Phenotypic and genotypic bacterial antimicrobial resistance in liquid pig manure is variously associated with contents of tetracyclines and sulfonamides

Antibiotic Residues and Zinc Concentrations in the Livers and Kidneys of Portuguese Piglets-Relationship to Antibiotic and Zinc Resistance in Intestinal Escherichia coli

Metal ions such as zinc and copper have been used as alternatives to antibiotics, to improve animal health and growth rates in pig farming. This study aims to determine antibiotic residues and Zn concentration in piglets' livers (n = 56) and kidneys (n = 60); and to examine the correlation between the use of Zn and antibiotics, and resistance to Zn and antibiotics of Escherichia coli isolated from piglets' faeces (n = 60). Samples were collected from randomly selected healthy piglets (n = 60); antibiotic residues were quantified by ultra-high-performance-liquid-chromatography time-of-flight mass spectrometry (UHPLC-ToF-MS); Zn was quantified using flame atomic absorption spectrometry (FAAS); microbiological methods were used for E. coli isolation, antibiotic susceptibility, and Zn minimal inhibitory concentration; and Real-Time PCR was used for gene detection. The presence of antibiotic residues and Zn concentrations in the liver was found to be negatively correlated, whilst no significant difference was observed in the kidney. In E. coli isolated from piglet faeces considered to be susceptible or multi-drug-resistant, no significant difference was found between Zn concentrations in the liver and in the kidney, which appears to indicate that Zn accumulated in the liver and in the kidney does not promote resistance to antibiotics in E. coli. The isolates showed tolerance to Zn which would suggest that antibiotic resistance and phenotypic tolerance to Zn in these isolates are not related. The genes zitB and zntA associated to Zn tolerance, were predominantly found in the more resistant Zn isolates. The findings provide insights on how Zn use in pig production maintains antibiotic resistance and metal tolerance in bacteria, with implications for One Health.

Adsorption and transformation of tetracyclines on alpha alumina particles with surface modification by anionic surfactant

The adsorption and transformation of tetracyclines (TCs) antibiotics, including oxytetracycline (OTC), chlortetracycline (CTC), and tetracycline (TC), on the sodium dodecyl sulfate (SDS) surfactant-modified α-Al₂O₃ particles were comprehensively investigated in this study. The TCs adsorption was significantly enhanced by using the modified adsorbents compared with the use of the unmodified adsorbents. The experimental conditions were systematically optimized and found to be pH 4, NaCl 1 mM, the contact time of 180 min, and the adsorbent dosage of 25 mg. mL^-1. The high maximum adsorption capacities were approximately 320, 85, and 91 mg. g^-1 for TC, OTC, and CTC, respectively. Meanwhile, the great removal efficiencies of the three antibiotics TC, OTC, and CTC were correspondingly 91.85, 88.4, and 98.3%. The TCs adsorption isotherm and kinetics on the SDS-modified α-Al₂O₃ particles mainly governed by the electrostatic and hydrophobic interactions were clarified by a suitable two-step model, the Fourier transform infrared spectroscopy (FT-IR) and zeta potential measurements. Meanwhile, the TCs structural transformation determined by the liquid chromatography with tandem mass spectrometry (LC-MS/MS) measurement was promoted through the adsorption on the α-Al₂O₃ surface. The TCs transformation rates strongly affected by the TCs adsorption were in the order of CTC > TC > OTC. The found results are promised that the SDS-modified α-Al₂O₃ particles might behave as high-performance adsorbents to remove the TCs from aqueous solutions.

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.

