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Journal of Global Antimicrobial... Dec 2023The aim of this study was to characterise the whole genome sequence of multidrug-resistant Streptococcus pluranimalium strain SP21-2 of swine origin in China.
OBJECTIVES
The aim of this study was to characterise the whole genome sequence of multidrug-resistant Streptococcus pluranimalium strain SP21-2 of swine origin in China.
METHODS
Illumina Miseq (200X coverage) and Nanopore PromethION platform (100X coverage) were used for genome sequencing. Rapid Annotation using Subsystem Technology (RAST) was used to annotate the genome of SP21-2. The antimicrobial resistance genes (ARGs) were identified using ResFinder-4.1.
RESULTS
The assembled circular genome of S. pluranimalium SP21-2 was 1,987,058 bp in length with a GC content of 39.54%, and no plasmid sequence was detected. A total of 2086 coding sequences were predicted by RAST. Oxazolidinone-phenicol resistance gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), are both located on chromosomes, associated with IS1216 and ISS1S, respectively. In addition, SP21-2 harbours lnu(B) (lincosamide), ant (6)-Ia and aac(6')-aph(2") (aminoglycoside), erm(B) (macrolide), and tet(O) (tetracycline).
CONCLUSION
We firstly report the oxazolidinone-phenicol gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), in S. pluranimalium. In this strain, we firstly identified ISS1S and IS1216 carrying ARGs in S. pluranimalium, which will provide a valuable reference to understanding potential transfer mechanisms of ARGs in S. pluranimalium.
Topics: Animals; Swine; Streptogramin A; Anti-Bacterial Agents; Lincosamides; Anti-Infective Agents; Oxazolidinones; Chromosomes; Pleuromutilins
PubMed: 37709136
DOI: 10.1016/j.jgar.2023.09.007 -
Journal of Dairy Science Dec 2023The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use...
The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 10 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.
Topics: Animals; Cattle; Female; Acidosis; Animal Feed; Archaea; Bacteria; Diet; Fermentation; Fructose; Histamine; Hydrogen-Ion Concentration; Lactates; Monensin; RNA, Ribosomal, 16S; Rumen; Saccharomyces cerevisiae; Starch
PubMed: 37678787
DOI: 10.3168/jds.2023-23486 -
Scientific Reports Sep 2023This study aimed to assess the impact of a commercial blend of functional oils, specifically cashew nutshell liquid and castor oil (FO), in two physical forms (solid: P;...
This study aimed to assess the impact of a commercial blend of functional oils, specifically cashew nutshell liquid and castor oil (FO), in two physical forms (solid: P; liquid: S), in comparison to a combination of virginiamycin and anticoccidials on the gut health of broilers challenged with coccidiosis. A total of 1760 1-day-old male chicks were randomly distributed in a study design with eight treatments. The treatments included: a control group (without additive), OFS_0.75_kg/t (FO spray), OFP_1.0_kg/t (FO powder), OFP_1.5_kg/t (FO liquid spray), Sal (anticoccidials), Sal_Vir (virginiamycin and anticoccidials), Sal_OFS_0.5_ kg/t (anticoccidials plus FO spray), and Sal_OFP_1.0_kg/t (anticoccidials plus FO powder). All birds were challenged with Eimeria spp. at 14 days. The physical form of FO did not affect performance and intestinal health parameters. At 42 days, broilers from the control and OFS_0.75 treatments were the lightest, while those from the Sal_Vir and Sal_OFP_1.0 treatments were the heaviest (P < 0.05). FO reduced the presence of Clostridium perfringens. The individual phytogenic additives did not prevent weight loss in birds challenged with Eimeria, but they mitigated the effects of the infection by modulating the intestinal microbiota. A synergistic effect was observed between the FO and anticoccidials, yielding satisfactory results in substituting virginiamycin.
