Prevalence and quantitative analysis of ESBL and AmpC beta-lactamase producing Enterobacteriaceae in broiler chicken during slaughter in Germany

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Antibiotic resistance and virulence profiles of Proteus mirabilis isolated from broiler chickens at abattoir in South Africa

BACKGROUND

Proteus mirabilis has been identified as an important zoonotic pathogen, causing several illnesses such as diarrhoea, keratitis and urinary tract infections.

OBJECTIVE

This study assessed the prevalence of P. mirabilis in broiler chickens, its antibiotic resistance (AR) patterns, ESBL-producing P. mirabilis and the presence of virulence genes.

METHODS

A total of 26 isolates were confirmed as P. mirabilis from 480 pooled broiler chicken faecal samples by polymerase chain reaction (PCR). The disk diffusion method was used to evaluate the antibacterial susceptibility test, while nine virulence genes and 26 AR genes were also screened by PCR.

RESULTS

All 26 P. mirabilis isolates harboured the ireA (siderophore receptors), ptA, and zapA (proteases), ucaA, pmfA, atfA, and mrpA (fimbriae), hlyA and hpmA (haemolysins) virulence genes. The P. mirabilis isolates were resistant to ciprofloxacin (62%) and levofloxacin (54%), while 8 (30.7%) of the isolates were classified as multidrug resistant (MDR). PCR analysis identified the blaCTX-M gene (62%), blaTEM (58%) and blaCTX-M-2 (38%). Further screening for AMR genes identified mcr-1, cat1, cat2, qnrA, qnrD and mecA, 12%, 19%, 12%, 54%, 27% and 8%, respectively for P. mirabilis isolates. The prevalence of the integron integrase intI1 and intI2 genes was 43% and 4%, respectively.

CONCLUSIONS

The rise of ciprofloxacin and levofloxacin resistance, as well as MDR strains, is a public health threat that points to a challenge in the treatment of infections caused by these zoonotic bacteria. Furthermore, because ESBL-producing P. mirabilis has the potential to spread to humans, the presence of blaCTX -M -producing P. mirabilis in broilers should be kept under control. This is the first study undertaken to isolate P. mirabilis from chicken faecal samples and investigate its antibiotic resistance status as well as virulence profiles in South Africa.

Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020

Introduction

Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK.

Methods

In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020.

Results

The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission.

Discussion

We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.

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

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

Occurrence of Antibiotic-Resistant Bacteria in Fish and Seafood from Slovak Market

The consumption of sushi or poke has grown globally. However, this type of dish often contains raw fish or seafood; therefore, it can pose a microbial risk for consumers. This study deals with the occurrence of total and antibiotic-resistant coliform bacteria and enterococci in fish and seafood as well as sushi and poke bought from Slovak retail (restaurants and fast food). Total coliforms have ranged in sushi, poke samples and samples of fish and seafood from cooling counters from 0.6 to 5.1 log CFU/g. Ampicillin resistance has been predominantly observed in all types of samples. Tetracycline resistance was detected in 16% of all tested samples and gentamicin resistance in 13%. Total enterococci has been detected in 74% of sushi samples, 100% of poke samples and 62% of samples obtained from supermarkets. The majority of enterococci were resistant to ampicillin. Vancomycin resistance was observed in five samples. Forty-eight resistant coliforms were identified mainly as Enterobacter spp. and Klebsiella spp. Antibiotic-resistant isolates were predominantly resistant to gentamicin, chloramphenicol and tetracycline. In 13% of resistant isolates was detected efflux pumps overproduction, and in four isolates was detected the tetA resistance gene. Our results point to poor hygiene in some establishments. The prevention of the antibiotic-resistant bacteria spread would be in better stewardship and improved monitoring of sanitation.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

Enumeration, antimicrobial resistance and genomic characterization of extended-spectrum β-lactamases producing Escherichia coli from supermarket chicken meat in the United Arab Emirates

