Detection of mcr-1-1 Positive Enteropathogenic Escherichia coli Isolates Associated with Post-Weaning Diarrhoea in an Organic Piglet-Producing Farm in Austria.

Postweaning diarrhoea (PWD) is a frequent multifactorial disease occurring in swine stocks worldwide. Since pathogenic Escherichia (E.) coli play a pivotal role in the pathogenesis of PWD and porcine E. coli are often resistant to different antibiotics, colistin is frequently applied to treat piglets with PWD. However, the application of colistin to livestock has been associated with the emergence of colistin resistance. This case report describes the detection of the colistin resistance gene mcr-1-1 in two E. coli isolated from piglets with PWD in an Austrian organic piglet-producing farm, which was managed by two farmers working as nurses in a hospital. Both mcr-1-positive E. coli were further analysed by Illumina short-read-sequencing, including assemblies and gene prediction. Both isolates belonged to the same clonal type and were positive for eaeH and espX5, which are both virulence genes associated with enteropathogenic E. coli (EPEC). Due to the detection of mcr-1-positive EPEC and based on the results of the antimicrobial resistance testing, the veterinarian decided to apply gentamicin for treatment instead of colistin, leading to improved clinical signs. In addition, after replacing faba beans with whey, PWD was solely observed in 2/10 weaned batches in the consecutive months.

Comparison of Lipid Properties and Cadmium and Lead Content in Red Deer (Cervus elaphus) Meat from Three Feeding Grounds.

The aim of the study was to compare the properties of lipids and the content of cadmium and lead in the meat of red deer (Cervus elaphus) kept in a forest feeding ground (FFG) and on organic and conventional farms in Poland. Longissimus lumborum (LL) and Musculus semimembranosus (SM) muscles were collected for the study from 36 red deer carcasses in an equal sex and age ratio (3 and 4 years old). From April to October, the animals consumed only the vegetation growing in the feeding grounds. The floristic and phytoncide composition, as well as the fodder value, of the feeding grounds were assessed. Additionally, the intramuscular fat and cholesterol content, the profile, sum, and ratios of fatty acids (FAs), lipid nutraceutical parameters, and cadmium and lead content were determined in LL and SM. The plant composition comprised 116 species in the organic feeding ground (OFG) and 78 species in the conventional feeding ground (CFG). The LL and SM muscles of the red deer from the organic and forest feeding grounds exhibited significantly lower amounts of fat and cholesterol than those from the conventional system. The differences in the fatty acid composition between the three groups were quite small. Differences in intramuscular fat content contributed to a higher percentage of PUFAs in the FFG and OFG, in comparison to the CFG. In all types of feeding ground, the cadmium (0.002 to 0.008 mg/kg) and lead (0.009 to 0.019 mg/kg) content determined in the meat did not pose a threat to consumers.

Plant Microbial Biostimulants as a Promising Tool to Enhance the Productivity and Quality of Carrot Root Crops.

The interest in studies focused on applying probiotic microorganisms is increasing due to sustainable agriculture development. In this research, we aimed to evaluate the impact of two commercial plant probiotics-ProbioHumus and NaturGel on carrot growth, yield, and quality in organic and nonorganic production systems. The research was carried out under laboratory and field conditions. Plants were treated with probiotics (2 L/ha) at the nine leaves stage. Biometrical measurements and chemical analyses were performed at a maturation stage. The average weight of carrot roots increased by 17 and 20 g in the test variant with ProbioHumus as compared to the control in the organic and nonorganic farms, respectively. Plant microbial biostimulants ProbioHumus and NaturGel had a positive effect on the quality of carrots from organic and nonorganic farms: applied in couple they promoted the accumulation of monosaccharides, ascorbic acid, carotenoids, phenols, and increased antioxidant activity. Quantitative nitrate analysis regardless of the biostimulant used revealed about twofold lower nitrate content of carrots from organic than nonorganic farms, and probiotics did not show a significant effect on nitrate accumulation. Finally, ProbioHumus and NaturGel were effective at low doses. The use of microbial biostimulants can be recommended as an element of cultivation for creating ecologically friendly technologies.

Design and implementation of a survey quantifying winter housing and bedding types used on Vermont organic dairy farms.

