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On-farm welfare assessment gives the opportunity to monitor and improve the quality of the animal life on the farm. In order to build the first Italian public standard for the welfare of indoor reared beef cattle, a list of 25 potential hazards and 22 potential promoters of beef cattle welfare was judged by a group of national experts by taking into account their negative or positive impacts on the welfare-state of the target population. In addition, the experts were asked to rank a list of 11 animal-based measures for identifying the most appropriate and important for measuring negative welfare outcomes in beef cattle. Based on experts' ratings, an "impact score" (IS

A clinical strain of Klebsiella pneumoniae typed as sequence type 307 carrying three different alleles of the flu gene encoding the Escherichia coli virulence factor antigen 43 associated with biofilm formation was detected and characterized. The flu alleles are located in the chromosome inside putative integrative conjugative elements. The strain displays the phenotypes associated with Ag43, i.e. bi-phasic colony morphology and enhanced biofilm production. Furthermore, the strain produces low amount of capsule known to affect Ag43 function. Analysis of 1431 worldwide deposited genomes revealed that 3.7% Klebsiella pneumoniae carry one or two flu alleles.

This study aims to describe trends of mcr-positive Enterobacterales in humans based on laboratory surveillance with a defined catchment population. The data source is the Micro-RER surveillance system, established in Emilia-Romagna region (Italy), to monitor the trend of mcr resistance. Enterobacterales isolates from human clinical samples with minimum inhibitory concentration (MIC) ≥ 2mg/L for colistin were sent to the study reference laboratory for the detection of mcr genes. Isolates prospectively collected in the period 2018–2020 were considered for the assessment of population rates and trends; further analyses were carried out for the evaluation of clonality and horizontal mcr gene transfer. Previous isolates from local laboratory collection were also described. In the period 2018–2020, 1164 isolates were sent to the reference laboratory, and 51 (4.4%) were confirmed as mcr-positive: 50 mcr-1 (42 Escherichia coli, 6 Klebsiella pneumoniae, 2 Salmonella enterica) and 1 mcr-4 (Enterobacter cloacae). The number of mcr-positive isolates dropped from 24 in the first half of 2018 to 3 in the whole of 2020 (trend p value < 0.001). Genomic analyses showed the predominant role of the horizontal transfer of mcr genes through plasmids or dissemination of transposable elements compared to clonal dissemination of mcr-positive microorganisms. The study results demonstrate a substantial decrease in the circulation of mcr-1 plasmid genes in Emilia-Romagna Region.

Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to food safety. Analysis of the distribution of Salmonella enterica serovar Derby (S. Derby) subtypes in human and swine identified isolates with a distinct PFGE profile that were significantly under-represented in human infections, consistent with further host adaptation to swine. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within S. Derby and exhibit a profound reduction in invasion of human epithelial cells, and a relatively small reduction in swine epithelial cells. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was present in the adapted lineage. The missense mutation resulted in a loss of function of HilD that accounted for reduced invasion in human epithelial cells. The relatively small impact of the mutation on interaction with swine cells was consistent with an alternative mechanism of invasion in this pathogen-host combination.

Mathematical models are formal and simplified representations of the knowledge related to a phenomenon. In classical epidemic models, a major simplification consists in assuming that the infectious period is exponentially distributed, then implying that the chance of recovery is independent on the time since infection. Here, we first attempt to investigate the consequences of relaxing this assumption on the performances of time-variant disease control strategies by using optimal control theory. In the framework of a basic susceptible–infected–removed (SIR) model, an Erlang distribution of the infectious period is considered and optimal isolation strategies are searched for. The objective functional to be minimized takes into account the cost of the isolation efforts per time unit and the sanitary costs due to the incidence of the epidemic outbreak. Applying the Pontryagin’s minimum principle, we prove that the optimal control problem admits only bang–bang solutions with at most two switches. In particular, the optimal strategy could be postponing the starting intervention time with respect to the beginning of the outbreak. Finally, by means of numerical simulations, we show how the shape of the optimal solutions is affected by the different distributions of the infectious period, by the relative weight of the two cost components, and by the initial conditions.

