Transmission of ESBL/AmpC-producing Escherichia coli from broiler chicken farms to surrounding areas

CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure

The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system CRISPR-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its anti-plasmid efficacy in an agricultural niche - manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.

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.

Comparison of Three Preharvest Sampling Strategies to Monitor Pathogens in Cattle Lairage Areas

The objective of this study was to compare preharvest monitoring strategies by evaluating three different sampling methods in the lairage area to determine pathogen recovery for each sampling method and incoming pathogen prevalence from the cattle to inform in-plant decision making. Samples were gathered over a 5-month period, from February to June 2022, at a harvesting and processing facility located in Eastern Nebraska. Sampling methods included (i) fecal pats, (ii) boot swabs, and (iii) MicroTally swab. A total of 329 samples were collected over the study period (fecal pats: n = 105, boot swabs: n = 104, and MicroTally swabs: n = 120). Specific media combinations, an incubation temperature of 42°C, and incubation timepoints (18-24 h) were utilized for each matrix and the prevalence of Salmonella, Escherichia coli O157:H7, and six non-O157 Shiga-toxin producing E. coli (STEC) was evaluated using the BAX system Real-Time PCR assay. Overall, results from the study concluded that boot swabs were an effective sampling method for pathogen detection in the cattle lairage area. Boot swabs (97.1%) were statistically more likely to detect for Salmonella (p < 0.05) when compared to fecal pats (67.6%) and MicroTally swab (77.5%) methods. For E. coli O157:H7 and STEC - O26, O121, O45, and O103 prevalence, boot swabs were significantly better at detecting for these pathogens (p < 0.05) than MicroTally swabs (OR = 3.16 - 11.95) and a comparable sampling method to fecal pats (OR = 0.93 - 2.01, p > 0.05). Lastly, all three sampling methods detected a very low prevalence for E. coli O111 and O145; therefore, no further analysis was conducted. The boot swab sampling method was strongly favored because they require little training to implement, are inexpensive, and they do not require much sampling labor; therefore, would be a simple and effective sampling method to implement within the industry to evaluate pathogen prevalence preharvest.

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

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

Prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli in young calves on Dutch dairy farms

In young calves on dairy farms the animal prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-EC) is significantly higher compared with the animal prevalence in young stock and dairy cows. Hitherto it was unknown at what age antimicrobial resistant bacteria appear for the first time in the gut of calves on dairy farms, and how long these infections persist. The aim of this study was to examine the prevalence of ESBL/AmpC-EC, the number of excreted ESBL/AmpC-EC (in cfu/g of feces), as well as the ESBL/AmpC genotypes in young dairy calves (0-21 d of age) and the variation of these parameters between calves of different ages. Next to this, the course of shedding ESBL/AmpC-EC during the first year in dairy calves was studied. In a cross-sectional study, fecal samples from 748 calves, from 0 to 88 d of age, on 188 Dutch dairy farms were collected. The prevalence of calves testing positive for ESBL/AmpC-EC in a phenotypic assay was determined for different age categories (per 2 d of age). Positive samples were subjected to a semiquantitative test to determine the numbers of ESBL/AmpC-EC per gram of feces and for a selection of ESBL/AmpC-EC isolates the ESBL/AmpC genotype was determined. Ten of the 188 farms were selected for a longitudinal study based on the presence of at least 1 female calf with ESBL/Amp-EC in the cross-sectional study. These farms were additionally visited 3 times with a 4-mo interval. All calves that were sampled in the cross-sectional study were, if still present, resampled during the follow-up visits. Results show that from the day of birth ESBL/AmpC-EC can be present in the gut of calves. The phenotypic prevalence of ESBL/AmpC-EC was 33.3% in 0- to 21-d-old calves and 28.4% in 22- to 88-d-old calves. The prevalence of ESBL/AmpC-EC positive calves varied per age category among calves up to 21 d of age: significant increases and decreases at an early age were shown. Results of the longitudinal study show that after 4, 8, and 12 mo the prevalence of ESBL/AmpC-EC positive calves dropped to 3.8% (2/53), 5.8% (3/52), and 2.0% (1/49), respectively. This indicates that early gut colonization in young calves with ESBL/AmpC-EC is transient and does not lead to long-term shedding of these bacteria.

Effectiveness Evaluation of a UV-C-Photoinactivator against Selected ESKAPE-E Pathogens

Healthcare-associated infections (HAI) worldwide includes infections by ESKAPE-E pathogens. Environmental surfaces and fomites are important components in HAI transmission dynamics, and shoe soles are vectors of HAI. Ultraviolet (UV) disinfection is an effective method to inactivate pathogenic microorganisms. In this study, we investigated whether the SANITECH UV-C shoe sole decontaminator equipment that provides germicidal UV-C radiation could effectively reduce this risk of different pathogens. Six standard strains and four clinical MDR strains in liquid and solid medium were exposed to a UV-C System at specific concentrations at other times. Bacterial inactivation (growth and cultivability) was investigated using colony counts and resazurin as metabolic indicators. SEM was performed to assess the membrane damage. Statistically significant reduction in cell viability for all ATCCs strains occurred after 10 s of exposure to the UV-C system, except for S. enterica, which only occurred at 20 s. The cell viability of P. aeruginosa (90.9%), E. faecalis and A. baumannii (85.3%), S. enterica (82.9%), E. coli (79.2%) and S. aureus (71.9%) was reduced considerably at 20 s. In colony count, after 12 s of UV-C exposure, all ATCC strains showed a 100% reduction in CFU counts, except for A. baumannii, which reduced by 97.7%. A substantial reduction of colonies above 3 log₁₀ was observed at 12 and 20 s in all bacterial strains tested, except for A. baumannii ATCC 19606 (12 s). The exposure of ATCCs bacterial strains to the UV-C system for only 2 s was able to reduce 100% in the colony forming units (CFU) count in all ATCCs strains, S. aureus, P. aeruginosa, E. coli, A. baumannii, E. faecalis, except the S. enterica strain which had a statistically significant reduction of 99.7%. In ATCC strains, there was a substantial decrease in colonies after 4 s (sec) of exposure to the UV-C system, with a reduction ranging from 3.78-4.15 log₁₀ CFU/mL. This reduction was observed in MDR/ESKAPE-E strains within 10 s, showing that UV-C could eliminate above 3.84 log₁₀ CFU/mL. SEM showed a reduction of pili-like appendages after UV-C treatment in all strains except for E. coli (ATCC 25922). The Sanitech UV-C shoe sole decontaminator equipment from Astech Serv. and Fabrication Ltd. (Petrópolis, Brazil), effectively killed in vitro a series of ATCCs and MDR/ESKAPE-E bacteria of sanitary interest, commonly found in the hospital environment.

