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Colistin has been re-assessed as a critically important antimicrobial in humans due to its efficacy against multi-drug resistant Gram-negative bacteria, in particular P. aeruginosa, A. baumannii, and K. pneumoniae. The recent discovery of mobile colistin resistance (mcr) determinants in humans and animals has brought concerns regarding the future of this antimicrobial. In this paper, we aim to highlight the current challenges with colistin resistant bacteria and to summarize reliable global data on colistin resistance in poultry production. In addition, we present and compare data from a screening for colistin resistance carried out on a collection of clinical Escherichia coli isolated from poultry in Italy. In Europe, resistance rates for Salmonella and E. coli are in general low with sporadic incidence of high colistin resistance levels. Absence of resistance or very low rates have been recorded in countries where colistin is either not employed (e.g. Norway) or used in minimal amounts (e.g. Denmark) in food-producing animals. In large poultry meat producing countries, such as China and Brazil, the widespread use of colistin has resulted in the dissemination of resistance determinants in diverse bacterial species. Worryingly, these bacteria are often co-resistant to other critically important antimicrobials, such as extended-spectrum cephalosporins. The data gap for many countries and for zoonotic bacteria, the role of the “phantom resistome” and the circulation of mcr-carriers expressing resistance phenotypes close or below the current ECOFF values, should be considered in future investigations. The importance of poultry as a cheap protein source and the global effort to mitigate colistin resistance and preserve this essential antimicrobial require a thorough re-assessment of colistin use in poultry. [ABSTRACT FROM AUTHOR]

Poultry are the main reservoir for thermophilic Campylobacter spp., which is the most common causative agent of human bacterial gastroenteritis. The epidemiology of Campylobacter in poultry, particularly in turkeys, is not completely understood. This study aimed at identifying potential sources and transmission routes of thermophilic Campylobacter spp. in commercial turkey farms. C. jejuni and C. coli isolates from breeders (n = 29, 20 C. jejuni and 9 C. coli) and their progeny (n = 51, 18 C. jejuni and 33 C. coli) reared in two different farms for three sequential production cycles were analysed by multilocus sequence typing (MLST). Strains (n = 88, 42 C. jejuni and 46 C. coli) isolated from environmental (i.e. anteroom and in-house overshoes), water (i.e. drinkers and water line), and pest (i.e. flies, Alphitobius diaperinus, and mice) sources were also examined. MLST of C. jejuni and C. coli isolates resulted in 13 and 12 different sequence types (STs) belonging to six and one previously-described clonal complexes (CCs), respectively. Three novel STs were identified. Genetic similarities were detected between isolates from fattening turkeys and the considered environmental, water, and pest sources, and with the breeders to a lesser extent. Source attribution analysis estimated that environmental and water sources accounted for most (∼75%) of fattening turkey isolates and were therefore identified as the most likely sources of flock colonization, followed by pests (∼20%) and breeders (∼5%). These sources may thus be targeted by control measures to mitigate the risk of Campylobacter colonization in commercial turkeys. RESEARCH HIGHLIGHTS High occurrence of C. jejuni and C. coli in commercial turkey flocks. High genetic diversity of C. jejuni and C. coli in commercial turkey flocks. Horizontal transmission responsible for Campylobacter colonization of commercial turkey flocks. Environmental and water sources involved in Campylobacter colonization of commercial turkey flocks. Strategies for prevention and control of Campylobacter colonization of commercial turkey flocks are needed. [ABSTRACT FROM AUTHOR]

Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980, 2007 and 2011, and two commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and may be involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains. [ABSTRACT FROM AUTHOR]

The dispersion of antibiotics in livestock farming represents a health concern worldwide, contributing to the spread of antimicrobial-resistant bacteria through animals, the environment, and humans. Phenolic compounds could be alternatives to antibiotics, once drawbacks such as their low water solubility, bioavailability, and reduced stability are overcome. Although nano- or micro-sized formulations could counter these shortcomings, they do not represent cost-effective options. In this study, three phenolic compounds, obtained from wood-processing manufacturers, were characterized, revealing suitable features such as their antioxidant activity, size, and chemical and colloidal stability for in-field applications. The minimum inhibitory concentration (MIC) of these colloidal suspensions was measured against six bacterial strains isolated from livestock. These particles showed different inhibition behaviors: Colloidal chestnut was effective against one of the most threatening antibiotic-resistant pathogens, i.e., S. aureus, but ineffective toward E. coli. Instead, colloidal pine showed a weak effect on S. aureus but specificity toward E. coli. The present proof-of-concept points at colloidal polyphenols as valuable alternatives for antimicrobial substitutes in the livestock context. [ABSTRACT FROM AUTHOR]

The article discusses a study on the presence of class 1 and 2 integrons in Campylobacter jejuni and Campylobacter coli. The strains in the study originated from industrial poultry farms and flocks throughout Italy. The authors concluded the absence of class 1 and 2 integrons in these strains isolated from poultry.

Norovirus, an ssRNA + virus of the family Caliciviridae, is a leading disease burden in humans worldwide, causing an estimated 600 million cases of acute gastroenteritis every year. Since the discovery of norovirus in the faeces of swine in Japan in the 1990s, swine norovirus has been reported in several countries on several continents. The identification of the human-associated GII.4 genotype in swine has raised questions about this animal species as a reservoir of norovirus with zoonotic potential, even if species-specific P-types are usually detected in swine. This review summarises the available data regarding the geographic distribution of norovirus in swine, the years of detection, the genotype characterisation, and the prevalence in specific production groups. Furthermore, we discuss the major bottlenecks for the detection and characterisation of swine noroviruses. [ABSTRACT FROM AUTHOR]

