Antimicrobial-Resistant Escherichia coli Survived in Dust Samples for More than 20 Years

Dissemination and characterization of Escherichia coli resistant to extended-cephalosporins in feedlot lambs: A two-year two-population study

Dissemination of antimicrobial resistance in food animals is a One Health concern, but sheep production has been overlooked. This study aimed to explore the dissemination of Escherichia coli resistant to extended-spectrum cephalosporins (ESC) in feedlot lambs. Two pens were sampled on two occasions, and carcasses and other mammals living around were also tested. E. coli were recovered and antibiotic resistance determined. blaCTX-M/CMY genes and their genetic localization were characterized. Whole genome sequencing (WGS) was performed to confirm clonal relationship. The most prevalent ESC-resistance genes in the 108 E. coli isolates were blaCTX-M-55 (53.7 %), blaCTX-M-2 (14.8 %) and blaCMY-2 (13.9 %). Most blaCTX-M-55 genes were found on the chromosome, but IncA/C, IncHI1, IncHI2 and IncF plasmids were also identified. Genetic diversity was observed even though ST6448 was by far the most frequent ST. WGS analysis showed high similarity among isolates recovered from feedlot lambs, animals in the surroundings and lambs' carcasses, proving the clonal and plasmidic dissemination.

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.

Resistance to β-lactams in Enterobacteriaceae isolated from vegetables: a review

Vegetables are crucial for a healthy human diet due to their abundance of essential macronutrients and micronutrients. However, there have been increased reports of antimicrobial-resistant Enterobacteriaceae isolated from vegetables. Enterobacteriaceae is a large group of Gram-negative bacteria that can act as commensals, intestinal pathogens, or opportunistic extraintestinal pathogens. Extraintestinal infections caused by Enterobacteriaceae are a clinical concern due to antimicrobial resistance (AMR). β-lactams have high efficacy against Gram-negative bacteria and low toxicity for eukaryotic cells. These antimicrobials are widely used in the treatment of Enterobacteriaceae extraintestinal infections. This review aimed to conduct a literature survey of the last five years (2018-2023) on the occurrence of β-lactam-resistant Enterobacteriaceae in vegetables. Research was carried out in PubMed, Web of Science, Scopus, ScienceDirect, and LILACS (Latin American and Caribbean Health Sciences Literature) databases. After a careful evaluation, thirty-seven articles were selected. β-lactam-resistant Enterobacteriaceae, including extended-spectrum β-lactamases (ESBLs)-producing, AmpC β-lactamases, and carbapenemases, have been isolated from a wide variety of vegetables. Vegetables are vectors of β-lactam-resistant Enterobacteriaceae, contributing to the dissemination of resistance mechanisms previously observed only in the hospital environment.

Biofilm Formation and Antimicrobial Susceptibility of E. coli Associated With Colibacillosis Outbreaks in Broiler Chickens From Saskatchewan

The global poultry industry has grown to the extent that the number of chickens now well exceeds the number of humans on Earth. Escherichia coli infections in poultry cause significant morbidity and economic losses for producers each year. We obtained 94 E. coli isolates from 12 colibacillosis outbreaks on Saskatchewan farms and screened them for antimicrobial resistance and biofilm formation. Fifty-six isolates were from broilers with confirmed colibacillosis, and 38 isolates were from healthy broilers in the same flocks (cecal E. coli). Resistance to penicillins, tetracyclines, and aminoglycosides was common in isolates from all 12 outbreaks, while cephalosporin resistance varied by outbreak. Most E. coli were able to form biofilms in at least one of three growth media (1/2 TSB, M63, and BHI broth). There was an overall trend that disease-causing E. coli had more antibiotic resistance and were more likely to form biofilms in nutrient-rich media (BHI) as compared to cecal strains. However, on an individual strain basis, there was no correlation between antimicrobial resistance and biofilm formation. The 21 strongest biofilm forming strains consisted of both disease-causing and cecal isolates that were either drug resistant or susceptible. Draft whole genome sequencing indicated that many known antimicrobial resistance genes were present on plasmids, with disease-causing E. coli having more plasmids on average than their cecal counterparts. We tested four common disinfectants for their ability to kill 12 of the best biofilm forming strains. All disinfectants killed single cells effectively, but biofilm cells were more resistant, although the difference was less pronounced for the disinfectants that have multiple modes of action. Our results indicate that there is significant diversity and complexity in E. coli poultry isolates, with different lifestyle pressures affecting disease-causing and cecal isolates.

