Assays to measure SARS-CoV-2-specific neutralizing antibodies are important to monitor seroprevalence, to study asymptomatic infections and to reveal (intermediate) hosts. A recently developed assay, the surrogate virus-neutralization test (sVNT) is a quick and commercially available alternative to the "gold standard" virus neutralization assay using authentic virus, and does not require processing at BSL-3 level. The assay relies on the inhibition of binding of the receptor binding domain (RBD) on the spike (S) protein to human angiotensin-converting enzyme 2 (hACE2) by antibodies present in sera. As the sVNT does not require species- or isotype-specific conjugates, it can be similarly used for antibody detection in human and animal sera. In this study, we used 298 sera from PCR-confirmed COVID-19 patients and 151 sera from patients confirmed with other coronavirus or other (respiratory) infections, to evaluate the performance of the sVNT. To analyze the use of the assay in a One Health setting, we studied the presence of RBD-binding antibodies in 154 sera from nine animal species (cynomolgus and rhesus macaques, ferrets, rabbits, hamsters, cats, cattle, mink and dromedary camels). The sVNT showed a moderate to high sensitivity and a high specificity using sera from confirmed COVID-19 patients (91.3% and 100%, respectively) and animal sera (93.9% and 100%), however it lacked sensitivity to detect low titers. Significant correlations were found between the sVNT outcomes and PRNT 50 and the Wantai total Ig and IgM ELISAs. While species-specific validation will be essential, our results show that the sVNT holds promise in detecting RBD-binding antibodies in multiple species., Competing Interests: The authors declare that there is no conflict of interest., (© 2021 The Author(s).)

Objective: Unprecedented SARS-CoV-2 infections in farmed minks raised immediate concerns regarding transmission to humans and initiated intensive environmental investigations to assess occupational and environmental exposure., Methods: Air sampling was performed at infected Dutch mink farms, at farm premises and at nearby residential sites. A range of other environmental samples were collected from minks' housing units, including bedding materials. SARS-CoV-2 RNA was analysed in all samples by quantitative PCR., Results: Inside the farms, considerable levels of SARS-CoV-2 RNA were found in airborne dust, especially in personal inhalable dust samples (approximately 1000-10 000 copies/m 3 ). Most of the settling dust samples tested positive for SARS-CoV-2 RNA (82%, 75 of 92). SARS-CoV-2 RNA was not detected in outdoor air samples, except for those collected near the entrance of the most recently infected farm. Many samples of minks' housing units and surfaces contained SARS-CoV-2 RNA., Conclusions: Infected mink farms can be highly contaminated with SARS-CoV-2 RNA. This warns of occupational exposure, which was substantiated by considerable SARS-CoV-2 RNA concentrations in personal air samples. Dispersion of SARS-CoV-2 to outdoor air was found to be limited and SARS-CoV-2 RNA was not detected in air samples collected beyond farm premises, implying a negligible risk of environmental exposure to nearby communities. Our occupational and environmental risk assessment is in line with whole genome sequencing analyses showing mink-to-human transmission among farm workers, but no indications of direct zoonotic transmission events to nearby communities., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

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., (© 2021. The Author(s).)

Prior regional studies found a high risk of pneumonia for people living close to poultry and goat farms. This epidemiological study in the Netherlands used nationwide antibiotic prescription data as a proxy for pneumonia incidence to investigate whether residents of areas with poultry and goat farms use relatively more antibiotics compared to areas without such farms. We used prescription data on antibiotics most commonly prescribed to treat pneumonia in adults and livestock farming data, both with nationwide coverage. Antibiotic use was expressed as defined daily doses per (4-digit Postal Code (PC4) area)-(age group)-(gender)-(month) combination for the year 2015. We assessed the associations between antibiotic use and farm exposure using negative binomial regression. The amoxicillin, doxycycline, and co-amoxiclav use was significantly higher (5-10% difference in use) in PC4 areas with poultry farms present compared to areas without, even after adjusting for age, gender, smoking, socio-economic status, and goat farm presence. The adjusted models showed no associations between antibiotic use and goat farm presence. The variables included in this study could only partly explain the observed regional differences in antibiotic use. This was an ecological study that precludes inference about causal relations. Further research using individual-level data is recommended.

Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing ( n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB , tetW , sul2 , and aph3'-III ; ( n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) ( n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.

Background: Despite the recognition of the importance of indoor microbial exposures on children's health, the role of different microbial agents in development and aggravation of respiratory symptoms and diseases is only poorly understood. This study aimed to assess whether exposure to microbial aerosols within the indoor environment are associated with respiratory symptoms among children under-5 years of age., Methods: A systematic literature search was conducted on PubMed, Web of Science, GreenFILE, ScienceDirect, EMBASE and Cochrane library through February 2020. Studies that investigated the exposure-response relationship between components of the indoor microbial communities and respiratory symptoms among under-five children were eligible for inclusion. A random-effect meta-analysis was applied to estimate pooled relative risk (RR) and 95% confidence interval (CI) for study specific high versus low microbial exposures. The potential effect of individual studies on the overall estimate was evaluated using leave-one-out analysis, while heterogeneity was evaluated by I 2 statistics using RevMan 5.3., Results: Fifteen studies were eligible for inclusion in a meta-analysis. The pooled risk estimate suggested that increased microbial exposure was associated with an increased risk of respiratory symptoms [pooled relative risk (RR): 1.24 (1.09, 1.41), P = 0.001]. The association was strongest with exposure to a combination of Aspergillus, Penicillium, Cladosporium and Alternaria species [pooled RR: 1.73 (1.30, 2.31), P = 0.0002]. Stratified analysis revealed an increased risk of wheeze [pooled RR: 1.20 (1.05, 1.37), P = 0.007 and allergic rhinitis [RR: 1.18 (0.94, 1.98), P = 0.16] from any microbial exposure., Conclusions: Microbial exposures are, in general, associated with risk of respiratory symptoms. Future studies are needed to study the indoor microbiome more comprehensively, and to investigate the mechanism of these associations.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect many animal species, including minks, cats, and dogs. To gain insights into SARS-CoV-2 infections in cats and dogs, we developed and validated a set of serologic assays, including ELISA and virus neutralization. Evaluation of samples from animals before they acquired coronavirus disease and samples from cats roaming SARS-CoV-2-positive mink farms confirmed the suitability of these assays for specific antibody detection. Furthermore, our findings exclude SARS-CoV-2 nucleocapsid protein as an antigen for serologic screening of cat and dog samples. We analyzed 500 serum samples from domestic cats and dogs in the Netherlands during April-May 2020. We showed 0.4% of cats and 0.2% of dogs were seropositive. Although seroprevalence in cats and dogs that had unknown SARS-CoV-2 exposure was low during the first coronavirus disease wave, our data stress the need for development of continuous serosurveillance for SARS-CoV-2 in these 2 animal species.

We report the genome sequence of a Minacovirus strain identified from a fecal sample from a farmed mink ( Neovison vison ) in The Netherlands that was tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using real-time PCR (RT-PCR). The viral genome sequence was obtained using agnostic deep sequencing., (Copyright © 2021 Kwok et al.)

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., (Copyright © 2021, American Association for the Advancement of Science.)