Tracking Antimicrobial Resistant E. coli from Pigs on Farm to Pork at Slaughter

Antimicrobial-resistant bacteria might be transferred via the foodchain. However, that risk is rarely tracked along different production steps, e.g., from pigs at farm to meat. To close that gap, we performed a prospective study in four conventional and two organic farms from the moment pigs entered the farm until meat sampling at slaughter. Antimicrobial use was recorded (0 to 11 agents). Antimicrobial susceptibility (AMS) against 26 antibiotics, including critically important substances, was tested by microdilution, and tetA-tetB-sulI-sulII-strA-strB-bla-CTXM-qacEΔ1 were included in PCR-genotyping. From 244 meat samples of 122 pigs, 54 samples (22.1%) from 45 animals were positive for E. coli (n = 198). MICs above the breakpoint/ECOFF occurred for all antibiotics except meropenem. One isolate from organic farming was markedly resistant against beta-lactams including fourth-generation cefalosporines. AMS patterns differed remarkably between isolates from one piece of meat, varying from monoresistance to 16-fold multiresistance. Amplicon-typing revealed high similarity between isolates at slaughter and on farm. Prior pig lots andeven the farmer might serve as reservoirs for E. coli isolated from meat at slaughter. However, AMS phenotyping and genotyping indicate that antimicrobial resistance in E. coli is highly dynamic, impairing reliable prediction of health risks from findings along the production chain.

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil

Antibiotic residues and antibiotic resistance genes can enter the environment via fertilization with calf and pig manure. In a longitudinal study, nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) and 56 antibiotic residues were investigated in 288 soil samples and 8 corresponding slurry samples from 6 pig farms and 2 veal farms using qPCR and LC-MS/MS, respectively. A significant increase in gene copy number of tet(M), erm(B), erm(F) and sul2 was observed in all the soil layers between sampling times prior to (T1) and 2-3 weeks after fertilization (T3). Tet(B), tet(Q) and tet(L) were least abundant in the soil among the genes tested. From 7 classes of antibiotics, 20 residues were detected in soil and slurry using an optimized and validated extraction method. Flumequine was detected in all soil samples in concentrations below 100 μg/kg despite being detected in only half of the corresponding slurry samples. Doxycycline, oxytetracycline, lincomycin and sulfadiazine were also frequently detected in concentrations ranging from 0.1 μg/kg to 500 μg/kg and from 2 μg/kg and 9480 μg/kg in soil and slurry, respectively. Furthermore a positive association between the presence of antibiotic residues (total antibiotic load) and antibiotic resistance genes in soil was found. One possible explanation for this is a simultaneous introduction of antibiotic residues and resistance genes upon application of animal slurry.

Microbially-mediated synthesis of activated carbon derived from cottonseed husks for enhanced sulfanilamide removal

This study provided a novel pathway to develop activated carbon with enhanced adsorption performance via feedstock pretreatment by fungi. The growth of Pleurotus ostreatus on cottonseed husks offered this feedstock an advantageous pore size for porous carbon making. The prepared activated carbons derived from cottonseed husks (CSH-ACs) during different fungal growth periods exhibited extraordinary performance than commercial activated carbon for sulfanilamide adsorptive removal. Their experimental data of adsorption capacities for sulfanilamide were 139.43, 146.15, and 146.16 mg g^-1, respectively. The adsorption behaviors of sulfanilamide on CSH-ACs were evaluated by kinetic, isotherm and thermodynamic models. Pore filling, hydrogen-bond forming and π-π staking interactions all contributed to the rapid sulfanilamide removal. The microporous-mesoporous structure, stronger hydrophilicity, and richer functional groups moieties owing to the lignocellulose decomposition in the plant wall significantly strengthened the adsorption process on the microbial-mediated activated carbon. The effects of pH and water impurities (H₂PO₄^-, CO₃^2-, SO₄^2-, Cl^-, and humic acid) on sulfanilamide removal were investigated by a single factor experimental design. Results indicated that CSH-ACs were suitable for sulfanilamide removal in actual wastewater treatment with wide pH adaptability and resilience to interference.

Plasmid-Encoded AmpC and Extended-Spectrum Beta-Lactamases in Multidrug-Resistant Escherichia coli Isolated from Piglets in Portugal