Simple Summary: Biosecurity is essential for safeguarding the health and welfare of poultry flocks; however, its implementation may face many challenges. The challenges of implementing biosecurity measures in Italian poultry farms and the selection and validation of supporting measures (SMs) to improve compliance were addressed in this study. The methodology included stakeholder surveys, virtual farm tours, group discussions, and farmer coaching. While the level of biosecurity implementation was generally high, individual factors such as personality and behavior influenced its compliance. Virtual farm tours and group discussions proved effective in facilitating interaction and knowledge exchange among stakeholders. However, farmers' preferences for minor changes due to time and cost constraints were highlighted during coaching sessions. Alternative methodologies like virtual farm tours and coaching have shown to be promising in engaging farmers and stakeholders, but further research on personal traits and attitudes is necessary to optimize compliance. This paper describes the selection and validation of supporting measures (SMs) aimed at enhancing biosecurity compliance within Italian poultry farms. A tailored methodology, based on a stakeholders' survey involving farmers and advisors, included a virtual farm tour, group discussion, and farmer coaching. Virtual farm tours and group discussions were delivered during two meetings targeting meat and egg production stakeholders, separately. Coaching was validated in 26 pilot farms (PFs) by assessing farmers' attitudes towards change (i.e., ADKAR®) and farms' biosecurity score (i.e., Biocheck.UgentTM) before and after a minimum six-month period. A total of 20 out of 26 farmers agreed to implement at least one action plan (AP). Full implementation of the agreed APs was observed in ten farms, while others only partially implemented (n = 7) or did not implement (n = 3) the improvement. Most APs focused on enhancing house hygiene locks (n = 7), followed by bacterial auto-control after cleaning and disinfection (n = 4). Scoring tools indicated minimal or no variations in farmers' attitudes towards change and farm biosecurity. Virtual farm tours and group discussions were found to be effective in fostering interaction and facilitating the exchange of experiences and knowledge among farmers and stakeholders of poultry production. Coaching indicated that farmers might prefer implementing minor changes possibly influenced by time and cost constraints associated with structural interventions. These limitations could have also impacted the scores of the farmer/farm. The findings of this study provide a foundation for further application of SMs to improve biosecurity in Italian poultry farms. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: The prevention of the spread of poultry diseases within and among farms largely depends on the adoption of good biosecurity practices. Through the process of profiling European poultry producers, we were able to identify the particular aspects that influence the adoption of biosecurity practices. The results suggest a wide and varied attitude towards biosecurity in the poultry farming community. Generally, most producers appear to be aware of the risks associated with poor biosecurity and the outcomes of carrying out or not carrying out certain practices. Yet, compared with producers of laying hens or parent breeding stock, meat poultry producers (broiler, turkeys, and ducks) appear to have more blocking components with regard to biosecurity. The education level had a positive effect on perception about biosecurity. Poultry producers are not a homogeneous group, and to change their attitudes and actions, approaches must consider the producers' mindset and need to be tailored to the specific needs of the producers. Poultry producers' attitudes towards biosecurity practices were assessed by using the ADKAR® (Awareness, Desire, Knowledge, Ability, and Reinforcement) behavioral change model. Conventional poultry producers (n = 155) from different production types including broilers (n = 35), layers (n = 22), breeders (n = 24), turkeys (n = 19), ducks (n = 23), free-range broilers (n = 11), free-range layers (n = 11), and hatcheries (n = 10) from seven European countries were scored for each ADKAR element (1 = total absence to 5 = perfect fulfilment). Each country performed selected interventions (e.g., coaching, participatory meetings, etc.) to improve biosecurity compliance. After the interventions, significant change was observed in three of the four attitude elements. The overall mean scores ( x ¯ ± SD) obtained during the initial assessment (n = 130) were 4.2 ± 0.6 for Awareness, 4.1 ± 0.7 for Desire, 3.8 ± 0.8 for Knowledge, and 4.0 ± 0.7 for Ability, whereas after intervention, the scores were A = 4.3 ± 0.6, D = 4.2 ± 0.7, K = 4.1 ± 0.7, and Ab = 4.1 ± 0.7. The Reinforcement component was only evaluated after the change and obtained a score of 3.7 ± 0.7 on average. Identifying the elements influencing poultry producers and their behavior related to farm management decisions was useful in guiding our educational interventions to effectively change their behavior. [ABSTRACT FROM AUTHOR]

Farm biosecurity has gained increasing attention worldwide during the last decades because of its role in reducing the occurrence of diseases and improving animal performance. Recently, recommendations to reinforce the concept of farm biosecurity in lower- and middle-income countries have been advised. Therefore, this review aims to provide a comprehensive description of the methods and tools used to assess biosecurity compliance in livestock farms in Africa and formulate recommendations. The present review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis extension for scoping reviews guidelines. Peer-reviewed studies reporting biosecurity assessment in poultry, cattle, pig, goat, or sheep farms in Africa were included. Five databases were searched with no date restrictions. A total of 41 studies across 17 countries were finally selected. Selected studies were all published after 2008, and an increasing trend in the number of papers published per year was noticed. In total, 41 different methods for biosecurity assessment were found to be used in African countries, meaning that even within the same country, the same animal species, and the same farming system, different methods were utilized. In many papers, the methods used for biosecurity evaluation were poorly described. In addition, during the biosecurity assessment, measures related to the purchase of laying hens, egg transport and management, calves, calving and dairy management, and nursery units were almost not considered. These measures should be contemplated in future studies since they are related to important risk factors for the introduction and dissemination of infectious diseases. Interestingly, some measures not considered in European biosecurity tools were identified in the selected studies. The observed high difference in methods used may be due to the lack of regulations on biosecurity in African countries; therefore, the authors recommend the development and implementation of a harmonized and contextualized method for the assessment of biosecurity in livestock farms in Africa. [ABSTRACT FROM AUTHOR]

Colibacillosis, a disease caused by Escherichia coli in broiler chickens has serious implications on food safety, security, and economic sustainability. Antibiotics are required for treating the disease, while vaccination and biosecurity are used for its prevention. This systematic review and meta-analysis, conducted under the COST Action CA18217—European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT), aimed to assess the efficacy of E. coli vaccination in broiler production and provide evidence-based recommendations. A comprehensive search of bibliographic databases, including, PubMed, CAB Abstracts, Web of Science and Agricola, yielded 2,722 articles. Following a defined protocol, 39 studies were selected for data extraction. Most of the studies were experimental infection trials, with only three field studies identified, underscoring the need for more field-based research. The selected studies reported various types of vaccines, including killed (n = 5), subunit (n = 8), outer membrane vesicles/protein-based (n = 4), live/live-attenuated (n = 16), and CpG oligodeoxynucleotides (ODN) (n = 6) vaccines. The risk of bias assessment revealed that a significant proportion of studies reporting mortality (92.3%) or feed conversion ratio (94.8%) as outcomes, had "unclear" regarding bias. The meta-analysis, focused on live-attenuated and CpG ODN vaccines, demonstrated a significant trend favoring both vaccination types in reducing mortality. However, the review also highlighted the challenges in reproducing colibacillosis in experimental setups, due to considerable variation in challenge models involving different routes of infection, predisposing factors, and challenge doses. This highlights the need for standardizing the challenge model to facilitate comparisons between studies and ensure consistent evaluation of vaccine candidates. While progress has been made in the development of E. coli vaccines for broilers, further research is needed to address concerns such as limited heterologous protection, practicability for application, evaluation of efficacy in field conditions and adoption of novel approaches. [ABSTRACT FROM AUTHOR]

Simple Summary: In poultry production, biosecurity is essential for preventing the entry and spread of pathogens in/within farms, with positive impacts on animal health and welfare. This becomes crucial in countries in which the production reaches high productive standards, such as Italy. Although the importance of implementing biosecurity measures (BMs) in poultry farms is well recognized, compliance may not be always optimal. According to the perceptions of interviewed Italian poultry farmers and advisors, biosecurity is implemented well, with different opinions between them. Compared to farmers, advisors claim a lower level of biosecurity implementation, probably because the former have limited outlooks focused on their own farms or consider some BMs not useful and/or effective, while advisors possess a more comprehensive picture of the implementation of biosecurity due to their involvement in multiple farms and productive categories. Stakeholders, mainly advisors, provided useful suggestions for encouraging farmers and workers at poultry farms to adopt BMs they remain reluctant to implement. The level of implementation of biosecurity measures (BMs), the reasons for not implementing BMs and the effectiveness of BMs were assessed according to the perceptions of stakeholders (i.e., farmers and advisors) in Italian poultry farms. For this purpose, data were collected using a questionnaire administered to advisors (n = 37) and farmers (n = 30) of conventional broiler (n = 13) and layer (n = 13), free-range broiler (n = 8) and layer (n = 10), turkey (n = 13), duck (n = 3) and breeder (n = 7) farms between April and September 2021. The frequency of the implementation of BMs was 66.97% and 81.14% according to the answers provided by the advisors and farmers, respectively, with the breeder sector showing the highest level of implementation (85.71%). "Not knowing advantages" (21.49% for advisors) and "other/specific reasons" (21.49% for advisors and 38.32% for farmers) were the most common answers regarding the lack of implementation of BMs for all poultry sectors. Only 31.09% of farmers acknowledged the effectiveness of not-implemented BMs in contrast to 61.02% of advisors, with the layers' stakeholders being the most aware. The findings of this study may be useful for identifying failures in biosecurity and failures to develop intervention strategies to fulfil the biosecurity gaps still present in Italian poultry farms. [ABSTRACT FROM AUTHOR]