The occurrence and counts of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in retail chicken sold in the United Arab Emirates (UAE) were investigated in this study. Results indicated that 79.68 % of chicken carcasses (251/315) sampled from UAE supermarkets harbored ESBL-producing E. coli. About half (51.75 % [163/315]) of the tested samples had an ESBL-producing E. coli count range between ≥3 log₁₀ and < 5 log₁₀ CFU/g. The antimicrobial resistance profiles of a subset of 100 isolates showed high rates of non-susceptibility to clinically significant antibiotics, particularly ciprofloxacin (80 %) and cefepime (46 %). Moreover, 7 % of the isolates exhibited resistance to colistin, with PCR-based screening revealing the presence of the mcr-1 gene in all colistin-resistant isolates. Multiplex PCR screening identified bla_CTX-M and bla_TEM genes as the most frequently presented genes among the phenotypically confirmed ESBL-producing E. coli. Further whole-genome sequencing and bioinformatic analysis of 27 ESBL-producing E. coli isolates showed that the gene family bla_CTX group 1 was the most prevalent, notably CTX-M-55 (55.55 % [15/27]), followed by CTX-M-15 (22.22 % [6/27]). The most common sequence types (STs) were ST359 and ST1011, with three evident clusters identified based on phylogenomic analysis, aligned with isolates from specific production companies. Analysis of plasmid incompatibility types revealed IncFIB, IncFII, Incl2, and IncX1 as the most commonly featured plasmids. The findings of this study indicate a noticeable prevalence and high counts of ESBL-producing E. coli in chicken sampled from supermarkets in the UAE. The high rates of antimicrobial resistance to clinically important antibiotics highlight the potential public health risk associated with consuming chicken contaminated with ESBL-producing E. coli. Overall, this study emphasizes the importance of continued antimicrobial resistance monitoring in the UAE food chain and calls for further exposure risk assessment of the consumption of ESBL-producing E. coli via chicken meat.

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

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

Transmission of antimicrobial resistance (AMR) during animal transport

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

Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments

Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.

Raw Meat Contaminated with Cephalosporin-Resistant Enterobacterales as a Potential Source of Human Home Exposure to Multidrug-Resistant Bacteria

The prevalence of cephalosporine-resistant (3GC-R) strains among United States community-related research samples ranged from 5.6 to 10.8%, while, in the European countries, it was 1.2% to 10.1%. Several studies suggest that meat of animal origin could be one of the reservoirs of 3GC-R bacteria. Here, 86 raw meat samples (turkey, pork, chicken and beef) were collected randomly and verified for the presence of 3GC-R bacteria. The 3GC-R bacteria were isolated, identified and characterized phenotypically (antibiotic resistance, motility and biofilm) and genotypically (repetitive-sequence-based rep-PCR) to elucidate any correlations with principal component analysis (PCA). From 28 3GC-R positive samples, 41 strains were isolated, from which the majority belonged to Serratia fonticola (39%), followed by Escherichia coli (19.5%), Enterobacter cloacae (17.1%) and Klebsiella pneumoniae (14.6%). The isolates of E. coli and S. fonticola presented diverse profiles in rep-PCR. Generally, 3GC-R strains were more resistant to antibiotics used in veterinary medicine than in human medicine. PCA derived from antibiotic resistance, motility and biofilm formation of S. fonticola and E. coli strains showed that resistance to beta-lactams was separated from the resistance to other antibiotic classes. Moreover, for the S. fonticola, E. coli and En. cloacae, the type of meat can create a specific tendency towards antibiotic resistance and phenotypic characteristics for S. fonticola, while these relationships were not found for other tested species.

Characterization of plasmid-mediated quinolone resistance genes and extended-spectrum beta-lactamases in non-typhoidal Salmonella enterica isolated from broiler chickens

Background and Aim:

Antibiotic-resistant Salmonella is a public health concern. Fluoroquinolones and extended-spectrum beta-lactams are widely used for the treatment of Salmonella infections. This study focused on the detection of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum beta-lactamase (ESBL) genes among multidrug-resistant (MDR) Salmonella enterica isolated from broilers.

