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Bovine respiratory disease (BRD) remains the leading infectious disease in beef cattle production systems. Host gene expression upon facility arrival may indicate risk of BRD development and severity. However, a time-course approach would better define how BRD development influences immunological and inflammatory responses after disease occurrences. Here, we evaluated whole blood transcriptomes of high-risk beef cattle at three time points to elucidate BRD-associated host response. Sequenced jugular whole blood mRNA from 36 cattle (2015: n = 9; 2017: n = 27) across three time points ( n = 100 samples; days [D]0, D28, and D63) were processed through ARS-UCD1.2 reference-guided assembly (HISAT2/Stringtie2). Samples were categorized into BRD-severity cohorts (Healthy, n = 14; Treated 1, n = 11; Treated 2+, n = 11) via frequency of antimicrobial clinical treatment. Assessment of gene expression patterns over time within each BRD cohort was modeled through an autoregressive hidden Markov model (EBSeq-HMM; posterior probability ≥ 0.5, FDR < 0.01). Mixed-effects negative binomial models (glmmSeq; FDR < 0.05) and edgeR (FDR < 0.10) identified differentially expressed genes between and across cohorts overtime. A total of 2,580, 2,216, and 2,381 genes were dynamically expressed across time in Healthy, Treated 1, and Treated 2+ cattle, respectively. Genes involved in the production of specialized resolving mediators (SPMs) decreased at D28 and then increased by D63 across all three cohorts. Accordingly, SPM production and alternative complement were differentially expressed between Healthy and Treated 2+ at D0, but not statistically different between the three groups by D63. Magnitude, but not directionality, of gene expression related to SPM production, alternative complement, and innate immune response signified Healthy and Treated 2+ cattle. Differences in gene expression at D63 across the three groups were related to oxygen binding and carrier activity, natural killer cell-mediated cytotoxicity, cathelicidin production, and neutrophil degranulation, possibly indicating prolonged airway pathology and inflammation weeks after clinical treatment for BRD. These findings indicate genomic mechanisms indicative of BRD development and severity over time., 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 © 2024 Scott, Valeris-Chacin, Thompson, Woolums and Karisch.)

Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.

Currently, control against bovine respiratory disease (BRD) primarily consists of mass administration of an antimicrobial upon arrival to facility, termed "metaphylaxis." The objective of this study was to determine the influence of six different antimicrobials used as metaphylaxis on the whole blood host transcriptome in healthy steers upon and following arrival to the feedlot. One hundred and five steers were stratified by arrival body weight (BW = 247 ± 28 kg) and randomly and equally allocated to one of seven treatments: negative control (NC), ceftiofur (CEFT), enrofloxacin (ENRO), florfenicol (FLOR), oxytetracycline (OXYT), tildipirosin (TILD), or tulathromycin (TULA). On day 0, whole blood samples and BW were collected prior to a one-time administration of the assigned antimicrobial. Blood samples were collected again on days 3, 7, 14, 21, and 56. A subset of cattle ( n  = 6) per treatment group were selected randomly for RNA sequencing across all time points. Isolated RNA was sequenced (NovaSeq 6,000; ~35 M paired-end reads/sample), where sequenced reads were processed with ARS-UCD1.3 reference-guided assembly (HISAT2/StringTie2). Differential expression analysis comparing treatment groups to NC was performed with glmmSeq (FDR ≤ 0.05) and edgeR (FDR ≤ 0.1). Functional enrichment was performed with KOBAS-i (FDR ≤ 0.05). When compared only to NC, unique differentially expressed genes (DEGs) found within both edgeR and glmmSeq were identified for CEFT ( n  = 526), ENRO ( n  = 340), FLOR ( n  = 56), OXYT ( n  = 111), TILD ( n  = 3,001), and TULA ( n  = 87). At day 3, CEFT, TILD, and OXYT shared multiple functional enrichment pathways related to T-cell receptor signaling and FcεRI-mediated NF-kappa beta (kB) activation. On day 7, Class I major histocompatibility complex (MHC)-mediated antigen presentation pathways were enriched in ENRO and CEFT groups, and CEFT and FLOR had DEGs that affected IL-17 signaling pathways. There were no shared pathways or Gene Ontology (GO) terms among treatments at day 14, but TULA had 19 pathways and eight GO terms enriched related to NF- κβ activation, and interleukin/interferon signaling. Pathways related to cytokine signaling were enriched by TILD on day 21. Our research demonstrates immunomodulation and potential secondary therapeutic mechanisms induced by antimicrobials commonly used for metaphylaxis, providing insight into the beneficial anti-inflammatory properties antimicrobials possess., 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 © 2023 Bigelow, Richeson, McClurg, Valeris-Chacin, Morley, Funk and Scott.)

