The broader context of antibiotic resistance: zinc feed supplementation of piglets increases the proportion of multi-resistant Escherichia coli in vivo

Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential

Even though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.

A history of antimicrobial drugs in animals: Evolution and revolution

The evolutionary process of antimicrobial drug (AMD) uses in animals over a mere eight decades (1940-2020) has led to a revolutionary outcome, and both evolution and revolution are ongoing, with reports on a range of uses, misuses and abuses escalating logarithmically. As well as veterinary therapeutic perspectives (efficacy, safety, host toxicity, residues, selection of drug, determination of dose and measurement of outcome in treating animal diseases), there are also broader, nontherapeutic uses, some of which have been abandoned, whilst others hopefully will soon be discontinued, at least in more developed countries. Although AMD uses for treatment of animal diseases will continue, it must: (a) be sustainable within the One Health paradigm; and (b) devolve into more prudent, rationally based therapeutic uses. As this review on AMDs is published in a Journal of Pharmacology and Therapeutics, its scope has been made broader than most recent reviews in this field. Many reviews have focused on negative aspects of AMD actions and uses, especially on the question of antimicrobial resistance. This review recognizes these concerns but also emphasizes the many positive aspects deriving from the use of AMDs, including the major research-based advances underlying both the prudent and rational use of AMDs. It is structured in seven sections: (1) Introduction; (2) Sulfonamide history; (3) Nontherapeutic and empirical uses of AMDs (roles of agronomists and veterinarians); (4) Rational uses of AMDs (roles of pharmacologists, clinicians, industry and regulatory controls); (5) Prudent use (residue monitoring, antimicrobial resistance); (6) International and inter-disciplinary actions; and (7) Conclusions.

Towards Zero Zinc Oxide: Feeding Strategies to Manage Post-Weaning Diarrhea in Piglets

Simple Summary

Zinc oxide (ZnO) supplementation at pharmacological doses in post-weaning piglets is a consolidated practice that allows efficient control of post-weaning diarrhea (PWD), a condition exacerbated by Escherichia coli F4 (K88) infections. Far from being completely elucidated, the multifactorial ZnO mechanism of action is in all likelihood exerted at the gastrointestinal level. However, increasing environmental concerns are arising from prolonged ZnO use. This article reviews the utilization of ZnO in piglets, the biological rationale behind its powerful activity, and the emerging threats that are leading towards a significant reduction in its use. Finally, a wide analysis of the strengths and weaknesses of innovative alternative strategies to manage PWD at the nutritional level is given.

Abstract

Zinc oxide (ZnO) at pharmacological doses is extensively employed in the pig industry as an effective tool to manage post-weaning diarrhea (PWD), a condition that causes huge economic losses because of its impact on the most pivotal phase of a piglet’s production cycle. In a multifactorial way, ZnO exerts a variety of positive effects along the entire gastrointestinal tract by targeting intestinal architecture, digestive secretions, antioxidant systems, and immune cells. ZnO also has a moderate antibacterial effect against Escherichia coli F4 (K88), the main causative agent of PWD. However, the environmental impact of ZnO and new emerging threats are posing serious questions to the sustainability of its extensive utilization. To work towards a future free from pharmacological ZnO, novel nutritional approaches are necessary, and many strategies have been investigated. This review article provides a comprehensive framework for ZnO utilization and its broad mode of action. Moreover, all the risks related to pharmacological ZnO levels are presented; we focus on European institutions’ decisions subsequently. The identification of a novel, complete solution against PWD should be accompanied by the adoption of holistic strategies, thereby combining good management practices to feeding approaches capable of mitigating Escherichia coli F4 (K88) infections and/or lowering ZnO utilization. Promising results can be obtained by adjusting diet composition or employing organic acids, natural identical compounds, polyphenol-rich extracts, prebiotics, and probiotics.

A reduced CP level without medicinal zinc oxide does not alter the intestinal morphology in weaned pigs 24 days post-weaning

The use of medicinal zinc oxide (ZnO) to prevent diarrhoea post-weaning will be banned in the EU from 2022. Therefore, new alternatives are needed to avoid an increase in diarrhoea and higher antibiotic use. A low dietary CP level has shown to lower the frequency of diarrhoea in pigs, due to lower microbial protein fermentation in the colon as well as improved conditions in the small intestine after weaning. The objective of this study was to examine the effect of decreased CP levels post-weaning as an alternative to medicinal ZnO on gut morphology and histopathology. Five hundred and sixty pigs were randomly assigned into one of six groups receiving a two-phase diet from 5.5 to 15 kg: positive control group (PC) with medicinal ZnO and standard levels of protein (19.1-18.4% CP), negative control group (NC) without medicinal ZnO and standard levels of protein (19.1-18.4% CP). The remaining four low protein groups were a low-standard (LS) CP level (16.6-18.4% CP), a low-low (LL) CP level (16.6-16.2% CP), a very low-high (VLH) CP level (14-19.3% CP) and a very low-medium (VLM) CP level (14-17.4% CP). Individual BW was recorded at day 0, 10 and 24 post-weaning, and all antibiotic treatments were recorded. Tissue samples from the small intestine (mid-jejunum) for morphological and histopathologic analysis, organ weights, blood and urine samples were collected at day 10 and 24 post-weaning from a total of 90 sacrificed weaners. The results demonstrated no differences in intestinal morphology between groups, but the histopathology showed a damaged brush border score in VLM and VLH pigs . In addition, a lower blood urea nitrogen in VLM pigs at 24 days was found. The LL and VLM pigs had a significantly decreased average daily gain in the overall trial period compared to PC and NC pigs. Conclusively, intestinal brush border was damaged by the very low protein diet at 24 days post-weaning, but intestinal morphology was unaffected by dietary strategy.

Effects of Zinc and Menthol-Based Diets on Co-Selection of Antibiotic Resistance among E. coli and Enterococcus spp. in Beef Cattle

Antibiotic resistance represents a growing crisis in both human and veterinary medicine. We evaluated the use of antibiotic alternatives-heavy metals and essential oils-in beef cattle feeding, and their effects on Gram-negative and Gram-positive bacteria. In this randomized controlled field trial, we measured the impact of supplemental zinc and menthol on antibiotic resistance among commensal enteric bacteria of feeder cattle. Fecal suspensions were plated onto plain- and antibiotic-supplemented MacConkey and m-Enterococcus agar for quantification of total and antibiotic-resistant Escherichia coli and Enterococcus spp., respectively. Temporal effects on overall E. coli growth were significant (p < 0.05), and menthol was associated with decreased growth on tetracycline-supplemented agar. Zinc was associated with significant increases in growth on erythromycin-supplemented m-Enterococcus agar. Cattle fed zinc exhibited significantly higher levels of macrolide resistance among fecal enterococci isolates.

Regulatory effects of transition metals supplementation/deficiency on the gut microbiota

Transition metal ions are essential micronutrients for all living organisms and exert a wide range of effects on human health. The uptake of transition metal ions occurs primarily in the gastrointestinal tract, which is colonized by trillions of bacterial cells. In recent years, increasing studies have indicated that transition metals have regulatory effects on the gut microbiota. In view of the significant effect of the gut microbiota on human health and involvement in the pathogenesis of a wide range of diseases, in this paper, we provide a comprehensive discussion on the regulatory effects of four kinds of transition metal ions on the gut microbiota. A total of 20 animal model and human studies concerning the regulatory effects of four types of transition metal ions (i.e., iron, copper, zinc, and manganese) on gut microbiota were summarized. Both the deficiency and supplementation of these transition metal ions on the gut microbiota were considered. Furthermore, the potential mechanisms governing the regulatory effects of transition metal ions on the gut microbiota were also discussed. KEY POINTS : • Regulatory effects of iron, copper, zinc, and manganese on gut microbiota were reviewed. • Both deficiency and supplementation of metal ions on gut microbiota were considered. • Mechanisms governing effects of metal ions on gut microbiota were discussed.