Survival of Escherichia coli in Airborne and Settled Poultry Litter Particles

Airborne Escherichia coli (E. coli) in the poultry environment can migrate inside and outside houses through air movement. The airborne E. coli, after settling on surfaces, could be re-aerosolized or picked up by vectors (e.g., caretakers, rodents, transport trucks) for further transmission. To assess the impacts of airborne E. coli transmission among poultry farms, understanding the survivability of the bacteria is necessary. The objective of this study is to determine the survivability of airborne E. coli, settled E. coli, and E. coli in poultry litter under laboratory environmental conditions (22–28 °C with relative humidity of 54–63%). To determine the survivability of airborne E. coli, an AGI-30 bioaerosol sampler (AGI-30) was used to collect the E. coli at 0 and 20 min after the aerosolization. The half-life time of airborne E. coli was then determined by comparing the number of colony-forming units (CFUs) of the two samplings. To determine the survivability of settled E. coli, four sterile Petri dishes were placed on the chamber floor right after the aerosolization to collect settled E. coli. The Petri dishes were then divided into two groups, with each group being quantified for culturable E. coli concentrations and dust particle weight at 24-h intervals. The survivability of settled E. coli was then determined by comparing the number of viable E. coli per milligram settled dust collected in the Petri dishes in the two groups. The survivability of E. coli in the poultry litter sample (for aerosolization) was also determined. Results show that the half-life time of airborne E. coli was 5.7 ± 1.2 min. The survivability of E. coli in poultry litter and settled E. coli were much longer with the half-life time of 15.9 ± 1.3 h and 9.6 ± 1.6 h, respectively. In addition, the size distribution of airborne E. coli attached to dust particles and the size distribution of airborne dust particles were measured by using an Andersen impactor and a dust concentration monitor (DustTrak). Results show that most airborne E. coli (98.89% of total E. coli) were carried by the dust particles with aerodynamic diameter larger than 2.1 µm. The findings of this study may help better understand the fate of E. coli transmitted through the air and settled on surfaces and evaluate the impact of airborne transmission in poultry production.

Treatment of pigs with enrofloxacin via different oral dosage forms – environmental contaminations and resistance development of Escherichia coli

Background

Antibacterial agents play important roles in the treatment of bacterial infections. However, the development of antimicrobial resistance (AMR) and carry-over of substances into the environment are several problems arising during oral treatment of bacterial infections. We assessed AMR development in commensal Escherichia coli (E. coli) in enrofloxacin treated and untreated animals. In addition, we examined fluoroquinolone in the plasma and urine of treated and untreated animals, and in sedimentation dust and aerosol.

Methods

In each trial, six pigs were treated with enrofloxacin via powder, granulate or pellet forms in two time periods (days 1–5 and 22–26). Four pigs served as untreated controls. The minimum inhibitory concentration (MIC) was determined to evaluate AMR development. Analysis of enro- and ciprofloxacin was performed with high performance liquid chromatography.

Results

Non-wildtype E. coli (MIC > 0.125 µg/mL) was detected in the pellet treated group after the first treatment period, whereas in the other groups, non-wildtype isolates were found after the second treatment period. E. coli with MIC > 4 µg/mL was found in only the pellet trial. Untreated animals showed similar susceptibility shifts several days later. Bioavailability differed among the treatment forms (granulate > pellet > powder). Enro- and ciprofloxacin were detected in aerosols and sedimentation dust (granulate, powder > pellet).

Conclusions

This study indicates that the kind of the oral dosage form of antibiotics affects environmental contamination and AMR development in commensal E. coli in treated and untreated pigs.

