Oral antimicrobials increase antimicrobial resistance in porcine E. coli – A systematic review

Risk Factor Analysis for Occurrence of Linezolid-Resistant Bacteria in the Digestive and Respiratory Tract of Food-Producing Animals in Belgium: A Pilot Study

Linezolid is a critically important antimicrobial used in human medicine. While linezolid is not licensed for food-producing animals, the veterinary use of other antimicrobials, such as phenicols (e.g., florfenicol), could cross/co-select for linezolid-resistant (LR) bacteria. Such LR strains pose a great concern for public health due to their potential transfer between animals and humans. This study explored possible associations between epidemiological risk factors, including phenicol use, and the occurrence of LR bacteria, such as enterococci and staphylococci, in poultry, pigs, and veal calves in Belgium. Florfenicol use significantly increased the likelihood of harboring LR bacteria in veal calves, sows, and fattening pigs, particularly for the digestive tract (odds ratio (OR): [3.19-5.29]) and the respiratory tract (OR: [6.11-9.09]). LR strains from feces from fattening pigs were significantly associated with production type (OR: [3.31-44.14]) and the presence of other animal species (OR: 0.41). The occurrence of LR strains in the respiratory tract from sows was also significantly associated with using antimicrobials other than florfenicol (OR: 10.07) and purchasing animals (OR: 7.28). Our study highlights the potential risks of using certain veterinary antimicrobials, such as florfenicol, in food-producing animals and emphasizes the need for responsible antimicrobial use to safeguard both animal and public health.

Impact of Veterinary Feed Directive Rules Changes on the Prevalence of Antibiotic Resistance Bacteria Isolated from Cecal Samples of Food-Producing Animals at US Slaughterhouses

This study examined the impact of the 2017 Veterinary Feed Directive (VFD) rule changes on the prevalence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella spp., Campylobacter spp., and Escherichia coli) in cecal samples of food animals (cattle, swine, chicken, and turkey) at US slaughterhouses. Multivariable logistic regression was used to analyze 2013-2019 cecal samples of food-producing animals surveillance data from the National Antimicrobial Resistance Monitoring System (NARMS) in the U.S. The variables included year (used to evaluate VFD rule changes), host, and quarter of year. The analysis of surveillance data showed that the VFD rule changes have varying effects on tetracycline-resistant and erythromycin-resistant bacteria in food animals. For example, the odds of detecting tetracycline-resistant Salmonella spp. decreased in cattle but increased in chickens following the implementation of the VFD rule changes. Similarly, the odds of detecting tetracycline-resistant Escherichia coli decreased in chickens but increased in swine after the VFD rule changes. The odds of detecting erythromycin-resistant Campylobacter spp. increased in cattle but decreased in chickens after the VFD rule changes. In conclusion, the implementation of VFD rule changes has been beneficial in reducing the odds of detecting tetracycline-resistant Escherichia coli and erythromycin-resistant Campylobacter spp. in chickens, as well as tetracycline-resistant Salmonella spp. in cattle at US slaughterhouses.

Risk factors associated with mcr-1 colistin-resistance gene in Escherichia coli broiler samples in northern Jordan

OBJECTIVES

The purpose of this study was to determine the prevalence of colistin-resistant Escherichia coli carrying mcr-1, and to identify risk factors associated with mcr gene-mediated resistance.

METHODS

In total, 385 cloacal samples were collected from 125 broiler farms and a questionnaire containing information about each farm was designed and filled.

RESULTS

Most of the antibiotics used in the disk diffusion method were highly resistant in all samples, with tetracycline and penicillin showing 100% and 99.7% resistance, respectively. Additionally, avian pathogenic E. coli (APEC) virulence genes frequency and percentage of APEC were identified, including sitA,iucC, and astA at 77%, 70.5%, and 62% respectively. In total, 214 of 360 isolates were positive for APEC (59.4%). Based on the minimum inhibitory (MIC) test, 58% of the isolates (n = 209 of 360) were resistant to colistin, with 39.7% displaying the mcr-1 gene. The statistical analysis of risk factors that influence colistin resistance prevalence revealed several significant factors, including commercial feed, farm management, sanitization, and antibiotic use. Irregular health checks for workers, non-dipping of feet before entering poultry houses, and the use of commercial poultry feeds all contributed to higher levels of colistin resistance as measured by MIC. On the other hand, doxycycline and commercial feed was 4 and 3.2 times more likely to occur based on the final logistic model of the mcr-1 gene, respectively.

CONCLUSION

Our results suggest that better biosecurity protocols should be implemented in poultry farms to reduce antibiotic-resistant bacteria. Additionally, antibiotics should be carefully monitored and used only when necessary.

Impact of In-Feed versus In-Water Chlortetracycline and Tiamulin Administrations on Fecal Prevalence and Antimicrobial Susceptibilities of Campylobacter in a Population of Nursery Pigs

Antimicrobial resistance (AMR) in bacteria is a major public health concern in the US and around the world. Campylobacter is an important foodborne pathogen that resides in the gut of pigs and is shed in feces, with the potential to be transmitted to humans. In pigs, the oral route, either in-feed or in-water, is by far the most common route of administration of antimicrobials. Because the distribution of the antibiotic in the gut and the dosages are different, the impact of in-feed vs. in-water administration of antibiotics on the development of AMR is likely to be different. Therefore, a study was conducted to compare in-feed vs. in-water administrations of chlortetracycline (CTC) and/or tiamulin on fecal prevalence and AMR profiles of Campylobacter among weaned nursery piglets. A total of 1,296 weaned piglets, allocated into 48 pens (27 piglets per pen), were assigned randomly to six treatment groups: Control (no antibiotic), in-feed CTC, in-water CTC, in-feed tiamulin, in-water tiamulin, or in-feed CTC and tiamulin. Fecal samples were collected randomly from 5 piglets from each pen during the pre-treatment (days 0, 7), treatment (days 14, 21), and post-treatment (days 28, 35) phases. Bacterial isolations and species identifications were conducted by culture and PCR, respectively. The microbroth dilution method with SensititreTM plates was used to determine the antimicrobial susceptibility and resistance of Campylobacter isolates. The results on resistance were interpreted based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cutoff values for Campylobacter. The overall prevalence of Campylobacter was 18.2% (262/1440). Speciation of Campylobacter isolates by PCR indicated the prevalence of only two species: Campylobacter hyointestinalis (17.9%; 258/1440) and C. coli (0.3%; 4/1440). Campylobacter isolates were resistant to tetracycline (98.5%), ciprofloxacin (89.3%), and nalidixic acid (60.3%). Neither the antibiotic nor the route of administration had an effect (p > 0.05) on the prevalence of AMR Campylobacter in the feces of piglets.

Assessing the Effect of Oxytetracycline on the Selection of Resistant Escherichia coli in Treated and Untreated Broiler Chickens

Oxytetracycline (OTC) is administered in the poultry industry for the treatment of digestive and respiratory diseases. The use of OTC may contribute to the selection of resistant bacteria in the gastrointestinal tract of birds or in the environment. To determine the effect of OTC on the selection of resistant Escherichia coli strains post-treatment, bacteria were isolated from droppings and litter sampled from untreated and treated birds. Bacterial susceptibility to tetracyclines was determined by the Kirby-Bauer test. A total of 187 resistant isolates were analyzed for the presence of tet(A), (B), (C), (D), (E), and (M) genes by PCR. Fifty-four strains were analyzed by PFGE for subtyping. The proportion of tetracycline-resistant E. coli strains isolated was 42.88%. The susceptibility of the strains was treatment-dependent. A high clonal diversity was observed, with the tet(A) gene being the most prevalent, followed by tet(C). Even at therapeutic doses, there is selection pressure on resistant E. coli strains. The most prevalent resistance genes were tet(A) and tet(C), which could suggest that one of the main mechanisms of resistance of E. coli to tetracyclines is through active efflux pumps.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Effects of Antimicrobial Administration Route on Growth and Antimicrobial Resistance in Weaned Piglets

This study aimed to determine how the route of antimicrobial administration affected the growth performance of weaned piglets. Additionally, we aimed to investigate potential differences between antimicrobial resistance developed by antimicrobials administered orally through drinking water, and those administered through feed, in weaned piglets. The research was undertaken on a farm housing 500 sows and involved 150 weaned piglets at 21 days of age. These piglets were evenly distributed into three groups of equal size: water, feed, and control. Antimicrobials were administered through drinking water and feed in the water and feed groups, respectively, while the control group received no antimicrobial treatment. The observation of piglets continued until they reached 70 days of age. The feed conversion ratio in the water group (1.7 ± 0.78) was significantly higher than in the control (2.4 ± 1.77) and feed (2.7 ± 1.68) groups. Additionally, the route of administration did not affect antimicrobial resistance rates. Based on these results, it can be inferred that administering antimicrobials through drinking water is advantageous for pig farming.

