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Neonatal calf diarrhea (NCD) remains a significant contributor to calf mortality within the first 3 weeks of life, prompting widespread antibiotic use with associated concerns about antimicrobial resistance and disruption of the calf gut microbiota. Recent research exploring NCD treatments targeting gut microbiota dysbiosis has highlighted probiotic supplementation as a promising and safe strategy for gut homeostasis. However, varying treatment outcomes across studies suggest the need for efficient treatment options. In this study, we evaluated the potential of probiotics Limosilactobacillus reuteri , formally known as Lactobacillus reuteri , isolated from healthy neonatal calves to treat NCD. Through in silico whole genome analysis and in vitro assays, we identified nine L. reuteri strains, which were then administered to calves with NCD. Calves treated with L. reuteri strains shed healthy feces and demonstrated restored gut microbiota and normal animal behavior. Leveraging a machine learning model, we evaluated microbiota profiles and identified bacterial taxa associated with calf gut health that were elevated by L. reuteri administration. These findings represent a crucial advancement towards sustainable antibiotic alternatives for managing NCD, contributing significantly to global efforts in mitigating antimicrobial resistance and promoting overall animal health and welfare., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Zhai, Kim, Fan, Rajeev, Kim, Driver, Galvão, Boucher and Jeong.)

This study aimed to synthesize phenytoin (PHT)-loaded water chestnut starch-based biomaterials and evaluate their drug release kinetics for use in transdermal drug delivery systems for antiepileptic therapy. Hierarchical microparticles (HMPs) extracted from human hair were also used to improve the PHT release efficiency. The physicochemical characteristics of PHT, HMPs, and the prepared biomaterials were evaluated by physical properties, antimicrobial activities, FE-SEM, FT-IR, XRD, 1 H NMR, and 13 C CPMAS solid-state NMR. The photothermal effect and the PHT release profile were confirmed through 808 nm NIR laser irradiation. After 30 min of the laser exposure, the temperature of the HMP-added biomaterials increased by 1.50-1.59 times compared to that of without the HMPs. PHT release in buffers and artificial skin test under NIR laser irradiation enhanced by 1.20-1.85 times owing to the photothermal effect. The release kinetics in pH buffer and artificial skin were determined using the Fickian diffusion and Korsmeyer-Peppas models. Additionally, to verify the transdermal penetration of PHT, drug-release simulations were conducted using rhodamine B in agar blocks and pig ears. The results implied that the photothermal effect of the HMPs enhanced the penetration of the drug., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Helcococcus ovis ( H. ovis ) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35 Helcococcus sp. clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes in vitro . Phylogenetic and average nucleotide identity analyses classified four Helcococcus isolates within a cryptic clade representing an undescribed species, for which we propose the name Helcococcus bovis sp. nov. By establishing this new species clade, we also resolve the longstanding question of the classification of the Tongji strain responsible for a confirmed human conjunctival infection. This strain did not neatly fit into H. ovis and is instead a member of H. bovis . We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31 H. ovis isolates. An overwhelming 97% of H. ovis strains (30 out of 31) harbor mobile tetracycline resistance genes and displayed significantly increased minimum inhibitory concentrations of tetracyclines in vitro . The high prevalence of mobile tetracycline resistance genes makes H. ovis a significant antimicrobial resistance gene reservoir in our food chain. Finally, the phylogenetic distribution of co-occurring high-virulence determinant genes of H. ovis across unlinked and distant loci highlights an instance of convergent gene loss in the species. In summary, this study showed that mobile genetic element-mediated tetracycline resistance is widespread in H. ovis , and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species. Finally, we introduced a novel Helcococcus species closely related to H. ovis , called H. bovis sp. nov., which has been reported to cause infection in humans., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Cunha, Zhai, Casaro, Jones, Hernandez, Bisinotto, Kariyawasam, Brown, Phillips, Jeong and Galvão.)

Vancomycin-resistant enterococci (VRE) commonly colonize the gut of individuals with hematologic malignancies or undergoing hematopoietic cell transplant (HCT) and may cause bacteremia. In 2012, we identified VRE isolates from patients and patients' rooms and showed transmission networks of highly genetically related daptomycin-resistant (DR)-VRE strains. This is a follow-up study performing whole-genome sequencing (WGS) and phylogenetic analyses on 82 clinical VRE strains isolated from stools and blood cultures of patients with leukemia and HCT between 2015 and 2019. Here, we observed transmission of highly genetically related strains between rooms on the same or on different floors, including a DR-VRE strain identified in 2012. Eleven of twenty-eight patients with DR-VRE were never exposed to daptomycin, suggesting horizontal transmission. Fifteen of the twenty-eight patients with DR-VRE died within 30 days of positive blood cultures. Amongst those, one DR-VRE strain belonging to ST1471 had the virulence gene bopD responsible for biofilm formation. Additionally, to our knowledge, this is the first report of a DR-VRE strain belonging to ST323 in the United States. In summary, our study demonstrated the emergence and persistence of VRE strains, especially DR-VRE, in our hospital. Adding WGS to routine infection control measures may timely identify potential horizontal VRE transmission including multi-drug-resistant isolates.

Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The objective was to evaluate the performance of exploratory models containing routinely available on-farm data, behavior data, and the combination of both to predict metritis self-cure (SC) and treatment failure (TF). Holstein cows (n = 1,061) were fitted with a collar-mounted automated-health monitoring device (AHMD) from -21 ± 3 to 60 ± 3 d relative to calving to monitor rumination time and activity. Cows were examined for diagnosis of metritis at 4 ± 1, 7 ± 1, and 9 ± 1 d in milk (DIM). Cows diagnosed with metritis (n = 132), characterized by watery, fetid, reddish/brownish vaginal discharge (VD), were randomly allocated to 1 of 2 treatments: control (CON; n = 62), no treatment at the time of metritis diagnosis (d 0); or ceftiofur (CEF; n = 70), subcutaneous injection of 6.6 mg/kg of ceftiofur crystalline-free acid on d 0 and 3 relative to diagnosis. Cure was determined 12 d after diagnosis and was considered when VD became mucoid and not fetid. Cows in CON were used to determine SC, and cows in CEF were used to determine TF. Univariable analyses were performed using farm-collected data (parity, calving season, calving-related disorders, body condition score, rectal temperature, and DIM at metritis diagnosis) and behavior data (i.e., daily averages of rumination time, activity generated by AHMD, and derived variables) to assess their association with metritis SC or TF. Variables with P-values ≤0.20 were included in the multivariable logistic regression exploratory models. To predict SC, the area under the curve (AUC) for the exploratory model containing only data routinely available on-farm was 0.75. The final exploratory model to predict SC combining routinely available on-farm data and behavior data increased the AUC to 0.87, with sensitivity (Se) of 89% and specificity (Sp) of 77%. To predict TF, the AUC for the exploratory model containing only data routinely available on-farm was 0.90. The final exploratory model combining routinely available on-farm data and behavior data increased the AUC to 0.93, with Se of 93% and Sp of 87%. Cross-validation analysis revealed that generalizability of the exploratory models was poor, which indicates that the findings are applicable to the conditions of the present exploratory study. In summary, the addition of behavior data contributed to increasing the prediction of SC and TF. Developing and validating accurate prediction models for SC could lead to a reduction in antimicrobial use, whereas accurate prediction of cows that would have TF may allow for better management decisions., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Mycoplasma hyopneumoniae ( M. hyopneumoniae ) is considered the primary causative agent of porcine enzootic pneumonia (EP), a chronic contagious respiratory disease that causes economic losses. Obtaining new pathogenic isolates and studying the genome and virulence factors are necessary. This study performed a complete sequencing analysis of two Brazilian strains, UFV01 and UFV02, aiming to characterize the isolates in terms of the virulence factors and sequence type. The complete genome analysis revealed the main virulence genes ( mhp385 , mhp271 , MHP_RS03455 , p102 , p97 , p216 , MHP_RS00555 , mhp107 ) and ST-123, the presence of three toxin-related genes ( tlyC , PLDc_2 and hcnC ), and some genetic groups specific to these two isolates. Subsequently, the pathogenicity of the isolates was evaluated via an experimental infection conducted in a swine model. The study was divided into three groups, namely a negative control group ( n  = 4) and two test groups ( n  = 8), totaling 20 animals. They were challenged at 35 days of age with 10 7 CCU (Color Changing Units) M. hyopneumoniae via the intratracheal route. The UFV01 group showed earlier and higher seroconversion (IgG) (100%), while only 50% of the UFV02 group seroconverted. The same trend was observed when analyzing the presence of IgA in the bronchoalveolar lavage fluid (BALF) at 35 days post-infection (dpi). The UFV01 group had a mean macroscopic lesion score of 11.75% at 35 dpi, while UFV02 had 3.125%. Microscopic lesions were more severe in the UFV01 group. Based on laryngeal swab samples evaluated by qPCR, and the detection began at 14 days. The UFV01 group showed 75% positivity at 14 dpi. The UFV02 group also started excreting at 14 dpi, with a positivity rate of 37.5%. The results indicate that the UFV01 isolate exhibits higher virulence than UFV02. These findings may aid in developing new vaccines and diagnostic kits and establishing experimental models for testing., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Toledo, de Souza, Pereira, Polveiro, Bressan, Yamatogi, Jeong, Marks, Diamantino, de Carvalho, Malcher, Petri, de Oliveira, Moreira and Silva-Júnior.)