The aim of this study was to assess the dynamics of microbial communities and antimicrobial resistance genes (ARGs) in the chicken gut following amoxicillin and thiamphenicol treatments and potential co-selection of ARGs. To this purpose, the microbial community composition, using 16S rRNA NGS, and the abundance of ARGs conferring resistance to β-lactams and phenicols, using qPCRs, were determined. Results revealed that the administered antimicrobials did not significantly reduce the gut microbiota diversity, but changed its composition, with taxa (e.g. Gallibacterium and Megamonas) being enriched after treatment and replacing other bacteria (e.g. Streptococcus and Bifidobacterium). Positive correlations were found between ARGs (e.g. cmlA, blaCMY-2, and blaSHV) and the relative abundance of specific taxa (e.g. Lactobacillus and Subdoligranulum). The selective pressure exerted by both amoxicillin and thiamphenicol resulted in an increased abundance of ARGs conferring resistance to β-lactams (e.g. blaTEM-1, blaSHV, and blaCTX-M1-like) and phenicols (e.g. floR and cmlA). These findings, together with the co-occurrence of genes conferring resistance to the two antimicrobial classes (e.g. blaTEM-1 and cmlA), suggest a possible interaction among antimicrobials on resistance emergence, possibly due to the presence of mobile genetic elements (MGEs) carrying multiple resistance determinants. [ABSTRACT FROM AUTHOR]

To assess and enhance the application of biosecurity measures in poultry farming, an objective measurement tool (Biocheck.UGent™) was already available for broiler and layer. This study describes the development, validation and application of a risk-based weighted scoring tool for breeder, turkey, duck, free-range layer and free-range broiler production. In collaboration with an expert panel (n= 38), five different questionnaires were developed, following the format of the existing Biocheck.UGent scoring tools. Weights were attributed to external (7–9 subcategories) and internal (3–4 subcategories) biosecurity categories, as well as to the corresponding individual questions within each subcategory. The biosecurity measures were prioritized and weighed based on their relative importance in preventing disease transmission. Upon completion of the questionnaire, and upload of all answers to the Biocheck.UGent website, the algorithm generates a biosecurity score varying between ''0" which equals the total absence of any biosecurity measure up to ''100" which refers to full application of all biosecurity measures. The final scoring systems are available online (https://biocheckgent.com/en) for free and have been used to assess biosecurity in 70 breeders, 100 turkeys, 23 ducks, 16 free-range broilers, and 15 free-range layer farms originating from 12 countries so far. On average, the overall biosecurity score (mean ± std. dev) was 78 ± 7 % for breeders, 73 ± 11 % for turkeys, 71 ± 8 % for ducks, 73 ± 8 % for free-range layers and 70 ± 13 % for free-range broilers. There were significant differences (p < 0.05) in biosecurity (both at the overall and subcategory levels) across different poultry types. The overall farm biosecurity score for breeders was significantly higher than that for turkey (p <.001) and duck production (p = 0.001). External biosecurity levels were highest in breeders in comparison to turkeys (p < 0.001), ducks (p = 0.008) and broiler free-range (p = 0.005). There was a notable difference in internal biosecurity levels between duck and turkey (p = 0.041) production as well. The study contributed to the poultry biosecurity database which allows benchmarking of the biosecurity levels of the users' farm results to national or international averages, indicating room for improvement and aiding to motivate stakeholders to enhance their biosecurity levels. [ABSTRACT FROM AUTHOR]

Simple Summary: In intensive animal farming, biosecurity represents a crucial point to guarantee animal welfare and health. Therefore, it is necessary that proper biosecurity measures are complied with and implemented. To date, several tools to assess biosecurity compliance in poultry farms are available with the general purpose of providing an evaluation of the implemented biosecurity measures. With this study, we aimed to assess the level of compliance with biosecurity measures in poultry farms located in the most densely populated Italian poultry area. Standardized biosecurity checklists according to national legislation were used to collect information. The main findings of our study show an overall good level of biosecurity implementation with some measures still requiring improvement. Our study may help to highlight the importance of biosecurity compliance in poultry farms by identifying the main achievements/challenges in a context in which measures are to be implemented by law and poultry production is vertically integrated. Biosecurity in poultry farms represents the first line of defense against the entry and spread of pathogens that may have animal health, food safety, and economic consequences. The aim of this study was to assess biosecurity compliance in poultry farms located in a densely populated poultry area in North East Italy. A total of 259 poultry farms (i.e., broilers, turkeys, and layers) were surveyed between 2018 and 2019 using standardized checklists, and differences in biosecurity compliance between the poultry sectors and years (only for turkey farms) were tested for significance. Among the three sectors, turkey farms showed the highest compliance. Farm hygiene, infrastructure condition, cleaning and disinfection tools, and procedures were the biosecurity measures most complied with. Some deficiencies were observed in the cleanliness of the farm hygiene lock in broiler farms, as well as the presence of the house hygiene lock in broiler and layer farms and an adequate coverage of built-up litter in turkey and broiler farms. In conclusion, this study highlighted a generally high level of biosecurity in the visited poultry farms (probably due to the stringent national regulation and the integration of the poultry industry) and identified some measures that still need to be improved. [ABSTRACT FROM AUTHOR]

Biosecurity is an essential tool for rearing healthy animals. Biosecurity measures (BMs) are well known in poultry production, but it is difficult to assess actual implementation on farms. The aims of this qualitative study were (1) to provide an overview of biosecurity implementation according to poultry farmers in Europe; and (2) to better understand the reported reasons and potential obstacles for not implementing the measures. In seven European Union Member States, 192 farmers (118 under contract with a company and 68 independents) working in seven different categories of poultry production were interviewed on 62 BMs to determine the frequency of implementation and the reasons for non-implementation. Most of the replies (n = 7791) concerning BM implementation were reported by the farmers as "always" implemented (81%), statistically higher for breeders (87%) and layers (82%) and lower for independent farms versus farms under contract with a company (79.5% and 82.5%, respectively). Regardless the poultry production category, the most frequently implemented BMs declared by the farmers were daily surveillance of birds, rodent control and feed storage protection. Standard hygiene practices were also mentioned as high-implementation measures for most production categories, with some deficiencies, such as rendering tank disinfection after each collection and, for meat poultry, disinfection of the feed silo and bacterial control of house cleaning and disinfection between each cycle. The entry of vehicles and individuals onto poultry farms, especially during critical points of eggs collection for breeders and layers, as well as the presence of other animals, such as the "all in/all out" practice, particularly in layers and ducks, were also reported as the least commonly practiced measures. The main reasons for not implementing the measures (n = 1683 replies) were low awareness and poor knowledge of the expected benefits of biosecurity ("no known advantages" 14%, and "not useful" 12%), the lack of training ("not enough training" 5% and "advice" 7%), lack of time (19%), and financial aspects (17%). Despite the good overall biosecurity mentioned by the farmers, these findings highlight certain deficiencies, suggesting room for improvement and the need for targeted and tailored support of poultry farmers in Europe. • 192 poultry farmers in 7 EU countries were interviewed on biosecurity implementation. • In most replies (81%), biosecurity measures were reported as "always implemented". • Main deficiencies were vehicle and personnel entry, and presence of other animals. • Reasons included lack of knowledge or training, lack of time, and cost. • There is room for improvement and a need for tailored support to farmers. [ABSTRACT FROM AUTHOR]

