Definition of Food Safety Criteria for Bacteria Food-Borne Pathogens in Ready to Eat products

The aims of this research study is to explore the opportunity to set up Performance Objectives (POs) parameters for specific risks in RTE products to propose for food industries and food authorities. In fact, even if microbiological criteria for Salmonella and Listeria monocytogenes Ready-to-Eat (RTE) products are included in the European Regulation, these parameters are not risk based and no microbiological criteria for Bacillus cereus in RTE products is present. For these reasons the behaviour of Salmonella enterica in RTE mixed salad, the microbiological characteristics in RTE spelt salad, and the definition of POs for Bacillus cereus and Listeria monocytogenes in RTE spelt salad has been assessed. Based on the data produced can be drawn the following conclusions: 1. A rapid growth of Salmonella enterica may occurr in mixed ingredient salads, and strict temperature control during the production chain of the product is critical. 2. Spelt salad is characterized by the presence of high number of Lactic Acid Bacteria. Listeria spp. and Enterobacteriaceae, on the contrary, did not grow during the shlef life, probably due to the relevant metabolic activity of LAB. 3. The use of spelt and cheese compliant with the suggested POs might significantly reduce the incidence of foodborne intoxications due to Bacillus cereus and Listeria monocytogenes and the proportions of recalls, causing huge economic losses for food companies commercializing RTE products. 4. The approach to calculate the POs values and reported in my work can be easily adapted to different food/risk combination as well as to any changes in the formulation of the same food products. 5. The optimized sampling plans in term of number of samples to collect can be derive in order to verify the compliance to POs values selected

Successful Treatment of Bloodstream Infection due to a KPC-Producing Klebsiella Pneumoniae Resistant to Imipenem/Relebactam in a Hematological Patient

Novel carbapenem-β-lactamase inhibitor combination, imipenem/relebactam (IMI-REL), has been recently approved for treatment of infections with limited or no alternative treatment options. In this study, we described the emergence of the IMI-REL-resistance in a KPC-producing Klebsiella pneumoniae (KPC-Kp) strain collected from a hematological patient with no evidence of prior colonization. Interestingly, IMI-REL-resistance was associated with meropenem/vaborbactam (MER-VAB) cross-resistance but was not associated with cross-resistance to ceftazidime/avibactam (CAZ-AVI). Although treatment with CAZ-AVI and gentamicin completely eradicated the infection due KPC-Kp cross-resistance to IMI-REL and MER-VAB, the patient became colonized subsequently by KPC-Kp strains susceptible to IMI-REL and MER-VAB. Whole-genome sequencing performed by hybrid approach using Illumina and Oxford Nanopore platforms demonstrated that all KPC-Kp strains isolated from hematological patient belonged to the ST512 and were clonally related. Analysis of antimicrobial and porins genes demonstrated that cross-resistance to IMI-REL and MER-VAB was associated with increased blaKPC-3 copy number and truncated OmpK35 and OmpK36 with GD134-135 insertion. Phylogenetic analysis demonstrated that KPC-Kp cross-resistance to IMI-REL and MER-VAB was clonally related to a KPC-Kp resistant to IMI-REL as previously described, demonstrating the spread of this multidrug resistant clone in the hematological unit. In conclusion, the results presented in this study reported the emergence of cross-resistance to MER-VAB and IMI-REL in a KPC-Kp strain isolated from a hematological patient and highlight the potential development and diffusion of new multidrug resistance traits

New technologies to enhance quality and safety of table eggs: ultra-violet treatment and modified atmosphere packaging