High-Zinc Supplementation of Weaned Piglets Affects Frequencies of Virulence and Bacteriocin Associated Genes Among Intestinal Escherichia coli Populations

To prevent economic losses due to post-weaning diarrhea (PWD) in industrial pig production, zinc (Zn) feed additives have been widely used, especially since awareness has risen that the regular application of antibiotics promotes buildup of antimicrobial resistance in both commensal and pathogenic bacteria. In a previous study on 179 Escherichia coli collected from piglets sacrificed at the end of a Zn feeding trial, including isolates obtained from animals of a high-zinc fed group (HZG) and a corresponding control group (CG), we found that the isolate collection exhibited three different levels of tolerance toward zinc, i.e., the minimal inhibitory concentration (MIC) detected was 128, followed by 256 and 512 μg/ml ZnCl2. We further provided evidence that enhanced zinc tolerance in porcine intestinal E. coli populations is clearly linked to excessive zinc feeding. Here we provide insights about the genomic make-up and phylogenetic background of these 179 E. coli genomes. Bayesian analysis of the population structure (BAPS) revealed a lack of association between the actual zinc tolerance level and a particular phylogenetic E. coli cluster or even branch for both, isolates belonging to the HZG and CG. In addition, detection rates for genes and operons associated with virulence (VAG) and bacteriocins (BAG) were lower in isolates originating from the HZG (41 vs. 65% and 22 vs. 35%, p < 0.001 and p = 0.002, resp.). Strikingly, E. coli harboring genes defining distinct pathotypes associated with intestinal disease, i.e., enterotoxigenic, enteropathogenic, and Shiga toxin-producing E. coli (ETEC, EPEC, and STEC) constituted 1% of the isolates belonging to the HZG but 14% of those from the CG. Notably, these pathotypes were positively associated with enhanced zinc tolerance (512 μg/ml ZnCl2 MIC, p < 0.001). Taken together, zinc excess seems to influence carriage rates of VAGs and BAGs in porcine intestinal E. coli populations, and high-zinc feeding is negatively correlated with enteral pathotype occurrences, which might explain earlier observations concerning the relative increase of Enterobacterales considering the overall intestinal microbiota of piglets during zinc feeding trials while PWD rates have decreased.

Low protein diets without medicinal zinc oxide for weaned pigs reduced diarrhea treatments and average daily gain

The use of medicinal zinc oxide (ZnO) in post-weaning diets must be phased out in the European Union by 2022, resulting in urgent needs for alternative strategies to prevent diarrhea in pigs. The objective of this study was to test the effect of four different dietary protein strategies with different amino acid profiles on diarrhea frequency and pig performance as alternative diet plans when medicinal ZnO was will be excluded from the diet. A total of 6 800 Duroc x (Danish Landrace x Yorkshire) pigs, weaned around 28 days of age, were randomly assigned by sex and size to six dietary treatments. The treatments were; standard CP levels (191, 184, 184 g/kg CP) and allocated 2 500 ppm ZnO in phase 1 (PC = positive control), standard CP levels (191, 184, 184 g/kg CP) and no added ZnO in phase 1 (NC = negative control), CP levels of 166, 184, 184 g/kg (LSS = low-standard-standard), CP levels of 166, 162, 192 g/kg (LLH = low-low-high), CP levels of 140, 193, 192 g/kg (VHH = very low-high-high), and lastly 140, 174, 192 g/kg CP levels (VMH = very low-medium-high). The pigs entered the trial at ~7 kg BW and exited at ~30 kg BW. As expected, the PC treatment resulted in 42% fewer diarrhea pen treatments in the total trial period compared to the NC group (P < 0.05), whereas both PC and LLH had fewer diarrhea treatment days per pig compared to NC pigs (P < 0.05). Additionally, at the point of treatment, the NC pens had 33% fecal floor samples positive for pathogens, compared to 80% samples positive for pathogens in the PC pens. This suggests that ZnO has a particular positive effect on non-infectious diarrhea without bacterial involvement. A reduction in dietary CP levels in phase 1 led to a reduced average daily gain (ADG) in LLH and VMH pigs and a poorer feed conversion ratio (FCR) in VHH pigs during the overall study period compared to the NC pigs (P < 0.05). Conclusively, a diet with low CP levels from weaning to about 15 kg BW had a reducing effect on diarrhea, but decreased ADG without affecting the FCR.

High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus

BACKGROUND

Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP.

RESULTS

The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain.

CONCLUSION

Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire

Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology. Metagenomic sequencing of colon microbiota revealed only clear differences at genus level for the group receiving 2500 ppm zinc oxide. However, a clear group differentiation according to dietary zinc concentration and source was observed at species level. Functional analysis revealed significant differences in genes related to stress response, mineral, and carbohydrate metabolism. Taxonomic and functional gene differences were accompanied with clear effects in microbial metabolite concentration. Finally, a selection of certain antibiotic resistance genes by dietary zinc was observed. This study sheds further light onto the consequences of concentration and chemical form of dietary zinc on microbial ecology measures and the resistome in the porcine colon.

Associations between sensitivity to antibiotics, disinfectants and heavy metals in natural, clinical and laboratory isolates of Escherichia coli

Bacteria in nature often encounter non-antibiotic antibacterials (NAAs), such as disinfectants and heavy metals, and they can evolve resistance via mechanisms that are also involved in antibiotic resistance. Understanding whether susceptibility to different types of antibacterials is non-randomly associated across natural and clinical bacteria is therefore important for predicting the spread of resistance, yet there is no consensus about the extent of such associations or underlying mechanisms. We tested for associations between susceptibility phenotypes of 93 natural and clinical Escherichia coli isolates to various NAAs and antibiotics. Across all compound combinations, we detected a small number of non-random associations, including a trio of positive associations among chloramphenicol, triclosan and benzalkonium chloride. We investigated genetic mechanisms that can explain such associations using genomic information, genetic knockouts and experimental evolution. This revealed some mutations that are selected for by experimental exposure to one compound and confer cross-resistance to other compounds. Surprisingly, these interactions were asymmetric: selection for chloramphenicol resistance conferred cross-resistance to triclosan and benzalkonium chloride, but selection for triclosan resistance did not confer cross-resistance to other compounds. These results identify genetic changes involved in variable cross-resistance across antibiotics and NAAs, potentially contributing to associations in natural and clinical bacteria.

Influence of zinc on CTX-M-1 β-lactamase expression in Escherichia coli

OBJECTIVE

Zinc oxide is used to prevent post-weaning diarrhoea in pigs as an alternative to antimicrobial growth promoters. This study aims to determine if the use of zinc oxide selects for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and affects the expression of bla_CTX-M-1 in E. coli.

METHODS

Using an in vitro faecal micro-cosmos model, the selective properties of zinc were investigated using an E. coli strain with bla_CTX-M-1 encoded by a natural IncI1 resistance plasmid (MG1655/pTF2) and another strain where the same gene was located on the chromosome (MG1655::bla_CTX-M-1). The micro-cosmos was seeded with faecal material containing an increasing concentration of zinc (0-8 mM). Outcome measurements consisted of colony-forming units (CFU) of the inoculated ESBL E. coli and naturally occurring coliforms as determined by plate counting on MacConkey with and without 5 mg/L cefotaxime as well as total viable bacteria determined on Luria agar without cefotaxime. Expression of bla_CTX-M-1 under the experimental zinc concentrations was determined by quantitative polymerase chain reaction.

RESULTS

The proportion of MG1655/pTF2 of the total viable bacteria was significantly higher at high zinc concentrations (6 and 8 mM) compared with low concentrations (0-4 mM). The messenger RNA (mRNA) levels of bla_CTX-M-1 in the two ESBL strains increased at increasing zinc concentrations and varied with the growth phase.