Pre-Treatment with Bromelain Prevents Intestinal Dysbiosis in Pigs with Post-Weaning Diarrhea, without Increasing Antimicrobial Resistance in Escherichia coli

Pigs are especially vulnerable to intestinal pathogens and dysbiosis in the first two weeks after weaning. Infection with enterotoxigenic strains of Escherichia coli (ETEC) in combination with poor nutrition and hygiene can lead to diarrhea, poor growth and increased mortality. While neomycin and zinc oxide can prevent post-weaning diarrhea (PWD), their broad-spectrum activity also kills commensal microbiota and can lead to the emergence of heavy metal and antimicrobial resistance. Bromelain prevents attachment of F4 ETEC to intestinal enterocytes by cleaving the host receptor. In controlled environmental facilities, weaned pigs treated with either therapeutic levels of neomycin sulfate, zinc oxide, bromelain or non-treated were monitored for diarrhea, weight gain, feed intake, feed efficiency, excretion of F4 ETEC, changes to their intestinal microbiomes and antimicrobial resistance in E. coli. The treatment effects were evaluated at weaning, during two weeks of treatment and for three weeks after treatments ceased. Minimal clinical signs of PWD were observed, except in zinc-treated pigs post treatment. Intestinal dysbiosis was observed in response to diarrhea and in pigs treated with both neomycin and zinc. Antimicrobial resistance increased in commensal E. coli isolated from neomycin- and zinc-treated pigs. In contrast, bromelain controlled PWD and prevented intestinal dysbiosis without inducing antimicrobial resistance.

Molecular Characterisation of Antimicrobial Resistance in E. coli Isolates from Piglets in the West Region of Romania

Antibiotics are widely used for prophylaxis and therapy, reducing morbidity and mortality produced by bacterial pathogensin pigs, including infections caused by Escherichia coli. The aim of this study was to characterise antibiotic resistance phenotypes and genotypes in E. coli isolates in pigs in West Romanian grower farms. Differential phenotypic susceptibility profiles and the contribution of resistance genes to phenotypic expression of susceptibility or resistance were evaluated. A total of 76 E. coli isolates were identified and confirmed by the MicroScan Walk Away System. The occurrence of four resistance genes, ampC, blaZ, blaTEM and tetK in strains resistant to 13 antibiotics was assessed. Of the E. coli isolates, 0% showed resistance to meropenem, 3.9% to tigecycline and 10.5% to piperacillin/tazobactam, whereas, in contrast, 100% were resistant to ampicillin and mezlocillin, 76.31% to piperacillin and 59.3% to tetracycline. The prevalence of resistance genes in resistant isolates detected by q-PCR analysis was 97.0% for ampC, 96% for blaZ, 32.9% for blaTEM and 58.8% for tetK. Penetrance (the proportion of individuals carrying a particular variant of a gene that also expresses an associated trait) was 50% for ampC (32% for amoxicillin/clavulanate, 62% for cefazolin, 32% for cefepime, 100% for cefotaxime, 56% for cefuroxime and 99% for ampicillin), 65% for blaZ (32% for amoxicillin/clavulanate and 99% for ampicillin), 51% for blaTEM (81% for piperacillin) and 44% for the tetK gene (83% for tetracycline). The result of phenotypic antibiotic resistance testing may indicate the presence of plasmid-borne resistance, with a diagnostic odds ratio of a positive phenotypic resistance for tetK being 4.52. As a management decision, the maximum penetrance admitted for using a specific antibiotic for E. coli infections in pigs is recommended to be less than 20%.

Evaluating Antimicrobial Resistance Trends in Commensal Escherichia coli Isolated from Cecal Samples of Swine at Slaughter in the United States, 2013-2019

The emergence of antimicrobial resistance (AMR) in commensal and pathogenic enteric bacteria of swine is a public health threat. This study evaluated publicly available AMR surveillance data collected by the National Antimicrobial Resistance Monitoring System (NARMS) by assessing AMR patterns and temporal trends in commensal E. coli isolated from cecal samples of swine at slaughter across the United States. We applied the Mann-Kendall test (MKT) and a linear regression trend line to detect significant trends in the proportion of resistant isolates to individual antimicrobials over the study period. A Poisson regression model assessed differences among years in the number of antimicrobials to which an E. coli isolate was resistant. Among the 3237 E. coli isolates, a very high prevalence of resistance for tetracycline (67.62%), and high resistance for streptomycin (24.13%), and ampicillin (21.10%) were identified. The MKT and the linear trend line showed a significantly increasing temporal trend for amoxicillin-clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftriaxone, and trimethoprim-sulfamethoxazole. Compared to 2013 the number of antimicrobials to which an E. coli isolate was resistant was significantly higher in the years 2017, 2018, and 2019. The increasing temporal trend of resistance to important antimicrobials for human medicine (e.g., third-generation cephalosporins) and the increase in multidrug resistance in the later years of the study are concerning and should be followed up by studies to identify sources and risk factors for the selection of AMR.

Antimicrobial Resistance and Virulence Factors of Proteus mirabilis Isolated from Dog with Chronic Otitis Externa

Otitis externa is among the most prevalent diseases in dogs. If the underlying cause is not addressed, bacterial reinfection becomes frequent, necessitating antibiotic administration for an extended period of time. Prolonged treatment promotes the emergence of antibiotic-resistant bacteria and increases the risk of their transmission from animals to humans. This study aimed to analyze the antibiotic resistance pattern of the emerging pathogen Proteus mirabilis to identify bacterial virulence and antibiotic selection. Samples were collected from randomly encountered dogs with chronic otitis externa. Thirty-two strains of P. mirabilis were isolated and identified, using MALDI-TOF. The Kirby-Bauer disk diffusion method was used to assess the antibiotic susceptibility of P. mirabilis to 11 antibiotics. The isolates (n = 32) were most resistant to cefazolin (75%), trimethoprim–sulfamethoxazole (72%), chloramphenicol (72%), amoxicillin–clavulanate (63%), ampicillin (59%), cefepime (56%), ciprofloxacin (53%), aztreonam (50%), ceftazidime avibactam (50%), gentamicin (22%), and amikacin (16%). Moreover, 75% of isolates were found to be multidrug-resistant bacteria. P. mirabilis was found to have a high resistance-pattern ratio. Although the exact cause is unknown, continuous antibiotic use is thought to be a major factor. We concluded that antibiotic use must be prudent and selective to prevent antibiotic resistance.

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs

BACKGROUND

Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups.

RESULTS

Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials.

CONCLUSIONS

The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.