Short-term and long-term effects of antimicrobial use on antimicrobial resistance in broiler and turkey farms

ABSTRACTAntimicrobials have been widely used in poultry, promoting antimicrobial resistance (AMR) emergence and spread. Resistant bacteria selected by antimicrobial use (AMU) can contaminate the farm environment and transfer resistance genes to other bacteria, providing opportunities for persistence and (re-)colonization of subsequent flocks and potentially jeopardizing antimicrobial treatments. We investigated the effects of AMU on AMR in poultry in the long-term (due to historical AMU in the farm) and in the short-term (due to current AMU in a flock). Litter samples from 35 broiler and 35 turkey farms in North-East Italy were sampled longitudinally for AMR testing of E. coli indicator bacteria in 2019/2020. Differences in AMR as a function of historical AMU (Defined Daily Doses in 2016-2018), current AMU in the sampled flock, farm size and season were tested using Generalized Estimating Equation regression analysis. In both broilers and turkeys, the highest resistance levels were observed for sulfamethoxazole (>70%), followed by ampicillin (54-60%). Only few positive associations between historical levels of penicillin use and the specific resistance levels to penicillin in broiler farms, and the overall historical AMU and resistance to trimethoprim in turkey flocks, were significant. Current AMU showed significant effects on resistance to sulfamethoxazole, trimethoprim, ciprofloxacin and tetracycline in turkey flocks. Significant effects of farm size on some AMR levels were also identified. We found a stronger association between current AMU and AMR compared to historical AMU and AMR. AMR persistence in the farm environment in absence of direct AMU pressure needs to be further investigated.

The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety

Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.

A review of antimicrobial resistance in imported foods

Antimicrobial resistance is one of the most serious threats to medical science. Food supply is recognized as a potential source of resistant bacteria, leading to the development of surveillance programs targeting primarily poultry, pork, and beef. These programs are limited in scope, not only in the commodities tested, but also in the organisms targeted (Escherichia coli, Salmonella, and Campylobacter); consequently, neither the breadth of food products available nor the organisms that may harbour clinically relevant and (or) mobile resistance genes are identified. Furthermore, there is an inadequate understanding of how international trade in food products contributes to the global dissemination of resistance. This is despite the recognized role of international travel in disseminating antimicrobial-resistant organisms, notably New Delhi metallo-beta-lactamase. An increasing number of studies describing antimicrobial-resistant organisms in a variety of imported foods are summarized in this review.

Aerosol is the optimal route of respiratory tract infection to induce pathological lesions of colibacillosis by a lux-tagged avian pathogenic Escherichia coli in chickens

Pathogenesis of colibacillosis caused by avian pathogenic Escherichia coli (APEC) in poultry is unclear and experimental studies reveal substantial inconsistency. In this study, the impact of three infection routes differing in the site of deposition of inoculum in the respiratory tract, were investigated. Two-weeks-old chickens were infected with a lux-tagged APEC strain via aerosol, intranasally or intratracheally, and sequentially sampled along with uninfected birds. At 1 and 3 days post infection (dpi), liver or spleen to body-weight ratios in all infected groups were significantly higher than in negative control, while at 7 dpi, such differences were significant in both organs in the aerosol-infected group. The infection-strain colonized tracheas and lungs in infected birds at 1 dpi and persisted until 7 dpi. Among infected groups, in lungs, bacterial load at 1 dpi was significantly lower in intranasally-inoculated birds. Histology revealed that, independent of infection route, lesions were mostly seen in the lower respiratory organs (lungs and air sacs) characterized by bronchitis/pneumonia and airsacculitis. Birds infected via aerosol showed the highest mean lesion score in lungs while intranasal application caused the mildest pathological changes, and difference between the two groups was significant at 1 dpi. In spleen, heterophilic infiltrations were prominent in affected birds. Interestingly, tracheas were pathologically unaffected. Altogether, the results demonstrated the importance of infection route, with aerosol being the most suitable to induce pathological lesions of colibacillosis without predisposing factors. Furthermore, the lux-tagged APEC strain was discriminated from native isolates enabling exact differentiation and enumeration.RESEARCH HIGHLIGHTS Lux-tagged APEC strain was used for infection to differentiate from native E. coli.Pathologically, lungs, air sacs and spleen but not trachea were affected.The route of infection strongly impacts the pathological outcome with APEC.The infection with APEC via aerosol caused the most severe lesions in chickens.

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.

