Extended-Spectrum-Beta-Lactamase- and Plasmid-Encoded Cephamycinase-Producing Enterobacteria in the Broiler Hatchery as a Potential Mode of Pseudo-Vertical Transmission

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.

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.

Comamonas testosteroni as the cause of mortality in embryonated chicken eggs of breeding broiler hens in Costa Rica

Mortality of chicken embryos and first-week chickens was reported in a commercial incubator company in Costa Rica. Six 1-day-old Cobb chickens and twenty-four embryonated chicken eggs were examined in the Laboratory of Avian Pathology and the Laboratory of Bacteriology of the National University of Costa Rica. Twelve dead-in-shell embryos showed maceration and were immersed in a putrid, turbid, slightly thick brown liquid. Additionally, the other 12 embryonated eggs had milky yellow-orange content. The livers of those embryos had congestion, haemorrhages and multifocal cream foci of necrosis. Granulocytic infiltration was observed in the bursa of Fabricius, myocardium, liver, lung and kidney. Livers and egg yolks from six embryonated chickens and all 1-day-old chickens were aseptically collected and cultured. In addition, tissues from six better conserved embryos and all 1-day-old chickens were fixed in buffered formalin and embedded in paraffin. Biochemical and molecular tests identified Comamonas testosteroni as the cause of the early, middle and late embryo mortality. As all the eggshells from the sampled embryonated eggs were dirty with soiled a fecal matter, contamination after manipulating the eggs was considered the source of infection. C. testosteroni is an environmental microorganism that has rarely been reported to cause human disease. To our knowledge, this is the first report of C. testosteroni causing mortality in a hatchery. Cleaning and disinfection using ozone were implemented in the hatchery to eliminate the embryo mortality associated with C. testosteroni.

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.

Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark

The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.

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.

Characterization and Comparative Genomic Analysis of Three Virulent E. coli Bacteriophages with the Potential to Reduce Antibiotic-Resistant Bacteria in the Environment

The emerging global crisis of antibiotic resistance demands new alternative antibacterial solutions. Although bacteriophages have been used to combat bacterial infections for over a century, a dramatic boost in phage studies has recently been observed. In the development of modern phage applications, a scientific rationale is strongly required and newly isolated phages need to be examined in detail. In this study, we present the full characterization of bacteriophages BF9, BF15, and BF17, with lytic activity against extended-spectrum β-lactamases (ESBLs)- and AmpC β-lactamases (AmpC)-producing Escherichia coli, the prevalence of which has increased significantly in livestock in recent decades, representing a great hazard to food safety and a public health risk. Comparative genomic and phylogenetic analysis indicated that BF9, BF15, and BF17 represent the genera Dhillonvirus, Tequatrovirus, and Asteriusvirus, respectively. All three phages significantly reduced in vitro growth of their bacterial host and retained the ability to lyse bacteria after preincubation at wide ranges of temperature (−20–40 °C) and pH (5–9). The results described herein indicate the lytic nature of BF9, BF15, and BF17, which, along with the absence of genes encoding toxins and bacterial virulence factors, represents an undoubted asset in terms of future phage application.

Research Note: A mixture of Bacteroides spp. and other probiotic intestinal anaerobes reduces colonization by pathogenic E. coli strain O78:H4-ST117 in newly hatched chickens

An experimental group of one-day-old chicken from a commercial hatchery was given a defined mixture of 7 gut anaerobes. The next day the chicks were inoculated by an APEC strain O78:H4-ST117 resistant to ciprofloxacin, alongside with the control group and monitored for 4 wk after the inoculation for the presence of the colonizing strains and ciprofloxacin-resistant E. coli. Significant reduction of colonization rates in the first 2 wk was recorded in the experimental group for the numbers of ciprofloxacin-resistant E. coli. The results show that colonization of chicken by defined anaerobic mixtures may provide a decisive protection during the critical period of the chicken intestinal microflora development.

Evaluation of Antimicrobial Resistance of Different Phylogroups of Escherichia coli Isolates from Feces of Breeding and Laying Hens

Animal and food sources are seen as a potential transmission pathway of multi-drug resistance (MDR) micro-organisms to humans. Escherichia. coli is frequently used as an indicator of fecal contamination in the food industry and known as a reservoir of antimicrobial resistance genes (ARGs). Microbial contamination as a major outcome for the poultry and egg industry and is a serious public health problem. In the present study we performed the quantification of β-glucoronidase positive E. coli in 60 fecal samples of breeding and laying hens collected in Portugal in 2019. Phylogenetic and pathotypic characterization, antimicrobial susceptibility, and detection of resistant extended-spectrum β-lactamase (ESBL) genes were assessed. The phylogenetic and pathogenic characterization and detection of ESBL genes were assessed by real-time PCR and antimicrobial susceptibility was evaluated using the disk diffusion method. Overall, E. coli quantification was 6.03 log CFU/g in breeding hens and 6.02 log CFU/g in laying hens. The most frequent phylogroups were B1. None of the isolates was classified as diarrheagenic E. coli (DEC). In total, 57% of the isolates showed MDR and 3.8% were positive for ESBL. Our study highlights that consumers may be exposed to MDR E. coli, presenting a major hazard to food safety and a risk to public health.

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.

