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Simple Summary: To the authors' knowledge, there is currently no standardised inventory on information on regularly collected routine data on zoonotic infections, meaning that they can spread from animals to humans and the other way around. We used a template with specific questions on the level of the data base and the different pathogens documented in each of these. To support further development in this sector, we gathered information on 37 different data bases, mainly from the human and veterinary sector, and showed opportunities and challenges in joint analysis of data from these data collections. Two-thirds of human infectious diseases are zoonotic diseases and routine data collections exist for each sector (human, veterinary, environmental). However, these operate separately and the collected data are not integrated across sectors. Publicly available information on these routine data collections in terms of metadata and the information collected is sparse. The aim was to create an inventory of routine data collections in the Federal State of Lower Saxony, Germany. A systematic screening of existing routine data collections from the human and veterinary sectors on zoonotic infectious diseases was carried out on the basis of expert interviews. A standardised template was used to collect relevant metadata on data collections and pathogens they contain. The template was transferred to Research Electronic Data Capture tools. We recorded metadata for 19 veterinary, 16 human and 2 other data collections, and for 69 different zoonotic pathogens. The frequencies of a selection of metadata were analysed descriptively. The data collections, which served different purposes, differed, e.g., in underlying population and sampling strategy, export format and access to the original data. We identified challenges for integrated analyses of data from different collections, which need to be addressed to develop a One Health monitoring and surveillance system. [ABSTRACT FROM AUTHOR]

Simple Summary: Among its role within the commensal bacterial flora, Escherichia coli (E. coli) is known as a cause of intestinal or extraintestinal diseases in pets and their owners. In order to reveal factors associated with the carriage of extended spectrum beta-lactamase-producing Escherichia coli in dogs, rectal swabs from 1000 dogs visiting a pet animal clinic in northern Germany within one year were tested. Additional data were sampled regarding, on the one hand, the dog's health and husbandry conditions and, on the other hand, information about the owner´s medical history. Thus, we were able to define seven factors associated with extended spectrum beta-lactamase-producing Escherichia coli carriage. The high number of dogs tested and the exceptional data volume concerning the dog and owner itself, as well as those habits and interactions, underline the importance of our study to avoid the carriage and spread of pathogens, especially regarding the One Health aspect. Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli are an emerging problem in veterinary and human medicine. Our study concentrated on the estimation of the prevalence and factors associated with the carriage of ESBL-producing E. coli in dogs who visited a veterinary clinic in northern Germany in 2017. For this reason, 1000 patients (healthy and sick dogs) were tested, resulting in 1000 samples originating from rectal swabs. Additional data were collected using a self-reported questionnaire that was completed by the dog owner. Factors associated with ESBL carriage were considered for further modeling if p < 0.05 using a two-sided Fisher test. Using a backward elimination procedure, the variables for the final multivariable logistic regression model were identified. In total, 8.9% of the dogs tested were positive for carriage of ESBL-producing E. coli. Seven factors were associated with the colonization of dogs with ESBL-E. coli within the multivariable model, namely husbandry system (p = 0.0019, OR = 3.00; 95% CI: 1.50–6.00), contact with puppies (p = 0.0044, OR = 2.43; 95% CI: 1.32–4.46), feeding of raw meat (p = 0.011, OR = 2.28; 95% CI: 1.21–4.31), food residues (p = 0.0151, OR = 2.31; 95% CI: 1.18–4.53) and food supplements (p = 0.0487, OR = 0.426; 95% CI: 0.18–0.96), and antibiotic treatments of dogs (p = 0.0005, OR = 3.030; 95% CI: 1.62–5.68) or owners (p = 0.041, OR = 2.74; 95% CI: 1.04–7.19) prior to the study. These factors refer to the animals themselves as well as to the owners and their habits or medical treatments. Although the causality and direction of transmission from owners to their dogs cannot be proven, the factor of antibiotic treatment of the owner is clearly associated with the dog's status. [ABSTRACT FROM AUTHOR]