Associations between antimicrobial resistance in fecal Escherichia coli isolates and antimicrobial use in Canadian turkey flocks

Antimicrobial resistance (AMR) in enteric bacteria continues to be detected in turkey flocks and retail products worldwide, including in Canada. However, studies assessing linkages between on-farm antimicrobial use (AMU) and the development of AMR are lacking. This study aims to identify AMU characteristics that impact the development of AMR in the indicator bacteria Escherichia coli in turkey flocks, building on the Canadian Integrated Program for Antimicrobial Resistance Surveillance methodology for farm-level AMU and AMR data integration. Two analytic approaches were used: (1) multivariable mixed-effects logistic regression models examined associations between AMU (any route, route-specific, and route-disease-specific indication) summarized as the number of defined daily doses in animals using Canadian standards ([nDDDvetCA]/1,000 kg-animal-days at risk) and AMR and (2) multivariable mixed-effects Poisson regression models studied the linkages between AMU and the number of classes to which an E. coli isolate was resistant (nCR E. coli ). A total of 1,317 E. coli isolates from a network of 16 veterinarians and 334 turkey producers across the five major turkey-producing provinces in Canada between 2016 and 2019 were used. Analysis indicated that AMR emerged with the use of related antimicrobials (e.g., tetracycline use-tetracycline resistance), however, the use of unrelated antimicrobial classes was also impacting AMR (e.g., aminoglycosides/streptogramins use-tetracycline resistance). As for studying AMU-nCR E. coli linkages, the most robust association was between the parenteral aminoglycosides use and nCR E. coli , though in-feed uses of four unrelated classes (bacitracin, folate pathway inhibitors, streptogramins, and tetracyclines) appear to be important, indicating that ongoing uses of these classes may slow down the succession from multidrug-resistant to a more susceptible E. coli populations. The analysis of AMU (route and disease-specific)-AMR linkages complemented the above findings, suggesting that treatment of certain diseases (enteric, late-stage septicemic conditions, and colibacillosis) are influential in the development of resistance to certain antimicrobial classes. The highest variances were at the flock level indicating that stewardship actions should focus on flock-level infection prevention practices. This study added new insights to our understanding of AMU-AMR linkages in turkeys and is useful in informing AMU stewardship in the turkey sector. Enhanced surveillance using sequencing technologies are warranted to explain molecular-level determinants of AMR.

Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon

Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall ‘low’ probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall ‘low’, but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.

National Monitoring of Veterinary-Dispensed Antimicrobials for Use on Pig Farms in Austria: 2015-2020

Antimicrobial use in livestock production systems is increasingly scrutinised by consumers, stakeholders, and the veterinary profession. In Austria, veterinarians dispensing antimicrobials for use in food-producing animals have been required to report these drugs since 2015. Here, we describe the national monitoring systems and the results obtained for Austrian pig production over a six-year period. Antimicrobial dispensing is described using the mass-based metric, milligrams per population correction unit (mg/PCU) and the dose-based metric, Defined Daily Dose (DDDvet) per year and divided into the European Medicines Agency's prudent use categories. Pig production was divided into breeding units, fattening farms, farrow-to-finish farms, and piglet-rearing systems. Over all six years and all pig production systems, the mean amount of antimicrobials dispensed was 71.6 mg/PCU or 2.2 DDDvet per year. Piglet-rearing systems were found to have the highest levels of antimicrobial dispensing in DDDvet, as well as the largest proportion of Category B antimicrobials, including polymyxins. Although progress has been made in promoting a more prudent use of antimicrobials in veterinary medicine in Austria, further steps need to be taken to proactively improve animal health and prevent disease to reduce the need for antimicrobials, particularly those critically important for human medicine, in the future.

Evaluation of the Impact of Antimicrobial Use Protocols in Porcine Reproductive and Respiratory Syndrome Virus-Infected Swine on Phenotypic Antimicrobial Resistance Patterns

A longitudinal study was conducted to assess the impact of different antimicrobial exposures of nursery-phase pigs on patterns of phenotypic antimicrobial resistance (AMR) in fecal indicator organisms throughout the growing phase. Based on practical approaches used to treat moderate to severe porcine reproductive and respiratory syndrome virus (PRRSV)-associated secondary bacterial infections, two antimicrobial protocols of differing intensities of exposure [44.1 and 181.5 animal-treatment days per 1000 animal days at risk (ATD)] were compared with a control group with minimal antimicrobial exposure (2.1 ATD). Litter-matched pigs (n = 108) with no prior antimicrobial exposure were assigned randomly to the treatment groups. Pen fecal samples were collected nine times during the wean-to-finish period and cultured for Escherichia coli and Enterococcus spp. Antimicrobial-susceptibility testing was conducted using NARMS Gram-negative and Gram-positive antibiotic panels. Despite up to 65-fold difference in ATD, few and modest differences were observed between groups and over time. Resistance patterns at marketing overall remained similar to those observed at weaning, prior to any antimicrobial exposures. Those differences observed could not readily be reconciled with the patterns of antimicrobial exposure. Resistance of E. coli to streptomycin was higher in the group exposed to 44.1 ATD, but no aminoglycosides were used. In all instances where resistances differed between time points, the higher resistance occurred early in the trial prior to any antimicrobial exposures. These minimal impacts on AMR despite substantially different antimicrobial exposures point to the lack of understanding of the drivers of AMR at the population level and the likely importance of factors other than antimicrobial exposure. IMPORTANCE Despite a recognized need for more longitudinal studies to assess the effects of antimicrobial use on resistance in food animals, they remain sparse in the literature, and most longitudinal studies of pigs have been observational. The current experimental study had the advantages of greater control of potential confounding, precise measurement of antimicrobial exposures which differed markedly between groups and tracking of pigs until market age. Overall, resistance patterns were remarkably stable between the treatment groups over time, and the differences observed could not be readily reconciled with the antimicrobial exposures, indicating the likely importance of other determinants of AMR at the population level.

Removal of antimicrobial prophylaxis and its effect on swine carriage of antimicrobial-resistant coliforms

The use of antimicrobials in the food animal industry has caused an increased prevalence of antimicrobial-resistant bacteria and antimicrobial resistance genes, which can be transferred to the microbiota of humans through the food chain or the environment. To reduce the development and spread of antimicrobial resistance, restrictions on antimicrobial use in food animals have been implemented in different countries. We investigated the impact of an antimicrobial restriction intervention during two generations of pigs. Fecal samples were collected in five growth phases. The frequency of antimicrobial-resistant coliforms and antimicrobial-resistant bacteria or antimicrobial resistance genes was analyzed. No differences in the richness or abundance of antimicrobial-resistant coliforms or antimicrobial resistance genes were found when animals fed with or without prophylactic antimicrobials were compared. Withholding antimicrobial supplementation did not negatively affect weight gain in pigs. Withdrawal of prophylactic antimicrobial consumption during two generations of pigs was not enough to reduce the prevalence of antimicrobial resistance genes, as measured by richness and abundance markers. This study indicates that the fitness costs associated with bacterial carriage of some antimicrobial resistance genes are low.

Antibiotic Resistance in Escherichia coli from Broiler Chickens After Amoxicillin Treatment in an Experimental Environment

Groupwise antibiotic treatments are common in broiler chicken production. They induce selection for antibiotic resistance in commensal Escherichia coli. This study aimed to investigate antibiotic resistance after individual (I, drenching) or groupwise treatment (G, by water) with amoxicillin, and after contact with I or G (KI or KG), compared with untreated broilers without contact with treated broilers (C), and pretreatment values. Finally, we compared antibiotic resistance from broilers (G) after a second treatment, with a treatment in the contact animals (KG), and a first treatment in the control animals (C). Resistance to ampicillin and other antibiotics was significantly increased in groups G and I within 2 days, suggesting (co-)selection of resistance. The increase was lower in groups KI, KG, and C during the first treatment (days 1-5). The increased resistance in group C was interpreted as a change in the microbiota after initial moving and first feeding. After treatment, resistance rates decreased to initial or lower values in all groups. During the second treatment period (days 34-38), all three groups' (G, KG, and C) resistance levels increased to equally high levels. Cephalosporin resistance was low, and did not change over the experimental period. On days 3 and 38, resistance rates of E. coli from duodenum, jejunum, and cecum did not differ between segments and treatment routes. Overall, the baseline levels of antibiotic resistance in E. coli were high. Amoxicillin triggered an increase in resistance levels, irrespective of the mode of treatment. Substantial resistance dynamics in untreated controls warrant further investigation.