The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs. [ABSTRACT FROM AUTHOR]

Extended-spectrum β-lactamase (ESBL)- and plasmid mediated AmpC-type cephalosporinase (pAmpC)-producing Escherichia coli (ESBL/pAmpC E. coli) in food-producing animals is a major public health concern. This study aimed at quantifying ESBL/pAmpC-E. coli occurrence and transfer in Italy’s broiler production pyramid. Three production chains of an integrated broiler company were investigated. Cloacal swabs were taken from parent stock chickens and offspring broiler flocks in four fattening farms per chain. Carcasses from sampled broiler flocks were collected at slaughterhouse. Samples were processed on selective media, and E. coli colonies were screened for ESBL/pAmpC production. ESBL/pAmpC genes and E. coli phylogroups were determined by PCR and sequencing. Average pairwise overlap of ESBL/pAmpC E. coli gene and phylogroup occurrences between subsequent production stages was estimated using the proportional similarity index, modelling uncertainty in a Monte Carlo simulation setting. In total, 820 samples were processed, from which 513 ESBL/pAmpC E. coli isolates were obtained. We found a high prevalence (92.5%, 95%CI 72.1–98.3%) in day-old parent stock chicks, in which blaCMY-2 predominated; prevalence then dropped to 20% (12.9–29.6%) at laying phase. In fattening broilers, prevalence was 69.2% (53.6–81.3%) at the start of production, 54.2% (38.9–68.6%) at slaughter time, and 61.3% (48.1–72.9%) in carcasses. Significantly decreasing and increasing trends for respectively blaCMY-2 and blaCTX-M-1 gene occurrences were found across subsequent production stages. ESBL/pAmpC E. coli genetic background appeared complex and bla-gene/phylogroup associations indicated clonal and horizontal transmission. Modelling revealed that the average transfer of ESBL/pAmpC E. coli genes between subsequent production stages was 47.7% (42.3–53.4%). We concluded that ESBL/pAmpC E. coli in the broiler production pyramid is prevalent, with substantial transfer between subsequent production levels. [ABSTRACT FROM AUTHOR]

Custom immuno-magnetic devices are desirable tools for biomedical and biotechnological applications. Herein, surface active maghemite nanoparticles (SAMNs) are proposed as a versatile platform for developing tailored immuno-magnetic nano-carriers by simple wet reactions. Two examples for conjugating native and biotinylated antibodies were presented along with their successful applications in the recognition of specific foodborne pathogens. Nanoparticles were functionalized with rhodamine B isothiocyanate (RITC), leading to a fluorescent nano-conjugate, and used for binding anti-Campylobacter fetus antibodies (SAMN@RITC@Anti-Cf). The microorganism was selectively captured in the presence of two other Campylobacter species (C. jejuni and C. coli), as verified by PCR. Alternatively, SAMNs were modified with avidin, forming a biotin-specific magnetic nano-carrier and used for the immobilization of biotinylated anti-Listeria monocytogenes antibodies (SAMN@avidin@Anti-Lm). This immuno-magnetic carrier was integrated in piezoelectric quartz crystal microbalance (QCM) sensor for the detection of L. monocytogenes in milk, showing a detection limit of 3 bacterial cells. The present work presents a new category of customized immuno-magnetic nano-carriers as a competitive option for suiting specific applications.ᅟ [ABSTRACT FROM AUTHOR]

Due to the great number of greater flamingos in captivity and their long life span, studying their behavior and welfare might be useful to improve the husbandry and breeding of this species in zoos. This study aimed to investigate factors affecting the breeding activity of captive greater flamingos (Phoenicopterus roseus) from 2012 to 2016. To estimate reproductive success, the number of pairs, eggs laid, and hatchlings were recorded. In addition, information on age, egg-laying history of the partners, and pair composition was collected. An increase in the number of pairs, eggs, and hatchlings was reported over the years. For each breeding season, there were pairs who laid more than once, especially in 2014 and 2015. Approximately 50% of pairs were monogamous between consecutive years; however, the percentage dropped gradually when comparing nonconsecutive years. Senescence and previous experience seemed to affect the reproductive success of the study flamingos. In conclusion, different factors can influence the reproduction of greater flamingos in zoos. All these factors are related to nonhuman animal welfare and need to be considered in developing and improving management practices. [ABSTRACT FROM AUTHOR]

The aim was to investigate occurrence and diversity of plasmid-mediated resistance to third-generation cephalosporins (3GC) and quinolones in clinical Escherichia coli from 200 industrial poultry farms across Italy. E. coli was isolated from colibacillosis lesions in turkeys ( n  = 109), broilers ( n  = 98) and layers ( n  = 22) between 2008 and 2012. 3GC-resistant isolates were screened for extended-spectrum and AmpC β-lactamase (ESBL/AmpC), while all isolates were tested for plasmid-mediated quinolone resistance (PMQR) genes. ESBL/AmpC- and PMQR-positive isolates were typed by pulsed-field gel electrophoresis and antimicrobial susceptibility testing, and their plasmids were characterised by replicon typing, multilocus sequence typing, restriction fragment length polymorphism and conjugation. EBSL/AmpC genes ( bla CTX-M-1 , bla CTX-M-14 , bla CTX-M-2 , bla SHV-12 and bla CMY-2 ) were detected in 7%, 9% and 4% of isolates from turkeys, broilers and layers, respectively. We identified seven ESBL/AmpC-encoding plasmid types, usually conjugative (78%), with a marked prevalence of IncI1/pST3 plasmids carrying bla CTX-M-1 . PMQR occurred less frequently among isolates from turkeys (0.9%) compared to those from broilers (5%) and layers (4%). The PMQR genes qnrS , qnrB19 and oqxA/B were located on three plasmid types and two non-typeable plasmids, mostly (85%) conjugative. ESBL/AmpC- and PMQR-positive isolates were genetically unrelated and 64% of them were additionally resistant to aminoglycosides, sulfonamides and tetracyclines. Our data show that 3GC- and quinolone-resistant clinical E. coli in Italian poultry production represent a highly diverse population often resistant to most antimicrobials available for poultry. These findings underline the crucial need to develop new strategies for prevention and control of colibacillosis. [ABSTRACT FROM AUTHOR]