Purpose of Review: This review describes recent prospective and retrospective work exploring the incidence and clinical consequence of sugammadex-induced bradycardia and an update of recent evidence and adverse event reports to the United States Food and Drug Administration regarding the incidence of sugammadex induced bradycardia., Recent Findings: This work suggests that the incidence of sugammadex-induced bradycardia can range from 1 to 7% depending on the definition to reverse moderate to deep neuromuscular blockade. For most instances, the bradycardia is inconsequential. For those instances that have hemodynamic instability, the adverse physiology is easily treated with appropriate vasoactive agents. One study demonstrated that the incidence of bradycardia from sugammadex is less than with neostigmine. There are several case reports that describe marked bradycardia with cardiac arrest from reversal with sugammadex. The incidence of this type of reaction to sugammadex appears to be very rare. Data from the United States Food and Drug Administration's Adverse Event Reporting System public dashboard corroborates this presence of this rare finding., Summary: Sugammadex-induced bradycardia is common and, in most instances, of minimal clinical consequence. Nevertheless, anesthesia providers should maintain proper monitoring and vigilance to treat hemodynamical instability with each administration of sugammadex., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Experimental bovine respiratory syncytial virus (BRSV) infection can enhance Histophilus somni (Hs) disease in calves; we thus hypothesized that modified-live virus (MLV) vaccines containing BRSV may alter Hs carriage. Our objective was to determine the effects of an intranasal (IN) trivalent (infectious bovine rhinotracheitis virus [IBRV], parainfluenza-3 virus [PI3V], and BRSV) respiratory vaccine with parenteral (PT) bivalent bovine viral diarrhea virus (BVDV) type I + II vaccine, or a PT pentavalent (BVDV type I and II, IBRV, BRSV, and PI3V) respiratory vaccine, on health, growth, immunity, and nasal pathogen colonization in high-risk beef calves. Calves (n = 525) were received in five truckload blocks and stratified by body weight (213 ± 18.4 kg), sex, and presence of a pre-existing ear-tag. Pens were spatially arranged in sets of three within a block and randomly assigned to treatment with an empty pen between treatment groups consisting of: 1) no MLV respiratory vaccination (CON), 2) IN trivalent MLV respiratory vaccine with PT BVDV type I + II vaccine (INT), or 3) PT pentavalent, MLV respiratory vaccine (INJ). The pen was the experimental unit, with 15 pens/treatment and 11 to 12 calves/pen in this 70-d receiving study. Health, performance, and BRSV, Hs, Mycoplasma bovis (Mb), Mannheimia haemolytica (Mh), and Pasteurella multocida (Pm) level in nasal swabs via rtPCR was determined on days 0, 7, 14, and 28, and BRSV-specific serum neutralizing antibody titer, and serum IFN-γ concentration via ELISA, were evaluated on days 0, 14, 28, 42, 56, and 70. Morbidity (P = 0.83), mortality (P = 0.68) and average daily gain (P ≥ 0.82) did not differ. Serum antibodies against BRSV increased with time (P < 0.01). There was a treatment × time interaction (P < 0.01) for Hs detection; on days 14 and 28, INT (21.1% and 57.1%) were more frequently (P < 0.01) Hs positive than CON (3.6% and 25.3%) or INJ (3.4 % and 8.4%). Also, INT had reduced (P = 0.03) cycle time of Hs positive samples on day 28. No difference (P ≥ 0.17) was found for IFN-γ concentration and Mb, Mh, or Pm detection. The proportion of Mh positive culture from lung specimens differed (P < 0.01); INT had fewer (0.0%; 0 of 9) Mh positive lungs than INJ (45.5%; 6 of 13) or CON (74.0%; 14 of 19). Vaccination of high-risk calves with MLV did not clearly impact health or growth during the receiving period. However, INT was associated with an altered upper respiratory microbial community in cattle resulting in increased detection and level of Hs., (© 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.)

