Vertical transmission of a fluoroquinolone-resistant Escherichia coli within an integrated broiler operation

Detection and characterization of multidrug resistant Escherichia coli carrying virulence gene isolated from broilers in Bangladesh

BACKGROUND

The emergence and dissemination of multidrug resistant (MDR) bacteria pose a severe threat to public health by limiting clinical treatment and prophylactic options.

OBJECTIVES

This study investigates the prevalence of Escherichia coli in broilers, their phenotypic antimicrobial resistance (AMR) profiles and the presence of virulence-associated genes (VAGs) and antimicrobial resistance genes (ARGs) using polymerase chain reaction (PCR).

MATERIALS AND METHODS

A total of 216 pooled cloacal samples were collected from 1080 broilers across six districts of Bangladesh. Each pooled sample comprised randomly selected cloacal swabs from five birds per farm. E. coli isolates were identified using standard bacteriological approach, followed by biochemical assays and PCR. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method, and the presence of ARGs and VAGs was determined via PCR. Five selected isolates were partially sequenced for five VAGs using Sanger sequencing.

RESULTS

A total of 177 E. coli isolates (81.94%, 95% confidence interval: 76.24%-86.53%) were identified. The isolates showed the highest resistance to ampicillin (93.79%), followed by tetracycline (91.53%), erythromycin (89.27%) and ciprofloxacin (87%). Conversely, ceftriaxone (80.79%) showed highest susceptibility, followed by gentamicin (37.29%) and neomycin (31.07%). All isolates were MDR, with a multiple antibiotic resistance indexes were <0.3. A significant percentage (16.38%) of E. coli isolates were MDR to five antimicrobial classes and harboured blaTEM, sul1, ere (A), tetA, tetB and tetC genes. The highest prevalent ARGs were blaTEM (88.14%) followed by ere (A) (83.62%) and sul 1 (72.32%). The prevalence of VAGs was astA (56.50%), iucD (31.07%), iss (21.47%), irp2 (15.82%) and cva/cvi (3.39%), respectively.

CONCLUSIONS

This study highlights the presence of ARGs contributing to the development of MDR in E. coli carrying VAGs in broilers. Effective monitoring and surveillance of antimicrobial usage in poultry production systems are urgently required to prevent emergence and dissemination of AMR.

Persistence of commensal multidrug-resistant Escherichia coli in the broiler production pyramid is best explained by strain recirculation from the rearing environment

Despite the success of mitigation policies in several countries to reduce the use of antibiotics in veterinary medicine, pathogenic and commensal bacteria resistant to antibiotics are still circulating in livestock animals. However, factors contributing the most to antimicrobial resistance (AMR) persistence in these settings are yet not clearly identified. The broiler production, with its highly segmented, pyramidal structure offers an ideal context to understand and control the spread of resistant bacteria. By taking advantage of an experimental facility reproducing the whole broiler production pyramid, we demonstrate that resistant E. coli persist in our system primarily though recirculation of a few commensal clones surviving in the rearing environment. No vertical transmission from hens to offspring nor strain acquisition at the hatchery were detected, while import of new strains from outside the facility seems limited. Moreover, each clone carries its own resistance-conferring plasmid(s), and a single putative plasmid horizontal transfer could have been inferred. These results, observed for now in a small experimental facility with high level of biosecurity, must be confirmed in a commercial farm context but still provide invaluable information for future mitigation policies.

Vaccinating parent flocks against colibacillosis reduces broiler mortality - A retrospective observational study from 2016 to 2019 in Finland

Colibacillosis is one of the most important infectious diseases in modern poultry production. The complex nature of colibacillosis has made it challenging to produce an effective vaccine. As a control measure for colibacillosis outbreak in Finland, a vaccination program with a commercial colibacillosis vaccine and later also an autogenous vaccine was started for parent flocks in 2017. In this retrospective observational study from years 2016-2019, we evaluated first week and total mortality of broiler flocks (n= 6969) originating from parents with different colibacillosis vaccination status. Broiler flocks were divided into three groups according to vaccination status of their parent flocks. First group were flocks from parents with no colibacillosis vaccines; second group was flocks from parents vaccinated with commercial vaccine only; and third group was flocks from parents with both commercial and autogenous vaccine. Bayesian modelling was used to predict posterior distributions of first week mortality and total mortality of the broiler flocks. Results of the modelling revealed that broiler flocks from unvaccinated parents had the highest mortality rates (mean first week mortality 1.40 % and mean total mortality 4.33 %, respectively) whereas flocks from parents with a combination of commercial and autogenous vaccinations had the lowest mortality rates (mean first week mortality 0,91 % and mean total mortality 3,14 %). The mortalities from broilers flocks from parents with only commercial vaccine fell in between these groups. Also, standard deviations of mortality rates were lower in broilers from parents with commercial or both vaccines. This demonstrates that in addition to lowering the mean mortality rates, the vaccinations made high mortality broiler flocks less common. Best performance was obtained when autogenous vaccine was combined to the commercial vaccine. The autogenous vaccine consists of the same type of Escherichia coli strain that was causing most colibacillosis cases during the study period in Finland. This study adds to the evidence of benefits of colibacillosis vaccines during outbreaks. It also demonstrates the importance of the knowledge of the types of APEC strains causing outbreaks to produce effective autogenous vaccines.

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.

Avian Pathogenic Escherichia coli (APEC) in Broiler Breeders: An Overview

Poultry meat is one of the major animal protein sources necessary to meet the global protein demand. Sustainability in broiler production is the key to achieving its continuous supply, and broiler breeders play a critical role in maintaining this sustainability by providing good quality chicks. Colibacillosis, the disease caused by avian pathogenic Escherichia coli (APEC), causes severe economic losses to the poultry industry globally. Moreover, APEC causes an additional burden among broiler breeders, such as a decrease in egg production and mortality among these birds. There is vertical transmission of APEC to the broiler chicks through eggs, resulting in increased first-week mortality and subsequent horizontal transmission at the hatchery. In this regard, the vertical transmission of antibiotic resistance genes is another concern that needs attention. Controlling several diseases in broiler breeders would possibly reduce the first-week mortality in chicks, thereby maintaining the production level. For that, constant monitoring of the bacterial populations is critical. Moreover, amidst the increased antibiotic resistance pattern, more focus on alternative treatment strategies like vaccines, probiotics, and bacteriophages is necessary. Future research focusing on strategies to mitigate APEC in broiler breeders would be one of the finest solutions for sustainable broiler production.