The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes

Avian Pathogenic E. coli (APEC) is the causative agent of avian colibacillosis, resulting in economic losses to the poultry industry through morbidity, mortality and carcass condemnation, and impacts the welfare of poultry. Colibacillosis remains a complex disease to manage, hampered by diagnostic and classification strategies for E. coli that are inadequate for defining APEC. However, increased accessibility of whole genome sequencing (WGS) technology has enabled phylogenetic approaches to be applied to the classification of E. coli and genomic characterization of the most common APEC serotypes associated with colibacillosis O1, O2 and O78. These approaches have demonstrated that the O78 serotype is representative of two distinct APEC lineages, ST-23 in phylogroup C and ST-117 in phylogroup G. The O1 and O2 serotypes belong to a third lineage comprised of three sub-populations in phylogroup B2; ST-95, ST-140 and ST-428/ST-429. The frequency with which these genotypes are associated with colibacillosis implicates them as the predominant APEC populations and distinct from those causing incidental or opportunistic infections. The fact that these are disparate clusters from multiple phylogroups suggests that these lineages may have become adapted to the poultry niche independently. WGS studies have highlighted the limitations of traditional APEC classification and can now provide a path towards a robust and more meaningful definition of the APEC pathotype. Future studies should focus on characterizing individual APEC populations in detail and using this information to develop improved diagnostics and interventions.

Antibiotic Resistance in Escherichia coli from Broiler Chickens After Amoxicillin Treatment in an Experimental Environment

Groupwise antibiotic treatments are common in broiler chicken production. They induce selection for antibiotic resistance in commensal Escherichia coli. This study aimed to investigate antibiotic resistance after individual (I, drenching) or groupwise treatment (G, by water) with amoxicillin, and after contact with I or G (KI or KG), compared with untreated broilers without contact with treated broilers (C), and pretreatment values. Finally, we compared antibiotic resistance from broilers (G) after a second treatment, with a treatment in the contact animals (KG), and a first treatment in the control animals (C). Resistance to ampicillin and other antibiotics was significantly increased in groups G and I within 2 days, suggesting (co-)selection of resistance. The increase was lower in groups KI, KG, and C during the first treatment (days 1-5). The increased resistance in group C was interpreted as a change in the microbiota after initial moving and first feeding. After treatment, resistance rates decreased to initial or lower values in all groups. During the second treatment period (days 34-38), all three groups' (G, KG, and C) resistance levels increased to equally high levels. Cephalosporin resistance was low, and did not change over the experimental period. On days 3 and 38, resistance rates of E. coli from duodenum, jejunum, and cecum did not differ between segments and treatment routes. Overall, the baseline levels of antibiotic resistance in E. coli were high. Amoxicillin triggered an increase in resistance levels, irrespective of the mode of treatment. Substantial resistance dynamics in untreated controls warrant further investigation.

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.

Influence of farm management on the dynamics of Salmonella enterica serovar Infantis shedding and antibiotic resistance during the growing period of broiler chickens

BACKGROUND

Salmonella enterica serovar Infantis is a zoonotic pathogen isolated in broilers causing great economic losses in the European poultry sector. It is demonstrated that an investment in management measures at farm level could directly affect the control of food chain microorganisms. The aim of this study was to investigate the development of S. Infantis antimicrobial resistance (AMR) patterns during the growing period, according to flock density and ventilation management, without antibiotic administration.

METHODS

The experiment was performed in two identical poultry houses, evaluating commercial and optimal farm conditions. At 24 h of rearing, 20% of the animals were orally infected with a S. Infantis strain susceptible to all the antibiotics tested. To study Salmonella shedding, faeces samples from each experimental group were taken weekly and analysed as per ISO/TS 6579-2:2017. Antibiotic susceptibility was assessed according to Decision 2013/653.

RESULTS

Salmonella shedding showed that the lowest counts were observed in the first week post-infection and highest at slaughter day for both groups. Moreover, 100% of the isolates were multi-resistant.

CONCLUSION

The acquisition of AMR by S. Infantis starts at the onset of the production cycle and is maintained until the end, demonstrating the importance of transmission of AMR in zoonotic bacteria at farm level.

Commensal Escherichia coli Antimicrobial Resistance and Multidrug-Resistance Dynamics during Broiler Growing Period: Commercial vs. Improved Farm Conditions

Simple Summary

This experiment was designed to evaluate the differences in antimicrobial and multidrug resistance dynamics in broilers reared under two different farm conditions (commercial vs. improved) during the growing period, using Escherichia coli as sentinel bacterium. Although no antibiotics were applied during rearing for two different management conditions tested, high rates of antimicrobial and multidrug-resistant bacteria were observed throughout rearing, with the percentages of resistant bacteria observed being of particular concern in day-old chicks on arrival day and in chickens at the end of the growing period, just before delivery to the slaughterhouse.

Abstract

New measures applied to reduce antimicrobial resistances (AMR) at field level in broiler production are focused on improving animals’ welfare and resilience. However, it is necessary to have better knowledge of AMR epidemiology. Thus, the aim of this study was to evaluate AMR and multidrug resistance (MDR) dynamics during the rearing of broilers under commercial (33 kg/m² density and max. 20 ppm ammonia) and improved (17 kg/m² density and max. 10 ppm ammonia) farm conditions. Day-old chicks were housed in two poultry houses (commercial vs. improved), and no antimicrobial agents were administered at any point. Animals were sampled at arrival day, mid-period and at slaughter day. High AMR rates were observed throughout rearing. No statistical differences were observed between groups. Moreover, both groups presented high MDR at slaughter day. These results could be explained by vertical or horizontal resistance acquisition. In conclusion, AMR and MDR are present throughout rearing. Moreover, although a lower level of MDR was observed at mid-period in animals reared under less intensive conditions, no differences were found at the end. In order to reduce the presence of AMR bacteria in poultry, further studies are needed to better understand AMR acquisition and prevalence in differing broiler growing conditions.