The study assessed Salmonella carriage in wild boars (Sus scrofa) and compared their isolates with those recovered from the domestic swine population of the same area of northern Italy (Emilia-Romagna), characterized by intensive pig farming and rather high density of wild boars. A total of 189 wild boars hunted during twelve months (2017-2018) were tested for Salmonella in mesenteric lymph nodes (MLN) and faecal samples. Antimicrobial resistance of recovered strains was tested against 14 antimicrobials. Salmonella was detected in 33/189 wild boars (17.5%), specifically from 30/189 MLN (15.9%) and 6/189 faecal samples (3.2%). Three animals were positive in both samples. Thirteen Salmonella serovars were identified, i.e. Typhimurium (the most common), Bovismorbificans, Coeln, Derby, Enteritidis, Gaminara, Hessarek, Houtenae IV, Kottbus, Napoli, Stanleyville, Thompson and Veneziana. Salmonella carriage was higher in warm than in cold months (P = 0.0013). Pregnancy status was never associated with Salmonella carriage, with significant difference in the recovery of the pathogen between non-pregnant and pregnant females (P = 0.003). Only one resistance pattern to streptomycin and tetracycline was found in 15 isolates (41.7%) belonging to Typhimurium (14/14; 100%) and Kottbus (1/3; 33.3%) serovars. Overlap with isolates from farmed pigs was limited at serotype level (Typhimurium, Derby, Enteritis, Bovismorbificans, Kottbus) and absent at PFGE level, and also antimicrobial resistance patterns were substantially different. This evidence indicates a substantial segregation of the two animal populations with regard to infectious contacts, possibly suggesting that biosecurity measures in place at industrial farm level limit the exchange of Salmonella.

Background Listeria monocytogenes is a foodborne pathogen with low incidence but severe manifestations in at risk categories (up to 30% fatality rate in YOPI). L. monocytogenes can form biofilm and persist in food processing environments for decades. In the Lombardy Region up to 50% of listeriosis cases have been attributed to dairy products. This study aimed at investigating a L. monocytogenes clone widely present in one of the most important Italian cheese production chain. Methods Through a retrospective analysis of the Lombardy Region PFGE database a cluster comprising isolates from eight PDO Gorgonzola and Taleggio dairies (2013-2019) was identified. A representative subset of 33 isolates was typed with MLVA and MLST. All isolates were further typed with WGS and compared to all Lombardy clinical isolates (n = 9) that shared the same Sequence Type (ST). Genomic relationship among isolates were investigated with cgMLST and SNP analysis. Results All isolates had the same MVLA/MLST profile (ST325). cgMLST and SNP analysis divided the isolates in two clusters that however shared a very high similarity (99.4%). Interestingly, isolates collected from same production plants clustered separately. Conversely, isolates collected in different years and plants clustered together. By querying the L. monocytogenes MLVA database it was possible to identify isolates of the same production chain with identical profile back to the year 2005. ST325 clinical isolates represented 2% of all typed clinical isolates and have an incidence of 0.007 cases/100000 inhabitants. Due to the high genomic similarity, it was not possible to link any clinical isolate to a putative source. Conclusions Our data suggest a persistent contamination by a L. monocytogenes ST325 clone traced back to the year 2005 present in the dairy production chain of Lombardy. Given the high similarity among the isolates further analyses with a larger dataset and are needed to elucidate the epidemiology of this clone. Key messages A highly clonal contamination by L. monocytogenes is widespread in the Lombardy Region dairy production chain. The low incidence of ST325 among the population suggests a low pathogenicity of the strain, however the occurrence of an ongoing long-term outbreak cannot be excluded.

With several human cases reported annually since 2008 and the unapparent risk of infection of blood donors, the West Nile virus (WNV) is emerging as an important health issue in Europe. Italy, as well as other European countries, experienced a recrudescence of the virus circulation in 2018, which led to an increased number of human cases. An integrated surveillance plan was activated in the Emilia-Romagna and Lombardy regions (Northern Italy) since 2008 in order to monitor the intensity and timing of WNV circulation. A fundamental part of this plan consists in entomological surveillance. In 2018, the surveillance plan made it possible to collect 385,293 mosquitoes in 163 stations in the two Regions. In total 269,147 Culex mosquitoes were grouped into 2,337 pools and tested for WNV, which was detected in 232 pools. Circulation started in the central part of the Emilia-Romagna region in the middle of June, about one month before the previous seasons. Circulation suddenly expanded to the rest of the region and reached the Lombardy region in the middle of July. WNV circulated more intensively in the eastern part of the surveyed area, as confirmed by the highest number of human cases. A relationship between the number of mosquitoes collected and the virus incidence emerged, but the data obtained highlighted that the probability of detecting the virus in a given site was less than expected with a higher number of collected mosquitoes. A significant relationship was observed between the temperature recorded one week before the sampling and the number of collected mosquitoes, as well as between the estimated number of WNV-positive mosquitoes and the temperature recorded two weeks before the sampling. The two weeks delay in the influence of temperature on the positive mosquitoes is in line with the time of the virus extrinsic incubation in the mosquito. This finding confirms that temperature is one of the principal drivers in WNV mosquito infection. The surveillance system demonstrated the ability to detect the virus circulation early, particularly in areas where circulation was more intense. This allowed evaluating the effect of mosquito abundance and weather factors on virus circulation.