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

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

Background

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

Results

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

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

Conclusions

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

Prevalence and Genetic Relationship of Predominant Escherichia coli Serotypes Isolated from Poultry, Wild Animals, and Environment in the Mekong Delta, Vietnam

Avian pathogenic Escherichia coli (APEC) is the main causative agent of avian colibacillosis, which is an important systemic disease of profound economic and clinical consequences for the poultry industry worldwide. In this study, 975 E. coli strains were isolated from 2,169 samples collected from cloacal swabs of chickens, in-farm wild animals (ants, geckos, flies, and rats), and environment. The highest proportion of E. coli isolation was obtained from chicken cloacal swabs with 71.05% (95% confidence interval (CI) 66.69-75.05%) followed by the proportions of 38.15% (95% CI 35.41-40.97%) and 38.11% (95% CI 34.15-42.24%) from wild animals or environment, respectively. Distribution of O-antigen serotypes of the E. coli isolates, including O1, O2, O18, and O78, was determined by PCR. The most predominant serotype was O18 (10.56%) followed by O2 (9.44%), O1 (7.79%), and O78 (6.56%). Of note, serotype O18 was more likely distributed in the examined wild animals, especially in geckos. Polymorphic DNA fingerprints, generated by ERIC-PCR, of representative E. coli strains of each serotype revealed genetic heterogeneity of the examined E. coli, and O18 was more divergent with 63 clusters formed from 66 isolates. Furthermore, several E. coli strains from different sample sources shared high DNA fingerprint relatedness, suggesting that there exists complex transmission of E. coli from chickens to wild animals and environment and vice versa in poultry husbandry settings. Although pathotypes of the examined E. coli were not determined in this study, our results provided important findings of epidemiological and genetic characteristics of E. coli in the Mekong Delta and highlighted the prerequisite of stricter biocontainment to reduce the prevalence and consequences of APEC in poultry production.

Airborne Dissemination of Bacteria (Enterococci, Staphylococci and Enterobacteriaceae) in a Modern Broiler Farm and Its Environment

Simple Summary

In this study, the density and diversity of relevant groups of bacteria at a broiler farm have been studied, in the inside and outside air and in litter samples. A high number of bacteria was detected in the litter and in the inside air, but a low emission of bacteria was found in the outside air. Moreover, the bacteria detected in the outside air decreased with the distance to the farm. A total of 544 isolates were identified from all the samples (146 from the litter, 142 from inside air and 256 from outside air). From these, 162 staphylococci, 176 Enterobacteriaceae, and 190 enterococci were detected. E. hirae was the predominant species and the detection of identical DNA profiles in E. hirae isolates from inside and outside samples suggests the role of the air in bacterial dissemination from the inside of the broiler farm to the immediate environment. It is necessary to consider the relevance of air as a vehicle of disseminating bacteria at the farm level, which can involve potentially pathogenic bacteria and bacteria carrying antimicrobial resistance genes.

Abstract

The role of the air as a vehicle of bacteria dissemination in the farming environment has been previously reported, but still scarcely studied. This study investigated the bacteria density/diversity of the inside and outside air and of litter samples at a broiler farm. Samples were collected considering two seasons, three outside air distances (50/100/150 m) and the four cardinal directions. Selective media was used for staphylococci, enterococci, and Enterobacteriaceae recovery. A high number of bacteria was detected in the litter (2.9 × 10⁵–5.8 × 10⁷ cfu/g) and in the inside air (>10⁵ cfu/m³), but a low emission of bacteria was evidenced in the outside air (<6 cfu/m³). Moreover, the bacteria detected in the farm’s outside air decreased the further from the farm the sample was taken. A total of 544 isolates were identified by MALDI-TOF (146 from the litter, 142 from inside air and 256 from outside air). From these, 162 staphylococci (14 species; S. saprophyticus 40.7%), 176 Enterobacteriaceae (4 species; E. coli 66%) and 190 enterococci (4 species; E. hirae 83%) were detected. E. hirae was the predominant species, and identical PFGE clones were detected in inside and outside samples. The detection of identical DNA profiles in E. hirae isolates from inside and outside samples suggests the role of the air in bacterial dissemination from the inside of the broiler farm to the immediate environment.

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.