We conducted a descriptive observational study to quantify the frequency and diversity of winter housing and bedding types used by organic dairy farmers in Vermont. This report describes the survey methods, results, successes, limitations, and lessons learned from administering the survey. Beginning in December 2018, a short questionnaire was administered by web, mail, and telephone to a source population defined as all producers of organic dairy cow milk in Vermont (n = 177) listed in the United States Department of Agriculture Organic Integrity database. Our approach yielded an 82% (n = 145) response from certified organic farms producing cow milk in Vermont at the time of the survey. The 3 most common housing and bedding material combinations used by respondents were tiestall housing with wood (sawdust or shavings) bedding materials (45%), freestall housing with wood bedding materials (14%), and freestall housing with sand bedding (12%). Fifteen percent of respondents reported using more than one type of facility for winter housing of lactating cattle. The median number of lactating cows on farms among respondents was 59.5 (range: 2-400), and the odds of using more than one type of facility to house lactating cows increased positively with the number of lactating cows reported for a herd. Breed distribution was similar across the housing and bedding type categories. An association between frequency of individual cow milk somatic cell count testing and housing type was identified; respondents using freestall sand facilities tested less frequently than respondents using tiestalls with wood bedding. Although the questionnaire length limited the amount of information gathered, the response proportion was exceptional, and overall our survey results provide valuable insight on Vermont organic dairy housing and bedding practices that should inform future extension and outreach efforts for this sector of the dairy industry.

A Case of Infectious Laryngotracheitis in an Organic Broiler Chicken Farm in Greece.

Infectious laryngotracheitis is an economically significant viral disease of chickens, that mainly affects the upper respiratory tract, and is present worldwide. This case reports the first outbreak of infectious laryngotracheitis in a four-week-old organic broiler farm and surrounding flocks in Greece, with typical clinical symptoms and lesions, allegedly provoked by a wild strain of infectious laryngotracheitis virus. Our findings contradict the general perception indicating that the disease appears mainly in older birds and that vaccine strains are the primary cause of infectious laryngotracheitis outbreaks in most continents. A recombinant vectored vaccine was administered, supplementary to biosecurity measures, containing the viral spread. The responsible strain was potentially circulating in the area; therefore, an industry-wide holistic approach was applied, including the vaccination of neighboring broilers and breeders with the same vaccine, the rapid molecular diagnosis of the disease, and strict biosecurity protocols. The results of this holistic effort were effective because, following the application of vaccine and management protocols, manifestations of the disease in regional flocks dropped significantly, and there was no recurrence to date. These findings suggest that vaccination protocols should be modified, especially for organic broilers, to include vaccination against infectious laryngotracheitis.

Data set of smallholder farm households in banana-coffee-based farming systems containing data on farm households, agricultural production and use of organic farm waste.

The data was collected in the Karagwe and Kyerwa districts of the Kagera region in north-west Tanzania. It encompasses 150 smallholder farming households, which were interviewed on the composition of their household, agricultural production and use of organic farm waste. The data covers the two previous rainy seasons and the associated vegetation periods between September 2016 and August 2017. The knowledge of experts from the following institutions was included in the discussion on the selection criteria: two local non-profit organisations, i.e., WOMEDA and the MAVUNO Project; the International Institute of Tropical Agriculture (IITA); and the National Land Use Planning Commission (NLUPC). Households were selected for inclusion if all of the following applied to them: 1) less than 10 acres of land (4.7 ha) registered in the village offices, 2) no agricultural training, and 3) decline in the fertility of their land since they started farming (self-reported). We selected 150 smallholder households out of a pool of 5,000 households known to WOMEDA in six divisions of the Kyerwa and Karagwe districts. The questionnaire contained 54 questions. The original language of the survey was Kiswahili. All interviews were audio recorded. The answers were digitalised and translated into English. The data set contains the raw data with 130 quantitative and qualitative variables. For quantitative variables, the only analysis that was made was the conversion of units, e.g., land area was converted from acres to hectares, harvest from buckets to kilograms and then to tons, and heads of livestock to Tropical Livestock Units (TLU). Qualitative variables were summarised into categories. All data has been anonymised. The data set includes geographical variables, household information, agricultural information, gender-specific responsibilities, economic data, farm waste management, and water, energy and food availability (Water-Energy-Food (WEF) Nexus). Variables are written in italics. The following geographical variables are part of the data set: district, division, ward, village, hamlet, longitude, latitude, and altitude. Household information includes start of farming, household size, gender and age of household members. Agricultural information includes land size, size of homegarden, crops, livestock and livestock keeping, trees, and access to forest. Gender-specific responsibilities includes producing and exchanging seeds, weed control, terracing, distributing organic material to the fields, care of annual and perennial crops, harvesting of crops, decisions about the harvest and animal products, selling and buying products, working on their own farm and off-farm, cooking, storing food, collecting and caring for drinking water, washing, and toilet cleaning. Economic data includes distance to the market, journey time to market, transport methods, labourers employed by the household, working off-farm, and assets such as type of house. Variables relevant to the WEF Nexus are drinking water source and treatment, meals per day, months without food, cooking fuel, and type of toilet. Variables on farm waste management are the use of crop residues, food and kitchen waste, livestock manure, cooking ash, animal bones, and human urine and faeces. The data can be potentially reused and further developed for the purpose of agricultural production analysis, socio-economic analysis, comparison to other regions, conceptualisation of waste and nutrient management, establishment of land use concepts, and further analysis on food security and healthy diets.

