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This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Var-iants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected through-out the country. A total of 332 wastewater samples were collected from 20 Italian Regions/Autonomous Provinces (APs) within the framework of national SARS-CoV-2 environmental surveillance. Of these, 164 were collected in the first week of October and 168 in the first week of November. A similar to 1600 bp fragment of the spike protein was sequenced by Sanger (for individual samples) and long-read nanopore sequencing (for pooled Region/AP samples).In October, mutations characteristic of Omicron BA.4/BA.5 were detected in the vast majority (91 %) of the samples amplified by Sanger sequencing. A fraction of these sequences (9 %) also displayed the R346T mutation. Despite the low prevalence documented in clinical cases at the time of sampling, amino acid substitutions characteristic of sublineages BQ.1 or BQ.1.1 were detected in 5 % of sequenced samples from four Regions/APs. A significantly higher variability of sequences and variants was documented in November 2022, when the rate of se-quences harbouring mutations of lineages BQ.1 and BQ1.1 increased to 43 %, and the number of Regions/APs positive for the new Omicron subvariant more than tripled (n = 13) compared to October. Moreover, an increase in the number of sequences with the mutation package BA.4/BA.5 + R346T (18 %), as well as the detection of variants never observed before in wastewater in Italy, such as BA.2.75 and XBB.1 (the latter in a Region where no clinical cases asso-ciated with this variant had ever been documented) was recorded.The results suggest that, as predicted by the ECDC, BQ.1/BQ.1.1 is rapidly becoming dominant in late 2022. Environ-mental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population.

Background The serovar Typhimurium (4, [5],12:i:1,2), is the most frequently isolated serovar in case of salmonellosis in pigs in Europe and its monophasic variant (4, [5],12:i:-) has been increasingly responsible for Salmonella outbreaks in humans. A total of 25,215 samples were collected, during the years 2002–2017, from 1359 pig farms located in Northern Italy. Samples were collected from different material sources including fecal samples, rectal swabs, gut content and different organs. Results Salmonella was isolated in 15.80% of samples and, among the isolates, 733 were typed as Salmonella Typhimurium (ST) or its monophasic variant (MST). Over time, there was an increase of isolation of MST which outnumbered ST. Most of the strains were isolated in animals during the weaning stage and the growing – fattening period whereas the clinical cases were mainly present in young pigs after weaning. Conclusions This study confirms the presence of ST and MST in pig farms although, considering the total of isolated serotypes, with lower percentages than previously reported. In the last few years, ST has increasingly been replaced by MST suggesting that MST has a competitive advantage over ST, probably due to its different antigenicity and pathogenicity which renders the infection stealthier to recognize and control.

Background Genotypic variability in M. hyopneumoniae has been reported within and among herds. However, information regarding VNTR types within single lung lobes is lacking. The objective of his study was to analyse M. hyopneumoniae infections and their association with VNTR types and lung lesions at the lobe level. Lungs from 300 pigs from 10 farms experiencing an enzootic pneumonia outbreak were collected and scored. M. hyopneumoniae was detected by real-time PCR and genotyped by MLVA assay in all samples. Results The results showed genotypic variability within single pigs and among lung lobes. At the lobe level, infection with one VNTR type (SN infection) was dominant. Lobes with lesion scores > 0 were associated with positive results for real-time PCR. At the lobe level, no relationship was observed between infections with more than one genotype (MX infections) and the proportion of Mycoplasma-like lesions. Lesion-free lobes presented a higher proportion of MX infections than lobes scored > 0. M. hyopneumoniae was detected more frequently in the right lobe of the lung (p M. hyopneumoniae genotype analyses, including lung lobes with no visible lesions. Conclusion The results did not show a significant association between the number of detected genotypes and the severity of the lesions at the lung lobe level, but revealed the unexpected detection of M. hyopneumoniae genotypes in lesion-free lobes. These results imply that a representative sampling of all lobes may lead to an accurate identification of the VNTR-type distribution. Further studies including factors that can affect pathogenetic evolution of this bacterium could shed light on the complexity of the relationship between genotypes and the lung lesions magnitude.

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool.

The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies, however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.