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

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

Research Note: Characterization of antibiotic resistant phenotypes and linked genes of Escherichia coli and Klebsiella pneumoniae from healthy broiler chickens, Karnataka, India

The study was carried out to estimate the burden and pattern of antibiotic resistance and to identify antibiotic resistance genes with focus on ESBL producers, plasmid mediated quinolone resistance, and tetracycline efflux genes, in faecal bacterial isolates collected from poultry farms of coastal Southern Karnataka, India. High resistance to fluoroquinolones was observed with 94% Escherichia coli and 80% Klebsiella pneumoniae being resistant to both ciprofloxacin and levofloxacin. All the Escherichia coli strains were resistant to tetracycline (100%). qnrB (38%) was the most common gene detected followed by qnrS (27%) and qnrA (21.5%). All Klebsiella pneumoniae isolates resistant to tetracycline harbored tetA gene. Most of the isolates in our study had high MAR indices indicating rampant use of antibiotics.

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

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

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

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

Characterization of Pseudomonas aeruginosa isolated from various environmental niches: New STs and occurrence of antibiotic susceptible "high-risk clones"

The aim of this study was to investigate the antimicrobial phenotypes, major virulence factors, and the molecular typing of 66 P. aeruginosa isolates collected from various sources: human patients and hospital environment, raw milk, poultry meat, chicken/sheep fecal samples, wastewater, thermal water, and seawater. All isolates, except one, were susceptible to all tested antibiotics. exoA, lasB, rhlR, and lasR genes were harbored by 60 isolates. Forty-six, 18, and 2 isolates amplified exoS, exoU, and exoS+exoU genes, respectively. Twenty-one isolates showed high elastase and pigment production. The PFGE typing identified 26 pulsotypes. Some pulsotypes included isolates from different environmental niches and areas. Twelve selected isolates were typed by MLST and eight different STs were found, three of them were new. Our results highlighted the dissemination of some clones amongst different settings and the occurrence of antibiotic susceptible 'high-risk clones' that might be very harmful when acquiring genes encoding antibiotic resistance.

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.

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.

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

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

MOLECULAR CHARACTERIZATION OF FECAL ESCHERICHIA COLI ISOLATED FROM ZOO ANIMALS

Accredited zoos and animal parks play an important role in animal health research and conservation, providing important insights on matters of public health including zoonotic infectious diseases and antimicrobial resistance (AMR). The emergence and spread of AMR is a complex phenomenon that jeopardizes human and animal health and also threatens the long-term survival of endangered species. The presence of β-lactamases in clinical isolates is particularly significant as they can jeopardize the efficacy of critically important antimicrobials. Although the presence of β-lactamases and extended-spectrum β-lactamases (ESBLs) producing Enterobacteriaceae in zoo animals has been reported, data are not available for northern European countries. In addition, few data are available on phylogenetic grouping of Escherichia coli isolated from zoo animals that can provide additional information on the host-bacterium relationship and on the pathogenicity of isolates. This study aimed to characterize fecal E. coli isolated from 33 healthy zoo animals from 22 species in Ireland, using conventional and molecular microbiological methods. All E. coli isolates were ampicillin resistant, but combined resistance to amoxicillin and clavulanic acid was not detected. Three E. coli isolates sampled from one Amur tiger, one Bornean orangutan, and one Southern white rhino were multidrug resistant, and blaTEM was detected in E. coli recovered from the Amur tiger and the Bornean orangutan. Other β-lactamases, including ESBLs and AmpCs and plasmid-mediated mcr-1 and mcr-2, were not detected. Overall, E. coli isolates investigated were susceptible to the majority of the antimicrobials tested, and only two animals shed E. coli carrying β-lactamase-encoding genes. The majority of isolates belonged to phylogenetic group B1. The screening of the AMR phenotype and genotype of zoo animal E. coli provides useful data that is relevant to antimicrobial stewardship in the zoo veterinary services and relevant to the bank of knowledge needed for tackling AMR.

Prevalence of extended-spectrum β-lactamases in the local farm environment and livestock: challenges to mitigate antimicrobial resistance

The effectiveness of antibiotics has been challenged by the increasing frequency of antimicrobial resistance (AR), which has emerged as a major threat to global health. Despite the negative impact of AR on health, there are few effective strategies for reducing AR in food-producing animals. Of the antimicrobial resistant microorganisms (ARMs), extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae are an emerging global threat due to their increasing prevalence in livestock, even in animals raised without antibiotics. Many reviews are available for the positive selection of AR associated with antibiotic use in livestock, but less attention has been given to how other factors including soil, water, manure, wildlife, and farm workers, are associated with the emergence of ESBL-producing bacteria. Understanding of antibiotic resistance genes and bacteria transfer at the interfaces of livestock and other potential reservoirs will provide insights for the development of mitigation strategies for AR.

PM2.5 from a broiler breeding production system: The characteristics and microbial community analysis

Particulate matter (PM) released from the processes of livestock production has a negative impact on the health of animals and workers. Herein, the concentration, major chemical components, morphology and microbiological compositions of particulate matter 2.5 (PM_2.5, particles with aerodynamic diameter less than 2.5 μm) in a broiler breeding house were investigated. The results showed that the PM_2.5 distribution in the chicken house was affected by the illumination, draught fans, chicken frame structure and activity of the chickens in the broiler breeding house. Component analysis showed that organic carbon (OC) accounted for the largest proportion, and followed by element carbon (EC), SO₄^2-, NO₃^-, NH₄⁺, Na⁺, K⁺ and Ca²⁺. Ultrastructural observations revealed that the shape of PM_2.5 had a round, rectangular, chain-like and irregular shape. The concentration of endotoxin was approximately 0.3 EU/m³. Microbiological analysis showed that at the genus level, the pathogenic bacteria included Staphylococcus, Corynebacterium, Enterococcus, Parabacteroides, Escherichia and Megamonas. The abundant harmful fungi were Aspergillus, Scopulariopsis, Wallemia, and Fusarium. Through redundancy analysis (RDA) analysis, we determined that OC, EC, Na⁺, K⁺, and NH₄⁺ had strong correlations with Brachybacterium, Brevibacterium, Corynebacterium, Escherichia, Scopulariopsis and Microascus. SO₄^2- was closely related to Scopulariopsis and Salinicoccus. Salinicoccus was also strongly correlated with NO₃^-. Our results indicated that feed, faeces, and outside soot are contributed to the increase in PM_2.5 concentration in the chicken house, while the sources of the dominant bacterial and fungi might be feed, faeces, suspended outside soil and cereal crops.

