Longitudinal monitoring of extended-spectrum-beta-lactamase/AmpC-producing Escherichia coli at German broiler chicken fattening farms

Evolution of the Antibiotic Resistance Levels, Multi-Resistance Patterns, and Presence of Antibiotic Resistance Genes in E. coli Isolates from the Feces of Breeding Hens during the Rearing Period

The food chain acts as an entry point for antibiotic resistance to reach humans and environment. Because of the importance of the poultry sector, we investigated the prevalence and evolution of antibiotic resistance in Escherichia coli isolates from a series of 14,500 breeding hens and their farm environment during the rearing period. Samples included meconium from one-day-old breeders and fecal samples and boot swabs from the breeding sheds of pullets and adult hens. All E. coli isolates from one-day-old chicks, 77% from feces and 61% from boot swabs, were resistant to at least one antibiotic. Cefotaxime and multi-drug resistance in fecal isolates decreased during the rearing period from 41.2% and 80.8% in one-day-old chicks to 3.8% and 33.8% in adults. All genes studied were detected in E. coli from feces and boot swabs, the most common being blaTEM (75%), blaSHV (72%), and qnrB (67%). blaCMY-2 was detected in 100% of one-day-old breeders. The combination of at least one cephalosporin and one quinolone resistance gene was detected in 68.7% of fecal and boot swab isolates. Our results highlight the need to monitor the prevalence of antibiotic resistance on farms and to take appropriate measures to reduce the risk to public and environmental health.

In-silico insights of ESBL variants and tracking the probable sources of ESBL-producing Escherichia coli in a small-scale poultry farm

Commercial broiler farms face challenges of extended spectrum beta-lactamase (ESBL)-producing Escherichia coli transmitted from both vertical and horizontal routes. Understanding the dynamics of ESBL-E. coli transmission in compromised biosecurity settings of small-scale rural poultry farms is essential. This study aimed to elucidate the probable transmission pathways of ESBL-E. coli in such settings, employing phylogenetic analysis and molecular docking simulations to explore the catalytic properties of β-lactamase variants. Sampling was conducted on a small-scale poultry farm in West Bengal, India, collecting 120 samples at three intervals during the broiler production cycle. E. coli isolates underwent resistance testing against eight antimicrobials, with confirmation of ESBL production. Genotypic analysis of ESBL genes and sequencing were performed, alongside molecular docking analyses and phylogenetic comparisons with publicly available sequences. Among 173 E. coli isolates, varying resistance profiles were observed, with complete resistance to cefixime and high resistance to amoxicillin and tetracycline. The incidence of ESBL-E. coli fluctuated over the production cycle, with dynamic changes in the prevalence of blaCTX-M-type and blaSHV-type genes. Phylogenetic analysis indicated partial clonal relationships with human clinical strains and poultry strains from the Indian subcontinent. Molecular docking confirmed the catalytic efficiencies of these ESBL variants. The study highlights probable vertical transmission of ESBL-E. coli and emphasizes drinking water as a potential source of horizontal transmission in small-scale poultry farms. Strict biosecurity measures could prevent the spread of antimicrobial-resistant bacteria in birds and their products in a small scale poultry farm.

Survival of highly related ESBL- and pAmpC- producing Escherichia coli in broiler farms identified before and after cleaning and disinfection using cgMLST

BACKGROUND

Broiler chickens are frequently colonized with Extended-Spectrum Beta-Lactamase- (ESBL-) and plasmid mediated AmpC Beta-Lactamase- (pAmpC-) producing Enterobacterales, and we are confronted with the potential spread of these resistant bacteria in the food chain, in the environment, and to humans. Research focused on identifying of transmission routes and investigating potential intervention measures against ESBL- and pAmpC- producing bacteria in the broiler production chain. However, few data are available on the effects of cleaning and disinfection (C&D) procedures in broiler stables on ESBL- and pAmpC- producing bacteria.

RESULTS

We systematically investigated five broiler stables before and after C&D and identified potential ESBL- and pAmpC- colonization sites after C&D in the broiler stables, including the anteroom and the nearby surrounding environment of the broiler stables. Phenotypically resistant E. coli isolates grown on MacConkey agar with cefotaxime were further analyzed for their beta-lactam resistance genes and phylogenetic groups, as well as the relation of isolates from the investigated stables before and after C&D by whole genome sequencing. Survival of ESBL- and pAmpC- producing E. coli is highly likely at sites where C&D was not performed or where insufficient cleaning was performed prior to disinfection. For the first time, we showed highly related ESBL-/pAmpC- producing E. coli isolates detected before and after C&D in four of five broiler stables examined with cgMLST. Survival of resistant isolates in investigated broiler stables as well as transmission of resistant isolates from broiler stables to the anteroom and surrounding environment and between broiler farms was shown. In addition, enterococci (frequently utilized to detect fecal contamination and for C&D control) can be used as an indicator bacterium for the detection of ESBL-/pAmpC- E. coli after C&D.

CONCLUSION

We conclude that C&D can reduce ESBL-/pAmpC- producing E. coli in conventional broiler stables, but complete ESBL- and pAmpC- elimination does not seem to be possible in practice as several factors influence the C&D outcome (e.g. broiler stable condition, ESBL-/pAmpC- status prior to C&D, C&D procedures used, and biosecurity measures on the farm). A multifactorial approach, combining various hygiene- and management measures, is needed to reduce ESBL-/pAmpC- E. coli in broiler farms.

A comprehensive study of colisepticaemia progression in layer chickens applying novel tools elucidates pathogenesis and transmission of Escherichia coli into eggs

Colisepticaemia caused by avian pathogenic Escherichia coli (APEC) is a challenging disease due to its high economic importance in poultry, dubious pathogenesis and potential link with zoonosis and food safety. The existing in vitro studies can't define hallmark traits of APEC isolates, suggesting a paradigm shift towards host response to understand pathogenesis. This study investigated the comprehensive pathological and microbial progression of colisepticaemia, and transmission of E. coli into eggs using novel tools. In total 48 hens were allocated into three groups and were inoculated intratracheally with ilux2-E. coli PA14/17480/5-/ovary (bioluminescent strain), E. coli PA14/17480/5-/ovary or phosphate buffered saline. Infection with both strains led to typical clinical signs and lesions of colibacillosis as in field outbreaks. Based on lung histopathology, colisepticaemia progression was divided into four disease stages as: stage I (1-3 days post infection (dpi)), stage II (6 dpi), stage III (9 dpi) and stage IV (16 dpi) that were histologically characterized by predominance of heterophils, mixed cells, pyogranuloma, and convalescence, respectively. As disease progressed, bacterial colonization in host organs also decreased, revealed by the quantification of bacterial bioluminescence, bacteriology, and quantitative immunohistochemistry. Furthermore, immunofluorescence, immunohistochemistry, and bacteria re-isolation showed that E. coli colonized the reproductive tract of infected hens and reached to egg yolk and albumen. In conclusion, the study provides novel insights into the pathogenesis of colisepticemia by characterizing microbial and pathological changes at different disease stages, and of the bacteria transmission to table eggs, which have serious consequences on poultry health and food safety.

Quantifying health risks from ESBL-producing Escherichia coli in Dutch broiler production chains and potential interventions using compartmental models

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) in animals are considered a human health threat, because this type of bacteria can serve as a reservoir of antibiotic resistant genes and act as a continuous threat of the emergence of new resistant bacteria, in addition to the direct effect of making infection untreatable. Although the prevalence of ESBL producing bacteria in broilers was drastically reduced in the Netherlands, chicken meat still has the highest prevalence among meat products. Therefore, further control of the ESBL-producing E. coli in the broiler production chain is important to reduce public health risks. The main objectives of this study were to evaluate the effectiveness of intervention scenarios to reduce the transmission of ESBL-producing E. coli in the broiler production chain and to quantitatively estimate the risk to public health. In this study, we developed two different types of transmission models that described the observed time-related decline in prevalence during a production round: one with time-dependent decline in susceptibility and one with partial immunity to phylogenetic groups. Both models incorporated the environmental contamination effect between production rounds and within flocks. The parameter values, including transmission rate and recovery rate, were estimated by Approximate Bayesian computation (ABC) method using data from a longitudinal study in a Dutch organic broiler farm. We applied the models to the three production stages in the broiler production chain, beginning from the Parent Stock (PS) farms, the hatcheries, and to the broiler farms. In our models, eggs were collected from different parent stock farms and transported to the hatchery and from there to a broiler farm.The size of a flock and the number of farms were adjusted to the Dutch situation. Both models were able to describe the observed dynamics within and between the production stages equally well, with estimated ESBL-producing E. coli prevalence of 8.98% and 11.47% in broilers at slaughter and 0.12% and 0.15% in humans due to chicken consumption. Both models indicated that improving farm management to eliminate the bacteria from the environment was the most effective intervention, making this outcome robust. Although chicken meat consumption is not a major risk factor for human carriage of the bacteria according to our models, reducing the bacteria in the PS and broiler farm environment to at least one percent can further decrease the prevalence in humans.

Molecular detection of Shiga toxin and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from sheep and goats

BACKGROUND

The Shiga toxin (Stx)-producing Escherichia coli (STEC) have become important global public health concerns. This study investigated the prevalence, antimicrobial resistance profile, and extended-spectrum beta-lactamase-producing E. coli in sheep and goat faeces.