CONCLUSION

The growth of the inoculated CTX-M-1-encoding E. coli MG1655 strains and naturally occurring coliforms was impacted differently when exposed to zinc oxide. The bla_CTX-M-1 mRNA expression levels seemed to increase with increasing zinc concentrations, but varied with growth phase, but not gene location.

Zinc phosphate-based nanoparticles as alternatives to zinc oxide in diet of weaned piglets

BACKGROUND

The high doses of zinc oxide (ZnO) administered orally to piglets for the prevention of diarrhea and increase of growth rate can contaminate pig farms and the surrounding environment. Therefore, there is a need to find a replacement of high doses of dietary ZnO with an equally effective alternative. In the present study, the effect of two formulations of zinc phosphate-based nanoparticles (ZnA and ZnC NPs) on growth performance, intestinal microbiota, antioxidant status, and intestinal and liver morphology was evaluated. A total of 100 weaned piglets were randomly divided into 10 equal groups with the base diet (control) or the base diet supplemented with ZnA, ZnC, or ZnO at concentrations 500, 1000, and 2000 mg Zn per kilogram of diet. Supplements were given to animals for 10 days. Fecal samples were collected on day 0, 5, 10 and 20. At the end of the treatment (day 10), three piglets from each group were sacrificed and analyzed.

RESULTS

Comparing to that of control, the significantly higher piglet weight gain was observed in all piglet groups fed with ZnA (P < 0.05). Differences in the total aerobic bacteria and coliform counts in piglet feces after NPs supplementation compared to that of control and ZnO groups were also found (P < 0.05). The majority of aerobic culturable bacteria from the feces represented Escherichia (28.57-47.62%), Enterococcus (3.85-35.71%), and Streptococcus (3.70-42.31%) spp. A total of 542 Escherichia coli isolates were screened for the virulence genes STa, STb, Stx2, F4, and F18. The substantial occurrence of E. coli virulence factors was found on day 5, mainly in fimbrillary antigen and thermostable toxins, except for piglets fed by ZnC. Zn treatment decreased Zn blood levels in piglets fed with ZnO and ZnA (500 mg/kg) and increased in ZnC (2000 mg/kg) compared to that of control (P < 0.05). The antioxidant status of piglets was affected only by ZnA. While some changes in the liver and the intestinal morphology of piglets with NPs were observed, none were serious as reflected by the normal health status and increased weigh gain performance.

CONCLUSIONS

Our results indicate that ZnA NPs have a positive effect on the piglet growth performance even at the lowest concentration. The prevalence of E. coli virulence factors was lowest in pigs supplemented with ZnC. Zinc phosphate-based nanoparticles may be an effective alternative to ZnO.

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces

Oral antibiotics are a critical tool for fighting bacterial infections, yet their use can have negative consequences, such as the disturbance of healthy gut bacterial communities and the dissemination of antibiotic residues in feces. Altering antibiotic administration route may limit negative impacts on intestinal microbiota and reduce selective pressure for antimicrobial resistance genes (ARG) persistence and mobility. Thus, a study was performed in pigs to evaluate route of therapeutic oxytetracycline (oxytet) administration, an antibiotic commonly used in the U.S. swine industry, on intestinal microbial diversity and ARG abundance. Given that oral antibiotics would be in direct contact with intestinal bacteria, we hypothesized that oral administration would cause a major shift in intestinal bacterial community structure when compared to injected antibiotic. We further postulated that the impact would extend to the diversity and abundance of ARG in swine feces. At approximately 3 weeks-of-age, piglets were separated into three groups (n = 21–22 per group) with two groups receiving oxytet (one via injection and the second via feed) and a third non-medicated group. Oxytet levels in the plasma indicated injected antibiotic resulted in a spike 1 day after administration, which decreased over time, though oxytet was still detected in plasma 14 days after injection. Conversely, in-feed oxytet delivery resulted in lower but less variable oxytet levels in circulation and high concentrations in feces. Similar trends were observed in microbial community changes regardless of route of oxytet administration; however, the impact on the microbial community was more pronounced at all time points and in all samples with in-feed administration. Fecal ARG abundance was increased with in-feed administration over injected, with genes for tetracycline and aminoglycoside resistance enriched specifically in the feces of the in-feed group. Sequencing of plasmid-enriched samples revealed multiple genetic contexts for the resistance genes detected and highlighted the potential role of small plasmids in the movement of antibiotic resistance genes. The findings are informative for disease management in food animals, but also manure management and antibiotic therapy in human medicine for improved antibiotic stewardship.

The Effects of the Marine-Derived Polysaccharides Laminarin and Chitosan on Aspects of Colonic Health in Pigs Challenged with Dextran Sodium Sulphate

This study examined the effects of dietary supplementation with laminarin or chitosan on colonic health in pigs challenged with dextran sodium sulphate (DSS). Weaned pigs were assigned to: (1) a basal diet (n = 22); (2) a basal diet + laminarin (n = 10); and (3) a basal diet + chitosan (n = 10). On d35, the basal group was split, creating four groups: (1) the basal diet (control); (2) the basal diet + DSS; (3) the basal diet + laminarin + DSS; and (4) the basal diet + chitosan + DSS. From d39-42, the pigs were orally challenged with DSS. On d44, colonic tissue/digesta samples were collected. The basal DSS group had reduced growth, higher pathology score and an increased expression of MMP1, IL13 and IL23 compared with the controls (p < 0.05); these parameters were similar between the DSS-challenged groups (p > 0.05). In the basal DSS group, the relative abundance of beneficial taxa including Prevotella and Roseburia were reduced while Escherichia/Shigella were increased, compared with the controls (p < 0.05). The relative abundance of Escherichia/Shigella was reduced and the molar proportions of acetate were increased in the laminarin DSS group compared with the basal DSS group (p < 0.01), suggesting that laminarin has potential to prevent pathogen proliferation and enhance the volatile fatty acid profile in the colon in a porcine model of colitis.

Effects of Hydrolysable Tannins as Zinc Oxide Substitutes on Antioxidant Status, Immune Function, Intestinal Morphology, and Digestive Enzyme Activities in Weaned Piglets

Simple Summary

Zinc oxide (ZnO) is generally used to control diarrhea and improve gut health in weaned piglets. To protect weaned pigs from intestinal injuries and to decrease environmental zinc load, it is essential to find an alternative to ZnO. In the present study, hydrolysable tannins (HT) showed decreased diarrhea rate and improving gut health via multiple pathways. Herein we demonstrate that HT supplementation may be a potential alternative of ZnO in weaned piglets.

Abstract

Zinc oxide (ZnO) has negative environmental effects and bioavailability in weaned piglets. Thus, finding safe and effective ZnO substitutes to improve intestinal health and to prevent diarrhea of weaned piglets is urgently required. Therefore, this experiment was conducted to evaluate the effects of hydrolysable tannins (HT), ZnO and HT versus ZnO on growth performance, antioxidant status, serum immunity, intestinal morphology, and digestive enzyme activities in weaned pigs. A total of 144 piglets (28 d-old, initial body weight 7.81 ± 0.99 kg) were assigned to 4 treatments with 6 replicates of 6 piglets each. The experiment lasted 28 d (d 1 to 14 as for phase 1 and d 15 to 28 as for phase 2). The dietary treatments include a corn-soybean meal basal diet (CON); ZnO diet (CON + 2000 mg/kg ZnO in phase 1 and 137.5 mg/kg ZnO in phase 2); HT diet (CON + 1000 mg/kg HT in the overall period (d 1 to 28); HT + ZnO diet (CON + 2000 mg/kg ZnO + 1000 mg/kg HT in phase 1, and 137.5 mg/kg ZnO + 1000 mg/kg HT in phase 2). In phase 1, the incidence of diarrhea was lower (p < 0.05) in the HT + ZnO group than CON. Serum catalase (CAT) and glutathione peroxidase (GSH-Px) were increased (p < 0.01) and malondialdehyde (MDA) was decreased (p < 0.01) in the HT + ZnO group than CON. Compared with CON, immunoglobulin M (IgM), immunoglobulin A (IgA) were increased (p < 0.05) in the HT + ZnO group. In phase 2, both HT and HT + ZnO had a trend to improve (p < 0.10) daily gain. The concentration of total antioxidant capacity (T-AOC) and IgM in serum was higher (p < 0.01) in HT compared with CON. Supplementation of HT improved (p < 0.01) GSH-Px activities in ileum mucosa than the ZnO group. Compared with CON, trypsin, lipase activities, and villus height of jejunum were improved (p < 0.05) in HT and HT + ZnO. The ratio of villus height to crypt depth in the jejunum was improved (p < 0.05) in the HT + ZnO group and which also was increased (p < 0.05) in ileum in the HT group compared with CON. Propionic acid, butyric acid, and acetic acid concentrations in the colon were increased (p < 0.05) in the HT group than CON. Overall, HT + ZnO treatments could be used to replace ZnO for reducing diarrhea and improving antioxidant capacity, immunity, and digestive enzyme activities in weaned piglets.