Hepatitis E virus (HEV) is a singlestrand RNA virus that causes an acute viral hepatitis in humans. Among its eight recognized genotypes, HEV-3 and HEV-4 are zoonotic, infecting humans, pigs and wild boars. Recently, HEV-3 has been also detected in red deer, which represents another reservoir of HEV. Consumption of raw pork products (mainly liver sausages), undercooked wild boar meat, raw wild boar liver and deer meat has been responsible for foodborne HEV human worldwide. From November 2018 to March 2019, liver samples collected from 97 wild boars hunted in Emilia-Romagna region (Northern Italy) were tested for HEV RNA. The hunting area included two territories for an extension of 33 km2, named A (about 13 km2, natural park, deciduous wood) and B (about 20 km2, cultivated fields in proximity of a river) areas. Distance between the two areas ranged between 8 to 10 km. A total of 73 wild boars were hunted in area A, and 24 in area B. HEV RNA was detected by Realtime RT–PCR in 23/73 liver samples of wild boars living in area A only (31.5% - 95% CI: 22.0-42.8%). The HEV sequences (n=13) clustered within genotype 3. The majority of positives belonged to animals < 12 months (12/25; 48%), followed by subadults (13-24 months) (7/16; 43.8%) and adults (4/32; 12.5%). This difference was found to be statistically significant (p=0.0024). In absence of pig farms, the restriction of HEV-positive animals to a well-defined territory of 13 km2 (Boschi di Carrega Regional Park) could hypothetically be related to the presence of red deer (Cervus elaphus), which lived in area A at the beginning of the hunting season. Further studies are needed to confirm or deny our hypothesis.

International audience; In 2016 and 2017, 509 raw milk samples were collected from bulk milk tanks in 315 dairy farms in Parma province, Italy. Yersinia pseudotuberculosis was never detected. Yersinia enterocolitica was isolated from 17 (3.1%) bulk milk samples by culture methods. Estimated apparent prevalence was 3.91% in 2016, and 2.63% in 2017, with no significant difference between the two years (df ¼ 1; p-value ¼ 0.419). Five BT 2/ O:5,27 and 12 BT 1A isolates were detected. The most common virulence genes (ail, inv, virF, yadA, ystA, ystB, myfA, irp2, fyuA) were screened and the genes ail, virF, yadA, ystA were harboured only by 2 O:5,27 isolates. The Italian strains were very close by SNP analysis. The 2 O:5,27 isolates showed a unique antimicrobial resistance pattern, being resistant to amoxicillin, cefoxitin, cephalexin and amoxicillin-clavulanic acid. The study suggests that consumption of raw or improperly pasteurised milk may be hazardous for the consumers.

The population structure of human isolates of Listeria monocytogenes in Emilia-Romagna, Italy, from 2012 to 2018 was investigated with the aim of evaluating the presence of genomic clusters indicative of possible outbreaks, the proportion of cluster-associated vs. sporadic isolates and different methods and metrics of genomic analysis for use in routine surveillance. In the 2012–2018 period the notification rate of confirmed invasive cases in Emilia-Romagna was 0.91 per 100,000 population per year, more than twice the average rate of EU countries. Out of the total 283 cases, 268 (about 95%) isolates were typed through whole genome sequencing (WGS) for cluster detection with methods based on core-genome multi-locus sequence typing and single nucleotide polymorphisms. Between 66 and 72% of listeriosis cases belonged to genomic clusters which included up to 27 cases and lasted up to 5 years. This proportion of cluster-associated cases is higher than previously estimated in other European studies. Rarefaction analysis, performed by reducing both the number of consecutive years of surveillance considered and the proportion of isolates included in the analysis, suggested that the observed high proportion of cluster-associated cases can be ascribed to the long surveillance duration (7 years) and the high notification and typing rates of this study. Our findings show that a long temporal perspective and high surveillance intensity, intended as both exhaustiveness of the system to report cases and high WGS-typing rate, are critical for sensitive detection of possible outbreaks within a WGS-based surveillance of listeriosis. Furthermore, the power and complexity of WGS interpretation emerged from the integration of genomic and epidemiological information in the investigation of few past outbreaks within the study, indicating that the use of multiple approaches, including the analysis of the accessory genome, is needed to accurately elucidate the population dynamics of Listeria monocytogenes.