Materials and Methods:

A total of 40 non-typhoidal S. enterica isolates were collected from 28 broiler chicken farms in four Iraqi Governorates. These isolates were examined for their susceptibility to 10 antimicrobial agents by disk-diffusion method followed by polymerase chain reaction assay for the detection of PMQR determinants and ESBLs genes.

Results:

Salmonella strains revealed high levels of resistance to the following antibiotics: Nalidixic acid 100%, levofloxacin (LEV) 97.5%, amoxicillin-clavulanic acid 95.0%, tetracycline 92.5%, and nitrofurantoin 80.0%. Otherwise, all isolates were susceptible to cefotaxime and ceftriaxone. All isolates were MDR, with 15 different profiles observed. Among 38 amoxicillin/clavulanic acid-resistant Salmonella isolates, 20 (52.6%) had the blaTEM gene, while blaSHV, blaCTX-M, and blaOXA genes were not detected. Only 5 (12.8%) out of 39 LEV-resistant isolates were positive for qnrB, three of which had blaTEM. No qnrC or qnrD, qnrS, aac(6`)-Ib-cr, qunA, and oqxAB genes were found in any of the tested isolates.

Conclusion:

This study demonstrates that broiler chickens may be considered a potential source for spreading MDR non-typhoidal Salmonella and ESBL traits in poultry production. Therefore, it is important to continuously monitor ESBL and PMQR genes to avoid the spread of resistant strains in the food chain and impact public health.

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

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

Prevalence and Characterization of ESBL/AmpC Producing Escherichia coli from Fresh Meat in Portugal

The present study aimed to characterize the extended-spectrum β-lactamases and plasmid-mediated AmpC β-lactamases (ESBL/PMAβ) among Escherichia coli producers isolated from beef, pork, and poultry meat collected at retail, in Portugal. A total of 638 meat samples were collected and inoculated on selective medium for the search of E. coli resistant to 3rd generation cephalosporins. Isolates were characterized by antimicrobial susceptibility testing, molecular assays targeting ESBL/AmpC, plasmid-mediated quinolone resistance (PMQR), and plasmid-mediated colistin resistance (PMCR) encoding genes. The highest frequency of E. coli non-wild type to 3rd generation cephalosporins and fluoroquinolones was observed in broiler meat (30.3% and 93.3%, respectively). Overall, a diversity of acquired resistance mechanisms, were detected: bla_ESBL [bla_CTX-M-1 (n = 19), bla_CTX-M-15 (n = 4), bla_CTX-M-32 (n = 12), bla_CTX-M-55 (n = 8), bla_CTX-M-65 (n = 4), bla_CTX-M-27 (n = 2), bla_CTX-M-9 (n = 1), bla_CTX-M-14 (n = 11), bla_SHV-12 (n = 27), bla_TEM-52 (n = 1)], bla_PMAβ [bla_CMY-2 (n = 8)], PMQR [qnrB (n = 27), qnrS (n = 21) and aac(6')-Ib-type (n = 4)] and PMCR [mcr-1 (n = 8)]. Our study highlights that consumers may be exposed through the food chain to multidrug-resistant E. coli carrying diverse plasmid-mediated antimicrobial resistance genes, posing a great hazard to food safety and a public health risk.

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.

Comparative Analysis of Consumer Exposure to Resistant Bacteria through Chicken Meat Consumption in Germany