Considering the concept of "One Health," the aim of this study was to determine susceptibility profiles of Escherichia coli in piglets' intestinal microbiota from different farms in Portugal. Beyond antimicrobial susceptibility, the occurrence of multiple antibiotic resistance and detection of phenotypic/genotypic extended-spectrum beta-lactamases (ESBLs) and plasmid mediated AmpC beta-lactamases (pAmpC) were done. From 10 different pig farms, 340 E. coli isolates were obtained from 75 feces samples. Susceptibility to amoxicillin-clavulanic acid (AMC), piperacillin (PIP), cefoxitin (FOX), ceftazidime (CAZ), cefepime (FEP), aztreonam (AZT), imipenem (IP), amikacin (AK), ciprofloxacin (CIP), and trimethoprim-sulfamethoxazole (SXT) was determined. Five-gene panel for amplification of bla genes was used for ESBL (TEM, SHV, CTX-M) and pAmpC (CMY-2, ACC). Among E. coli isolates, 209 were distributed in three resistance profiles: 57.7% MDR, 3.5% extensively drug-resistance (XDR) (resistant to CIP, SXT, and beta-lactams, except IP, with variability to AK) and 0.3% pandrug-resistance (PDR) (resistant to all antibiotics used). pAmpC and/or ESBLs genes were presented in 65% of the isolates. Presence of different associations of bla genes in the same isolate was the most observed (31%), and the most common were an ESBL (TEM) and a pAmpC (CMY-2). Presence of three or four bla genes in various associations were detected. These isolates were very resistant, especially those with four genes, which were resistant to beta-lactams (except IP), CIP, and SXT. This study showed a surprisingly high rate of MDR E. coli isolated in Portuguese piglets, with enzymes that impair activity of the most used antibiotics in human therapeutic.

Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants

Studies considering environmental multidrug-resistant Acinetobacter spp. are scarce. The application of manure on agricultural fields is one source of multidrug-resistant bacteria from livestock into the environment. Here, Acinetobacter spp. were quantified by quantitative polymerase chain reaction in manure applied to biogas plants and in the output of the anaerobic digestion, and Acinetobacter spp. isolated from those samples were comprehensively characterized. The concentration of Acinetobacter 16S ribosomal ribonucleic acid (rRNA) gene copies per g fresh weight was in range of 106-108 in manure and decreased (partially significantly) to a still high concentration (105-106) in digestates. 16S rRNA, gyrB-rpoB and blaOXA51-like gene sequencing identified 17 different Acinetobacter spp., including six A. baumannii strains. Multilocus sequence typing showed no close relation of the six strains with globally relevant clonal complexes; however, they represented five novel sequence types. Comparative genomics and physiological tests gave an explanation how Acinetobacter could survive the anaerobic biogas process and indicated copper resistance and the presence of intrinsic beta-lactamases, efflux-pump and virulence genes. However, the A. baumannii strains lacked acquired resistance against carbapenems, colistin and quinolones. This study provided a detailed characterization of Acinetobacter spp. including A. baumannii released via manure through mesophilic or thermophilic biogas plants into the environment.

Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil?

The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.

Sulfamethoxazole affects the microbial composition and antibiotic resistance gene abundance in soil and accumulates in lettuce

Pot experiments were set up to simulate the soil contamination by three initial concentrations of sulfamethoxazole (SMX) (S1, 100 mg/kg; S2, 200 mg/kg; S3, 300 mg/kg). The content of SMX in soil and its accumulation in lettuce were analysed. Additionally, the effects of SMX on soil microorganisms and antibiotic resistance genes were studied by Illumina high-throughput sequencing and droplet digital polymerase chain reaction (ddPCR). The results demonstrated that the SMX content in soil reduced by 97%, 86% and 75% in the S1, S2 and S3 treatment groups after 120 days, respectively. The accumulated SMX in lettuce was positively correlated with the initial concentration of SMX in soil. SMX contamination significantly reduced the bacterial diversity and altered the composition of bacterial and fungal communities in soil. The dominant bacterial and fungal genera in the SMX-contaminated soil were obviously different from those in the control soil. The relative abundance of sul1 (sulfonamide resistance gene) remarkably increased in the SMX-contaminated soil, while that of other ARGs, such as sul2 and tetracycline and quinolone resistance genes, showed no significant change.

Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants

BACKGROUND

Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted.

RESULTS

VRE isolates, including E. faecalis (n = 24), E. faecium (n = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium (p < 0.001) and E. faecalis (p < 0.001) and with the number of AMR genes in E. faecium (p = 0.005). Genes conferring vancomycin resistance, including vanA and vanM (E. faecium), vanG (E. faecalis), and vanC (E. casseliflavus/E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium, than E. casseliflavus and E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers.