Our objective was to evaluate the effects of combinations of Saccharomyces cerevisiae and Megasphaera elsdenii as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 10 8 colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 ( S. cerevisiae and M. elsdenii strain 1), YM2 ( S. cerevisiae and M. elsdenii strain 2), and YMM ( S. cerevisiae and half of the doses of M. elsdenii strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, P  = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum Proteobacteria ( P  = 0.05) and family Succinivibrioceae ( P  = 0.05) in the solid fraction and tended to increase abundance of family Succinivibrioceae ( P  = 0.10) and genus Succinivibrio ( P  = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of Proteobacteria ( r  = 0.36, P  = 0.04) and Succinivibrioceae ( r  = 0.36, P  = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed., Competing Interests: The authors have not stated any conflicts of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Endometrial inflammation is associated with reduced pregnancy per artificial insemination (AI) and increased pregnancy loss in cows. It was hypothesized that induced endometritis alters histotroph composition and induces inflammatory signatures on conceptus that compromise development. In Experiment 1, lactating cows were assigned to control (CON; n = 23) or to an intrauterine infusion of Escherichia coli and Trueperella pyogenes (ENDO; n = 34) to induce endometritis. Cows received AI 26 days after treatment, and the uterine fluid and conceptuses were collected on day 16 after AI. In Experiment 2, Holstein heifers were assigned to CON (n = 14) or ENDO (n = 14). An embryo was transferred on day 7 of the estrous cycle, and uterine fluid and conceptuses were recovered on day 16. Composition of histotroph and trophoblast and embryonic disc gene expression were assessed. Bacterial-induced endometritis in lactating cows altered histotroph composition and pathways linked to phospholipid synthesis, cellular energy production, and the Warburg effect. Also, ENDO reduced conceptus length in cows and altered expression of genes involved in pathogen recognition, nutrient uptake, cell growth, choline metabolism, and conceptus signaling needed for maternal recognition of pregnancy. The impact of ENDO was lesser on conceptuses from heifers receiving embryo transfer; however, the affected genes and associated pathways involved restricted growth and increased immune response similar to the observed responses to ENDO in conceptuses from lactating cows. Bacterial-induced endometrial inflammation altered histotroph composition, reduced conceptus growth, and caused embryonic cells to activate survival rather than anabolic pathways that could compromise development., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Microbial biofilms are prevalent in various environments and pose significant challenges to food safety and public health. The biofilms formed by pathogens can cause food spoilage, foodborne illness, and infectious diseases, which are difficult to treat due to their enhanced antimicrobial resistance. While the composition and development of biofilms have been widely studied, their profound impact on food, the food industry, and public health has not been sufficiently recapitulated. This review aims to provide a comprehensive overview of microbial biofilms in the food industry and their implication on public health. It highlights the existence of biofilms along the food-producing chains and the underlying mechanisms of biofilm-associated diseases. Furthermore, this review thoroughly summarizes the enhanced understanding of microbial biofilms achieved through machine learning approaches in biofilm research. By consolidating existing knowledge, this review intends to facilitate developing effective strategies to combat biofilm-associated infections in both the food industry and public health., Competing Interests: Conflict of interestThe authors declare no conflicts of interest., (© The Korean Society of Food Science and Technology 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Objectives of this experiment were to study the effect of infusing utero-pathogenic bacteria to induce endometrial inflammation on productive performance in early lactation and subsequent reproduction. Although endometritis is associated with perturbed reproduction, numerous factors may contribute to the observed association. It was hypothesized that induced endometrial inflammation, resulting in localized and systemic inflammatory responses, compromises production and reproduction. Holstein cows without clinical disease and with less than 18% polymorphonuclear leukocytes (PMN) in endometrial cytology on d 31 ± 3 postpartum had their estrous cycle synchronized. Cows were blocked by parity and genomic breeding value for cow conception rate and, within block, assigned randomly to remain as untreated controls (CON; n = 37) or to receive an intrauterine infusion of 5.19 × 10 8 cfu Escherichia coli and 4.34 × 10 8 cfu Trueperella pyogenes during the luteal phase to induce endometrial inflammation (INF; n = 48). Endometrial cytology was taken on d 2 and 7 after treatment to evaluate the proportion of PMN. Rectal temperature, dry matter intake, and yields of milk and components were measured in the first 7 d after treatment. Blood serum was analyzed for concentration of haptoglobin. Leukocytes were isolated from blood on d 2 and 7 after treatment and on d 19 after artificial insemination (AI) and mRNA was quantified for a select group of genes. Cows received AI and reproduction was followed for 300 d postpartum. Bacterial infusion induced endometrial inflammation with increased proportions of PMN in the endometrial cytology on d 2 (4.4 ± 0.7 vs. 26.3 ± 2.8%) and 7 (10.9 ± 1.7 vs. 17.4 ± 2.1%) after treatment, resulting in increased mean prevalence of subclinical endometritis (>10% PMN; 23.3 ± 6.3 vs. 80.9 ± 5.1%). Rectal temperature did not differ between CON and INF, but the concentration of haptoglobin in serum tended to increase in INF compared with CON (113 ± 14 vs. 150 ± 16 µg/mL). Induced endometrial inflammation reduced yields of milk (44.9 ± 0.8 vs. 41.6 ± 0.8 kg/d), protein (1.19 ± 0.03 vs. 1.12 ± 0.03 kg/d), and lactose (2.17 ± 0.04 vs. 2.03 ± 0.04 kg/d) and tended to reduce dry matter intake (20.7 ± 0.5 vs. 19.4 ± 0.6 kg/d) in the first 7 d after treatment. Indeed, the reduction in milk yield lasted 4 wk. However, treatment did not affect yields of energy-corrected milk or fat because treatment with INF increased the concentration of fat in milk (3.54 ± 0.10 vs. 3.84 ± 0.10%). Induced endometrial inflammation reduced pregnancy per AI at all inseminations (33.4 ± 5.1 vs. 21.6 ± 3.7%) and the hazard of pregnancy (0.61; 95% CI = 0.36-1.04), which extended the median days open by 24 d. Blood leukocytes from INF cows had increased mRNA expression of the pro-inflammatory gene IL1B on d 2 and 7 after treatment, but reduced expression of the IFN-stimulated genes ISG15 and MX2 on d 19 after AI. Induced endometrial inflammation depressed production and caused long-term negative effects on reproduction in lactating dairy cows., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The objective of this study was to evaluate the effects of feeding sugars as a replacement for starch on the ruminal microbiome using a dual-flow continuous culture system. Four periods of 10 days each were conducted with 8 fermenters in a 4 × 4 replicated Latin square design. Treatments included: 1) control with corn-CON, 2) molasses-MOL, 3) untreated condensed whey permeate-CWP, and 4) CWP treated with a caustic agent-TCWP as a partial substitute for corn. Sugars were defined as the water-soluble carbohydrates (WSC) concentration. Diets were formulated by replacing 4% of the diet DM in the form of starch from corn with the sugars in byproducts. Microbial samples for DNA analysis were collected from the solid and liquid effluent containers at 3, 6, and 9 h after feeding. Bacterial community composition was analyzed with sequencing the V4 region of the 16S rRNA gene using Illumina MiSeq platform. Data were analyzed with R 4.1.3 packages vegan, lmer, and ggplot to determine the effects of treatment on the relative abundance of taxa in the solid and liquid fractions, as well as the correlation of Acetate: Propionate ratio and pH to taxa relative abundance. Treatments did not affect alpha or beta diversity. At the phylum level the relative abundance of Proteobacteria was increased in CON compared to sugars in the solid fraction. In the liquid fraction, Firmicutes had greater relative abundance in sugar treatments while Bacteroidota and Spirochaetota were present in lower relative abundance in CWP. For solid and liquid samples, the family Lachnospiraceae had greater relative abundance in sugar treatments compared to CON. The decreased relative abundance of Christensenellaceae and Rikenellaceae paired with the greater relative abundance of Selenomonadaceae in CWP could help explain greater propionate molar proportion and decreased ruminal pH previously observed for this treatment. The genera Olsenella a lactic acid-producing bacterium, had the greatest relative abundance in MOL. Incorporating TCWP or MOL as a partial replacement for starch was more conservative of fibrolytic bacterial taxa compared to CWP. Additionally, TCWP did not increase bacterial taxa associated with synthesis of lactate as compared to MOL. Overall, replacing starch with sugars is mostly conservative of the ruminal microbiome; however, changes observed coincide with differences observed in acetate and propionate proportions and ruminal pH., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Our objective was to evaluate the effects of bacteria ( Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus lichenformis, Bacillus subtilis, and Enterococcus faecium ), enzymes (amylase, hemicellulose, and xylanase), and yeast as additives on the ruminal microbiome. We hypothesized that inclusion of bacteria, enzymes, and yeast would impact butyric bacterial populations. Eight fermenters were arranged in a duplicated 4 × 4 Latin square with the following treatments: 1) control without additives (CTRL); 2) bacterial culture and enzyme blend (EB); 3) bacterial culture and enzyme blend with a live yeast and yeast culture blend (EBY); and 4) double dose of bacterial culture and enzyme blend and the yeast products blend (2X). We conducted four fermentation periods of 10 d each, with the last 3 d for collection of samples. Overall, 64 solid and liquid samples were analyzed by amplification of the V4 region of bacterial 16S rRNA. Data were analyzed with R and SAS. The following orthogonal contrasts were used: 1) ADD-the control compared to all treatments with additives (CTRL vs. EB, EBY, and 2X); 2) YEAST-treatment without yeast compared to those with yeast (EB vs. EBY and 2X); and 3) DOSE-the single dose of enzymes, bacteria, and yeast compared to the doubled dose (EBY vs. 2X). Family Prevotellaceae was more abundant when additives were added (ADD). Additives (ADD) also increased relative abundance of Prevotellaceae Ga6A1 and YAB2003 in solid fraction, and of Prevotellaceae Ga6A1 and two members of Lachnospiracea family in liquid fraction. Yeast (YEAST) decreased relative abundance of Succinivibrionaceae UCG-001 and increased abundance of Ruminococcus and Prevotellaceae UCG-003 in solid fraction. Doubling the dose of enzymes and microbial additives (DOSE) decreased the abundance of Succiniclasticum in solid fraction and Selenomonadaceae in the liquid. Molar proportion of butyrate was highly correlated with abundance of Prevotellaceae Ga6A1 in solid ( r = 0.68) and liquid fraction ( r = 0.79), and with Unclassified Lachnospiraceae in liquid ( r = 0.70). Our results demonstrate that YEAST decreases abundance of succinate synthesizing bacteria, while DOSE decreases abundance of bacteria that metabolize succinate into propionate. Combined bacteria, enzymes, and yeast increase the relative abundance of specific genera primarily within the Prevotellaceae family, which may explain the increase in butyrate molar proportion observed with ADD., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Our objective was to evaluate the inclusion of calcium-magnesium carbonate [CaMg(CO 3 ) 2 ] and calcium-magnesium hydroxide [CaMg(OH) 4 ] in corn silage-based diets and their impact on ruminal microbiome. Our previous work showed a lower pH and molar proportion of butyrate from diets supplemented with [CaMg(CO 3 ) 2 ] compared to [CaMg(OH) 4 ]; therefore, we hypothesized that ruminal microbiome would be affected by Mg source. Four continuous culture fermenters were arranged in a 4 × 4 Latin square with the following treatments defined by the supplemental source of Mg: 1) Control (100% MgO, plus sodium sesquicarbonate as a buffer); 2) CO 3 [100% CaMg(CO 3 ) 2 ]; 3) OH [100% CaMg(OH) 4 ]; and 4) CO 3 /OH [50% Mg from CaMg(CO 3 ) 2 , 50% Mg from CaMg(OH) 4 ]. Diet nutrient concentration was held constant across treatments (16% CP, 30% NDF, 1.66 MCal NEl/kg, 0.67% Ca, and 0.25% Mg). We conducted four fermentation periods of 10 d, with the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 16 solid and 16 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R and SAS to determine treatment effects on taxa relative abundance of liquid and solid fractions. Correlation of butyrate molar proportion with taxa relative abundance was also analyzed. Treatments did not affect alpha and beta diversities or relative abundance of phylum, class and order in either liquid or solid fractions. At the family level, relative abundance of Lachnospiraceae in solid fraction was lower for CO 3 and CO 3 /OH compared to OH and Control ( P < 0.01). For genera, abundance of Butyrivibrio ( P = 0.01) and Lachnospiraceae ND3007 ( P < 0.01) (both from Lachnospiraceae family) was lower and unclassified Ruminococcaceae ( P = 0.03) was greater in CO 3 than Control and OH in solid fraction; while abundance of Pseudobutyrivibrio ( P = 0.10) and Lachnospiraceae FD2005 ( P = 0.09) (both from Lachnospiraceae family) and Ruminobacter ( P = 0.09) tended to decrease in CO 3 compared to Control in liquid fraction. Butyrate molar proportion was negatively correlated to Ruminococcaceae ( r = -0.55) in solid fraction and positively correlated to Pseudobutyrivibrio ( r = 0.61) and Lachnospiraceae FD2005 ( r = 0.61) in liquid. Our results indicate that source of Mg has an impact on bacterial taxa associated with ruminal butyrate synthesis, which is important for epithelial health and fatty acid synthesis., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Antibiotic-resistant microorganisms (ARMs) are widespread in natural environments, animals (wildlife and livestock), and humans, which has reduced our capacity to control life threatening infectious disease. Yet, little is known about their transmission pathways, especially at the wildlife-livestock interface. This study investigated the potential transmission of ARMs and antibiotic resistance genes (ARGs) between cattle and wildlife by comparing gut microbiota and ARG profiles of feral swine (Sus scrofa), coyotes (Canis latrans), cattle (Bos taurus), and environmental microbiota. Unexpectedly, wild animals harbored more abundant ARMs and ARGs compared to grazing cattle. Gut microbiota of cattle was significantly more similar to that of feral swine captured within the cattle grazing area where the home range of both species overlapped substantially. In addition, ARMs against medically important antibiotics were more prevalent in wildlife than grazing cattle, suggesting that wildlife could be a source of ARMs colonization in livestock., (© 2022. The Author(s).)