Background West Nile virus (WNV) transmission was much greater in 2018 than in previous seasons in Europe. Focusing on Emilia-Romagna region (northern Italy), we analyzed detailed entomological and epidemiological data collected in 2013–2018 to quantitatively assess environmental drivers of transmission and explore hypotheses to better understand why the 2018 epidemiological season was substantially different than the previous seasons. In particular, in 2018 WNV was detected at least two weeks before the observed circulation in 2013–2017 and in a larger number of mosquito pools. Transmission resulted in 100 neuroinvasive human cases in the region, more than the total number of cases recorded between 2013 and 2017. Methodology We used temperature-driven mathematical models calibrated through a Bayesian approach to simulate mosquito population dynamics and WNV infection rates in the avian population. We then estimated the human transmission risk as the probability, for a person living in the study area, of being bitten by an infectious mosquito in a given week. Finally, we translated such risk into reported WNV human infections. Principal findings The estimated prevalence of WNV in the mosquito and avian populations were significantly higher in 2018 with respect to 2013–2017 seasons, especially in the eastern part of the region. Furthermore, peak avian prevalence was estimated to have occurred earlier, corresponding to a steeper decline towards the end of summer. The high mosquito prevalence resulted in a much greater predicted risk for human transmission in 2018, which was estimated to be up to eight times higher than previous seasons. We hypothesized, on the basis of our modelling results, that such greater WNV circulation might be partially explained by exceptionally high spring temperatures, which have likely helped to amplify WNV transmission at the beginning of the 2018 season., Author summary West Nile virus (WNV) is one of the most recent emerging mosquito-borne diseases in Europe and North America. While most human infections are asymptomatic, about 1% of them can result in severe neurological diseases which might be fatal. WNV transmission was unusually greater in 2018 than in previous years in many European countries, resulting in a large number of human infections. Focusing on Emilia-Romagna region (Italy), we developed an epidemiological model informed by entomological data; through that we found that exceptionally high spring temperatures might have contributed at amplifying WNV transmission at the beginning of the season, causing greater WNV prevalence in mosquito and avian populations during the summer, which resulted in a higher estimated risk for human transmission. Thus, weather anomalies at the beginning of the mosquito breeding season, which are likely to become more common under the projected scenarios of climate change, might act as an early warning signal for public health authorities, enabling them to design efficient surveillance and prevention strategies.

Consumption of milk and dairy products is considered one of the main routes of human exposure to Mycobacterium avium subsp. paratuberculosis (MAP). Quantitative data on MAP load in raw cows’ milk are essential starting point for exposure assessment. Our study provides this information on a regional scale, estimating the load of MAP in bulk tank milk (BTM) produced in Emilia‐Romagna region (Italy). The survey was carried out on 2934 BTM samples (88.6% of the farms herein present) using two different target sequences for qPCR (f57 and IS900). Data about the performances of both qPCRs are also reported, highlighting the superior sensitivity of IS900‐qPCR. Seven hundred and eighty‐nine samples tested MAP‐positive (apparent prevalence 26.9%) by IS900 qPCR. However, only 90 of these samples were quantifiable by qPCR. The quantifiable samples contained a median load of 32.4 MAP cells mL −1 (and maximum load of 1424 MAP cells mL −1). This study has shown that a small proportion (3.1%) of BTM samples from Emilia‐Romagna region contained MAP in excess of the limit of detection (1.5 × 101 MAP cells mL −1), indicating low potential exposure for consumers if the milk subsequently undergoes pasteurization or if it is destined to typical hard cheese production.