Campylobacter species are known to be able to produce biofilm, which represents an ideal protective environment for the maintenance of such fragile bacteria. Since the genetic mechanisms promoting biofilm formation are still poorly understood, in this study we assessed the ability of C. jejuni (n = 7) and C. coli (n = 3) strains isolated from diseased poultry, and previously characterized by whole genome sequencing, to form biofilm. The in vitro analyses were carried out by using a microtiter based protocol including biofilm culturing and fixation, staining with crystal violet, and measurement of the optical density (OD 570). The ability to form biofilm was categorized into four classes (no, weak, moderate, and strong producers). Potential correlations between OD 570 and the presence/absence of virulence determinants were examined. The C. jejuni were classified as no (n = 3), weak (n = 2), and moderate (n = 2) biofilm producers; however, all possessed genes involved in chemotaxis, adhesion, and invasion to the host cells. No genes present exclusively in biofilm producers or in non-biofilm producers were identified. All C. coli were classified as weak producers and showed a similar set of virulence genes between each other. A trend of increased mean OD 570 was observed in the presence of flaA and maf7 genes. No association between biofilm production classes and the explanatory variables considered was observed. The results of this study suggest that further investigations are needed to better identify and characterize the genetic determinants involved in extra-intestinal Campylobacter biofilm formation. • Extra-intestinal Campylobacter jejuni and C. coli are able to produce biofilm. • Motility and adherence factors may be involved in Campylobacter biofilm formation. • flaA and maf7 genes may contribute to biofilm production in Campylobacter. • Biofilm-producing Campylobacter spp. may be a threat for public health. [ABSTRACT FROM AUTHOR]

Background: Campylobacter fetus is a pathogen of major concern for animal and human health. The species shows a great intraspecific variation, with three subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum. Campylobacter fetus fetus affects a broad range of hosts and induces abortion in sheep and cows. Campylobacter fetus venerealis is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus testudinum has been proposed recently based on genetically divergent strains isolated from reptiles and humans. Both C. fetus fetus and C. fetus testudinum are opportunistic pathogens for immune-compromised humans. Biochemical tests remain as the gold standard for identifying C. fetus but the fastidious growing requirements and the lack of reliability and reproducibility of some biochemical tests motivated the development of molecular diagnostic tools. These methods have been successfully tested on bovine isolates but fail to detect some genetically divergent strains isolated from other hosts. The aim of the present study was to develop a highly specific molecular assay to identify and quantify C. fetus strains. Results: We developed a highly sensitive real-time PCR assay that targets a unique region of the 16S rRNA gene. This assay successfully detected all C. fetus strains, including those that were negative for the cstA gene-based assay used as a standard for molecular C. fetus identification. The assay showed high specificity and absence of cross-reactivity with other bacterial species. The analytical testing of the assay was determined using a standard curve. The assay demonstrated a wide dynamic range between 102 and 107 genome copies per reaction, and a good reproducibility with small intra- and inter-assay variability. Conclusions: The possibility to characterize samples in a rapid, sensitive and reproducible way makes this assay a good option to establish a new standard in molecular identification and quantification of C. fetus species. [ABSTRACT FROM AUTHOR]

Background: Campylobacter fetus is a pathogen of major concern for animal and human health. The species shows a great intraspecific variation, with three subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum. Campylobacter fetus fetus affects a broad range of hosts and induces abortion in sheep and cows. Campylobacter fetus venerealis is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus testudinum has been proposed recently based on genetically divergent strains isolated from reptiles and humans. Both C. fetus fetus and C. fetus testudinum are opportunistic pathogens for immune-compromised humans. Biochemical tests remain as the gold standard for identifying C. fetus but the fastidious growing requirements and the lack of reliability and reproducibility of some biochemical tests motivated the development of molecular diagnostic tools. These methods have been successfully tested on bovine isolates but fail to detect some genetically divergent strains isolated from other hosts. The aim of the present study was to develop a highly specific molecular assay to identify and quantify C. fetus strains. Results: We developed a highly sensitive real-time PCR assay that targets a unique region of the 16S rRNA gene. This assay successfully detected all C. fetus strains, including those that were negative for the cstA gene-based assay used as a standard for molecular C. fetus identification. The assay showed high specificity and absence of cross-reactivity with other bacterial species. The analytical testing of the assay was determined using a standard curve. The assay demonstrated a wide dynamic range between 102 and 107 genome copies per reaction, and a good reproducibility with small intra- and inter-assay variability. Conclusions: The possibility to characterize samples in a rapid, sensitive and reproducible way makes this assay a good option to establish a new standard in molecular identification and quantification of C. fetus species. [ABSTRACT FROM AUTHOR]

The aim of the study was to determine the multilocus sequence types of Escherichia coli from diseased farm rabbits and apparently healthy wild lagomorphs, and the genetic relatedness among them. Fifty-five enteropathogenic E. coli from reared rabbits and 32 from wild rabbits and hares were characterised by multilocus sequence typing (MLST) according to the Michigan State University EcMLST scheme. Isolates were differentiated into 37 sequence types (STs), which were grouped into 8 clonal complexes (CCs). The most common ST was ST140 (CC31), followed by ST238 and ST119 (CC17). MLST analysis revealed 22 novel STs. Phylogenetic analyses showed a heterogeneous distribution of STs into 3 clusters of genetically related strains. The genetic relationship among STs of different origin and the detection of new, as well as previously described STs as human pathogens, indicate a widespread distribution and adaptability of particular lineages to different hosts. These findings highlight the need for further research to improve the knowledge about E. coli populations colonising the gut of lagomorphs and their zoonotic potential. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the occurrence of class 1 and 2 integrons in avian pathogenic Escherichia coli (APEC) from poultry in northern Italy. Strains were tested for phenotypic resistance to aminoglycosides and sulphonamides, and the association between the presence of integrons and the resistance to these antimicrobials was evaluated. A total of 299 isolates (158 from turkeys, 110 from broilers, and 31 from layer hens) were collected from 200 industrial farms. Antimicrobial susceptibility test by the disk diffusion method was performed in accordance with the Clinical and Laboratory Standards Institute (CLSI) guidelines. All strains were screened for the presence of class 1 and 2 integrons by PCR and sequencing. About 55% of APEC contained integrons (class 1, 49.8%; class 2, 10.4%). Different variants of the aadA (5 variants) and the dfrA (4 variants) genes, encoding for streptomycin and trimethoprim resistance respectively, were detected in integron-positive isolates. Less common gene cassettes, such as sat, estX, and orfF, were also identified. Fifteen and 4 gene cassette arrays were found among class 1 and 2 integrons, respectively. High levels of resistance were observed for triple sulphonamides (79.3%), streptomycin (67.2%), and sulfamethoxazole combined with trimethoprim (62.2%), whereas resistance against gentamycin (16.7%), kanamycin (14.7%), and apramycin 3.0%) was low. Integron positivity was significantly higher in isolates phenotypically resistant to aminoglycosides (63.6% vs. 37.8%, P < 0.001) and sulfonamides (64.1% vs. 21.1%, P < 0.001) than in susceptible ones. Integron-borne aminoglycoside and sulfonamide resistance in APEC represents a concern for the poultry industry in Italy, since they are among the most commonly used antimicrobials in poultry therapy. [ABSTRACT FROM AUTHOR]