METHODS AND RESULTS

A total of 53 E. coli isolates were confirmed by PCR targeting the uidA [β-D glucuronidase] gene. The Shiga toxin genes stx1 and stx2, as well as bfpA, vir, eaeA, lt and aafII virulence genes, were detected in this study. Of the 53 isolates confirmed to be STEC, 100% were positive for stx2 and 47.2% for stx1. Three isolates possessed a combination of stx1 + stx2 + eaeA, while four isolates harboured stx1 + stx2 + vir virulence genes. The isolates displayed phenotypic antimicrobial resistance against erythromycin (66.04%), colistin sulphate (43.4%), chloramphenicol (9.4%) and ciprofloxacin (1.9%). A total of 28.8% of the strains were phenotypically considered ESBL producers and contained the beta-lactamase blaCTX-M-9 and blaCTX-M-25 gene groups. A larger proportion of the E. coli strains (86.8%) contained the antibiotic sulphonamide resistant (sulII) gene, while 62.3%, 62.3%, 52.8%, 43.4%, 41.5%, 20.8%, 18.9%, 11.3%, 11.3%, 9.4%, 9.4% and 5.7% possessed mcr-4, floR, mcr-1, tet(A), sulI, tet(O), tet(W), parC, mcr-2, ampC 5, qnrS and ermB genes, respectively. Thirteen isolates of the ESBL-producing E. coli were considered multi-drug resistant (MDR). One Shiga toxin (stx2) and two beta-lactamase genes (blaCTX-M-9 and blaCTX-M-25 groups) were present in 16 isolates. In conclusion, the E. coli isolates from the small stock in this study contained a large array of high antibiotic resistance and virulence profiles.

CONCLUSIONS

Our findings highlight the importance of sheep and goats as sources of virulence genes and MDR E. coli. From a public health and veterinary medicine perspective, the characterization of ESBL producers originating from small livestock (sheep and goats) is crucial due to their close contact with humans.

Detection of Extended-Spectrum β-Lactamase (ESBL) E. coli at Different Processing Stages in Three Broiler Abattoirs

The European Food Safety Authority (EFSA) identified extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)-producing E. coli as one of the main priority hazards for poultry. Different studies detected ESBL-producing E. coli at broiler fattening farms and in abattoirs, concluding that poultry meat is a potential source of human infection. Broiler breast skin samples taken in three abattoirs with different scalding techniques were examined for ESBL-producing Escherichia (E.) coli and their phylogenetic groups. A total of 307 ESBL-producing E. coli isolates were found, and the abattoir with conventional immersion scalding with thermal treatment of the water had the lowest incidence. Phylogroups D/E and B1 were mostly detected, while phylogroups C, D, and E were not detected. Phylogroup B2 was detected in low proportions. The phylogroups B2 and D are important as they have been associated with urinary tract infections in humans, but were only detected in low proportions at different processing stages in this study. Since the risk for the consumer of being infected via chicken meat with ESBL-producing E. coli and E. coli of highly pathogenic phylogroups cannot be excluded, good kitchen hygiene is of great importance.

Lactiplantibacillus plantarum, lactiplantibacillus pentosus and inulin meal inclusion boost the metagenomic function of broiler chickens

BACKGROUND

The inclusion of alternative ingredients in poultry feed is foreseen to impact poultry gut microbiota. New feeding strategies (probiotics/prebiotics) must be adopted to allow sustainable productions. Therefore, the current study aimed to use metagenomics approaches to determine how dietary inclusion of prebiotic (inulin) plus a multi-strain probiotic mixture of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus affected microbiota composition and functions of the gastro-intestinal tract of the broilers during production. Fecal samples were collected at the beginning of the trial and after 5, 11 and 32 days for metataxonomic analysis. At the end of the trial, broilers were submitted to anatomo-pathological investigations and caecal content was subjected to volatilome analysis and DNAseq.

RESULTS

Probiotic plus prebiotic inclusion did not significantly influence bird performance and did not produce histopathological alterations or changes in blood measurements, which indicates that the probiotic did not impair the overall health status of the birds. The multi-strain probiotic plus inulin inclusion in broilers increased the abundance of Blautia, Faecalibacterium and Lachnospiraceae and as a consequence an increased level of butyric acid was observed. In addition, the administration of probiotics plus inulin modified the gut microbiota composition also at strain level since probiotics alone or in combination with inulin select specific Faecalibacterium prausnitzi strain populations. The metagenomic analysis showed in probiotic plus prebiotic fed broilers a higher number of genes required for branched-chain amino acid biosynthesis belonging to selected F. prausnitzi strains, which are crucial in increasing immune function resistance to pathogens. In the presence of the probiotic/prebiotic a reduction in the occurrence of antibiotic resistance genes belonging to aminoglycoside, beta-lactamase and lincosamide family was observed.

CONCLUSIONS

The positive microbiome modulation observed is particularly relevant, since the use of these alternative ingredients could promote a healthier status of the broiler's gut.

Biosecurity and Hygiene Procedures in Pig Farms: Effects of a Tailor-Made Approach as Monitored by Environmental Samples

In livestock, the importance of hygiene management is gaining importance within the context of biosecurity. The aim of this study was to monitor the implementation of biosecurity and hygiene procedures in 20 swine herds over a 12-month period, as driven by tailor-made plans, including training on-farm. The measure of adenosine triphosphate (ATP) environmental contents was used as an output biomarker. The presence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) was also investigated as sentinels of antibiotic resistance. A significant biosecurity improvement (p = 0.006) and a reduction in the ATP content in the sanitised environment (p = 0.039) were observed. A cluster including 6/20 farms greatly improved both biosecurity and ATP contents, while the remaining 14/20 farms ameliorated them only slightly. Even if the ESBL-E. coli prevalence (30.0%) after the hygiene procedures significantly decreased, the prevalence of LA-MRSA (22.5%) was unaffected. Despite the promising results supporting the adoption of tailor-made biosecurity plans and the measure of environmental ATP as an output biomarker, the high LA-MRSA prevalence still detected at the end of the study underlines the importance of improving even more biosecurity and farm hygiene in a one-health approach aimed to preserve also the pig workers health.

Prevalence and Persistence of Ceftiofur-Resistant Escherichia coli in A Chicken Layer Breeding Program

We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were bla_CTX-M-55, bla_CMY and bla_NDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms.

Assessing the Load, Virulence and Antibiotic-Resistant Traits of ESBL/Ampc E. coli from Broilers Raised on Conventional, Antibiotic-Free, and Organic Farms

Poultry is the most likely source of livestock-associated Extended Spectrum Beta-Lactamase (ESBL) and plasmid-mediated AmpC (pAmpC)-producing E. coli (EC) for humans. We tested the hypothesis that farming methods have an impact on the load of ESBL/pAmpC-EC in the gut of broilers at slaughter. Isolates (n = 156) of antibiotic-free (AF), organic (O), and conventional (C) animals were characterized for antibiotic susceptibility and antibiotic resistance genes. Thirteen isolates were whole-genome sequenced. The average loads of ESBL/pAmpC-EC in cecal contents were 4.17 Log CFU/g for AF; 2.85 Log CFU/g for O; and 3.88 Log CFU/g for C type (p < 0.001). ESBL/pAmpC-EC isolates showed resistance to antibiotic classes historically used in poultry, including penicillins, tetracyclines, quinolones, and sulfonamides. Isolates from O and AF farms harbored a lower proportion of resistance to antibiotics than isolates from C farms. Among the determinants for ESBL/pAmpC, CTX-M-1 prevailed (42.7%), followed by TEM-type (29%) and SHV (19.8%). Avian pathogenic E. coli (APEC), belonging to ST117 and ST349, were identified in the collection. These data confirm the possible role of a broiler as an ESBL/AmpC EC and APEC reservoir for humans. Overall, our study suggests that antibiotic-free and organic production may contribute to a reduced exposure to ESBL/AmpC EC for the consumer.

Transmission of antimicrobial resistance (AMR) during animal transport

The transmission of antimicrobial resistance (AMR) between food-producing animals (poultry, cattle and pigs) during short journeys (< 8 h) and long journeys (> 8 h) directed to other farms or to the slaughterhouse lairage (directly or with intermediate stops at assembly centres or control posts, mainly transported by road) was assessed. Among the identified risk factors contributing to the probability of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), the ones considered more important are the resistance status (presence of ARB/ARGs) of the animals pre-transport, increased faecal shedding, hygiene of the areas and vehicles, exposure to other animals carrying and/or shedding ARB/ARGs (especially between animals of different AMR loads and/or ARB/ARG types), exposure to contaminated lairage areas and duration of transport. There are nevertheless no data whereby differences between journeys shorter or longer than 8 h can be assessed. Strategies that would reduce the probability of AMR transmission, for all animal categories include minimising the duration of transport, proper cleaning and disinfection, appropriate transport planning, organising the transport in relation to AMR criteria (transport logistics), improving animal health and welfare and/or biosecurity immediately prior to and during transport, ensuring the thermal comfort of the animals and animal segregation. Most of the aforementioned measures have similar validity if applied at lairage, assembly centres and control posts. Data gaps relating to the risk factors and the effectiveness of mitigation measures have been identified, with consequent research needs in both the short and longer term listed. Quantification of the impact of animal transportation compared to the contribution of other stages of the food-production chain, and the interplay of duration with all risk factors on the transmission of ARB/ARGs during transport and journey breaks, were identified as urgent research needs.

Comparison of approaches for source attribution of ESBL-producing Escherichia coli in Germany

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.