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

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

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

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

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.

Insights into Livestock-Related Microbial Concentrations in Air at Residential Level in a Livestock Dense Area

Microbial air pollution from livestock farms has raised concerns regarding public health. Little is known about airborne livestock-related microbial levels in residential areas. We aimed to increase insights into this issue. Air measurements were performed in 2014 and 2015 at 61 residential sites in The Netherlands. Quantitative-PCR was used to assess DNA concentrations of selected bacteria (commensals: Escherichia coli and Staphylococcus spp.; a zoonotic pathogen: Campylobacter jejuni) and antimicrobial resistance (AMR) genes ( tetW, mecA) in airborne dust. Mixed models were used to explore spatial associations (temporal adjusted) with livestock-related characteristics of the surroundings. DNA from commensals and AMR genes was detectable even at sites furthest away from farms (1200 m), albeit at lower levels. Concentrations, distinctly different between sites, were strongly associated with the density of farms in the surroundings especially with poultry and pigs. C. jejuni DNA was less prevalent (42% of samples positive). Presence of C. jejuni was solely associated with poultry (OR: 4.7 (95% CI: 1.7-14), high versus low poultry density). Residential exposure to livestock-related bacteria and AMR genes was demonstrated. Identified associations suggest contribution of livestock farms to microbial air pollution in general and attribution differences between farm types. This supports the plausibility of recent studies showing health effects in relation to residential proximity to farms.

Extended-spectrum beta-lactamase and ampicillin Class C beta lactamase-producing Escherichia coli from food animals: A review

Antimicrobial resistance has gained global notoriety due to its public health concern, the emergence of multiple drug-resistant bacteria, and lack of new antimicrobials. Extended-spectrum beta-lactamase (ESBL)/ampicillin Class C (AmpC)- producing Escherichia coli and other zoonotic pathogens can be transmitted to humans from animals either through the food chain, direct contact or contamination of shared environments. There is a surge in the rate of resistance to medically important antibiotics such as carbapenem, ESBL, aminoglycosides, and fluoroquinolones among bacteria of zoonotic importance. Factors that may facilitate the occurrence, persistence and dissemination of ESBL/AmpC-Producing E. coli in humans and animal includes; 1). o ral administration of antimicrobials to humans primarily (by physician and health care providers) and secondarily to animals, 2). importation of parent stock and day-old chickens, 3). farm management practice and lack of water acidification in poultry, 4). contamination of feed, water and environment, 5). contamination of plants with feces of animals. Understanding these key factors will help reduce the level of resistance, thereby boosting the therapeutic effectiveness of antimicrobial agents in the treatment of animal and human infections. This review highlights the occurrence, risk factors, and public health importance of ESBL/AmpC-beta-lactamase producing E. coli isolated from livestock.

[Transmission pathways for resistant bacteria between animals and humans: antibiotics resistance in the One Health context]

People and animals share the same environment and antibiotics are used in both. Thus, antibiotics resistance is a major common issue for human and veterinary medicine. The potential impact of antibiotics use in animals on resistance in humans is frequently the focus of debate. In this paper the transmission pathways of resistant bacteria between animals and humans are described and the question is addressed whether a reduction in antibiotics use in animals contributes to the improvement of the resistance situation in humans. Direct contact between humans and animals, transmission of bacteria via food, and indirect transmission via emissions in the environment and the subsequent exposure of humans via the environment are the major transmission routes to be considered. It can thus be established that the relevance of these various transmission routes varies significantly among bacterial species. Furthermore, despite numerous investigations, the exact significance of transmission pathways and the bacteria transferred for the resistance situation in humans cannot yet be precisely quantified. There is evidence that antibiotics use in animals fosters the spread of resistant organisms in animals. Recent studies also suggest that there might be a relationship between antibiotics use in animals and the occurrence of resistance in humans. However, this relationship is complex, and for a better understanding of it and the role of the various transmission pathways, further collaborative studies between veterinary and medical science are needed.

Optimization of a wet scrubber with electrolyzed water spray-Part II: Airborne culturable bacteria removal