The worldwide spread of Extra-intestinal Pathogenic Escherichia coli (ExPEC), together with the antimicrobial resistance linked with extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (pAmpCs) are pressing threats for public health. This study aimed to investigate the presence of ExPEC genes in third-generation cephalosporin (3 GC)-resistant E. coli and to study their distribution in broiler carcasses at the slaughterhouse after the chilling process. To this purpose, isolates from a collection of 3 GC-resistant E. coli from carcasses of broilers originating from twelve broiler farms and three production chains were investigated. Several multivariate statistical approaches were adopted to elucidate the relationships among features. Phylogroup F was predominant in all broiler batches and was mainly associated with bla TEM and ESBL genes but less correlated to ExPEC genes. Another remarkable finding was the predominance of ExPEC strains assigned to uncommon phylogroups, such as B2, D, E and Clade I, commonly found into the environment. This study represents a first step for a comprehensive characterization of ExPEC genes harboured by 3 GC-resistant E. coli. These findings may be valuable for the identification of potential risks associated to broiler carcasses as source of uncommon E. coli phylogroups. • ExPEC in 26% of 3 GC resistant E. coli from broiler carcasses. • Phylogroup F predominant in broiler carcasses. • Phylogroup F associated with bla TEM and ESBL, but less correlated with ExPEC. • ExPEC associated to minor E. coli phylogroups (B2, D, E and Clade I). [ABSTRACT FROM AUTHOR]

This study was aimed at assessing the antimicrobial resistance (AMR) of Campylobacter isolates from broilers and turkeys reared in industrial farms in Northern Italy, given the public health concern represented by resistant campylobacters in food-producing animals and the paucity of data about this topic in our country. Thirty-six Campylobacter jejuni and 24 Campylobacter coli isolated from broilers and 68 C. jejuni and 32 C. coli from turkeys were tested by disk diffusion for their susceptibility to apramycin, gentamicin, streptomycin, cephalothin, cefotaxime, ceftiofur, cefuroxime, ampicillin, amoxicillin+clavulanic acid, nalidixic acid, flumequine, enrofloxacin, ciprofloxacin, erythromycin, tilmicosin, tylosin, tiamulin, clindamycin, tetracycline, sulfamethoxazole+trimethoprim, chloramphenicol. Depending on the drug, breakpoints provided by Comité de l'antibiogramme de la Société Française de Microbiologie, Clinical and Laboratory Standards Institute, and the manufacturer were followed. All broiler strains and 92% turkey strains were multidrug resistant. Very high resistance rates were detected for quinolones, tetracycline, and sulfamethoxazole+trimethoprim, ranging from 65% to 100% in broilers and from 74% to 96% in turkeys. Prevalence of resistance was observed also against ampicillin (97% in broilers, 88% in turkeys) and at least three cephalosporins (93-100% in broilers, 100% in turkeys). Conversely, no isolates showed resistance to chloramphenicol and tiamulin. Susceptibility prevailed for amoxicillin+clavulanic acid and aminoglycosides in both poultry species, and for macrolides and clindamycin among turkey strains and among C. jejuni from broilers, whereas most C. coli strains from broilers (87.5%) were resistant. Other differences between C. jejuni and C. coli were observed markedly in broiler isolates, with the overall predominance of resistance in C. coli compared to C. jejuni. This study provides updates and novel data on the AMR of broiler and turkey campylobacters in Italy, revealing the occurrence of high resistance to several antimicrobials, especially key drugs for the treatment of human campylobacteriosis, representing a potential risk for public health. [ABSTRACT FROM AUTHOR]

This study aimed to identify and characterize class 1 and 2 integrons and plasmid-mediated quinolones resistance (PMQR) genes in a collection of 113 multidrug resistance (MDR) Escherichia coli isolated from farm and wild lagomorphs between 2006 and 2008 in Northern Italy. Strains were examined for antimicrobial susceptibility by agar disk diffusion method and E-test for colistin (COL); integrons and gene cassettes content by real-time polymerase chain reaction (PCR) and DNA sequencing; PMQR genes by PCR and DNA sequencing; clonal relatedness by multilocus sequence typing; and plasmids by PCR-based replicon typing. Class 1 integrons were detected in 69 isolates (47 farm rabbits, 14 wild rabbits, and 8 wild hares). No class 2 integrons were found. Five different gene cassettes arrays were identified ( aadA1, dfrA1-aadA1, orf in682-dhfrA5, orf in682-dfrA5-orfD ins21, and dfrA17-aadA5). Fifteen percent (17/113) of isolates carried oqxAB, no other PMQR determinants. All but one oqxAB-positive E. coli strains were recovered from farm rabbits. Seven out of 17 strains were associated with the predominant ST238 and carried from three to six different plasmid types, such as IncF, IncHI1, IncI1, IncN, IncP, IncX1, IncY, and ColE. COL resistance was identified in 6/113 strains (5.3%). This study provides new insights on the resistance phenotypes and the prevalence and dissemination of oqxAB in E. coli from farm and wild lagomorphs, suggesting that these animals may be reservoir of these genetic determinants in Italy and thus a potential source of PMQR E. coli for humans. PMQR mediated by oqxAB has not been detected in farm and wild lagomorphs before. [ABSTRACT FROM AUTHOR]

The aim of the study was to carry out a serological survey of Encephalitozoon cuniculi in commercially reared rabbit does (Oryctolagus cuniculi) in Veneto region (Northern Italy). Two hundred and sixty blood samples from 13 farms were examined by a carbon immunoassay (CIA test) to detect the presence of antibodies anti-E. cuniculi. All sampled rabbit does were clinically healthy. Seropositivity against E. cuniculi was found in 196/260 (75.4%) sera and in all the sampled farms (100%). Logistic regression analysis showed that the size of the farm had no statistically significant effect on E. cuniculi positivity; whereas rabbits of the hybrid X showed a higher seropositivity (p < 0.01) than rabbits belonging to other commercial breeds. Moreover, the age seemed to influence the seropositivity (p < 0.05). This serological survey showed a high prevalence of E. cuniculi infection suggesting that this parasite may be endemic in industrial rabbitries in Northern Italy. [ABSTRACT FROM AUTHOR]

• Campylobacter jejuni and C. coli can invade chicken parenchymatous organs. • Motility and adherence factors may be involved in Campylobacter spp. extra-intestinal spread. • Colonization of chicken parenchymatous organs may result in lesions resembling those of AVH/SLD. • Environmental factors may contribute to the development of lesions in parenchymatous organs. • Campylobacter spp. in extra-intestinal tissues may be a threat for public health. Campylobacter jejuni and Campylobacter coli have commonly been considered harmless commensal inhabitants of the chicken gut; however, these Campylobacter spp. are known to be able to multiply in the gut and invade other tissues, negatively affecting host health and performance. In this study, fourteen Campylobacter spp. were isolated from chickens showing foci of necrosis on the liver surface resembling lesions observed in cases of avian vibrionic hepatitis/spotty liver disease. The whole genome sequences of the fourteen isolates were analysed and their virulomes compared to those of Campylobacter reference sequences, aiming to investigate the possible association between virulence genes and the observed pathological lesions. Nine C. jejuni and five C. coli were studied. These Campylobacter shared twelve virulence factors with other isolates originated from chicken livers and hosted a higher number of virulence-associated genes in comparison to the reference genomes, including genes encoding for factors involved in adherence to and invasion of the intestinal epithelial cells. Our findings seem to point out that these twelve common virulence-associated genes, together with the presence of a high number of virulence factors involved in adherence, invasion and motility, might be responsible for the extra-intestinal spread of our isolates and the colonization of parenchymatous tissues, possibly causing the pathological lesions observed. [ABSTRACT FROM AUTHOR]