Topics: Male; Animals; Chickens; Eimeria; Powders; Castor Oil; Virginiamycin
PubMed: 37670021
DOI: 10.1038/s41598-023-41743-9 -
Microorganisms Jul 2023Antimicrobial growth promoters (AGP) are used in chicken production to suppress pathogens in the gut and improve performance, but such products tend to suppress...
An Immobilized Form of a Blend of Essential Oils Improves the Density of Beneficial Bacteria, in Addition to Suppressing Pathogens in the Gut and Also Improves the Performance of Chicken Breeding.
Antimicrobial growth promoters (AGP) are used in chicken production to suppress pathogens in the gut and improve performance, but such products tend to suppress beneficial bacteria while favoring the development and spread of antimicrobial resistance. A green alternative to AGP with the ability to suppress pathogens, but with an additional ability to spare beneficial gut bacteria and improve breeding performance is urgently required. We investigated the effect of supplementation of a blend of select essential oils (cinnamon oil, carvacrol, and thyme oil, henceforth referred to as EO; at two doses: 200 g/t and 400 g/t feed) exhibiting an ability to spare Lactobacillus while exhibiting strong inhibition ability under in vitro tests and immobilized in a sunflower oil and calcium alginate matrix, to broiler chickens and compared the effects with those of a probiotic yeast (Y), an AGP virginiamycin (V), and a negative control (C). qPCR analysis of metagenomic DNA from the gut content of experimental chickens indicated a significantly ( < 0.05) lower density of in the EO groups as compared to other groups. Amplicon sequence data of the gut microbiome indicated that all the additives had specific significant effects (DESeq2) on the gut microbiome, such as enrichment of uncultured Clostridia in the V and Y groups and uncultured Ruminococcaceae in the EO groups, as compared to the control. LEfSe analysis of the sequence data indicated a high abundance of beneficial bacteria Ruminococcaceae in the EO groups, Faecalibacterium in the Y group, and Blautia in the V group. Supplementation of the immobilized EO at the dose rate of 400 g/ton feed improved body weight gain (by 64 g/bird), feed efficiency (by 5 points), and cellular immunity (skin thickness response to phytoheamagglutinin lectin from by 58%) significantly ( < 0.05), whereas neither yeast nor virginiamycin showed a significant effect on performance parameters. Expression of genes associated with gut barrier and immunity function such as , , , , and were significantly higher in the EO groups. This study showed that the encapsulated EO mixture can improve the density of beneficial microbes in the gut significantly, with concomitant suppression of potential pathogens such as and improved performance and immunity, and hence, has a high potential to be used as an effective alternative to AGP in poultry.
PubMed: 37630519
DOI: 10.3390/microorganisms11081960 -
Bioelectrochemistry (Amsterdam,... Oct 2023Virginiamycin (VIR), a feed additive, is used to promote pig and poultry growth. However, it is hazardous to human health. This work described a label-free...
Virginiamycin (VIR), a feed additive, is used to promote pig and poultry growth. However, it is hazardous to human health. This work described a label-free electrochemical immunosensor based on silver nanoparticles-reduced graphene oxide (AgNPs-rGO) nanocomposites and staphylococcal protein A (SPA) for the first time to directly detect the residual marker VIR M1. Good catalytic currents for oxygen reduction reaction were apparently obtained after the modification of nanocomposites on gold electrode. Nanocomposites were characterized using UV-Vis, X-ray diffraction (XRD) patterns, Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). SPA was targeted to immobilize VIR M1 monoclonal antibody (mAb) by binding to Fc region of antibody. The proposed immunosensor showed a wide linear range from 0.25 ng mL to 100 ng mL, providing detection limit (LOD) of 0.18 ng mL of VIR M1. Recovery rates ranged from 92.27% to 98.84%, and relative standard deviation (RSD) was not above 6.6%, indicating the immunosensor could detect VIR M1 in actual samples with high accuracy. The sensor showed good selectivity, reproducibility and stability and could be considered as a potential tool for detection of VIR M1 in feed and animal derived food.