CONCLUSIONS

There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.

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.

Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history

Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.

Influence of metal ions on sulfonamide antibiotics biochemical behavior in fiber coexisting system

Metal ions and fiber are common compounds in the livestock and poultry manure, which will affect the fate of organic compounds in aqueous environment. However, limited research has addressed the effect of coexisting metal ions and fiber on the biodegradation of sulfonamide antibiotics. Accordingly, a compositing study was performed to assess the effect of metal ions (Fe³⁺ and Cu²⁺) on the biodegradation of sulfadimethoxine sodium salt (SDM) in the presence of fiber. The enhanced adsorption of SDM onto fiber in the presence of metal ions can be attributed to the π⁺-π electron donor acceptor (EDA) interaction. The microbial (Phanerochaete chrysosprium) could easily attach onto fiber forming attached microbial, and the degradation rates of SDM of immobilized bacteria in the presence of Fe³⁺ were 100%, which were significantly higher than those of free bacteria (45%). This study indicates that Fe³⁺ and fiber could enhance the biodegradation of SDM. Fiber acts as adsorbent, carrier, and substrate which enhanced the removal of SDM.

Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis

This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.

Review of antibiotic resistance in China and its environment

Antibiotic resistance is a global health crisis linked to increased, and often unrestricted, antibiotic use in humans and animals. As one of the world's largest producers and consumers of antibiotics, China is witness to some of the most acute symptoms of this crisis. Antibiotics and antibiotic resistance genes (ARGs) are widely distributed in surface water, sewage treatment plant effluent, soils and animal wastes. The emergence and increased prevalence of ARGs in the clinic/hospitals, especially carbapenem-resistant gram negative bacteria, has raised the concern of public health officials. It is important to understand the current state of antibiotic use in China and its relationship to ARG prevalence and diversity in the environment. Here we review these relationships and their relevance to antimicrobial resistance (AMR) trends witnessed in the clinical setting. This review highlights the issues of enrichment and dissemination of ARGs in the environment, and also future needs in mitigating the spread of antibiotic resistance in the environment, particularly under the 'planetary health' perspective, i.e., the systems that sustain or threaten human health.

Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics

Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days' incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs.

Comparative genomics of Enterococcus spp. isolated from bovine feces

Background

Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics.

Results

We present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance.

Conclusions

This study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0962-1) contains supplementary material, which is available to authorized users.

Effect of different sulfadimidine addition methods on its degradation behaviour in swine manure

Sulfadimidine (SM2) is commonly used in the swine industry and enters the environment via faeces. In recent years, advances in the ecotoxicology of SM2 have become a popular research interest with two common research methods including swine manure collection from swine fed with a diet containing SM2 and directly adding SM2. The purpose of this experiment was to compare SM2 degradation behaviour in pig manure with two different SM2 addition methods. The results showed that the degradation half-lives of SM2 in manure from SM2-fed swine treatment were 33.2 and 32.0 days at the initial addition level of SM2 at 32.1 and 64.3 mg/kg, respectively. This was significantly longer than that in manure directly adding SM2 treatment with the half-lives of 21.4 and 14.8 days. The metabolite of SM2 N⁴-acetyl-sulfamethazine occurred in manure from SM2-fed swine treatment but was not detected in directly adding SM2 treatment. The pH in manure from SM2-fed swine treatment was significantly lower than that in directly adding SM2 treatment, but the values of organic carbon, total nitrogen, and electrical conductivity in manure from SM2-fed swine treatment were significantly higher than those in manure directly adding SM2 treatment. Meanwhile, although the copy number of bacteria had no significant difference between two treatments, there was a significant difference in bacteria diversity. Results of the present study demonstrated that the presence of the metabolites, chemical property, and microbial diversity might be the reason for different SM2 degradation behaviours on different addition methods. Thus, the method using manure with SM2 collected from swine could obtain more accurate results for the ecotoxicological study of SM2.

