Assessing the occurrence and transfer dynamics of ESBL/pAmpC-producing Escherichia coli across the broiler production pyramid

Extended-spectrum \u3b2-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

Campylobacter: Animal Reservoirs, Human Infections, and Options for Control

Campylobacteriosis is a frequently diagnosed disease in humans. Most infections are considered foodborne and are caused by Campylobacter jejuni and C. coli. The animal reservoirs of these Campylobacter species, and the sources and routes of transmission, are described and discussed in this chapter. Most warm-blooded animals can be colonized by Campylobacter, but avian species, and in particular poultry, are preferred hosts. Much of the world’s poultry production is colonized by Campylobacter. Source attribution studies estimate that 20–40% of cases are attributed to the handling and consumption of chicken meat, while up to 80% of cases are due to Campylobacter found in the chicken reservoir. The difference suggests that routes other than through the food chain, i.e., environmental contamination, are important. The epidemiology of infections in humans differs between industrialized and low- and middle-income countries. Thus, the most effective interventions would be targeted to primary production. To date, only improved biosecurity is available. If effectively implemented, strict biosecurity can reduce the number of Campylobacter-positive flocks, but implementation to this level has proved difficult for the poultry industry. Available interventions in chicken processing plants can substantially reduce Campylobacter numbers on carcasses and consequently reduce the risk to humans. Public health strategies therefore utilize control programs, which aim at reducing the level of Campylobacter by measures along the food chain. It is now recognized that commercially acceptable complementary interventions for primary production, such as vaccines and feed additives, are urgently needed. Once Campylobacter in poultry is controlled then other minor sources of Campylobacter including contaminated drinking water, direct contact with (pet) animals, and other food items (e.g., red meat and milk) can be addressed

Assessing Biosecurity Compliance in Poultry Farms: A Survey in a Densely Populated Poultry Area in North East Italy

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

Risk factors for sporadic campylobacteriosis: a systematic review and meta-analysis

Campylobacter spp. is an important causative agent of diarrheal illness worldwide. The disease is frequently associated with foodborne transmission, but other routes of exposure are increasingly recognized. A systematic review and meta-analysis of case-control studies were performed to determine the main risk factors associated with sporadic campylobacteriosis. Suitable scientific articles published up to March 2017 were identified through a systematic literature search and subject to methodological quality assessment. From each study, odds ratios (OR) as measures of association were extracted or calculated, as well as study characteristics such as study population, design, type of model used and risk factor categorization. Mixed-effects meta-analytical models were adjusted by population type to appropriate data partitions. From 4453 identified references, the quality assessment stage was passed by 71 case-control studies focusing on sporadic campylobacteriosis. The eligible studies were conducted between 1981 and 2012 and provided 1336 ORs for meta-analysis. The meta-analysis identified international travel (pooled OR=4.626), recent use of gastric antacids (pooled OR=2.911), occupational exposure to animals/carcasses (pooled OR=3.022), and food consumption (in particular raw or undercooked eggs, poultry, beef, and dairy) as the main risks factors for sporadic campylobacteriosis in the mixed population. In the child population, the main risk factors concerned environmental/animal transmission routes (e.g. drinking untreated water (pooled OR=3.261), exposure to recreational water (pooled OR=3.156), exposure to farm/rural environment (pooled OR=3.128), contact with farm animals (pooled OR=2.747), person-to-person transmission (pooled OR=2.736) and consumption of raw milk (pooled OR =2.603). The results of this meta-analysis highlight the importance of overlooked routes and vehicles of transmission (environment, animal contact, and other food vehicles) of Campylobacter that should be explored in dedicated studies.The authors would like to thank Anses staff and the members of the Anses Working Group on Source Attribution of Foodborne Diseases: Moez Sanaa, Laurence Watier, Jean Christophe Augustin, Frédéric Carlin, Laurent Guillier, Nathalie Jourdan-Da Silva, Alexandre Leclercq, Anne Thébault, Nicole Pavio, Isabelle Villena. U. Gonzales-Barron and V. Cadavez are grateful to the Foundation for Food Science and Technology (FCT, Portugal) and FEDER under Programme PT2020 for financial support to CIMO ( UID/AGR/00690/2019 ). U. Gonzales-Barron thanks the national funding by FCT , P.I., through the Institutional Scientific Employment Program contract.info:eu-repo/semantics/publishedVersio

Amoxicillin and thiamphenicol treatments may influence the co-selection of resistance genes in the chicken gut microbiota

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, bla CMY-2, and bla SHV) 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. bla TEM-1, bla SHV, and bla CTX-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. bla TEM-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

Sources and trends of human salmonellosis in Europe, 2015-2019: An analysis of outbreak data

