Risk factors for antimicrobial resistance in Escherichia coli found in GB turkey flocks

Decrease in the prevalence of antimicrobial resistance in Escherichia coli isolates of Canadian turkey flocks driven by the implementation of an antimicrobial stewardship program

The emergence of antimicrobial-resistant organisms at the human-animal-environment interface has raised global concern prompting governments and various stakeholders to take action. As a part of the stewardship initiative, Canadian turkey producers have implemented an antimicrobial use (AMU) strategy to manage antimicrobial resistance (AMR) in their sector. This study evaluated farm-level AMU and AMR data collected between 2016 and 2021 in major turkey-producing provinces/regions through the Canadian Integrated Program for Antimicrobial Resistance Surveillance to assess the progress of the strategy by characterizing the prevalence of homologous and multidrug resistance (MDR) in Escherichia coli isolated from turkeys. Multivariable mixed-effect logistic regression models assessed temporal and provincial/regional variations in AMR and MDR. Negative binomial regression models examined the temporal and regional variations in the total AMU. The total AMU (measured in mg/kg turkey biomass) significantly decreased in all provinces/regions in 2020 and 2021. Escherichia coli isolates from turkey flocks showed a significant decrease in resistance to gentamicin, sulfisoxazole, and tetracyclines during the six-year study period, consistent with the timing of the AMU reduction strategy. The prevalence of MDR isolates was significantly lower in 2020 and 2021 compared to 2016. Higher prevalence was observed in the Western region compared to Québec and Ontario. Two common AMR patterns were identified: ampicillin-streptomycin-tetracyclines and streptomycin-sulfisoxazole-tetracyclines. These AMR patterns indicate possible cross-resistances (same class), co-selection (unrelated classes) for resistance, or potential carryover of resistance determinants from previous production cycles. The decreasing prevalence of resistance to homologous antimicrobials, MDR, and AMU quantity are suggestive that the turkey sector's AMU strategy is achieving its desired impact. However, antimicrobials previously eliminated for preventive use in turkey flocks and the use of highly important antimicrobials in human medicine suggest that the AMU reduction strategy should be monitored and re-evaluated periodically to mitigate the emergence of MDR bacteria and safeguard animal and public health.

Genetic diversity and risk factor analysis of drug-resistant Escherichia coli recovered from broiler chicken farms

A total of 38 Escherichia coli isolates were recovered from 120 samples collected from various sources of broiler chicken farms (n = 10 each) in Andhra Pradesh and Telangana states. Though the recovered E. coli isolates were found variably resistant to the tested antibiotics, all the tested isolates were susceptible to meropenem. Alarming multi-drug resistance (MDR) was observed (34/38) among the recovered isolates, wherein antibiotic-resistant genes (bla_TEM, bla_SHV, and tetA) were detected, except for bla_CTX-M-9. The heatmap with cluster analysis exhibited that majority of the E. coli isolates recovered from different sources and regions clustered together based on their phenotypic resistance suggesting co-sharing of resistance. However, the pulsed-field gel electrophoresis (PFGE) typing revealed an extremely diverse genotypic profile. Further, a significant statistical association was not observed between hypothesized risk factors and recovered MDR- E. coli isolates from various sources, although a significant statistical association between antibiotic resistance with large flock size, poor biosecurity practices, poor workers' hygiene, and poor disinfection practices was noticed. Since the study highlighted an alarming level of drug resistance among the recovered E. coli isolates, further in-depth research in similar veins is required to ensure the prudent use of antimicrobials in the poultry sector and the implementation of an antimicrobial surveillance system.

Transmission of antimicrobial resistance (AMR) during animal transport

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

A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project)

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

Risk factors for third-generation cephalosporin-resistant and extended-spectrum β-lactamase-producing Escherichia coli carriage in domestic animals of semirural parishes east of Quito, Ecuador