Staphylococcus aureus (S. aureus) is one of the most important causes of mastitis in dairy cattle. Control and eradication programs of S. aureus intra-mammary infections (IMI) are based on different factors included the correct detection and management of the infected cows. The present study aimed at evaluating the efficacy of composite milk samples (CMS) analysis, compared to quarter milk samples (QMS) analysis, for the bacteriological detection of S. aureus intra-mammary infections. During 2016, 661 CMS (hygienically collected) and 2644 QMS (aseptically collected) were obtained from 661 cows in 5 herds. All the samples were submitted to S. aureus bacteriological culture and somatic cell count (SCC) analysis. QMS bacteriological analysis on blood agar plates was able to detect 236 cows excreting S. aureus, while the bacteriological analysis of CMS, using selective agar, identified 229 positive cows. The concordance was 95% with an excellent Cohen's κ (0.89). Relative sensitivity and specificity of CMS vs QMS, considered as the reference test, were 91.5% ± 2.1 and 96.9% ± 1.3 (CI 95%), respectively. In addition, the relative sensitivity of CMS improved as the number of infected quarters per cow and the number of colony forming units (cfu) per sample increased. The predictive value of CMS results was better when paired with SCC data, in particular CMS showed better negative predictive value when SCC was200,000 cells/mL and better positive predictive value when SCC was200,000 cells/mL. The probability for a cow to be S. aureus positive was 56.4% in case of SCC 200,000 cells/mL, while it was 18.6% in case of SCC 200,000 cells/mL. The average SCC in CMS was significantly higher in positive cows and the value rose as the number of infected quarters per cow increased. Given the intermittent excretion of S. aureus in milk from dairy cows, it could be more advantageous to carry out several serial CMS, rather than few QMS, being CMS an easier to collect and less expensive milk sampling method. Thus, bacteriological examination of CMS, combined with SCC data of the same sample, could be extremely useful for the success of S. aureus IMI control plans, because repeated CMS are easier to be performed and could be more easily proposed to the farmers.

During 2014-2015, 300 pig carcasses before chilling and 85 food contact surfaces (FCSs) at cutting lines were tested for Salmonella in three slaughterhouses (namely A, B, and C) of northern Italy. In slaughterhouses A and B, four carcass sites of 100 cm2 each (from both the exterior and interior side) were swabbed with a single sponge. In abattoir C, four 100 cm2 sites of the exterior and the interior sides were swabbed with two independent sponges. The population average prevalence of Salmonella-positive carcasses (which takes into account the structure of the study design, with multiple samples collected in a single day) in slaughterhouses A and B was 12.3%, while in slaughterhouse C it was 11.2%. Presence of Salmonella on exterior and interior sides of carcasses showed a low level of concordance (only 3/12 of the contaminated carcasses were positive on both sides). No significant difference was found for FCSs contamination in the three slaughterhouses, with a population average prevalence of Salmonella-positive FCSs of 19.9%. In addition, we found that the clustering due to the day of sampling account for more than 36% and 60% of the overall prevalence variation on carcasses and FCSs, respectively. Eight serovars were identified, with Salmonella Derby as the most common type. The counting of Salmonella on carcasses showed large variability. It was low (

Background and aim Epidemiology of human non-typhoid salmonellosis is characterised by recurrent emergence of new clones of the pathogen over time. Some clonal lines of Salmonella have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for Salmonella 4,[5],12:i:-, a monophasic variant of serotype Typhimurium. The same clonal behaviour is recognisable at sub-serotype level where single outbreaks or more generalised epidemics are attributable to defined clones. The aim of this study was to understand the dynamics of a clone of Salmonella 4,[5],12:i:- over a 3-year period (2012–15) in a province of Northern Italy where the clone caused a large outbreak in 2013. Furthermore, the role of candidate outbreak sources was investigated and the accuracy of multilocus variable-number tandem repeat analysis (MLVA) was evaluated. Methods: we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion. Results: The study showed the transient nature of the clone in the population, possibly as a consequence of its occasional expansion in a food-processing facility. We demonstrated that important weaknesses characterise conventional typing methods applied to clonal pathogens such as Salmonella 4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking. Conclusions: The study provided evidence for the remarkable prevention potential of whole genome sequencing used as a routine tool in systems that integrate human, food and animal surveillance.

Background and aim Epidemiology of human non-typhoid salmonellosis is characterised by recurrent emergence of new clones of the pathogen over time. Some clonal lines of Salmonella have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for Salmonella 4,[5],12:i:-, a monophasic variant of serotype Typhimurium. The same clonal behaviour is recognisable at sub-serotype level where single outbreaks or more generalised epidemics are attributable to defined clones. The aim of this study was to understand the dynamics of a clone of Salmonella 4,[5],12:i:- over a 3-year period (2012–15) in a province of Northern Italy where the clone caused a large outbreak in 2013. Furthermore, the role of candidate outbreak sources was investigated and the accuracy of multilocus variable-number tandem repeat analysis (MLVA) was evaluated. Methods: we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion. Results: The study showed the transient nature of the clone in the population, possibly as a consequence of its occasional expansion in a food-processing facility. We demonstrated that important weaknesses characterise conventional typing methods applied to clonal pathogens such as Salmonella 4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking. Conclusions: The study provided evidence for the remarkable prevention potential of whole genome sequencing used as a routine tool in systems that integrate human, food and animal surveillance.