Prevalence of Potential Pathogenic and Antimicrobial Resistant Escherichia coli in Danish Broilers

Avian pathogenic Escherichia coli (APEC) are important bacteria in broiler production in terms of economy, welfare, and use of antibiotics. During a previous outbreak of APEC in the Nordic countries, it was suggested that the pathogenic clones of E. coli causing the outbreak originated from grandparent stock and were transmitted to the offspring, causing increased first week mortality. This study investigated whether the pathogenic potential of E. coli at the parent and broiler level differs in relation to pathogenic potential described by the level of virulence-associated genes and pattern of antimicrobial resistance. The hypothesis was that, due to higher biosecurity at the parent level, the E. coli population will show a lower level of antimicrobial resistance and carry fewer virulence-associated genes, as a result of fewer E. coli infections observed. From four parent flocks and eight broiler flocks, 715 E. coli were isolated from cloacal swabs of newly hatched chickens (Ross 308). The isolated E. coli were characterized by eight virulence-associated genes and phenotypic resistance against six antimicrobials. It was found that the prevalence of virulence-associated genes and phenotypic antimicrobial resistance varied significantly between flocks, and the virulence-associated genes papC and irp2 and resistance against ampicillin were significantly more prevalent in breeder flocks compared to broiler flocks.

Comparative analysis of antimicrobial resistance and genetic characteristics of Escherichia coli from broiler breeder farms in Korea

Broiler breeder farms could be a reservoir of Escherichia coli, disseminating antimicrobial resistance and virulence factors. We investigated the antimicrobial resistance of E. coli from nine broiler breeder farms and characterised their resistance and virulence genes. A total of 256 E. coli showed a high level of resistance to tetracycline, nalidixic acid, ampicillin, and cephalothin, followed by trimethoprim-sulfamethoxazole and chloramphenicol. The resistance to nalidixic acid, ampicillin, trimethoprim–sulfamethoxazole, and chloramphenicol showed significant differences among the farms. Among 202 β-lactam-resistant E. coli, 138 carried β-lactamase genes. The most prevalent β-lactamase gene was blaTEM-1, of which the presence differed significantly across the farms. Out of 197 tetracycline-resistant E. coli isolates, tetA and tetB were detected in 164 and 50, with significant differences among the farms. Also, 45 of 196 nalidixic acid-resistant E. coli carried qnrS while 67 of 149 trimethoprim–sulfamethoxazole-resistant E. coli carried sul2. Among the five virulence genes tested, ompT was the most prevalent, and all genes except for iutA distributed significantly different among the farms. The phenotypic and genotypic characteristics of E. coli were significantly different among the farms; therefore, management at the breeder level is required to control the vertical transmission of E. coli.

Antimicrobial Resistance of Campylobacter jejuni, Escherichia coli and Enterococcus faecalis Commensal Isolates from Laying Hen Farms in Spain

Simple Summary

Antimicrobial resistance (AMR) is a global threat for human and animal health. Few studies have been carried out in laying hens. We evaluated the antimicrobial susceptibility of commensal Campylobacter jejuni, Escherichia coli, and Enterococcus faecalis isolates in Spanish laying hens in 2018. C. jejuni was highly resistant, and a medium proportion of the isolates were susceptible to all the antimicrobials studied. E. coli showed medium to high percentages of resistance to the antibiotic categories of highest public health risk concern (A and B). Only a low proportion of the isolates were susceptible to all antimicrobials. The E. faecalis resistance to antimicrobials was variable, and very few isolates were susceptible to all antimicrobials. Novel data on AMR in laying hen commensal isolates in Spain was provided, and the AMR levels differed from those reported for poultry in the EU. High resistance to key drugs used in human medicine was found. Therefore, laying hens could be a source of AMR for humans, thus, representing a public health risk.

Abstract

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

High incidence of multidrug resistance and class 1 and 2 integrons in Escherichia coli isolated from broiler chickens in South of Iran

The objective was to investigate the multidrug resistance and presence of class 1 and 2 integrons in 300 Escherichia coli isolates obtained from 20 broiler farms during three rearing periods (one-day-old chicks, thirty-day-old chickens, and one day before slaughter) in Fars, South Iran. Results showed that 81.00%, 82.00%, and 85.00% of isolates were multidrug-resistant on the first day, thirty-day-old chickens, and one day before slaughter, respectively. Multidrug-resistant E. coli isolates were further examined for the presence of class 1 and 2 integrons using PCR assay. The existence of class 1 integron-integrase gene (intI1) was confirmed in 68.40%, 72.70%, and 60.90% of multidrug-resistant isolates from stage 1, stage 2, and stage 3 of the rearing period, respectively. The frequency of class 2 integron-integrase gene (intI2) during the first to the third stage of sampling was 2.60%, 25.50%, and 30.40%. Also, sequence analysis of the cassette arrays within class 1 integron revealed the presence of the genes associated with resistance for trimethoprim (dfrA), streptomycin (aadA), erythromycin (ereA), and orfF genes. The results revealed that percentages of antimicrobial resistance in E. coli isolates were significantly higher in the middle and end stages of the rearing period. In conclusion, widespread dissemination of class 1 integrons in all three stages and rising trends of class 2 integrons existence in E. coli isolates during the rearing period of broiler chickens could exacerbate the spread of resistance factors among bacteria in the poultry industry. Future research is needed to clarify its implication for human health.