High-Frequency Detection of fosA3 and bla CTX-M-55 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms

Considering the worrying emergence of multidrug resistance, including in animal husbandry and especially in food-producing animals, the need to detect antimicrobial resistance strains in poultry environments is relevant, mainly considering a One Health approach. Thus, this study aimed to conduct longitudinal monitoring of antimicrobial resistance in broiler chicken farms, with an emphasis on evaluating the frequency of resistance to fosfomycin and β-lactams. Escherichia coli was isolated from broiler chicken farms (cloacal swabs, meconium, poultry feed, water, poultry litter, and Alphitobius diaperinus) in northern Paraná from 2019 to 2020 during three periods: the first period (1st days of life), the second period (20th to 25th days of life), and third period (40th to 42nd days of life). Antibiogram tests and the detection of phenotypic extended-spectrum β-lactamase (ESBL) were performed, and they were confirmed by seaching for genes from the bla_CTX–M group. The other resistance genes searched were mcr-1 and fosA3. Some ESBL bla_CTX–M–1 group strains were selected for ESBL identification by sequencing and enterobacterial repetitive intergenic consensus-polymerase chain reaction analysis. To determine the transferability of the bla_{CTX–M–1–} and fosA3-carrying plasmids, strains were subjected to conjugation experiments. A total of 507 E. coli were analyzed: 360 from cloacal swabs, 24 from meconium samples, 3 from poultry feed samples, 18 from water samples, 69 from poultry litter samples, and 33 from A. diaperinus samples. Among the strain isolate, 80% (406/507) were multidrug-resistant (MDR), and 51% (260/507) were ESBL-positive, with the bla_CTX–M–1 group being the most frequent. For the fosA3 gene, 68% (344/507) of the strains isolated were positive, deserves to be highlighted E. coli isolated from day-old chickens (OR 6.34, CI 2.34–17.17), when compared with strains isolated from other origins (poultry litter, A. diaperinus, water, and poultry feed). This work alerts us to the high frequency of the fosA3 gene correlated with the CTX-M-1 group (OR 3.57, CI 95% 2.7–4.72, p < 0.05), especially the bla_CTX–M–55 gene, in broiler chickens. This profile was observed mainly in day-old chicken, with a high percentage of E. coli that were MDR. The findings emphasize the importance of conducting longitudinal monitoring to detect the primary risk points during poultry production.

Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Livestock feces with antimicrobial resistant bacteria reaches the farm floor, manure pit, farm land and wider environment by run off and aerosolization. Little research has been done on the role of dust in the spread of antimicrobial resistance (AMR) in farms. Concentrations and potential determinants of antimicrobial resistance genes (ARGs) in farm dust are at present not known. Therefore in this study absolute ARG levels, representing the levels people and animals might be exposed to, and relative abundances of ARGs, representing the levels in the bacterial population, were quantified in airborne farm dust using qPCR. Four ARGs were determined in 947 freshly settled farm dust samples, captured with electrostatic dustfall collectors (EDCs), from 174 poultry (broiler) and 159 pig farms across nine European countries. By using linear mixed modeling, associations with fecal ARG levels, antimicrobial use (AMU) and farm and animal related parameters were determined. Results show similar relative abundances in farm dust as in feces and a significant positive association (ranging between 0.21 and 0.82) between the two reservoirs. AMU in pigs was positively associated with ARG abundances in dust from the same stable. Higher biosecurity standards were associated with lower relative ARG abundances in poultry and higher relative ARG abundances in pigs. Lower absolute ARG levels in dust were driven by, among others, summer season and certain bedding materials for poultry, and lower animal density and summer season for pigs. This study indicates different pathways that contribute to shaping the dust resistome in livestock farms, related to dust generation, or affecting the bacterial microbiome. Farm dust is a large reservoir of ARGs from which transmission to bacteria in other reservoirs can possibly occur. The identified determinants of ARG abundances in farm dust can guide future research and potentially farm management policy.

Modeling the Impact of Management Changes on the Infection Dynamics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in the Broiler Production

Livestock animals, especially poultry, are a known reservoir for extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli). They may enter the pen either via positive day-old chicks or via the environment. We developed a mathematical model to illustrate the entry and dissemination of resistant bacteria in a broiler pen during one fattening period in order to investigate the effectiveness of intervention measures on this infection process. Different management measures, such as varying amounts of litter, a slow-growing breed or lower stocking densities, were tested for their effects on broiler colonization. We also calculated the impact of products that may influence the microbiota in the chicks' digestive tract, such as pre- or probiotics, feed supplements or competitive exclusion products. Our model outcomes show that a contaminated pen or positive chicks at the beginning of the fattening period can infect the entire flock. Increasing the amount of litter and decreasing the stocking density were shown to be effective in our model. Differences in the route of entry were found: if the chicks are already positive, the litter quantity must be increased to at least six times the standard of 1000 g/m2, whereas, if the pen is contaminated on the first day, three times the litter quantity is sufficient. A reduced stocking density of 20 kg/m2 had a significant effect on the incidence of infection only in a previously contaminated pen. Combinations of two or three measures were effective in both scenarios; similarly, feed additives may be beneficial in reducing the growth rate of ESBL-producing E. coli. This model is a valuable tool for evaluating interventions to reduce the transmission and spread of resistant bacteria in broiler houses. However, data are still needed to optimize the model, such as growth rates or survival data of ESBL-producing E. coli in different environments.

Antimicrobial resistance in Escherichia coli isolated from on-farm and conventional hatching broiler farms in Ireland

Background

On-farm hatching (OH) systems are becoming more common in broiler production. Hatching conditions differ from conventional farms as OH chicks avoid exposure to handling, transport, post-hatch water and feed deprivation. In contrast, chicks in conventional hatching conditions (CH) are exposed to standard hatchery procedures and transported post hatching. The objectives of this pilot study were to investigate the prevalence and frequency of Escherichia coli resistant to antimicrobials, including presumptive ESBL/AmpC-producing E. coli, isolated from environmental and faecal samples from OH versus CH hatching systems, and to investigate the presence of ESBL/AmpC-producing encoding genes.

Results

Environmental samples were collected from one flock in 10 poultry farms (5 OH farms, 5 CH farms) on day 0 post disinfection of the facilities to assess hygiene standards. On D10 and D21 post egg/chick arrival onto the farm, samples of faeces, boot swabs and water drinker lines were collected.

E. coli were isolated on MacConkey agar (MC) and MacConkey supplemented with cefotaxime (MC+). Few E. coli were detected on D0. However, on D10 and D21 E. coli isolates were recovered from faeces and boot swabs. Water samples had minimal contamination. In this study, 100% of cefotaxime resistant E. coli isolates (n=33) detected on selective media and 44% of E. coli isolates (84/192) detected on nonselective media were multidrug resistant (MDR). The antimicrobial resistance (AMR) genotype for the 15 ESBL/AmpC producing isolates was determined using multiplex PCR. Six of these were selected for Sanger sequencing of which two were positive for bla_CMY-2, two for bla_TEM-1 and two were positive for both genes.

Conclusions

There was no difference in E. coli isolation rates or prevalence of AMR found between the OH versus CH systems, suggesting that the OH system may not be an additional risk of resistant E. coli dissemination to broilers compared to the CH systems. The frequency of β-lactam resistant E. coli in boot swab and faeces samples across both OH (24/33 (73%)) and CH (9/33 (27%)) systems may indicate that hatcheries could be a reservoir and major contributor to the transmission of AMR bacteria to flocks after entry to the rearing farms.

Antibiotic-resistant bacteria, antibiotic resistance genes, and antibiotic residues in wastewater from a poultry slaughterhouse after conventional and advanced treatments

Slaughterhouse wastewater is considered a reservoir for antibiotic-resistant bacteria and antibiotic residues, which are not sufficiently removed by conventional treatment processes. This study focuses on the occurrence of ESKAPE bacteria (Enterococcus spp., S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.), ESBL (extended-spectrum β-lactamase)-producing E. coli, antibiotic resistance genes (ARGs) and antibiotic residues in wastewater from a poultry slaughterhouse. The efficacy of conventional and advanced treatments (i.e., ozonation) of the in-house wastewater treatment plant regarding their removal was also evaluated. Target culturable bacteria were detected only in the influent and effluent after conventional treatment. High abundances of genes (e.g., bla_TEM, bla_CTX-M-15, bla_CTX-M-32, bla_OXA-48, bla_CMY and mcr-1) of up to 1.48 × 10⁶ copies/100 mL were detected in raw influent. All of them were already significantly reduced by 1–4.2 log units after conventional treatment. Following ozonation, mcr-1 and bla_CTX-M-32 were further reduced below the limit of detection. Antibiotic residues were detected in 55.6% (n = 10/18) of the wastewater samples. Despite the significant reduction through conventional and advanced treatments, effluents still exhibited high concentrations of some ARGs (e.g., sul1, ermB and bla_OXA-48), ranging from 1.75 × 10² to 3.44 × 10³ copies/100 mL. Thus, a combination of oxidative, adsorptive and membrane-based technologies should be considered.

Multiresistant Gram-Negative Pathogens—A Zoonotic Problem

BACKGROUND

Extended-spectrum-β-lactamase-producing, carbapenemase-producing, and colistin-resistant Enterobacteriaceae (ESBL-E, CPE, and Col-E) are multiresistant pathogens that are increasingly being encountered in both human and veterinary medicine. In this review, we discuss the frequency, sources, and significance of the zoonotic transmission of these pathogens between animals and human beings.

METHODS

This review is based on pertinent publications retrieved by a selective literature search. Findings for Germany are presented in the global context.