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.

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.

New strategies to prevent and control avian pathogenic Escherichia coli (APEC)

Avian pathogenic Escherichia coli (APEC) infections are associated with major economical losses and decreased animal welfare. In broiler production, APEC infections have traditionally been controlled by antibiotics, resulting in an increased prevalence of antibiotic-resistant E. coli. Concerns have been raised that transfer of antibiotic-resistant APEC via the food chain may result in risks for extra-intestinal infection of humans related to zoonotic transfer and increased difficulties in the treatment of human infections caused APEC-related E. coli types. In this review, the risks associated with APEC are presented based on new knowledge on transmission, virulence and antibiotic resistance of APEC. A major new change in our understanding of APEC is the high degree of genuine vertical transfer of APEC from parents to offspring. A new strategy for controlling APEC, including control of antibiotic-resistant APEC, has to focus on limiting vertical transfer from parents to offspring, and subsequent horizontal transmission within and between flocks and farms, by using all-in-all-out production systems and implementing a high level of biosecurity. Vaccination and the use of competitive exclusion are important tools to be considered. A specific reduction of antibiotic-resistant APEC can be obtained by implementing culling strategies, only allowing the use of antibiotics in cases where animal welfare is threatened. Strategies to reduce APEC, including antibiotic-resistant APEC, need to be implemented in the whole production pyramid, but it has to start at the very top of the production pyramid.

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.

Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017

Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3-0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73-0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56-15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29-0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26-0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29-0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR.

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.

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.

Research Note: Tracing pathways of entry and persistence of facultative pathogenic and antibiotic-resistant bacteria in a commercial broiler farm with substantial health problems

On a commercial broiler farm with substantial health problems, shown by a reported loss rate of approx. 10% and regular antibiotic use, samples were taken at different locations in 2 barns, with the aim of analyzing possible entry routes and persistence of pathogens and antibiotic-resistant bacteria as well as revealing weak points in sanitation. Therefore, swab samples for biofilm and water samples from animal drinking water lines and the spray cooling system were taken twice immediately before restocking. In addition, swab samples from drain holes and air samples were collected. At restocking, hatchlings that died during transportation and chick paper were sampled. All samples were analyzed for the occurrence of Pseudomonas aeruginosa, total coliform count, and antibiotic-resistant bacteria, namely, methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, Klebsiella spp., Citrobacter spp., Enterobacter spp., Acinetobacter baumannii, P. aeruginosa, and vancomycin-resistant Enterococci (VRE). No MRSA or VRE were detectable. In all samples from drinking water and sprinkler system pipes, P. aeruginosa was detectable; in most cases, antibiotic-resistant P. aeruginosa was also detected, with varying resistance profiles. Samples from the hatchlings and chick paper were contaminated with antibiotic-resistant Enterobacter spp., with resistance to piperacillin, fosfomycin, and the third-generation cephalosporins cefotaxime and ceftazidime. Therefore, the initial entry of antibiotic-resistant Enterobacteriaceae likely occurred via exposure at the hatchery, resulting in colonization of the chicks. Animals on the fattening farm were treated with colistin, amoxicillin, and lincomycin in the 3 production cycles before sampling. Owing to the frequent administration of several antibiotic classes during the fattening period via piped water in both barns, resistance of isolates from water pipes accumulated, showing additional resistance to chloramphenicol and frequently to ciprofloxacin and levofloxacin. To prevent the development of secondary diseases caused by the facultative pathogen P. aeruginosa in chicks with a weak immune status, the hygiene management for drinking water lines and the spray cooling system was changed. These changes resulted in an improvement in water line sanitation, shown by the absence of antibiotic-resistant bacteria and rare detection of P. aeruginosa.

Genotyping and molecular characterization of antimicrobial resistance in thermophilic Campylobacter isolated from poultry breeders and their progeny in Eastern Spain

Thermophilic Campylobacter spp. are recognized as a major cause of acute bacterial diarrhea in humans, with broiler meat being the most common source of human infection. Antibiotic therapy is usually necessary for severe or prolonged infections, especially in immunocompromised populations such as young or elderly individuals. However, different studies have demonstrated a close association between antibiotic use in animal production and antimicrobial resistance (AMR) in humans. In this sense, there is social pressure to reduce antibiotic administration and find adequate alternatives to control the presence of bacterial infections in farms. However, there is a lack of information related to Campylobacter AMR dynamics through the entire production system from breeders to their progeny. It is unknown if resistance genes are a result of adaptation through chromosomal mutation or through horizontal gene transfer, instead of vertical transmission of DNA from the parent to their progeny. Thus, the main objectives of this study were to assess the main AMR rates present in a poultry production system, to study the relationship between Campylobacter AMR profiles from breeders and their progeny, and to study the presence and distribution of antibiotic resistance genes in poultry production. Regarding AMR rates, ciprofloxacin was classified as extremely high, followed by nalidixic acid and tetracyclines that were classified as very high. Moreover, this study demonstrated a relationship between the AMR patterns and genes found from Campylobacter strains isolated in breeders and those present in their progeny.

Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic

Background

Avian pathogenic Escherichia coli (APEC) can cause various extraintestinal infections in poultry, resulting in massive economic losses in poultry industry. In addition, some avian E. coli strains may have zoonotic potential, making poultry a possible source of infection for humans. Due to its extreme genetic diversity, this pathotype remains poorly defined. This study aimed to investigate the diversity of colibacillosis-associated E. coli isolates from Central European countries with a focus on the Czech Republic.

Results

Of 95 clinical isolates subjected to preliminary characterization, 32 were selected for whole-genome sequencing. A multi resistant phenotype was detected in a majority of the sequenced strains with the predominant resistance to β-lactams and quinolones being associated with TEM-type beta-lactamase genes and chromosomal gyrA mutations respectively. The phylogenetic analysis confirmed a great diversity of isolates, that were derived from nearly all phylogenetic groups, with predominace of B2, B1 and C phylogroups. Clusters of closely related isolates within ST23 (phylogroup C) and ST429 (phylogroup B2) indicated a possible local spread of these clones. Besides, the ST429 cluster carried bla_{CMY-2, − 59} genes for AmpC beta-lactamase and isolates of both clusters were generally well-equipped with virulence-associated genes, with considerable differences in distribution of certain virulence-associated genes between phylogenetically distant lineages. Other important and potentially zoonotic APEC STs were detected, incl. ST117, ST354 and ST95, showing several molecular features typical for human ExPEC.

Conclusions

The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.

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.

Preliminary study: Health and performance assessment in broiler chicks following application of six different hatching egg disinfection protocols

As part of a Germany-wide project that evaluates strategies for the reduction of multi-resistant bacteria along the poultry production chain, the impact of different hatching egg disinfectants on hatchability and health of the broiler chicks was evaluated. Animal trials were conducted with extended-spectrum beta-lactamase- (ESBL) producing Escherichia (E.) coli contaminated hatching eggs and six disinfection protocols that used formaldehyde, hydrogen peroxide, low-energy electron irradiation, peracetic acid and an essential oil preparation. Each protocol was tested on a group of 50 chicks. Equally sized positive and negative control groups were carried along for each trial. Hatchability, mortality and body weight were recorded as performance parameters. During necropsy of half of the animals in each group on day 7 and 14 respectively, macroscopic abnormalities, body weight, weights of liver and gut convolute were recorded and a range of tissue samples for histological examination were collected as part of the health assessment. A decrease in hatchability was recorded for spray application of essential oils. Body weight development was overall comparable, in several groups even superior, to the Ross308 performance objectives, but a reduced performance was seen in the hydrogen peroxide group. Histologically, lymphoid follicles were regularly seen in all sampled organs and no consistent differences were observed between contaminated and non-contaminated groups. Significances were infrequently and inconsistently seen. In conclusion, remarkable findings were a decrease in hatchability caused by the essential oils spray application and a reduced body weight development in the hydrogen peroxide group. Therefore, the essential oils preparation as spray application was deemed inappropriate in practice, while the application of hydrogen peroxide was considered in need of further research. The other trial results indicate that the tested hatching egg disinfectants present a possible alternative to formaldehyde.

Contribution of the Broiler Breeders' Fecal Microbiota to the Establishment of the Eggshell Microbiota

In broiler chicken production, microbial populations on the eggshell surface following oviposition are still poorly characterized, though they may significantly impact both poultry and public health. The aim of this study was to describe the microbiota of both broiler breeder hens’ feces and the surface of their eggs to assess the contribution of the parental fecal microbiota to the eggshell microbiota. A total of twelve breeder flocks in Quebec, Canada, were sampled at two different times, and a total of 940 feces and 16,400 egg surface samples were recovered. Using 16S rRNA gene sequencing, we showed that even if the microbiota of both feces and eggshells were mainly composed of the phyla Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes, the bacterial community compositions and structures differed between both types of samples. Our results also showed that both the sampling time and the flock identity significantly influenced the alpha- and the beta-diversities of the studied microbiomes. Using a Venn diagram, we showed that 1790 operational taxonomic units (OTUs) were shared between feces and eggshell samples. Sequences associated with genera of potentially pathogenic and spoilage bacteria, Acinetobacter, Campylobacter, Escherichia/Shigella, Helicobacter, Listeria, Proteus, Pseudomonas, Salmonella, and Staphylococcus, were shared between sample types. Some OTUs highly represented in the fecal microbiota and associated with Lactobacillus and Streptococcus genera, were absent from eggshells, suggesting a selection during the microbiota transfer and/or the potential role of environmental contamination. To the best of our knowledge, this is the first study using 16S rRNA sequencing to describe the contribution of the transfer from the fecal microbial ecosystem of laying breeder hens to the establishment of the microbiota on the surface of laid eggs, as well as the bacterial communities at both the broiler breeder feces and the eggshell levels.

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.