Antimicrobial use, biosecurity, herd characteristics, and antimicrobial resistance in indicator Escherichia coli in ten Finnish pig farms

We investigated connections between antimicrobial use (AMU), biosecurity, and the numbers of pigs and staff in ten Finnish farrow-to-finish herds. Data on AMU in each herd were collected for 12 months. AMU was quantified as treatment incidences per 1000 days at risk (TI) using the consensus defined daily dose calculation. Biosecurity was scored using the Biocheck.UGent™ system. We also examined antimicrobial resistance patterns of indicator E. coli isolated from faeces of selected pigs. In each herd, two groups of five pigs were formed: 1) antimicrobial treatment group (ANT: at least one pig in the litter was identified as sick and treated with antimicrobials) and 2) non-antimicrobial treatment group (NON: the litter was not medicated). Faecal samples were taken from these pigs at 5 and 22 weeks of age, cultured, and indicator E. coli isolates were tested for antimicrobial susceptibilities. The AMU varied considerably between the herds. Altogether, most of the antimicrobial treatment courses were assigned to weaned piglets. When AMU was quantified as TIs, suckling piglets had the highest TI (mean 46.6), which was significantly higher (P < 0.05) than TIs in fatteners and breeders (9.3 and 7.3, respectively). The difference between TI in suckling and TI in weaned piglets (19.1) was not statistically significant. There was a tendency for a negative correlation between the TI in breeders and the number of sows (r = -0.56, P = 0.09). Larger herds had higher external biosecurity scores than smaller herds (LS-means; 72 vs. 66, P < 0.05). The proportions of E. coli isolates resistant to at least one antimicrobial were higher in pigs at 5 weeks than in pigs at 22 weeks of age (Binomial proportion means; 40.5 % vs. 15.5 %, P < 0.05); as well as proportions of isolates resistant to at least three antimicrobial classes (23.0 % vs. 3.7 %, P < 0.01). These proportions did not differ between the ANT and NON groups at either 5 or 22 weeks of age (P> 0.05). We found few connections: enhanced external biosecurity levels found in the large herds co-occurred with lower use of antimicrobials and herds with low biosecurity scores - especially in the internal subcategories - appeared to have higher proportions of resistant isolates. Conclusively, we suggest that enhancing internal biosecurity might contribute to a reduction in the spreading of antimicrobial resistance in pig herds.

Geographic Drivers of Antimicrobial Use and Resistance in Pigs in Khon Kaen Province, Thailand

In Thailand, pig production has increased considerably in the last decades to meet a growing demand for pork. Antimicrobials are used routinely in intensive pig production to treat infections and increase productivity. However, the use of antimicrobials also contributes to the rise of antimicrobial resistance with potential consequences for animal and human health. Here, we quantify the association between antimicrobial use and resistance rates in extensive and intensive farms with a focus on geographic proximity between farm and drugstores. Of the 164 enrolled farms, 79% reported using antimicrobials for disease prevention, treatment, or as a feed additive. Antimicrobial-resistant E. coli were present in 63% of farms. These drugs included critically important antimicrobials, such as quinolones and penicillins. Medium-scale farms with intensive animal production practices showed higher resistance rates than small-scale farms with extensive practices. Farms with drug-resistant Escherichia coli were located closer to drugstores and a had a higher proportion of disease than farms without drug-resistant E. coli. We found no association between the presence of resistance in humans and antimicrobial use in pigs. Our findings call for actions to improve herd health to reduce the need for antimicrobials and systematic training of veterinarians and drugstore owners on judicious use of antimicrobials in animals to mitigate resistance.

Risk factors associated with faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli among dogs in Southeast Brazil

Faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R E. coli) in dogs has been reported worldwide and can reduce the effectiveness of treatments against bacterial infections. However, the drivers that influence faecal carriage of ESC-R E. coli in dogs are poorly understood. The aims of this study were to estimate the prevalence of ESC-R E. coli among dogs prior to their admission to a veterinary teaching hospital and to identify risk factors associated with the faecal carriage of ESC-R E. coli. Rectal swabs (n = 130) were collected from dogs and screened for ESC-R E. coli using MacConkey agar supplemented with cefotaxime (2 μg/mL). E. coli species was confirmed by MALDI-TOF and screening of extended-spectrum beta-lactamase (ESBL) genes was conducted by multiplex PCR. Questionnaires were completed by each dog's owner to test several human and dog characteristics associated with ESC-R E. coli. The prevalence of faecal carriage of ESC-R E. coli was 9.2 % and 67 % of ESC-R E. coli isolates harboured ESBL genes including CTX-M alone or in combination with TEM. All ESC-R E. coli isolates were resistant to ceftriaxone, cefpodoxime, and cefotaxime and were susceptible to cefoxitin and carbapenems. The likelihood of carrying ESC-R E. coli was 15 times higher (OR = 14.41 [95 % CI: 1.80-38.02], p < 0.01) if the dog was treated with antibiotics 3-12 months prior to sampling and 8 times higher (OR = 7.96 [95 % CI: 2.96-92.07], p < 0.01) if the dog had direct contact with livestock, but 15 times lower (OR = 0.07 [95 % CI: 0.01-0.32], p < 0.01) if the dog was dewormed during the previous year. Our findings confirm the faecal carriage of ESC-R E. coli in subclinical dogs and call for further investigation regarding the impact of deworming on antibiotic-resistant bacteria in companion animals.

From Farm-to-Fork: E. Coli from an Intensive Pig Production System in South Africa Shows High Resistance to Critically Important Antibiotics for Human and Animal Use

Antibiotic resistance profiles of Escherichia coli were investigated in an intensive pig production system in the uMgungundlovu District, South Africa, using the 'farm-to-fork' approach. Four hundred seventeen (417) samples were collected from pig and pig products at different points (farm, transport, and abattoir). E. coli was isolated and enumerated using the Colilert^® 18/Quanti-Tray^® 2000 system. Ten isolates from each Quanti-tray were selected randomly and putatively identified on eosin methylene blue agar. Real-time PCR targeting the uidA gene was used to confirm isolates to the genus level. The Kirby-Bauer disc diffusion method was used to determine the isolates' antibiotic susceptibility profiles against 20 antibiotics. A total of 1044 confirmed E. coli isolates were obtained across the three critical points in the food chain. Resistance was observed to all the antibiotics tested with the highest and lowest rates obtained against tetracycline (88.5%) and meropenem (0.2%), respectively. Resistance was also observed to chloramphenicol (71.4%), ampicillin (71.1%), trimethoprim-sulfamethoxazole (61.3%), amoxicillin-clavulanate (43.8%), cephalexin (34.3%), azithromycin (23.9%), nalidixic acid (22.1%), cefoxitin (21.1%), ceftriaxone (18.9%), ciprofloxacin (17.3%), cefotaxime (16.9%), gentamicin (15.5%), cefepime (13.8%), ceftazidime (9.8%), amikacin (3.4%), piperacillin-tazobactam (1.2%), tigecycline (0.9%), and imipenem (0.3%). Multidrug resistance (MDR) was observed in 71.2% of the resistant isolates with an overall multiple antibiotic resistance (MAR) index of 0.25, indicating exposure to high antibiotic use environments at the farm level. A high percentage of resistance was observed to growth promoters and antibiotics approved for veterinary medicine in South Africa. Of concern was resistance to critically important antibiotics for animal and human use and the watch and reserve categories of antibiotics. This could have adverse animal and human health consequences from a food safety perspective, necessitating efficient antibiotic stewardship and guidelines to streamline antibiotic use in the food-animal production chain.