Our objectives were to compare the antifungal activity of 5 lignosulfonates, and 2 chitosans against fungi isolated from spoiled hay, and assess the effects of an optimized lignosulfonate, chitosan, and propionic acid (PRP) on high-moisture alfalfa hay. In experiment 1, we determined the minimum inhibitory concentration and minimum fungicidal concentration of 4 sodium lignosulfonates, 1 magnesium lignosulfonate, 2 chitosans, and PRP (positive control) against Aspergillus amoenus, Mucor circinelloides, Penicillium solitum, and Debaromyces hansenii at pH 4 and 6. Among sodium lignosulfonates, the one from Sappi Ltd. (NaSP) was the most antifungal at pH 4. However, chitosans had the strongest fungicidal activity with the exception of M. circinelloides at both pH 4 and 6. PRP had more antifungal effects than NaSP and was only better than chitosans for M. circinelloides. In experiment 2, we evaluated the effects of 3 additives (ADV): optimized NaSP (NaSP-O, UMaine), naïve chitosan (ChNv, Sigma-Aldrich), and PRP on high-moisture alfalfa hay. The experimental design was a randomized complete block design replicated 5 times. Treatment design was the factorial combination of 3 ADV× 5 doses (0, 0.25, 0.5, 1, and 2% w/w fresh basis). Additives were added to 35 g of sterile alfalfa hay (71.5 ± 0.23% DM), inoculated with a mixture of previously isolated spoilage fungi (5.8 log cfu/fresh g), and aerobically incubated in vitro for 23 d (25°C). After incubation, DM losses were reduced by doses as low as 0.25% for both NaSP-O and PRP (x¯=1.61) vs. untreated hay (24.0%), partially due to the decrease of mold and yeast counts as their doses increased. Also, hay NH3-N was lower in NaSP-O and PRP, with doses as low as 0.25%, relative to untreated hay (x¯=1.13 vs. 7.80% of N, respectively). Both NaSP-O and PRP increased digestible DM recovery (x¯=69.7) and total volatile fatty acids (x¯=94.3), with doses as low as 0.25%, compared with untreated hay (52.7% and 83.8 mM, respectively). However, ChNv did not decrease mold nor yeast counts (x¯=6.59 and x¯=6.16 log cfu/fresh g, respectively) and did not prevent DM losses relative to untreated hay. Overall, when using an alfalfa hay substrate in vitro, NaSP-O was able to prevent fungal spoilage to a similar extent to PRP. Thus, further studies are warranted to develop NaSP-O as a hay preservative under field conditions., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Acquisition of acquired chemoresistance during treatment cycles in urothelial carcinoma of the bladder (UCB) is the major cause of death through enhancing the risk of cancer progression and metastasis. Elevated glucose flux through the abnormal upregulation of O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) controls key signaling and metabolic pathways regulating diverse cancer cell phenotypes. This study showed that OGT expression levels in two human UCB cell models with acquired resistance to gemcitabine and paclitaxel were significantly upregulated compared with those in parental cells. Reducing hyper-O-GlcNAcylation by OGT knockdown (KD) markedly facilitated chemosensitivity to the corresponding chemotherapeutics in both cells, and combination treatment with OGT-KD showed more severe growth defects in chemoresistant sublines. We subsequently verified the suppressive effects of OGT-KD monotherapy on cell migration/invasion in vitro and xenograft tumor growth in vivo in chemoresistant UCB cells. Transcriptome analysis of these cells revealed 97 upregulated genes, which were enriched in multiple oncogenic pathways. Our final choice of suspected OGT glycosylation substrate was VCAN, S1PR3, PDGFRB, and PRKCG, the knockdown of which induced cell growth defects. These findings demonstrate the vital role of dysregulated OGT activity and hyper-O-GlcNAcylation in modulating treatment failure and tumor aggression in chemoresistant UCB.