Effects of different types of zinc supplement on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn dairy calves

Neonatal diarrhea in dairy calves causes huge economic and productivity losses in the dairy industry. Zinc is an effective anti-diarrheal agent, but high doses may pose a threat to the environment. Therefore, we aimed to evaluate the effects of low-dose zinc supplementation on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn Holstein dairy calves. Thirty newborn calves were allocated to either a control group (without extra zinc supplementation), or groups supplemented with either 104 mg of zinc oxide (ZnO, equivalent to 80 mg of zinc/d) or 457 mg of zinc methionine (Zn-Met, equivalent to 80 mg of zinc/d) and studied them for 14 d. The rectal contents were sampled on d 1, 3, 7, and 14, and blood samples were collected at the end of the study. Supplementation with ZnO reduced the incidence of diarrhea during the first 3 d of life, and increased serum IgG and IgM concentrations. The Zn-Met supplementation increased growth performance and reduced the incidence of diarrhea during the first 14 d after birth. The results of fecal microbiota analysis showed that Firmicutes and Proteobacteria were the predominant phyla, and Escherichia and Bacteroides were the dominant genera in the recta of the calves. As the calves grew older, rectal microbial diversity and composition significantly evolved. In addition, dietary supplementation with ZnO reduced the relative abundance of Proteobacteria in 1-d-old calves, and increased that of Bacteroidetes, Lactobacillus, and Faecalibacterium in 7-d-old calves, compared with the control group. Supplementation with Zn-Met increased the relative abundance of the phylum Actinobacteria and the genera Faecalibacterium and Collinsella on d 7, and that of the genus Ruminococcus after 2 wk, compared with the control group. Thus, the rectal microbial composition was not affected by zinc supplementation but significantly evolved during the calves' early life. Zinc supplementation reduced the incidence of diarrhea in young calves. In view of their differing effects, we recommend ZnO supplementation for dairy calves during their first 3 d of life and Zn-Met supplementation for the subsequent period. These findings suggest that zinc supplementation may be an alternative to antibacterial agents for the treatment of newborn calf diarrhea.

Effects of alternative feed additives to medicinal zinc oxide on productivity, diarrhoea incidence and gut development in weaned piglets

The use of medicinal zinc oxide (ZnO) must be phased out by 2022, thus prompting an urgent need for alternative strategies to prevent diarrhoea in weaner piglets. The objectives of this study were to assess the impact on weaner piglet performance, diarrhoea incidence and gut development, when (1) dietary ZnO supplementation was substituted by alternative commercial products based on macroalgae, specific probiotics or synbiotics, or (2) dietary ZnO inclusion was reduced from 2500 to 1500 ppm. A total of 4680 DLY piglets (DanBred, Herlev, Denmark), weaned around 35 days of age, were randomly assigned according to sex and BW to six different dietary treatment groups. A basal diet was supplemented with no ZnO (NC = negative control), 2500 ppm ZnO (PC = positive control), 1500 ppm ZnO (RDZ = reduced dose of ZnO) or commercial macroalgae (OceanFeed™ Swine = OFS), probiotic Miya-Gold or synbiotic GærPlus products. The piglets entered and exited the weaner unit at ~7.0 and 30 kg BW, respectively. In-feed ZnO was provided the first 10 days post-weaning, while the alternative supplements were fed throughout the weaner period. As expected, the average daily feed intake, average daily weight gain (ADG), feed conversion ratio (FCR) and diarrhoea incidence were improved in the PC compared to NC group (P < 0.05) during phase 1 consistent with improved indices of villi development observed in subgroups of piglets sacrificed 11 days post-weaning. Reduction of ZnO to 1500 ppm lowered ADG (P < 0.05) and slightly increased incidence of diarrhoea during the first 10 days after weaning (but not later) without affecting FCR. None of the three alternative dietary additives, including a 10-fold increased dose of GærPlus than recommended, improved piglet performance, gut health and gut development above that of NC piglets. The OFS piglets sacrificed 11 days after weaning had significantly lower weights of hindgut tissue and contents compared to the PC group, consistent with antimicrobial activity of the product, which was detected from anaerobic in vitro fermentation. In conclusion, dietary ZnO supplementation during the first 10 days post-weaning may be reduced from 2500 to 1500 ppm without major negative implications for weaner piglet performance and health in herds under a high management level. However, none of the alternative dietary supplements were able to improve piglet performance or gut health, when ZnO was omitted from the diet.

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 zinc resistance does not correlate with antimicrobial multi-resistance in fecal E. coli isolates of piglets

Background

Following the ban on antimicrobial usage for growth promotion in animal husbandry in the EU, non-antimicrobial agents including heavy metal ions (e.g. zinc and copper), prebiotics or probiotics have been suggested as alternatives. Zinc has extensively been used in pig farming, particularly during weaning of piglets to improve animal health and growth rates. Recent studies, however, have suggested that high dietary zinc feeding during weaning of piglets increases the proportion of multi-drug resistant E. coli in the gut, contraindicating the appropriateness of zinc as an alternative. The underlying mechanisms of zinc effects on resistant bacteria remains unclear, but co-selection processes could be involved. In this study, we determined whether E. coli isolates from intestinal contents of piglets that had been supplemented with high concentrations of zinc acquired a higher tolerance towards zinc, and whether multi-drug resistant isolates tolerated higher zinc concentrations. In addition, we compared phenotypic zinc and copper resistance of E. coli isolates for possible correlation between phenotypic resistance/tolerance to different bivalent ionic metals.

Results

We screened phenotypic zinc/copper tolerance of 210 isolates (including antimicrobial resistant, multi-drug resistant, and non-resistant E. coli) selected from two, independent zinc-feeding animal trials by determining a zinc/copper minimal inhibitory concentration (Merlin, Bornheim-Hersel, Germany). In both trials, groups of piglets were supplemented either with high dietary zinc (> 2000 ppm) or control (50–70 ppm, background) concentrations. Our observations showed that high concentration zinc exposure did not have an effect on either zinc or copper phenotypic tolerance of E. coli isolates from the animals. No significant association was found between antimicrobial resistance and phenotypic zinc/copper tolerance of the same isolates.

Conclusion

Our findings argue against a co-selection mechanism of antimicrobial drug-resistance and zinc tolerance after dietary zinc supplementation in weaning piglets. An explanation for an increase in multi-drug resistant isolates from piglets with high zinc dietary feeding could be that resistant bacteria to antimicrobial agents are more persistent to stresses such as zinc or copper exposure.