Airborne microorganisms, especially the pathogenic microorganisms, emitted from animal feeding operations (AFOs) may harm the environment and public health and threaten the biosecurity of the farm and surrounding environment. Electrolyzed water (EW), which was considered to be an environmentally friendly disinfectant, may be a potential spraying medium of wet scrubber for airborne microorganism emission reduction. A laboratory test was conducted to investigate the airborne bacteria (CB) removal efficiency of the wet scrubber by EW spray with different designs and operating parameters. Both the available choline (AC) initial loss rate and AC traveling loss rate of acidic electrolyzed water (AEW; pH = 1.35) were much higher than those of slightly acidic electrolyzed water (SAEW; pH = 5.50). Using one spraying stage with 4 m sec^-1 air speed in the duct, the no detect lines (NDLs) of SAEW (pH = 5.50) for airborne Escherichia coli, Staphylococcus aureus, and Salmonella enteritidis removal were all 50 mg L^-1, whereas the NDLs of AEW (pH = 1.35) for airborne E. coli, S. aureus, and S. enteritidis removal increased to 70, 90, and 90 mg L^-1, respectively. The NDLs of SAEW (pH = 5.50) for airborne E. coli, S. aureus, and S. enteritidis were lower than those of AEW (pH = 1.35) at single spraying stage. Increase in the number of stages lowered the NDLs of both SAEW (pH = 5.50) and AEW (pH = 1.35) for airborne E. coli, S. aureus, and S. enteritidis. EW with a higher available chlorine concentration (ACC) was needed at air speed of 6 m sec^-1 to reach the same airborne CB removal efficiency as that at air speed of 4 m sec^-1. The results of this study demonstrated that EW spray wet scrubbers could be a very effective and feasible airborne CB mitigation technology for AFOs. Implications: It is difficult to effectively reduce airborne bacteria emitted from animal feeding operations (AFOs). Electrolyzed water (EW) with disinfection effect and acidity is a potential absorbent for spray in wet scrubber to remove microorganisms and ammonia. Based on the field test results, a laboratory experiment we conducted this time was to optimize the design and operation parameters to improve the airborne bacteria removal efficiency. A better understanding of the EW application in the wet scrubber can contribute to the mitigation of airborne bacteria from animal houses and improve the atmosphere air quality.

Antimicrobial Resistance and Potential Pathogenicity of Escherichia coli Isolates from Healthy Broilers in Québec, Canada

Antimicrobial resistance (AMR) is a global health issue, particularly when it affects critically important antimicrobials such as third-generation cephalosporins (3GC). The objective of this study was to characterize Escherichia coli isolates from healthy chickens in Québec in farms where ceftiofur has been administered to chickens in ovo over a long period with regard to their AMR, multidrug resistance (MDR), potential virulence, clonality, and possession of plasmids of the incompatibility groups carrying extended-spectrum beta-lactamases (ESBLs)/AmpC genes. More than 62% of indicator isolates were MDR with resistance observed for each of the nine classes of antimicrobials tested by disk diffusion. 3GC resistance was encoded by the bla_CMY-2 gene (26.7% in indicator isolates), whereas bla_CTX-M was only detected in isolates selected after supplementation with ceftriaxone (3 bla_CTX-M-1 isolates). Examination of bla_CMY-2-positive isolates by pulsed-field gel electrophoresis showed clustering of isolates originating from different floors of the livestock building within farms. The bla_CMY-2 gene was carried on replicon plasmids FIB, I1, K/B, and B/O, whereas bla_CTX-M-1 gene was located on I1 as demonstrated by transformation experiments; some of these plasmids cotransferred nonsusceptibility against tetracycline or sulfonamides. In addition, six isolates, of which three were AmpC-producers, were defined as potential human extraintestinal pathogenic E. coli. In summary, this study showed that ESBLs/AmpC-producing E. coli isolates from apparently healthy chickens in Québec, Canada predominantly possess bla_CMY-2 rather than bla_CTX-M maybe because of the in ovo use of ceftiofur to prevent omphalitis and may be spread through clones or plasmids, and that some of these isolates could be capable of infecting humans.

Diversity in prevalence and characteristics of ESBL/pAmpC producing E. coli in food in Germany

The spread of extended-spectrum β-lactamases (ESBLs) in Escherichia coli is a major public health issue and ESBL-producing bacteria are frequently reported in livestock. For the assessment of the role of the foodborne transmission pathway in Germany, detailed data on the prevalence and characteristics of isolates of food origin are necessary. The objective of this study was to describe the prevalence of cefotaxime resistant E. coli as well as ESBL/pAmpC-producing E. coli and their characteristics in foods in Germany. Out of 2256 food samples, the highest prevalence of cefotaxime resistant E. coli was observed in chicken meat (74.9%), followed by turkey meat (40.1%). Prevalence in beef, pork and minced meat was considerably lower (4.2-15.3%). Whereas 18.0% of the raw milk samples, collected at farm level were positive, this was true only for few cheese samples (1.3%). In one out of 399 vegetable samples a cefotaxime-resistant E. coli was isolated. ESBL resistance genes of the CTX-M-group (10.1% of all samples) were most frequently detected, followed by genes of the pAmpC (2.6%), SHV (2.0%) and TEM (0.8%) families. Distribution of ESBL/AmpC-encoding E. coli resistance genes and E. coli phylogroups was significantly different between the chicken related food samples and all other food items. Our study results reflect that consumers might get exposed to ESBL/pAmpC-producing E. coli through several food chains. These results together with those collected at primary production and in the human population in other studies will allow more detailed analysis of the foodborne pathways, considering transmission from livestock populations to food at retail and to consumers in Germany.

Assessment of the Exposure of Turkey Farmers to Antimicrobial Resistance Associated with Working Practices

The objective of the present study was the identification of farming practices in the production of turkeys for human consumption, and their ranking in terms of the occupational probability of exposure to antimicrobial resistant (AMR) bacteria, for farm workers. We gathered evidence and data from scientific literature, on risk factors for AMR in farmers, and on the prevalence of those hazards across farming phases. We administered semi-structured interviews to public and private veterinarians in Northern Italy, to obtain detailed information on turkey farming phases, and on working practices. Data were then integrated into a semi-quantitative Failure Modes and Effect Analysis (FMEA). Those working practices, which are characterized by direct contact with numerous animals, and which are carried out frequently, with rare use of personal protection devices resulted as associated with the greatest probability of exposure to AMR. For methicillin resistant Staphylococcus aureus (MRSA), these included vaccination and administration of any individual therapy, and removal and milling of litter, given the exposure of farmers to high dust level. Indeed, levels of occupational exposure to MRSA are enhanced by its transmission routes, which include direct contact with animal, as well as airborne transmission. Level of exposure to extended spectrum beta lactamase (ESBL) is more strictly associated with direct contact and the oral-fecal route. Consequently, exposure to ESBL resulted and associated with the routinely tipping over of poults turned on their back, and with the individual administration of therapies.