Highlights • A total of 469 isolates originating from 150 livestock farms in Germany were investigated. • In pig and cattle isolates, blaCTX-M family genes were most frequent (94.0%). • Phylogroups A (44.6%) and B1 (35.0%) were the most frequent. • Isolates from broilers differed substantially from those of other isolates. • Associations of farm-related factors with isolate characteristics are demonstrated. Abstract Resistance to β-lactam antibiotics, including third-generation cephalosporins, is of major concern for animal and human health. In this study, extended-spectrum β-lactamase (ESBL) / plasmid-mediated AmpC (pAmpC) β-lactamase -producing Escherichia coli isolates from German livestock farms were characterised and associations of these isolate characteristics with farm-related factors were investigated across different types of livestock. A total of 469 isolates originating from 150 farms (34 broiler farms, 38 fattening pig farms, 43 dairy cattle farms, 35 beef cattle farms) was included in the analyses. ESBL-gene family, phylogroup and phenotypic antimicrobial susceptibility for several antimicrobial agents were determined. This data was used to define different profiles characterising the isolates. Multivariate analyses using a distance-based non-parametric approach were performed to investigate associations between the profiles of the isolates and farm-related factors (e.g. management, husbandry, and environment of the farms). Co-occurrence of ESBL-gene families were not found in any of the isolates analysed. Sixty-eight percent of the isolates carried bla CTX-M variant genes. The frequency of phylogroups was as follows: A (55%), B1 (35%), D (17%) and B2 (3%). The most frequent phenotypic non-wildtype profile was non-wildtype status of solely cefepime (27%). Profiles of isolates from broilers differed substantially from those of other isolates. Associations between farm-related factors and characteristics profiles differed, depending on the isolate characteristics included in the analyses. Some factors describing the farm environment, like waterfowl in the surrounding of the farm, were associated with all tested profiles. The epidemiological method applied defines distances between isolates on basis of isolate characteristics data and is capable of analysing associations between isolate characteristics and epidemiological factors. As additional data, such as plasmid characteristics, gene type, or sequence information could be included in future studies, the method is suitable to identify points of action to reduce the occurrence of antimicrobial resistant bacteria. [ABSTRACT FROM AUTHOR]

Within the scope of a cross-sectional investigation on fattening pig farms conducted in 2011 and 2012, 48 fattening farms in different agricultural regions of Germany were sampled. Primary cultures of boot swabs and collective faecal samples were stored at −80 °C and screened for the presence of the mcr-1 colistin–resistance gene. The laboratory results were linked to farm–related data collected via questionnaire. Logistic regression models were used to investigate the association between occurrence of mcr-1 and farm–related data. Escherichia coli carrying the mcr-1 gene were isolated from 26 of 216 (12.0%) mixed bacterial cultures originating from 12 of 48 (25.0%) farms. Results of the logistic regression analyses indicate that the transmission between pigs or their direct environment is crucial for the occurrence of these resistant bacteria. However, there was no statistically significant association between antimicrobial use and the occurrence of the mcr-1 gene. [ABSTRACT FROM AUTHOR]

Methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) producing enterobacteria (ESBL-E) have emerged in livestock. This study prospectively investigates the prevalence of MRSA and ESBL-E on pig farms and in nasal and stool samples from farmers and compares molecular characteristics of these ESBL-E isolates. In 2014, samples were derived at 51 pig farms in Germany. Per farm, five dust and five fecal samples were collected; one nasal and one stool sample were retrieved from farmers. ESBL-E isolates from humans and environmental isolates from the respective farms were characterized using whole genome sequencing for classical multilocus sequence typing (MLST), determination of ESBL-encoding genes and an ad hoc core genome MLST (cgMLST) analysis. MRSA and ESBL-E were detected on 49 (96%) and 31 (61%) of the farms, respectively; in most cases (59%) simultaneously. Nasal MRSA carriage was detected in 72 of 85 (84.7%) farmers and five of 84 (6.0%) farmers carried ESBL-E. ESBL- Escherichia coli isolates from farmers belonged to MLST STs/ESBL-genes ST10/CTX-M-1, ST196/TEM-52, ST278/TEM-52, ST410/CTX-M-15 and ST453/CTX-M-1. In one case, the human ESBL-E isolate was clonally identical to isolates from the farm environment; in the other four cases typing results indicated potential exchange of resistance determinants between human and environmental isolates, but, comparing the isolates within a minimum spanning tree indicated differences in cgMLST-patterns between the farms (p = 0.076). This study demonstrated rectal ESBL-E carriage rates among farmers, which were similar to those in the general population. Molecular typing suggested that cross-transmission between the farmers and the farm environment is possible. [ABSTRACT FROM AUTHOR]

