Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries (original) (raw)
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Gut Microbiomes of Pigs Grown in Organic and Conventional Dietary Regimens
Journal of Veterinary Science and Animal Husbandry, 2017
In animal production, antibiotics are used at sub-therapeutic and therapeutic levels for growth promotion and disease prevention. Using antibiotics can result in selecting for drug resistant microorganisms that may spread to humans through consumption of contaminated food. Lately, an increased interest in organic farming, where animals are grown without antibiotics, has been popular amongst the consumers. It is believed that organic farming will reduce antimicrobial resistance in microorganisms. However, the animals grown organically may be prone to diseases, and other microorganisms may thrive in the gut, that may be potentially harmful to humans. We analyzed the DNA of fecal samples of pigs grown under conventional and organic dietary regimens and detected the presence of genes that causes antibiotic resistance. The microbiomes of gut in swine grown under these two dietary regimens exhibited little difference in composition and exhibited the presence of Bacteriodetes, Firmicutes and Proteobacteria at the phyla level and Prevotella, Lactobacillus, Barnesiella, Proteus, Fecalibacteria, Escherichia coli and Shigella at the genus level. Presence of eighty seven antibiotic resistance genes, tested by real-time PCR, exhibited the presence of more antibiotic resistance genes in guts of swine grown in conventional diet than under organic conditions. This pilot study may lead to comprehensive research on the composition of microbiomes in pigs in large production environment allowing formulation of strategies that may eventually reduce prevalence and dissemination of antibiotic resistance genes in the guts of animals.
Microbiome
Background The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Results Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on thos...
Journal of Antimicrobial Chemotherapy, 2022
Objectives The occurrence and zoonotic potential of antimicrobial resistance (AMR) in pigs and broilers has been studied intensively in past decades. Here, we describe AMR levels of European pig and broiler farms and determine the potential risk factors. Methods We collected faeces from 181 pig farms and 181 broiler farms in nine European countries. Real-time quantitative PCR (qPCR) was used to quantify the relative abundance of four antimicrobial resistance genes (ARGs) [aph(3′)-III, erm(B), sul2 and tet(W)] in these faeces samples. Information on antimicrobial use (AMU) and other farm characteristics was collected through a questionnaire. A mixed model using country and farm as random effects was performed to evaluate the relationship of AMR with AMU and other farm characteristics. The correlation between individual qPCR data and previously published pooled metagenomic data was evaluated. Variance component analysis was conducted to assess the variance contribution of all factors....
International Conference on the Epidemiology and Control of Biological, Chemical and Physical Hazards in Pigs and Pork
Antimicrobials have been widely used in veterinary medicine for disease treatment, disease prevention, and growth promotion. Although, the mechanisms about in-feed additives use are still not completely understood, it is accepted that its use improves feed efficiency by reducing the microbial load in the intestinal tract, thereby reducing the pressure on the immune system and increasing energy availability for the animal. However, disruption to commensal bacterial communities by antibiotics in some cases can increase the gut colonization by pathogenic bacteria. In this sense, the aim of this study was to evaluate the Escherichia coli antibiotic resistance and the gut microbiota profile from pigs raised in Brazilian farms with different in-feed antimicrobials protocols. Pigs from four farms with distinct antibiotic usage, including one farm that used no antibiotics, were followed from weaning to finishing, and the frequency of antimicrobial resistance and gut bacterial profile by 16S rRNA gene sequencing were evaluated. The gut microbial community structure was the same among all groups of pigs despite different antibiotic use on the farms; however, the antimicrobial resistance profiles of E. coli isolates were different between groups. One farm administered seven antibiotics at different times, and E. coli isolates from these pigs showed higher frequency of resistance and multidrug resistance as compared with samples from the farm that did not administer in-feed antimicrobials. The phenotypes included resistance to drugs considered critically important antimicrobial agents in veterinary medicine (ampicillin, ciprofloxacin, florfenicol, sulfonamide and tetracycline) as well as one highly important antibiotic in human medicine (colistin). Resistant E. coli strains were screened for the presence of the mcr-1 gene by PCR. The colistin-resistant strains were positive for the presence of the mcr-1 gene. These results suggest that although different antibiotic uses on-farm might not impact microbial community structure, it does impact bacterial functions, namely antibiotic resistance. Our results show that prudent use of antimicrobials is important for decreasing selective pressure for antibiotic resistance gene evolution.