Topics: Animals; Humans; Swine; Electrochemical Techniques; Staphylococcal Protein A; Streptogramin A; Biosensing Techniques; Reproducibility of Results; Metal Nanoparticles; Immunoassay; Silver; Graphite; Nanocomposites; Gold; Antibodies; Limit of Detection
PubMed: 37354640
DOI: 10.1016/j.bioelechem.2023.108489 -
Scientific Reports May 2023Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family...
Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family Pseudonocardiaceae has abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently, Kutzneria chonburiensis SMC256 has been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256 (genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256 and other publicly available Kutzneria species. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256 is most closely related to Kutzneria sp. 744, Kutzneria kofuensis, Kutzneria sp. CA-103260 and Kutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among the Kutzneria genomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256genome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific in Kutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome of Kutzneria chonburiensis contains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in the Kutzneria.
Topics: Actinomycetales; Genomics; Secondary Metabolism; Multigene Family; Phylogeny
PubMed: 37258607
DOI: 10.1038/s41598-023-36039-x -
Microbiology Spectrum Jun 2023Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) isolates ( = 178) collected in the national resistance...
Genomic Diversity of Methicillin-Resistant Staphylococcus aureus CC398 Isolates Collected from Diseased Swine in the German National Resistance Monitoring Program GE-Vet from 2007 to 2019.
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) isolates ( = 178) collected in the national resistance monitoring program GE-Vet from diseased swine in Germany from 2007 to 2019 were investigated for their genomic diversity with a focus on virulence and antimicrobial resistance (AMR) traits. Whole-genome sequencing was followed by molecular typing and sequence analysis. A minimum spanning tree based on core-genome multilocus sequence typing was constructed, and antimicrobial susceptibility testing was performed. Most isolates were assigned to nine clusters. They displayed close phylogenetic relationships but a wide molecular variety, including 13 types and 19 known and four novel types. Several toxin-encoding genes, including , , , , and , were detected. The isolates harbored a wide range of AMR properties mirroring the proportions of the classes of antimicrobial agents applied in veterinary medicine in Germany. Multiple novel or rare AMR genes were identified, including the phenicol-lincosamide-oxazolidinone-pleuromutilin-streptogramin A resistance gene , the lincosamide-pleuromutilin-streptogramin A resistance gene (C), and the novel macrolide-lincosamide-streptogramin B resistance gene (54). Many AMR genes were part of small transposons or plasmids. Clonal and geographical correlations of molecular characteristics and resistance and virulence genes were more frequently observed than temporal relations. In conclusion, this study provides insight into population dynamics of the main epidemic porcine LA-MRSA lineage in Germany over a 13-year-period. The observed comprehensive AMR and virulence properties, most likely resulting from the exchange of genetic material between bacteria, highlighted the importance of LA-MRSA surveillance to prevent further dissemination among swine husbandry facilities and entry into the human community. The LA-MRSA-CC398 lineage is known for its low host specificity and frequent multiresistance to antimicrobial agents. Colonized swine and their related surroundings represent a considerable risk of LA-MRSA-CC398 colonization or infection for occupationally exposed people through which such isolates might be further disseminated within the human community. This study provides insight into the diversity of the porcine LA-MRSA-CC398 lineage in Germany. Clonal and geographical correlations of molecular characteristics and resistance and virulence traits were detected and may be associated with the spread of specific isolates through livestock trade, human occupational exposure, or dust emission. The demonstrated genetic variability underlines the lineage's ability to horizontally acquire foreign genetic material. Thus, LA-MRSA-CC398 isolates have the potential to become even more dangerous for various host species, including humans, due to increased virulence and/or limited therapeutic options for infection control. Full-scale LA-MRSA monitoring at the farm, community, and hospital level is therefore essential.