Zinc and Copper Reduce Conjugative Transfer of Resistance Plasmids from Extended-Spectrum Beta-Lactamase-Producing Escherichia coli

The present work addresses the effect of excess levels of ZnCl₂ and CuSO₄ in the growth medium on the conjugative transfer of plasmids carrying the antibiotic resistance gene bla_CMY-2 from extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. Norwegian poultry are not treated prophylactically with antibiotics, but still, ESBL-producing E. coli are found in the chicken populations. Chickens receive higher amounts of Zn and Cu than their biological need, and several metals have been shown to act as drivers of antimicrobial resistance. In the present study, ESBL-producing E. coli strains collected from retail chicken meat were mated in broth containing various concentrations of ZnCl₂ and CuSO₄. Manual counting of transconjugants showed that ZnCl₂ and CuSO₄ reduced the conjugation frequency between E. coli strains in a concentration-dependent manner. Quantitative real-time PCR analyses showed that the presence of ZnCl₂ and CuSO₄ in the growth media reduced expression of the conjugation genes traB and nikB. By propagating monocultures over several generations, it was found that the bla_CMY-2 plasmids remained stable in the recipient strains. Together the results show that exposure of ESBL-producing E. coli to Zn and Cu reduce horizontal transfer of the bla_CMY-2 resistance plasmid by reducing expression of genes involved in conjugation in the plasmid donor strain.

Comparative effects of low zinc oxide dose with or without probiotics relative to high zinc oxide dose on the performance, nutrient digestibility, blood metabolites, and noxious gases emission in weaned piglets

The objective of this study was to assess the effects of low-dose zinc oxide (ZnO) supplemented with or without probiotic complex compared with pharmacological ZnO (3000 mg kg−1) on the performance, digestibility, blood metabolites, fecal Lactobacillus and enterobacteria counts of weaned piglets. One-hundred and twenty crossbred piglets were randomly allocated to three treatments based on their initial body weight (BW). Treatments consisted of corn–soybean-meal-based basal diet supplemented with 3000 mg kg−1 ZnO as positive control (ZH), basal diet supplemented with 300 mg kg−1 ZnO as negative control (ZL), and ZL + 0.1% probiotic complex (ZLP). At the end of the experiment, fecal samples were collected by direct rectal massage to determine nutrient digestibility, Lactobacillus and enterobacteria counts, and gas emission, whereas blood samples were taken via jugular venipuncture for determination of blood metabolites. The BW of piglets at week 6, and the average daily gain (ADG) at week 6 and during overall period were higher (P < 0.05) in pigs fed ZH diet compared with those fed ZL diet. The supplementation of ZLP increased the ADG during week 6 and overall making it comparable with ZH diet (P < 0.05). However, other parameters described above were comparable with ZH in pigs fed ZLP diet.

Effects of a Four-Week High-Dosage Zinc Oxide Supplemented Diet on Commensal Escherichia coli of Weaned Pigs

Strategies to reduce economic losses associated with post-weaning diarrhea in pig farming include high-level dietary zinc oxide supplementation. However, excessive usage of zinc oxide in the pig production sector was found to be associated with accumulation of multidrug resistant bacteria in these animals, presenting an environmental burden through contaminated manure. Here we report on zinc tolerance among a random selection of intestinal Escherichia coli comprising of different antibiotic resistance phenotypes and sampling sites isolated during a controlled feeding trial from 16 weaned piglets: In total, 179 isolates from "pigs fed with high zinc concentrations" (high zinc group, [HZG]: n = 99) and a corresponding "control group" ([CG]: n = 80) were investigated with regard to zinc tolerance, antimicrobial- and biocide susceptibilities by determining minimum inhibitory concentrations (MICs). In addition, in silico whole genome screening (WGSc) for antibiotic resistance genes (ARGs) as well as biocide- and heavy metal tolerance genes was performed using an in-house BLAST-based pipeline. Overall, porcine E. coli isolates showed three different ZnCl₂ MICs: 128 μg/ml (HZG, 2%; CG, 6%), 256 μg/ml (HZG, 64%; CG, 91%) and 512 μg/ml ZnCl₂ (HZG, 34%, CG, 3%), a unimodal distribution most likely reflecting natural differences in zinc tolerance associated with different genetic lineages. However, a selective impact of the zinc-rich supplemented diet seems to be reasonable, since the linear mixed regression model revealed a statistically significant association between "higher" ZnCl₂ MICs and isolates representing the HZG as well as "lower ZnCl₂ MICs" with isolates of the CG (p = 0.005). None of the zinc chloride MICs was associated with a particular antibiotic-, heavy metal- or biocide- tolerance/resistance phenotype. Isolates expressing the 512 μg/ml MIC were either positive for ARGs conferring resistance to aminoglycosides, tetracycline and sulfamethoxazole-trimethoprim, or harbored no ARGs at all. Moreover, WGSc revealed a ubiquitous presence of zinc homeostasis and - detoxification genes, including zitB, zntA, and pit. In conclusion, we provide evidence that zinc-rich supplementation of pig feed selects for more zinc tolerant E. coli, including isolates harboring ARGs and biocide- and heavy metal tolerance genes - a putative selective advantage considering substances and antibiotics currently used in industrial pork production systems.

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.

Heavy metal pollution and co-selection for antibiotic resistance: A microbial palaeontology approach

Frequent and persistent heavy metal pollution has profound effects on the composition and activity of microbial communities. Heavy metals select for metal resistance but can also co-select for resistance to antibiotics, which is a global health concern. We here document metal concentration, metal resistance and antibiotic resistance along a sediment archive from a pond in the North West of the United Kingdom covering over a century of anthropogenic pollution. We specifically focus on zinc, as it is a ubiquitous and toxic metal contaminant known to co-select for antibiotic resistance, to assess the impact of temporal variation in heavy metal pollution on microbial community diversity and to quantify the selection effects of differential heavy metal exposure on antibiotic resistance. Zinc concentration and bioavailability was found to vary over the core, likely reflecting increased industrialisation around the middle of the 20th century. Zinc concentration had a significant effect on bacterial community composition, as revealed by a positive correlation between the level of zinc tolerance in culturable bacteria and zinc concentration. The proportion of zinc resistant isolates was also positively correlated with resistance to three clinically relevant antibiotics (oxacillin, cefotaxime and trimethoprim). The abundance of the class 1 integron-integrase gene, intI1, marker for anthropogenic pollutants correlated with the prevalence of zinc- and cefotaxime resistance but not with oxacillin and trimethoprim resistance. Our microbial palaeontology approach reveals that metal-contaminated sediments from depths that pre-date the use of antibiotics were enriched in antibiotic resistant bacteria, demonstrating the pervasive effects of metal-antibiotic co-selection in the environment.

Nutrition Related Stress Factors Reduce the Transfer of Extended-Spectrum Beta-Lactamase Resistance Genes between an Escherichia coli Donor and a Salmonella Typhimurium Recipient In Vitro

The transfer of extended spectrum β-lactamase (ESBL)-genes occurs frequently between different bacteria species. The aim of this study was to investigate the impact of nutrition related stress factors on this transfer. Thus, an Escherichia coli donor and a Salmonella Typhimurium recipient were co-incubated for 4 h in media containing different levels of the stress factors' pH, osmolality, copper, zinc and acetic, propionic, lactic, and n-butyric acid, as well as subtherapeutic levels of cefotaxime, sulfamethoxazole/trimethoprim, and nitrofurantoin. Conjugation frequencies were calculated as transconjugants per donor, recipient, and total bacterial count. A correction factor for the stress impact on bacterial growth was used. Acetic, lactic, and n-butyric, acid, as well as pH, showed no significant impact. In contrast, increasing concentrations of propionate, zinc, copper, and nitrofurantoin, as well as increased osmolality reduced conjugation frequencies. Sulfamethoxazole/trimethoprim and cefotaxime showed increased transconjugants per donor, which decreased after correction for stress. This study showed, for the model mating pair, that conjugation frequencies decreased under different physiological stress conditions, and, thus, the hypothesis that stress factors may enhance conjugation should be viewed with caution. Furthermore, for studies on in vitro gene transfer, it is vital to consider the impact of studied stressors on bacterial growth.