Our objective was to evaluate the effects of unprotected choline chloride (Cho) on the ruminal microbiome at 2 dietary neutral detergent fiber (NDF) concentrations. We hypothesized that the effects of Cho on ruminal bacterial populations would depend on NDF. Eight dual-flow continuous-culture fermentors were arranged in a duplicated 4 × 4 Latin square as a 2 × 2 factorial with the following treatments: (1) 30% NDF-control (30% NDF diet, no supplemental choline); (2) 30% NDF-Cho (30% NDF diet plus 1.9 g of choline ion per kg of dry matter); (3) 40% NDF-control (40% NDF diet, no supplemental choline); and (4) 40% NDF-Cho (40% NDF diet plus 1.9 g of choline ion per kg of dry matter). We did 4 fermentation periods of 10 d each and used the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 32 solid and 32 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R (R Project for Statistical Computing) and SAS (SAS Institute Inc.) to determine effects of Cho, NDF, and NDF × Cho on taxa relative abundance. The correlation of propionate molar proportion with taxa relative abundance was also analyzed. At the phylum level, relative abundance of Firmicutes in the liquid fraction tended to be greater when Cho was supplemented with a 30% NDF diet. At the order level, Cho increased Coriobacteriales in solid fraction and decreased Fibrobacterales in liquid fraction. Moreover, Cho decreased abundance of Clostridiales and increased Selenomonadales in the solid fraction, only with the 30% NDF diet. For genera, lower abundance of Pseudobutyrivibrio resulted from Cho in solid and liquid fractions. Greater abundance of Succinivibrio in solid and Selenomonas and Selenomonas 1 in liquid resulted from Cho with the 30% NDF diet. Propionate molar proportion was positively correlated with relative abundance of order Selenomonadales in solid and liquid fractions, and with genus Succinivibrio in solid and genera Selenomonas and Selenomonas 1 in liquid. Our results indicate that Cho primarily decreases abundance of bacteria involved in fiber degradation and increases abundance of bacteria mainly involved in nonstructural carbohydrate degradation and synthesis of propionate, particularly when a diet with 30% NDF is provided., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The objective of this study was to evaluate ruminal microbiome changes associated with feeding Lactobacillus plantarum GB-LP1 as direct-fed microbials (DFM) in high-producing dairy cow diets. A dual-flow continuous culture system was used in a replicated 4 × 4 Latin square design. A basal diet was formulated to meet the requirements of a cow producing 45 kg of milk per day (16% crude protein and 28% starch). There were 4 experimental treatments: the basal diet without any DFM (CTRL); a mixture of Lactobacillus acidophilus, 1 × 10 9 cfu/g, and Propionibacterium freudenreichii, 2 × 10 9 cfu/g [MLP = 0.01% of diet dry matter (DM)]; and 2 different levels of L. plantarum, 1.35 × 10 9 cfu/g (L1 = 0.05% and L2 = 0.10% of diet DM). Bacterial samples were collected from the fluid and particulate effluents before feeding and at 2, 4, 6, and 8 h after feeding; a composite of all time points was made for each fermentor within their respective fractionations. Bacterial community composition was analyzed through sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequenced data were analyzed on DADA2, and statistical analyses were performed in R (RStudio 3.0.1, https://www.r-project.org/) and SAS 9.4 (SAS Institute Inc.); orthogonal contrasts were used to compare treatments. Different than in other fermentation scenarios (e.g., silage or beef cattle high-grain diets), treatments did not affect pH or lactic acid concentration. Effects were mainly from overall DFM inclusion, and they were mostly observed in the fluid phase. The relative abundance of the phylum Firmicutes, family Lachnospiraceae, and 6 genera decreased with DFM inclusion, with emphasis on Butyrivibrio&#95;2, Saccharofermentans, and Ruminococcus&#95;1 that are fibrolytic and may display peptidase activity during fermentation. Lachnospiraceae&#95;AC2044&#95;group and Lachnospiraceae&#95;XPB1014&#95;group also decreased in the fluid phase, and their relative abundances were positively correlated with NH 3 -N daily outflow from the fermentors. Specific effects of MLP and L. plantarum were mostly in specific bacteria associated with proteolytic and fibrolytic functions in the rumen. These findings help to explain why, in the previous results from this study, DFM inclusion decreased NH 3 -N concentration without altering pH and lactic acid concentration., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The source and route of bacterial colonization of the uterus are still not established. The objective was to investigate the source and route of bacterial colonization of the uterus by exploring the genetic relationship among E. coli strains isolated from the gastrointestinal and the reproductive tract of dairy cows pre- and postpartum. Secondarily, uterine health status (metritis vs. healthy) was evaluated. Cows (n = 34) had the rectoanal junction (RAJ), vulva, and vagina swabbed every three days starting six days before expected calving until nine days postpartum. The uterus was swabbed postpartum. A blood sample was collected at all time points, but cultures were negative. Whole-genome sequencing was performed on 44 isolates recovered from eight cows (four metritic and four healthy) with growth on selective E. coli media from the RAJ, vulva and/or vagina and uterus. Clonal isolates were found in the RAJ or the vulva prepartum and in the vulva, vagina or uterus postpartum. Clonal isolates were also found in the RAJ, the vulva, the vagina and the uterus postpartum. Clonal isolates were found in individual cows and different cows. Absence of clustering based on virulence factor genes and all genes indicate no strain specificity to body site or uterine health status. These findings indicate that the gastrointestinal tract is the likely source of bacteria that colonize the reproductive tract via ascending colonization of the uterus through the lower genital tract. Additionally, cow to cow transmission occurs, and strains are not specific to body site or to health status., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Bacillus cereus, a foodborne pathogen, is capable of forming spores and biofilms as methods to withstand environmental stresses. These bacterial structures are an issue for food safety as they aid the bacteria survive heat sterilisation processes of foods and food contact surfaces. This study was conducted to investigate the role of the biofilm structure in providing an extra layer of protection to spores against heat treatments. For this, heat resistance of B. cereus spores in intact biofilms was compared to that of planktonic spores in vitro and in a Cheonggukjang jjigae food model. Using methods developed in this study to measure the wet and dry heat resistance of spores in intact biofilms, it was found that B. cereus spores have significantly higher heat resistances when present in biofilms rather than as planktonic spores, and that dry heat is less effective than wet heat at killing spores in biofilms. In further detail, for wet heat treatments, spores in biofilms of the strain isolated from Cheonggukjang (Korean fermented whole soybean), B. cereus CH3, had generally higher wet heat resistances than the reference strain, B. cereus ATCC 10987, both in vitro and in the Cheonggukjang jjigae food model. However, the spores in biofilms of the two strains showed similar heat resistance to dry heat, with some exceptions, when biofilms were formed in vitro or in Cheonggukjang jjigae broth. Meanwhile, B. cereus ATCC 10987 spores in biofilms had higher or similar wet heat resistances in vitro compared to in Cheonggukjang jjigae broth. Wet heat resistances of B. cereus CH3 spores in biofilms were all statistically similar regardless of biofilm formation media (brain heart infusion and Cheonggukjang jjigae broths). For dry heat, spores in biofilms of both B. cereus strains were more heat resistant when biofilms were formed in the Cheonggukjang jjigae food model rather than in vitro. Altogether, heat resistances of spores in biofilms formed in vitro and in the food environment were found to be different depending on the tested B. cereus strain, but higher than planktonic spores in any case. This is the first study examining the heat resistance of B. cereus spores in intact biofilms matrices attached to the surface, both in vitro and in a food model. Therefore, this research is valuable to understand the protective effects of biofilms formed in food environments and to reduce the food safety risks associated with B. cereus., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Antimicrobial resistance is one of the greatest global threats. Particularly, multidrug resistant extended-spectrum β-lactamase (ESBL)-producing pathogens confer resistance to many commonly used medically important antibiotics, especially beta-lactam antibiotics. Here, we developed an innovative combination approach to therapy for multidrug resistant pathogens by encapsulating cephalosporin antibiotics and β-lactamase inhibitors with chitosan nanoparticles (CNAIs). The four combinations of CNAIs including two cephalosporin antibiotics (cefotaxime and ceftiofur) with two β-lactamase inhibitors (tazobactam and clavulanate) were engineered as water-oil-water emulsions. Four combinations of CNAIs showed efficient antimicrobial activity against multidrug resistant ESBL-producing Enterobacteriaceae. The CNAIs showed enhanced antimicrobial activity compared to naïve chitosan nanoparticles and to the combination of cephalosporin antibiotics and β-lactamase inhibitors. Furthermore, CNAIs attached on the bacterial surface changed the permeability to the outer membrane, resulting in cell damage that leads to cell death. Taken together, CNAIs have provided promising potential for treatment of diseases caused by critically important ESBL-producing multidrug resistant pathogens., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Calf diarrhea is one of the most concerning challenges facing both the dairy and beef cattle industry. Maintaining healthy gut microbiota is essential for preventing gastrointestinal disorders. Here, we observed significantly less bacterial richness in the abnormal feces with watery or hemorrhagic morphology compared to the normal solid feces. The normal solid feces showed high relative abundances of Osllospiraceae , Christensenellaceae , Barnesiella , and Lactobacillus , while the abnormal feces contained more bacterial taxa of Negativicutes , Tyzzerella , Parasutterella , Veillonella , Fusobacterium , and Campylobacter . Healthy calves had extensive bacterial-bacterial correlations, with negative correlation between Lactobacillus and potential diarrheagenic Escherichia coli-Shigella , but not in the abnormal feces. We isolated Lactobacillus species ( L. reuteri , L. johnsonii , L. amylovorus , and L. animalis ), with L. reuteri being the most abundant, from the healthy gut microbiota. Isolated Lactobacillus strains inhibited pathogenic strains including E. coli K88 and Salmonella Typhimurium. These findings indicate the importance of a diverse gut microbiota in newborn calf's health and provide multiple potential probiotics that suppress pathogen colonization in the gastrointestinal tract to prevent calf diarrhea., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Fan, Kim, Liu, Zhai, Liu, Driver and Jeong.)