Ways to minimize bacterial infections, with special reference to Escherichia coli, to cope with the first-week mortality in chicks: an updated overview

On the commercial level, the poultry industry strives to find new techniques to combat bird's infection. During the first week, mortality rate increases in birds because of several bacterial infections of about ten bacterial species, especially colisepticemia. This affects the flock production, uniformity, and suitability for slaughter because of chronic infections. Escherichia coli (E. coli) causes various disease syndromes in poultry, including yolk sac infection (omphalitis), respiratory tract infection, and septicemia. The E. coli infections in the neonatal poultry are being characterized by septicemia. The acute septicemia may cause death, while the subacute form could be characterized through pericarditis, airsacculitis, and perihepatitis. Many E. coli isolates are commonly isolated from commercial broiler chickens as serogroups O₁, O₂, and O₇₈. Although prophylactic antibiotics were used to control mortality associated with bacterial infections of neonatal poultry in the past, the commercial poultry industry is searching for alternatives. This is because of the consumer's demand for reduced antibiotic-resistant bacteria. Despite the vast and rapid development in vaccine technologies against common chicken infectious diseases, no antibiotic alternatives are commercially available to prevent bacterial infections of neonatal chicks. Recent research confirmed the utility of probiotics to improve the health of neonatal poultry. However, probiotics were not efficacious to minimize death and clinical signs associated with neonatal chicks' bacterial infections. This review focuses on the causes of the increased mortality in broiler chicks during the first week of age and the methods used to minimize death.

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.

Effects of in ovo probiotic administration on the incidence of avian pathogenic Escherichia coli in broilers and an evaluation on its virulence and antimicrobial resistance properties

Avian pathogenic Escherichia coli (APEC) causes colibacillosis in poultry, which has been traditionally controlled by the prophylactic in-feed supplementation of antibiotics. However, antibiotics are being removed from poultry diets owing to the emergence of multidrug-resistant (MDR) bacteria. Therefore, alternatives to control APEC are required. This study aimed to evaluate the effects of in ovo inoculation of probiotics on the incidence of APEC in broilers and evaluate the virulence and antimicrobial resistance properties of the APEC isolates. On embryonic day 18, 4 in ovo treatments (T) were applied: T1 (Marek's vaccine [MV]), T2 (MV and Lactobacillus animalis), T3 (MV and Lactobacillus reuteri), and T4 (MV and Lactobacillus rhamnosus). A total of 180 male broilers per treatment were randomly placed in 10 pens. The heart, liver, spleen, and yolk sac were collected on day 0, 14, 28, and 42. Presumptive E. coli isolates were confirmed by real-time PCR. The positive isolates were screened for the APEC-related genes (iroN, ompT, hlyF, iss, and iutA), and E. coli isolates containing one or more of these genes were identified as APEC-like strains. A total of 144 APEC-like isolates were isolated from 548 organ samples. No differences (P > 0.05) among treatments were observed for the incidence of APEC-like strains in all organs when averaged over sampling days. However, when averaged over treatments, the incidence in the heart, liver, and yolk sac was different among sampling days; a significant increase was observed in these organs on day 14 compared with day 0. Twenty-five antimicrobial resistance genes were evaluated for all APEC-like isolates, and 92.4% of the isolates carried at least one antimicrobial resistance gene. Thirty-seven isolates were then selected for antimicrobial susceptibility testing; MDR strains accounted for 37.8% of the isolates. In conclusion, the in ovo inoculation of a single probiotic strain did not confer protection against APEC strains in broilers. The high prevalence of MDR isolates indicates that further research on antibiotic alternatives is required to prevent APEC infections in broilers.

Diversity of Escherichia coli strains isolated from day-old broiler chicks, their environment and colibacillosis lesions in 80 flocks in France

Avian colibacillosis is the most common bacterial disease affecting broilers. To better evaluate the diversity and the origin of the causative Escherichia coli strains infecting birds, we conducted a study on 80 broiler flocks. Just before the arrival of chicks on the farm, samples were collected in the farm environment (walls, feeders, air inlets, etc.) and, upon delivery, day-old chicks (DOCs) and the transport boxes were also sampled. Isolates were obtained from these samples, and from organs of chickens exhibiting typical colibacillosis symptoms. The isolates were characterized using high-throughput qPCR to detect a range of genetic markers (phylogroups, main serogroups virulence markers, etc.). A total of 967 isolates were studied, including 203 from 28 colibacillosis episodes, 484 from DOCs, 162 from transport boxes and 118 from the farm environment. These isolates yielded 416 different genetic profiles, of which 267 were detected in single isolates, and the others were observed in up to 44 isolates from nine farms. The distributions of isolates across phylogroups and the main serogroups varied with the origin of isolation. The isolates obtained from colibacillosis cases either shared a single genetic profile or were different. In a few cases, we observed the same profile for isolates obtained from DOCs and colibacillosis lesions in the same flock or different flocks. However, some flocks receiving DOCs contaminated with isolates bearing the genetic profile of colibacillosis cases identified in other flocks remained healthy. This study highlights the huge diversity among avian E. coli isolated from diseased and non diseased birds.

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.

Antimicrobial Susceptibility of Escherichia coli and ESBL-Producing Escherichia coli Diffusion in Conventional, Organic and Antibiotic-Free Meat Chickens at Slaughter

Simple Summary

Following the spread of antibiotic resistance and the high consumption of chicken meat, conventional poultry-producing companies have turned to antibiotic-free and organic lines of products. Our work investigated E. coli susceptibility to different antimicrobials and extended-spectrum β-lactamase (ESBL) E. coli diffusion from samples collected in slaughterhouse from conventional (C), organic (O) and reared without antibiotics (ABF) chickens. Conventional samples showed the highest number of E. coli strains resistant to ampicillin (89.6%), trimethoprim/sulfamethoxazole (62.2%), nalidixic acid (57.8%), ciprofloxacin (44.4%), and cefotaxime (43.7%), with prevalent patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%). The highest numbers of ESBL E. coli were observed in conventional and the lowest in organic. Our results are relevant with an influence of farming typology regarding the susceptibility of E. coli and the presence of ESBL E. coli. Conventional farms, in which the use of antibiotics is allowed, showed samples with the highest number of strains resistant to antimicrobials commonly used in poultry as well as the highest amounts of ESBL E. coli. Organic samples exhibited the lowest value for ESBL due to a lack of antimicrobial treatment in chickens and the possibility to have access to the outdoors, limiting contact with litter as a potential source of resistant bacteria.