Objectives: The aim of this study is to assess whether medication use for obstructive airway diseases is associated with environmental exposure to livestock farms. Previous studies in the Netherlands at a regional level suggested that asthma and chronic obstructive pulmonary disease (COPD) are less prevalent among persons living near livestock farms., Methods: A nationwide population-based cross-sectional study was conducted among 7,735,491 persons, with data on the dispensing of drugs for obstructive airway diseases in the Netherlands in 2016. Exposure was based on distances between home addresses and farms and on modelled atmospheric particulate matter (PM 10 ) concentrations from livestock farms. Data were analysed for different regions by logistic regression analyses and adjusted for several individual-level variables, as well as modelled PM 10 concentration of non-farm-related air pollution. Results for individual regions were subsequently pooled in meta-analyses., Results: The probability of medication for asthma or COPD being dispensed to adults and children was lower with decreasing distance of their homes to livestock farms, particularly cattle and poultry farms. Increased concentrations of PM 10 from cattle were associated with less dispensing of medications for asthma or COPD, as well (meta-analysis OR for 10th-90th percentile increase in concentration of PM 10 from cattle farms, 95%CI: 0.92, 0.86-0.97 for adults). However, increased concentrations of PM 10 from non-farm sources were positively associated (meta-analysis OR for 10th-90th percentile increase in PM 10 -concentration, 95%CI: 1.29, 1.09-1.52 for adults)., Conclusions: The results show that the probability of dispensing medication for asthma or COPD is inversely associated with proximity to livestock farms and modelled exposure to livestock-related PM 10 in multiple regions within the Netherlands. This finding implies a notable prevented risk: under the assumption of absence of livestock farms in the Netherlands, an estimated 2%-5% more persons (an increase in tens of thousands) in rural areas would receive asthma or COPD medication., (Copyright © 2020 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Background: High antimicrobial use (AMU) and antimicrobial resistance (AMR) in veal calves remain a source of concern. As part of the EFFORT project, the association between AMU and the abundance of faecal antimicrobial resistance genes (ARGs) in veal calves in three European countries was determined., Methods: In 2015, faecal samples of veal calves close to slaughter were collected from farms located in France, Germany and the Netherlands (20 farms in France, 20 farms in the Netherlands and 21 farms in Germany; 25 calves per farm). Standardized questionnaires were used to record AMU and farm characteristics. In total, 405 faecal samples were selected for DNA extraction and quantitative polymerase chain reaction to quantify the abundance (16S normalized concentration) of four ARGs [aph(3')-III, ermB, sul2 and tetW] encoding for resistance to frequently used antimicrobials in veal calves. Multiple linear mixed models with random effects for country and farm were used to relate ARGs to AMU and farm characteristics., Results: A significant positive association was found between the use of trimethoprim/sulfonamides and the concentration of sul2 in faeces from veal calves. A higher weight of calves on arrival at the farm was negatively associated with aph(3')-III and ermB. Lower concentrations of aph(3')-III were found at farms with non-commercial animals present. Furthermore, farms using only water for the cleaning of stables had a significantly lower abundance of faecal ermB and tetW compared with other farms., Conclusion: A positive association was found between the use of trimethoprim/sulfonamides and the abundance of sul2 in faeces in veal calves. Additionally, other relevant risk factors associated with ARGs in veal calves were identified, such as weight on arrival at the farm and cleaning practices., (Copyright © 2020 Elsevier Ltd and International Society of Antimicrobial Chemotherapy. All rights reserved.)