Topics: Animals; Humans; Swine; Methicillin-Resistant Staphylococcus aureus; Phylogeny; Streptogramin A; Staphylococcal Infections; Anti-Bacterial Agents; Genomics; Lincosamides; Livestock; Pleuromutilins
PubMed: 37154741
DOI: 10.1128/spectrum.00770-23 -
Frontiers in Veterinary Science 2023Although efforts to improve antimicrobial stewardship should include the collection of antimicrobial use data, most antimicrobial datasets collected at the national...
Although efforts to improve antimicrobial stewardship should include the collection of antimicrobial use data, most antimicrobial datasets collected at the national level consist of antimicrobial sales data which cannot inform stewardship. These data lack context, such as information regarding target species, disease indication, and regimen specifics like dose, route and duration. Therefore, the goal of this study was to develop a system for collecting data on the use of antimicrobials in the U.S. broiler chicken industry. This study utilized a public-private partnership to enable collection and protection of sensitive data from an extremely large industry while releasing deidentified and aggregated information regarding the details of antimicrobial use on U.S. broiler chicken farms over time. Participation was voluntary. Data were collected for the period 2013 through 2021 and are reported on a calendar year basis. Using production statistics from USDA:NASS as a denominator, the data supplied by participating companies represented approximately 82.1% of broiler chicken production in the U.S. in 2013, approximately 88.6% in 2017, and approximately 85.0% in 2021. The data that were submitted for 2021 are based on approximately 7,826,121,178 chickens slaughtered and 50,550,817,859 pounds liveweight produced. Granular flock-level treatment records were available for 75-90% of the birds represented in the 2018-2021 dataset. There was no use of antimicrobials in the hatchery for the years 2020 and 2021. Medically important in-feed antimicrobial use decreased substantially, with all in-feed tetracycline use being eliminated by 2020, and the use of virginiamycin being reduced by more than 97% since 2013. Medically important water-soluble antimicrobials are used for the treatment of disease in broiler production. Use decreased substantially for most water-soluble antimicrobials. The most important diseases necessitating treatment were necrotic enteritis and gangrenous dermatitis as well as -related disease. A focus on reducing the incidence of these diseases would reduce the need for antimicrobial therapy but will require an investment in research to find efficacious and cost-effective interventions for these diseases.
PubMed: 37138912
DOI: 10.3389/fvets.2023.1139908 -
Frontiers in Veterinary Science 2023Feedlot cattle are usually adapted to high-concentrate diets containing sodium monensin (MON) in more than 14 days. However, considering that the dry matter intake DMI...
Shortening the adaptation of Nellore cattle to high-concentrate diets using only virginiamycin as sole feed additive negatively impacts ruminal fermentation and nutrient utilization.
Feedlot cattle are usually adapted to high-concentrate diets containing sodium monensin (MON) in more than 14 days. However, considering that the dry matter intake DMI is usually lower during adaptation when compared to the finishing period, the use of MON during adaptation may decrease even further the DMI, and virginiamycin (VM) may be an alternative. This study was designed to investigate the effects of shortening the adaptation length from 14 to 9 or 6 days on ruminal metabolism, feeding behavior, and nutrient digestibility of Nellore cattle fed high-concentrate diets containing only VM as the sole feed additive. The experimental design was a 5 × 5 Latin square, where each period lasted 21 days. Five 17 mo-old Nellore yearling bulls were used (415 ± 22 kg of body weight), which were assigned to five treatments: (1) MON (30 mg/kg) and adaptation for 14 days; (2) MON (30 mg/kg) + VM (25 mg/kg) and adaptation for 14 days; (3) VM (25 mg/kg) and adaptation for 14 days; (4) VM (25 mg/kg) and adaptation for 9 days, and (5) VM (25 mg/kg) and adaptation for 6 days. A quadratic effect for adaptation length when only VM was fed was observed for mean pH ( = 0.03), duration of pH below 5.2 ( = 0.01) and 6.2 ( = 0.01), where cattle consuming VM adapted for 9 days had higher mean pH and shorter period of pH below 5.2 and 6.2. Cattle that consumed only MON had a lower concentration of butyrate ( = 0.02) and a higher concentration of propionate ( = 0.04) when compared to those consuming VM and adapted for 14 days. As the adaptation length decreased for animals consuming only VM, the rumen degradability of dry matter ( < 0.01), neutral detergent fiber ( < 0.01), and starch ( < 0.01) decreased; however, protozoa numbers of and total protozoa increased. It is not recommended to shorten the adaptation length of these animals to either 6 or 9 days without negatively impacting nutrient disappearance and ruminal fermentation patterns.