New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae pose a great threat to public health globally. Most known NDM-producing Enterobacteriaceae are associated with human hospital or community infections. Here, we report the draft genome sequence of an NDM-1-encoding Klebsiella pneumoniae strain isolated from feral swine (Sus scrofa) captured in Florida, USA.

The objective was to investigate the economic effect of treating dairy cows with metritis using ceftiofur-free acid or leaving them untreated at the time of diagnosis. Cows with a fetid, watery, red-brownish vaginal discharge were diagnosed with metritis (d 0). Data from 875 dairy cows (506 primiparous and 369 multiparous) from 1 herd in northern Florida that had been part of a larger study evaluating different treatments for metritis were used for the economic analysis. Holstein cows with metritis had been randomly assigned to: Ceftiofur (CEF, n = 239) = subcutaneous injection of 6.6 mg/kg of ceftiofur crystalline-free acid in the base of the ear at d 0 and d 3; Untreated (UNT, n = 233) = no treatment applied at metritis diagnosis. Both groups could receive escape therapy if condition worsened. A group of nonmetritic healthy cows (NMET; n = 403) from the same cohort was randomly selected for comparison. Continuous outcomes such as 300-d milk production (kg/cow), milk sales ($/cow), cow sales ($/cow), treatment cost by 60 days in milk ($/cow), reproduction cost ($/cow), replacement cost ($/cow), feeding cost ($/cow), and gross profit per cow ($/cow) were analyzed using the ANOVA (MIXED procedure of SAS version 9.4). Dichotomous outcomes such as pregnancy and culling by 300 d were analyzed using logistic regression (GLIMMIX procedure of SAS). Models included the fixed effects of treatment, parity, and the interaction between treatment and parity. A stochastic analysis was performed with 10,000 iterations using the observed results from each group. The CEF treatment resulted in greater treatment cost by 60 DIM than UNT ($112 vs. $37), but resulted in a greater proportion of pregnant cows (71 vs. 61%) and decreased culling by 300 DIM (29 vs. 39%) compared with UNT. Gross profit was lesser for UNT than NMET ($2,969 vs. $3,426), and CEF was intermediate ($3,219). The stochastic analysis showed that the mean difference in gross profit between UNT and NMET was -$457; saleable milk (49%) and replacement cost (24%) accounted for most of the variation. The mean difference in gross profit between CEF and NMET group was -$207; saleable milk (82%) and initial metritis treatment cost (9%) accounted for most of the variation. The mean difference in gross profit between the UNT and the CEF group was -$250; replacement cost (41%) and cow sales (31%) accounted for most of the variation. In summary, metritis caused large economic losses when left untreated, and CEF reduced those losses by improving fertility, reducing culling and replacement cost, and reducing milk yield losses., (Copyright © 2021 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we evaluated the hindgut microbiota and its association with animal growth and immunity across life. We evaluated three different growth stages in an Angus-Brahman multibreed population with a graduated spectrum of genetic variation, raised under variable environmental conditions and diets. We found the gut microbiota structure was changed significantly during growth when preweaning, and fattening calves experienced large variations in diet and environmental changes. However, regardless of the growth stage, we found gut microbiota is significantly influenced by breed composition throughout life. Host genetics explained the relative abundances of 52.2%, 40.0%, and 37.3% of core bacterial taxa at the genus level in preweaning, postweaning, and fattening calves, respectively. Sutterella, Oscillospira, and Roseburia were consistently associated with breed composition at these three growth stages. Especially, butyrate-producing bacteria, Roseburia and Oscillospira, were associated with nine single-nucleotide polymorphisms (SNPs) located in genes involved in the regulation of host immunity and metabolism in the hindgut. Furthermore, minor allele frequency analysis found breed-associated SNPs in the short-chain fatty acids (SCFAs) receptor genes that promote anti-inflammation and enhance intestinal epithelial barrier functions. Our findings provide evidence of dynamic and lifelong host genetic effects upon gut microbiota, regardless of growth stages. We propose that diet, environmental changes, and genetic components may explain observed variation in critical hindgut microbiota throughout life., (© 2021. The Author(s).)

Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232 T ), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508 T , CSL7591 T ). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232 T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius , and the 16S rRNA gene of CSL7508 T and CSL7591 T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium . All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232 T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508 T and CSL7591 T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus . Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus , for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232 T (=NCTC 14341 T =DSM 110741 T =CCUG 74371 T ), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508 T (=NCTC 14410 T =DSM 110742 T =CCUG 74374 T ) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591 T (=NCTC 14455 T =DSM 111148 T =CCUG 74655 T ). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232 T , CSL7508 T , and CSL7591 T , respectively.

Background: NDM-producing Enterobacteriaceae are a major clinical concern worldwide. We characterized NDM-positive pathogens isolated from patients and assessed the dissemination patterns of the bla NDM genes in a hospital setting., Methods: Eleven NDM-positive Enterobacteriaceae (three Enterobacter hormaechei , six Klebsiella pneumoniae and two Escherichia coli ) were isolated from nine patients over a 1 year period. Antimicrobial susceptibility was assessed by MICs. A combination of short- and long-read WGS was used for genome analysis. Clinical treatment history of patients was linked with genetic features of individual isolates to investigate the dissemination patterns of the bla NDM genes and NDM-positive strains., Results: bla NDM in clonal K. pneumoniae were transmitted between two patients. In other instances, an identical IncC plasmid encoding NDM-1 was transmitted between E. coli and K. pneumoniae isolated from the same patient, and an IncX3 plasmid, carrying bla NDM-1 or bla NDM-5 , was harboured in non-clonal E. hormaechei . Varying patterns of IS elements were identified as a critical transmission mechanism in association with bla NDM genes., Conclusions: Multiple transmission patterns were identified in hospitalized patients, including dissemination of clonal bacterial strains carrying resistance genes and horizontal transfer of resistance genes among divergent bacterial strains. Controlling spread of NDM is complex: while attention to standard infection control practices is critically important, this needs to be matched by aggressive efforts to limit unnecessary antimicrobial use, to minimize the selection for and risk of transfer of 'high mobility' resistance genes among Enterobacteriaceae., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.)

Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens with high transmissibility and mortality. Here, we report the draft genome sequence of a Bcc strain isolated from a deep abscess culture in an immunocompetent patient with no relevant prior medical history., (Copyright © 2021 Zhai et al.)

Antibiotic use in livestock accounts for 80% of total antibiotic use in the United States and has been described as the driver for resistance evolution and spread. As clinical infections with multidrug-resistant pathogens are rapidly rising, there remains a missing link between agricultural antibiotic use and its impact on human health. In this study, two species of filth flies from a livestock operation were collected over the course of 11 mo: house flies Musca domestica (L.) (Diptera: Muscidae), representing a generalist feeder, and stable flies Stomoxys calcitrans (L.) (Diptera: Muscidae), representing a specialist (blood) feeder. The prevalence of flies carrying cefotaxime-resistant (CTX-R) bacteria in whole bodies and dissected guts were assayed by culturing on antibiotic-selective media, with distinct colonies identified by Sanger sequencing. Of the 149 flies processed, including 81 house flies and 68 stable flies, 18 isolates of 12 unique bacterial species resistant to high-level cefotaxime were recovered. These isolates also showed resistance to multiple classes of antibiotics. The CTX-R isolates were predominantly recovered from female flies, which bore at least two resistant bacterial species. The majority of resistant bacteria were isolated from the guts encompassing both enteric pathogens and commensals, sharing no overlap between the two fly species. Together, we conclude that house flies and stable flies in the field could harbor multidrug-resistant bacteria. The fly gut may serve as a reservoir for the acquisition and dissemination of resistance genes., (© The Author(s) 2020. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Intramammary bacterial infection, the most common cause of mastitis, is the most costly disease in dairy cattle in the US and reason for antibiotic usage. Ceftiofur, a third-generation cephalosporin, is generally used to treat such disease, but it has a high treatment failure rate. Though the reason is not known clearly, it is hypothesized that multiple factors are associated with the treatment failure. In this study, we analyzed 169 milk samples from cows with mastitis in two independent dairy farms (Farm A and B) in which 19.4% (Farm A) and 14.3% (Farm B) of the antibiotic treated cows were not cured. The prevalence of cephalosporin-resistant bacteria (CRB) in milk was 72.0% and 42.1% in Farm A and B, respectively. Nineteen and nine bacterial genera were identified in Farm A and B respectively, with the most abundant genus being Staphylococcus (27.1%; Farm A) and Bacillus (63.5%; Farm B). However, no strong relationship between the treatment failure rate and the CRB prevalence was observed. Furthermore, the metagenomic analysis showed no significant differences in the α- and β-diversities of microbiota in milk samples from cured and uncured cows, suggesting that antibiotic-resistant bacteria were not the sole reason for the antibiotic treatment failure. KEY POINTS: • The mastitic milk samples had high prevalence of cephalosporin-resistant bacteria (CRB). • The CRB identified belong to diversified species. • Antibiotic treatment failure was not solely caused by the abundance of CRB.

Bacterial resistance to antibiotics is a critical public health concern. Alternatives of antibiotics are needed urgently. Herein, we designed and engineered a new nano-antimicrobial, chitosan nanoparticles (CNs)-antimicrobial peptide microcin J25 (MccJ25) conjugates (CNMs). The engineered CNMs proved to be highly active against Gram-negative and Gram-positive bacteria, and the activity of CNMs and CNs was stable in various thermal and pH environments. Escherichia coli K88 strain treated with CNMs did not acquire resistance in serial passage assays over a period of 18 days. Risk assessment with cell lines showed that CNMs did not cause toxicity. Additionally, CNMs did not reduce the lifespan of C. elegans. In summary, this study demonstrated that CNMs can serve as an excellent novel antimicrobial agent against multi-drug resistance pathogens., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Due to increasing reports of multidrug-resistant (MDR) Vibrio cholerae O1, the goal of this study was to characterize the in vitro antimicrobial activity of chitosan microparticles (CMs) to evaluate their potential as a novel therapeutic agent for cholera. We examined the antimicrobial activity of CMs against toxigenic V. cholerae O1 using direct enumeration, microscopy, and fluorescence microplate assays. Bacterial viability kinetics were measured with different concentrations of CMs, solution pH, and salt content using a live/dead staining technique. Growth inhibition of CM-exposed V. cholerae strains was conducted using a redox-sensitive stain and compared between wild-type and isogenic outer membrane (OM) mutants. CM concentrations above 0.1 wt % were sufficient to kill V. cholerae O1 suspensions with approximately 10 8 CFU/mL within 3 h. The nonviable cells demonstrated increased OM permeability that corresponded to gross morphological changes observed through scanning electron microscopy. CMs exhibited dose-dependent bactericidal activity that increased predictably at lower pH and decreased with salt addition. V. cholerae O1 strains lacking O-antigen were twice as susceptible to growth inhibition by CMs, whereas those with glycine modification to lipid A were ten times more resistant. We propose that CMs exert vibriocidal activity via electrostatic surface interactions between their positively charged amine groups and the negatively charged Gram-negative bacterial OM, resulting in disruption, increased permeability, decreased redox metabolism, and subsequent loss of cellular viability. Further research should be conducted in vivo to evaluate the efficacy of CMs as luminal agents to treat infections caused by MDR, toxigenic V. cholerae and other diarrheal pathogens.

The objective of this study was to evaluate the effect of chitosan microparticles on the uterine microbiome of cows with metritis. Dairy cows with metritis ( n  = 89) were assigned to 1 of 3 treatments: chitosan microparticles ( n  = 21), in which the cows received an intrauterine infusion of chitosan microparticles at metritis diagnosis (day 0), day 2, and day 4; ceftiofur ( n  = 25), in which the cows received a subcutaneous injection of ceftiofur on day 0 and day 3; and no intrauterine or subcutaneous treatment ( n  = 23). Nonmetritic cows ( n  = 20) were healthy cows matched with cows with metritis by the number of days postpartum at metritis diagnosis. Uterine swab samples collected on days 0, 3, 6, 9, and 12 were used for 16S rRNA gene sequencing and 16S RNA gene copy number quantification by quantitative PCR. Principal-coordinate analysis showed that the microbiome of the ceftiofur-treated and metritic untreated groups progressed toward that of the nonmetritic group by day 3, whereas that of the chitosan microparticle-treated group remained unchanged. The differences on day 3 were mainly due to a greater relative abundance of Fusobacteria , particularly Fusobacterium , in the chitosan microparticle-treated group than in the ceftiofur-treated and metritic untreated groups. Furthermore, the microbiome of the ceftiofur-treated group became similar to that of the nonmetritic group by day 9, whereas the microbiome of the chitosan microparticle-treated and metritic untreated groups became similar to that of the nonmetritic group only by day 12. The total bacterial 16S rRNA gene counts in the chitosan microparticle-treated group were greater than those in the metritic untreated controls on days 6 and 9, whereas the ceftiofur treatment group was the only group in which the total bacterial 16S rRNA gene count became similar to that in the nonmetritic group by day 12. In summary, chitosan microparticles slowed the progression of the uterine microbiome toward a healthy state, whereas ceftiofur hastened the progression toward a healthy state. IMPORTANCE Third-generation cephalosporins, such as ceftiofur, are commonly used to treat metritis in dairy cows. Chitosan microparticles has been shown to have a broad spectrum of activity in vitro and to be effective against uterine pathogens in vivo ; therefore, they have been hailed as a possible alternative to traditional antibiotics. Nonetheless, in the present study, we saw that chitosan microparticle treatment slowed the progression of the uterine microbiome of cows with metritis toward a healthy state, whereas ceftiofur treatment hastened the progression toward a healthy state. Given the lack of an effective alternative to traditional antibiotics and an increased concern about antimicrobial resistance, a greater effort should be devoted to the prevention of metritis in dairy cows., (Copyright © 2020 American Society for Microbiology.)