Minimum Inhibitory Concentration of Glyphosate and a Glyphosate-Containing Herbicide in Salmonella enterica Isolates Originating from Different Time Periods, Hosts, and Serovars

Glyphosate, the active compound of Roundup, is one of the most used pesticides in the world. Its residues are often detected in animal feed, but the impact on the animal gut microbiota and on pathogens of the intestine has not intensively been investigated. In this study, we analyzed the minimum inhibitory concentration (MIC) of glyphosate isopropylamine salt and a common glyphosate-containing herbicide formulation in 225 Salmonella enterica isolates by broth microdilution. A bacteriostatic effect of glyphosate on Salmonella growth was detected at the concentration range of 10 to 80 mg/mL for both the active ingredient and the ready-to-use formulation. Time/year of isolation, host species, and serovars revealed a statistically significant influence on MIC values. Recently collected Salmonella isolates had significantly higher MIC values for glyphosate and the glyphosate-containing product compared with isolates collected between 1981 and 1990. Isolates from pigs showed significantly higher MIC values compared with isolates from poultry, and isolates of the Salmonella serovar Typhimurium had significantly higher MIC values than Salmonella Enteritidis and Infantis isolates.

Antibiotic resistance in Escherichia coli from pigs from birth to slaughter and its association with antibiotic treatment

The purpose of this longitudinal study was to describe the occurrence of antibiotic resistance in faecal Escherichia coli isolated from pigs between birth and slaughter and its association with antibiotic treatment. Four objectives were addressed: comparison of antibiotic resistance in isolates from a) treated vs. non-treated pigs, b) follow-up vs. initial samples of treated and non-treated pigs, c) pigs receiving treatments via different administration routes and d) sows and their piglets. Each comparison addressed the following antibiotic groups used for treatment: beta-lactams, tetracyclines, polymyxins and macrolides, and the susceptibility of E. coli isolates to the respective agents: ampicillin, tetracycline, colistin and azithromycin. Between 2014 and 2016, 406 focal animals from 29 commercial breeding herds were followed from birth to the end of the relevant fattening periods. All antibiotic treatments in these pigs were documented. Faecal samples were collected from the focal pigs once while suckling, once after weaning and three times during fattening, and from their dams once around farrowing. Escherichia coli isolated from these samples was tested for antibiotic susceptibility. In total, 264 animals from 19 breeding herds were treated with an antibiotic at least once during their lifetime. Beta-lactams, tetracyclines and colistin were used most frequently. Piglets were treated individually by injection (n = 108 treatments) or via drench (9); weaners via feed (192) or water (56) and fatteners via feed (30) or injection (15). Resistance to ampicillin and tetracycline in E. coli was already common prior to antibiotic treatment. Resistance proportions were higher for beta-lactam-, tetracycline-, colistin- and macrolide-treated pigs compared to untreated pigs at different sampling periods (p < 0.05; Fisher's exact test). In the logistic analysis, the difference was confirmed for beta-lactam-treated vs. untreated pigs. In E. coli from macrolide-untreated pigs, resistance to azithromycin was more frequent compared to pre-treatment values. Route of application did not affect rates of antibiotic resistance in the logistic analysis even though Fisher's exact test indicated associations for beta-lactams (feed/water vs. injection), tetracyclines (feed/water vs. non-treatment) and macrolides (tulathromycin-injection vs. tylosin in feed). Piglets were more likely to carry an E. coli resistant to ampicillin or azithromycin if their dams did so as well. Our results suggest further research on resistance effects by administration routes is required. Reducing antibiotic resistance in sows might lead to a lower level of beta-lactam or macrolide-resistant E. coli among their progeny. To preserve treatment options for bacterial infections, antibiotic use should be restricted to necessary cases.

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes

The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem. Finally, we frame microbiomes as open systems subject to acquisition of novel information from foreign ecosystems through invasion by outsider microbes.

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.

Effects of supplemental zinc sulfate on growth performance, carcass characteristics, and antimicrobial resistance in feedlot heifers

Effects of supplemental Zn as Zn sulfate on feedlot performance, carcass traits, and antimicrobial resistance were evaluated using 480 crossbred heifers (BW = 385 kg ± 13.08) in a randomized complete block design. Heifers were blocked by BW and randomly assigned within block to diets with 0, 30, 60, or 90 mg supplemental Zn/kg DM. Heifers were housed in dirt-surfaced pens (20 animals per pen; 6 pens per treatment) equipped with fence-line feed bunks and automatic water fountains. Heifers were fed once daily to ensure ad libitum intake. Plasma was collected on day 0 from five randomly selected heifers per pen and repeated on days 63 and 115 to determine plasma Zn concentrations. Random samples of freshly voided feces were collected from the surface of each pen the day of harvest to determine antibiotic resistance. Heifers were transported on day 144 to a commercial abattoir where hot carcass weight (HCW) and incidence of liver abscesses were recorded at harvest and HCW, dressed yield, ribeye area, 12th rib fat, quality and yield grades were recorded after 36 h of refrigeration. Plasma Zn concentration increased (P = 0.02) linearly in response to increasing concentrations of dietary Zn. Final BW and ADG were unaffected by supplementation (P ≥ 0.29). Quantified levels of resistance to ceftriaxone and tetracycline among fecal Escherichia coli were not impacted (P > 0.05) by dietary zinc concentrations. Increasing Zn concentrations tended to decrease (linear effect, P = 0.07) DMI, resulting in a linear (P = 0.03) and tendency for quadratic (P = 0.12) improvement in feed efficiency with increasing Zn concentration. No differences were detected for HCW, dressed yield, ribeye area, 12th rib fat, percentages of carcasses grading Select or Choice, or yield grade (P > 0.53), but added Zn tended to affect percentage of carcasses that graded Prime, peaking at 60 mg/kg added Zn (quadratic effect, P = 0.07). In vitro fermentations were performed using ruminal fluid cultures containing 0, 30, 60, 90, 120, or 150 mg Zn/kg substrate DM to determine impact of Zn on gas production, VFA concentrations, and in vitro DM disappearance (IVDMD). There were no effects of Zn on in vitro gas production, IVDMD, or most VFA (P > 0.15), but isovalerate decreased linearly in response to added Zn (P = 0.05). Supplementing finishing heifers up to 60 mg Zn/kg diet DM improved feed efficiency compared to other treatments.

Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat

Misuse/over use of antibiotics increases the threats to human health since this is a main reason behind evolution of antibiotic resistant bacterial pathogens. However, metals such as mercury, lead, zinc, copper and cadmium are accumulating to critical concentration in the environment and triggering co-selection of antibiotic resistance in bacteria. The co-selection of metal driven antibiotic resistance in bacteria is achieved through co-resistance or cross resistance. Metal driven antibiotic resistant determinants evolved in bacteria and present on same mobile genetic elements are horizontally transferred to distantly related bacterial human pathogens. Additionally, in marine environment persistent pollutants like microplastics is recognized as a vector for the proliferation of metal/antibiotics and human pathogens. Recently published research confirmed that horizontal gene transfer between phylogenetically distinct microbes present on microplastics is much faster than free living microbes. Therefore, microplastics act as an emerging hotspot for metal driven co-selection of multidrug resistant human pathogens and pose serious threat to humans which do recreational activities in marine environment and ingest marine derived foods. Therefore, marine environment co-polluted with metal, antibiotics, human pathogens and microplastics pose an emerging health threat globally.

Resistance to Metals Used in Agricultural Production

Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.