RESULTS

ESBL-E are common in Germany in both animals and human beings, with a 6-10% colonization rate in the general human population. A major source of ESBL-E is human-tohuman transmission, partly through travel. Some colonizations are of zoonotic origin (i.e., brought about by contact with animals or animal-derived food products); in the Netherlands, more than 20% of cases are thought to be of this type. CPE infections, on the other hand, are rare in Germany in both animals and human beings. Their main source in human beings is nosocomial transmission. Col-E, which bear mcr resistance genes, have been described in Germany mainly in food-producing animals and their meat. No representative data are available on Col-E in human beings in Germany; in Europe, the prevalence of colonization is less than 2%, with long-distance travel as a risk factor. The relevance of animals as a source of Col-E for human beings is not yet entirely clear.

CONCLUSION

Livestock farming and animal contact affect human colonization with the multiresistant Gram-negative pathogens CPE, ESBL-E and Col-E to differing extents. Improved prevention will require the joint efforts of human and veterinary medicine.

Influence of yeast hydrolysate supplement on growth performance, nutrient digestibility, microflora, gas emission, blood profile, and meat quality in broilers

A total of 1512 Ross 308 broilers (one - day - old) were assigned (random blocks) to 1of 3 dietary treatments with 28 replicates of 18 chicks/cage. The dietary treatments were Corn-soybean-meal based basal diet supplemented with 0%, 0.1%, and 0.2% of commercial yeast hydrolysate (YH [Saccharomyces cerevisiae]). The graded level of YH supplementation has linearly increased broilers body weight gain on d 21, 35, and overall (p = 0.044, 0.029, and 0.036, respectively) experimental period. In addition, the increased level of YH supplementation has linearly reduced feed conversation ratio of broilers on d 21, 35, and overall trial period (p = 0.041, 0.052, and 0.032, respectively). However, the feed intake and mortality of broilers were not affected by the graded level of YH supplementation. Though nutrient digestibility of dry matter (p = 0.012) and nitrogen (p = 0.021) was linearly increased in broilers fed YH supplementation, at the end of the trial it fails to affect the total track digestible energy. Dietary inclusion of YH supplementation showed a beneficial effect on the microbial population as linearly improved lactobacillus (p = 0.011) and reduced Escherichiacoli counts (p = 0.042). An increasing level of YH supplementation has tended to decrease NH₃ (p = 0.069) and linearly decrease H₂S (p = 0.027) of noxious gas emission in broilers. Moreover, dietary YH supplements trend to increase the glucose (p = 0.066) and reduced cholesterol (p = 0.069) level. At the end of the test, YH supplementation elicited a linear reduction in drip loss on days 5 and 7, respectively (p = 0.045, and 0.021). Furthermore, dietary inclusion of YH supplementation had linearly increased villus height (p = 0.051) but fails to affect crypt depth. Therefore, in terms of positive effects on the broiler’s overall performance, we suggest that dietary supplements containing graded YH levels in the broilers diet could serve as a potential alternative for growth promoters.

Are There Effective Intervention Measures in Broiler Production against the ESBL/AmpC Producer Escherichia coli?

Extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase (AmpC) producing Enterobacteriaceae occur frequently in livestock animals and the subsequent stages of the meat production chain and are therefore considered a risk for human health. Strict biosecurity measures and optimal farm management should reduce or even prevent poultry flock colonization at farm level. This review summarizes and evaluates published information on the effectiveness of specific intervention measures and farm management factors aiming to reduce the occurrence and spread of ESBL/AmpC producing or commensal or pathogenic E. coli in broiler chicken farms. In this systematic literature review, a total of 643 publications were analyzed, and 14 studies with significant outcome about the effectiveness of specific measures against E. coli and ESBL/AmpC producing E. coli in broiler chicken farms were found. Different feed additives seem to have an impact on the occurrence of those microorganisms. The measures ‘cleaning and disinfection’ and ‘competitive exclusion’ showed strong effects in prevention in some studies. In summary, some intervention measures showed potential to protect against or eliminate ESBL/AmpC-producing, commensal or pathogenic E. coli at farm level. Due to the high variability in the outcome of the studies, more specific, detailed investigations are needed to assess the potential of the individual intervention measures.

Longitudinal study on antibiotic susceptibility in commensal E. coli from geese raised in free-range production systems

The transmission of antimicrobial resistance bacteria from animals to humans has become an important concern. The extended-spectrum beta-lactamase (ESBL) -AmpC- producing Escherichia coli (ESBL-AmpC EC) and quinolones resistant E. coli are of particular interest. The present study aimed to evaluate the load and prevalence of antibiotic-resistant commensal E. coli along the goose production cycle on 2 free-range farms in central Italy. On A farm, oxytetracycline was administered, while the B farm did not use antibiotics during the geese productive cycle. One hundred geese of 1-day-old from the same batch were divided into the two farms. At hatching, the animals showed an average of E. coli loads was 6.83 ± 0.48 log CFU/g, and 0.28 ± 0.28, 0, 5.12 ± 0.54 log CFU/g for E. coli resistant to nalidixic acid (E. coli^nal), to cefotaxime (E. coli^cef) and to tetracyclines (E. coli^tet), respectively. The loads of E. coli, E. coli^nal, E. coli^cef and E. coli^tet on 224 environmental faecal pools were determined at 8 time points. Antimicrobial susceptibility and molecular characterization of E. coli^cef isolates were performed. The ANOVA was used to assess the difference in bacterial loads between the two farms. We described more than 50% of resistances for tetracyclines in both farms, and sulphonamides and cephazolin in the A farm. The loads of E. coli and E. coli^nal in faeces were estimated at approximately 6–7 log (CFU/g) and 5–6 log (CFU/g) in the two farms, respectively. The average load of extended-spectrum beta-lactamase Escherichia coli (ESBL EC) in goose faeces varied broadly along the production cycle: in the first weeks, a sharp increase was observed in both farms, while later on A farm, the burden of ESBL EC remained steady until the end of the production cycle and on B farm the load dramatically decreased from 6 wk of age onward. An increase in the proportion of E. coli^nal was observed on A farm shortly after the antibiotic administration. Our study shows that the dynamics of antibiotic-resistant E. coli in farmed geese are similar to the ones observed in broilers. However, the risk of the emergence of antibiotic-resistant commensal E. coli, might be mitigated by the adoption of good management practices, including prudent use of antibiotics.

Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms

Biocides are frequently applied as disinfectants in animal husbandry to prevent the transmission of drug-resistant bacteria and to control zoonotic diseases. Concerns have been raised, that their use may contribute to the selection and persistence of antimicrobial-resistant bacteria. Especially, extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli have become a global health threat. In our study, 29 ESBL-/AmpC-producing and 64 NON-ESBL-/AmpC-producing E.coli isolates from three German broiler fattening farms collected in 2016 following regular cleaning and disinfection were phylogenetically characterized by whole genome sequencing, analyzed for phylogenetic distribution of virulence-associated genes, and screened for determinants of and associations between biocide tolerance and antibiotic resistance. Of the 30 known and two unknown sequence types detected, ST117 and ST297 were the most common genotypes. These STs are recognized worldwide as pandemic lineages causing disease in humans and poultry. Virulence determinants associated with extraintestinal pathogenic E.coli showed variable phylogenetic distribution patterns. Isolates with reduced biocide susceptibility were rarely found on the tested farms. Nine isolates displayed elevated MICs and/or MBCs of formaldehyde, chlorocresol, peroxyacetic acid, or benzalkonium chloride. Antibiotic resistance to ampicillin, trimethoprim, and sulfamethoxazole was most prevalent. The majority of ESBL-/AmpC-producing isolates carried bla_CTX-M (55%) or bla_CMY-2 (24%) genes. Phenotypic biocide tolerance and antibiotic resistance were not interlinked. However, biocide and metal resistance determinants were found on mobile genetic elements together with antibiotic resistance genes raising concerns that biocides used in the food industry may lead to selection pressure for strains carrying acquired resistance determinants to different antimicrobials.

Dietary Inclusion of Blood Plasma with Yeast (Saccharomyces cerevisiae) Supplementation Enhanced the Growth Performance, Nutrient Digestibility, Lactobacillus Count, and Reduced Gas Emissions in Weaning Pigs

This experiment was performed to examine the hypothesis that blood plasma (BP) with yeast (Saccharomyces cerevisiae) supplement in the diet of weaning pigs could provoke the growth performance, nutrient digestibility, fecal microbial, and reduce harmful gas excretion. A total of one hundred and eighty healthy piglets were taken and assigned (complete random blocks) to three dietary treatments as: Phase 1: Treatment (TRT) 1-6% BP; TRT 2-3% BP + 3% yeast; TRT 3-6% yeast. Phase 2: TRT 1-3%; BP., TRT 2-1.5% BP + 1.5% yeast; TRT 3- 3% yeast. Phase 3: TRT 1- Control (CON) (Basal diet); TRT 2- CON; TRT 3- CON for six- weeks. Each treatment had twelve replicates and five (three gilts and two barrows) pigs per pen. Dietary inclusion of BP with yeast supplementation significantly increased the body weight of piglets during phase 2 (p = 0.003) and phase 3 (p = 0.032). In addition, TRT2 group piglets had a significant improvement in average daily gain at the end of each phase and overall (p = 0.047, 0.025, 0.018 and 0.012, respectively). At phase 3, TRT2 group piglets showed a significant improvement on nutrient digestibility of dry matter (p = 0.012) and nitrogen (p = 0.040). The fecal microbiota of TRT2 group piglets showed a tendency to increase the number of Lactobacillus counts at phase 1 (p = 0.07) and phase 2 (p = 0.06) as well as, a significant improvement at phase 3 (p = 0.021). In addition, TRT2 group piglets had trend to decrease NH3 (p = 0.074) and H2S (p = 0.069) during phase 2, and significantly reduced NH3 (p = 0.038) and H2S (p = 0.046) at phase 3. However, the fecal score of piglets remains unaffected during the entire trial. At the end of phase 1 piglets' IgG (p = 0.008) was significantly increased with the inclusion of BP with yeast supplementation. Based on the positive effects on body weight, average daily gain, nutrient digestibility, Lactobacillus count, and reduced gas emission, we suggest that dietary supplement with BP and yeast in the diet of weaned piglet could serve as an excellent alternative to antibiotics growth promoters.