• Prevalence of ESBL/pAmpC-producing E. coli is highest in chicken meat. • Characteristics of isolates from turkey meat are significantly different to those from chicken. • Prevalence of CTX-M group among the ESBL/pAmpC producing E. coli isolates was highest in turkey (26.0%) and chicken (24.0 %). • Minced meat from beef or pork is contaminated at higher frequency than beef or pork. • Vegetables are contaminated only at a very low level in Germany. The spread of extended-spectrum β-lactamases (ESBLs) in Escherichia coli is a major public health issue and ESBL-producing bacteria are frequently reported in livestock. For the assessment of the role of the foodborne transmission pathway in Germany, detailed data on the prevalence and characteristics of isolates of food origin are necessary. The objective of this study was to describe the prevalence of cefotaxime resistant E. coli as well as ESBL/pAmpC-producing E. coli and their characteristics in foods in Germany. Out of 2256 food samples, the highest prevalence of cefotaxime resistant E. coli was observed in chicken meat (74.9%), followed by turkey meat (40.1%). Prevalence in beef, pork and minced meat was considerably lower (4.2–15.3%). Whereas 18.0% of the raw milk samples, collected at farm level were positive, this was true only for few cheese samples (1.3%). In one out of 399 vegetable samples a cefotaxime-resistant E. coli was isolated. ESBL resistance genes of the CTX-M-group (10.1% of all samples) were most frequently detected, followed by genes of the pAmpC (2.6%), SHV (2.0%) and TEM (0.8%) families. Distribution of ESBL/AmpC-encoding E. coli resistance genes and E. coli phylogroups was significantly different between the chicken related food samples and all other food items. Our study results reflect that consumers might get exposed to ESBL/pAmpC-producing E. coli through several food chains. These results together with those collected at primary production and in the human population in other studies will allow more detailed analysis of the foodborne pathways, considering transmission from livestock populations to food at retail and to consumers in Germany. [ABSTRACT FROM AUTHOR]

Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli are an emerging problem in veterinary and human medicine. Our study concentrated on the estimation of the prevalence and factors associated with the carriage of ESBL-producing E. coli in dogs who visited a veterinary clinic in northern Germany in 2017. For this reason, 1000 patients (healthy and sick dogs) were tested, resulting in 1000 samples originating from rectal swabs. Additional data were collected using a self-reported questionnaire that was completed by the dog owner. Factors associated with ESBL carriage were considered for further modeling if p < 0.05 using a two-sided Fisher test. Using a backward elimination procedure, the variables for the final multivariable logistic regression model were identified. In total, 8.9% of the dogs tested were positive for carriage of ESBL-producing E. coli . Seven factors were associated with the colonization of dogs with ESBL- E. coli within the multivariable model, namely husbandry system ( p = 0.0019, OR = 3.00; 95% CI: 1.50-6.00), contact with puppies ( p = 0.0044, OR = 2.43; 95% CI: 1.32-4.46), feeding of raw meat ( p = 0.011, OR = 2.28; 95% CI: 1.21-4.31), food residues ( p = 0.0151, OR = 2.31; 95% CI: 1.18-4.53) and food supplements ( p = 0.0487, OR = 0.426; 95% CI: 0.18-0.96), and antibiotic treatments of dogs ( p = 0.0005, OR = 3.030; 95% CI: 1.62-5.68) or owners ( p = 0.041, OR = 2.74; 95% CI: 1.04-7.19) prior to the study. These factors refer to the animals themselves as well as to the owners and their habits or medical treatments. Although the causality and direction of transmission from owners to their dogs cannot be proven, the factor of antibiotic treatment of the owner is clearly associated with the dog's status.

Antimicrobial resistance in livestock is a matter of general concern. To develop hygiene measures and methods for resistance prevention and control, epidemiological studies on a population level are needed to detect factors associated with antimicrobial resistance in livestock holdings. In general, regression models are used to describe these relationships between environmental factors and resistance outcome. Besides the study design, the correlation structures of the different outcomes of antibiotic resistance and structural zero measurements on the resistance outcome as well as on the exposure side are challenges for the epidemiological model building process. The use of appropriate regression models that acknowledge these complexities is essential to assure valid epidemiological interpretations. The aims of this paper are (i) to explain the model building process comparing several competing models for count data (negative binomial model, quasi-Poisson model, zero-inflated model, and hurdle model) and (ii) to compare these models using data from a cross-sectional study on antibiotic resistance in animal husbandry. These goals are essential to evaluate which model is most suitable to identify potential prevention measures. The dataset used as an example in our analyses was generated initially to study the prevalence and associated factors for the appearance of cefotaxime-resistant Escherichia coli in 48 German fattening pig farms. For each farm, the outcome was the count of samples with resistant bacteria. There was almost no overdispersion and only moderate evidence of excess zeros in the data. Our analyses show that it is essential to evaluate regression models in studies analyzing the relationship between environmental factors and antibiotic resistances in livestock. After model comparison based on evaluation of model predictions, Akaike information criterion, and Pearson residuals, here the hurdle model was judged to be the most appropriate model.