Broiler chickens are an important source of Campylobacter to humans and become colonized on the farm, but the role of the litter in the ecology of Campylobacter is still not clear. The aim of this study was to examine the relationship between Campylobacter and the changes in the litter microbiome throughout the broiler production cycle. Twenty-six commercial broiler flocks representing two production types (small and big broilers) were followed from 1 to 2 weeks after placement to the end of the production cycle. Composite litter samples from the broiler chicken house were collected weekly. Litter DNA was extracted and used for Campylobacter jejuni and Campylobacter coli qPCR as well as for 16S rRNA gene V4 region sequencing. Campylobacter jejuni concentration in litter significantly differed by production type and flock age. Campylobacter jejuni concentration in litter from big broilers was 2.4 log 10 units higher, on average, than that of small broilers at 3 weeks of age. Sixteen amplicon sequence variants (ASVs) differentially abundant over time were detected in both production types. A negative correlation of Campylobacter with Bogoriella and Pseudogracilibacillus was observed in the litter microbiome network at 6 weeks of flock age. Dynamic Bayesian networks provided evidence of negative associations between Campylobacter and two bacterial genera, Ornithinibacillus and Oceanobacillus , at 2 and 4 weeks of flock age, respectively. In conclusion, dynamic associations between Campylobacter and the litter microbiome were observed during grow-out, suggesting a potential role of the litter microbiome in the ecology of Campylobacter colonization and persistence on farm. IMPORTANCE This study interrogated the longitudinal association between Campylobacter and broiler litter microbiome in commercial broiler flocks. The results of this investigation highlighted differences in Campylobacter dynamics in the litter throughout the broiler production cycle and between small and big broilers. Besides documenting the changing nature of the microbial networks in broiler litter during grow-out, we detected bacterial genera ( Oceanobacillus and Ornithinibacillus ) negatively associated with Campylobacter abundance and concentration in litter via the Bayesian network framework. These bacteria should be investigated as possible antagonists to Campylobacter colonization of the broiler environment.

Bovine Respiratory Disease (BRD) represents a significant burden to the health of feedlot cattle and the profitability of the beef industry in the US. Mannheimia haemolytica is widely regarded as the primary bacterial pathogen driving acute BRD. While Mycoplasma bovis is most commonly implicated in chronic cases of BRD, this agent's potential role in acute stages of BRD is unclear. Therefore, this study aimed to evaluate potential associations between M. bovis and M. haemolytica during acute BRD in feedlot cattle. Nasal swabs ( n = 1,044) were collected over time from feedlot cattle ( n = 270) enrolled in an experiment assessing the effect of vaccination for Bovine Respiratory Syncytial Virus (BRSV). Swabs were analyzed for detection of M. bovis, M. haemolytica, Pasteurella multocida, Histophilus somni , and BRSV via multiplex qPCR assays. Data were analyzed using inverse conditional probability weighted (ICPW) logistic regression models to investigate potential effects of M. bovis presence on arrival (d0), day seven (d7) and day 14 (d14) post-arrival on M. haemolytica prevalence on day 28 (d28) post-arrival, adjusting for the previous history of P. multocida, H. somni , BRSV, BRD morbidity, and body weight. The potential association between time-to-BRD detection and M. bovis presence on d0, d7, and d14 post-arrival, was inferred via an ICPW time-to-event model. The presence of M. bovis in nasal swabs collected on d7 post-arrival was significantly associated with an increase in the prevalence of M. haemolytica on d28 (prevalence difference: 45%; 95% Confidence Interval: 31%, 60%; P -value < 0.001). Significant time-varying coefficients for M. bovis presence were detected at d0, d7, and d14 post-arrival in the ICPW time-to-event model ( P -value < 0.001). The shortest median time-to-BRD detection was 29 days in cattle that were M. bovis positive on d0, d7, and d14 post-arrival and in those that were positive on d0 and d14 post-arrival. Under the conditions of this study, our findings suggest that M. bovis may be influencing the respiratory environment during the acute phase of BRD, increasing the abundance of M. haemolytica , which could have important impacts on the occurrence of BRD., 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 © 2022 Valeris-Chacin, Powledge, McAtee, Morley and Richeson.)