Low airborne tenacity and spread of ESBL-/AmpC-producing Escherichia coli from fertilized soil by wind erosion

ESBL-/AmpC-producing Escherichia coli from organic fertilizers were previously detected on soil surfaces of arable land and might be emitted by wind erosion. To investigate this potential environmental transmission path, we exposed ESBL-/AmpC-positive chicken litter, incorporated in agricultural soils, to different wind velocities in a wind tunnel and took air samples for microbiological analysis. No data exist concerning the airborne tenacity of ESBL-/AmpC-producing E. coli. Therefore, we explored the tenacity of two ESBL/AmpC E. coli strains and E. coli K12 in aerosol chamber experiments at different environmental conditions. In the wind tunnel, ESBL/AmpC-producing E. coli were detected in none of the air samples (n = 66). Non-resistant E. coli were qualitatively detected in 40.7% of air samples taken at wind velocities exceeding 7.3 m s^-1 . Significantly increased emission of total viable bacteria with increasing wind velocity was observed. In the aerosol chamber trials, recovery rates of airborne E. coli ranged from 0.003% to 2.8%, indicating a low airborne tenacity. Concluding, an emission of ESBL/AmpC E. coli by wind erosion in relevant concentrations appears unlikely because of the low concentration in chicken litter compared with non-resistant E. coli and their low airborne tenacity, proven in the aerosol chamber trials.

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

Detection of ESBL/AmpC-Producing and Fosfomycin-Resistant Escherichia coli From Different Sources in Poultry Production in Southern Brazil

This study discussed the use of antimicrobials in the commercial chicken production system and the possible factors influencing the presence of Extended-spectrum β-lactamase (ESBL)/AmpC producers strains in the broiler production chain. The aim of this study was to perform longitudinal monitoring of ESBL-producing and fosfomycin-resistant Escherichia coli from poultry farms in southern Brazil (Paraná and Rio Grande do Sul states) and determine the possible critical points that may be reservoirs for these strains. Samples of poultry litter, cloacal swabs, poultry feed, water, and beetles (Alphitobius sp.) were collected during three distinct samplings. Phenotypic and genotypic tests were performed for characterization of antimicrobial resistant strains. A total of 117 strains were isolated and 78 (66%) were positive for ESBL production. The poultry litter presented ESBL positive strains in all three sampled periods, whereas the cloacal swab presented positive strains only from the second period. The poultry litter represents a significant risk factor mainly at the beginning poultry production (odds ratio 6.43, 95% confidence interval 1-41.21, p < 0.05). All beetles presented ESBL positive strains. The predominant gene was bla CTX-M group 2, which occurred in approximately 55% of the ESBL-producing E. coli. The cit gene was found in approximately 13% of the ESBL-producing E. coli as AmpC type determinants. A total of 19 out of 26 fosfomycin-resistant strains showed the fosA3 gene, all of which produced ESBL. The correlation between fosA3 and bla CTX-M group 1 (bla CTX-M55 ) genes was significant among ESBL-producing E. coli isolated from Paraná (OR 3.66, 95% CI 1.9-9.68) and these genetic determinants can be transmitted by conjugation to broiler chicken microbiota strains. Our data revealed that poultry litter and beetles were critical points during poultry production and the presence of fosfomycin-resistant strains indicate the possibility of risks associated with the use of this antimicrobial during production. Furthermore, the genetic determinants encoding CTX-M and fosA3 enzymes can be transferred to E. coli strains from broiler chicken microbiota, thereby creating a risk to public health.

Impact of different management measures on the colonization of broiler chickens with ESBL- and pAmpC- producing Escherichia coli in an experimental seeder-bird model

The colonization of broilers with extended-spectrum β-lactamase- (ESBL-) and plasmid-mediated AmpC β-lactamase- (pAmpC-) producing Enterobacteriaceae has been extensively studied. However, only limited data on intervention strategies to reduce the colonization throughout the fattening period are available. To investigate practically relevant management measures for their potential to reduce colonization, a recently published seeder-bird colonization model was used. Groups of 90 broilers (breed Ross 308) were housed in pens under conventional conditions (stocking of 39 kg/m2, no enrichment, water and feed ad libitum). Tested measures were investigated in separate trials and included (I) an increased amount of litter in the pen, (II) the reduction of stocking density to 25 kg/m2, and (III) the use of an alternative broiler breed (Rowan x Ranger). One-fifth of ESBL- and pAmpC- negative broilers (n = 18) per group were orally co-inoculated with two E. coli strains on the third day of the trial (seeder). One CTX-M-15-positive E. coli strain (ST410) and one CMY-2 and mcr-1-positive E. coli strain (ST10) were simultaneously administered in a dosage of 102 cfu. Colonization of all seeders and 28 non-inoculated broilers (sentinel) was assessed via cloacal swabs during the trials and a final necropsy at a target weight of two kilograms (= d 36 (control, I-II), d 47 (III)). None of the applied intervention measures reduced the colonization of the broilers with both the ESBL- and the pAmpC- producing E. coli strains. A strain-dependent reduction of colonization for the ESBL- producing E. coli strain of ST410 by 2 log units was apparent by the reduction of stocking density to 25 kg/m2. Consequently, the tested management measures had a negligible effect on the ESBL- and pAmpC- colonization of broilers. Therefore, intervention strategies should focus on the prevention of ESBL- and pAmpC- colonization, rather than an attempt to reduce an already existing colonization.

Longitudinal monitoring of multidrug resistance in Escherichia coli on broiler chicken fattening farms in Shandong, China

The extensive use of antibiotics has, in recent years, caused antimicrobial resistance and multidrug resistance in Escherichia coli to gradually develop into a worldwide problem. These resistant E. coli could be transmitted to humans through animal products and animal feces in the environment, thereby creating a problem for bacterial treatment for humans and animals and resulting in a public health issue. Monitoring the resistance of E. coli throughout the broiler fattening period is therefore of great significance for both the poultry industry and public health. In this longitudinal study, samples were taken from 6 conventional broiler fattening farms in Shandong Province, China, at 3 different times within 1 fattening period. The overall isolation rate of E. coli was 53.04% (375/707). Antibiotic resistance was very common in the E. coli isolated from these farms, and differed for different antibiotics, with ampicillin having the highest rate (92.86%) and cefoxitin the lowest (10.12%). Multidrug resistance was as high as 91.07%. More importantly, both the resistance rate of E. coli to the different drugs and the detection rate of drug resistance genes increased over time. The mobile colistin resistance (mcr-1) gene was detected in 24.40% of the strains, and these strains often carried other drug resistance genes, such as those conferring aminoglycoside, β-lactamase, tetracycline, and sulfonamide resistance. Antimicrobial resistance and drug resistance genes in E. coli were least common in the early fattening stage. The individual detection rates of sul1, sul3, aacC4, aphA3, and mcr-1 were significantly lower (P < 0.05) for the early fattening stage than for the middle and late stages. The rational use of antibiotics, in conjunction with the improvement of the breeding environment during the entire broiler fattening cycle, will be helpful in the development of the poultry industry and the protection of public health.

Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers

Extended spectrum beta-lactamase (ESBL)-producing bacteria are resistant to extended-spectrum cephalosporins and are common in broilers. Interventions are needed to reduce the prevalence of ESBL-producing bacteria in the broiler production pyramid. This study investigated two different interventions. The effect of a prolonged supply of competitive exclusion (CE) product and compartmentalization on colonization and transmission, after challenge with a low dose of ESBL-producing Escherichia coli, in broilers kept under semi-field conditions, were examined. One-day-old broilers (Ross 308) (n = 400) were housed in four experimental rooms, subdivided in one seeder (S/C1)-pen and eight contact (C2)-pens. In two rooms, CE product was supplied from day 0 to 7. At day 5, seeder-broilers were inoculated with E. coli strain carrying bla CTX-M- 1 on plasmid IncI1 (CTX-M-1-E. coli). Presence of CTX-M-1-E. coli was determined using cloacal swabs (day 5-21 daily) and cecal samples (day 21). Time until colonization and cecal excretion (log10 CFU/g) were analyzed using survival analysis and linear regression. Transmission coefficients within and between pens were estimated using maximum likelihood. The microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing in cecal content of broilers on days 5 and 21. None of the CE broilers was CTX-M-1-E. coli positive. In contrast, in the untreated rooms 187/200 of the broilers were CTX-M-1-E. coli positive at day 21. Broilers in C2-pens were colonized later than seeder-broilers (Time to event Ratio 3.53, 95% CI 3.14 to 3.93). The transmission coefficient between pens was lower than within pens (3.28 × 10-4 day-2, 95% CI 2.41 × 10-4 to 4.32 × 10-4 vs. 6.12 × 10-2 day-2, 95% CI 4.78 × 10-2 to 7.64 × 10-2). The alpha diversity of the cecal microbiota content was higher in CE broilers than in control broilers at days 5 and 21. The supply of a CE product from day 0 to 7 prevented colonization of CTX-M-1-E. coli after challenge at day 5, likely as a result of CE induced effects on the microbiota composition. Furthermore, compartmentalization reduced transmission rate between broilers. Therefore, a combination of compartmentalization and supply of a CE product may be a useful intervention to reduce transmission and prevent colonization of ESBL/pAmpC-producing bacteria in the broiler production pyramid.