Abstract

As a result of public health concerns regarding antimicrobial resistance in animal-based food products, conventional poultry companies have turned to ‘raised without antibiotics’ (ABF) and organic farming systems. In this work, we evaluated the influence of rearing systems on antimicrobial susceptibility in E. coli and extended-spectrum β-lactamase (ESLB) E. coli diffusion in conventional (C), organic (O) and antibiotic free (ABF) chicken samples collected from cloacal swabs and skin samples in slaughterhouse. The E. coli isolates from conventional (135), antibiotic-free (131) and organic (140) samples were submitted to the Kirby–Bauer method and ESBL E. coli were analyzed by the microdilution test. Conventional samples showed the highest number of strains resistant to ampicillin (89.6%; p < 0.01), cefotaxime (43.7%; p < 0.01), nalidixic acid (57.8%; p < 0.01), ciprofloxacin (44.4%; p < 0.001), and trimethoprim/sulfamethoxazole (62.2%; p < 0.01), with patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%), whereas most of the E. coli isolated from antibiotic-free and organic chicken samples revealed a co-resistance pattern (29.2% and 39%, respectively). The highest number of ESBL E. coli was observed in conventional, in both cloacal and skin samples and the lowest in organic (p < 0.001). Our results are consistent with the effect of conventional farming practices on E. coli antimicrobial resistance and ESBL E. coli number, due to the use of antimicrobials and close contact with litter for most of the production cycle.

Decreased detection of ESBL- or pAmpC-producing Escherichia coli in broiler breeders imported into Sweden

In the spring of 2010, it was discovered that a large proportion of broilers in Sweden were colonized with Escherichia coli producing extended-spectrum beta-lactamases (ESBL) or plasmid mediated AmpC (pAmpC). It was hypothesized that the high prevalence was due to transfer from an upper level in the production pyramid and sampling upwards in the production pyramid was initiated. From 2010 to 2019, all shipments (n = 122) of broiler breeders were screened on arrival to Sweden for the occurrence of ESBL- or pAmpC-producing E. coli using selective methods. Samples of paper linings from shipments of breeders were cultured on MacConkey agar supplemented with cefotaxime (1 mg/L) after pre-enrichment in either MacConkey broth with cefotaxime (1 mg/L), or from late June 2015 in buffered peptone water without antibiotics. ESBL- or pAmpC-producing E. coli was isolated from 43 (35%) of these. Over the years, the proportion of positive imports have decreased and during 2018 and 2019 all imports were negative. In conclusion, the occurrence of ESBL- or pAmpC-producing E. coli in broiler breeders on arrival to Sweden has decreased. Such bacteria have not been detected in any shipments since 2017.

Decrease in fluoroquinolone use in French poultry and pig production and changes in resistance among E. coli and Campylobacter

This paper presents the impact on antimicrobial resistance (AMR) in poultry and pig bacteria of the French EcoAntibio plan, a public policy to reduce antimicrobial use in animals. The analysis was performed using sales data of veterinary antimicrobials and AMR data from bacteria obtained at slaughterhouse and from diseased animals. From 2011-2018, fluoroquinolones exposure decreased by 71.5 % for poultry and 89.7 % for pigs. For Campylobacter jejuni isolated from broilers at slaughterhouses, ciprofloxacin resistance increased from 51 % in 2010 to 63 % in 2018, whereas for turkeys the percentages varied from 56 % in 2014 to 63 % in 2018. For commensal E. coli isolated from the caecal content of broilers at slaughterhouses, the resistance to ciprofloxacin - assessed using an epidemiological cut-off value - increased in broiler isolates from 30.7 % in 2010 to 38.1 % in 2018. In turkeys, the percentage of resistant E. coli isolates decreased from 21.3 % in 2014 to 15.2 % in 2018, whereas in pigs, it increased from 1.9 % in 2009 to 5.5 % in 2017. However, for E. coli isolated from diseased animals, when the breakpoints of 2018 were applied, resistance to fluoroquinolones significantly decreased between 2010 and 2018 from 9.0%-5.4% for broilers/hens, from 7.4 % to 3.4 % for turkeys and from 9.4 % to 3.6 % for pigs. These data show that the major, rapid decrease in the exposition to fluoroquinolones had contrasting effects on resistance in the diverse bacterial collections. Co-selection or fitness of resistant strains may explain why changes in AMR do not always closely mirror changes in use.

Resistance Reservoirs and Multi-Drug Resistance of Commensal Escherichia coli From Excreta and Manure Isolated in Broiler Houses With Different Flooring Designs

Carriage of resistant bacteria and spread of antimicrobial resistance (AMR) in the environment through animal manure pose a potential risk for transferring AMR from poultry and poultry products to the human population. Managing this risk is becoming one of the most important challenges in livestock farming. This study focused on monitoring the prevalence of multi-drug resistance (MDR) bacteria and development of AMR depending on flooring. In two experiments (2 × 15,000 birds), broilers were always divided in two different stables. In the control group, the entire floor pen was covered with litter material and in the experimental group, the flooring system was partly modified by installing elevated slat platforms equipped with water lines and feed pans. Over the whole fattening period, excreta and manure samples were taken (days 2, 22, and 32). In total, 828 commensal E. coli isolates were collected. The development and prevalence of resistance against four different antibiotic classes (quinolones, β-lactams, tetracyclines, and sulfonamides) were examined by using broth microdilution. At the end of the trials, the amount of manure per square metre was twice as high below the elevated platforms compared to the control group. Approximately 58% of E. coli isolates from excreta showed resistance against at least one antibacterial agent at day 2. During and at the end of the fattening period, resistant E. coli isolates at least against one of the four antibacterial agents were observed in excreta (46 and 46%, respectively), and manure samples (14 and 42%, respectively), despite the absence of antibacterial agent usage. In spite of less contact to manure in the experimental group, the prevalence of resistant E. coli isolates was significantly higher. Birds preferred the elevated areas which inevitably led to a local high population density. Animal-to-animal contact seems to be more important for spreading antimicrobial resistant bacteria than contact to the litter-excreta mixture. Therefore, attractive areas in poultry housing inducing crowding of animals might foster transmission of AMR. In poultry farming, enrichment is one of the most important aims for future systems. Consequently, there is a need for keeping birds not carrying resistant bacteria at the start of life.