Infection with Campylobacter species is one of the leading causes of bacterial diarrhea in humans in the US. Chickens, which become colonized on the farm, are important reservoirs of this bacterium. Campylobacter can establish itself in the broiler house via a variety of sources, can survive in the litter of the house, and possibly persist over successive flock cycles. However, the role of the broiler litter microbiome on Campylobacter persistence is not clear. A matched case-control study was conducted to determine whether the broiler litter microbiome composition was associated with Campylobacter isolation within the broiler house. Flocks were classified as cases when either Campylobacter jejuni or Campylobacter coli was isolated in boot sock samples, or as controls otherwise. Case and control flocks were matched at the broiler house level. Composite broiler litter samples were collected and used for DNA extraction and 16S rRNA gene V4 region sequencing. Reads were processed using the DADA2 pipeline to obtain a table of amplicon sequence variants. Alpha diversity and differential bacterial relative abundance were used as predictors of Campylobacter isolation status in conditional logistic regression models adjusting for flock age and sampling season. Beta diversity distances were used as regressors in stratified PERMANOVA with Campylobacter isolation status as predictor, and broiler house as stratum. When Campylobacter was isolated in boot socks, broiler litter microbiome richness and evenness were lower and higher, respectively, without reaching statistical significance. Campylobacter isolation status significantly explained a small proportion of the beta diversity (genus-level Aitchison dissimilarity distance). Clostridium and Anaerostipes were positively associated with Campylobacter isolation status, whereas Bifidobacterium, Anaerosporobacter , and Stenotrophomonas were negatively associated. Our results suggest the presence of bacterial interactions between Campylobacter and the broiler litter microbiome. The negative association of Campylobacter with Bifidobacterium, Anaerosporobacter , and Stenotrophomonas in litter could be potentially exploited as a pre-harvest control strategy., 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 Valeris-Chacin, Pieters, Hwang, Johnson and Singer.)

The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae ) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis , Glaesserella parasuis , and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.

The aim of this study was to assess the genetic variability of Mycoplasma hyopneumoniae within various swine production flows. Four M. hyopneumoniae positive production flows, composed of 4 production stages, were selected for this study. Laryngeal and/or bronchial swabs were collected from each production stage within a flow, for a period of 4 months up to 3 years. A multiple-locus variable-number tandem repeat analysis was performed to assess the genetic variation of M. hyopneumoniae within and across production flows through the identification of variable-number tandem repeat (VNTR) types. A maximum of 6 M. hyopneumoniae VNTR types were identified in a single flow, in which VNTR types appeared to be flow specific. An identical VNTR type was detected across several production stages for up to 3 years. In this study, minimal M. hyopneumoniae genetic variation was evidenced within and across production flows., Competing Interests: Conflict of Interest The author(s) declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. Drs. Fano and Sponheim are employed by Boehringer Ingelheim Animal Health USA Inc. However, no commercial products were evaluated in this investigation. Dr. Singer has received funding from Boehringer Ingelheim Animal Health USA Inc., (Copyright and/or publishing rights held by the Canadian Veterinary Medical Association.)