Salmonella enterica serovar Napoli (serovar Napoli) is an emerging cause of human salmonellosis in Northern Italy. No specific reservoirs of serovar Napoli have been identified in Italy, so far. However, the environment, especially surface waters, has been hypothesized as an important source of infection based on the observation that genotypically different clusters of serovar Napoli are detected in different geographical macro-areas. To further support the hypothesis of a spatially-restricted pattern of serovar Napoli diffusion, a spatial segregation of serovar Napoli lineages should be observed also at smaller geographical scale. However, classical genotyping techniques used for Salmonella, such as pulsed-field gel electrophoresis (PFGE), did not possess enough discriminatory power to highlight spatial clustering of serovar Napoli within the macro-areas. To this purpose, we performed phylogeographical analyses based on genome-wide single nucleotide polymorphisms to test whether spatio-temporal evolution patterns of serovar Napoli in Northern Italy could be recognized with high geographical resolution, i.e. at local level. Specifically, we analyzed the local spread of the main PFGE clonal group, responsible for more than 60% of human infections in the study area, that did not show any geographical differentiation by PFGE within Northern Italy, i.e. the macro-area considered in the study. Both discrete and continuous phylogeography highlighted the existence of two main geographically-restricted clades: a Southern clade corresponding to the Po Valley and a Northern clade corresponding to the Pre-Alps area. Furthermore, the phylogeographical analyses suggested that the most probable site of origin of the clone was in an area of the Po Valley at the confluence of the Po and Ticino rivers, one of the most important Italian wetlands. These findings provide further support to the hypothesis that environmental transmission may play an important role in the ecology of serovar Napoli.

Infectious diseases in livestock can be transmitted through fomites: objects able to convey infectious agents. Between-farm spread of infections through fomites is mostly due to indirect contacts generated by on-farm visits of personnel that can carry pathogens on their clothes, equipment, or vehicles. However, data on farm visitors are often difficult to obtain because of the heterogeneity of their nature and privacy issues. Thus, models simulating disease spread between farms usually rely on strong assumptions about the contribution of indirect contacts on infection spread. By using data on veterinarian on-farm visits in a dairy farm system, we built a simple simulation model to assess the role of indirect contacts on epidemic dynamics compared to cattle movements (i.e. direct contacts). We showed that including in the simulation model only specific subsets of the information available on indirect contacts could lead to outputs widely different from those obtained with the full-information model. Then, we provided a simple preferential attachment algorithm based on the probability to observe consecutive on-farm visits from the same operator that allows overcoming the information gaps. Our results suggest the importance of detailed data and a deeper understanding of visit dynamics for the prevention and control of livestock diseases.

We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients ( n = 15) and food, feed, animal, and environmental sources ( n = 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system.

International audience; Brown rot, caused by Monilinia spp., is a major disease of stone fruit and, in favorable environmental conditions and in the absence of fungicide treatments, it causes important economic losses. In the present work, we propose a modification of classical susceptible, exposed, infectious and removed compartmental models to grasp the peculiarities of the progression of brown rot epidemics in stone fruit orchards in the last stage of the fruit growth (i.e., from the end of the pit hardening to harvest time). Namely, we took into account (i) the lifespan of airborne spores; (ii) the dependence of the latent period on the cuticle crack surface area, which itself varies in time with fruit growth; (iii) the impossibility of recovery in infectious fruit; and (iv) the abrupt interruption of disease development by the elimination of the host fruit at harvest time. We parametrized the model by using field data from a peach Prunus persica orchard infected by Monilinia laxa and M. fructicola in Avignon (southern France). The basic reproduction number indicates that the environmental conditions met in the field were extremely favorable to disease development and the model closely fitted the temporal evolution of the fruit abundance in the different epidemiological compartments. The model permits us to highlight crucial mechanisms undergoing brown rot build up and to evaluate the consequences of different agricultural practices on the quantity and quality of the yield. We found that winter sanitation practices (which decrease the initial infection incidence) and the control of the fruit load (which affects the host fruit density and the single fruit growth trajectory) can be effective in controlling brown rot in conjunction with or in place of fungicide treatments.