Antimicrobial resistance due to the content of potentially toxic metals in soil and fertilizing products

Potentially toxic metals (PTM), along with PTM-resistant bacteria and PTM-resistance genes, may be introduced into soil and water through sewage systems, direct excretion, land application of biosolids (organic matter recycled from sewage, especially for use in agriculture) or animal manures as fertilizers, and irrigation with wastewater or treated effluents. In this review article, we have evaluated whether the content of arsenic (As), cadmium (Cd), chromium (CrIII + CrVI), copper (Cu), lead (Pb), mercury (Hg), nickel (Ni), and zinc (Zn) in soil and fertilizing products play a role in the development, spreading, and persistence of bacterial resistance to these elements, as well as cross- or co-resistance to antimicrobial agents. Several of the articles included in this review reported the development of resistance against PTM in both sewage and manure. Although PTM like As, Hg, Co, Cd, Pb, and Ni may be present in the fertilizing products, the concentration may be low since they occur due to pollution. In contrast, trace metals like Cu and Zn are actively added to animal feed in many countries. In several studies, several different bacterial species were shown to have a reduced susceptibility towards several PTM, simultaneously. However, neither the source of resistant bacteria nor the minimum co-selective concentration (MCC) for resistance induction are known. Co- or cross-resistance against highly important antimicrobials and critically important antimicrobials were identified in some of the bacterial isolates. This suggest that there is a genetic linkage or direct genetic causality between genetic determinants to these widely divergent antimicrobials, and metal resistance. Data regarding the routes and frequencies of transmission of AMR from bacteria of environmental origin to bacteria of animal and human origin were sparse. Due to the lack of such data, it is difficult to estimate the probability of development, transmission, and persistence of PTM resistance. Abbreviations: PTM: potentially toxic metals; AMR: antimicrobial resistance; ARG: antimicrobial resistance gene; MCC: minimum co-selective concentration; MDR: multidrug resistance; ARB: antimicrobial resistant bacteria; HGT: horizontal gene transfer; MIC: minimum inhibitory concentration.

Heavy metal resistance in bacteria from animals

Resistance to metals and antimicrobials is a natural phenomenon that existed long before humans started to use these products for veterinary and human medicine. Bacteria carry diverse metal resistance genes, often harboured alongside antimicrobial resistance genes on plasmids or other mobile genetic elements. In this review we summarize the current knowledge about metal resistance genes in bacteria and we discuss their current use in the animal husbandry.

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut

High levels of zinc oxide are used frequently as feed additive in pigs to improve gut health and growth performance and are still suggested as an alternative to antimicrobial growth promoters. However, we have recently described an increase of multi-resistant E. coli in association to zinc feeding in piglets. This previous study focused on clonal diversity of E. coli, observing the effect on multi-resistant strains by chance. To shed further light into this highly important topic and falsify our previous findings, we performed a zinc pig feeding trial where we specifically focused on in-depth analysis of antimicrobial resistant E. coli. Under controlled experimental conditions, piglets were randomly allocated to a high dietary zinc (zinc group) and a background zinc feeding group (control group). At different ages samples were taken from feces, digesta, and mucosa and absolute E. coli numbers were determined. A total of 2665 E. coli isolates were than phenotypically tested for antimicrobial resistance and results were confirmed by minimum inhibitory concentration testing for random samples. In piglets fed with high dietary zinc, we detected a substantial increase of multi-resistant E. coli in all gut habitats tested, ranging from 28.9–30.2% multi-resistant E. coli compared to 5.8–14.0% in the control group. This increase was independent of the total number of E. coli. Interestingly, the total amount of the E. coli population decreased over time. Thus, the increase of the multi-resistant E. coli populations seems to be linked with persistence of the resistant population, caused by the influence of high dietary zinc feeding. In conclusion, these findings corroborate our previous report linking high dietary zinc feeding of piglets with the occurrence of antimicrobial resistant E. coli and therefore question the feeding of high dietary zinc oxide as alternative to antimicrobial growth promoters.

Zinc strengthens the jejunal barrier by reversibly tightening the paracellular route

During the postweaning period, piglets are prone to gastrointestinal infections. The resulting impairment of intestinal barrier function may cause diarrhea associated with growth retardation or even death of piglets. Orally applied Zn is commonly used to prevent and treat diarrhea, but its mode of action still needs to be elucidated. To analyze the molecular mechanism whereby Zn acts on porcine intestinal barrier function, ex vivo studies on piglet jejunum and accompanying in vitro studies on a porcine jejunal epithelial cell line, IPEC-J2/PS, were performed with electrophysiological tools. Feeding pharmacological Zn doses exerted no significant electrophysiologically ascertainable short- and long-term effects on jejunal barrier function ex vivo. However, in IPEC-J2/PS, basolateral Zn was cytotoxic since its application caused a release of lactate dehydrogenase and an irreversible breakdown of the epithelial barrier. In contrast, apical Zn application caused an immediate increase in paracellular resistance and a decrease in permeability to the paracellular marker fluorescein, reflecting overall barrier strengthening in vitro. Apical effects were fully reversible upon washout. This indicates that Zn supplemented to feed was completely washed out during ex vivo jejunum preparation. We conclude that there is no evidence for long-term barrier effects through prophylactic Zn supplementation and that extracellular Zn acts acutely and reversibly from the apical side via tightening the paracellular route, thus counteracting leak-flux diarrhea.NEW & NOTEWORTHY Therapeutically administered Zn successfully treats diarrhea in veterinary and human medicine. Here we present data that Zn strengthens the porcine jejunal epithelial barrier by reversibly tightening the paracellular route for inorganic ions and small solutes. Acute or long-lasting Zn effects on transcellular transport (Cl^- secretion) were not detected. We therefore conclude that Zn is useful for acutely treating leak-flux diarrhea rather than secretory diarrhea. Suitability as prophylactic feed supplement, however, is questionable.

Distribution of optrA and cfr in florfenicol-resistant Staphylococcus sciuri of pig origin

A novel transferable oxazolidinone-phenicol resistance gene, optrA, which confers resistance to linezolid, the next-generation oxazolidinone tedizolid, and also to chloramphenicol and florfenicol, has been identified in enterococcal and staphylococcal species. Here, we investigated the epidemiology of optrA in florfenicol-resistant Staphylococcus spp. isolates of pig origin, and characterized the genetic context of oxazolidinone resistance genes in 20 optrA-positive florfenicol- and methicillin-resistant S. sciuri isolates, 11 (55%) of which also harbored the multi-resistance gene cfr. Pulsed-field gel electrophoresis and direct repeat unit (dru) typing of the 20 optrA-positive S. sciuri isolates revealed 17 patterns and four distinct dru types, respectively. Nine and six different arrangements of the optrA and cfr gene regions, respectively, were identified among the isolates. The arrangements optrA-araC-Tn558 or optrA-ΔTn558 were present in all optrA-positive isolates, and in three of them, ISEnfa5 and cfr were located immediately downstream of optrA. The cfr-carrying segment in eight isolates was similar to the corresponding region of the staphylococcal plasmid pWo28-3, in which the coexistence of cfr and optrA was identified for the first time.

Comparison of porous and nano zinc oxide for replacing high-dose dietary regular zinc oxide in weaning piglets

The aim of this study was to compare the effect of dietary supplementation with low dose of porous and nano zinc oxide (ZnO) on weaning piglets, and to evaluate the possibility of using them as an alternative to high dose of regular ZnO. Piglets were randomly allocated into four treatment groups fed with four diets: (1) basal diet (NC), (2) NC+ 3000 mg/kg ZnO (PC), (3) NC + 500 mg/kg porous ZnO (HiZ) and (4) NC + 500 mg/kg nano ZnO (ZNP). The result showed that piglets in HiZ group had less diarrhea than ZNP group (P < 0.05). Besides, there was no significant difference between PC, HiZ and ZNP groups in terms of serum malondialdeyhde (MDA) concentration and glutathione peroxidase (GSH-Px) activity (P > 0.05). Analysis of trace metal elements revealed that piglets fed with high dose of regular ZnO had the highest Zn level in kidney (P < 0.05), which may induce kidney stone formation. Additionally, a decrease in ileal crypt depth was observed in PC, HiZ and ZNP group, suggesting an effective protection against intestinal injury. Results of mRNA analysis in intestine showed that ZNP supplementation had better effects on up-regulated trefoil factor 3 (TFF3) and nuclear factor erythroid 2-related factor 2 (Nrf2) levels in duodenum and jejunum than HiZ did (P < 0.05), implying that nano ZnO may possess higher anti-inflammatory capacity than porous ZnO. In conclusion, dietary supplementation with low dose of porous and nano ZnO had similar (even better) effect on improving growth performance and intestinal morphology, reducing diarrhea and intestinal inflammatory as high dose of regular ZnO in weaning piglets. Compared with nano ZnO, porous ZnO had better performance on reducing diarrhea but less effect on up-regulation of intestinal TFF3 and Nrf2.