The dynamic of antibiotic resistance in commensal Escherichia coli throughout the growing period in broiler chickens: fast-growing vs. slow-growing breeds

Antimicrobial resistance (AMR) is an important threat to public health worldwide. Furthermore, different studies have demonstrated a close association between antibiotic use in animal production and AMR in humans. It is well known that it is necessary to reduce antibiotic administration in farms by finding effective alternative treatments, using more resistant breeds and improving animal welfare. However, to be able to assess the alternatives proposed, it is essential to study the epidemiology of AMR under production conditions. Hence, the aim of this study was to investigate the AMR dynamic in 2 genetic poultry breeds during the growing period. The study was performed in 2 experimental poultry houses to simulate real production conditions, and no antibiotics were administered during the growing period. In addition, 2 poultry breeds were used, fast-growing and slow-growing. To evaluate AMR evolution, Escherichia coli was selected as indicator bacterium. To this end, animals from each experimental group were sampled at different times: on day of arrival, at mid-period, and at slaughter day. In the laboratory, cecal content was removed and inoculated in selective media. Then, biochemical tests were performed to confirm E. coli. Finally, antibiotic susceptibility was assessed according to Decision 2013/653. At the onset of the cycle, significant differences were observed between breeds, as the E. coli strains isolated from fast-growing 1-day-old-chicks showed higher AMR rates. However, at the end of the period, no significant differences were found between breeds and their presence of resistant bacteria (above 95%). Therefore, although no antibiotics were administered during the growing period, a high level of AMR at slaughter day was demonstrated. Further studies are necessary to determine the main risk factors that increase the level of AMR throughout the productive cycle in broiler chickens. In conclusion, it is important to highlight that although it is crucial to control both antibiotic use and animal welfare during the growing period, measures should be taken at all levels of the production chain.

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.

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.

Differences in antimicrobial resistance of commensal Escherichia coli isolated from caecal contents of organically and conventionally raised broilers in Austria, 2010-2014 and 2016

The prevalence of antimicrobial resistance in commensal Escherichia coli isolated from organically raised broiler flocks was compared to the prevalence in isolates from conventional flocks. From 2010 to 2014, and in 2016, resistance trends and multidrug resistance in isolates from the caecal contents of flocks from both broiler production forms were analyzed. Samples were taken in four abattoirs accounting for at least 90% of the national slaughtered broiler population. In total, 962 commensal E. coli were obtained from organically raised broiler flocks (n = 142) and from conventionally raised broiler flocks (n = 820). The mean prevalence of commensal E. coli isolates, which were fully susceptible to the antimicrobials tested, was 43.3% in organically raised broiler flocks and thus significantly higher (P < 0.001) compared to 16.7% in conventionally operated flocks. During the study period, the proportion of fully susceptible isolates increased significantly in both broiler populations. Antimicrobial resistance rates were significantly lower in commensal E. coli isolated from organic compared to conventional production regarding ciprofloxacin (33.3% versus 69.1%), nalidixic acid (33.7% versus 67.4%), sulfamethoxazole (26.7% versus 39.9%), ampicillin (19.0% versus 33.8%) and trimethoprim (12.8% versus 24.9%). Regarding tetracycline, tigecycline and ceftazidime resistance rates were slightly but not significantly higher in isolates from organic flocks (27.6% versus 25.9%; 4.0% versus 1.4%; 2.0% versus 1.9%). This fact is surprising for tetracycline, as none of the investigated organic flocks had been treated with this antimicrobial during their lifetime. No resistances were found in isolates from both production forms against colistin and meropenem, and from organic flocks against azithromycin. The annual prevalence of resistance against ciprofloxacin and nalidixic acid decreased significantly in isolates from both broiler production forms. In isolates from organic flocks, it also decreased regarding ampicillin and sulfamethoxazole. Significant increasing trends were observed in the resistance prevalence against trimethoprim and borderline significantly for ampicillin in commensal E. coli from conventional flocks. Multidrug resistance was detected at a significantly higher prevalence in isolates from conventionally raised flocks (35.1%) compared to organic flocks (22.7%). Findings from this study clearly indicate the influences of organic compared to conventional broiler production practices on the prevalence of antimicrobial resistance in commensal E. coli from broiler flocks.

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

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

Prevalence of antimicrobial resistance and potential pathogenicity, and possible spread of third generation cephalosporin resistance, in Escherichia coli isolated from healthy chicken farms in the region of Dakar, Senegal

Escherichia coli is a normal inhabitant of the intestinal microbiota of chickens, a small proportion of which may be avian pathogenic E. coli (APEC) or potential extraintestinal pathogenic E. coli (ExPEC), capable of causing disease in humans. These E. coli may also be resistant to antimicrobials of critical importance in human or veterinary health. This study aims to 1) determine the prevalence of antimicrobial resistance (AMR) and resistance genes, multidrug resistance (MDR), chromosomal mechanisms of quinolone-resistance and virulence profiles of E. coli isolated from healthy chicken farms in the region of Dakar, Senegal, 2) investigate the spread of third-generation cephalosporins (3GC) resistance in E. coli isolated from healthy chicken farms with respect to virulence and resistance genes, serogroups, Pulsed-Field Gel Electrophoresis (PFGE), phylogenetic groups, plasmid types and transferability and 3) determine whether nonsusceptibility against 3GC on farms could be linked to risk factors. More than 68% of isolates from environmental faecal and drinking water samples, carcasses and carcass washes collected on 32 healthy chicken farms were multidrug resistant (MDR), resistance to antimicrobials critical in human health (3GC or ciprofloxacin) being found in all types of samples. Ciprofloxacin resistance was due to mutations in the gyrA and parC genes, 95% of tested farms harboring isolates carrying three mutations, in gyrA (Ser83Ile and Asp87Asn) and parC (Ser80Ile). Nine of the 32 farms (28.1%) demonstrated the presence of one or more 3GC-nonsusceptible indicator isolates but none of the potential risk factors were significantly associated with this presence on farms. Following ceftriaxone enrichment, presumptive extended-spectrum beta-lactamase/AmpC-beta-lactamase (ESBL/AmpC)-producer isolates were found in 17 of the 32 farms. 3GC resistance was mediated by blaCMY-2 or blaCTX-M genes, blaCTX-M being of genotypes blaCTX-M-1, blaCTX-M-8 and for the first time in chickens in Senegal, the genotype blaCTX-M-15. Clonally related ESBL/AmpC-producer isolates were found on different farms. In addition, blaCTX-M genes were identified on replicon plasmids I1 and K/B and blaCMY-2 on K/B, I1 and B/O. These plasmids were found in isolates of different clusters. In addition, 18 isolates, some of which were ESBL/AmpC-producers, were defined as potential human ExPEC. In conclusion, E. coli isolates potentially pathogenic for humans and demonstrating MDR, with resistance expressed against antimicrobials of critical importance in human health were found in healthy chickens in Senegal. Our results suggest that both clonal spreading and horizontal gene transfer play a role in the spread of 3GC-resistance and that chickens in Senegal could be a reservoir for AMR and ExPEC for humans. These results highlight the importance of raising awareness about compliance with biosecurity measures and prudent use of antimicrobials.