Inactivation of ESBL-/AmpC-producing Escherichia coli during mesophilic and thermophilic anaerobic digestion of chicken manure

The high prevalence of extended-spectrum-ß-lactamase (ESBL)-/AmpC-producing Escherichia (E.) coli in European broiler farms leads to the possible dissemination of antibiotic-resistant strains into the environment using contaminated feces as organic fertilizer. The aim of the present study was to determine the influence of temperature on the reduction kinetics of two artificially added ESBL-/AmpC-producing E. coli strains during lab-scale mesophilic (37 °C, 42 °C) and thermophilic (55 °C) anaerobic digestion of chicken manure. The decimal reduction times (D-value) were approximately 3-6 days at 37 °C, 1.5 days at 42 °C and 48 min at 55 °C. Starting with initial E. coli counts of 7 log₁₀ colony forming units (CFU) per milliliter, both E. coli strains were below the detection limit after 35 days at all temperatures; however, at 37 °C and 42 °C, ESBL-producing E. coli were still partially detectable by enrichment. Temperature and retention time were the main inactivation factors. No direct correlation could be found between pH, volatile fatty acids (VFA) or ammonia (NH₃) and E. coli reduction. D-values were predicted for several temperatures between 37 °C and 55 °C and may help define time-temperature guidelines. Thermophilic digestion is an adequate method to rapidly inactivate ESBL-producing E. coli in chicken manure. At mesophilic temperatures, however, strict compliance of retention times and the prevention of short-circuiting become essential to gain an ESBL-producing E. coli free digestate.

Dissemination and characterisation of Escherichia coli producing extended-spectrum β-lactamases, AmpC β-lactamases and metallo-β-lactamases from livestock and poultry in Northeast India: A molecular surveillance approach

OBJECTIVES

The aim of this study was to identify and characterise probable extended-spectrum β-lactamase (ESBL)-, AmpC lactamase- and/or metallo-β-lactamase (MBL)-producing Escherichia coli variants circulating in the livestock and poultry environment to establish their epidemiological significance, genetic diversity, antimicrobial resistance (AMR) trends and virulence.

METHODS

The culture method and E. coli-specific multiplex PCR identified 78 E. coli strains from faecal samples of healthy livestock and poultry. The antibiogram was determined by the disk diffusion and minimum inhibitory concentration (MIC) methods. Antimicrobial-resistant E. coli isolates were screened for the presence of ESBL, AmpC and MBL genes. Isolates were further characterised by plasmid replicon typing, integron assay and virulence gene analysis. Genetic diversity was assessed by random amplification of polymorphic DNA (RAPD) analysis and multilocus sequence typing (MLST).

RESULTS

ESBL (CTX-M group 1, CTX-M group 4, TEM), AmpC (EBC, FOX, CMY, DHA) and MBL (IMP, SIM) resistance determinants were identified in 75%, 19% and 6% of isolates, respectively. Nine plasmid replicon types were distributed among resistant E. coli strains, with the most common plasmid replicon types being L/M and Y. Integrons were detected in 19% of E. coli isolates. RAPD analysis categorised the E. coli isolates into three clusters. MLST revealed seven different sequence types (STs), with ST10 being the most common.

CONCLUSIONS

This study demonstrated a high prevalence of animals carrying potential ESBL- and AmpC-producing E. coli and emphasises the need for rigorous surveillance in the animal sector to identify critical control points conducive to prevent the rapid dissemination of AMR.

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

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

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

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

Detection of multi-drug resistant (MDR) Escherichia coli and tet gene prevalence at a pig farm in Kupang , Indonesia

OBJECTIVE

The purpose of this study was to detect the incidence of multi-drug resistant (MDR) and the spread of tet genes that encode tetracycline (TE) resistance in E. coli in pig farms in the city of Kupang, Indonesia.

MATERIALS AND METHODS

Samples of pig feces have been obtained from 96 pig farms in Kupang city, Indonesia. Escherichia coli bacteria were isolated and identified morphologically and biochemically, and finally confirmed by the API test. The disk diffusion method has been used to observe the antibiotic sensitivity effects and has been followed by observing resistant genes encoding TE resistance using the multiplex polymerase chain reaction (m-PCR) method to detect the presence of tet genes such as tet (A), tet (B), tet (C), tet (D), and tet (E), respectively.

RESULTS

A total of 82 (85.4%) of E. coli isolates have been found in all pig feces samples obtained from 96 pig farms in Kupang city. This study has shown a high level of antibiotic resistance dominated by erythromycin (85.4%) and cephalothin (58.5%) and followed by several other antibiotics with a percentage below 34.1%. The prevalence of MDR E. coli was 57.3% by showing 39 different patterns. The most common pattern was showed by the Cephalothin-Colistin-Erythromycin pattern. The resistance of E. coli to TE appears to be related to the presence of tet (A) and tet (E) genes.

CONCLUSION

This study has encouraged the need for public awareness (farmers) of the wise use of antibiotics in preventing the spread of resistant bacteria that can cause health problems in animals and humans.