Bacteriocin production by Leuconostoc citreum ST110LD isolated from organic farm soil, a promising biopreservative.

AIMS: The objective of this study was to isolate a bacteriocin-producing strain and to characterize the expressed bacteriocin for the control of Listeria monocytogenes with aim of biopreservation application. METHODS AND RESULTS: Soil samples from a Korean organic farm were subjected to microbiological analysis for isolation of potential bacteriocinogenic LAB, based on a three-level approach, using L. monocytogenes ATCC 15313 as an indicator test micro-organism. From a total of 17 isolates with inhibitory potential, seven were confirmed to be bacteriocin producers. The selected isolates were differentiated based on their morphology, catalase reaction, sugar fermentation profile obtained by API50CHL and by RAPD-PCR generating two unique profiles. One of the isolates, ST110LD, a specific strong producer of anti-Listeria bacteriocins (12 800 AU ml-1 ) was identified as Leuconostoc citreum. The proteinaceous nature of the inhibitory compound produced by Leuc. citreum ST110LD was confirmed through treatment with pepsin and α-chymotrypsin. Bacteriocin activity was observed to be not affected by the presence of milk, NaCl, SDS, Tween 80 or glycerol. Bacteriocin ST110LD effectively inhibited the growth of exponentially growing L. monocytogenes ATCC 15313 during a 10-h incubation period in BHI at 37°C. In addition, this bacteriocin showed specific inhibition of only Listeria spp., but did not inhibit the growth of beneficial cultures included in the microbial test panel for assessment of the spectrum of activity. CONCLUSIONS: Leuconostoc citreum ST110LD was evaluated as safe bacterium strain, producing bacteriocin with high specificity against listerial and enterococcal species. Specificity of producer strain and expressed bacteriocin can be explored in biopreservation of different fermented food products or applied in biotherapy of antibiotic resistant listerial or enterococcal infections. SIGNIFICANCE AND IMPACT OF THE STUDY: To the best of our knowledge, this is the first report of bacteriocin produced by Leuc. citreum strain with highly specific antimicrobial activity against Listeria sp. and Enterococcus sp.

Blood profile and productive performance after partial substitution of maize grain with ancient wheat lines by-products in organic laying hens' diet.

The aim of this research was to evaluate the effects of the partial substitution of maize grain with local ancient wheats by-products in an organic laying hens farm on animal performance and blood profile, as well as on eggs quality. A total of 80 Hy-Line W-36 Single Comb White Leghorn, 18 weeks old hens were homogenously divided into two groups. The two groups (40 laying hens each, 8 replicates, 5 hens/replicate) were fed two isoprotein and isoenergetic diets: the Control group (C) was fed a standard, organic maize-soybean meal diet whereas in the Ancient Grains group (AG) part of the maize grain was replaced by a mix of ancient grains middling, consisting in 50:50 of Triticum aestivum var. spelta (spelt) and Triticum durum dicoccum L. (emmer wheat). The birds fed the maize based-diet (C) showed a higher (P < 0.01) egg weight and feed intake than the Ancient Grains (AG) group. By contrary, the feed conversion ratio was more favourable (P < 0.05) in hens fed the Ancient Grains diet. The eggs produced by the hens fed the Control diet showed higher length and width than the other group (P < 0.01). The shell thickness and strength were also higher in the Control group (P < 0.01 and P < 0.05, respectively). The experimental dietary treatment positively affected some blood parameters. The Control group showed higher levels of cholesterol and triglycerides (P < 0.05) as well as of alanine aminotransferase (ALT) and gamma-glutamyl transferase (GGT) (P < 0.01). In addition, butyrate, which may have great implications for the regulation of the immune response, resulted significantly higher in the caecal content of hens from the Ancient Grains group. Overall, the Ancient Grains diet seemed to be able to guarantee the production performances with positive effects on the animal health.