Multidrug-resistant enterobacteria colonize commercial day-old broiler chicks in Nigeria

Aim:

This study was conducted to isolate generic enterobacteria from day-old broiler chicks in Nigeria, determine the antibacterial resistance profile, and assess multidrug resistance.

Materials and Methods:

The birds were sourced from five purposively-selected hatcheries (identified as A, B, C, D and E) in Southwest Nigeria. Non-duplicate cloacal swabs were collected from a total of 75 (15 birds per hatchery) randomly selected apparently healthy birds. Sampling was done in three batches of five chicks per batch at 2-week interval. Isolation of enterobacteria was done using MacConkey agar. The resistance of the isolates was determined using the disk diffusion method.

Results:

Of 15 processed samples of birds from each hatchery, all samples from hatcheries B, D, and E, 10 (66.7%) and 14 (93.3%) samples from hatcheries A and C, respectively, yielded pure cultures of Escherichiacoli. Klebsiella was also isolated from 1 (7.1%) of the 14 and 2 (13.2%) of the 15 growth-positive samples from hatcheries C and D, respectively. The range of resistance among E. coli isolates was tetracycline (86.7-100%), ampicillin (80-100%), gentamicin (60-85.7%), sulfamethoxazole-trimethoprim (46.7-92.9%), enrofloxacin (40-100%), ciprofloxacin (26.7-86.7%), streptomycin (10-80%), cefotaxime (26.7-73.3%), amoxicillin-clavulanic acid (13.3-60%), and ceftazidime (6.7-40%). Klebsiella and all E. coli isolate from chicks of hatcheries B, C, and E, 80 and 93.3% of those from chicks of hatcheries A and D, respectively, exhibited resistance to three or more classes of antibacterial agents.

Conclusion:

Commercial day-old broiler chicks in Nigeria are colonized by multidrug-resistant coliforms (E. coli and Klebsiella) and are potential reservoirs and disseminators of these organisms.

Direct vertical transmission of ESBL/pAmpC-producing Escherichia coli limited in poultry production pyramid

Extended-spectrum beta-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli are found in the poultry production even without antibiotic use. The spread of these bacteria has been suggested to occur via imported parent birds, enabling transmission to production level broilers vertically via eggs. We studied transmission of ESBL/pAmpC-producing E. coli and E. coli without antibiotic selection by sampling imported parent birds (n = 450), egg surfaces prior to and after the incubation period (n = 300 and n = 428, respectively) and the laying house environment (n = 20). Samples were additionally taken from embryos (n = 422). To study the prevention of transmission, a competitive exclusion (CE) solution was added onto freshly laid eggs prior to incubation period (n = 150). Results showed carriage of ESBL/pAmpC-producing E. coli in parent birds (26.7%), the environment (5%) and egg surfaces before the incubation period (1.3%), but not from egg surfaces or embryos after the incubation period. Whole genome sequencing revealed ESBL/pAmpC-producing E. coli isolates belonging to clonal lineages ST429 and ST2040. However, the finding of E. coli cultured without antibiotic selection in two (2.2%) embryos strengthens the need to study E. coli transmission in poultry production in more depth. Since ESBL/pAmpC-producing E. coli seem not to persist on egg surfaces, there is no need to use CE solution ex ovo as a prevention method. The results indicate that other routes, such as for example transmission through fomites or horizontal gene transfer by other bacterial species, could be more important than vertical transmission in the spread of resistance in broiler production.

Transmission routes of ESBL/pAmpC producing bacteria in the broiler production pyramid, a literature review

Plasmid mediated Extended Spectrum Beta-Lactamase and AmpC Beta-Lactamase (ESBL/pAmpC) producing bacteria are resistant to beta-lactam antimicrobials and are widespread in humans, the environment and animals. Animals, especially broilers, are an important reservoir of ESBL/pAmpC producing bacteria. To control ESBL/pAmpC prevalence in broilers, transmission within the entire broiler production pyramid should be considered. This study, including 103 articles originating from two electronic databases, searched for evidence for possible routes of transmission of ESBL/pAmpC producing bacteria in the broiler production pyramid. Possible routes of transmission were categorised as 1) vertical between generations, 2) at hatcheries, 3) horizontal on farm, and 4) horizontal between farms and via the environment of farms. This review presents indications for transmission of ESBL/pAmpC producing bacteria for each of these routes. However, the lack of quantitative results in the literature did not allow an estimation of the relative contribution or magnitude of the different routes. Future research should be specifically targeted towards such information as it is crucial to guide reduction strategies for the spread of ESBL/pAmpC producing bacteria in the broiler production chain.

