Effects of Intensive Agricultural Management Practices on Soil Microbial Assembly and Recruitment

Soil microbial communities play an important role in ecosystems in various ways to promote healthy and fertile soil. However, intensive agricultural practices with excessive tillage and fertilizer applications can affect the abundance and community structure of microbial communities in soil as well as their assembly and recruitment by plant roots. Using amplicon sequencing and microscopy, we have examined bacterial and fungal communities under different tillage and fertilizer treatments in a 34-year-old field-trial at the Carrington Research Extension Center of NDSU. We observed that fertilizer application has a significantly stronger effect than tillage on soil properties, as well as the overall soil microbial abundance and community structure. Significantly higher mycorrhizal colonization was found under organic manure application. Overall, the results of this study can improve our understanding of the effects of fertilizer application on soil microbial communities and how management practices can be optimized to reduce the imprints of intensive agriculture

The speciation and genotyping of Cronobacter isolates from hospitalised patients

The World Health Organization (WHO) has recognised all Cronobacter species as human pathogens. Among premature neonates and immunocompromised infants, these infections can be life-threatening, with clinical presentations of septicaemia, meningitis and necrotising enterocolitis. The neurological sequelae can be permanent and the mortality rate as high as 40 – 80 %. Despite the highlighted issues of neonatal infections, the majority of Cronobacter infections are in the elderly population suffering from serious underlying disease or malignancy and include wound and urinary tract infections, osteomyelitis, bacteraemia and septicaemia. However, no age profiling studies have speciated or genotyped the Cronobacter isolates. A clinical collection of 51 Cronobacter strains from two hospitals were speciated and genotyped using 7-loci multilocus sequence typing (MLST), rpoB gene sequence analysis, O-antigen typing and pulsed- field gel electrophoresis (PFGE). The isolates were predominated by C. sakazakii sequence type 4 (63 %, 32/51) and C. malonaticus sequence type 7 (33 %, 17/51). These had been isolated from throat and sputum samples of all age groups, as well as recal and faecal swabs. There was no apparent relatedness between the age of the patient and the Cronobacter species isolated. Despite the high clonality of Cronobacter , PFGE profiles differentiated strains across the sequence types into 15 pulsotypes. There was almost complete agreement between O-antigen typing and rpoB gene sequence analysis and MLST profiling. This study shows the value of applying MLST to bacterial population studies with strains from two patient cohorts, combined with PFGE for further discrimination of strains

Survey of the prevalence of Salmonella species on laying hen farms in Kosovo

A survey on the prevalence of Salmonella (S.) species was carried out on 39 layer farms in Kosovo between April and September 2012. In total 367 samples, comprising feces, dust, eggs, and internal organs from dead birds, were investigated using bacteriological culture methods. Additionally, data on the location of the farm, the total number of birds on the farm, age of birds, and laying performance were collected. Salmonella were isolated from 38 samples obtained from 19 (49%) farms. The most common serovar identified was Salmonella enteritidis, found on 18 farms. The most common S. enteritidis phage type was PT29 followed by PT6, PT7, PT21, PT13a, PT8, PT14b, and PT4. One S. enteritidis isolate was not typable. Six farms had more than one phage type. Furthermore, serovar S. Bovismorbificans also was found in samples from 3 farms. Flock size or production stage was not associated with the probability of isolating Salmonella. The only flock factor found to be significantly associated was percent hen/day production: It was 2.8 times more likely to isolate Salmonella from flocks with production above 80% hen/day production compared to flocks producing at a lower level. Analysis of antimicrobial resistance patterns of 30 isolates revealed that all isolates were sensitive to gentamicin, ampicillin, sulphamethoxazole trimethoprim, and oxytetracycline, and 29 (97%) were sensitive to ciprofloxacin. All isolates showed intermediate resistance or were resistant to minocycline and cloxacillin. Twenty-six isolates (86%) had intermediate resistance to amoxicillin and 27 isolates (90%) were fully resistant to streptomycin. The present survey revealed a high prevalence of Salmonella enteritidis in layer flocks in Kosovo, indicating that table eggs have to be suspected as an important source of human salmone-llosis

EFSA Panel on Biological Hazards (BIOHAZ) Panel; Scientific Opinion on the risk posed by pathogens in food of non-animal origin. Part 1 (outbreak data analysis and risk ranking of food/pathogen combinations)

Food of non-animal origin (FoNAO) is consumed in a variety of forms, and a major component of almost all meals. These food types have the potential to be associated with large outbreaks as seen in 2011 associated with VTEC O104. A comparison of the incidence of human cases linked to consumption of FoNAO and of food of animal origin (FoAO) was carried out to provide an indication of the proportionality between these two groups of foods. It was concluded that outbreak data reported as part of EU Zoonoses Monitoring is currently the only option for EU-wide comparative estimates. Using this data from 2007 to 2011, FoNAO were associated with 10% of the outbreaks, 26% of the cases, 35% of the hospitalisations and 46% of the deaths. If the data from the 2011VTEC O104 outbreak is excluded, FoNAO was associated with 10% of the outbreaks, 18% of cases, but only 8% of the hospitalisations and 5% of the deaths. From 2008 to 2011 there was an increase in the numbers of reported outbreaks, cases, hospitalisations and deaths associated with food of non-animal origin. In order to identify and rank specific food/pathogen combinations most often linked to human cases originating from FoNAO in the EU, a model was developed using seven criteria: strength of associations between food and pathogen based on the foodborne outbreak data from EU Zoonoses Monitoring (2007-11), incidence of illness, burden of disease, dose-response relationship, consumption, prevalence of contamination and pathogen growth potential during shelf life. Shortcomings in the approach using outbreak data were discussed. The top ranking food/pathogen combination was Salmonellaspp. and leafy greens eaten raw followed by (in equal rank) Salmonellaspp. and bulb and stem vegetables, Salmonellaspp. and tomatoes, Salmonellaspp. and melons, and pathogenic Escherichia coli and fresh pods, legumes or grain

