Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples.

Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a method implementing TruSeq high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant gene targets representing a full-spectrum of antibiotic resistance classes common to environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within complex environmental samples originated from manure, soil, and livestock feces, in addition to a mock-community reference to assess sensitivity and specificity.

Genomic Changes within a Subset of IncI2 Plasmids Associated with Dissemination of Genes and Other Important Antimicrobial Resistance Determinants.

IncI2 plasmids appear to have only recently become associated with resistance genes; however, their tendency to carry resistance to the antibiotics of last resort and their widespread distribution increase their relative importance. In this study, we describe lineages within this plasmid family that have an increased likelihood of acquisition of antimicrobial resistance genes. Globally distributed -carrying IncI2 plasmids were found to cluster with other IncI2 plasmids carrying extended-spectrum beta-lactamase genes, and separately from the non-resistant IncI2 plasmids.

Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome.

Piglets are often weaned between 19 and 22 days of age in North America, although in some swine operations this may occur at 14 days or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown.

Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. isolated from pigs subjected to different antimicrobial administration protocols.

The antimicrobial resistance (AMR) in human and animal pathogens is a global concern, and antimicrobial use (AMU) is considered the most important driver for its increase. The aim of this study was to assess AMR in Escherichia coli and Enterococcus spp. in faecal samples of pigs subjected to four different AMU protocols from birth to finishing: G1, no in-feed antimicrobials; G2: a total average dose 6018 mg antimicrobials/pig; G3: a total average dose 8127 mg antimicrobials/pig; and G4: a total average dose 15,678 mg antimicrobials/pig.

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.

Recto-Anal Junction (RAJ) and Fecal Microbiomes of Cattle Experimentally Challenged With O157:H7.

Cattle are the asymptomatic reservoirs of O157:H7 (O157) that preferentially colonizes the bovine recto-anal junction (RAJ). Understanding the influence of O157 on the diversity of the RAJ microbiota could give insights into its persistence at the RAJ in cattle. Hence, we compared changes in bovine RAJ and fecal microbiota following O157 challenge under experimental conditions.

Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli.

Objective: Extraintestinal Pathogenic E. coli (ExPEC), are responsible for host diseases such as Neonatal Meningitis Escherichia coli (NMEC), the second-leading cause of neonatal bacterial meningitis, Avian Pathogenic E. coli (APEC), a cause of extraintestinal disease in poultry, and Uropathogenic E.

Cattle intestinal microbiota shifts following O157:H7 vaccination and colonization.

Vaccination-induced Escherichia coli O157:H7-specific immune responses have been shown to reduce E. coli O157:H7 shedding in cattle. Although E.

Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems.

Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin.

Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administration.

The impacts of antibiotic treatment and dosing regimen of an antibiotic on the swine respiratory microbiota are poorly defined. To begin to address this, this study characterized the impact of oxytetracycline administration, given either parenterally or in feed, on the diversity of the nasal and tonsil microbiotas of post-weaned pigs over a two-week period. One group received a single intramuscular injection (IM) of oxytetracycline, the second was treated with oxytetracycline mixed in feed (IF), and the control group received non-medicated (NON) feed.

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine.

Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift conditions toward health by promoting the growth of beneficial microbes that produce metabolites capable of modulating host cells. This study's objective was to assess how a dietary prebiotic could impact host tissues via modulation of the intestinal microbiota.

Paenibacillus 79R4, a potential rumen probiotic to enhance nitrite detoxification and methane mitigation in nitrate-treated ruminants.

The effects of supplemental nitrate administered alone or with a denitrifying ruminal bacterium, designated Paenibacillus 79R4 (79R4) intentionally selected for enhanced nitrate- and nitrite-metabolizing ability, on select rumen fermentation characteristics was examined in vivo. Rumen and blood samples were collected from cannulated Holstein steers one day prior to and one day after initiation of treatments applied as three consecutive intra-ruminal administrations of nitrate, to achieve the equivalent of 83 mg sodium nitrate/kg body weight day, given alone or with the nitrite-selected 79R4 (provided to achieve 10 cells/mL rumen fluid). Results revealed a day effect on methane-producing activity, with rates of methane production by ruminal microbes being more rapid when collected one day before than one day after initiation of treatments.

Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves.

Gastrointestinal tract (GIT) microbiota and stress can impact animal health. Studies have shown that perturbations in the GIT microbiota can influence host health and productivity by affecting physiological homeostasis, metabolism, hematopoiesis and inflammation. The present study aimed to evaluate possible effects of dehorning and castration stress on the GIT microbiota of dairy calves.