Occurrence of antibiotic resistance genes and microbial source tracking markers in the water of a karst spring in Germany

The emergence of antimicrobial resistances causes serious public health concerns worldwide. In recent years, the aquatic ecosystem has been recognized as a reservoir for antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). The prevalence of 11 ARGs, active against six antibiotic classes (β-lactams, aminoglycosides, tetracycline, macrolides, trimethoprim, and sulfonamides), was evaluated at a karst spring (Gallusquelle) in Germany, using molecular biological methods. In addition, fecal indicator bacteria (FIB), turbidity, electrical conductivity, spring discharge, and microbial source tracking markers specific for human, horse, chicken, and cow were determined. The ARGs most frequently detected were ermB (42.1%), tet(C) (40.8%), sul2 (39.5%), and sul1 (36.8%), which code for resistance to macrolides, tetracycline and sulfonamides, respectively. After a heavy rain event, the increase in FIB in the spring water was associated with the increase in ARGs and human-specific microbial source tracking (MST) markers. The determined correlations of the microbiological parameters, the observed overflow of a combined sewer overflow basin a few days before the increase of these parameters, and the findings of previous studies indicate that the overflow of this undersized basin located 9 km away from the spring could be a factor affecting the water quality of the karst spring. Our results provide a scientific basis for minimization of the input of fecal pollution and thus ARGs into the karst spring.

A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.

Effects of glucose oxidase on growth performance, immune function, and intestinal barrier of ducks infected with Escherichia coli O88

The negative effects of dietary antibiotics have become a widespread concern. It is imperative to search for a new type of green, safe, and efficient feed additive that can replace antibiotics. This study was to investigate the effects of glucose oxidase (GOD) on growth performance, immune function, and intestinal barrier in ducks infected with Escherichia coli O88. First, we established the E. coli challenge model of ducks through a preliminary experiment and then carried out the formal experiment by using 144 1-day-old male lean Peking ducklings (50 ± 2.75 g). All ducks were randomly assigned to 1 of 3 dietary treatment groups of basal diet (control), 30 mg/kg virginiamycin (antibiotic), and 200 U/kg GOD (1,000 U/g). Each group consisted of 6 replications with 8 birds per replicate. At day 7, all ducks were orally administered 0.2 mL E coli O88 (3 × 10⁹ cfu/mL) twice, 8 h apart based on the preliminary experiment. The experiment lasted for 28 d. Dietary supplementation with GOD improved growth performance of ducks infected with E. coli. The GOD increased contents of Ig in plasma and secreted Ig A in jejunal mucosa. The GOD group had lower concentrations of inflammatory cytokines (tumor necrosis factor-α, IL-1β, and IL-6) and their upstream regulator Toll-like receptor 4 in the jejunum of ducks than the control group. Supplementation with GOD increased villus height and decreased crypt depth in the jejunum. The gene expression of tight junction proteins (zonula occludens-1, claudin-1 and claudin-2) was enhanced by adding GOD. The GOD decreased intestinal permeability by reducing the concentrations of diamine oxidase and D-lactic in plasma of ducks. There were no significant differences in almost all the indices tested between the GOD and the antibiotic groups. In conclusion, supplementation of GOD improved growth performance, immune function, and intestinal barrier of ducks infected with E. coli O88. Glucose oxidase may serve as a promising alternative therapy to antibiotics to relieve or prevent colibacillosis in ducks.

Efficacy of six disinfection methods against extended-spectrum beta-lactamase (ESBL) producing E. coli on eggshells in vitro

The presence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli on poultry products is an important issue for veterinary and human health due to the zoonotic infection risk for producers and consumers. The present study focuses on testing the efficacy of six different disinfection methods on eggshell samples, aiming to reduce ESBL producing E. coli contamination on the hatching egg. Sterile eggshell cutouts were artificially contaminated with 10⁸ cfu/ml CTX-M-1 producing E. coli and used as a carrier model to analyze the efficacy of six disinfection methods. The contaminated samples were separated into two groups; 1) contaminated and disinfected, 2) contaminated and non-disinfected. Six independent disinfection protocols were performed following product specifications and protocols. Each eggshell sample was separately crushed, and the total viable bacterial count was calculated to determine the disinfection efficacy. Five out of six tested methods (formaldehyde gassing, hydrogen peroxide + alcohol spray, essential oils spray, peracetic acid foam, and low energetic electron radiation) demonstrated a reduction or completely eliminated the initial ESBL producing E. coli contamination. One method (essential oils as cold fog) only partly reached the expected efficacy threshold (reduction of >10² cfu/ml) and the result differed significantly when compared to the reference method i.e. formaldehyde gassing.

Occurrence of extended-spectrum beta-lactamase-producing Enterobacteriaceae, microbial loads, and endotoxin levels in dust from laying hen houses in Egypt

Background

Poultry houses are often highly contaminated with dust, which might contain considerable amounts of microorganisms and endotoxins. The concentrations of microorganisms and endotoxins in dust from laying hen houses in Egypt are unknown. However, to estimate the risks for birds, the environment, and people working in laying hen houses, it is important to gather information about the composition of these dusts. Here we report the microbial loads, the occurrence of antimicrobial-resistant bacteria, and endotoxin concentrations in dust samples from 28 laying hen farms in Dakahliya Governorate, Egypt, and discuss the results relevant to the literature.

Results

Pooled settled dust samples (n = 28) were analyzed for total viable counts of bacteria and fungi (CFU/g), the occurrence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Salmonella spp., and methicillin-resistant Staphylococcus aureus (MRSA), and endotoxin concentrations (ng/g). The means and standard deviations of total viable counts were 7.10 × 10⁸ ± 2.55 × 10⁹ CFU/g for bacteria and 5.37 × 10⁶ ± 7.26 × 10⁶ CFU/g for fungi. Endotoxin levels varied from 2.9 × 10⁴ to 6.27 × 10⁵ ng/g. None of the tested samples contained Salmonella spp. or MRSA. In contrast, by direct plating, Enterobacteriaceae were found frequently (57%; n = 16), and suspected ESBL-producing Enterobacteriaceae occurred in 21% (n = 6) of the sampled barns. Using an enrichment method, the detection of Enterobacteriaceae and suspected ESBL-producing Enterobacteriaceae increased to 20 and 16 positive barns, respectively. Taking results from both methods into account, Enterobacteriaceae and suspected ESBL-producing Enterobacteriaceae were detected in 23 barns Overall, 100 ESBL suspected isolates (Escherichia coli, n = 64; Enterobacter cloacae, n = 20; and Klebsiella pneumoniae n = 16) were identified to species level by MALDI-TOF MS. Isolates from 20 barns (71% positive barns) were confirmed as ESBL producing Enterobacteriaceae by the broth microdilution test.

Conclusions

Dust in Egyptian laying hen houses contains high concentrations of microorganisms and endotoxins, which might impair the health of birds and farmers when inhaled. Furthermore, laying hens in Egypt seem to be a reservoir for ESBL-producing Enterobacteriaceae. Thus, farmers are at risk of exposure to ESBL-producing bacteria, and colonized hens might transmit these bacteria into the food chain.

Early life supply of competitive exclusion products reduces colonization of extended spectrum beta-lactamase-producing Escherichia coli in broilers

Broilers are an important reservoir of extended spectrum beta-lactamase and AmpC beta-lactamase (ESBL/pAmpC)-producing bacteria. In previous studies, a single supply of a competitive exclusion (CE) product before challenge with a high dose of ESBL/pAmpC-producing Escherichia coli led to reduced colonization, excretion, and transmission, but could not prevent colonization. The hypothesized mechanism is competition; therefore, in this study the effect of a prolonged supply of CE products on colonization, excretion, and transmission of ESBL-producing E. coli after challenge with a low dose at day 0 or day 5 was investigated. Day-old broilers (Ross 308) (n = 220) were housed in isolators. Two CE products, containing unselected fermented intestinal bacteria (CEP) or a selection of pre- and probiotics (SYN), were supplied in drinking water from day 0 to 14. At day 0 or 5, broilers were challenged with 0.5 mL with 10¹ or 10² cfu/mL E. coli encoding the beta-lactamase gene bla_CTX-M-1 on an IncI plasmid (CTX-M-1-E. coli). Presence and concentration of CTX-M-1-E. coli were determined using cloacal swabs (days 0–14, 16, 19, and 21) and cecal content (day 21). Cox proportional hazard model and a mixed linear regression model were used to determine the effect of the intervention on colonization and excretion (log₁₀ cfu/g). When challenged on the day of hatch, no effect of CEP was observed. When challenged at day 5, both CEP and SYN led to a prevention of colonization with CTX-M-1-E. coli in some isolators. In the remaining isolators, we observed reduced time until colonization (hazard ratio between 3.71 × 10⁻³ and 3.11), excretion (up to −1.60 log₁₀ cfu/g), and cecal content (up to −2.80 log₁₀ cfu/g), and a 1.5 to 3-fold reduction in transmission rate. Colonization after a low-dose challenge with ESBL-producing E. coli can be prevented by CE products. However, if at least 1 bird is colonized it spreads through the whole flock. Prolonged supply of CE products, provided shortly after hatch, may be applicable as an intervention to reduce the prevalence of ESBL/pAmpC-producing bacteria in the broiler production chain.