Dissipation kinetics of oxytetracycline, tetracycline, and chlortetracycline residues in soil

The dissipation of different residual states of tetracycline antibiotics (TCs) including oxytetracycline (OTC), tetracycline (TC), and chlortetracycline (CTC) laboratory microcosm systems was investigated in this study. The residues were fractionated by stepwise extractions into aqueous state (KCl solution extracts), organic state (MeOH extracts), residual state I (citric acid-sodium citrate buffer and ethyl acetate extracts) and residual state II (acetonitrile-EDTA-McIlvaine buffer extracts) for accurate evaluation of TCs pollution. The antibiotics in the aqueous state were hardly detected, whereas the antibiotics in the organic state dissipated relatively fast (not detectable within 15 days after application) and followed simple first-order kinetics (SFOK) (R (2) from 0.929 to 0.990). While first-order double-exponential decay model (FODED) (R (2) from 0.840 to 0.999) and availability-adjusted first-order model (AAFO) (R (2) from 0.939 to 0.999) had a better fit on the dissipation of both residue state I and II than SFOK. TCs in these states were likely sequestered into a dormant undegradable phase since no degradation product was detected during the entire experiment. In addition, the overall 50 % dissipation values (i.e., stability) of the three TCs were OTC > TC > CTC. The TCs tend to dissipate faster in the high water content and organic matter soil.

Sampling and Pooling Methods for Capturing Herd Level Antibiotic Resistance in Swine Feces using qPCR and CFU Approaches

The aim of this article was to define the sampling level and method combination that captures antibiotic resistance at pig herd level utilizing qPCR antibiotic resistance gene quantification and culture-based quantification of antibiotic resistant coliform indicator bacteria. Fourteen qPCR assays for commonly detected antibiotic resistance genes were developed, and used to quantify antibiotic resistance genes in total DNA from swine fecal samples that were obtained using different sampling and pooling methods. In parallel, the number of antibiotic resistant coliform indicator bacteria was determined in the same swine fecal samples. The results showed that the qPCR assays were capable of detecting differences in antibiotic resistance levels in individual animals that the coliform bacteria colony forming units (CFU) could not. Also, the qPCR assays more accurately quantified antibiotic resistance genes when comparing individual sampling and pooling methods. qPCR on pooled samples was found to be a good representative for the general resistance level in a pig herd compared to the coliform CFU counts. It had significantly reduced relative standard deviations compared to coliform CFU counts in the same samples, and therefore differences in antibiotic resistance levels between samples were more readily detected. To our knowledge, this is the first study to describe sampling and pooling methods for qPCR quantification of antibiotic resistance genes in total DNA extracted from swine feces.

Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA

Universal primers targeting the bacterial 16S-rRNA-gene allow quantification of the total bacterial load in variable sample types by qPCR. However, many universal primer pairs also amplify DNA of plants or even of archaea and other eukaryotic cells. By using these primers, the total bacterial load might be misevaluated, whenever samples contain high amounts of non-target DNA. Thus, this study aimed to provide primer pairs which are suitable for quantification and identification of bacterial DNA in samples such as feed, spices and sample material from digesters. For 42 primers, mismatches to the sequence of chloroplasts and mitochondria of plants were evaluated. Six primer pairs were further analyzed with regard to the question whether they anneal to DNA of archaea, animal tissue and fungi. Subsequently they were tested with sample matrix such as plants, feed, feces, soil and environmental samples. To this purpose, the target DNA in the samples was quantified by qPCR. The PCR products of plant and feed samples were further processed for the Single Strand Conformation Polymorphism method followed by sequence analysis. The sequencing results revealed that primer pair 335F/769R amplified only bacterial DNA in samples such as plants and animal feed, in which the DNA of plants prevailed.

Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup

Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.

Diverse antibiotic resistance genes in dairy cow manure

Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings.

The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.

Insusceptibility to disinfectants in bacteria from animals, food and humans-is there a link to antimicrobial resistance?