Identification and selection of food safety-related risk factors to be included in the Canadian Food Inspection Agency's Establishment-based Risk Assessment model for Hatcheries

Towards the continuous improvement of its inspection system, the Canadian Food Inspection Agency (CFIA) is developing an Establishment-based Risk Assessment model for Hatcheries to allocate inspection resources based on the food safety risk associated with the Canadian hatcheries falling under its jurisdiction. The objectives of the current study were to identify and select critical food safety-related risk factors that would be included in this model, with a main focus on Salmonella. A literature review was used to develop a comprehensive list of risk factors that could potentially contribute to the food safety risk attributed to Canadian hatcheries operating in all production streams (breeders, layers, broilers, turkeys, waterfowl and game birds). The development of this list used a selection process that was conducted according to the availability of data sources, the clarity of definition and the measurability of the selected risk factors. A panel of experts reviewed and adjusted the identified risk factors. A final list of 29 risk factors was generated; 20 originated from the scientific literature and nine from the expert panel. Risk factors were grouped in three clusters according to whether they pertained to the inherent risk (nine factors identified), risk mitigation (nine factors identified) or compliance of a hatchery with its preventive control plan and regulatory requirements (11 factors identified). Criteria for assessing each risk factor were defined based on common practices used in the Canadian hatchery industry. This comprehensive list of risk factors and criteria represents useful information to support the design and implementation of a Canadian risk assessment model for hatcheries, but could also be used by like-minded food safety authorities.

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.

Optimization of Antimicrobial Treatment to Minimize Resistance Selection

Optimization of antimicrobial treatment is a cornerstone in the fight against antimicrobial resistance. Various national and international authorities and professional veterinary and farming associations have released generic guidelines on prudent antimicrobial use in animals. However, these generic guidelines need to be translated into a set of animal species- and disease-specific practice recommendations. This article focuses on prevention of antimicrobial resistance and its complex relationship with treatment efficacy, highlighting key situations where the current antimicrobial drug products, treatment recommendations, and practices may be insufficient to minimize antimicrobial selection. The authors address this topic using a multidisciplinary approach involving microbiology, pharmacology, clinical medicine, and animal husbandry. In the first part of the article, we define four key targets for implementing the concept of optimal antimicrobial treatment in veterinary practice: (i) reduction of overall antimicrobial consumption, (ii) improved use of diagnostic testing, (iii) prudent use of second-line, critically important antimicrobials, and (iv) optimization of dosage regimens. In the second part, we provided practice recommendations for achieving these four targets, with reference to specific conditions that account for most antimicrobial use in pigs (intestinal and respiratory disease), cattle (respiratory disease and mastitis), dogs and cats (skin, intestinal, genitourinary, and respiratory disease), and horses (upper respiratory disease, neonatal foal care, and surgical infections). Lastly, we present perspectives on the education and research needs for improving antimicrobial use in the future.

Serological diversity, molecular characterisation and antimicrobial sensitivity of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in Kashmir, India

The present study has determined the serological diversity, virulence-gene profile and in vitro antibiogram of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in India suspected to have died of colibacillosis. The virulence-gene profile of APEC was compared with that of the Escherichia coli isolates from faeces of apparently healthy chickens, called avian faecal E. coli (AFEC). In total, 90 representative isolates of APEC and 63 isolates of AFEC were investigated in the present study. The APEC were typed into 19 serogroups, while some isolates were rough and could not be typed. Most prevalent serogroup was O2 (24.44%). Among the eight virulence genes studied, the prevalence of seven genes (iss, iucD, tsh, cva/cvi, irp2, papC and vat) was significantly higher in APEC than in AFEC isolates. However, there was no significant difference between APEC and AFEC isolates for possession of astA gene. The most frequent gene detected among the two groups of organisms was iss, which was present in 98.88% and 44.44% of APEC and AFEC isolates respectively. The in vitro antibiogram showed that the majority (96.6%) of APEC isolates were resistant to tetracycline, while 82.2% were resistant to cephalexin, 78.8% to cotrimoxazole, 68.8% to streptomycin and 63.3% to ampicillin. However, most of them (84.45%) were sensitive to gentamicin. Thus, it is concluded that APEC from the broiler chickens carried putative virulence genes that attributed to their pathogenicity. Furthermore, the majority of APEC isolates were found to be multi-drug resistant, which, in addition to leading treatment failures in poultry, poses a public health threat.

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.

Antibiotic-resistant Escherichia coli from retail poultry meat with different antibiotic use claims

Background

We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional.

Results

We collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category.

Conclusion

The high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1322-5) 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®.

Dynamics of cefotaxime resistant Escherichia coli in broilers in the first week of life

Extended-spectrum beta-lactamase producing E. coli (ESBL-E) are wide spread among broilers, with the highest prevalence among individual birds at broiler production farms. Previous research describes low prevalences among individual birds at arrival at the farm (below 30%), and a rapid increase up to 100% within the first week. Our goal was to investigate whether this rapid increase was due to latent contamination of ESBL-E or to contamination at the broiler farm. Two broiler groups, one hatched at a conventional hatchery and the other individually hatched in an ESBL-free environment, were housed individually in an experimental ESBL-free environment. A third group was hatched at a conventional hatchery and kept at a conventional broiler farm. The birds were sampled daily during the first week after hatch and tested for the presence of ESBL-E. In addition ESBL-E presence in eggs that were not incubated was investigated. All birds and eggs came from one ESBL-E positive parent flock. ESBL/AmpC genes, plasmids and E. coli sequence types were determined for a selection of isolates. ESBL-E was never found in the two groups kept in the ESBL-free experimental environment or in the sampled eggs, whereas all broilers sampled at the conventional farm became positive for ESBL-E within three days. One dominant E. coli strain (ST88) carrying bla_CTX-M-1 gene on an IncI1/pST3 plasmid was found in parent and broiler samples. We conclude that the rapid increase in ESBL-E prevalence in the first week of life is not caused by a latent contamination of the majority of birds at arrival, but that this increase must be caused by other factors.