A Probabilistic Transmission Model for the Spread of Extended-Spectrum-β-Lactamase and AmpC-β-Lactamase-Producing Escherichia Coli in the Broiler Production Chain

Direct contact between humans and live broilers, as well as the consumption of chicken meat, have been suggested as pathways for transmission of extended-spectrum-β-lactamase (ESBL) and AmpC-β-lactamase (AmpC)-producing Escherichia coli. One approach to design intervention strategies to control the transmission of such bacteria between animals and humans is to study the transmission pathways of such bacteria between the animals themselves. The rationale is that controlling the process of the underlying source, here transmission between animals, can provide hints on how to control a higher-level process, here the transmission between animals and humans. The focus of this article is the transmission of the above-mentioned bacteria between broilers and broiler flocks in meat production with regards to the establishment of possible intervention strategies to reduce the transfer of these bacteria between animals. The objective of this work is to design a mathematical transmission model describing the effects of vertical and horizontal bacterial transmission in the broiler production chain, from the parent generation to the slaughterhouse level. To achieve this objective, an existing transmission model for Campylobacter was adapted for the case of E. coli. The model keeps track of prevalence among flocks (flock prevalence) and of prevalence among animals within one flock (animal prevalence). Flock and animal prevalences show different dynamics in the model. While flock prevalence increases mainly through horizontal transmission in hatcheries, animal prevalence increases mainly at the broiler-fattening farm. Transports have rather small effects just as the vertical transmission from parents to chicks.

Environmental adaptation and vertical dissemination of ESBL-/pAmpC-producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

High prevalence numbers of extended-spectrum beta-lactamase- (ESBL-)/plasmid-mediated AmpC beta-lactamase- (pAmpC-) producing Escherichia coli in broiler chicken and their distribution along the broiler production chain is an ongoing problem in food production. We, therefore, investigated resistant isolates along the broiler production chain to determine whether there is a constantly occurring direct vertical transmission of the ESBL-/pAmpC-producing E. coli from the parent flocks to their offspring or not. We, furthermore, analysed the isolates concerning the occurrence of virulence factors and their ability to form biofilms to estimate their potential to effectively colonize broiler chickens and/or persist and survive in the environment of the broiler production facilities. Using whole genome sequencing, we could show that ESBL-/pAmpC-producing E. coli were likely transferred in a step-wise process along the broiler production chain but not directly from the parent flock to the fattening flock with every single batch of offspring chickens. Additionally, resistant E. coli strains showing an extraintestinal pathogenic genotype as well as high numbers of virulence-associated genes including the production of curli fibres and cellulose have high capabilities to persist and spread in the broiler production chain.

Reviewing Interventions against Enterobacteriaceae in Broiler Processing: Using Old Techniques for Meeting the New Challenges of ESBL E. coli?

Extended-spectrum beta-lactamase- (ESBL-) producing Enterobacteriaceae are frequently detected in poultry and fresh chicken meat. Due to the high prevalence, an impact on human colonization and the spread of antibiotic resistance into the environment is assumed. ESBL-producing Enterobacteriaceae can be transmitted along the broiler production chain but also their persistence is reported because of insufficient cleaning and disinfection. Processing of broiler chickens leads to a reduction of microbiological counts on the carcasses. However, processing steps like scalding, defeathering, and evisceration are critical concerning fecal contamination and, therefore, cross-contamination with bacterial strains. Respective intervention measures along the slaughter processing line aim at reducing the microbiological load on broiler carcasses as well as preventing cross-contamination. Published data on the impact of possible intervention measures against ESBL-producing Enterobacteriaceae are missing and, therefore, we focused on processing measures concerning Enterobacteriaceae, in particular E. coli or coliform counts, during processing of broiler chickens to identify possible hints for effective strategies to reduce these resistant bacteria. In total, 73 publications were analyzed and data on the quantitative reductions were extracted. Most investigations concentrated on scalding, postdefeathering washes, and improvements in the chilling process and were already published in and before 2008 (n=42, 58%). Therefore, certain measures may be already installed in slaughterhouse facilities today. The effect on eliminating ESBL-producing Enterobacteriaceae is questionable as there are still positive chicken meat samples found. A huge number of studies dealt with different applications of chlorine substances which are not approved in the European Union and the reduction level did not exceed 3 log10 values. None of the measures was able to totally eradicate Enterobacteriaceae from the broiler carcasses indicating the need to develop intervention measures to prevent contamination with ESBL-producing Enterobacteriaceae and, therefore, the exposure of humans and the further release of antibiotic resistances into the environment.