Background: By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.e. pig and poultry farmers, employees and family members and pig slaughterhouse workers) and a control population (Lifelines cohort) in the Netherlands. In addition, we sought to identify determinants for the human resistome and bacteriome composition by applying a combination of multivariate (NMDS, PERMANOVA, SIMPER and DESeq2 analysis) and multivariable regression analysis techniques., Results: Pig slaughterhouse workers and pig farmers carried higher total ARG abundances in their stools compared to broiler farmers and control subjects. Tetracycline, β-lactam and macrolide resistance gene clusters dominated the resistome of all studied groups. No significant resistome alpha diversity differences were found among the four populations. However, the resistome beta diversity showed a separation of the mean resistome composition of pig and pork exposed workers from broiler farmers and controls, independent of their antimicrobial use. We demonstrated differences in resistome composition between slaughter line positions, pig versus poultry exposed workers, as well as differences between farmers and employees versus family members. In addition, we found a significant correlation between the bacteriome and resistome, and significant differences in the bacteriome composition between and within the studied subpopulations. Finally, an in-depth analysis of pig and poultry farms - of which also farm livestock resistomes were analysed - showed positive associations between the number of on-farm working hours and human faecal AMR loads., Conclusion: We found that the total normalized faecal ARG carriage was larger in persons working in the Dutch pork production chain compared to poultry farmers and controls. Additionally, we showed significant differences in resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. The number of on-farm working hours and the farm type (pig or broiler) that persons live or work on are determinants for the human faecal resistome. Overall, our results may suggest direct or indirect livestock contact as a determinant for human ARG carriage. Future studies should further focus on the connection between the human and livestock resistome (i.e. transmission routes) to substantiate the evidence for livestock-associated resistome acquisition., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust., Objectives: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored., Methods: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool., Results: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study., Conclusion: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The aim of this study was to gain more insight in the association between prevalence of diverse acute non-specific symptoms (NSS) and livestock density as a possible risk factor among residents of livestock-dense and non-dense regions, taking into account socio-demographic factors and psychological morbidity. Prevalence of NSS and psychological morbidity were assessed for the year 2017, based on electronic health records from 39 general practices in the Netherlands. The study group consisted of people who lived in rural areas with high numbers of livestock (n = 74093), while the control group included people in rural areas with low numbers of livestock (n = 50139). For a large portion of the study group, exposure estimates (to livestock) were calculated. Multiple logistic multilevel regression analyses were performed. Two methods were used: 1) area comparisons between study and control areas in relation to health problems, and 2) estimates of livestock exposure (to goats, poultry, pigs, and cattle) within the study area. It was found that prevalence of diarrhea, headache, sleep disturbance, respiratory symptoms, and skin problems were higher in the study group. The data suggest that there may be a protective effect of livestock exposure: in general, there was a lower risk of NSS closer to livestock (within the exposure analyses). The study suggests that the previously identified higher risk of respiratory health problems in livestock dense areas might also apply to the prevalence of various other NSS. Longitudinal research taking into account different or more individual and contextual characteristics could possibly elucidate why prevalence of NSS in closer proximity to livestock is lower compared to people who live further away, whilst a more overarching analysis indicated that living in livestock dense areas was associated with more NSS., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

SARS-CoV-2, the causative agent of COVID-19, caused respiratory disease outbreaks with increased mortality in 4 mink farms in the Netherlands. The most striking postmortem finding was an acute interstitial pneumonia, which was found in nearly all examined mink that died at the peak of the outbreaks. Acute alveolar damage was a consistent histopathological finding in mink that died with pneumonia. SARS-CoV-2 infections were confirmed by detection of viral RNA in throat swabs and by immunohistochemical detection of viral antigen in nasal conchae, trachea, and lung. Clinically, the outbreaks lasted for about 4 weeks but some animals were still polymerase chain reaction-positive for SARS-CoV-2 in throat swabs after clinical signs had disappeared. This is the first report of the clinical and pathological characteristics of SARS-CoV-2 outbreaks in mink farms.