Influenza D virus (IDV), a new member of the Orthomyxoviridae family, was first reported in 2011 in swine in Oklahoma, and consequently found in cattle across North America and Eurasia. To investigate the circulation of IDV among pigs in Italy, in the period between June 2015 and May 2016, biomolecular and virological tests were performed on 845 clinical samples collected from 448 pig farms affected by respiratory distress located in the Po Valley. Serological tests were conducted on 3698 swine sera, including archive sera collected in 2009, as well as samples collected in 2015 from the same region. Viral genome was detected in 21 (2.3%) samples from 9 herds (2%), while virus was successfully isolated from 3 samples. Genetic analysis highlighted that Italian swine IDVs are closely related to the D/swine/Oklahoma/1334/2011 cluster. Sera collected in 2015 showed a high prevalence of IDV antibody titers (11.7%), while archive sera from 2009 showed statistically significant lower positivity rates (0.6%). Our results indicate an increasing epidemiological relevance of the pathogen and the need for in-depth investigations towards understanding its pathogenesis, epidemiology and possible zoonotic potential of this emerging virus.

An expert opinion elicitation, based on a modified Delphi technique, was organized to collect the opinion of 16 Italian veterinarians with the aim of conducting a hazard and a welfare promoter characterization for defining and weighing a list of management and housing factors potentially associated with negative or positive welfare outcomes in dairy cows kept in loose housing systems. In addition, the 16 experts judged a set of animal-based measures in order to rate them by appropriateness and by the level of animal pain and suffering due to the welfare consequences they measure. Veterinary experts were asked to score 52 hazards, 47 welfare promoters and 18 animal-based measures. Management and housing hazards, that were determined to be associated with a very high impact on the welfare of dairy cows, were mainly referred to lactating cows (absence of bedding material, presence of inadequate or slippery floor in walking areas, wrong design of the lying area), but also the use of harmful tools for animal handling and the lack of scheduled foot inspection, trimming and foot bathing reached very high impact scores. Management and housing welfare promoters dealing with optimal cow comfort around resting obtained the highest ratings, together with the presence of experienced and trained stockpersons, the implementation of an attentive animal grouping strategy and the control of temperature, humidity and ventilation. Considering animal-based measures, the highest ranking of importance was given to observation of lameness, records of mortality of adult cows and calves, observation of integument alterations and body condition scoring. This study has been the starting point for the development of the first Italian national protocol for the assessment of the welfare of dairy cows farmed in loose housing systems.

Highlights • We study the problem of minimizing the epidemic duration in SIR models. • Minimize the outbreak duration is crucial, especially in livestock diseases. • We investigate vaccination, isolation, culling, and reduction of transmission. • The optimal control is bang–bang with at most one switch that delays the control. • Then, minimize the epidemic duration may not imply minimize the infectious burden., We investigate the time-optimal control problem in SIR (Susceptible-Infected-Recovered) epidemic models, focusing on different control policies: vaccination, isolation, culling, and reduction of transmission. Applying the Pontryagin’s Minimum Principle (PMP) to the unconstrained control problems (i.e. without costs of control or resource limitations), we prove that, for all the policies investigated, only bang–bang controls with at most one switch are admitted. When a switch occurs, the optimal strategy is to delay the control action some amount of time and then apply the control at the maximum rate for the remainder of the outbreak. This result is in contrast with previous findings on the unconstrained problems of minimizing the total infectious burden over an outbreak, where the optimal strategy is to use the maximal control for the entire epidemic. Then, the critical consequence of our results is that, in a wide range of epidemiological circumstances, it may be impossible to minimize the total infectious burden while minimizing the epidemic duration, and vice versa. Moreover, numerical simulations highlighted additional unexpected results, showing that the optimal control can be delayed also when the control reproduction number is lower than one and that the switching time from no control to maximum control can even occur after the peak of infection has been reached. Our results are especially important for livestock diseases where the minimization of outbreaks duration is a priority due to sanitary restrictions imposed to farms during ongoing epidemics, such as animal movements and export bans.

The total number of infections (epidemic size) and the time needed for the infection to go extinct (epidemic duration) represent two of the main indicators for the severity of infectious disease epidemics in human and livestock. However, few attempts have been made to address the problem of minimizing at the same time the epidemic size and duration from a theoretical point of view by using optimal control theory. Here, we investigate the multi-objective optimal control problem aiming to minimize, through either vaccination or isolation, a suitable combination of epidemic size and duration when both maximum control effort and total amount of resources available during the entire epidemic period are limited. Application of Pontryagin's Maximum Principle to a Susceptible-Infected-Removed epidemic model, shows that, when the resources are not sufficient to maintain the maximum control effort for the entire duration of the epidemic, the optimal vaccination control admits only bang-bang solutions with one or two switches, while the optimal isolation control admits only bang-bang solutions with one switch. We also find that, especially when the maximum control effort is low, there may exist a trade-off between the minimization of the two objectives. Consideration of this conflict among objectives can be crucial in successfully tackling real-world problems, where different stakeholders with potentially different objectives are involved. Finally, the particular case of the minimum time optimal control problem with limited resources is discussed.