Simple Summary: Antimicrobial resistance (AMR) is a global threat for human and animal health. Few studies have been carried out in laying hens. We evaluated the antimicrobial susceptibility of commensal Campylobacter jejuni, Escherichia coli, and Enterococcus faecalis isolates in Spanish laying hens in 2018. C. jejuni was highly resistant, and a medium proportion of the isolates were susceptible to all the antimicrobials studied. E. coli showed medium to high percentages of resistance to the antibiotic categories of highest public health risk concern (A and B). Only a low proportion of the isolates were susceptible to all antimicrobials. The E. faecalis resistance to antimicrobials was variable, and very few isolates were susceptible to all antimicrobials. Novel data on AMR in laying hen commensal isolates in Spain was provided, and the AMR levels differed from those reported for poultry in the EU. High resistance to key drugs used in human medicine was found. Therefore, laying hens could be a source of AMR for humans, thus, representing a public health risk. Antimicrobial resistance (AMR) is a global threat for human and animal health. Few studies have been carried out in laying hens. We evaluated the antimicrobial susceptibility of commensal Campylobacter jejuni, Escherichia coli, and Enterococcus faecalis isolates in Spanish laying hens in 2018. The Minimum Inhibitory Concentration (MIC) was used to identify any AMR of the studied isolates by means of a broth microdilution method. C. jejuni was highly resistant to the B category antimicrobials, and 52% of the isolates were susceptible to all the antimicrobials tested. E. coli showed medium and high percentages of resistance to the B and A antibiotic categories, respectively, and 33.33% of the isolates were susceptible to all antimicrobials. The E. faecalis resistance to A category antimicrobials was variable, and 4.62% of the isolates were susceptible to all antimicrobials. In our work, novel data on AMR in laying hen commensal isolates in Spain is provided, and the AMR levels differ from those reported for poultry in the EU. A high resistance to key drugs for human medicine was found, representing a public health risk. [ABSTRACT FROM AUTHOR]

Antimicrobials are commonly used in conventional livestock production and manure is widely applied to agricultural lands as fertilizer. This practice raises questions regarding the effects of fertilization on (i) soil microbiota composition and (ii) spread of antimicrobials and antimicrobial resistance (AMR) in the environment. This study was conducted in a high-density farming area of Northern Italy and aimed at assessing the impact of (dairy cattle, chickens and swine) manure application on soil microbiome, antimicrobial concentrations and antimicrobial resistance gene (ARG) abundance. We found the microbial community composition in manure to be different and less diverse than in soil, with manure application altering only marginally the soil microbiome. Exceptions were the phyla Firmicutes, Tenericutes and Cloacimonetes, which significantly enriched in fertilized soil. Of the antimicrobials investigated, only flumequine concentrations increased after manure application, albeit non-significantly. ARGs were more abundant in manure, with ermA , ermB , bla OXA-1 and oqxA being significantly enriched in fertilized soil. Positive correlations between oqxA and qnrS abundances and flumequine concentrations were observed, together with the co-occurrence of some ARGs and microbial taxa (e.g. oqxA correlated with Acidobacteria and Gemmatimonadetes). This study showed that manure application has little effect on soil microbiome but may contribute to the dissemination of specific ARGs into the environment. Moreover, flumequine residues seem to enhance the emergence of oqxA and qnrS in soil. Unlabelled Image • Manure application does not strongly influence soil microbiome. • Fertilization enriches the abundance of some ARGs (i.e. ermA , ermB , bla oxa-1 and oqxA) harboured in agricultural soil. • Manure-derived ARGs in soil display different dissipation patterns. • Flumequine residues correlate with oqxA and qnrS abundances. • Higher ARG abundances are present in swine vs. dairy and poultry manure. [ABSTRACT FROM AUTHOR]

• Presence of campylobacters potentially pathogenic for humans in captive reptiles. • Three taxa of Campylobacter recently described in chelonians were all isolated. • Data suggest reptilian-associated Campylobacter are not pathogenic for chelonians. • It is crucial to further investigate the epidemiology of Campylobacter in chelonians. The aim of this study was to investigate the occurrence and diversity of Campylobacter species in chelonians. From July 2016 to September 2017, a total of 452 individuals from a large variety of tortoises (n = 366) and turtles/terrapins (n = 86) kept in private collections and breeding centres, wildlife rescue centres, zoos, pet shops, and veterinary clinics from Northern Italy was sampled and subjected to microbiological examination. Campylobacter genus and species confirmation was performed by single and multiplex PCRs. Out of 452 samples, five (1.1%) tested positive: three for C. iguaniorum (two Testudo graeca and one Testudo hermanni), one for C. fetus subsp. testudinum (Stigmochelys pardalis) and one for C. geochelonis (Testudo hermanni). This study suggests that Campylobacter spp. are not common in chelonians, but a variety of species can be detected in these hosts, including those potentially pathogenic for humans. Further studies are needed to understand the epidemiology and the pathogenic potential for both animals and humans of reptile-associated Campylobacter spp. [ABSTRACT FROM AUTHOR]

• ESBL/pAmpC-EC prevalence at the isolate level reflects host colonisation levels. • ESBL/pAmpC-EC were overall subdominant to intestinal E. coli of broilers. • High sample prevalence is not associated with high levels of resistance in broilers. • Acquired genotypes did not differ between the two methodologies. • Correlation between ESBL/pAmpC-EC and total E. coli was found in carcasses. Presence of extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in humans and animals is alarming due to the associated risks of antibiotic therapy failure. ESBL/pAmpC-EC transmission between the human and animal compartments remains controversial. Using cefotaxime-supplemented (selective) media, we recently showed high sample prevalence of ESBL/pAmpC-EC in an integrated broiler chain [i.e. Parent Stock (PS), offspring broilers and their carcasses]. Here, we used a different approach. In parallel with the selective isolation, samples were processed on non-selective media. E. coli isolates were tested for ESBL/pAmpC-production and those found positive were genotyped. For carcasses, total E. coli were enumerated. This approach enabled us to estimate prevalence at the isolate level, which mirrors ESBL/pAmpC-EC colonisation levels. We showed that although present in many animals, ESBL/pAmpC-EC were overall subdominant to intestinal E. coli , indicating that high sample prevalence is not associated with high levels of resistance in individual hosts. This is a relevant aspect for risk assessments, especially regarding the immediate exposure of farm personnel. An exception was a particularly dominant B2/ bla CMY-2 lineage in the gut of imported PS chicks. This predominance obscured presence of latent genotypes, however bias towards particular ESBL/pAmpC-EC genotypes from the selective method or underestimation by the non-selective approach did not occur. At the slaughterhouse, we showed a link between total E. coli and ESBL/pAmpC-EC on carcasses. Mitigation strategies for reducing consumers' exposure should aim at suppressing ESBL/pAmpC-EC in the broiler gut as well as controlling critical points in the processing line. [ABSTRACT FROM AUTHOR]