A nationwide study on the occurrence of extended-spectrum β-lactamase (ESBL)/AmpC in nonhospitalized horses in the Netherlands was performed. Molecular characterization was done, and questionnaires were analyzed to identify factors associated with carriage. In total, 796 horse owners were approached; 281 of these submitted a fecal sample from their horse(s), resulting in 362 samples. All samples were cultured qualitatively in Luria-Bertani (LB) broth and subsequently on MacConkey agar, both supplemented with 1 mg/liter cefotaxime (LB+ and MC+). Positive samples were subsequently cultured quantitatively on MC+. Initial extended-spectrum-β-lactamase (ESBL)/AmpC screening was performed by PCR, followed by whole-genome sequencing on selected strains. Associations between ESBL/AmpC carriage and questionnaire items were analyzed using a univariate generalized estimating equation (GEE) regression analysis, followed by a multiple GEE model for relevant factors. In total, 39 of 362 samples (11%) were determined to be positive for ESBL/AmpC. bla CTX-M-1 -carrying isolates were obtained from 77% of positive samples ( n  = 30). Other ESBL/AmpC genes observed included bla CTX-M-2 , bla CTX-M-14 , bla CTX-M-15 , bla CTX-M-32 , bla SHV-12 , bla CMY-2 , and bla ACT-10 A high association between the presence of bla CTX-M-1 and IncHI1 plasmids was observed (46% of samples; n  = 18). Based on core genome analysis ( n  = 48 isolates), six Escherichia coli clusters were identified, three of which represented 80% of the isolates. A negative association between ESBL/AmpC carriage and horses being in contact with other horses at a different site was observed. The presence of a dog on the premises and housing in a more densely human-populated region were positively associated. IMPORTANCE Extended-spectrum β-lactamases (ESBLs) are widespread in human and animal populations and in the environment. Many different ESBL variants exist. The dissemination of ESBLs within and between populations and the environment is also largely influenced by genetic mobile elements (e.g., plasmids) that facilitate spread of these ESBLs. In order to identify potential attributable ESBL sources for, e.g., the human population, it is important to identify the different ESBL variants, the bacteria carrying them, and the potential risk factors for ESBL carriage from other potential sources. This nationwide study focuses on ESBL carriage in the open horse population and investigated the molecular characteristics, geographical distribution throughout the Netherlands, and potential risk factors for fecal ESBL carriage in horses. These data can be used for future attribution studies in order to reduce potential transmission of ESBL-producing bacteria between sources., (Copyright © 2020 American Society for Microbiology.)

The association between household air pollution and lower respiratory tract infections (LRTI) among children under five years of age has been well documented; however, the extent to which the microbiome within the indoor environment contributes to this association is uncertain. The home assessment of indoor microbiome (HAIM) study seeks to assess the abundance of indoor microbiota (IM) in the homes of under-five children (U-5Cs) with and without LRTI. HAIM is a hospital- and community-based study involving 200 cases and 200 controls recruited from three children's hospitals in Ibadan, Nigeria. Cases will be hospital-based patients with LRTI confirmed by a pediatrician, while controls will be community-based participants, matched to cases on the basis of sex, geographical location, and age (±3 months) without LRTI. The abundance of IM in houses of cases and controls will be investigated using active and passive air sampling techniques and analyzed by qualitative detection of bacterial 16SrRNA gene (V3-V4), fungal ITS1 region, and viral RNA sequencing. HAIM is expected to elucidate the relationship between exposure to IM and incidence of LRTI among U-5Cs and ultimately provide evidence base for strategic interventions to curtail the burgeoning burden of LRTI on the subcontinent.

Living close to livestock farms has been associated with increased symptoms in patients with chronic obstructive pulmonary disease (COPD). The causes of these effects are still poorly understood. This panel study attempts to assess the acute effects of livestock-related air pollution in patients with COPD living in an area with intensive livestock farming in the Netherlands. Between February 2015 and July 2016, 82 participants took spirometry measurements twice daily (morning and evening) during a 3-month period, resulting in 12,672 FEV 1 and PEF records. Participants also kept a diary on respiratory symptoms as well as livestock-related odor annoyance. Daily average ammonia (NH 3 ) (a proxy for livestock-related air pollution) and fine particulate matter (PM 10 ) levels were collected from monitoring stations in the area. Lung function was analyzed as decrements of >10% and >20% from their median as well as absolute values. Self-reported odor annoyance was analyzed as a dichotomous variable. All analyses were done using generalized estimated equations. We adjusted for humidity, temperature, linear trend, and took multiple testing into account. We found an odds ratio of 1.14 95%CI [1.05; 1.25] for decrements >20% in morning FEV 1 per interquartile range (12 µg/m 3 ) increase in NH 3 concentration (lag 2). Odor annoyance was negatively associated with evening PEF (-4.46 l/min 95%CI [-7.59; -1.33]). Sensitivity analyses showed a stronger effect in participants with worse baseline lung function. No associations with symptoms were found. Our results show acute effects of livestock-related air pollution on lung function in COPD patients living in close proximity to livestock farms., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)