Efficacy of a competitive exclusion culture against extended-spectrum β-lactamase-producing Escherichia coli strains in broilers using a seeder bird model

Background

Administration of a competitive exclusion culture (CE culture) has the potential to induce protective effects in very young chicks against caecal colonisation by EEC (= extended-spectrum β-lactamases [ESBL] and AmpC-type [AmpC] beta-lactamases producing Escherichia coli). The study aimed to verify the protective capacity of a CE culture in broilers using the seeder bird model against EEC exposure of the chicks.

Results

Introduction of infected seeder birds resulted in rapid and strong caecal colonisation of four different EEC challenge strains tested in untreated contact broilers. Compared to controls the broilers pre-treated with the CE culture showed a considerable decrease in caecal load of different EEC challenge strains from about 3.0–3.5 log₁₀ units (P < 0.05) on day 9 of life to 2.5–3.0 log₁₀ units (P < 0.05) on day 37. A slightly higher protective level of the CE culture in layer birds than in broilers raises the question on reasons for possible differences in the efficacy of CE culture in broiler and layer breeds. Whether the diet’s protein content has an impact on both normal intestinal flora composition and the efficacy of CE cultures against EEC or other pathogens remains open and needs further elucidation.

Conclusions

Our findings suggest that CE cultures of undefined composition can be valuable to reduce the intestinal colonisation by EEC in newly hatched broilers.

Individual training for farmers based on results from protein and ATP rapid tests and microbiological conventional cultural methods improves hygiene in pig fattening pens

Optimal hygiene management is an essential part of maintaining a high standard of health in conventional pig production systems and for the successful interruption of infection chains. Currently, efficiency assessments on cleaning and disinfection are only performed by visual inspection or are neglected completely. The aim of this study was to evaluate the available methods for on farm monitoring of hygiene, identify critical points in pig pens and use the data obtained for training purposes. In addition to visual inspection by assessing the cleanliness, microbiological swab samples, i.e., aerobic total viable count (TVC), total coliform count, methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum β-lactamases-producing bacteria (ESBL), swab samples for ATP as well as protein residues and agar contact plates combined with 3 different culture media, were applied and ranked according to their suitability for livestock farming. Samples were collected on at least 15 critical points from one representative pen on 6 pig fattening farms with various hygiene management practices after cleaning and disinfection. After the first sampling, farmers were trained with their individual results, and sampling was repeated 6 mo after training. Nipple drinkers, feeding tubes (external and inner surface), and troughs (external and inner surface) showed the greatest bacterial loads (TVC: 4.5-6.7 log10 cfu cm-2) and values for ATP and protein residues; therefore, these surfaces could be identified as the most important critical points. Spearman rank correlations (P < 0.01) were found between the different assessment methods, especially for the TVC and ATP (r = 0.82, P < 0.001). For rapid assessment on farms, ATP tests represented an accurate and cost-efficient alternative to microbiological techniques. Training improved cleaning performance as indicated by a lower rating for visual inspection, TVC, ATP, MRSA, and ESBL in the second assessment. The monitoring of cleaning efficiency in pig pens followed by training of the staff constitutes a valuable strategy to limit the spread of infectious diseases and antibiotic-resistant bacteria. Special attention should be paid to the sufficient hygiene of drinkers and feeders.

Clinically Relevant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates From Food Animals in South Korea

Extended-spectrum β-lactam antimicrobials have been broadly used in food animals and humans to control infectious diseases. However, the emergence and rapid spread of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, mainly Escherichia coli, have seriously threatened global health in recent decades. In this study, we determined the prevalence, antimicrobial susceptibility, and genetic properties of ESBL-producing E. coli (ESBL-EC) strains isolated from food animals in South Korea. A total of 150 fecal samples from healthy chickens (n = 34), pigs (n = 59), and cattle (n = 57) were screened from January to July 2018. Among these, 77 non-duplicate cefotaxime-resistant ESBL-EC strains were isolated from 32 chicken, 41 pig, and 4 cattle samples, with the corresponding occurrence rates of 94.1, 69.5, and 7.0%, respectively. All the isolates showed multidrug resistance (MDR) and produced at least one type of β-lactamase, including CTX-M (98.7%) and TEM (40.3%). CTX-M-14 (53.1%), CTX-M-55 (53.7%), and CTX-M-65 (50.0%) were the predominant genotypes in the chicken, pig, and cattle samples, respectively. Multilocus sequence typing revealed 46 different sequence types (STs), including the human-associated extraintestinal pathogenic E. coli ST131 (n = 2), ST10 (n = 5), ST38 (n = 1), ST410 (n = 4), ST354 (n = 2), ST58 (n = 3), ST117 (n = 1), and ST457 (n = 1). To the best of our knowledge, this is the first report of pandemic E. coli ST131 in non-human isolates in South Korea. Our results demonstrate the high prevalence and diversity of MDR-ESBL-EC in food animals and highlight them as potential pathogenic ESBL-EC reservoirs that may pose a high risk to human health.

Impact of short-term storage on the quantity of extended-spectrum beta-lactamase-producing Escherichia coli in broiler litter under practical conditions

Applying broiler litter containing extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) to arable land poses a potential risk for humans to get colonized by contact with contaminated soil or vegetables. Therefore, an inactivation of these bacteria before land application of litter is crucial. We performed 2 short-term litter storage trials (one in summer and winter, respectively), each covering a time span of 5 D to investigate the effectiveness of this method for inactivation of ESBL-producing E. coli in chicken litter. Surface and deep litter samples were taken from a stacked, ESBL-positive chicken litter heap in triplicates in close sampling intervals at the beginning and daily for the last 3 D of the experiments. Samples were analyzed quantitatively and qualitatively for ESBL-producing E. coli, total E. coli, and enterococci. Selected isolates were further characterized by whole-genome sequencing (WGS). In the depth of the heap ESBL-producing E. coli were detected quantitatively until 72 h and qualitatively until the end of the trial in winter. In summer detection was possible quantitatively up to 36 h and qualitatively until 72 h. For surface litter samples a qualitative detection of ESBL-producing E. coli was possible in all samples taken in both trials. In the deep samples a significant decrease in the bacterial counts of over 2 Log10 was observed for total E. coli in the winter and for total E. coli and enterococci in the summer. Genetic differences of the isolates analyzed by WGS did not correlate with survival advantage. In conclusion, short-term storage of chicken litter stacked in heaps is a useful tool for the reduction of bacterial counts including ESBL-producing E. coli. However, incomplete inactivation was observed at the surface of the heap and at low ambient temperatures. Therefore, an extension of the storage period in winter as well as turning of the heap to provide aerobic composting conditions should be considered if working and storage capacities are available on the farms.

ESKAPE Bacteria and Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolated from Wastewater and Process Water from German Poultry Slaughterhouses

The wastewater of livestock slaughterhouses is considered a source of antimicrobial-resistant bacteria with clinical relevance and may thus be important for their dissemination into the environment. To get an overview of their occurrence and characteristics, we investigated process water (n = 50) from delivery and unclean areas as well as wastewater (n = 32) from the in-house wastewater treatment plants (WWTPs) of two German poultry slaughterhouses (slaughterhouses S1 and S2). The samples were screened for ESKAPE bacteria (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli Their antimicrobial resistance phenotypes and the presence of extended-spectrum-β-lactamase (ESBL), carbapenemase, and mobilizable colistin resistance genes were determined. Selected ESKAPE bacteria were epidemiologically classified using different molecular typing techniques. At least one of the target species was detected in 87.5% (n = 28/32) of the wastewater samples and 86.0% (n = 43/50) of the process water samples. The vast majority of the recovered isolates (94.9%, n = 448/472) was represented by E. coli (39.4%), the A. calcoaceticus-A. baumannii (ACB) complex (32.4%), S. aureus (12.3%), and K. pneumoniae (10.8%), which were widely distributed in the delivery and unclean areas of the individual slaughterhouses, including their wastewater effluents. Enterobacter spp., Enterococcus spp., and P. aeruginosa were less abundant and made up 5.1% of the isolates. Phenotypic and genotypic analyses revealed that the recovered isolates exhibited diverse resistance phenotypes and β-lactamase genes. In conclusion, wastewater effluents from the investigated poultry slaughterhouses exhibited clinically relevant bacteria (E. coli, methicillin-resistant S. aureus, K. pneumoniae, and species of the ACB and Enterobacter cloacae complexes) that contribute to the dissemination of clinically relevant resistances (i.e., blaCTX-M or blaSHV and mcr-1) in the environment.IMPORTANCE Bacteria from livestock may be opportunistic pathogens and carriers of clinically relevant resistance genes, as many antimicrobials are used in both veterinary and human medicine. They may be released into the environment from wastewater treatment plants (WWTPs), which are influenced by wastewater from slaughterhouses, thereby endangering public health. Moreover, process water that accumulates during the slaughtering of poultry is an important reservoir for livestock-associated multidrug-resistant bacteria and may serve as a vector of transmission to occupationally exposed slaughterhouse employees. Mitigation solutions aimed at the reduction of the bacterial discharge into the production water circuit as well as interventions against their further transmission and dissemination need to be elaborated. Furthermore, the efficacy of in-house WWTPs needs to be questioned. Reliable data on the occurrence and diversity of clinically relevant bacteria within the slaughtering production chain and in the WWTP effluents in Germany will help to assess their impact on public and environmental health.