Human exposure to bacteria carrying antimicrobial resistance (AMR) genes through the consumption of food of animal origin is a topic which has gained increasing attention in recent years. Bacterial transmission can be enhanced, particularly in situations in which the consumer pays less attention to hygiene practices, and consumer exposure to foodborne resistant bacteria through ready-to-eat foods could be increased. It has been demonstrated that even methicillin-resistant Staphylococcus aureus (MRSA) bacteria, which have low prevalence and concentration in raw chicken meat in Germany, may reach the consumer during barbecue events after failures in hygiene practices. This study aimed to quantify the consumer exposure to extended-spectrum beta-lactamase- (ESBL) or ampicillinase class C (AmpC) beta-lactamase-producing E. coli in Germany through the consumption of chicken meat and bread during household barbecues. The study considered cross-contamination and recontamination processes from raw chicken meat by using a previously-developed probabilistic consumer exposure model. In addition, a comparative analysis of consumer exposure was carried out between ESBL-/AmpC-producing E. coli and MRSA. Our results demonstrated that the probability of ESBL-/AmpC-producing E. coli reaching the consumer was 1.85 × 10^-5 with the number of bacteria in the final serving averaging 332. Given the higher prevalence and concentration of ESBL-/AmpC-producing E. coli in raw chicken meat at retail compared to MRSA, comparative exposure assessment showed that the likelihood and extent of exposure were significantly higher for ESBL-/AmpC-producing E. coli than for MRSA. ESBL-/AmpC-producing E. coli was determined to be 7.6 times likelier (p-value < 0.01) than MRSA to reach the consumer, with five times the concentration of bacteria in the final serving (p-value < 0.01).

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

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

Characterization of extended-spectrum beta-lactamase-producing Enterobacterales from organic and conventional chicken meats

This study was conducted to isolate and identify extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in conventional and organic chicken meats, which were sold in Turkey. A total of 200 raw chicken meat sample (100 conventional and 100 organic) were used as material. Classic culture technique based on chromogenic method was used for the isolation of bacteria, and the identification was performed with VITEK MS. Phenotypic ESBL production was detected by combined disc diffusion method. Gene regions responsible for ESBL production were determined by PCR. MIC values of isolates were detected by VITEK 2. Phenotypic ESBL-producing Enterobacterales were detected in 46% of conventional chicken meats and in 22% of organic chicken meats. Of the 115 isolates obtained, 97 (84%) were Escherichia coli, 12 (10%) were Klebsiella pneumoniae, four (3·48%) were Serratia fonticola, one (0·87%) was Rahnella aquatilis, and one (0·87%) was Serratia liquefaciens. PCR analysis revealed that 109 of 115 isolates (94·78%) contained at least one of the bla_CTX-M , bla_TEM , and bla_SHV genes. Of the 115 ESBL-producing isolates, 103 (89·57%) were found resistant to at least one antibiotic except for the β-lactam group. The contamination level of ESBL-producing Enterobacterales was higher in conventional chicken meats (P < 0·001).

Impact of On-Farm Interventions against CTX-Resistant Escherichia coli on the Contamination of Carcasses before and during an Experimental Slaughter

Cefotaxime (CTX)-resistant Enterobacteriaceae are still an ongoing challenge in human and veterinary health. High prevalence of these resistant bacteria is detected in broiler chickens and the prevention of their dissemination along the production pyramid is of major concern. The impact of certain on-farm interventions on the external bacterial contamination of broiler chickens, as well as their influence on single processing steps and (cross-) contamination, have not yet been evaluated. Therefore, we investigated breast skin swab samples of broiler chickens before and during slaughter at an experimental slaughter facility. Broiler chickens were previously challenged with CTX-resistant Escherichia coli strains in a seeder-bird model and subjected to none (control group (CG)) or four different on-farm interventions: drinking water supplementation based on organic acids (DW), slow growing breed Rowan × Ranger (RR), reduced stocking density (25 kg/sqm) and competitive exclusion with Enterobacteriales strain IHIT36098(CE). Chickens of RR, 25 kg/sqm, and CE showed significant reductions of the external contamination compared to CG. The evaluation of a visual scoring system indicated that wet and dirty broiler chickens are more likely a vehicle for the dissemination of CTX-resistant and total Enterobacteriaceae into the slaughterhouses and contribute to higher rates of (cross-) contamination during processing.