On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses. Ministry of Education (MOE) National Research Foundation (NRF) Published version This research is supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program funding to the Singapore-MIT Alliance for Research and Technology (SMART) Antimicrobial Resistance Interdisciplinary Research Group (AMR IRG) and the Intra-CREATE Thematic Grant (Cities) grant NRF2019-THE001- 0003a to JT and EJA and funding from the Singapore Ministry of Education and National Research Foundation through an RCE award to Singapore Centre for Environmental Life Sciences Engineering (SCELSE). FW is supported by the Faculty Startup funding from the Center of Infectious Diseases at UTHealth and the UT system Rising STARs award.

Simple Summary In dairy production, antimicrobial resistance (AMR) is both a health and economic issue that may lead to treatment failures and the spread of multidrug-resistant pathogens. Epidemiological and farm data on AMR are instrumental for selecting the appropriate therapy. However, such data are not always available. We investigated the AMR profile of 2612 Escherichia coli strains isolated from cases of calf diarrhea over a 15-year period (2002–2016). Furthermore, the AMR profiles and major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves were examined, with a comparison made between those treated with antimicrobials (n = 406) and not treated (n = 99) as well as between the two age groups to evaluate the potential effects of treatments on AMR and pathogenicity. Resistance to tetracycline was the most common, followed by resistance to sulfamethoxazole/trimethoprim and flumequine. Treated calves showed a higher rate of AMR and virulence genes. These results highlight the risk of the frequent use of antimicrobials on calf microflora in leading to potentially ineffective treatments. A higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol was found in 1-week-old calves, suggesting the environment as a possible AMR source. In conclusion, measures such as improved hygiene in the calving pen, antimicrobial stewardship, and monitoring for resistant pathogens in manure should be promoted to prevent the spread of AMR. Abstract The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.

Simple Summary Antimicrobial resistance (AMR) represents a complex global issue due to the many factors involved. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli deserves attention for its broad repercussions on public health. Moreover, wild host species are of interest, particularly wild boar. Indeed, the constantly increasing population densities and the limited data on AMR in this species lead to health risks where spatial overlap with humans and domestic animals occurs. Therefore, 1504 wild boar fecal samples were analyzed to investigate ESBL/AmpC-producing E. coli and the effects of host-related factors and of human population density on their spread. A high prevalence of ESBL/AmpC-producing E. coli emerged in wild boar, species not treated with antibiotics, supporting that infection may be acquired through environmental contamination, whether of human or animal origin. Young animals were more colonized than older ones, demonstrating higher susceptibility as seen in domestic animals. Moreover, a positive association recorded between frequency of the TEM resistance gene and human population density suggests that spatial overlap may influence the infection in wild boar. Further analyses would be desirable to investigate the origin of the recorded environmental contamination, although a role of wild boar as a maintenance host of AMR strains emerged. Abstract The complex health problem of antimicrobial resistance (AMR) involves many host species, numerous bacteria and several routes of transmission. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli are among the most important strains. Moreover, wildlife hosts are of interest as they are likely antibiotics free and are assumed as environmental indicators of AMR contamination. Particularly, wild boar (Sus scrofa) deserves attention because of its increased population densities, with consequent health risks at the wildlife–domestic–human interface, and the limited data available on AMR. Here, 1504 wild boar fecal samples were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing E. coli and, through generalized linear models, the effects of host-related factors and of human population density on their spread. A prevalence of 15.96% of ESBL/AmpC-producing E. coli, supported by blaCTX-M (12.3%), blaTEM (6.98%), blaCMY (0.86%) and blaSHV (0.47%) gene detection, emerged. Young animals were more colonized by ESBL/AmpC strains than older subjects, as observed in domestic animals. Increased human population density leads to increased blaTEM prevalence in wild boar, suggesting that spatial overlap may favor this transmission. Our results show a high level of AMR contamination in the study area that should be further investigated. However, a role of wild boar as a maintenance host of AMR strains emerged.

A whole virus, inactivated, Porcine Circovirus 2b (PCV2b) vaccine was submitted to a quantal assay of potency, as explained in detail in our companion paper [1]. To this purpose, twenty, 45-day old piglets, checked for maternally-derived antibody (MDA), were allocated to four groups of 5 animals each; these were vaccinated with 800/266/88/0 nanograms, respectively, of an inactivated PCV2b strain, consisting of two distinct virion populations. Twenty-six days later, all the pigs were challenged intranasally with the homologous PCV2b strain. In the presence of a clear dose-dependent protection in terms of viremia, no such effect was observed in terms of weight gain after challenge. The 800 and 266-ng payloads were associated with neutralizing antibody titers above the MDA levels in oral fluids. Higher levels of viremia in control and 88-ng groups [1] coincided with a higher Natural Killer activity of tracheobronchial lymph node cells from PCV2-infected pigs. The PCV2 ORF2-specific ELISPOT assay for IFN-g– secreting cells showed very few (2–4) ORF2-specific cells/105 peripheral blood mononuclear cells beyond the basal levels under our experimental conditions (non-significant differences among groups). Also, no significant differences were observed in the degree of lymphoid tissue hyperplasia among the different groups.