Salmonella remains a major cause of foodborne outbreaks in Europe despite the implementation of harmonized control programmes. Outbreak data are observed at the public health endpoint and provide a picture of the most important sources of human salmonellosis at the level of exposure. To prioritize interventions, it is important to keep abreast of the sources and trends of salmonellosis outbreaks. The objective of this study was to determine the main food sources and recent trends of Salmonella outbreaks in Europe. Salmonella outbreak data from 34 European countries in 2015-2019 were obtained from the European Food Safety Authority (EFSA). For the source attribution analysis, implicated foods were categorized according to EFSA's zoonosis catalogue classification scheme. An established probabilistic source attribution model was applied using the information on the implicated foods, overall and by region and serotype. To assess significant trends in outbreak occurrence, overall and by region and serotype, mixed-effects Poisson models were used. Overall, the most important food source of salmonellosis outbreaks was eggs (33 %, 95 % Uncertainty Interval [UI]: 31-36 %), followed by pork (7 %, 95 % UI: 6-8 %), and (general) meat products (6 %, 95 % UI: 5-8 %). While eggs were the most important food source in all regions, pork was the second most common food source in Northern and Western Europe, and (general) meat products in Eastern and Southern Europe. Outbreaks caused by S. Enteritidis (SE) and other known serotypes (other than SE and S. Typhimurium and its monophasic variant [STM]) were mostly attributed to eggs (37 %, 95 % UI: 34-41 % and 17 %, 95 % UI: 11-25 %, respectively), whereas outbreaks caused by STM were mainly attributed to pork (34 %, 95 % UI: 27-42 %). Overall, there was a significant increase in the number of outbreaks reported between 2015 and 2019, by 5 % on average per year (Incidence Rate Ratio [IRR]: 1.05, 95 % Confidence Interval [CI]: 1.01-1.09). This was driven by a significantly increased number of outbreaks in Eastern Europe, particularly those caused by SE (IRR: 1.15, 95 % CI: 1.09-1.22), whereas in Northern and Southern Europe, outbreaks caused by SE decreased significantly from 2015 to 2019 (IRR: 0.72, 95 % CI: 0.61-0.85; IRR: 0.70, 95 % CI: 0.62-0.79, respectively). Regional, temporal and serotype-associated differences in the relative contributions of the different sources were also observed

Risk factors for sporadic salmonellosis: a systematic review and meta-analysis

Non-typhoidal Salmonella is an important causative agent of diarrheal illness worldwide. A systematic review and meta-analysis of case-control studies were performed to determine the main risk factors associated with sporadic salmonellosis. Suitable scientific articles published up to 2017 were identified through a systematic literature search and subject to methodological quality assessment. From each study, odds ratios (OR) were extracted or calculated, as well as study characteristics such as population type, design, type of model used and risk factor categorization. Mixed-effects meta-analytical models were adjusted by population type to appropriate data partitions. From 3858 identified references, the quality assessment stage was passed by 62 case-control studies focusing on sporadic salmonellosis which provided 1154 ORs for meta-analysis. The meta-analysis identified host-specifics factors, travel, environmental, animal and food exposures as significant risk factors of salmonellosis in the mixed population. For the mixed population, foods significantly associated with salmonellosis were eggs and egg products, composite foods, and meat (pork, red meats other than beef and poultry meats). In the child population, the main risk factors were found for person-to-person transmission, recent use of gastric anti-acids or antibiotics, contact with pets and farm animals, environmental, and food vehicles. Breastfeeding was found to be a protective factor for children. The food vehicles identified in children comprised dairy (milk formula), produce, meat and eggs products. Untreated drinking water was a risk factor for the children and mixed population. The result of the meta-analysis conducted at the international level is very important in the context of increasing international trade in foodstuffs and changes in food consumption patterns.The authors would like to thank Anses staff and the members of the Anses Working Group on Source Attribution of Foodborne Diseases: Moez Sanaa, Jean Christophe Augustin, Fr´ed´eric Carlin, Alexandre Leclercq, Nicole Pavio, Isabelle Villena, and Laurence Watier. U. Gonzales-Barron and V. Cadavez are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to CIMO (UIDB/00690/2020). U. Gonzales- Barron acknowledges the national funding by FCT, P.I., through the institutional scientific employment program contract.info:eu-repo/semantics/publishedVersio

Assessing risk and building resilience to accelerate the transition towards circular food systems

There is potential for circular food systems to improve quality of life for humans, farmed animals, and ecosystems. However, increasing circularity in the food system brings with it novel risks that should be managed to avoid negative unintended consequences. Under circularity, the interconnectivity of food subsystems is likely to increase. For example, waste streams are proposed to be used as feed or fertilizer. Creating such loops brings novel risks that may become reinforcing. Risk is interdependent across system scales and may related to animal welfare, pollution, spread of disease, or international trade. If these risks are not identified and managed, the project of circular food systems may be undermined. We propose a new framework for managing and governing risk within circular food systems, more specifically within the EU including the context of the Green Deal. Our framework places an emphasis on building resilience of food subsystems as a pathway to managing risk. We explore how the current movement toward restructuring of interconnections within the food system to increase circularity may introduce novel and unintended risk factors, and how this connectivity can be managed to mitigate these risks. We outline how risk owners can be identified and connected to improve governance across food system scales. Finally, we explain how resilience principles can be applied to manage changing risk associated with transition to a circular food system