Mycoplasma hyopneumoniae (M. hyopneumoniae) continues to be a prevalent and economically important swine respiratory pathogen. For M. hyopneumoniae surveillance, blood samples and/or oral fluids are commonly collected from incoming replacement gilts prior to entering sow farms. However, limitations to this approach exist, particularly due to low sensitivity during acute stages of natural infection, leading to diagnostic uncertainty. Therefore, the objective of this study was to evaluate the natural transmission and detection of M. hyopneumoniae based on the introduction of one infected gilt to a naïve population. Twenty-nine naïve gilts were housed with one M. hyopneumoniae naturally exposed gilt for 8 weeks. Deep tracheal catheters, laryngeal swabs, and blood samples were individually collected from each gilt at 0, 1, 2, 4, 6, and 8 weeks post-contact (wpc), along with one pen-based oral fluid sample. Blood samples were assayed by ELISA, while all other samples were tested by real-time PCR. The transmission rate of M. hyopneumoniae (ꞵ) was estimated using a Bayesian mixed-effects generalized linear model. At 8 wpc, 27 % (8/29) of the naïve gilts had become infected (ꞵ = 0.73 new infected gilts/gilt-week). Seroconversion was detected in 3% of contact gilts at 8 wpc. Oral fluids were negative for M. hyopneumoniae at all samplings. In this study, the natural transmission of M. hyopneumoniae was slow and detection varied based on sample type and timing. Thus, M. hyopneumoniae surveillance protocols should include lower respiratory tract samples that are tested by real-time PCR to avoid the introduction of potentially infected gilts into naïve sow farms., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Mycoplasma hyopneumoniae is an important respiratory pathogen causing significant losses in the swine industry. Eradication of this bacterium from herds results in increased pig performance, productivity, and animal welfare. The objective of this study was to compare the time-to-detection of M. hyopneumoniae in breed-to-wean farms after the application of one of two methods for M. hyopneumoniae eradication. The two methods compared in this study were: 1) Herd closure and medication, and 2) Whole herd medication without extended closure. Fifty-six breed-to-wean farms located in the US Midwest constituted the cohort for this investigation. Herd closure and medication was applied in 45 farms, while whole herd medication was applied in 11 farms. Two mutually exclusive events were recorded for each farm, either detection of M. hyopneumoniae, which was considered the event of interest, or end of follow-up, which was the right-censored event. Farms were monitored until recording the event of interest, or until the end of follow-up, whichever occurred first. Detection of M. hyopneumoniae was assessed by identification of antibodies against the bacterium in sentinel pigs using a commercially available ELISA assay within 6 months post-eradication completion. Moreover, clinical presentation of disease was recorded if observed post-eradication completion. The censored event occurred at the end of the study in November 2016 (administrative censoring). Time-to-detection of M. hyopneumoniae was analyzed with a Cox proportional hazards model. The proportional hazards assumption was assessed using graphical methods. A sensitivity analysis to evaluate the assumption of outcome-independent censoring was also performed. The cumulative incidence of M. hyopneumoniae detection at the end of follow-up was 18.6 % (95% CI: 6.5%, 46.8%) for herd closure and medication, and 36.4% (95% CI: 15.5%, 70.3%) for whole herd medication. An interaction term between the type of eradication method and follow-up time was included in the model to account for the non-proportional hazards. An overall effect of eradication method was present (P = 0.0442). The hazard ratio associated to the time-invariant effect of eradication method was 29.2 (95% CI: 0.95, 894; P = 0.053). The hazard ratio associated with the interaction term was 0.88 (95% CI: 0.65, 1.2; P = 0.405). Under these conditions, eradication using herd closure and medication reduced the likelihood of detecting cases of M. hyopneumoniae in breed-to-wean farms compared to whole herd medication. Detection of M. hyopneumoniae was concentrated during the first 64 months of follow-up in herd closure and medication, and in the first 8 months in whole herd medication., (Copyright © 2019 Elsevier B.V. All rights reserved.)