Control of Salmonella and Pathogenic E. coli Contamination of Animal Feed Using Alternatives to Formaldehyde-Based Treatments

This study compared a novel non-formaldehyde combination product developed for pathogen control in animal feed Finio (A), with a panel of three commonly used organic acid feed additive products: Fysal (B), SalCURB K2 (C) and Salgard (D). Products were evaluated for their ability to reduce Salmonella Typhimurium DT104 and avian pathogenic Escherichia coli in poultry feed. A commercial layer-hen mash was treated with each product and then mixed with feed previously contaminated (via inoculated meat and bone meal) with either Salmonella or E. coli. After 24 hours at room temperature, 10 replicate samples were taken from each preparation and plate counts were performed using a selective agar. All concentrations of product A (0.5, 1.0, 1.5, 2.0 and 2.5 kg per metric tonne (MT)) plus the higher concentration of products B and D (6.0 kg MT-1) significantly reduced Salmonella counts compared with those in the untreated control group (p < 0.05). Product C did not significantly reduce levels of Salmonella under these conditions. Because of the poor recovery of E. coli, statistical comparisons for this organism were limited in scope, but only product A at the highest concentration appeared to have eliminated it.

Management factors influencing the occurrence of cellulitis in broiler chickens

One of the main reasons for condemning fattening broiler chickens during meat inspection is cellulitis, which demonstrates the great economic issue concerning this topic. The aim of this epidemiological study was therefore to identify risk factors in order to draw conclusions on how to prevent the occurrence of cellulitis in broilers by implementing management changes. The data were collected between April and November 2018 on conventional broiler farms (n = 100) in the north of Germany with one to fourteen poultry houses per farm. In total, data were collected from 199 broiler flocks with a total of 5,332,767 broilers. Data on the type of management (feeding- and drinking management, housing, lighting management, litter type and animal health) were collected via a questionnaire, with additional data on condemnation rates being provided by the abattoirs. It was found that litter additives like fennel, eucalyptus and probiotics as well as a moist litter quality were associated with lower cellulitis condemnation rates. Flocks fattened in windowless barns, but with relatively higher lux-values as well as those broilers examined in a lower number of housing inspections had significantly lower cellulitis condemnation rates compared to other husbandry systems. In addition, lower cellulitis rates were seen when housing capacities were smaller, regardless of stocking density. The source of the breeders and hatchery also had a significant influence on the occurrence of cellulitis. No correlation was found between the condemnation rates due to cellulitis and the performance of thinning, the water source used, the use of drinking additives, observational skills and number of herd managers monitoring the broilers, participation in an animal welfare programme, the technique of heating and ventilation systems used, the feed supplier, litter material, the broiler breed, the length of darkness periods and chick losses during the first seven days. We concluded that management decisions that lead to stress reduction in the broiler flocks are beneficial in terms of chicken welfare and occurrence of cellulitis.

Occurrence of extended-spectrum beta-lactamase-producing Enterobacteriaceae, microbial loads, and endotoxin levels in dust from laying hen houses in Egypt

Background

Poultry houses are often highly contaminated with dust, which might contain considerable amounts of microorganisms and endotoxins. The concentrations of microorganisms and endotoxins in dust from laying hen houses in Egypt are unknown. However, to estimate the risks for birds, the environment, and people working in laying hen houses, it is important to gather information about the composition of these dusts. Here we report the microbial loads, the occurrence of antimicrobial-resistant bacteria, and endotoxin concentrations in dust samples from 28 laying hen farms in Dakahliya Governorate, Egypt, and discuss the results relevant to the literature.

Results

Pooled settled dust samples (n = 28) were analyzed for total viable counts of bacteria and fungi (CFU/g), the occurrence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Salmonella spp., and methicillin-resistant Staphylococcus aureus (MRSA), and endotoxin concentrations (ng/g). The means and standard deviations of total viable counts were 7.10 × 10⁸ ± 2.55 × 10⁹ CFU/g for bacteria and 5.37 × 10⁶ ± 7.26 × 10⁶ CFU/g for fungi. Endotoxin levels varied from 2.9 × 10⁴ to 6.27 × 10⁵ ng/g. None of the tested samples contained Salmonella spp. or MRSA. In contrast, by direct plating, Enterobacteriaceae were found frequently (57%; n = 16), and suspected ESBL-producing Enterobacteriaceae occurred in 21% (n = 6) of the sampled barns. Using an enrichment method, the detection of Enterobacteriaceae and suspected ESBL-producing Enterobacteriaceae increased to 20 and 16 positive barns, respectively. Taking results from both methods into account, Enterobacteriaceae and suspected ESBL-producing Enterobacteriaceae were detected in 23 barns Overall, 100 ESBL suspected isolates (Escherichia coli, n = 64; Enterobacter cloacae, n = 20; and Klebsiella pneumoniae n = 16) were identified to species level by MALDI-TOF MS. Isolates from 20 barns (71% positive barns) were confirmed as ESBL producing Enterobacteriaceae by the broth microdilution test.