Zinc oxide enriched peat influence Escherichia coli infection related diarrhea, growth rates, serum and tissue zinc levels in Norwegian piglets around weaning: five case herd trials

Background

Zinc oxide (ZnO), commonly used to control post-weaning diarrhea in piglets, has been highlighted as of potential concern from an environmental perspective. The aim of this field trial was to examine effects of different sources and levels of ZnO added to peat on average daily weight gain (ADG), fecal score in pens and serum and tissue zinc (Zn) levels around time of weaning in order to reduce the environmental impact without loss of the beneficial effect of ZnO on intestinal health and growth. Five case herds with enterotoxic colibacillosis challenges were included. The piglets entered the study aged three or five weeks. All piglets received a commercial diet containing <150 mg Zn/ per kg of complete feed. Four treatment groups received commercial peat added A: uncoated ZnO, B: lipid microencapsulated ZnO, C: solely commercial peat or D: no peat (Farms 2 and 3).

Results

At Farms 1, 2 and 3, a significant effect of treatment was identified for fecal score (P < 0.05). Treatment A led to lower fecal scores compared to treatments C (P < 0.05) and D (P < 0.01). At Farms 2 and 3, there was a significant difference in individual average daily weight gain (iADG) between treatment A and D (P < 0.05). The iADG of piglets receiving treatment B did not differ significantly from treatment A.

Conclusions

In 2016, The European Medicines Agency’s Committee on Veterinary Medicinal Products concluded that the benefits of ZnO for the prevention of diarrhea in pigs do not outweigh the risks to the environment. Effective alternative measures to reduce the accumulation of Zn in the environment have not been identified. Our results imply that peat added low concentration of both coated and uncoated ZnO influences the gut health of weaned piglets reflected by enhanced weight gain and reduced occurrence of diarrhea. This preventive approach certainly represents a favourable alternative in the “One Health” perspective. It will also contribute to reduced antibiotic use in pig farming while diminishing the environmental consequences caused by ZnO.

Types and prevalence of extended-spectrum beta-lactamase producing Enterobacteriaceae in poultry

For several billion years, bacteria have developed mechanisms to resist antibacterial substances. In modern time, antibiotics are frequently used in veterinary and human medicine for prevention and treatment of diseases, globally still also for their growth promoting effects as feed additives. This complex situation has evolved in accelerating development and prevalence of multi-drug resistant bacteria in livestock and people. Extended-spectrum beta-lactamase (ESBL) producing bacteria are resistant to a wide range of ß-lactam antibiotics. They are currently considered as one of the main threats for the treatment of infections in humans and animals. In livestock and animal products, poultry and poultry products show the highest prevalence of ESBL-producers with CTX-M-1, TEM-52 and SHV-12 being the most common ESBL-types in poultry. Escherichia coli and Salmonella spp. are the bacteria in poultry, which carry ESBL-genes most frequently. ESBL-producing bacteria are present at every level of the poultry production pyramid and can be detected even in the meconium of newly hatched chicks. The environment close to poultry barns shows high prevalence rates of these bacteria and contributes to an ongoing infection pressure with further ESBL-types. Probiotics have been shown to successfully reduce ESBL-producers in chicken, as well as ESBL-gene transfer. Other feed additives, such as zinc and copper, increase the prevalence of ESBL-producing bacteria when fed to animals. To our best knowledge, this is the first publication presenting a comparative overview of the prevalence of ESBL-types using data from different countries. To reduce the hazard for public health from poultry carrying high numbers of ESBL-producers, preventive measurements must include the surrounding environment and avoidance of antibiotic usage at all levels of the production pyramid. The first results, of the research on the impact of feed additives on the spread of ESBL-genes, indicate the diet as a further, possible magnitude of influence.

Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health

Weaning is a critical event in the pig's life cycle, frequently associated with severe enteric infections and overuse of antibiotics; this raises serious economic and public health concerns. In this review, we explain why gut microbiota dysbiosis, induced by abrupt changes in the diet and environment of piglets, emerges as a leading cause of post-weaning diarrhea, even if the exact underlying mechanisms remain unclear. Then, we focus on nonantimicrobial alternatives, such as zinc oxide, essential oils, and prebiotics or probiotics, which are currently evaluated to restore intestinal balance and allow a better management of the crucial weaning transition. Finally, we discuss how in vitro models of the piglet gut could be advantageously used as a complement to ex vivo and in vivo studies for the development and testing of new feed additives.

Copper and Zinc Tolerance in Bacteria Isolated from Fresh Produce

The continued agricultural exposure of bacteria to metals such as copper and zinc may result in an increased copper tolerance through the food chain. The aim of this study was to determine the Cu and Zn tolerance of bacteria from fresh produce (cucumber, zucchini, green pepper, tomato, lettuce, vegetable salad, broccoli, cabbage, carrot, green onion, onion, and mango). Isolates (506 aerobic mesophiles) from 12 different food produce products were tested for growth in a range of Cu and Zn concentrations. Selected isolates were identified using 16S rDNA sequencing, and the presence of metal resistance genes was studied using PCR amplification. More than 50% of the isolates had MICs for copper sulfate greater than 16 mM, and more than 40% had MICs greater than 4 mM for zinc chloride. Isolates with high levels of tolerance to Cu and Zn were detected in all the produce products investigated. A selection of 51 isolates with high MICs for both Cu and Zn were identified as belonging to the genera Pseudomonas (28), Enterobacter (7), Serratia (4), Leclercia (1), Bacillus (10), and Paenibacillus (1). A study of the genetic determinants of resistance in the selected gram-negative isolates revealed a high incidence of genes from the pco multicopper oxidase cluster, from the sil cluster involved in Cu and silver resistance, and from the chromate resistance gene chrB. A high percentage carried both pco and sil. The results suggest that Cu and Zn tolerance, as well as metal resistance genes, is widespread in bacteria from fresh produce.

Post weaning diarrhea in pigs: risk factors and non-colistin-based control strategies

Post-weaning diarrhea (PWD) is one of the most serious threats for the swine industry worldwide. It is commonly associated with the proliferation of enterotoxigenic Escherichia coli in the pig intestine. Colistin, a cationic antibiotic, is widely used in swine for the oral treatment of intestinal infections caused by E. coli, and particularly of PWD. However, despite the effectiveness of this antibiotic in the treatment of PWD, several studies have reported high rates of colistin resistant E. coli in swine. Furthermore, this antibiotic is considered of very high importance in humans, being used for the treatment of infections due to multidrug-resistant (MDR) Gram-negative bacteria (GNB). Moreover, the recent discovery of the mcr-1 gene encoding for colistin resistance in Enterobacteriaceae on a conjugative stable plasmid has raised great concern about the possible loss of colistin effectiveness for the treatment of MDR-GNB in humans. Consequently, it has been proposed that the use of colistin in animal production should be considered as a last resort treatment only. Thus, to overcome the economic losses, which would result from the restriction of use of colistin, especially for prophylactic purposes in PWD control, we believe that an understanding of the factors contributing to the development of this disease and the putting in place of practical alternative strategies for the control of PWD in swine is crucial. Such alternatives should improve animal gut health and reduce economic losses in pigs without promoting bacterial resistance. The present review begins with an overview of risk factors of PWD and an update of colistin use in PWD control worldwide in terms of quantities and microbiological outcomes. Subsequently, alternative strategies to the use of colistin for the control of this disease are described and discussed. Finally, a practical approach for the control of PWD in its various phases is proposed.