Microbiota is the entire collection of microorganisms in a specific environment and microbiome is all the genetic material within it. This is a complex system influenced by variations in its ecosystem itself, i.e. soil and gut. Bovine manure is commonly used for the fertilization of agricultural soils and it comprises the intestinal microbiota influenced both by feed and possible residues of drugs used for therapy. The excessive use of antibiotics in animal husbandry and subsequent land application of animal wastes may introduce massive quantities of antimicrobial drugs (AMD) and resistant bacteria into the soil environment. A research project has been granted by the Italian Ministry of School Education, University and Research (PRIN 2015KA3XFH) to evaluate the role of intensive animal farming as potential source of environmental antimicrobial contamination and resistance. To this aim samples of manure and soil (before and 30 days after fertilization) were collected from intensive dairy cow farms located in Veneto and Lombardia regions, where intensive animal farming is widespread. All samples were screened for detecting and quantifying the commonly used AMDs (i.e. beta-lactams, fluoroquinolones, polymyxins and macrolides) by HPLC-MS methods. The microbiome of the samples was determined by employing a culture independent approach based on metagenomics and NGS-sequencing. All samples were negative for AMDs selected. The manure microbiome was homogenous among the different farms and regions, but very different from the soil one. In manure a higher presence of Porphyromonadaceae, Lachnospiraceae, Clostridiaceae, Pseudomonadaceae and Ruminococcaceae families was observed, whereas in soil the Chitinophagaceae family was the most represented. After fertilization, the microbiome composition was not modified in soil, however the absence of drugs concentration in manure may have had a role in this process. The research project will be completed by assessing the prevalence and the diversity of antimicrobial resistance genes to multiple antimicrobial classes by quantitative real time PCR. This is one of the first studies that evaluates the modifications in the microbial communities of manure and soil before and after fertilization. Thanks to the metagenomics analysis, this research project may elucidate the role of intensive animal farming in the diffusion of antimicrobial resistance in the environment. [ABSTRACT FROM AUTHOR]

The presence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-EC) in food-producing animals can negatively affect human and animal health. This study aimed to determine the occurrence of ESBL/AmpC-EC in the whole broiler production pyramid in Italy by sampling three production chains. For each chain, we sampled Parent Stock (PS) chickens at the age of one-day and during the laying period. The offspring of the sampled PS was tracked and sampled in four commercial broiler farms during the first week of life and during the last week before slaughter. Carcasses of these broilers at the slaughterhouse and tissue swabs from colibacillosis cases were also collected. All samples (cloacal swabs from chickens and rinsates from carcasses) were processed on both Eosin Methylene Blue agar (EMB) and EMB supplemented with 1mg/L cefotaxime (CTX-EMB) except for tissue samples, which were analysed only on EMB. Three confirmed E. coli colonies (2 from EMB and 1 from CTX-EMB) were subjected to disk-diffusion test for ESBL/AmpC-production according to CLSI guidelines. Detection rates using CTX-EMB demonstrated the presence of ESBL/AmpC-EC at all levels of the broiler production pyramid. Extremely-high percentages (92.5% on average) were encountered in one-day-old PS chickens, which dropped significantly to moderate ratios (20% on average) during the laying period. Persistent occurrence of ESBL/AmpC-EC was found in broiler farms at both sampling times with an average detection rate of 64.2% (range 25-100%) for day-old broilers to 42.9% before slaughter (range 15-95%). Also at the bottom of the production pyramid, carcasses were highly contaminated with ESBL/AmpC-EC (51.3% on average, range 15-75%). Conversely, detection rates of ESBL/AmpC-EC with EMB were substantially lower. The proportion of positive samples was seven times lower on average compared to CTX-EMB and for 14 out of 42 sampled flocks, no samples were found positive on EMB. Additionally, only 6.6% (10/152) of clinical E. coli showed phenotypic ESBL/AmpC-production. This finding suggests that, although present, ESBL/AmpC-EC colonise the broiler gut at low levels. [ABSTRACT FROM AUTHOR]

In intensive animal farming, antimicrobial drugs (AMD) are used for individual therapy, but also for mass medication involving use of large amounts of drugs. Some of the AMDs are eliminated as such and others as metabolites. Manure is commonly used for the fertilization of agricultural soils potentially resulting in an environmental load of drug residues. The environmental consequences from the soil fertilization with drug-contaminated manure represent a topic of increasing interest. The evaluation of the environmental risks deriving from the use of veterinary medicinal products is mandatory for all the new marketing authorizations in the EU. For the already authorized veterinary drugs this requirement does not exist. Thus, the real scenario of environmental exposure to AMDs remains incomplete. Besides soil and water contamination with undesirable substances, the persistence of veterinary AMDs in the environment may represent a toxicological risk for non-target species (e.g. fishes, plants, aquatic and terrestrial organisms). Additionally, an emerging concern is the occurrence and spread of antimicrobial resistance (AMR) in the environment. Along with its impact on the soil and water resistome, the distribution of drug-contaminated manure can affect the composition and functional properties of microbial communities or microbiome. The reservoir of resistance in the environment is a mix of naturally occurring resistance genes and those added via animal and human waste. Moreover, the selective effects of antimicrobials may have potential serious ecological and public health implications. Indeed, there is an increasing concern that environmental resistance may be transferred to humans. A research project has been granted by the Italian Ministry of School Education, University and Research (PRIN 2015KA3XFH) to evaluate the role of intensive animal farming (poultry, cattle and swine located in two Italian regions), as potential source of environmental antimicrobial contamination and resistance and as potential cause of toxic effects on non-target organisms. Analyses are carried out in order to generate data on antimicrobial concentrations, antimicrobial resistance genes (ARGs) and microbial community composition of animal manure and soil before and after the application of manure. The toxic effects on non-target organisms of the soil and freshwater compartments will be also investigated. [ABSTRACT FROM AUTHOR]

Objective: The emergence of metallo-β-lactamase-producing Enterobacteriaceae is a worldwide health concern. In this study, the first evaluation of MBL genes, blaIMP and blaVIM, in Escherichia coli resistant to imipenem isolated from urine and blood specimens in Qom, Iran is described. Three hundred urine and blood specimens were analysed to detect the presence of E. coli. Resistance to imipenem and other antimicrobials was determined by disk diffusion and MIC. MBL production was screened using CDDT. PCR was also carried out to determine the presence of blaIMP and blaVIM genes in imipenem-resistant isolates. Results: In total, 160 E. coli isolates were collected from March to May 2016. According to disk diffusion, high-level of resistance (20%) to cefotaxime was observed, whereas the lowest (1%) was detected for tetracycline. In addition, five isolates showed resistance to imipenem with a MIC ≥ 4 µg/mL. CDDT test confirmed that five isolates were MBL-producing strains, but no blaIMP and blaVIM genes were detected. Results of this study show a very low level of resistance to imipenem in our geographical area. [ABSTRACT FROM AUTHOR]