We applied optimal control theory to an SI epidemic model to identify optimal culling strategies for diseases management in wildlife. We focused on different forms of the objective function, including linear control, quadratic control, and control with limited amount of resources. Moreover, we identified optimal solutions under different assumptions on disease-free host dynamics, namely: self-regulating logistic growth, Malthusian growth, and the case of negligible demography. We showed that the correct characterization of the disease-free host growth is crucial for defining optimal disease control strategies. By analytical investigations of the model with negligible demography, we demonstrated that the optimal strategy for the linear control can be either to cull at the maximum rate at the very beginning of the epidemic (reactive culling) when the culling cost is low, or never to cull, when culling cost is high. On the other hand, in the cases of quadratic control or limited resources, we demonstrated that the optimal strategy is always reactive. Numerical analyses for hosts with logistic growth showed that, in the case of linear control, the optimal strategy is always reactive when culling cost is low. In contrast, if the culling cost is high, the optimal strategy is to delay control, i.e. not to cull at the onset of the epidemic. Finally, we showed that for diseases with the same basic reproduction number delayed control can be optimal for acute infections, i.e. characterized by high disease-induced mortality and fast dynamics, while reactive control can be optimal for chronic ones.

The first case of plasmid-mediated resistance to colistin due to the mcr-1 gene was reported in China in late 2015 ([1][1]). Soon after, the same gene was detected by a number of retrospective analyses ([2][2]). Resistance to colistin is generally believed to be related to its use in animal

A questionnaire survey about on farm dairy cow mortality was carried out among veterinary practitioners in Italy between January 2013 and May 2014. The study aimed at investigating the main circumstances of death in dairy cows (euthanasia, emergency slaughter or unassisted death), the primary causes and the risk factors of death. Out of 251 dead cows involved (across 137 farms), 54.6% died assisted and 45.4% were found dead. The main causes of death were metabolic/digestive disorders (22.3%) and mastitis/udder problems (17.1%), while in 14.7% of all cases, reasons of death were unknown. From the univariable generalised linear mixed models, dry cows showed a significantly higher odds to die unassisted compared to lactating cows (OR=3.2); dry cows also had higher odds of dying from unknown reasons (OR=11.7). Season was not significantly related to the risk of dying unassisted and for unknown reasons, but during the summer (characterised by hot and muggy weather in Northern Italy) cows died mostly for problems at calving. 54.2% of cows died during the first 30days in milk (DIM). Half of the multiparous cows that died, died in the first 29.5 DIM, while half of the primiparous cows that died, died in the first 50 DIM. Results pointed out that, especially in dry cows, around calving and during the summer, some failure in management practices and daily inspections may occur. Improvements should be done in monitoring activities and in recognising early symptoms of diseases among stockperson. In addition, in case of diagnosed diseases with poor prognosis, euthanasia procedures should be implemented to prevent cows from dying unassisted.

Ninety pig carcasses and twenty one food contact surfaces (FCSs) were tested for Salmonella in a slaughterhouse processing ca. 380 pigs/h between 2014-2015. Sampling was performed during seven sessions. Four carcass sites of 100 cm2 each (back, belly, jowl externally, and the diaphragmatic area internally) were swabbed after evisceration. Meat conveyors and dressing tables were tested swabbing areas of 200 to 400 cm2. After pre-enrichment in buffered peptone water, samples were tested by Salmonella MDS® assay and the presumptive positives were confirmed by the ISO 6579 method. Salmonella isolates were serotyped following the Kauffman- White-Le Minor scheme and genotyped by XbaI pulsed field gel electrophoresis. Salmonella was isolated from 16/90 [17.8%; confidence interval (CI) 95%=11.2-26.9] carcasses and 4/21 (19.0%; CI 95%=7.7-40.0) FCSs. Four serovars were identified on carcasses. S. enterica 4,[5],12:i:- was the most prevalent (43.75%), followed by S. Rissen (31.25%), S. Derby (12.5%) and S. Bovismorbificans (12.5%). Two serovars were found on FCSs, namely S. Derby (75%) and S. Livingstone (25%). During one sampling session, a failure in carcass dehairing occurred and caused significantly higher prevalence of carcass contamination (60%) than in the remaining sessions. Moreover, in the same session, Salmonella prevalence was marginally significantly higher on FCSs than in the remaining sampling days, suggesting that dehairing affects contamination not only on carcasses, but also on the working surfaces.