Enterococcus faecalis (n = 834) and Enterococcus faecium (n = 135) from blood and feces of hospitalized humans, from feces of outpatients and livestock and from food were screened for their susceptibility to a quaternary ammonium compound (didecyldimethylammoniumchloride, DDAC) and to 28 antibiotics by micro-/macrodilution. The maximum DDAC-MIC in our field study was 3.5 mg/l, but after adaptation in the laboratory, MIC values of 21.9 mg/l were observed. Strains for which DDAC had MICs > 1.4 mg/l ("non-wildtype," in total: 46 of 969 isolates/4.7%) were most often found in milk and dairy products (14.6%), while their prevalence in livestock was generally low (0-4%). Of human isolates, 2.9-6.8% had a "non-wildtype" phenotype. An association between reduced susceptibility to DDAC, high-level-aminoglycoside resistance and aminopenicillin resistance was seen in E. faecium (p < 0.05). No indications for a common source of non-wildtype strains were found by RAPD-PCR; however, several non-wildtype E. faecalis shared the same variant of the emeA-gene. In addition, bacteria (n = 42) of different genera were isolated from formic acid based boot bath disinfectant (20 ml of 55% formic acid/l). The MICs of this disinfectant exceeded the wildtype MICs up to 20-fold (staphylococci), but were still one to three orders of magnitude below the used concentration of the disinfectant (i. e., 1.1% formic acid). In conclusion, the bacterial susceptibility to disinfectants still seems to be high. Thus, the proper use of disinfectants in livestock surroundings along with a good hygiene praxis should still be highly encouraged. Hints to a link between antibiotic resistance and reduced susceptibility for disinfectants-as seen for E. faecium-should be substantiated in further studies and might be an additional reason to confine the use of antibiotics.

Effects of hydrothermal liquefaction on the fate of bioactive contaminants in manure and algal feedstocks

This study investigated the effects of hydrothermal liquefaction (HTL) on the fate of bioactive compounds (BACs) often present with wet biosolids from wastewater, manure, or algae. Tracking radiolabeled (14)C for two BACs showed that 60-79% of the carbon was transferred to the HTL raw oil product, and most of the rest was found in the aqueous product. In the presence of both swine manure and Spirulina biomass feedstocks, HTL provided essentially complete removal of three BACs when operated at 300°C for ≥ 30 min. Experiments with both natural transformation and high-efficiency transformation showed that HTL provided complete deactivation of antibiotic resistant genes for all tested HTL conditions (250-300°C, 15-60 min reaction time). Thus, incorporating HTL into wastewater treatment systems can simultaneously produce valuable bio-crude oil, provide effective removal of BACs and disrupt the natural pathways for antibiotic resistant gene transfer from manure and wastewater biosolids to the environment.

Quantitatively modeling soil-water distribution coefficients of three antibiotics using soil physicochemical properties

Using 14 parameters featuring soil physicochemical properties and the partial least squares (PLSs) regression method, three quantitative models were respectively developed for the soil-water distribution coefficients (logK(d)) of oxytetracycline (OTC), sulfamethazine (SMZ) and norfloxacin (NOR) in 23 Chinese natural soil samples from cultivated lands in 19 provinces of China. The cross-validated correlation coefficients (Q(cum)(2)) of three models are 0.866, 0.765 and 0.868, and the standard deviations (SDs) are 0.16, 0.21 and 0.15 respectively. The high Q(cum)(2) and low SD values indicate that three models have high robustness and precise predictability. Six parameters including pH, clay content, free Fe oxides (DCB-Fe), free Al oxides (DCB-Al), Ca content and Al content are greatly significant in the OTC model, three ones including pH, clay content and DCB-Fe are greatly significant in the SMZ model, and five ones including pH, clay content, DCB-Fe, Ca content and organic matter (OM) are greatly significant in the NOR model. The high VIP values of pH (1.17-1.24), clay content (0.81-1.10) and DCB-Fe (0.90-0.99) show that the three sorts of soil physicochemical properties play dominant roles in governing the partition balance between soil and water of three antibiotics.