Genotype by environment interaction for female fertility traits under conventional and organic production systems in Danish Holsteins.

Conventional and organic production systems mainly differ in feeding strategies, outdoor and pasture access, and the use of antibiotic treatments. These environmental differences could lead to a genotype by environment interaction (G × E) and a requirement for including G × E in breeding decisions. The objectives of this study were to estimate variance components and heritabilities for conventional and organic production systems and investigate G × E under these 2 production systems for female fertility traits in Danish Holsteins. The analyzed traits included the interval from calving to first insemination (ICF), the interval from first to last insemination, number of inseminations per conception (NINS), and non-return rate within 56 d after the first insemination. Records of female fertility in heifers and the first 3 lactations in cows as well as grass ratio of feed at herd level were collected during the period from 2011 to 2016. The performances of a trait in heifers and cows (lactation 1 to 3) were considered as different traits. The (co)variance components and the resulting heritabilities and genetic correlations were estimated using 2 models. One was a bivariate model treating performances of a trait under organic and conventional production systems as 2 different traits using a reduced data set, and the other was a reaction norm model with random regression on the production system and the grass ratio of feed using a full data set. The full data set comprised records of 37,836 females from 112 organic herds and 513,599 females from 1,224 conventional herds, whereas the reduced data set comprised records from all these 112 organic herds and 92,696 females from 185 convention herds extracted from the full data set with grass ratio of feed lower than 0.20. All female fertility performances of the organic production system were superior to those of the conventional production system. Besides, heterogeneities in additive genetic variances and heritabilities were observed between conventional and organic production systems for all traits. Furthermore, genetic correlations between these 2 production systems ranged from 0.607 to 1.000 estimated from bivariate models and from 0.848 to 0.999 estimated from reaction norm models. Statistically significant G × E were observed for NINS in heifers, non-return rate within 56 d after the first insemination in heifers, and ICF from the bivariate model, and for ICF and NINS in cows from the reaction norm model.

A Case Study on Converting Organic Farm Waste Vegetables to Biogas Using a Cartridge Design Anaerobic Digester.

Anaerobic digestion of multiple waste vegetables collected from an organic farm in Central Illinois was carried out using a new cartridge design anaerobic digestion system. Waste vegetables, including carrot, cucumber, bell pepper, onion, lettuce, and potato, were chopped and then mixed together to be used as the digestion feedstock. Three cartridges in the digestion chamber were rotated every week. Results showed that the system was stable, in terms of biogas and methane yields, ammonium-nitrogen concentration, and pH value, throughout the 90-day operation. On average, the daily and accumulative methane yield were 23.38 L/day/kg-VS and 490.98 L/kg-VS (21-day retention time), respectively. Rotation of cartridge significantly affected methane yield, methane concentration in biogas, and hydrogen sulfide concentration in biogas. Especially, the average hydrogen sulfide concentration decreased from 1145 ppm, to 695 ppm, and then to 539 ppm, in biogas samples taken on 2 days, 4 days, and 7 days after rotation. No liquid waste was generated throughout the test. A rough estimate of the potential biogas yield shows that if all the waste vegetables and crop residues collected from this farm were used in this new anaerobic digestion system, US$4711 in energy can be saved in a year.