ESBL-Producing Klebsiella pneumoniae in the Broiler Production Chain and the First Description of ST3128

ESBL-producing Klebsiella pneumoniae (K. pneumoniae) represent an increasing problem both in human and veterinary medicine. As SHV-2 - encoding K. pneumoniae were recently detected in the broiler production we were interested in investigating a possible transmission along the broiler production chain and furthermore, in evaluating their possible impact on human health. Therefore, 41 ESBL-producing K. pneumoniae originating from a parent flock, from the hatcherys' environment during the hatching of that parent flocks' chickens, and from an associated fattening flock were investigated on an Illumina Miseq. Whole genome sequences were analyzed concerning their MLST-type, cgMLST-type, genotypic and phenotypic resistance, plasmid profiles and virulence genes. Irrespective of the origin of isolation all investigated isolates were multi-drug resistant, harbored the same ESBL-gene bla_SHV−2, shared the same sequence type (ST3128) and displayed 100% similarity in core genome multilocus sequence typing (cgMLST). In addition, in silico plasmid typing found several Inc/Rep types associated with ESBL-plasmids. Summarizing, identical clones of SHV-2—producing K. pneumoniae were detected in different stages of the industrial broiler production in one out of seven investigated broiler chains. This proves the possibility of pseudo-vertical transmission of multi-resistant human pathogens from parent flocks to hatcheries and fattening flocks. Furthermore, the importance of cross-contamination along the production chain was shown. Although the ESBL-producing K. pneumoniae clone detected here in the broiler production has not been associated with clinical settings so far, our findings present a potential public health threat.

Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany

Background

Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal ampC gene, acquisition of plasmid-encoded ampC genes, e.g. bla_CMY-2, has been described worldwide in E. coli from humans and animals. To investigate a possible transmission of bla_CMY-2 along the food production chain, we conducted a next-generation sequencing (NGS)-based analysis of 164 CMY-2-producing E. coli isolates from humans, livestock animals and foodstuff from Germany.

Results

The data of the 164 sequenced isolates revealed 59 different sequence types (STs); the most prevalent ones were ST38 (n = 19), ST131 (n = 16) and ST117 (n = 13). Two STs were present in all reservoirs: ST131 (human n = 8; food n = 2; animal n = 6) and ST38 (human n = 3; animal n = 9; food n = 7). All but one CMY-2-producing ST131 isolates belonged to the clade B (fimH22) that differed substantially from the worldwide dominant CTX-M-15-producing clonal lineage ST131-O25b clade C (fimH30). Plasmid replicon types IncI1 (n = 61) and IncK (n = 72) were identified for the majority of bla_CMY-2-carrying plasmids. Plasmid sequence comparisons showed a remarkable sequence identity, especially for IncK plasmids. Associations of replicon types and distinct STs were shown for IncK and ST57, ST429 and ST38 as well as for IncI1 and ST58. Additional β-lactamase genes (bla_TEM, bla_CTX-M, bla_OXA, bla_SHV) were detected in 50% of the isolates, and twelve E. coli from chicken and retail chicken meat carried the colistin resistance gene mcr-1.

Conclusion

We found isolates of distinct E. coli clonal lineages (ST131 and ST38) in all three reservoirs. However, a direct clonal relationship of isolates from food animals and humans was only noticeable for a few cases. The CMY-2-producing E. coli-ST131 represents a clonal lineage different from the CTX-M-15-producing ST131-O25b cluster. Apart from the ST-driven spread, plasmid-mediated spread, especially via IncI1 and IncK plasmids, likely plays an important role for emergence and transmission of bla_CMY-2 between animals and humans.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4976-3) contains supplementary material, which is available to authorized users.

The effect of a commercial competitive exclusion product on the selection of enrofloxacin resistance in commensal E. coli in broilers

The effect of a competitive exclusion product (Aviguard®) on the selection of fluoroquinolone resistance in poultry was assessed in vivo in the absence or presence of fluoroquinolone treatment. Two experiments using a controlled seeder-sentinel animal model (2 seeders: 4 sentinels per group) with one-day-old chicks were used. For both experiments, as soon as the chicks were hatched, the birds of two groups were administered Aviguard® and two groups were left untreated. Three days later, all groups were inoculated with an enrofloxacin-susceptible commensal E. coli strain. Five days after hatching, two birds per group were inoculated with either a bacteriologically fit or a bacteriologically non-fit enrofloxacin-resistant commensal E. coli strain. In experiment 2, all groups were orally treated for three consecutive days (days 8-10) with enrofloxacin. Throughout the experiments, faecal excretion of all inoculated E. coli strains was determined on days 2, 5, 8, 11, 18 and 23 by selective plating (via spiral plater). Linear mixed models were used to assess the effect of Aviguard® on the selection of fluoroquinolone resistance. The use of Aviguard® (P < 0.01) reduced the excretion of enrofloxacin-resistant E. coli when no enrofloxacin treatment was administered. However, this beneficial effect disappeared (P = 0.37) when the birds were treated with enrofloxacin. Similarly, bacterial fitness of the enrofloxacin-resistant E. coli strain used for inoculation had an effect (P < 0.01) on the selection of enrofloxacin resistance when no treatment was administered, whereas this effect was no longer present when enrofloxacin was administered (P = 0.70). Thus, enrofloxacin treatment cancelled the beneficial effects from administrating Aviguard® in one-day-old broiler chicks and resulted in an enrofloxacin-resistant flora. RESEARCH HIGHLIGHTS The effect of Aviguard® on the selection of enrofloxacin resistance was assessed in vivo. Without enrofloxacin, Aviguard® reduced the selection of enrofloxacin resistance. When enrofloxacin was administered, it cancelled the beneficial effect of Aviguard®.