Porcine reproductive and respiratory syndrome (PRRS) affects farmed swine causing heavy direct and indirect losses. The infections sustained by PRRS viruses (PRRSV-1 and PRRSV-2) may give rise to severe clinical cases. This highlights the issue of PRRSV pathogenicity and relevant markers thereof. Since PRRSV strains can be discriminated in terms of immunotypes, we aimed to detect possible correlates of virulence in vitro based on the profile of innate immune responses induced by strains of diverse virulence. To this purpose, 10 field PRRSV isolates were investigated in assays of innate immune response to detect possible features associated with virulence. Tumor necrosis factor-α, interleukin (IL)-1beta, IL-8, IL-10, and caspase-1 were measured in cultures of PRRSV-treated peripheral blood mononuclear cells of PRRS-naive pigs, unable to support PRRSV replication. Two reference PRRSV strains (highly pathogenic and attenuated, respectively), were included in the screening. The PRRSV strains isolated from field cases were shown to vary widely in terms of inflammatory cytokine responses in vitro, which were substantially lacking with some strains including the reference, highly pathogenic one. In particular, neither the field PRRSV isolates nor the reference highly pathogenic strain gave rise to an IL-1beta response, which was consistently induced by the attenuated strain, only. This pattern of response was reversed in an inflammatory environment, in which the attenuated strain reduced the ongoing IL-1beta response. Results indicate that some pathogenic PRRSV strains can prevent a primary inflammatory response of PBMCs, associated with reduced permissiveness of mature macrophages for PRRSV replication in later phases.

Porcine Circovirus 2 (PCV2) vaccines are poorly standardized in terms of antigen payload and correlates of protection. Therefore, twenty, 45-day old piglets were divided into four groups of 5 animals each and vaccinated with 800 / 266 / 88 / 0 nanograms, respectively, of an inactivated PCV2b strain formulated in the same oil adjuvant. Twenty-six days later, all the pigs were challenged intranasally with the homologous PCV2b strain. No clinical signs were observed in the pigs under study. Viremia was observed after challenge in all the control pigs, as well as in 3 pigs of the 266 and 88-ng groups (one and two, respectively). No pigs of the 800-ng group developed viremia. On the basis of post challenge viremia, the PCV2b vaccine under study had a titer of 11 Protective Doses (PD) 50 %, and 1 PD50 amounted to 74 ng of PCV2b Ag. Neutralizing and ELISA Ab titers showed no obvious correlation with protection in the single animals, even though the 800-ng group developed a significantly higher mean Ab response. All the pigs with a PCV2-specific, IFN-gamma response at 3 weeks after vaccination in whole blood samples were protected against viremia. In lymphoid tissues (mainly tonsils and ileum) the presence of sparse reactive histiocytes and multinucleated giant cells was the only PCV2-associated feature and, by immunohistochemistry, only 3 out of 20 subjects showed a low viral load.

The blastogenic response of bovine peripheral blood mononuclear cells (PBMCs) to lipopolysaccharides (LPS) has been investigated for a long time in our laboratories. In particular, a possible correlation between the blastogenic response to LPS and the disease resistance of dairy cows has been suggested in previous studies. Isolated PBMCs from eight cows at three different time points during the transition period (T0 = 15 days before calving; T1 = 7 days post-calving; T2 = 21 days post-calving) were cultured in the presence or absence of LPS, and the blastogenic response was assayed 72 h after in vitro stimulation. Moreover, the gene expression of proinflammatory cytokines and kynurenine pathway molecules was investigated by real-time RT-PCR on both unstimulated and stimulated PBMCs. The cows were retrospectively divided into healthy and diseased, based on the development of peripartum diseases (subclinical ketosis and placenta retention). The comparison between healthy and diseased cows suggested that healthy animals seemed to better control the response to LPS. On the contrary, diseased animals showed a much higher inflammatory response to LPS. Moreover, cows were retrospectively classified as high and low responders based on the in vitro proliferative response of PBMCs to LPS, using the median value as a threshold. Unstimulated PBMCs of low responders showed higher expression of the proinflammatory cytokines Interleukin 1-β (IL-1β), Interleukin 6 (IL-6) and Tumor Necrosis Factor-α (TNF-α), compared to high responders. Our preliminary data suggest that, during the peripartum period, high responders seem to be more tolerant to endotoxins and develop a lower inflammatory response to different stressors. Instead, low responders could be more prone to the development of unwanted inflammatory conditions in response to mild/moderate stressors.