Heavy metals in liquid pig manure in light of bacterial antimicrobial resistance

Heavy metals are regularly found in liquid pig manure, and might interact with bacterial antimicrobial resistance. Concentrations of heavy metals were determined by atomic spectroscopic methods in 305 pig manure samples and were connected to the phenotypic resistance of Escherichia coli (n=613) against 29 antimicrobial drugs. Concentrations of heavy metals (/kg dry matter) were 0.08-5.30 mg cadmium, 1.1-32.0 mg chrome, 22.4-3387.6 mg copper, <2.0-26.7 mg lead, <0.01-0.11 mg mercury, 3.1-97.3 mg nickel and 93.0-8239.0 mg zinc. Associated with the detection of copper and zinc, resistance rates against β-lactams were significantly elevated. By contrast, the presence of mercury was significantly associated with low antimicrobial resistance rates of Escherichia coli against β-lactams, aminoglycosides and other antibiotics. Effects of subinhibitory concentrations of mercury on bacterial resistance against penicillins, cephalosporins, aminoglycosides and doxycycline were also demonstrated in a laboratory trial. Antimicrobial resistance in the porcine microflora might be increased by copper and zinc. By contrast, the occurrence of mercury in the environment might, due to co-toxicity, act counter-selective against antimicrobial resistant strains.

Feed supplemented with 3 different antibiotics improved food intake and decreased the activation of the humoral immune response in healthy weaned pigs but had differing effects on intestinal microbiota

The aim of this study was to determine the effects of 3 antibiotics used for pulmonary pathologies added in the feed of weaned pigs on growth performance, commensal microbiota, and immune response. At weaning, a total of 72 pigs were randomly assigned by BW and litter to 1 of the following diets: control (typical weaning diet), control + 400 mg of tilmicosin/kg, control + 600 mg of amoxicillin/kg, and control + 300 mg of doxycycline/kg. Individually penned pigs were slaughtered after 3 wk (12 pigs/treatment) or 4 wk (6 pigs/treatment). During the fourth week, all pigs received the control diet to test the residual effect of the antimicrobial supplementation. The antibiotic supplementation increased growth and feed intake during the first week (P < 0.01) and over the first 3 wk combined (P < 0.05). Gain-to-feed ratio tended to improve during the first week (P = 0.076) by the antibiotics compared with the control. Among the antibiotic treatments, no difference was observed in ADG and feed intake, which were also unchanged by the diet in the fourth week. The fecal enterobacteria counts were increased by amoxicillin on d 14 and 21 (P < 0.05 and 0.01, respectively) and were decreased by tilmicosin (P < 0.001) compared with the control. Amoxicillin decreased lactic acid bacteria (P < 0.01) counts compared with the control. The antibiotic supplementation tended to decrease total bacteria variability in the jejunum (Shannon index, P = 0.091) compared with the control. The antibiotic treatment decreased the mean total serum IgM concentration (P = 0.016) after 3 wk and did not change the mucosal histomorphometry of the small intestine. For tilmicosin, the observed positive action on piglet performance and feed intake can originate by the decreased costs of immune activation determined by the action on intestinal microbiota. For amoxicillin and doxycycline, the observation on intestinal and fecal microbiota seems to be not sufficient to explain their growth-promoting effect.

Adsorption of tetracycline on soil and sediment: effects of pH and the presence of Cu(II)

Tetracycline (TC) is frequently detected in the environment, however, knowledge on the environmental fate and transport of TC is still limited. Batch adsorption experiments of TC by soil and sediment samples were conducted. The distribution of charge and electrostatic potential of individual atoms of various TC species in the aqueous solution were determined using MOPAC version 0.034 W program in ChemBio3D Ultra software. Most of the adsorption isotherms on the soil, river and marine sediments were well fitted with the Freundlich and Polanyi-Manes (PMM) models. The single point organic carbon (OC)-normalized adsorption distribution coefficients (K(OC)) and PMM saturated adsorption capacity (Q(OC)(0)) values of TC were associated with the mesopore volume and clay content to a greater extent, indicating the mesopore volume of the soil and sediments and their clay content possibly influenced the fate and transport of TC in the natural environment. The adsorption of TC on soil and sediments strongly depended on the pH and presence of Cu(II). The presence of Cu(II) facilitated TC adsorption on soil and sediments at low pH (pH<5), possibly due to the metallic complexation and surface-bridging mechanism by Cu(II) adsorption on soil and sediments. The cation exchange interaction, metallic complexation and Coulombic interaction of mechanisms for adsorption of TC to soils and sediments were further supported by quantum chemical calculation of various TC species in different pH.