In the present study the effect of ultra-violet (UV) treatment alone and in combination with 100% CO2 modified atmosphere packaging (MAP) was evaluated both on the survival of naturally occurring bacteria, as well as on quality parameters of table eggs during 28 days of storage at 21\ub0C. Table eggs were collected from the conveyor belt after the UV module, and placed on carton trays. A representative number of carton trays were packed in a high barrier multilayer pouch filled with 100% CO2. All eggs were stored at 21\ub0C and analysed at 0, 1, 7, 14, 21 and 28 days of storage. Eggs not treated with UV and not packed were also included. On the eggshells total colony count, total coliforms and faecal coliforms counts, as well as the detection of Salmonella spp. were investigated. Moreover, chemical-functional parameters such as weight loss, albumen pH and Haugh Unit (HU) were evaluated. The total colony count on UV treated table eggs was approximately 1 log10 CFU/g lower than untreated eggs (2.27 vs 3.29 log10 CFU/g). During storage, CO2 packed eggs maintained the initial values of HU, whereas the albumen pH decreased up to 1.5-2 points in comparison to unpacked eggs. The UV treatment was effective in reducing the total colony count on the surface of table eggs. MAP showed a great potential in maintaining/enhance the technological properties of egg constituents (higher foam stability of the albumen for meringue preparation) without significantly impacting on the microbial load of table eggs

Evaluation of Real-Time PCR to complement ISO 6579:2004 method for the detection of Salmonella in pork cuts

According to Commission Regulation (EC) No 2073/2005 of 15 November 2005 on microbiological crite-ria for foodstuff , the analytical reference method for the detection of Salmonella in food is ISO 6579:2004. However this long and labor-intensive method is not in line with the short production times of the food industry. In the last years, Real-Time PCR is used more and more by scientists for the relia-ble, fast and specific detection of bacterial pathogens in food. The aim of the present study was to eval-uate the Salmonella detection capability of a validated Real-Time PCR assay on naturally contaminated pork cuts in comparison with the reference method ISO 6579:2004. Three sampling were performed and included 16 pork cut packaging. From each packaging, three aliquots of 10 g each were tested separate-ly by ISO 6579:2004 method and by Real-Time PCR. In particular this molecular method was applied on DNA samples extracted from pre-enrichment broth after 1 and 18 hours of incubation. Within the three sampling periods, Real-Time PCR detected Salmonella in 81%, 100% e 62,5% of pork cut samples respectively, whereas the corresponding percentages of detection of the reference method were 56%, 81% e 62,5% respectively. In conclusion the Real-Time PCR assay used in the present study might be a reliable tool for a fast detection of Salmonella on pork cuts, especially when large number of samples needs to be tested. The reference method might be applied only on positive samples for isolation purpos-es mandatory in epidemiological investigations

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Background Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.info:eu-repo/semantics/publishedVersio

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a ?One Health? perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identifed in the four candidate genes: 26% of them were not previously described; 29 variants afected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a frst step towards a ?One Health? perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the describedFE1B-06B2-126F | Jos? Pedro Pinto de Ara?joN/

Susceptibility of black bullhead Ameiurus melas to a panel of ranavirus isolates

Ranaviruses are considered a serious threat to lower vertebrates, including fish, amphibians and reptiles. However, epidemiological data on these agents are lacking, and further investigations are needed to understand the role of carriers and to update the list of susceptible hosts. We carried out various experimental infections under controlled conditions to contribute to the current knowledge on the susceptibility of black bullhead Ameiurus melas to European catfish virus (ECV) and other ranaviruses. A panel of 7 ranavirus isolates was used to challenge duplicate groups of A. melas juveniles maintained in aquaria supplied with running dechlorinated tap water. The experiments were performed at 15 and 25 degrees C. The results confirmed the high susceptibility of A. melas to ECV infection. Furthermore, a significant mortality associated with the typical signs of systemic viral infections was observed in groups challenged with Epizootic haematopoietic necrosis virus (EHNV) at 25 degrees C, and to a lesser extent, at 15 degrees C. No significant mortality was recorded in fish challenged with European sheatfish virus (ESV), Frog virus 3 (FV3), Rana esculenta virus-like (REV-like), Bohle iridovirus (BIV) or short-finned eel virus (SERV)