The main objective of this study was to evaluate the efficacy of intrauterine administration of chitosan microparticles (CM) in curing metritis in dairy cows. A secondary objective was to evaluate the effects of metritis treatments on milk yield, survival, and reproductive performance. Cows with a fetid, watery, red-brownish vaginal discharge were diagnosed with metritis. Holstein cows (n = 826) with metritis from 3 dairies located in northern Florida were blocked by parity (primiparous or multiparous) and, within each block, randomly assigned to one of 3 treatments: CM (n = 276) = intrauterine infusion of 24 g of CM dissolved in 40 mL of sterile distilled water at the time of metritis diagnosis (d 0), 2 (d 2), and 4 (d 4) d later; ceftiofur (CEF; n = 275) = subcutaneous injection of 6.6 mg/kg ceftiofur crystalline-free acid in the base of the ear at d 0 and d 3; Control (CON; n = 275) = no treatment applied at metritis diagnosis. All groups could receive escape therapy if condition worsened. Cure was considered when vaginal discharge became mucoid and not fetid. A group of nonmetritic (NMET; n = 2,436) cows was used for comparison. Data were analyzed by generalized linear mixed and Cox's proportional hazard models. Cows in CM and CON had lesser risk of metritis cure on d 12 than cows in CEF (58.6 ± 5.0 vs. 61.9 ± 4.9% vs. 77.9 ± 3.9, respectively). The proportion of cows culled within 60 days in milk (DIM) was greater for cows in CM than for cows in CEF and CON (21.5 ± 2.7 vs. 9.7 ± 1.9 vs. 11.3 ± 2.0%, respectively). Treatment did not affect rectal temperature or plasma nonesterified fatty acids, β-hydroxybutyrate, and haptoglobin concentrations. Milk yield in the first 60 DIM differed for all treatments, and it was lowest for CM (35.8 ± 0.3 kg/d), followed by CON (36.8 ± 0.3 kg/d) and CEF (37.9 ± 0.3 kg/d). The hazard of pregnancy up to 300 DIM was lesser for CM than CEF (hazard ratio = 0.62; 95% CI: 0.50-0.76), for CM than CON (hazard ratio = 0.77; 95% CI: 0.62-0.95) and for CON than CEF (hazard ratio = 0.80; 95% CI: 0.65-0.99). Culling was greater, and milk yield and fertility were lesser for CEF than NMET. In summary, CM did not improve the cure of metritis, and was detrimental to milk yield, survival, and fertility compared with CON. In contrast, CEF increased the cure of metritis, milk yield, and fertility compared with CM and CON. Finally, the negative effects of metritis on milk yield culling and fertility could not be completely reversed by CEF., (Copyright © 2020 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Postpartum uterine infection reduces fertility in dairy cattle; however, the mechanisms of uterine infection-mediated infertility are unknown. Paradoxically, infection-induced infertility persists after the resolution of disease. Oocytes are a finite resource, which are present at various stages of development during uterine infection. It is likely that oocyte development is influenced by uterine infection-induced changes to the follicular microenvironment. To better understand the impact of infection on oocyte quality we employed global transcriptomics of oocytes collected from heifers after receiving intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes . We hypothesized that the oocyte transcriptome would be altered in response to intrauterine infection. A total of 452 differentially expressed genes were identified in oocytes collected from heifers 4 days after bacteria infusion compared to vehicle infusion, while 539 differentially expressed genes were identified in oocytes collected from heifers 60 days after bacteria infusion. Only 42 genes were differentially expressed in bacteria-infused heifers at both Day 4 and Day 60. Interferon, HMGB1, ILK, IL-6, and TGF-beta signaling pathways were downregulated in oocytes collected at Day 4 from bacteria-infused heifers, while interferon, ILK, and IL-6 signaling were upregulated in oocytes collected at Day 60 from bacteria-infused heifers. These data suggest that bacterial infusion alters the oocyte transcriptome differently at Day 4 and Day 60, suggesting different follicle stages are susceptible to damage. Characterizing the long-term impacts of uterine infection on the oocyte transcriptome aids in our understanding of how infection causes infertility in dairy cattle., Competing Interests: The authors have nothing to declare., (© 2020 The Authors. FASEB BioAdvances published by the Federation of American Societies for Experimental Biology.)

The study evaluated the role of Enterococcus faecium in tyramine production and its response to fermentation temperature in a traditional Korean fermented soybean paste, Cheonggukjang . Tyramine content was detected in retail Cheonggukjang products at high concentrations exceeding the recommended limit up to a factor of 14. All retail Cheonggukjang products contained Enterococcus spp. at concentrations of at least 6 Log CFU/g. Upon isolation of Enterococcus strains, approximately 93% (157 strains) produced tyramine at over 100 µg/mL. The strains that produced the highest concentrations of tyramine (301.14-315.29 μg/mL) were identified as E . faecium through 16S rRNA sequencing. The results indicate that E. faecium is one of the major contributing factors to high tyramine content in Cheonggukjang . During fermentation, tyramine content in Cheonggukjang groups co-inoculated with E. faecium strains was highest at 45 °C, followed by 37 °C and 25 °C. The tyramine content of most Cheonggukjang groups continually increased as fermentation progressed, except groups fermented at 25 °C. At 45 °C, the tyramine content occasionally exceeded the recommended limit within 3 days of fermentation. The results suggest that lowering fermentation temperature and shortening duration may reduce the tyramine content of Cheonggukjang , thereby reducing the safety risks that may arise when consuming food with high tyramine concentrations.

Infection of the postpartum uterus with pathogenic bacteria is associated with infertility months later in dairy cattle. However, it is unclear whether these bacterial infections lead to long-term changes in the reproductive tract that might help explain this infertility. Here we tested the hypothesis that infusion of pathogenic bacteria into the uterus leads to changes in the transcriptome of the reproductive tract 3 months later. We used virgin Holstein heifers to avoid potential confounding effects of periparturient problems, lactation, and negative energy balance. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes (n = 4) and compared with control animals (n = 6). Three months after infusion, caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from ovarian follicles >8 mm diameter were profiled by RNA sequencing. Bacterial infusion altered the transcriptome of all the tissues when compared with control. Most differentially expressed genes were tissue specific, with 109 differentially expressed genes unique to caruncular endometrium, 57 in intercaruncular endometrium, 65 in isthmus, 298 in ampulla, and 83 in granulosa cells. Surprisingly, despite infusing bacteria into the uterus, granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there were changes in the transcriptome of the endometrium, oviduct and even granulosa cells, 3 months after intrauterine infusion of pathogenic bacteria. These findings imply that long-term changes throughout the reproductive tract could contribute to infertility after bacterial infections of the uterus.

While the soil microbiome may influence pathogen survival, determining the major contributors that reduce pathogen survival is inconclusive. This research was performed to determine the survival of E. coli O157 in autoclaved and natural (unautoclaved) sandy soils. Soils were inoculated with three different E. coli O157 strains (stx1+/stx2+, stx1-/stx2-, and stx1-/stx2+), and enumerated until extinction at 30°C. There was a significant difference in the survival of E. coli O157 based on soil treatment (autoclaved versus natural) at 30°C on days 1 (P = 0.00022), 3, (P = 2.53e-14), 7 (P = 5.59e-16), 14 (P = 1.072e-12), 30 (P = 7.18e-9), and 56 (P = 0.00029), with greater survival in autoclaved soils. The time to extinction (two consecutive negative enrichments) for all three strains was 169 and 84 days for autoclaved and natural soils, respectively. A separate E. coli O157 trial supplemented with 16S rRNA gene sequencing of the soil microbiome was performed at 15°C and 30°C on days 0, 7, 14, and 28 for each soil treatment. Greater species richness (Chao1, P = 2.2e-16) and diversity (Shannon, P = 2.2e-16) was observed in natural soils in comparison with autoclaved soils. Weighted UniFrac (beta-diversity) showed a clear distinction between soil treatments (P = 0.001). The greatest reduction of E. coli O157 was observed in natural soils at 30°C, and several bacterial taxa positively correlated (relative abundance) with time (day 0 to 28) in these soils (P < 0.05), suggesting that the presence of those bacteria might cause the reduction of E. coli O157. Taken together, a clear distinction in E. coli O157 survival, was observed between autoclaved and natural soils along with corresponding differences in microbial diversity in soil treatments. This research provides further insights into the bacterial taxa that may influence E. coli O157 in soils., Competing Interests: The authors have declared that no competing interests exist.

Shiga toxin (Stx)-producing Escherichia coli (STEC) O157:H7 is an enteric pathogen that causes life-threatening disease in humans, with cattle being major natural reservoirs. A group of STEC O157:H7 with a dramatic combination of high virulence potentials and super-shedder bovine origin have been isolated. Here, an STEC O157:H7 isolate, JEONG-1266, was analyzed by comparative genomics, stx genotyping, and phenotypic analyses. The phylogenetic typing and whole-genome comparison consistently showed that JEONG-1266 is genetically close to EC4115 (one of 2006 Spinach outbreak isolates) and SS17 (an isolate from super-shedder cattle) strains, all of which belong to lineage I/II and Clade 8. Both lineage I/II and Clade 8 are known to be mostly associated with clinical strains with high virulence and severe clinical symptoms. Further, JEONG-1266, like EC4115 and SS17, harbors stx2a/stx2c genes, and carries Stx-encoding prophages, specifically the φ stx2a -γ subtype. Possession of the φ stx2a -γ subtype of Stx-encoding prophages and production of Stx2a have been shown to be a key signature associated with hypervirulent STEC O157:H7 strains. In silico virulence typing elucidated JEONG-1266, EC4115, and SS17 shared a highly conserved profile of key virulence genes at the nucleotide sequence level. Consistently, phenotypic data showed that JEONG-1266 expressed a high level of Stx2 toxins and had the full capacity of adhesion in vitro . Taken together, our study suggests that JEONG-1266 may represent an emerging STEC O157:H7 group, which are hypervirulent strains that originate from super-shedders, that can be a threat to food safety and public health., (Copyright © 2020 Teng, Lee, Park and Jeong.)