The Animal-foods-environment interface of Klebsiella pneumoniae in Germany: an observational study on pathogenicity, resistance development and the current situation

Klebsiella (K.) pneumoniae as a multi-drug resistant (MDR) pathogen is an emerging challenge for clinicians worldwide. Virulence factors are capsular antigens, adherence factors, the O-lipopolysaccharide, and siderophores promoting infectivity. Mechanisms of antimicrobial resistance are inactivation of compounds via enzymes, change of membrane permeability, and alteration of the target site of the antimicrobial compound. In addition to environmental resistance, K. pneumoniae can survive increasing concentrations of disinfectants, if exposed. This review describes the temporal and spatial distribution of K. pneumoniae in the past decades in Germany, with emphases on the development of resistance in the non-human columns of the One-Health concept. In general, K. pneumoniae is a neglected pathogen in veterinary and environmental health, and the risk of human infection concerning animal contact and food consumption is barely investigated. Few reports exist (n = 26) on antibiotic resistance of isolates from non-human origin. Multi-drug resistance and extended-spectrum β-lactamase (MDR-ESBL) strains also resistant to carbapenems and antibiotics of the ß-lactam group harbor blaCTX-M, blaOXA, blaTEM, blaSHV, blaCMY, and PMQR have been found in animals, foods, and the environment. Colistin resistant strains carrying the mcr-1 gene were detected in wastewater. The blaCTX-M-15 and blaOXA-48 genes are the most frequently identified AMR genes in isolates of humans and were also the most predominant ESBL-genes in samples collected from animal hosts. Several aspects of the molecular epidemiology and resistance development of K. pneumoniae in farm animal populations, wildlife, and foods need intensive research. Environmental health has to be integrated into national research plans, as a lack of data is apparent. Increasing awareness of the fact that non-human sources can act as a reservoir for this pathogen has to be raised.

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

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

Detection of Tn7-Like Transposons and Antibiotic Resistance in Enterobacterales From Animals Used for Food Production With Identification of Three Novel Transposons Tn6813, Tn6814, and Tn6765

Enterobacterales are widely distributed in the gastro-intestinal system of animals and may cause opportunistic infections. Worse still, multidrug-resistant Enterobacterales also poses a serious threat to public health. Tn7-like transposons have been found in several species of the Enterobacterales order and play an important role in dissemination of antibiotic resistance. This study aimed to investigate the distribution and genetic characterization of Tn7-like transposons in Enterobacterales isolates from food animals and their association with antibiotic resistance. Enterobacterales isolated from the samples were identified and classified according to the 16S rDNA sequence. Tn7-like transposons and associated integrons were detected by polymerase chain reaction (PCR) and sequencing. The antibiotic resistance of each Tn7-like transposon positive isolate was detected according to the Kirby-Bauer disk diffusion method. Then, six representative strains were selected to study the genetic environment by whole-genome sequencing (WGS). In total, we isolated 377 Tn7-like transposons positive strains of Enterobacterales. Class 2 integrons were detected in 99.5% of the isolates, and there were high frequency mutation sites especially in base 535, a stop mutation. Many isolates (54.9%) were multidrug-resistant and observed high resistance rates to trimethoprim/sulfamethoxazole and streptomycin. Among these strains, we found three new types of Tn7-like transposons, named Tn6813, Tn6814, and Tn6765. This is the first comprehensive survey that shows Tn7-like transposons in Enterobacterales from animals used for food production in different regions of China. This study also provides an insight into the horizontal transfer of resistance genes associated with Tn7-like transposons.

Prevalence and Molecular Typing of Colistin-Resistant Pseudomonas aeruginosa (CRPA) Among β-Lactamase-Producing Isolates: A Study Based on High-Resolution Melting Curve Analysis Method

Background

The frequency and production of β-lactamase enzymes may be different in colistin-resistant Pseudomonas aeruginosa (CRPA) strains compared to susceptible strains. The purpose of this study was to investigate the relationship between colistin resistance and β-lactamase enzymes in different Sequence Types (ST) of P. aeruginosa.

Methods

A total of 101 P. aeruginosa isolates were collected from different samples. The antimicrobial susceptibilities of the bacterial isolates were examined by disk diffusion and MIC E-test methods. Also, real-time PCR and high-resolution melting curve analysis (HRMA) assay were performed to detect the resistance genes.