Higher Prevalence of Extended-Spectrum Cephalosporin-Resistant Enterobacterales in Dogs Attended for Enteric Viruses in Brazil Before and After Treatment with Cephalosporins

The extensive use of antibiotics is a leading cause for the emergence and spread of antimicrobial resistance (AMR) among dogs. However, the impact of using antibiotics to treat viral infections on AMR remains unknown. In this study, we compared the prevalence of extended-spectrum cephalosporin-resistant Enterobacterales (ESCR-E) between dogs with a suspected infection of canine parvovirus (CPV) and canine distemper (CDV) before and after treatment with third-generation cephalosporins. We found a higher prevalence of ESCR-E faecal carriage in dogs suspected of CPV (37%) and CDV (15%) compared to dogs with noninfectious pathologies (9%) even prior to the start of their treatment. A 7-day course of ceftriaxone or ceftiofur administrated to CPV and CDV-suspected dogs substantially increased their ESCR-E faecal carriage during treatment (85% for CPV and 57% for CDV), and 4 weeks after the treatment ended (89% for CPV and 60% for CDV) when dogs were back in their households. Most of the observed resistance was carried by ESCR-E. coli carrying bla_CTX-M genes. Our results suggest the need to optimize prophylactic antibiotic therapy in dogs treated for a suspected viral infection to prevent ESCR-E emergence and spread in the community.

Rational use of antibiotics for treatment of urinary infection in sows

Abstract The endemic character of urinary infections (UI) in sows makes collective antimicrobial therapies via feed a routine. This, however, generates sub-doses unable to heal and contribute to the selection of antibiotic-resistant bacteria. The use of individual therapy is the most appropriate procedure to be performed on animals with UI. With this study, we aimed to evaluate the occurrence of UI in sows housed in the western region of Paraná and the efficacy and cost-benefit of individual treatment. A total of 353 females were selected from five different herds, submitted to urine collection in the final third of pregnancy by spontaneous urination method. The samples were analyzed physically and chemically with the use of reagent strips, and the presence of nitrite was a determinant for positivity for UI. The animals with UI had urine submitted to a bacteriological evaluation, were treated with parenteral medication (marbofloxacin - single dose - 8 mg/kg), and submitted to a new urine collection 24h and 48h after the first. UI was observed in 4.53% of the females evaluated (16/353). Escherichia coli and Streptococcus sp. were the most frequently isolated agents. Seven days after the use of marbofloxacin 87.5% (14/16) of the animals were negative for UI, which demonstrates the efficacy of UI parenteral control. The diagnosis associated with individual therapy at the expense of collective medication was highly cost-effective, made it possible to drastically reduce the number of medicated animals, and was efficient in controlling UI. Thus, it is concluded that it is possible to make rational use of antibiotics by treating only sows that are proven to be positive for UI. This reduces the number of unnecessarily medicated animals and reduces the cost due to the use of antimicrobials only in sick animals.

Stability, Homogeneity and Carry-Over of Amoxicillin, Doxycycline, Florfenicol and Flubendazole in Medicated Feed and Drinking Water on 24 Pig Farms

The vast majority of medicines in pig rearing are administered via oral group medication through medicated feed and drinking water. However, relevant on-farm factors affecting the concentration of these drugs in feed and drinking water, such as the homogeneity, stability, and cross-contamination, are largely unknown. To characterize these factors, samples of medicated feed and drinking water were taken on 24 Belgian pig farms during treatment and 2 days thereafter, as well as at different on-farm sampling sites from production to feeding troughs or drinking nipples. The samples contained amoxicillin, doxycycline, florfenicol, or flubendazole. Additionally, a questionnaire was completed. In contrast to the results of medicated feed, results of medicated water showed a large between-farm variation in antimicrobial drug concentration. The therapeutic concentration range was only met in 2 out of 11 farms using medicated feed, and in 3 out of 13 farms using medicated water. Medicated feed concentrations were often below the therapeutic concentration range mentioned in the Summary of Product Characteristics, while drinking water concentrations were just as often above as they were below the advised target concentration range. Drug residues measured 2 days after the end of therapy with both feed and water medication rarely exceeded 1% of the lowest therapeutic concentration. This study demonstrates that recommendations on good clinical practices for oral group medication in the pig industry are highly needed.

Veterinary drug administration in German veal calves: An exploratory study on retrospective data

The aim of this cross-sectional study was to characterise the usage of antibiotic and non-antibiotic drugs with a withdrawal period in German veal calves in more detail. In Germany, the documentation of the usage of veterinary medicinal products in food producing animals is mandatory. In the German monitoring system antibiotic use in calves under the age of eight months is recorded irrespective of the production type and only some basic measures (50 % and 75 % percentiles of the entire distributions of the treatment frequencies) are published regularly. Within this study 57 farms were included contributing data of 169 veal calf groups with a total of 91,196 individual calves. To assess the drug use the treatment frequency (TF) was calculated. Most treatments were applied in the first weeks after arrival at the farm against respiratory and gastrointestinal disorders, accounting for 65.2 % and 28.6 % of the TF, respectively. Antibiotics account for 91 % of the TF. The antibiotics used most frequently were tetracyclines (35.6 %), beta-lactams (21.9 %), macrolides (12.7 %), sulphonamides (6.0 %) and trimethoprimes (5.3 %). Tetracyclines and polypeptides were administered as group treatments in more than half of the recorded applications. The number of antibiotic group treatments decreased considerably from the first to the second half of the fattening period. Logistic regression analyses revealed no statistically significant association between TF and groups size or mortality. Nevertheless, the results indicate a negative associated between TF and mortality. Concerning non-antibiotics mainly iron compounds, arylpropionic acids, mucolytics and avermectines were applied, accounting for about 5 % of the total TF. The present study provides basic data on antibiotic and non-antibiotic use in German veal calf production.

The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review

Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.

Isolates, Antimicrobial Susceptibility Profiles and Multidrug Resistance of Bacteria Cultured from Pig Submissions in New Zealand

Data on the scope of bacterial pathogens present and the frequency of antimicrobial resistance (AMR) in New Zealand's pigs are limited. This study describes bacterial isolates, antimicrobial susceptibility data, and multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) from New Zealand pig submissions. Porcine test data from June 2003 to February 2016 were obtained from commercial veterinary pathology laboratory records. In total, 470/477 unique submissions resulted in bacterial growth, yielding 779 isolates. Sample type was recorded for 360/477 (75.5%); lung (79/360; 21.9%), faecal (61/360; 16.9%) and intestinal (45/360; 12.5%) were most common. The most common isolates were Escherichia coli (186/779, 23.9%), Actinobacillus pleuropneumoniae (43/779; 5.5%), Streptococcus suis (43/779; 5.5%), unidentified Campylobacter spp. (38/779; 4.9%), alpha haemolytic Streptococci (32/779; 4.1%), coagulase negative Staphylococcus spp. (26/779; 3.3%), and Pasteurella multocida (25/779; 3.2%). Susceptibility results were available for 141/779 (18.1%) isolates from 62/470 (13.2%) submissions. Most were susceptible to trimethoprim-sulphonamide (75/81; 92.6%), but fewer were susceptible to penicillin (37/77; 48.1%), tilmicosin (18/43; 41.9%), or tetracyclines (41/114; 36.0%). No susceptibility data were available for Salmonella spp., Campylobacter spp., or Yersinia spp. isolates. MDR was present in 60/141 (42.6%) isolates. More data on sample submission drivers, antimicrobial drug use, and susceptibilities of important porcine bacterial isolates are required to inform guidelines for prudent antimicrobial use, to reduce their prevalence, human transmission, and to minimise AMR and MDR.

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

Antibiotic resistance genes (ARGs) including those from the bla_CTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.

Quantitative and qualitative analysis of antimicrobial usage patterns in 180 selected farrow-to-finish pig farms from nine European countries based on single batch and purchase data

OBJECTIVES

Farm-level quantification of antimicrobial usage (AMU) in pig farms.