In veterinary medicine, the issue of antimicrobial resistance was mainly addressed in food-producing animals (although companion animals also deserve attention). Indeed, these species may be reservoir of resistant microorganisms, such as extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing bacteria. Dogs in particular may transmit them to close-contact humans. Overall 266 faecal samples of healthy dogs were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing Escherichia coli and the effects of host and environmental factors on their spread. A prevalence of 25.9% of ESBL/AmpC-producing E. coli, supported by blaCTX-M (79.7%), blaTEM (47.8%), blaCMY (13%), and blaSHV (5.8%) gene detection, emerged. Dogs frequenting extra-urban environments showed significantly higher odds of being positive to ESBL/AmpC E. coli (30.2%) compared to urban dogs (16.7%) identifying the environment as a risk factor. About 88.4% of isolates were resistant to cephalosporins, 8.7% to cephalosporins and carbapenems, and 2.9% to cephalosporins, carbapenems, and penicillins. ESBL/AmpC-producing E. coli expressing blaCMY were significantly more resistant to cefoxitin, cefotaxime/clavulanic acid and ceftazidime/clavulanic acid, highlighting its negative effects. Our results suggest the role of domestic dogs as a maintenance host of ESBL/AmpC-producing E. coli leading to a constant health monitoring. The recorded resistances to carbapenems implies attention and further investigations.

Porcine Circovirus 2 (PCV2) vaccines are based on either inactivated whole virion, or recombinant ORF2 capsid protein assembled into Virus-like Particles (VLPs). No data are available instead about the immunizing properties of free, non-assembled capsid protein. To investigate this issue, ORF2 of a reference PCV2b strain was expressed in a Baculovirus-based expression system without assembly into VLPs. The free purified protein was formulated into an oil vaccine at three distinct Ag payloads: 10.8 / 3.6 / 1.2 micrograms /dose. Each dose was injected intramuscularly into five, 37-day old piglets, carefully matched for maternally-derived antibody. Five control piglets were injected with sterile PBS in oil adjuvant. Twenty-eight days later, all the pigs were challenged intranasally with 200,000 TCID50 of PCV2b strain DV6503. After challenge infection, all the pigs remained in good clinical conditions. The recombinant vaccine did not induce significant antibody and PCV2-specific IFN-gamma responses. ELISPOT and lymphocyte proliferation data confirmed poor induction of cell-mediated immunity. In terms of PCV2 viremia, there was no significant difference between vaccinated and control animals. The histological data indicated the absence of a detectable viral load and of PCVAD lesions in both vaccinated and control animals, as well as of histiocytes and multi-nucleated giant cells. We conclude that free, non-assembled ORF2 capsid protein does not induce protective immunity.

The complex health problem of antimicrobial resistance (AMR) involves many host species, numerous bacteria and several routes of transmission. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli are among the most important strains. Moreover, wildlife hosts are of interest as they are likely antibiotics free and are assumed as environmental indicators of AMR contamination. Particularly, wild boar (Sus scrofa) deserves attention because of its increased population densities, with consequent health risks at the wildlife–domestic–human interface, and the limited data available on AMR. Here, 1504 wild boar fecal samples were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing E. coli and, through generalized linear models, the effects of host-related factors and of human population density on their spread. A prevalence of 15.96% of ESBL/AmpC-producing E. coli, supported by blaCTX-M (12.3%), blaTEM (6.98%), blaCMY (0.86%) and blaSHV (0.47%) gene detection, emerged. Young animals were more colonized by ESBL/AmpC strains than older subjects, as observed in domestic animals. Increased human population density leads to increased blaTEM prevalence in wild boar, suggesting that spatial overlap may favor this transmission. Our results show a high level of AMR contamination in the study area that should be further investigated. However, a role of wild boar as a maintenance host of AMR strains emerged.