Conclusions

Dust in Egyptian laying hen houses contains high concentrations of microorganisms and endotoxins, which might impair the health of birds and farmers when inhaled. Furthermore, laying hens in Egypt seem to be a reservoir for ESBL-producing Enterobacteriaceae. Thus, farmers are at risk of exposure to ESBL-producing bacteria, and colonized hens might transmit these bacteria into the food chain.

Identification of antimicrobial resistant bacteria from plant-based food products imported into Canada

The role of plant-based foods in the epidemiology of antimicrobial resistance has been inadequately studied. In this investigation, resistant organisms from vegetables, fruits and spices imported into Canada were identified and characterized. A total of 143 products imported from primarily Asian and African countries were purchased from international markets in Saskatoon, Saskatchewan. Samples were selectively cultured for bacterial species where resistance is known to be emerging. The proportions of samples positive for each organism were as follows: E. coli (n = 13, 9.1%), Salmonella spp. (n = 2, 1.4%), ESBL producing Enterobacter spp. (n = 2, 1.4%) and K. pneumoniae (n = 2, 1.4%), S. aureus (n = 7, 4.9%) and Enterococcus spp. (n = 66, 46.2%). Antimicrobial minimum inhibitory concentrations were determined by broth micro-dilution and agar-dilution. Based on the susceptibility of each organism, isolates were screened for resistance genes (β-lactamases and plasmid mediated quinolones resistance determinants) by PCR. Extended-spectrum β-lactamase producing Enterobacteriaceae and methicillin resistant S. aureus (MRSA) were identified from 6/143 (4.2%) and 2/143 (1.4%) of samples respectively. The qnrB, qnrS and aac(6')-Ib-cr plasmid mediated quinolone resistance determinants were identified in 2/143 (1.4%) of samples tested. None of the Enterobacteriaceae isolates were resistant to meropenem or colistin. Similarly, all Enterococcus isolates remained susceptible to ampicillin, penicillin and vancomycin. Finding multi-drug resistant bacteria which are frequently isolated from human infections is concerning, although the contribution of the global food trade to the dissemination of resistance remains cryptic. These results suggest that imported plant-based foods may be an underappreciated source of clinically relevant resistant organisms. Further study is required to address these gaps in our understanding of the epidemiology of resistance, and the magnitude of the risk posed to human health by these organisms.

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

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

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.

Analysis of fluoroquinolones in dusts from intensive livestock farming and the co-occurrence of fluoroquinolone-resistant Escherichia coli

Fluoroquinolones are important therapeutics in human and veterinary medicine. This study aimed to retrospectively analyse sedimentation dusts from intensive-livestock-farming barns for fluoroquinolones and investigate the association between resistant Escherichia coli and the detected drugs. Sedimentation-dust samples (n = 125) collected (1980–2009) at 14 barns of unknown-treatment status were analysed by HPLC and tandem-mass spectroscopy to detect enrofloxacin, ciprofloxacin, marbofloxacin, and difloxacin. Recent microbiological data were included to investigate the relationship between fluoroquinolone presence and fluoroquinolone-resistant E. coli. Fifty-nine dust samples (47%) from seven barns contained fluoroquinolone residues. Up to three different fluoroquinolones were detected in pig and broiler barns. Fluoroquinolone concentrations ranged from 10-pg/mg to 46-ng/mg dust. Fluoroquinolone-resistant E. coli were isolated from four barns. Of all the dust samples, 22% contained non-susceptible isolates. Non-susceptible isolate presence in the dust was significantly associated (p = 0.0283) with detecting the drugs, while drug detection increased the odds (4-fold) of finding non-susceptible E. coli (odds ratio = 3.9877, 95% CI: 1.2854–12.3712). This retrospective study shows that fluoroquinolone usage leads to dust contamination. We conclude that farmers and animals inhale/swallow fluoroquinolones and fluoroquinolone-resistant bacteria due to drug application. Furthermore, uncontrolled drug emissions via air exhausted from the barns can be assumed.