Comparative analysis of the bacterial flora of vegetables collected directly from farms and from supermarkets in Germany

A total of 1,001 vegetables were collected from 13 farms and 11 supermarkets in Bavaria, Germany; 722 samples were positive for coliforms (mostly Enterobacter cloacae; n = 176). Escherichia coli were detected in 34, Pseudomonas spp. in 439, Salmonella spp. in 1, Enterococcus spp. in 682, and Listeria spp. in 11 samples. Prevalence of all investigated genera tended to be lower in samples collected at the supermarket. However, prevalence of Pseudomonas fluorescens was higher in supermarket samples. Cereals/bulbous vegetables were less contaminated than root vegetables/salads. Fruit vegetables seem to be often subsequently contaminated in the retail market. Compared to foods of animal origin, prevalence of pathogenic bacteria is low. Particularly, in 1,001 investigated vegetables, only four L. monocytogenes and one Salmonella enterica have been found. Almost all of the detected microorganisms are reported to be opportunistic pathogens, if only in rare cases. Therefore, fresh produce should be washed or peeled before it is eaten raw.

Antibiotic resistance gene spread due to manure application on agricultural fields

The usage of antibiotics in animal husbandry has promoted the development and abundance of antibiotic resistance in farm environments. Manure has become a reservoir of resistant bacteria and antibiotic compounds, and its application to agricultural soils is assumed to significantly increase antibiotic resistance genes and selection of resistant bacterial populations in soil. The genome location of resistance genes is likely to shift towards mobile genetic elements such as broad-host-range plasmids, integrons, and transposable elements. Horizontal transfer of these elements to bacteria adapted to soil or other habitats supports their environmental transmission independent of the original host. The human exposure to soil-borne resistance has yet to be determined, but is likely to be severely underestimated.

Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems

Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre- and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices.

Sewage sludge and liquid pig manure as possible sources of antibiotic resistant bacteria

Within the last decades, the environmental spread of antibiotic resistant bacteria has become a topic of concern. In this study, liquid pig manure (n=305) and sewage sludge (n=111) - used as agricultural fertilizers between 2002 and 2005 - were investigated for the presence of Escherichia coli, Enterococcus faecalis and Enterococcus faecium. Bacteria were tested for their resistance against 40 chemotherapeutics including several "reserve drugs". E. coli (n=613) from pig manure were at a significantly higher degree resistant to streptomycin, doxycycline, spectinomycin, cotrimoxazole, and chloramphenicol than E. coli (n=116) from sewage sludge. Enterococci (Ent. faecalis, n=387, and Ent. faecium, n=183) from pig manure were significantly more often resistant to high levels of doxycycline, rifampicin, erythromycin, and streptomycin than Ent. faecalis (n=44) and Ent. faecium (n=125) from sewage sludge. Significant differences in enterococcal resistance were also seen for tylosin, chloramphenicol, gentamicin high level, fosfomycin, clindamicin, enrofloxacin, moxifloxacin, nitrofurantoin, and quinupristin/dalfopristin. By contrast, aminopenicillins were more effective in enterococci from pig manure, and mean MIC-values of piperacillin+tazobactam and third generation cefalosporines were significantly lower in E. coli from pig manure than in E. coli from sewage sludge. 13.4% (E. coli) to 25.3% (Ent. faecium) of pig manure isolates were high-level multiresistant to substances from more than three different classes of antimicrobial agents. In sewage sludge, high-level-multiresistance reached from 0% (Ent. faecalis) to 16% (Ent. faecium). High rates of (multi-) resistant bacteria in pig manure emphasize the need for a prudent - cautious - use of antibiotics in farm animals.

Resistance to linezolid in a porcine Clostridium perfringens strain carrying a mutation in the rplD gene encoding the ribosomal protein L4

Coresistance to human reserve antibiotics can be selected by antibiotics used in veterinary medicine. A Clostridium perfringens strain isolated from pig manure was resistant to the reserve drug linezolid and, simultaneously, resistant against florfenicol and erythromycin. We detected a new mutation in a highly conserved region of rplD, encoding protein L4 of the 50S ribosomal subunit. This is the first genetic substantiation of linezolid resistance in the genus Clostridium.