Background: Docetaxel is the preferred chemotherapeutic agent for hormone-refractory prostate cancer (PC) patients. However, patients eventually develop docetaxel resistance, and no effective treatment options are available for them., Objective: We aimed to establish docetaxel resistance in castration-resistant prostate cancer (CRPC) cell lines (DU145/TXR, PC-3/TXR, and CWR22/TXR) and characterized transcriptional changes upon acquiring resistance to the docetaxel., Methods: Human PC cells (DU145, PC-3, CWR22) and all docetaxel-resistant cells were maintained in Roswell Park Memorial Institute Medium (RPMI) 1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. ABCB1 was detected by using both parental and docetaxel-resistant CRPCs prepared for flow cytometry. For the evaluation of tumor-suppressive effects under each chemotherapeutic agent, subcutaneous xenografts of DU145 or DU145/TXR were implanted at the mouse flank., Results: The P-glycoprotein-encoding gene ABCB1 was distinctively upregulated in the resistant cells, and its overexpression played an essential role in docetaxel resistance in CRPC. When tested for the cytotoxicity of gemcitabine, another option for chemotherapy, the docetaxel-resistant cells were shown to become sensitive to the drug, implying additional phenotypic transformation in the docetaxel-resistant cells. Studies using xenograft animal models demonstrated that the growth of tumors composed of both docetaxel-sensitive and docetaxel-resistant cells was deterred most profoundly when docetaxel and gemcitabine were administered together., Conclusion: This study suggests that when a drug develops therapeutic resistance, sensitivity tests could be another option, ultimately providing insight into a novel alternative clinical strategy., (© 2020 Wiley Periodicals, Inc.)

Shiga toxin-producing Escherichia coli (STEC) are critical foodborne pathogens, which cause serious human health issues, including hemolytic uremic syndrome. Illnesses caused by STEC lack effective treatments that target the elimination of these bacteria from the gastrointestinal tract without causing an adverse effect. Reducing this pathogen from a reservoir of STEC is an effective strategy, but the challenges remain due to the lack of efficient, selective antimicrobial agents. We developed specific antibody-conjugated chitosan nanoparticles (CNs) to selectively target and treat STEC in the gastrointestinal tract. Given the great broad-spectrum antimicrobial activity of CN, we conjugated antibodies to CN. Antibodies were raised and purified from egg yolks after immunization of hens with seven different O-side-chain antigens isolated from STEC (O26, O45, O103, O111, O121, O145, and O157). We prepared CN-immunoglobulin Y (IgY) conjugates by forming amide bonds at different ratios of CN:IgY (10:1, 10:2, and 10:4). The CN-IgY conjugated at a 10:2 ratio demonstrated significantly enhanced antimicrobial activity against E. coli O157:H7. Conjugates of CN and anti-STEC IgY antibodies killed corresponding STEC serotypes specifically and selectively, while showing no significant impact on nontargeted bacteria, including Salmonella enterica and Lactobacillus plantarum . The enhanced antimicrobial activity of CN-IgY against STEC was also confirmed in synthetic intestinal fluid, as well as an in vivo animal model of Caenorhabditis elegans . These results suggest that the CN-IgY conjugates have strong and specific antimicrobial activity and that they are also great candidates to eliminate pathogens selectively in the gastrointestinal tract without inhibiting beneficial bacteria.

The effectiveness of antibiotics has been challenged by the increasing frequency of antimicrobial resistance (AR), which has emerged as a major threat to global health. Despite the negative impact of AR on health, there are few effective strategies for reducing AR in food-producing animals. Of the antimicrobial resistant microorganisms (ARMs), extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae are an emerging global threat due to their increasing prevalence in livestock, even in animals raised without antibiotics. Many reviews are available for the positive selection of AR associated with antibiotic use in livestock, but less attention has been given to how other factors including soil, water, manure, wildlife, and farm workers, are associated with the emergence of ESBL-producing bacteria. Understanding of antibiotic resistance genes and bacteria transfer at the interfaces of livestock and other potential reservoirs will provide insights for the development of mitigation strategies for AR.

This study was conducted to examine the effects of clay (CL) and Saccharomyces cerevisiae fermentation product (SCFP) on the ruminal bacterial community of Holstein dairy cows challenged with aflatoxin B 1 (AFB 1 ). A second objective was to examine correlations between bacterial abundance and performance measures. Eight lactating dairy cows stratified by milk yield and parity were randomly assigned to 4 treatments in a 4 × 4 Latin square design with 2 replicate squares, four 33-d periods, and a 5-d washout between periods. The treatments included (1) control (basal diet, no additive); (2) T (control + 63.4 µg/kg AFB 1 , oral dose); (3) CL (T + 200 g/head per day of sodium bentonite clay, top-dress); and (4) CL+SCFP [CL + 19 g/head per day Diamond V NutriTek (Diamond V Inc., Cedar Rapids, IA) + 16 g/head per day MetaShield (Diamond V Inc.), top-dress]. Cows were adapted to diets containing no AFB 1 from d 1 to 25 (predosing period). From d 26 to 30 (dosing period), AFB 1 was orally dosed and then withdrawn for d 31 to 33 (withdrawal period). During the predosing period, compared with the control, feeding CL and CL+SCFP increased the relative abundance of the most dominant phylum, Bacteroidetes (55.1 and 55.8 vs. 50.6%, respectively), and feeding CL+SCFP increased Prevotella abundance (43.3 and 43.6 vs. 40.0%, respectively). During the dosing period, feeding AFB 1 did not affect the ruminal bacterial community, but the relative abundance of Fibrobacteraceae increased with CL+SCFP compared with T (1.45 vs. 0.97%); Fibrobacter abundance also tended to increase with CL+SCFP compared with T and control, respectively (1.45 vs. 0.97 and 1.05%, respectively). Feeding AFB 1 with or without CL or CL+SCFP did not affect ruminal pH or concentrations of NH 3 -N, total volatile fatty acids, or individual volatile fatty acids. Milk yield and milk component yields were positively correlated with the relative abundance of unclassified Succinivibrionaceae, unclassified YS2, or Coprococcus. Feed efficiency was positively correlated (r ≥ 0.30) with the relative abundance of unclassified YS2, Coprococcus, or Treponema. Feeding aflatoxin at 63 µg/kg, a common contamination level on farms, did not affect the abundance of dominant bacteria or rumen fermentation. When aflatoxin was fed, CL+SCFP increased the abundance of Fibrobacter, a major fibrolytic bacteria genus. Milk yield and DMI were positively correlated with abundance of Succinivibrionaceae and Coprococcus. Feed efficiency was positively correlated with abundance of Coprococcus, Treponema, and YS2. Future studies should speciate culture and determine the functions of the bacteria to elucidate their roles in the rumen and potential contribution to increasing the performance of dairy cows., (Copyright © 2020 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The emergence of extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase producing Escherichia coli represent a contemporary public health threat. ESBL and AmpC β-lactamase genes translocate between chromosomes and plasmids, facilitating rapid spread throughout the environment. In this study, ESBL/AmpC producing bacteria were isolated from beef cattle farms with seldom antibiotic use. Eleven farms out of 17 tested, had ESBL/AmpC producing E. coli in animals, soil, and forage samples. Fifty-nine CTX-M or CMY-2 positive E. coli isolates were further characterized with whole-genome sequencing. The isolates commonly carried CMY-2, TEM, or CTX-M genes, and over half encoded both CTX-M and TEM genes. Using comparative genomics, antimicrobial resistance genes from 12 classes of antimicrobial were identified and confirmed by antibiotic susceptibility test, revealing multidrug resistance against multiple classes of antibiotics. Virulence factors related to adherence, invasion, iron uptake, and bacterial secretion systems were shared by all isolates; some of which were identified as enteropathogenic E. coli . Phylogenetic analyses revealed a pattern of close genetic relatedness, suggesting that ESBL/AmpC producing E. coli were transmitted among farms as well as independent evolution within farms. Our results indicate that ESBL and AmpC β-lactamases prevail in food animal production system regardless antibiotic use and have the characteristics for zoonotic transmission., (Copyright © 2020 Lee, Teng, DiLorenzo, Weppelmann and Jeong.)