Identification of Enterococci, Staphylococci, and Enterobacteriaceae from Slurries and Air in and around Two Pork Farms

In this study, we investigated the airborne dissemination of bacteria from the inside of two very different pork farms (an intensively confined farm and an open-range farm) to the immediate environment. Samples were taken from the slurry, from the air inside the farms (area 0), and from their immediate surroundings at a distance of 50, 100, and 150 m in four directions (north, south, east, and west). A control sample in the air of a zone far away from human or animal activity was also taken. Identification of isolates was made by means of the matrix-assisted laser desorption-ionization time of flight system. A total of 1,063 isolates were obtained, of which a mere 7 came from the air of the control area. Staphylococci, enterococci, and Enterobacteriaceae were selectively targeted for isolation and represented 48.6, 27.2, and 21.6% of the isolates, respectively. The species identified from the air of surrounding areas ( Enterococcus faecalis, Enterococcus hirae, and Staphylococcus arlettae, mainly) were also present inside the farms studied. The results suggest that air is involved in bacterial dissemination, and pork farms should be considered a potential source of foodborne bacteria that might contaminate surrounding areas, including vegetable orchards. Wind direction appears as a factor involved in bacterial dispersion through the air, but its effect may be conditioned by existing vegetation and orographic conditions.

Reservoirs and Transmission Pathways of Resistant Indicator Bacteria in the Biotope Pig Stable and along the Food Chain: A Review from a One Health Perspective

The holistic approach of “One Health” includes the consideration of possible links between animals, humans, and the environment. In this review, an effort was made to highlight knowledge gaps and various factors that contribute to the transmission of antibiotic-resistant bacteria between these three reservoirs. Due to the broad scope of this topic, we focused on pig production and selected “indicator bacteria”. In this context, the role of the bacteria livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended spectrum beta-lactamases carrying Escherichia coli (ESBL-E) along the pig production was particularly addressed. Hotspots of their prevalence and transmission are, for example, pig stable air for MRSA, or wastewater and manure for ESBL-E, or even humans as vectors in close contact to pigs (farmers and veterinarians). Thus, this review focuses on the biotope “stable environment” where humans and animals are both affected, but also where the end of the food chain is not neglected. We provide basic background information about antibiotics in livestock, MRSA, and ESBL-bacteria. We further present studies (predominantly European studies) in tabular form regarding the risk potentials for the transmission of resistant bacteria for humans, animals, and meat differentiated according to biotopes. However, we cannot guarantee completeness as this was only intended to give a broad superficial overview. We point out sustainable biotope approaches to try to contribute to policy management as critical assessment points in pig housing conditions, environmental care, animal health, and food product safety and quality as well as consumer acceptance have already been defined.

Prevalence and Emergence of Extended-Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram Negative Bacteria of Animal Origin in the Mediterranean Basin

In recent years, extended ESBL and carbapenemase producing Gram negative bacteria have become widespread in hospitals, community settings and the environment. This has been triggered by the few therapeutic options left when infections with these multi-drug resistant organisms occur. The emergence of resistance to colistin, the last therapeutic option against carbapenem-resistant bacteria, worsened the situation. Recently, animals were regarded as potent antimicrobial reservoir and a possible source of infection to humans. Enteric Gram negative bacteria in animals can be easily transmitted to humans by direct contact or indirectly through the handling and consumption of undercooked/uncooked animal products. In the Mediterranean basin, little is known about the current overall epidemiology of multi-drug resistant bacteria in livestock, companion, and domestic animals. This review describes the current epidemiology of ESBL, carbapenemase producers and colistin resistant bacteria of animal origin in this region of the world. The CTX-M group 1 seems to prevail in animals in this area, followed by SHV-12 and CTX-M group 9. The dissemination of carbapenemase producers and colistin resistance remains low. Isolated multi-drug resistant bacteria were often co-resistant to non-beta-lactam antibiotics, frequently used in veterinary medicine as treatment, growth promoters, prophylaxis and in human medicine for therapeutic purposes. Antibiotics used in veterinary medicine in this area include mainly tetracycline, aminoglycosides, fluoroquinolones, and polymyxins. Indeed, it appears that the emergence of ESBL and carbapenemase producers in animals is not related to the use of beta-lactam antibiotics but is, rather, due to the co-selective pressure applied by the over usage of non-beta-lactams. The level of antibiotic consumption in animals should be, therefore, re-considered in the Mediterranean area especially in North Africa and western Asia where no accurate data are available about the level of antibiotic consumption in animals.

Extensive Genetic Commonality among Wildlife, Wastewater, Community, and Nosocomial Isolates of Escherichia coli Sequence Type 131 (H30R1 and H30Rx Subclones) That Carry blaCTX-M-27 or blaCTX-M-15

Escherichia coli sequence type 131 (ST131) is currently one of the leading causes of multidrug-resistant extraintestinal infections globally. Here, we analyzed the phenotypic and genotypic characteristics of 169 ST131 isolates from various sources (wildlife, wastewater, companion animals, community, and hospitals) to determine whether wildlife and the environment share similar strains with humans, supporting transmission of ST131 between different ecological niches. Susceptibility to 32 antimicrobials was tested by disc diffusion and broth microdilution. Antibiotic resistance genes, integrons, plasmid replicons, 52 virulence genes, and fimH-based subtypes were detected by PCR and DNA sequencing. Genomic relatedness was determined by pulsed-field gel electrophoresis (PFGE). The genetic context and plasmid versus chromosomal location of extended-spectrum beta-lactamase and AmpC beta-lactamase genes was determined by PCR and probe hybridization, respectively. The 169 ST131 study isolates segregated predominantly into bla_CTX-M-15H30Rx (60%) and bla_CTX-M-27H30R1 (25%) subclones. Within each subclone, isolates from different source groups were categorized into distinct PFGE clusters; genotypic characteristics were fairly well conserved within each major PFGE cluster. Irrespective of source, the bla_CTX-M-15H30Rx isolates typically exhibited virotype A (89%), an F2:A1:B- replicon (84%), and a 1.7-kb class 1 integron (92%) and had diverse structures upstream of the bla_CTX-M region. In contrast, the bla_CTX-M-27H30R1 isolates typically exhibited virotype C (86%), an F1:A2:B20 replicon (76%), and a conserved IS26-ΔISEcp1-bla_CTX-M-like structure. Despite considerable overall genetic diversity, our data demonstrate significant commonality between E. coli ST131 isolates from diverse environments, supporting transmission between different sources, including humans, environment, and wildlife.