Effects of the C/N ratio and moisture content on the survival of ESBL-producing Escherichia coli during chicken manure composting

Antibiotic-resistant bacteria are a threat to human and animal health. In recent years, the presence of extended-spectrum-β-lactamase (ESBL)-producing Escherichia (E.) coli in chicken manure, which is used as organic fertilizer, is a concern. The aim of the present study was to determine the effects of the carbon/nitrogen (C/N) ratio and moisture content (MC) on the survival of ESBL-producing E. coli during laboratory-scale composting of chicken manure. Nine different compost mixtures were enriched with an ESBL-producing E. coli strain to an initial concentration of 7 log₁₀ CFU/g, and the number of E. coli, temperature, and chemical conditions during composting were determined. The fastest decrease in E. coli occurred for all mixtures with a C/N ratio of 10:1. Additionally, dry mixtures with an MC of 20% and a C/N ratio of either 10:1 or 40:1 exhibited faster reductions in E. coli than the moist mixtures did, despite having lower maximum temperatures within the bioreactors. The decimal reduction times ranged from 0.27 days in a mixture with a C/N ratio of 10:1 and 40% MC to 4.82 days in a mixture with a C/N ratio of 40:1 and 40% MC. Both the C/N ratio and MC had a significant effect on the number of ESBL-producing E. coli and on temperature development; the C/N ratio additionally affected the pH value and content of ammoniacal nitrogen during chicken manure composting. The results of this study demonstrate a considerable range of mechanisms involved in the inactivation of E. coli during chicken manure composting.

bla CTX-M- 1/IncI1-Iγ Plasmids Circulating in Escherichia coli From Norwegian Broiler Production Are Related, but Distinguishable

Escherichia coli carrying bla_CTX–M–1 mediating resistance to extended-spectrum cephalosporins was recently described as a new genotype in Norwegian broiler production. The aim of this study was to characterize these isolates (n = 31) in order to determine whether the emergence of the genotype was caused by clonal expansion or horizontal dissemination of bla_CTX–M–1-carrying plasmids. All included isolates were subjected to whole genome sequencing. Plasmid transferability was determined by conjugation, and plasmid replicons in the transconjugants were described using PCR-based replicon typing. Plasmid sizes were determined using S1 nuclease digestion. Plasmids in a subset of strains were reconstructed and compared to plasmids from broiler production in other European countries. The isolates belonged to nine different sequence types (STs), with the largest group being ST57 (n = 12). The vast majority of bla_CTX–M–1-carrying plasmids were conjugative. All transconjugants were positive for the IncI1-Iγ replicon, and several also harbored the IncFIB replicon. Highly similar plasmids were present in different E. coli STs. Additionally, high similarity to previously published plasmids was detected. A reconstructed plasmid from an ST57 isolate harbored both IncI1-Iγ and IncFIB replicons and was considered to be co-integrated. The presence of one large plasmid was confirmed by S1 nuclease digestion. Our results show that dissemination of bla_CTX–M–1 in Norwegian broiler production is due to both clonal expansion and horizontal transfer of plasmids carrying bla_CTX–M–1. The bla_CTX–M–1/IncI1-Iγ plasmids grouped into two main lineages, namely clonal complex (CC)-3 and CC-7. The genetic diversity at both strain and plasmid level indicates multiple introductions to Norway. We also show that the bla_CTX–M–1 plasmids circulating in Norwegian broiler production are highly similar to plasmids previously described in other countries.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Impact of selective and non-selective media on prevalence and genetic makeup of ESBL/pAmpC-producing Escherichia coli in the broiler production pyramid

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.

Effect of challenge dose of plasmid-mediated extended-spectrum β-lactamase and AmpC β-lactamase producing Escherichia coli on time-until-colonization and level of excretion in young broilers

Plasmid-mediated extended-spectrum β-lactamase and AmpC β-lactamase (ESBL/pAmpC) producing bacteria are present at all levels of the broiler production pyramid. Young birds can be found positive for ESBL/pAmpC-producing Escherichia coli shortly after arrival at farm. The aim of this study was to determine the effect of different challenge doses of ESBL/pAmpC-producing E. coli on time-until-colonization and the level of excretion in young broilers. One-day-old broilers (specific-pathogen free (SPF) and conventional Ross 308) were housed in isolators and challenged with 0.5 ml ESBL/pAmpC-producing E. coli strains of varying doses (10¹-10⁵ CFU/ml). Presence and concentration (CFU/gram feces) of ESBL/pAmpC-producing E. coli and total E. coli were determined longitudinally from cloacal swabs, and in cecal content 72 h after challenge. Higher challenge doses resulted in shorter time-until-colonization. However, even the lowest dose (10¹ CFU/ml) resulted in colonization of the broilers which excreted >10⁶ CFU/gram feces 72 h after inoculation. Conventional broilers were colonized later than SPF broilers, although within 72 h after challenge all broilers were excreting ESBL/pAmpC-producing E. coli. A probabilistic model was used to estimate the probability of colonization by initial inoculation or transmission. The higher the dose the higher the probability of excreting ESBL/pAmpC-producing E. coli as a result of inoculation. In conclusion, low initial doses of ESBL/pAmpC-producing E. coli can result in rapid colonization of a flock. Interventions should thus be aimed to eliminate ESBL/pAmpC-producing bacteria in the environment of the hatchlings and measures focusing at reducing colonization and transmission of ESBL/pAmpC-producing E. coli should be applied shortly after hatching.

Occurrence of and risk factors for extended-spectrum cephalosporin-resistant Enterobacteriaceae determined by sampling of all Norwegian broiler flocks during a six month period

All broiler flocks reared and slaughtered in Norway from May-October 2016 (n = 2110) were screened for the presence of extended-spectrum cephalosporin (ESC) -resistant Enterobacteriaceae. Furthermore, we investigated possible risk factors for occurrence of such bacteria in broiler flocks. The odds of a flock being positive for ESC-resistant Enterobacteriaceae increased if the previous flock in the same house was positive, and if the flock was reared during September-October. However, we cannot exclude seasonal fluctuations in occurrence of ESC-resistant Enterobacteriaceae during the months November to April. The overall occurrence of ESC-resistant Enterobacteriaceae was 10.4%, and primarily linked to the presence of blaCMY (82.6%) in positive isolates. We describe the first findings of Escherichia coli with blaCTX-M-1, Klebsiella pneumoniae with both blaCTX-M-15 and blaSHV-12, and K. pneumoniae with blaCMY isolated from Norwegian broiler production. This study gives us a unique overview and estimate of the true occurrence of ESC-resistant Enterobacteriaceae in Norwegian broilers over a six-month period. To the best of our knowledge, this is the most comprehensive study performed on the occurrence of ESC-resistant Enterobacteriaceae in a broiler population.

Low Dose Colonization of Broiler Chickens With ESBL-/AmpC- Producing Escherichia coli in a Seeder-Bird Model Independent of Antimicrobial Selection Pressure

Extended-spectrum beta-lactamase- (ESBL-) and AmpC beta-lactamase- (AmpC-) producing Enterobacteriaceae pose a risk for both human and animal health. For livestock, highest prevalences have been reported in broiler chickens, which are therefore considered as a reservoir of multidrug-resistant bacteria. The possibility of transfer to humans either by a close contact to colonized broiler flocks or through contaminated retail meat results in the necessity to develop intervention measures for the entire broiler production chain. In this regard, a basic understanding of the colonization process is mandatory including the determination of the minimal bacterial load leading to a persistent colonization of broiler chickens. Therefore, we conducted a bivalent broiler colonization study close to real farming conditions without applying any antimicrobial selection pressure. ESBL- and AmpC- negative broiler chickens (Ross 308) were co- colonized on their third day of life with two strains: one CTX-M-15-producing Escherichia coli-ST410 and one CMY-2/mcr-1-positive E. coli-ST10. Colonization was assessed by cloacal swabs over the period of the trial, starting 24 h post inoculation. During the final necropsy, the contents of crop, jejunum, cecum, and colon were quantified for the occurrence of both bacterial strains. To define the minimal oral colonization dosage 104 to 101 colony forming units (cfu) were orally inoculated to four separately housed broiler groups (each n = 19, all animals inoculated) and a dosage of already 101 cfu E. coli led to a persistent colonization of all animals of the group after 3 days. To assure stable colonization, however, a dosage of 102 cfu E. coli was chosen for the subsequent seeder-bird trial. In the seeder-bird trial one fifth of the animals (seeder, n = 4) were orally inoculated and kept together with the non-inoculated animals (sentinel, n = 16) to mimic the route of natural infection. After 35 days of trial, all animals were colonized with both E. coli strains. Given the low colonization dosage and the low seeder/sentinel ratio, the rapid spread of ESBL- and AmpC- producing Enterobacteriaceae in conventional broiler farms currently seems inevitably resulting in an urgent need for the development of intervention strategies to reduce colonization of broilers during production.

Proteomic analysis of ESBL-producing Escherichia coli under bentonite condition

The dissemination of extended spectrum beta-lactamases (ESBL) genes through gene transfer attracts wide attention. Bentonite is widely used as a feed additive in an animal-breeding environment. In order to obtain a better understanding of the effect of bentonite on Escherichia coli carrying ESBL gene, proteomic analysis was carried out to screen the key proteins. The results showed that a total of 31 proteins were differentially expressed, including 21 up-regulated proteins and 10 down-regulated proteins. These proteins were involved in biosynthetic process, metabolic process, stress response, transport, anaerobic respiration, proteolysis, hydrolase, protein folding, transcription, salvage, and other. The transcriptional level of four genes (mipA, gntY, tldD, and arcA) was in consensus with proteomic results. This study revealed the differentially expressed proteins involved when E. coli was incubated under bentonite and PBS condition, which implied the possibility that bentonite may promote the transfer of ESBL gene between E. coli.