Results

Out of the 101 P. aeruginosa isolates, four isolates (3.96%) were resistant to colistin. Also, 39 isolates (38.61%) were considered as MDR, and eight isolates (7.92%) were considered as XDR. Further, 25 (24.75%) and 26 isolates (25.74%) were produced ESBL and carbapenemase enzymes, respectively. According to HRMA results, four isolates (3.96%) were positive for pmrA, three isolates (2.97%) were positive for mcr-1, 25 isolates (24.75%) were positive for blaTEM, 24 isolates (23.76%) were positive for blaSHV, 26 isolates (25.75%) were positive for blaKPC, and 23 isolates (22.77%) were positive for blaIMP genes. Furthermore, ST108 and ST250 showed the highest distribution in P. aeruginosa isolates. Also, ST217, ST1078, and ST3340 were reported as novel types in CRPA strains.

Conclusion

Concerns about the prevalence of CRPA strains should be taken seriously. Also, our results showed that the mcr-1 gene plays a vital role in the distribution of ESBL and KPC-producing P. aeruginosa strains.

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

Background

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

Results

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

Conclusions

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

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

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

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

Presence of extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in humans and animals is alarming due to the associated risks of antibiotic therapy failure. ESBL/pAmpC-EC transmission between the human and animal compartments remains controversial. Using cefotaxime-supplemented (selective) media, we recently showed high sample prevalence of ESBL/pAmpC-EC in an integrated broiler chain [i.e. Parent Stock (PS), offspring broilers and their carcasses]. Here, we used a different approach. In parallel with the selective isolation, samples were processed on non-selective media. E. coli isolates were tested for ESBL/pAmpC-production and those found positive were genotyped. For carcasses, total E. coli were enumerated. This approach enabled us to estimate prevalence at the isolate level, which mirrors ESBL/pAmpC-EC colonisation levels. We showed that although present in many animals, ESBL/pAmpC-EC were overall subdominant to intestinal E. coli, indicating that high sample prevalence is not associated with high levels of resistance in individual hosts. This is a relevant aspect for risk assessments, especially regarding the immediate exposure of farm personnel. An exception was a particularly dominant B2/bla_CMY-2 lineage in the gut of imported PS chicks. This predominance obscured presence of latent genotypes, however bias towards particular ESBL/pAmpC-EC genotypes from the selective method or underestimation by the non-selective approach did not occur. At the slaughterhouse, we showed a link between total E. coli and ESBL/pAmpC-EC on carcasses. Mitigation strategies for reducing consumers' exposure should aim at suppressing ESBL/pAmpC-EC in the broiler gut as well as controlling critical points in the processing line.

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

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

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

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

Antimicrobial resistance genes in Salmonella and Escherichia coli isolates from chicken droppings in Nairobi, Kenya

OBJECTIVE

Increase in antimicrobial resistance is a threat to health sector globally. Surveillance on the spread and emergence of antimicrobial resistance is therefore invertible. This study investigated prevalence of Salmonella and Escherichia coli, molecularly characterized their antimicrobial resistance patterns and spread among resistant isolates from chicken droppings.

RESULTS

A total of 150 chicken households were selected randomly within Nairobi and fresh chicken droppings collected. Salmonella and Escherichia coli were isolated and antimicrobial susceptibility test carried out. Beta-lactamase genes and class 1 integrons were determined among amoxicillin resistant isolates. Isolates carrying TEM gene were further subjected to (GTG)₅ PCR genotyping. Of the analysed samples, 57% and 12% contained Escherichia coli and Salmonella respectively. Most of the isolates were susceptible to the tested antibiotics with exemption of 53% of the isolates that were resistant to amoxicillin. The isolates were detected with TEM (46%), CTX-M (18%) resistance genes and class 1 integrons (25%). The study reveals presence of beta-lactamase genes and class 1 integrons across Salmonella and Escherichia coli isolates from droppings of reared chicken. Therefore, the wide distribution of chicken and their fecal waste is likely to increase development of antibiotic resistance.

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

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