Biogenic amines and mycotoxins concentrations in baled silage from organic and conventional farms / Concentrações de aminas biogênicas e micotoxinas em silagem embalada de fazendas orgânicas e convencionais

The aim of the current study was to investigate biogenic amines and mycotoxins concentrations in baled silage (mainly Poaceae family grasses) prepared in organic and conventional farms and to relate these parameters to fermentative parameters. The mean dry matter (DM) content was 364.10±93.31 and 424.70±95.93g/kg in the silage from organic and conventional farms respectively. The silage samples from organic farms had 17.00% higher (P≤ 0.05) tyramine (TY) than the silage from conventional farms. Conventional farm samples were characterized by 46.00% higher histamine (HIS) (P≤ 0.05), 9.80% higher putrescine (PUT) (P≤ 0.05), 17.30% higher cadaverine (CAD) (P≤ 0.05). Aflatoxins (AFL) (total) and zearalenone (ZEN), T-2/HT-2 concentrations were higher respectively 16.00% (P≤ 0.05) and 13.40% (P≤ 0.05), 1.80% (P≤ 0.05) in the silage prepared in organic farms. Deoxynivalenol (DON) concentration was higher 42.40% (P≤ 0.05) in silage from conventional farms. Volatile fatty acids (VFA), lactic acid, ethanol, pH and ammonia nitrogen showed that the silage samples from organic and conventional farms were of good quality. Our study suggests differences in biogenic amine formation or mycotoxins content in silage from organic and conventional farming, but, overall, the measured values are too low to be relevant for animal health. Furthermore, these differences might as well be due to the difference in dry matter content and plant maturity between the organic and conventional silage samples.(AU)

O objetivo do presente estudo foi investigar concentrações de aminas biogênicas micotoxinas em silagem embalada (principalmente gramíneas da família Poaceae) preparada em fazendas orgânicas e convencionais e relacionar esses parâmetros a parâmetros fermentativos. A massa seca média (MS) foi 364,10±93,31 e 424,70±95,93g/kg na silagem de fazendas orgânicas e convencionais, respectivamente. As amostras de silagem de fazendas orgânicas tinham 17% a mais de tyramina (TY) (p≤ 0,05) que as de fazendas convencionais. As amostras de fazendas convencionais foram caracterizadas por histamina (HIS) 46,00% mais alta (P≤ 0,05), 9,80% putrecina (PUT) mais alta (P≤ 0,05), 17,30% de cadaverina (CAD) mais alta (P≤ 0,05). Aflatoxnas (AFL) (total) e zearalenone (ZEN), T-2/HT-2 tinham concentrações mais altas em respectivamente 16,00% (P≤ 0,05) e 13,40% (P≤ 0,05), 1,80% (P≤ 0,05) na silagem preparada em fazendas orgânicas. Deoxinivalenol (DON) tinha concentração mais alta 42,40% (P≤ 0,05) na silagem de fazendas convencionais. Ácidos graxos voláteis (AGV), ácido lático, etanol, pH e nitrogênio de amônia mostraram que as amostras de silagem de fazendas orgânicas e convencionais tinham boa qualidade. Nosso estudo sugere diferenças na formação biogênica de amônia ou micotoxinas em silagem de fazendas orgânicas ou convencionais mas, em geral, os valores medidos foram muito baixos para serem relevantes à saúde animal. Ademais, essas diferenças podem ser devido à diferença na matéria sólida e maturidade da planta entre as amostras de silagem orgânica e convencional.(AU)

Description and Molecular Phylogeny of a Novel Hypotrich Ciliate from the Soil of Marche Region, Italy; Including Notes on the MOSYSS Project.

The morphology and morphogenesis during cell division of a new stylonychine hypotrich, Rigidocortex quadrinucleatus n. sp., were investigated using live observation and protargol staining. The new species was isolated from soil samples collected from an organic farm in the Marche Region, Italy, in framework of the MOSYSS project. Rigidocortex quadrinucleatus is characterized as follows: cell size about 180 × 80 µm in vivo; four ellipsoidal macronuclear nodules; 44 adoral membranelles: 18 fronto-ventral-transverse cirri consisting of three frontal, four frontoventral, one buccal, three ventral, two pretransverse, and five transverse cirri; dorsal kinety 3 with multiple fragmentation; resting cyst with hyaline ridges. Rigidocortex quadrinucleatus mainly differs from the type species R. octonucleatus in having four (vs. eight) macronuclear nodules. Rigidocortex quadrinucleatus can be easily confused with Sterkiella cavicola since both have a rather similar ventral ciliature; however, they can be separated by the slightly higher number of cirri in the left marginal row that runs along the posterior cell's margin in R. quadrinucleatus. Morphogenesis on the ventral surface is highly similar to that of Sterkiella species, but differs significantly on the dorsal surface (multiple vs. simple fragmentation of dorsal kinety 3). Phylogenetic analyses based on SSU rRNA gene sequences consistently place the new species within the stylonychine oxytrichids, clustering closer to Gastrostyla steinii than to S. cavicola.