METHODS

In a cross-sectional study, AMU data on group treatments administered to a single batch of fattening pigs from birth to slaughter (group treatment data) and antimicrobials purchased during 1 year (purchase data) were collected at 180 pig farms in nine European countries. AMU was quantified using treatment incidence (TI) based on defined (DDDvet) and used (UDDvet) daily doses and defined (DCDvet) and used (UCDvet) course doses.

RESULTS

The majority of antimicrobial group treatments were administered to weaners (69.5% of total TIDDDvet) followed by sucklers (22.5% of total TIDDDvet). AMU varied considerably between farms with a median TIDDDvet of 9.2 and 7.1 for a standardized rearing period of 200 days based on group treatment and purchase data, respectively. In general, UDDvet and UCDvet were higher than DDDvet and DCDvet, respectively, suggesting that either the defined doses were set too low or that group treatments were often dosed too high and/or administered for too long. Extended-spectrum penicillins (31.2%) and polymyxins (24.7%) were the active substances most often used in group treatments, with the majority administered through feed or water (82%). Higher AMU at a young age was associated with higher use in older pigs.

CONCLUSIONS

Collecting farm-level AMU data of good quality is challenging and results differ based on how data are collected (group treatment data versus purchase data) and reported (defined versus used daily and course doses).

Effect of Probiotics and Herbal Products on Intestinal Histomorphological and Immunological Development in Piglets

The aim of the study was to evaluate the effect of probiotics and herbal products on the intestinal histomorphological and immunological development in piglets. Accordingly, 2-week-old piglets were allocated in 4 groups: C (basal diet), Pro (basal diet + probiotics), Pro+B (basal diet + probiotics + buckwheat bran), and H (powder of herbs). After 6 weeks of the experiment, 4 piglets from each experimental group were randomly selected and slaughtered at a slaughterhouse. Samples of tissue and digestive content from the jejunum and colon were collected for bacteriological, histological, and immunohistochemical examination. The results showed that probiotics increased the number of Lactobacillus spp. in the small (p < 0.05) and large intestines. The intestinal histomorphology was improved (p < 0.05) in all experimental groups by an increased villus height, VH : CD ration, colon crypt depth, and number of Ki-67⁺ epithelial cells. A higher number (p < 0.05) of goblet cells and their acidification were observed in group Pro, while the density of goblet cells was decreased by the herbs. Probiotics increased (p < 0.05) the number of intraepithelial lymphocytes (IELs), density of CD3⁺ cells in Peyer's patches (PPs), and lamina propria (LP). In group H, a dual effect on the CD3⁺ cell distribution was observed. The herbs reduced (p < 0.05) the number of IELs and CD3⁺ in LP but increased the distribution of CD3⁺ cells in PPs. In the colon, herbs increased CD3⁺ cells in LP as well. It suggests that probiotics and herbs had influence on the intestinal histomorphology and the ability to modulate the mucosal immune system; however, the combination of probiotics and buckwheat bran was not so convincing, probably due to the inhibitory effect of the buckwheat bran on the probiotics used.

Antimicrobial Resistance Profiles and Characterization of Escherichia coli Strains from Cases of Neonatal Diarrhea in Spanish Pig Farms

Escherichia coli is considered one of the most common agents associated with neonatal diarrhea in piglets. The aim of this work was to characterize the pathogenic and antimicrobial resistance (AMR) profiles of 122 E. coli strains isolated from pigs suffering diarrhea (n = 94) and pigs without diarrhea (n = 28) of 24 farms in Spain. Virulence factors, toxins and AMR (ESBL and colistin) genes and AMR phenotypes of E. coli isolates were analyzed. Low prevalence of pathogenic E. coli strains (26%) was found in both groups. However, ETEC and VTEC strains were more frequently isolated from diarrheic piglets. Irrespectively of diarrhea occurrence, 97.5% of the strains showed a multidrug-resistance (MDR) profile to aminopenicillins, sulfonamides and tetracyclines. It was found that 22% of E. coli was CTX-M+, with CTX-M-14 being the principal allelic variant. Remarkably, 81.5% of CTX-M+ strains were isolated from diarrheic animals and presented an extended MDR profile to aminopenicillins, quinolones and aminoglycosides. Finally, low frequencies of colistin resistance genes mcr-1 (4/122) and mcr-4 (1/122) were found. MDR E. coli strains are circulating in pig farms of Spain, representing a serious threat to animal and public health. More appropriate diagnostic approaches (genetic and AMR phenotypic analysis) should be implemented in animal health to optimize antibiotic treatments.

Antibiotic resistance and virulence patterns of pathogenic Escherichia coli strains associated with acute gastroenteritis among children in Qatar

Background

The treatment of Enterobacteriaceae family including diarrheagenic E. coli (DEC) has been increasingly complicated due to the emergence of resistant strains. Here we report on the phenotypic resistance profiles and ESBL genotype and virulence profiles of Enteroaggregative E. coli (EAEC) and Enteropathogenic E. coli (EPEC) isolated from children hospitalized with acute gastroenteritis in Qatar (AGE).

Results

E. coli were isolated and characterized from 76 diarrheagenic stool positive samples, collected from hospitalized children less than 10 years old. Isolates were tested for antibiotic susceptibility against eighteen clinically relevant antibiotics using E-test method. Conventional PCR was performed to detect genes encoding ESBL and virulence factors. Chi-square test was performed to compare the individual antibiotic resistance between EPEC and EAEC.

A significant percentage (73.7%) of isolates were resistant to at least one antibiotic. Overall, high resistance (70%) was reported to the first-line antibiotics such as ampicillin, tetracycline (46.4%), and sulfamethoxazole-trimethoprim (42.9%). Further, 39.5% of the isolates were multidrug resistant (MDR), with 22.4% being ESBL producers. On the other hand, all isolates were susceptible to carbapenem, fosfomycin, amikacin and colistin. The incidences of resistance to the 18 antibiotics between EPEC and EAEC were not significantly different by Pearson chi -square test (P > 0.05). Genetic analysis revealed that 88.23% of ESBL production was bla_CTX-M-G1 (bla_CTX-M-15, bla_CTX-M-3) - encoded. Several different combinations of virulence markers were observed, however, there was no specific trend among the isolates apart from absence of the bundle-forming pilus (bfpA) gene, which encodes the type IV fimbriae in EPEC adherence factor (EAF) plasmid (pEAF), among all EPEC (atypical). 15% of the EAEC strains were positive for a combination of astA, aap & capU, while 10% were positive for three different combinations. The aap, aatA, capU and aggR virulence genes showed the highest frequency of 65, 60, 55 and 55% respectively. Others genes, east, astA, and aai, showed frequencies of 35, 30 and 20% respectively.

Conclusions

Atypical EPEC and EAEC were the primary etiological agents of diarrhea in children among DEC pathotypes. Our results indicated high rate of antimicrobial resistance pattern of DEC strains, which necessities the development of regulatory programs and reporting systems of antimicrobial resistance in DEC and other AGE-associated bacteria to insure effective control of diarrheal diseases. Results from this study demand a further research on identifying the phenotypic and genotypic profiles of more DEC pathotypes in various clinical samples.

Antimicrobial Usage and Resistance in Companion Animals: A Cross-Sectional Study in Three European Countries

Companion animals have been described as potential reservoirs of antimicrobial resistance (AMR), however data remain scarce. Therefore, the objectives were to describe antimicrobial usage (AMU) in dogs and cats in three European countries (Belgium, Italy, and The Netherlands) and to investigate phenotypic AMR. A questionnaire and one fecal sample per animal (n = 303) were collected over one year and AMU was quantified using treatment incidence (TI). Phenotypic resistance profiles of 282 Escherichia coli isolates were determined. Nineteen percent of the animals received at least one antimicrobial treatment six months preceding sampling. On average, cats and dogs were treated with a standard daily dose of antimicrobials for 1.8 and 3.3 days over one year, respectively. The most frequently used antimicrobial was amoxicillin-clavulanate (27%). Broad-spectrum antimicrobials and critically important antimicrobials for human medicine represented 83% and 71% of the total number of treatments, respectively. Resistance of E. coli to at least one antimicrobial agent was found in 27% of the isolates. The most common resistance was to ampicillin (18%). Thirteen percent was identified as multidrug resistant isolates. No association between AMU and AMR was found in the investigated samples. The issue to address, regarding AMU in companion animal, lies within the quality of use, not the quantity. Especially from a One-Health perspective, companion animals might be a source of transmission of resistance genes and/or resistant bacteria to humans.