Evaluation of disinfectants and antiseptics to eliminate bacteria from the surface of turkey eggs and hatch gnotobiotic poults

Bird eggs are in contact with intestinal microbiota at or after oviposition, but are protected from bacterial translocation by a glycoprotein cuticle layer, the shell, and internal membranes. In a preliminary study, turkey eggs were hatched in a germ-free environment. Firmicutes 16S rRNA gene was detected in the cecal microbiota of hatched poults, suggesting that poults may acquire spore-formers by exposure to shell contents during hatching. Generating gnotobiotic poults for research requires elimination of bacteria from the egg's surface without damaging the developing embryo. The ability of different disinfectants and antiseptics to eliminate eggshell bacteria without harming the developing embryo was tested. Different classes of disinfectants and antiseptics (halogens, biguanidines, and oxidants) were selected to target spores and vegetative bacteria likely present on the egg's surface. Eggs were treated by fully immersing in heated antiseptic (betadine or chlorhexidine) or disinfectant (alkaline bleach, acidified bleach, chlorine dioxide, Oxysept-333, or Virkon S) solutions for up to 15 minutes. Shells were aseptically harvested for aerobic and anaerobic culturing of bacteria. Toxicity to the developing embryo was assessed by gross evaluation of developmental changes in treated eggs incubated up to 27 d of embryonation. Halogen disinfectants acidified bleach and chlorine dioxide, and oxidants Oxysept-333 and Virkon-S eliminated viable bacteria from eggshells. However, addition of oxidants, alone or in combination with other treatments, produced significant (P < 0.05) embryotoxicity. The combination treatment of acidified bleach, chlorine dioxide, and betadine produced minimal embryotoxicity and eliminated viable bacteria from whole turkey eggs, and produced hatched poults in a gnotobiotic isolator. As a control, eggs were treated with PBS, incubated, and hatched under germ-replete conditions. After hatching, poults were euthanized and treated poults had no detectable bacterial growth or 16S rRNA gene qPCR amplification, demonstrating that acidified sodium hypochlorite, chlorine dioxide, and betadine safely hatched gnotobiotic poults. Generation of germ-free poults is an important tool and will be used to evaluate the host-pathogen interaction by foodborne pathogens such as Campylobacter spp.

Transmission and pathogenicity of Gallibacterium anatis and Escherichia coli in embryonated eggs

In laying hens, Escherichia coli (E. coli) and Gallibacterium anatis (G. anatis) are considered the two major pathogens causing reproductive tract disorders, either as single infections or as co-infections. Vertical transmission has been confirmed for E. coli but remains to be clearly demonstrated for G. anatis. The aim of the present study was to investigate the ability of both G. anatis and E. coli at eggshell transmission using an embryonated egg dipping model, and to investigate the possible interaction between the two organisms in an embryonated egg injection model. Embryonated eggs were dipped into brain heart infusion broth containing 10⁸ CFU/ml either of G. anatis 12656-12 liver, E. coli ST95 or E. coli ST141, respectively. E. coli ST95 and ST141 were re-isolated from the interior egg contents in 60% (12/20) and 85% (17/20) of the eggs, respectively, while G. anatis 12656-12 was only re-isolated from the interior egg contents in 6.7% (3/45) eggs. Eggs were injected with 10-1000 CFU of either G. anatis 12656-12, E. coli ST95 or ST141 into the allantoic cavity. As few as 10 CFU of G. anatis 12656-12 resulted in 100% mortality within 24 h post injection whereas the E. coli injected embryos all died at 48 h post injection. Significant difference in CFU counts were observed for G. anatis when compared G. anatis injection group with either of the two G. anatis - E. coli co-injection groups. Sixteen hours post injection, a significant difference in embryo mortality could be observed when comparing co-injected embryonated eggs (G. anatis and E. coli) and single-injected (G. anatis or E. coli) embryonated eggs. In conclusion, bacterial transmission via the eggshell was demonstrated for both G. anatis and E. coli although at different magnitudes. The embryonated egg injection model revealed that G. anatis in particular was highly pathogenic when exposed directly to the developing embryo.

Effects of different types of flooring design on the development of antimicrobial resistance in commensal Escherichia coli in fattening turkeys

The objective of this study was to evaluate the effects of different types of flooring designs on antimicrobial resistance in commensal Escherichia coli from turkeys treated with enrofloxacin. Two trials were performed with same feed, housing conditions and fattening duration, but with different flooring designs. Furthermore, the first trial was performed in an unchanged environment and the second trial in a changed environment. The flooring designs of the pens were assigned to four groups; G1 - entire floor pen covered with litter, G2 - floor pen with heating, G3 - partially slatted flooring including an area that was littered, G4 - fully slatted flooring with a sand bath. Enrofloxacin was given at days 10-14 via drinking water. The changed environment in the second trial was achieved by moving the animals to new pens with the respective same conditions as previously after antimicrobial administration at day 15. A total of 576 E. coli were isolated from cloacal swab and poultry manure samples. Sample collection was done before the treatment, after the treatment and at the end of the trials at day 35. The resistance of isolates to enrofloxacin and ampicillin was determined using broth microdilution A single treatment with enrofloxacin reduced the proportion of samples with susceptible E. coli isolates significantly in all flooring designs. Overall, frequencies of enrofloxacin resistance were significantly different between the unchanged and changed environment. At the same time, the proportion of ampicillin-resistant isolates increased in the first trial, although no ampicillin was applied in this study.