Extended-spectrum β-lactamase (ESBL)-producing and other antimicrobial resistant (AR) Escherichia coli threaten human and animal health worldwide. This study examined risk factors for domestic animal colonization with ceftriaxone-resistant (CR) and ESBL-producing E. coli in semirural parishes east of Quito, Ecuador, where small-scale food animal production is common. Survey data regarding household characteristics, animal care, and antimicrobial use were collected from 304 households over three sampling cycles, and 1195 environmental animal fecal samples were assessed for E. coli presence and antimicrobial susceptibility. Multivariable regression analyses were used to assess potential risk factors for CR and ESBL-producing E. coli carriage. Overall, CR and ESBL-producing E. coli were detected in 56% and 10% of all fecal samples, respectively. The odds of CR E. coli carriage were greater among dogs at households that lived within a 5 km radius of more than 5 commercial food animal facilities (OR 1.72, 95% CI 1.15-2.58) and lower among dogs living at households that used antimicrobials for their animal(s) based on veterinary/pharmacy recommendation (OR 0.18, 95% CI 0.04-0.96). Increased odds of canine ESBL-producing E. coli carriage were associated with recent antimicrobial use in any household animal (OR 2.69, 95% CI 1.02-7.10) and purchase of antimicrobials from pet food stores (OR 6.83, 95% CI 1.32-35.35). Food animals at households that owned more than 3 species (OR 0.64, 95% CI 0.42-0.97), that used antimicrobials for growth promotion (OR 0.41, 95% CI 0.19-0.89), and that obtained antimicrobials from pet food stores (OR 0.47, 95% CI 0.25-0.89) had decreased odds of CR E. coli carriage, while food animals at households with more than 5 people (OR 2.22, 95% CI 1.23-3.99) and located within 1 km of a commercial food animal facility (OR 2.57, 95% CI 1.08-6.12) had increased odds of ESBL-producing E. coli carriage. Together, these results highlight the complexity of antimicrobial resistance among domestic animals in this setting.

The Role of Biosecurity in the Control of Campylobacter: A Qualitative Study of the Attitudes and Perceptions of UK Broiler Farm Workers

Campylobacter is the leading cause of human bacterial diarrhoeal disease worldwide, with poultry meat products contributing to a large proportion of cases. Due to the ubiquitous presence of Campylobacter in the poultry farm environment, biosecurity is the main area for intervention to prevent colonisation of commercial broiler chicken flocks. However, research has repeatedly demonstrated that farmers' uptake of biosecurity recommendations is often poor. This study explored farmers' attitudes towards biosecurity and identified barriers to effective implementation of biosecurity protocols. Semi-structured interviews were conducted with 1–3 members of staff on each of 16 broiler farms; 6 owned by, and 10 contracted to, 3 different UK poultry integrators. In total, 28 interviewees participated, including farm owners, managers, and workers, with a range of industry experience. Thematic analysis of the interviews revealed high levels of recognition amongst broiler farmers of the importance of Campylobacter and the responsibility of the whole farm-to-fork chain within the poultry industry to reduce Campylobacter contamination of chicken meat for the benefit of public health. Participants' self-reported awareness and implementation of biosecurity has improved significantly following the industry-wide focus on Campylobacter control. However, there are frustrations with the industry's approach to tackling Campylobacter and the heavy burden of responsibility that has been put on interventions at the farm-level. There was also scepticism amongst participants as to the effectiveness of current biosecurity measures in the reduction of Campylobacter. Nevertheless, the interviewees' recognition of the benefit of improved biosecurity on broiler health and welfare and other important targets, such as reducing antimicrobial usage, leaves a legacy of which the UK broiler industry can be proud. There is scope for further farmer education about the evidence supporting biosecurity interventions, particularly in the control of Campylobacter, and a need to establish more effective channels of communication. Furthermore, to give all players within the industry agency and investment in industry targets, contributions from all levels should be permitted in the design of future biosecurity interventions. Biosecurity compliance may be improved through collaborative efforts, such as participatory and co-design practises, to facilitate knowledge co-creation and exchange.

OUP accepted manuscript

Objectives

The occurrence and zoonotic potential of antimicrobial resistance (AMR) in pigs and broilers has been studied intensively in past decades. Here, we describe AMR levels of European pig and broiler farms and determine the potential risk factors.

Methods

We collected faeces from 181 pig farms and 181 broiler farms in nine European countries. Real-time quantitative PCR (qPCR) was used to quantify the relative abundance of four antimicrobial resistance genes (ARGs) [aph(3′)-III, erm(B), sul2 and tet(W)] in these faeces samples. Information on antimicrobial use (AMU) and other farm characteristics was collected through a questionnaire. A mixed model using country and farm as random effects was performed to evaluate the relationship of AMR with AMU and other farm characteristics. The correlation between individual qPCR data and previously published pooled metagenomic data was evaluated. Variance component analysis was conducted to assess the variance contribution of all factors.

Results

The highest abundance of ARG was for tet(W) in pig faeces and erm(B) in broiler faeces. In addition to the significant positive association between corresponding ARG and AMU levels, we also found on-farm biosecurity measures were associated with relative ARG abundance in both pigs and broilers. Between-country and between-farm variation can partially be explained by AMU. Different ARG targets may have different sample size requirements to represent the overall farm level precisely.

Conclusions

qPCR is an efficient tool for targeted assessment of AMR in livestock-related samples. The AMR variation between samples was mainly contributed to by between-country, between-farm and within-farm differences, and then by on-farm AMU.

Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries

Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3′-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

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

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

Antimicrobial resistance prevalence in commensal Escherichia coli from broilers, fattening turkeys, fattening pigs and veal calves in European countries and association with antimicrobial usage at country level

The aim of this article is to report on antimicrobial resistance (AMR) in commensal Escherichia coli from livestock from several European countries. The relationships with antimicrobial usage (AMU) at country level and harmonized indicators to cover the most relevant AMR aspects for human health in animal production were also investigated. E. coli were isolated in faeces from broilers and fattening pigs (from nine countries), and fattening turkeys and veal calves (from three countries) and screened against a fixed antimicrobial panel. AMU data were collected at farm and average treatment incidences stratified by antimicrobial class, country and livestock species were calculated. Associations between AMR and AMU at country level were analysed. Independent of animal species, the highest resistance was observed for ampicillin, sulphamethoxazole, tetracycline and trimethoprim. E. coli from broilers showed the highest resistance level for (fluoro)quinolones, and multidrug resistance peaked in broilers and fattening turkeys. Colistin resistance was observed at very low levels with the exception of fattening turkeys. High resistance to third- and fourth-generation cephalosporins was detected in broilers and fattening turkeys. The lowest levels of resistance were for meropenem, azithromycin and tigecycline (<1 %). Significant correlations between resistance and usage at country level were detected in broilers for polymyxins and aminoglycosides, and in fattening pigs for cephalosporins, amphenicols, fluoroquinolones and polymyxins. None of the correlations observed between AMR and AMU were statistically significant for fattening turkey and veal calves. The strength of the analysis performed here is the correlation of aggregated data from the same farms at country level for both AMU and AMR within antimicrobial classes.

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.

Antimicrobial Resistance on Farms: A Review Including Biosecurity and the Potential Role of Disinfectants in Resistance Selection

Resistance to therapeutic antimicrobial agents is recognized as a growing problem for both human and veterinary medicine, and the need to address the issue in both of these linked domains is a current priority in public policy. Efforts to limit antimicrobial resistance (AMR) on farms have so far focused on control of the supply and use of antimicrobial drugs, plus husbandry measures to reduce infectious disease. In the United Kingdom and some other countries, substantial progress has been made recently against targets on agricultural antimicrobial drug use. However, evidence suggests that resistant pathogenic and commensal bacteria can persist and spread within and between premises despite declining or zero antimicrobial drug use. Reasons for this are likely complex and varied but may include: bacterial adaptations to ameliorate fitness costs associated with maintenance and replication of resistance genes and associated proteins, horizontal transmission of genetic resistance determinants between bacteria, physical transfer of bacteria via movement (of animals, workers, and equipment), ineffective cleaning and disinfection, and co-selection of resistance to certain drugs by use of other antimicrobials, heavy metals, or biocides. Areas of particular concern for public health include extended-spectrum cephalosporinases and fluoroquinolone resistance among Enterobacteriaceae, livestock-associated methicillin-resistant Staphylococcus aureus, and the emergence of transmissible colistin resistance. Aspects of biosecurity have repeatedly been identified as risk factors for the presence of AMR on farm premises, but there are large gaps in our understanding of the most important risk factors and the most effective interventions. The present review aims to summarize the present state of knowledge in this area, from a European perspective.

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.

Prevalence and risk factors for carriage of antimicrobial-resistant Escherichia coli on household and small-scale chicken farms in the Mekong Delta of Vietnam

OBJECTIVES

To describe the prevalence of antimicrobial resistance among commensal Escherichia coli isolates on household and small-scale chicken farms, common in southern Vietnam, and to investigate the association of antimicrobial resistance with farming practices and antimicrobial usage.

METHODS

We collected data on farming and antimicrobial usage from 208 chicken farms. E. coli was isolated from boot swab samples using MacConkey agar (MA) and MA with ceftazidime, nalidixic acid or gentamicin. Isolates were tested for their susceptibility to 11 antimicrobials and for ESBL production. Risk factor analyses were carried out, using logistic regression, at both the bacterial population and farm levels.

RESULTS

E. coli resistant to gentamicin, ciprofloxacin and third-generation cephalosporins was detected on 201 (96.6%), 191 (91.8%) and 77 (37.0%) of the farms, respectively. Of the 895 E. coli isolates, resistance to gentamicin, ciprofloxacin and third-generation cephalosporins was detected in 178 (19.9%), 291 (32.5%) and 29 (3.2%) of the isolates, respectively. Ciprofloxacin resistance was significantly associated with quinolone usage (OR = 2.26) and tetracycline usage (OR = 1.70). ESBL-producing E. coli were associated with farms containing fish ponds (OR = 4.82).

CONCLUSIONS

Household and small farms showed frequent antimicrobial usage associated with a high prevalence of resistance to the most commonly used antimicrobials. Given the weak biocontainment, the high prevalence of resistant E. coli could represent a risk to the environment and to humans.