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.

Phenotypic antimicrobial resistance in Escherichia coli strains isolated from swine husbandries in North Western Germany - temporal patterns in samples from laboratory practice from 2006 to 2017

Background

Since 2011, antibiotic usage has decreased continuously in livestock in Germany. Whether this is accompanied by a reduction in bacterial antimicrobial resistance has not been proven so far. In this study 3054 Escherichia coli (E. coli) isolates from pigs which had suffered from disease on 2161 farms in North Western Germany were evaluated retrospectively from 2006 to 2017 for trends in their antimicrobial resistance pattern. Data were substantially related to the “pre-reduction period” and were therefore suggested as a basis for this task.

Minimal inhibitory concentrations for selected antimicrobial substances were evaluated for E. coli strains isolated from different organs of diseased swine sampled for routine diagnostic. In total, 81% of E. coli were isolated from faeces or the gastrointestinal tract, 11% from the genito-urinary tract and 8% from other organs. Susceptibility testing and classification of isolates in accordance with clinical cut-offs followed the Clinical and Laboratory Standards Institute (CLSI). If no clinical cut-offs were available for the respective combination of species, substance and organ, other published clinical cut-offs were used.

Results

Differences in susceptibility patterns between isolates from the gastrointestinal and genito-urinary tract were found for most substances. Isolates from the genito-urinary tract were less frequently resistant to ampicillin, apramycin, colistin, neomycin, spectinomycin and tetracycline and more frequently resistant to enrofloxacin and florfenicol.

A multifactorial logistic regression model revealed time-dependent decreases in frequency of resistant isolates for neomycin, spectinomycin and tetracycline. For colistin, the highest percentage of resistant isolates with 16.0% was found in 2015 followed by a decrease to the level of 2009–2010 in 2017. A decrease in frequencies of ampicillin-resistant isolates was dependent on the age-group and time period. Irrespective of the year, less than 15% E. coli isolates were resistant to apramycin, cephalosporins, colistin, enrofloxacin, florfenicol, gentamicin and neomycin.

Conclusion

An overall time-dependent decrease in the percentage of resistant E. coli isolates was found for some substances. These data from diseased animals indicate an impact of a general reduction in antibiotic usage on development of bacterial antimicrobial resistance in the field and can support the decision-making of swine practitioners for treatment options in swine.

Effect of tetracycline treatment regimens on antibiotic resistance gene selection over time in nursery pigs

Background

The majority of antimicrobials given during the production of pigs are given to nursery pigs. The influence of antimicrobial use on the levels of antimicrobial resistant (AMR) genes is important to quantify to be able to assess the impact of resistance on the food chain and risk to human and animal health.

Results

This study investigated the response on the levels of nine AMR genes to five different treatment strategies with oxytetracycline, and the dynamics of gene abundance over time by following 1167 pigs from five different farms in Denmark.

The results showed no significant difference between treatments and an increase in abundance for the efflux pump encoding tet(A) gene and the genes encoding the ribosomal protection proteins tet(O) and tet(W) tetracycline resistant genes following treatment, while tet(M) showed no response to treatment. However, it was also observed that the levels of tet(O), tet(W), and ermB in some farms would drift more over time compared to a single treatment-course with antibiotic.

Conclusion

This study underlines the large variation in AMR levels under natural conditions and the need for increased investigation of the complex interactions of antimicrobial treatment and other environmental and managerial practices in swine production on AMR gene abundance.

Antimicrobial usage in pig production: Effects on Escherichia coli virulence profiles and antimicrobial resistance

Antimicrobials (AM) are used for growth promotion and therapy in pig production. Its misuse has led to the development of resistant organisms. We evaluated Escherichia coli virulence genes, and compared phenotypic-genotypic antimicrobial resistance (AMR) patterns of faecal E. coli from pigs receiving routine farm treatment without antimicrobial agents against pigs treated routinely with AM over 70 days. Recovered E. coli were tested for AMR using disk diffusion and polymerase chain reaction. Virulence genes were detected in 24.8% of isolates from antimicrobial group and 43.5% from non-antimicrobial group (p = 0.002). The proportion of virulence genes heat-stable enterotoxins a b (STa, STb), enteroaggregative heat stable enterotoxin 1 [EAST1] and Shiga toxin type 2e [Stx2e]) were 18.1%, 0.0%, 78.7% and 3.0% for antimicrobial group and 14.8%, 8.5%, 85.1% and 12.7% for non-antimicrobial groups, respectively. Resistance to oxytetracycline was most common (p = 0.03) in samples collected between days 10 and 21. Resistance shifted to amoxicillin on days 56-70, and trimethoprim resistance was observed throughout. Seventeen phenotypic AMR combinations were observed and eight were multidrug resistant. At least one tetracycline resistance gene was found in 63.9% of the isolates. tet (A) (23.3%) was most common in the antimicrobial group, whereas tet (B) (43.5%) was prevalent in the non-antimicrobial group. Usage or non-usage of antimicrobial agents in growing pigs does not preclude virulence genes development and other complex factors may be involved as previously described. Heavily used AM correspond to the degree of resistance and tetracycline resistance genes were detected during the growth phase.

Prevalence of antibiotic-resistant E. coli in broilers challenged with a multi-resistant E. coli strain and received ampicillin, an organic acid-based feed additive or a synbiotic preparation

The aim of this study was to evaluate the effect of ampicillin, an organic acid-based feed additive and a synbiotic preparation on the prevalence of antibiotic-resistant E. coli in the ceca of broilers. A total of 2000 broiler chickens (Ross 708) were randomly assigned to 5 groups with 8 replicates. The negative control group was the only group that was not subjected to avian pathogenic E. coli challenge, while all the other 4 groups received a multi-resistant E. coli strain that was resistant to ampicillin, cephalexin, and nalidixic acid as an oral challenge. The second group served as a challenge control, and the third group received the antibiotic ampicillin via water for 5 d. The fourth group received a feed additive based on organic acids and cinnamaldehyde, and the fifth group received a synbiotic preparation via feed and water. On day 17 and 38 of the trial, cecal samples from 3 birds from each of the 40 pens were obtained, and the E. coli counts and abundances of antibiotic-resistant E. coli were determined. Oral challenge with an avian pathogenic E. coli strain did not influence the performance, and there was no significant difference in growth performance between groups. The total E. coli count was lower (P < 0.05) in the group supplemented with the synbiotic than in the challenge control group on day 38 of the trial. Administration of an antibiotic for 5 d led to a significant increase in the abundance of E. coli strains resistant to ampicillin, amoxicillin-clavulanic acid, cefoxitin, and ceftriaxone. There was no increase in the abundance of antibiotic-resistant E. coli observed in the groups that received feed supplemented with an organic acid/cinnamaldehyde-based feed additive or a synbiotic. Moreover, the effects of the tested feed additives on the prevalence of resistant E. coli are demonstrated by the lower ceftriaxone minimal inhibitory concentration values for this group than for the antibiotic group. Additionally, the synbiotic group exhibited lower ceftriaxone minimal inhibitory concentration values than the antibiotic group.

[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.