PubMed: 37065251
DOI: 10.3389/fvets.2023.1089903 -
Journal of Animal Science Jan 2023Two experiments were designed to evaluate the impacts of supplementing lasalocid (LAS), narasin (NAR), or virginiamycin (VRM) on rumen fermentation parameters, apparent...
Two experiments were designed to evaluate the impacts of supplementing lasalocid (LAS), narasin (NAR), or virginiamycin (VRM) on rumen fermentation parameters, apparent nutrient digestibility, and blood parameters (Exp. 1), as well as feed intake and performance (Exp. 2) of Nellore cattle consuming a forage-based diet. In Exp. 1, 32 rumen-fistulated Nellore steers (initial shrunk body weight [BW] = 355 ± 4.4 kg) were assigned to a randomized complete block design. Within block, animals were randomly assigned to one of four treatments: 1) forage-based diet without feed additives (CON), 2) CON diet plus 13 mg/kg of dry matter (DM) of NAR, 3) CON diet plus 20 mg/kg of DM of sodium LAS, or 4) CON diet plus 20 mg/kg of DM of VRM. No treatment effects were detected (P ≥ 0.32) for intake and apparent digestibility of nutrients. Steers fed NAR had the lowest (P ≤ 0.01) molar proportion of acetate on day 28, 56, and 112 vs. CON, LAS, and VRM steers, whereas acetate did not differ (P ≥ 0.25) between LAS, VRM, and CON steers from day 28 to 84. On day 112, steers fed LAS had a lower (P < 0.02) molar proportion of acetate vs. VRM and CON, whereas it did not differ between CON and VRM (P > 0.33). Steers receiving NAR had a greater (P ≤ 0.04) ruminal propionate vs. CON, LAS, and VRM, whereas LAS steers had greater (P < 0.04) propionate vs. CON and VRM steers on day 28 and 112, and it did not differ (P > 0.22) between CON and VRM. In Exp. 2, 160 Nellore bulls were blocked by initial shrunk BW (212 ± 3.1 kg) in a 140-d feedlot trial. Diets contained the same treatments used in Exp. 1. Bulls fed NAR had greater (P < 0.02) average daily gain (ADG) vs. CON and VRM, and similar (P = 0.17) ADG between NAR and LAS, whereas ADG did not differ (P > 0.28) between LAS, VRM, and CON bulls. A treatment effect was detected (P = 0.03) for dry matter intake, being greater in NAR vs. CON, LAS, and VRM bulls, and similar (P > 0.48) between CON, LAS, and VRM bulls. A tendency was detected (P = 0.09) for feed efficiency, which was greater (P < 0.02) in NAR bulls vs. CON and VRM, and similar (P = 0.36) between NAR and LAS bulls. From day 112 to 140, bulls receiving NAR were heavier (P < 0.03) vs. CON, LAS, and VRM bulls, but no differences were observed (P > 0.51) between CON, LAS, and VRM bulls. Collectively, ruminal fermentation profile and intake were impacted by NAR supplementation, which partially contributed to the enhanced performance of Nellore bulls receiving a forage-based diet.
Topics: Cattle; Animals; Male; Dietary Supplements; Lasalocid; Propionates; Rumen; Animal Feed; Digestion; Diet; Body Weight; Fermentation
PubMed: 37042805
DOI: 10.1093/jas/skad108