[Detection of Salmonella Choleraesuis var. Kunzendorf in a fattening pig with septicaemic salmonellosis. A case report]. / Nachweis von Salmonella Choleraesuis var. Kunzendorf bei einem Mastschwein mit septikämischer Salmonellose. Ein Fallbericht.

The present case reports the detection of Salmonella (S.) Choleraesuis var. Kunzendorf and porcine circovirus type 2 in an organic fattening pig suffering from septicaemic salmonellosis and porcine dermatitis and nephropathy syndrome. Six weeks after pigs had been housed in an organic fattening farm, an increase in mortality, diarrhea and coughing was observed. In recent years, S. choleraesuis var. Kunzendorf has been frequently detected in wild boars in Germany, whereas the same serovar did not play an important role in the Western European domestic pig population. A direct transmission of this serovar from wild boars to domestic pigs in this case could not be proven. However, because wild boars are important reservoirs for the spread of epizootic diseases to the domestic pig population, this case emphasises the importance of taking epidemiological relationships under consideration and to comply with biosecurity measures according to German law (Schweinehaltungshygieneverordnung).

Transmission dynamics of extended-spectrum ß-lactamase and AmpC ß-lactamase-producing Escherichia coli in a broiler flock without antibiotic use.

Extended-spectrum and AmpC ß-lactamase-producing Escherichia coli (ESBL/AmpC-EC) are found throughout the broiler production pyramid. Transmission of resistance between broilers and humans could occur at any point, representing a potential public health issue. Insight in farm transmission dynamics could provide a basis for control, leading to fewer contaminated broilers. The aim was quantifying transmission rates and routes of ESBL/AmpC-EC, and specific phylogenetic groups, in an organic broiler flock without antibiotic use. In each of two consecutive production rounds, 80 randomly chosen broilers were followed individually. Cloacal swabs from these, 20 other randomly chosen broilers, and 11 environmental samples were taken at several moments from arrival till slaughter. ESBL/AmpC-EC were isolated by selective pre-enrichment, and ESBL/AmpC-genes and E. coli phylogenetic groups were determined. Transmission parameters (ß) were estimated using a Generalised Linear Model with a susceptible-infectious-susceptible model. Effect of direct broiler contact as compared to contact through the environment and previous carriage c.q. infectious status and their interaction were included as explanatory variables. Multiplying ß by the length of the infectious period gives the reproduction ratio (R). On day 1, prevalence was 28.8% (95%CI 19.2-40.0%) and 0.0% (95%CI 0.0-4.5%) among individually followed broilers, in round 1 and 2 respectively. In round 2, the environment was positive before arrival of day-old chicks. After 3 days, almost 100% of broilers and environmental samples were positive in both rounds. Most samples were positive for CTX-M-1 group genes, and A1 and B1 were predominant phylogenetic groups. From day 3 there was a shift towards more phylogenetic groups. R was 1.70 (95%CI 0.55-5.25) for total ESBL/AmpC-EC. Risk for broilers to become infectious was lower if previously infectious (ßpreviously infectious=0.02 vs. ßnot previously infectious=3.41; P<0.0001). For phylogenetic groups separately, R was 0.88 (95%CI 0.38-2.07), 0.51 (95%CI 0.27-0.98), 0.99 (95%CI 0.65-1.51) for A1, B1 and rest (i.e. A0, B2, D1, D2) groups, respectively. The interaction effect for A1 and B1 was reflected in the fact that when broilers were previous infectious, the environment was relatively more important for transmission of the A1 group, while this was direct contact between broilers for the B1 group. Positive day-old chicks and the environment both play a role in introduction and transmission of ESBL/AmpC-EC in flocks. These results suggest that, even without selective pressure from antibiotics, total ESBL/AmpC-EC persistence, and resulting endemic situation, seem to be caused by shifts in carriage of different phylogenetic groups. It implies that contaminated broilers enter the slaughterhouse.