Complete Genome Sequence of Avian Pathogenic Escherichia coli Strain APEC O2-211.

Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, a disease that affects poultry production worldwide and leads to multimillion-dollar losses annually. Here, we report the genome sequence of APEC O2-211, a sequence type 117 (ST117) strain isolated from a diseased chicken.

Complete Genome Sequence of the Multidrug-Resistant Neonatal Meningitis Escherichia coli Serotype O75:H5:K1 Strain mcjchv-1 (NMEC-O75).

Neonatal meningitis Escherichia coli (NMEC) is the second leading cause of neonatal bacterial meningitis worldwide. We report the genome sequence of the multidrug-resistant NMEC serotype O75:H5:K1 strain mcjchv-1, which resulted in an infant's death. The O75 serogroup is rare among NMEC isolates; therefore, this strain is considered an emergent pathogen.

Chlortetracycline Enhances Tonsil Colonization and Fecal Shedding of Multidrug-Resistant Serovar Typhimurium DT104 without Major Alterations to the Porcine Tonsillar and Intestinal Microbiota.

spp. are estimated to cause 1.2 million cases of human foodborne illness each year in the United States, and pigs can often be asymptomatically colonized with spp.

Isolation, characterization and strain selection of a Paenibacillus species for use as a probiotic to aid in ruminal methane mitigation, nitrate/nitrite detoxification and food safety.

The effects of dietary nitrate and Paenibacillus 79R4 (79R4), a denitrifying bacterium, when co-administered as a probiotic, on methane emissions, nitrate and nitrite-metabolizing capacity and fermentation characteristics were studied in vitro. Mixed populations of rumen microbes inoculated with 79R4 metabolized all levels of nitrite studied after 24 h in vitro incubation. Results from in vitro simulations resulted in up to 2 log colony forming unit reductions in E.

Butyricicoccus porcorum sp. nov., a butyrate-producing bacterium from swine intestinal tract.

A Gram-stain-positive, non-motile, butyrate-producing coccus was cultured from the distal ileum of swine. This organism was isolated on rumen-fluid medium, consumes acetate, and produces butyrate as its major end product when grown on mono- and di-saccharides. A phylogenetic analysis based on near full-length 16S rRNA gene sequences as well as whole-genome phylogenies suggests that this isolate is most closely related to species in the genus Butyricicoccus, with Butyricicoccus pullicaecorum being the closest named relative (93.

Porcine Response to a Multidrug-Resistant Salmonella enterica serovar I 4,[5],12:i:- Outbreak Isolate.

Salmonella enterica serovar I 4,[5],12:i:- has emerged as a common nontyphoidal Salmonella serovar to cause human foodborne illness. An interesting trait of serovar I 4,[5],12:i:- is that it only expresses the fliC gene for bacterial motility (i.e.

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance.

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes.

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.

Carbadox is a quinoxaline-di--oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction ; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases.

Meta-analysis To Define a Core Microbiota in the Swine Gut.

The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design.

Effect of sole or combined administration of nitrate and 3-nitro-1-propionic acid on fermentation and Salmonella survivability in alfalfa-fed rumen cultures in vitro.

Ruminal methanogenesis is a digestive inefficiency resulting in the loss of dietary energy consumed by the host and contributing to environmental methane emission. Nitrate is being investigated as a feed supplement to reduce rumen methane emissions but safety and efficacy concerns persist. To assess potential synergies of co-administering sub-toxic amounts of nitrate and 3-nitro-1-propionate (NPA) on fermentation and Salmonella survivability with an alfalfa-based diet, ruminal microbes were cultured with additions of 8 or 16mM nitrate, 4 or 12mM NPA or their combinations.

Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine.

Unlabelled: Studying the host-associated butyrate-producing bacterial community is important, because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl coenzyme A (CoA):acetate-CoA transferase (EC 2.3.

Prophylactic Administration of Vector-Encoded Porcine Granulocyte-Colony Stimulating Factor Reduces Salmonella Shedding, Tonsil Colonization, and Microbiota Alterations of the Gastrointestinal Tract in Salmonella-Challenged Swine.

Salmonella colonization of food animals is a concern for animal health and public health as a food safety risk. Various obstacles impede the effort to reduce asymptomatic Salmonella carriage in food animals, including the existence of numerous serovars and the ubiquitous nature of Salmonella. To develop an intervention strategy that is non-specific yet effective against diverse Salmonella serovars, we explored the prophylactic use of a cytokine to decrease Salmonella in swine by boosting the host's innate immune system.