2008
Background: The project "Antibiotic resistance in bacteria of animal origin-II" (ARBAO-II) was funded by the European Union (FAIR5-QLK2-2002-01146) for the period 2003-05. The aim of this project was to establish a program for the continuous monitoring of antimicrobial susceptibility of pathogenic and indicator bacteria from food animals using validated and harmonised methodologies. In this report the first data on the occurrence of antimicrobial resistance among bacteria causing infections in pigs are reported. Methods: Susceptibility data from 17,642 isolates of pathogens and indicator bacteria including Actinobacillus pleuropneumoniae, Streptococcus suis and Escherichia coli isolated from pigs were collected from fifteen European countries in 2002-2004.
Surveillance of Antimicrobial Resistance in Pigs using Escherichia coli faecal isolates
Background: Resistant and multi drug resistant bacteria in food animals threaten food security and public health worldwide. Thus, periodic surveillance of antibiotic resistance among bacteria isolated from food animals is recommended. Hence, 50 Escherichia coli strains isolated from 50 pig faecal samples, each from one pig farm in Ashanti region, Ghana were used as indicators of resistance in pigs using eight antibiotics. Results: 72% and 42% of the isolates were resistant and multi drug resistant respectively. Resistance to streptomycin (22%) was highest, followed by amoxicillin (20%), sulphamethoxazole-trimethoprim (10%), tetracycline (8%) and doxycycline (6%); these closely reflected the antibiotic usage patterns of the farmers. Most strains showed multi drug resistance to amoxicillin and streptomycin (26%) and amoxicillin, streptomycin and tetracycline (24%). Multidrug resistance to both tetracycline and sulphamethoxazole-trimethoprim (16%), tetracycline and doxycycline (12%) and streptomycin and norfloxacin (12%) were substantial. Cross resistance to antibiotics not used on the farms (tetracycline, doxycycline, amoxicillin and ciprofloxacin) was observed. Conclusion: The selection of resistant and multidrug resistant phenotypes in pigs is influenced by antibiotic use by pig farmers and could result in resistant food-borne bacterial infections to consumers, farmers and abattoir workers alongside environmental contamination with resistant genes. Prudent antibiotic use and better farm waste handling practices are advised to safeguard food security and public health
Microbiome profiling of commercial pigs from farrow to finish
Journal of animal science, 2018
Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig's baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction ...
Journal of Veterinary Research, 2020
Introduction Land application of manure that contains antibiotics and resistant bacteria may facilitate the establishment of an environmental reservoir of antibiotic-resistant microbes, promoting their dissemination into agricultural and natural habitats. The main objective of this study was to search for acquired antibiotic resistance determinants in the gut microbiota of wild boar populations living in natural habitats. Material and Methods Gastrointestinal samples of free-living wild boars were collected in the Zemplén Mountains in Hungary and were characterised by culture-based, metagenomic, and molecular microbiological methods. Bioinformatic analysis of the faecal microbiome of a hunted wild boar from Japan was used for comparative studies. Also, shotgun metagenomic sequencing data of two untreated sewage wastewater samples from North Pest (Hungary) from 2016 were analysed by bioinformatic methods. Minimum spanning tree diagrams for seven-gene MLST profiles of 104 E. coli stra...
Scientific reports, 2017
The external environment plays a critical role in shaping the structure of the gut microbiome. One potential health threat lies in the release of antibiotic resistant genes (ARGs) from cross-contaminated microbiomes. We focused this study on a comparison of fecal microbial composition and antibiotic resistant genes between farm workers, local villagers and swine. We used a high-throughput next-generation sequencing of 16S rRNA and real-time PCR for these studies. Our results indicated that workers had less species diversity as compared to the local villagers. Moreover, the bacterial communities of the farm workers, the local villagers and swine feces were clearly divided into three groups. The workers had a greater abundance of Proteobacteria as compared to swine and the local villagers. The Clostridiaceae in the workers and swine were more abundant than the local villagers. In addition, there were ARG differences between the farm workers or local villager's and swine feces. The...