Resistance of Enterococcus spp. in Dust From Farm Animal Houses: A Retrospective Study

In a retrospective study, the antimicrobial susceptibility of Enterococcus spp. isolated from stored sedimentation dust samples from cattle, pig and poultry barns to 16 antibiotics was determined using a microdilution test. The resistance phenotypes of 70 isolates from different timespans (8 from the 1980s, 15 from the 1990s, 43 from the 2000s and 4 from 2015) were determined. Resistant enterococci were detected in samples from all time periods. Resistances to three or more antibiotics occurred in 69 percent of all isolates. The oldest multidrug resistant isolate was an Enterococcus faecium obtained from a 35-year-old pig barn dust sample. No correlations (ρ = 0.16, p = 0.187) were found between the age of isolates and the number of resistances. Instead, the number of resistances was associated with the origin of the isolates. An exact logistic conditional regression analysis showed significant differences in resistance to ciprofloxacin, erythromycin, penicillin and tylosin between isolates from different animal groups. Interestingly, we isolated ciprofloxacin-resistant E. faecium from pig barn dust before fluoroquinolones were introduced into the market for use in animal husbandry. In conclusion, dust from farm animal houses is a reservoir and carrier of multidrug-resistant Enterococcus spp. People working in barns are unavoidably exposed to these bacteria. Furthermore, it can be hypothesized that emissions from barns of intensive livestock farming contaminate the environment with multidrug resistant enterococci.

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry

Antimicrobial resistance against colistin has emerged worldwide and is threatening the efficacy of colistin treatment of multi-resistant Gram-negative bacteria. In this study, PCRs were used to detect mcr genes (mcr-1, mcr-2, mcr-3) in 213 anal and 1,339 nasal swabs from pigs (n = 1,454) in nine provinces of China, and 1,696 cloacal and 1,647 oropharyngeal samples from poultry (n = 1,836) at live-bird markets in 24 provinces. The mcr-1 prevalences in pigs (79.2%) and geese (71.7%) were significantly higher than in chickens (31.8%), ducks (34.6%) and pigeons (13.1%). The mcr-2 prevalence in pigs was 56.3%, significantly higher than in chickens (5.5%), ducks (2.3%), geese (5.5%) and pigeons (0%). The mcr-3 prevalences in pigs (18.7%), ducks (13.8%) and geese (11.9%) were significantly higher than in chickens (5.2%) and pigeons (5.1%). In total, 173 pigs and three chickens were positive for all three mcr genes. The prevalences of the mcr were significantly higher in nasal/oropharyngeal swabs than in the anal /cloacal swabs. Phylogenetic studies identified 33 new mcr-2 variants and 12 new mcr-3 variants. This study demonstrates high prevalences of mcr in pigs and poultry in China, and indicates there is need for more thorough surveillance and control programs to prevent further selection of colistin resistance.

E. coli Surface Properties Differ between Stream Water and Sediment Environments

The importance of E. coli as an indicator organism in fresh water has led to numerous studies focusing on cell properties and transport behavior. However, previous studies have been unable to assess if differences in E. coli cell surface properties and genomic variation are associated with different environmental habitats. In this study, we investigated the variation in characteristics of E. coli obtained from stream water and stream bottom sediments. Cell properties were measured for 77 genomically different E. coli strains (44 strains isolated from sediments and 33 strains isolated from water) under common stream conditions in the Upper Midwestern United States: pH 8.0, ionic strength 10 mM and 22°C. Measured cell properties include hydrophobicity, zeta potential, net charge, total acidity, and extracellular polymeric substance (EPS) composition. Our results indicate that stream sediment E. coli had significantly greater hydrophobicity, greater EPS protein content and EPS sugar content, less negative net charge, and higher point of zero charge than stream water E. coli. A significant positive correlation was observed between hydrophobicity and EPS protein for stream sediment E. coli but not for stream water E. coli. Additionally, E. coli surviving in the same habitat tended to have significantly larger (GTG)₅ genome similarity. After accounting for the intrinsic impact from the genome, environmental habitat was determined to be a factor influencing some cell surface properties, such as hydrophobicity. The diversity of cell properties and its resulting impact on particle interactions should be considered for environmental fate and transport modeling of aquatic indicator organisms such as E. coli.