Resistance and Virulence Mechanisms of Escherichia coli Selected by Enrofloxacin in Chicken

This study aimed to investigate the genetic characteristics, antibiotic resistance patterns, and novel mechanisms involved in fluoroquinolone (FQ) resistance in commensal Escherichia coli isolates. The E. coli isolates were recovered from a previous clinical study and subjected to antimicrobial susceptibility testing and molecular typing. Known mechanisms of FQ resistance (target site mutations, plasmid-mediated quinolone resistance [PMQR] genes, relative expression levels of efflux pumps and porins) were detected using DNA sequencing of PCR products and real-time quantitative PCR. Whole-genome shotgun sequencing was performed on 11 representative strains to screen for single nucleotide polymorphisms (SNPs). The function of a key SNP (A1541G) was investigated by site-directed mutagenesis and allelic exchange. The results showed that long-term enrofloxacin treatment selected multidrug-resistant (MDR) E. coli isolates in the chicken gut and that these E. coli isolates had diverse genetic backgrounds. Multiple genetic alterations, including double mutations on GyrA (S83L and D87N), a single mutation on ParC (S80I) and ParE (S458E), activation of efflux pumps, and the presence of the QnrS1 protein, contributed to the high-level FQ resistance (enrofloxacin MIC [MIC_ENR] ≥ 128 μg/ml), while the relatively low-level FQ resistance (MIC_ENR = 8 or 16 μg/ml) was commonly mediated by decreased expression of the porin OmpF, besides enhancement of the efflux pumps. No significant relationship was observed between resistance mechanisms and virulence genes. Introduction of the A1541G mutation on aegA was able to increase FQ susceptibility by 2-fold. This study contributes to a better understanding of the development of MDR and the differences underlying the mechanisms of high-level and low-level FQ resistance in E. coli.

Characterization of antimicrobial prescription frequency and diversity in a large animal veterinary medical teaching hospital

Antimicrobials are commonly used in veterinary medicine for therapeutic and prophylactic purposes, but little is known about the frequency with which they are prescribed or the quantity administered, especially in large animals. Furthermore, there are no standardized metrics for characterizing antimicrobial use, which can lead to confusion when comparing antimicrobial use among different units (institution, clinical service, clinician). Because there is no gold standard metric, the most comprehensive characterization of antimicrobial use will be achieved using a variety of metrics. The goal of this study was to characterize antimicrobial use from 2013 to 2018 at a tertiary care teaching hospital for large animals using different metrics, including novel ones. We found that at least one antimicrobial was prescribed in 42% of visits and that antimicrobials were prescribed at a rate of 919 animal-defined daily doses (ADDs) per 1000 animal days. A median of 3.6 ADDs and a mean of 2 different classes of antimicrobial were prescribed per patient, and penicillin was the most commonly used antimicrobial. The prescription diversity, a metric accounting for richness and evenness (similarity of frequencies) of different types of antimicrobials, was 0.82, with 1.0 representing maximal richness and diversity. Antimicrobial use differed significantly by species and by organ system affected for all metrics, though in general antimicrobials were prescribed most frequently and with the largest amounts in animals presenting with integumentary or respiratory signs. Many of our findings were consistent with those of other studies examining antimicrobial use in the species represented in our patient population, but more research is needed to determine how to best characterize antimicrobial use and assess appropriateness of prescribing.

Nanoemulsion-loaded hydrogel coatings for inhibition of bacterial virulence and biofilm formation on solid surfaces

The indiscriminate use of antibiotics has led to the emergence of drug-resistant bacteria which has become one of the biggest challenges of the twenty-first century for the researchers to combat and in turn search for novel targets which could lead to the development of effective and sustainable therapies. Inhibition of biofilm formation and virulence of bacterial pathogens is an emerging approach to address the challenges related to bacterial infections. To suppress the virulence and biofilm formation by Escherichia coli O157:H7 (ECOH), we developed stable nanoemulsion (NE) of Gaultheria fragrantissima Wall. essential oil’s (EO) bioactive compounds, viz., eugenol (E-NE) and methyl salicylate (MS-NE) that showed significantly higher anti-biofilm and anti-virulence activities as compared to eugenol and methyl salicylate without affecting ECOH planktonic cell growth. Transcriptional analysis showed that E-NE and MS-NE reduced the expression of genes, including curli, type I fimbriae, Shiga-like toxins, quorum sensing, and ler-controlled toxins, which are needed for biofilm formation, pathogenicity, and attachment. E-NE and MS-NE loaded hydrogel coatings showed superior anti-biofilm activity against ECOH on glass, plastic and meat surfaces as compared to eugenol and methyl salicylate loaded coatings. Conclusively, NE-loaded hydrogel coatings could be used in combating ECOH infection on solid surfaces through anti-biofilm and anti-virulence strategies.

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments

Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.

Placebo-controlled study on the effects of oral administration of Allium sativum L in postweaning piglets

Postweaning diarrhoea (PWD) due to Escherichia coli is an economically important disease in pig production. In this placebo-controlled study performed in Switzerland, the effects of oral supplementation of Allium sativum L. (garlic, AS) on performance (bodyweight (BW) and daily weight gain (DWG)) and health (body condition and clinical score) were investigated in postweaning piglets. Piglets (n=600) were randomly assigned to the treatment groups (placebo, AS or colistin) and observed from birth until three weeks postweaning. The treatments were administered for the first two weeks postweaning. Faecal dry matter (FDM) and coliform bacteria on pen level were measured weekly. Data were analysed using generalised mixed-effect models in R. BW and DWG of the AS group were significantly higher compared with placebo in the third week postweaning. No differences in body condition and FDM were observed. The clinical score of AS-treated animals was significantly better compared with the colistin group. About 33 per cent of the piglets of the AS and the placebo group had to be treated with antibiotics due to the occurrence of severe PWD. The major finding of this study showed that AS supplementation increased growth performance and improved clinical health, but did not reduce the incidence and severity of PWD.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Antimicrobial resistance of Escherichia coli and Enterococcus spp. isolated from Estonian cattle and swine from 2010 to 2015

BACKGROUND

The prevalence of resistant Escherichia coli and Enterococcus spp. in food-producing animals has increased worldwide. The objective of the study was to investigate the occurrence of antimicrobial resistance of Escherichia coli, Enterococcus faecium and Enterococcus faecalis isolated from healthy and diseased swine and cattle in Estonia. Clinical specimen and faecal samples were collected during 2010 to 2015. The in vitro antimicrobial susceptibility was determined using the microdilution method.

RESULTS

The most prevalent resistance of E. coli isolates from clinically healthy swine was observed against streptomycin (39.2%), tetracycline (32.5%) and sulfamethoxazole (30.0%), whereas in clinically healthy cattle, the resistance was the highest against aminoglycosides (7.0-8.8%) and tetracycline (7.0%). The E. coli isolates from clinically healthy swine showed significantly higher multidrug-resistance compared to isolates originated from clinically healthy cattle. E. coli isolates from diseased swine showed highest resistance to sulfamethoxazole (68.6%), tetracycline (60.2%) and streptomycin (54.6%). The proportion of resistant E. coli isolates from diseased cattle (clinical submissions) was highest to streptomycin (63.5%), sulfamethoxazole (60.3%) and tetracycline (58.8%). The proportion of multidrug-resistant isolates did not differ significantly between animal species. Among E. coli isolates, four strains representing AmpC phenotypes were found. One plasmid-encoded AmpC type β-lactamases producing E. coli from clinically healthy cattle was found to harbour the blaCMY-1 gene, and another from clinically healthy swine carried the blaCMY-2 gene. Among nine E. coli strains exhibiting an ESBL phenotype three strains was found to be the same genotype blaTEM-52C. Enterococci from healthy swine and cattle showed high resistance to tetracycline and erythromycin. Regarding enterococci, the number of multidrug-resistant strains was significantly higher in swine isolates compared to isolates originated from cattle.

CONCLUSIONS

The antimicrobial resistance of E. coli isolates was high in both Estonian swine and cattle. However, swine isolates, especially E. coli from healthy swine, had developed a higher level of resistance. The amount of multidrug-resistant E. coli isolates was also significantly higher in clinically healthy swine compared to that in cattle.

Optimization of Antimicrobial Treatment to Minimize Resistance Selection

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