Expanded spectrum β-lactamase producing Escherichia coli isolated from chickens with colibacillosis in Egypt

Throughout the world, expanded spectrum β-lactamases (ESBL) are increasing among clinical isolates of Enterobacteriaceae, both in humans and animals. Unfortunately, there is a paucity of data on ESBL or Ampicillin class C β-lactamase (AmpC) in Egypt, although antimicrobial consumption is high in this developing country. This study aims to characterize the resistance mechanisms to expanded spectrum cephalosporins among resistant veterinary Escherichia coli isolates in Egypt. We investigated 50 clinical multi-resistant E. coli strains isolated from 20 chicken farms for production of ESBL or AmpC. Antibiotic susceptibility was tested by Clinical and Laboratory Standards Institute (CLSI) disk diffusion and ESBL confirmatory tests. PCR and sequencing were performed to screen for plasmid mediated ESBL genes and genes encoding AmpC β-lactamases. All the isolates were phylogentically classified, investigated for harboring class 1 integrons, and genotyped by amplified fragment length polymorphism (AFLP). Three strains showed ESBL and 6 strains AmpC phenotypic patterns, respectively, with confirmed ESBL genes of blaTEM-57, blaSHV-12, blaCTX-M-14, and blaCMY-2 for AmpC producing strains. All ESBL strains belonged to phylogroup D with different clones isolated from different flocks, while most of the AmpC strains belonged to phylogroup B1 (4/6) and were assigned to the same genotype distributed in 2 different farms. Class 1 integrons were disseminated in 60% of all tested strains and in 100% of ESBL and AmpC strains. These results highlight the antimicrobial resistance problem in Egypt, caused in all probability by unwise use of antimicrobials in animal husbandry. The results call for a nationwide surveillance program to monitor antimicrobial resistance.

In Vivo Transfer and Microevolution of Avian Native IncA/C2blaNDM-1-Carrying Plasmid pRH-1238 during a Broiler Chicken Infection Study

The emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) in wildlife and livestock animals pose an important safety concern for public health. With our in vivo broiler chicken infection study, we investigated the transfer and experimental microevolution of the blaNDM-1-carrying IncA/C2 plasmid (pRH-1238) introduced by avian native Salmonella enterica subsp. enterica serovar Corvallis without inducing antibiotic selection pressure. We evaluated the dependency of the time point of inoculation on donor (S Corvallis [12-SA01738]) and plasmid-free Salmonella recipient [d-tartrate-fermenting (d-Ta+) S Paratyphi B (13-SA01617), referred to here as S Paratyphi B (d-Ta+)] excretion by quantifying their excretion dynamics. Using plasmid profiling by S1 nuclease-restricted pulsed-field gel electrophoresis, we gained insight into the variability of the native plasmid content among S Corvallis reisolates as well as plasmid acquisition in S Paratyphi B (d-Ta+) and the enterobacterial gut microflora. Whole-genome sequencing enabled us to gain an in-depth insight into the microevolution of plasmid pRH-1238 in S Corvallis and enterobacterial recipient isolates. Our study revealed that the fecal excretion of avian native carbapenemase-producing S Corvallis is significantly higher than that of S Paratyphi (d-Ta+) and is not hampered by S Paratyphi (d-Ta+). Acquisition of pRH-1238 in other Enterobacteriaceae and several events of plasmid pRH-1238 transfer to different Escherichia coli sequence types and Klebsiella pneumoniae demonstrated an interspecies broad host range. Regardless of the microevolutionary structural deletions in pRH-1238, the single carbapenem resistance marker blaNDM-1 was maintained on pRH-1238 throughout the trial. Furthermore, we showed the importance of the gut E. coli population as a vector of pRH-1238. In a potential scenario of the introduction of NDM-1-producing S Corvallis into a broiler flock, the pRH-1238 plasmid could persist and spread to a broad host range even in the absence of antibiotic pressure.

Systematic Review: Impact of point sources on antibiotic-resistant bacteria in the natural environment

Point sources such as wastewater treatment plants and agricultural facilities may have a role in the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG). To analyse the evidence for increases in ARB in the natural environment associated with these point sources of ARB and ARG, we conducted a systematic review. We evaluated 5,247 records retrieved through database searches, including both studies that ascertained ARG and ARB outcomes. All studies were subjected to a screening process to assess relevance to the question and methodology to address our review question. A risk of bias assessment was conducted upon the final pool of studies included in the review. This article summarizes the evidence only for those studies with ARB outcomes (n = 47). Thirty-five studies were at high (n = 11) or at unclear (n = 24) risk of bias in the estimation of source effects due to lack of information and/or failure to control for confounders. Statistical analysis was used in ten studies, of which one assessed the effect of multiple sources using modelling approaches; none reported effect measures. Most studies reported higher ARB prevalence or concentration downstream/near the source. However, this evidence was primarily descriptive and it could not be concluded that there is a clear impact of point sources on increases in ARB in the environment. To quantify increases in ARB in the environment due to specific point sources, there is a need for studies that stress study design, control of biases and analytical tools to provide effect measure estimates.