EFSA BIOHAZ Panel (EFSA Panel on Biologicial Hazards), 2013. Scientific Opinion on the public health hazards to be covered by inspection of meat (solipeds)

A risk ranking process identified Trichinella spp. as the most relevant biological hazard in the context of meat inspection of domestic solipeds. Without a full and reliable soliped traceability system, it is considered that either testing all slaughtered solipeds for Trichinella spp., or inactivation meat treatments (heat or irradiation) should be used to maintain the current level of safety. With regard to general aspects of current meat inspection practices, the use of manual techniques during current post-mortem soliped meat inspection may increase microbial cross-contamination, and is considered to have a detrimental effect on the microbiological status of soliped carcass meat. Therefore, the use of visual-only inspection is suggested for “non-suspect” solipeds. For chemical hazards, phenylbutazone and cadmium were ranked as being of high potential concern. Monitoring programmes for chemical hazards should be more flexible and based on the risk of occurrence, taking into account Food Chain Information (FCI), covering the specific on-farm environmental conditions and individual animal treatments, and the ranking of chemical substances, which should be regularly updated and include new hazards. Sampling, testing and intervention protocols for chemical hazards should be better integrated and should focus particularly on cadmium, phenylbutazone and priority “essential substances” approved for treatment of equine animals. Implementation and enforcement of a more robust and reliable identification system throughout the European Union is needed to improve traceability of domestic solipeds. Meat inspection is recognised as a valuable tool for surveillance and monitoring of animal health and welfare conditions. If visual only post-mortem inspection is implemented for routine slaughter, a reduction in the detection of strangles and mild cases of rhodococcosis would occur. However, this was considered unlikely to affect the overall surveillance of both diseases. Improvement of FCI and traceability were considered as not having a negative effect on animal health and welfare surveillance

Estimation of the incidence of invasive meningococcal disease using a capture– recapture model based on two independent surveillance systems in Catalonia, Spain

Microbiologia de diagnòstic; Epidemiologia; Control d'infecció; Diagnòstic molecularMicrobiología de diagnóstico; Epidemiología; Control de infección; Diagnóstico molecularDiagnostic microbiology; Epidemiology; Infection control; Molecular diagnosticsObjectives: Invasive meningococcal disease (IMD) is an urgent notifiable disease and its early notification is essential to prevent cases. The objective of the study was to assess the sensitivity of two independent surveillance systems and to estimate the incidence of IMD. Design: We used capture-recapture model based on two independent surveillance systems, the statutory disease reporting (SDR) system and the microbiological reporting system (MRS) of the Public Health Agency of Catalonia, between 2011 and 2015. The capture-recapture analysis and 95% CIs were calculated using the Chapman formula. Multivariate vector generalised linear model was performed for adjusted estimation. Measures: The variables collected were age, sex, year of report, size of municipality (<10 000 and ≥10 000), clinical form, death, serogroup, country of birth and type of reporting centre (private and public). Results: The sensitivity of the two combined surveillance systems was 88.5% (85.0-92.0). SDR had greater sensitivity than the MRS (67.9%; 62.7-73.1 vs 64.7%; 59.4-70.0). In 2014-2015, the sensitivity of both systems was higher (80.6%; 73.2-87.9 vs 73.4%; 65.2-81.6) than in 2011-2013 (59.3%; 52.6-66.0 vs 58.3%; 51.6-65.1). In private centres, the sensitivity was higher for SDR than for MRS (100%; 100-100 vs 4.8%; -4.4-13.9). The adjusted estimate of IMD cases was lower than that obtained using the Chapman formula (279; 266-296 vs 313; 295-330). The estimated adjusted incidence of IMD was 0.7/100 000 persons-year. Conclusions: The sensitivity of enhanced surveillance through the combination of two complementary sources was higher than for the sources individually. Factors associated with under-reporting in different systems should be analysed to improve IMD surveillance.This work was supported partially by CIBER of Epidemiology and Public Health (CIBERESP), Carlos III Health Institute and the Catalan Agency for the Management of Grants for University Research (AGAUR grant number 2017/SGR 1342). The funding sources played no part in the design of the study and collection, analysis and interpretation of data and in writing the manuscript

Effect of cut-type on quality of minimally processed papaya

BACKGROUND: This research was undertaken to study the effects of different cut-types (cube, parallelepiped, cylinder and sphere) on the quality and shelf-life of papaya cv. Sunrise Solo. Physicochemical analyses were carried out during 10 days of storage at 4 ◦C to determine colour, firmness, pH, titratable acidity, total soluble solids, weight loss and vitamin C content. Microbiological analysis and sensory evaluation were also performed. RESULTS: Papaya spheres (1.55cm radius) presented the most favourable physicochemical and microbiological properties (smaller changes in colour parameters L∗, a∗, b∗, chroma and hue angle, firmer texture, lower increase in pH, higher titratable acidity, almost constant total soluble solids, reduced weight loss, high vitamin C content and lower microbial loads) and sensory characteristics on day 10, while papaya cubes (1.4cm side) proved to be the least acceptable. CONCLUSION: The results of physicochemical,microbiological and sensory analyses performed on different cuttypes of papaya indicated acceptable fresh-cut produce during 10 days of storage at 4 ◦C. The potential shelf-life at 4 ◦C is therefore 10 days, provided that no contamination occurs in the postharvest period and during minimal processing operations