Longitudinal study of transmission of Escherichia coli from broiler breeders to broilers

Escherichia coli is of major importance in industrial broiler production as the main cause of salpingitis and peritonitis in broiler breeders. Furthermore E. coli is the most common cause of first week mortality in broiler chickens. The aim of the present study was to investigate the transmission of E. coli, isolated from broiler breeders with salpingitis, to the progeny and the possibility of subsequent first week mortality. Four parent flocks were followed during the whole production period (20-60 weeks) by post mortem and bacteriological examination of randomly selected dead birds. Newly hatched chickens from each flock were swabbed in the cloaca on four occasions (parent age 30, 40, 50, 60 weeks) and E. coli was isolated. Causes of first week mortality were determined pathologically and bacteriologically. E. coli isolates from parents, newly hatched chickens and first week mortality were selected for Pulsed-Field-Gel-Electrophoresis (PFGE) and Multi-Locus-Sequence-Typing (MLST) to determine their clonal relationships. E. coli was the main cause of both salpingitis in parents and first week mortality in broilers, and E. coli dominated the bacterial flora of the cloaca of newly hatched chickens. PFGE of E. coli showed identical band patterns in isolates from the three different sources indicating a transmission of E. coli from parent birds to chickens. In conclusion, E. coli isolated from salpingitis in broiler parents were found to be transmitted to broilers in which some sequence types contributed to the first week mortality.

Antimicrobial resistance of Escherichia coli isolated in newly-hatched chickens and effect of amoxicillin treatment during their growth

The use of antimicrobials in food animals is the major determinant for the propagation of resistant bacteria in the animal reservoir. However, other factors may also play a part, and in particular vertical spread between the generations has been suggested to be an important transmission pathway. The objective of this paper was to determine the resistance patterns of Escherichia coli isolated from newly-hatched chickens as well as to study the antibiotic pressure effect when amoxicillin was administered during their growing period. With this aim, meconium from 22 one-day-old Ross chickens was analysed. In addition, during their growth period, amoxicillin treatments at days 7, 21 and 35 were carried out. Results showed a high number of E. coli-resistant strains were isolated from the treated one-day-old chickens, and were the highest for β-lactams group, followed by quinolone and tetracyclines. After treatment with amoxicillin, the highest percentage of resistances were detected for this antibiotic compared to the others analysed, with significant differences in resistance percentages between control and treated broilers detected in relation to ampicillin, cephalothin, streptomycin, kanamycin, gentamicin, chloramphenicol and tetracycline. Differences in resistances to ciprofloxacin and nalidixic acid between control and treated animals were not observed and there was lack of resistance for amikacin and ceftriaxone. These results suggest the possibility of vertical transmission of resistant strains to newly-hatched chicks from parent flocks, and seem to indicate that the treatment with amoxicillin increased the resistance of E. coli to other antibiotics.

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

Antimicrobial resistance through extended-spectrum beta-lactamases (ESBLs) and transferable (plasmid-encoded) cephamycinases (pAmpCs) represents an increasing problem in human and veterinary medicine. The presence of ESBL-/pAmpC-producing commensal enterobacteria in farm animals, such as broiler chickens, is considered one possible source of food contamination and could therefore also be relevant for human colonization. Studies on transmission routes along the broiler production chain showed that 1-day-old hatchlings are already affected. In this study, ESBL-/pAmpC-positive broiler parent flocks and their corresponding eggs, as well as various environmental and air samples from the hatchery, were analyzed. The eggs were investigated concerning ESBL-/pAmpC-producing enterobacteria on the outer eggshell surface (before/after disinfection), the inner eggshell surface, and the egg content. Isolates were analyzed concerning their species, their phylogroup in the case of Escherichia coli strains, the respective resistance genes, and the phenotypical antibiotic resistance. Of the tested eggs, 0.9% (n = 560) were contaminated on their outer shell surface. Further analyses using pulsed-field gel electrophoresis showed a relationship of these strains to those isolated from the corresponding parent flocks, which demonstrates a pseudo-vertical transfer of ESBL-/pAmpC-producing enterobacteria into the hatchery. Resistant enterobacteria were also found in environmental samples from the hatchery, such as dust or surfaces which could pose as a possible contamination source for the hatchlings. All 1-day-old chicks tested negative directly after hatching. The results show a possible entry of ESBL-/pAmpC-producing enterobacteria from the parent flocks into the hatchery; however, the impact of the hatchery on colonization of the hatchlings seems to be low.

IMPORTANCE

ESBL-/pAmpC-producing enterobacteria occur frequently in broiler-fattening farms. Recent studies investigated the prevalence and possible transmission route of these bacteria in the broiler production chain. It seemed very likely that the hatcheries play an important role in transmission and/or contamination events. There are only few data on transmission investigations from a grandparent or parent flock to their offspring. However, reliable data on direct or indirect vertical transmission events in the hatchery are not available. Therefore, we conducted our study and intensively investigated the broiler hatching eggs from ESBL-/pAmpC-positive broiler parent flocks as well as the hatchlings and the environment of the hatchery.

Quantitative assessment of antimicrobial resistance in livestock during the course of a nationwide antimicrobial use reduction in the Netherlands

OBJECTIVES

To quantify associations between antimicrobial use and acquired resistance in indicator Escherichia coli over a period of time which involved sector-wide antimicrobial use reductions in broilers and pigs (years 2004-14), veal calves (2007-14) and dairy cattle (2005-14). Prevalence estimates of resistance were predicted for a hypothetical further decrease in antimicrobial use.

METHODS

Data reported annually for the resistance surveillance programme in the Netherlands were retrieved. Two multivariate random-effects logistic models per animal sector were used to relate total and class-specific antimicrobial use (as defined daily dosages per animal per year, DDDA/Y) with the probability of E. coli resistance to a panel of 10 antimicrobial agents.

RESULTS

Positive dose-response relationships (ORs) were obtained from all models. Specific resistance phenotypes were more often associated with total antimicrobial use than with class-specific use. The most robust associations were found in pigs and veal calves. Resistance to historically widely used antimicrobials (e.g. penicillins, tetracyclines) was, in relative terms, less influenced by drug use changes over time than resistance to newer or less prescribed antimicrobials (e.g. third-/fourth-generation cephalosporins, fluoroquinolones). In pigs and veal calves, prevalence estimates for the most common resistance phenotypes were projected to decline ∼5%-25% during 2014-16 if total antimicrobial use reduction reached 80%; projections for poultry and dairy cows were more modest.

CONCLUSIONS

Epidemiological evidence indicated that drug use history and co-selection of resistance are key elements for perpetuation of resistance. Data suggest that recent Dutch policies aimed at reducing total use of antimicrobials have decreased E. coli resistance in the pig and veal calf production sectors while the impact on the dairy cattle and poultry sectors is less clear.

Persistence of vancomycin resistance in multiple clones of Enterococcus faecium isolated from Danish broilers 15 years after the ban of avoparcin

The occurrence and diversity of vancomycin-resistant Enterococcus faecium (VREF) were investigated in 100 Danish broiler flocks 15 years after the avoparcin ban. VREF occurred in 47 flocks at low fecal concentrations detectable only by selective enrichment. Vancomycin resistance was prevalently associated with a transferable nontypeable plasmid lineage occurring in multiple E. faecium clones. Coselection of sequence type 842 by tetracycline use only partly explained the persistence of vancomycin resistance in the absence of detectable plasmid coresistance and toxin-antitoxin systems.

Impact of third-generation-cephalosporin administration in hatcheries on fecal Escherichia coli antimicrobial resistance in broilers and layers

We investigated the impact of the hatchery practice of administering third-generation cephalosporin (3GC) on the selection and persistence of 3GC-resistant Escherichia coli in poultry. We studied 15 3GC-treated (TB) and 15 non-3GC-treated (NTB) broiler flocks and 12 3GC-treated (TL) and 10 non-3GC-treated (NTL) future layer flocks. Fecal samples from each flock were sampled before arrival on the farm (day 0), on day 2, on day 7, and then twice more. E. coli isolates were isolated on MacConkey agar without antibiotics and screened for 3GC resistance, and any 3GC-resistant E. coli isolates were further analyzed. 3GC-resistant E. coli isolates were found in all 3GC-treated flocks on at least one sampling date. The percentages of 3GC-resistant E. coli isolates were significantly higher in TB (41.5%) than in NTB (19.5%) flocks and in TL (49.5%) than in NTL (24.5%) flocks. In the day 2 samples, more than 80% of the E. coli strains isolated were 3GC resistant. 3GC-resistant E. coli strains were still detected at the end of the follow-up period in 6 out of 27 3GC-treated and 5 out of 25 non-3GC-treated flocks. Many 3GC-resistant E. coli strains were resistant to tetracycline, and there were significant differences in the percentages of resistance to sulfamethoxazole-trimethoprim, streptomycin, or gentamicin between treated and nontreated flocks. blaCTX-M and blaCMY-2 were the most frequently detected genes. These results clearly demonstrated that 3GC-resistant strains are introduced early in flocks and that the use of 3GC in hatcheries promotes the selection of 3GC-resistant E. coli. Measures must be implemented to avoid the spread and selection of 3GC-resistant strains.

Effect of berberine and other herbal extracts on gyrA gene mutations in multidrug resistant Escherichia coli

AIM: To investigate if berberine and other herbal extracts have an effect on gyrA gene mutations in multidrug resistant Escherichiae coli (E. coli).

METHODS: The multidrug resistance of E. coli to ofloxacin, ciprofloxacin and norfloxacin was determined by K-B method. Multidrug resistant E. coli was cultured in the presence of berberine or other herbal extracts and passaged once every 2 d for a total of 15 times. E. coli DNA was extracted to amplify the gyrA gene by PCR, and gyrA gene sequence was analyzed to check the mutation status before and after treatment.

RESULTS: The multidrug resistant E. coli had gyrA gene mutations, mainly C-T mutation at nt83 and G-A mutation at nt87. After treatment with berberine or other herbal extracts for 30 d, no significant changes were found in the gyrA gene mutations.

CONCLUSION: Multidrug resistant E. coli to quinolones carry gyrA gene mutations, and berberine and other herbal extracts have no significant impact on these mutations.

The contribution of systemic Escherichia coli infection to the early mortalities of commercial broiler chickens

Avian pathogenic Escherichia coli (APEC) are a substantial burden to the global poultry industry. APEC cause a syndromic poultry infection known as colibacillosis, which has been previously associated with broiler chickens over 2 weeks old. We recently reported that the intestinal tract of 1-day-old broilers harbours a rich reservoir of potentially pathogenic E. coli. Prior infections of the reproductive tract of breeders, egg hygiene and transportation all contribute to early colonization of the neonatal gut. Up to one-half of all flock deaths occur in the first week of production, but few data are available describing the contribution of E. coli. In the present study, all dead birds collected on the first daily welfare walk 48 and 72 h after chick placement underwent post-mortem examination. Diseased tissues were selectively cultured for E. coli and isolates subsequently virulotyped using 10 APEC virulence-associated genes (VAGs): astA, iss, irp2, iucD, papC, tsh, vat, cvi, sitA and ibeA. Approximately 70% of birds displayed signs of colibacillosis. Thirty distinct virulence profiles were identified among 157 E. coli. Isolates carried between zero and seven VAGs; ∼ 30% of E. coli isolates carried five to seven VAGs, with 12.7% sharing the same VAG profile (astA, iss, irp2, iucD, tsh, cvi and sitA). Overall, this study demonstrates the significant contribution of E. coli infections to early broiler mortalities. The identification of a diverse E. coli population is unsurprising based on our previous findings. This work emphasizes the need for an effective vaccination programme and provides preliminary data for vaccine production.

Characterization and antimicrobial resistance analysis of avian pathogenic Escherichia coli isolated from Italian turkey flocks

This study investigated the occurrence of avian pathogenic Escherichia coli (APEC) in a finishing turkey commercial farm, carrying out longitudinal surveys involving 3 consecutive flocks. The diversity and the distribution of the E. coli strains detected during colisepticemia outbreaks were examined. The strains were isolated, serogrouped, assessed for the presence of virulence-associated genes, typed by random amplification of polymorphic DNA (RAPD), and antimicrobial resistance analysis was then carried out. Escherichia coli O78 and O2 were predominantly found. Moreover, based on the somatic antigens used in the study, strains were recovered that were nontypeable. On one occasion, an E. coli O111 strain was found in turkeys. The E. coli isolates differed in terms of antibiotic resistance and RAPD profile. All strains possessed the virulence genes that enabled them to be considered APEC. Strains not only differed between flocks, but also within the same flock. These findings point out the importance of addressing colibacillosis therapy on the basis of a sensitivity test.