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 haemolyticais widely regarded as the primary bacterial pathogen driving acute BRD. WhileMycoplasma bovisis 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 betweenM. bovisandM. haemolyticaduring 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 ofM. bovis, M. haemolytica, Pasteurella multocida, Histophilus somni, and BRSVviamultiplex qPCR assays. Data were analyzed using inverse conditional probability weighted (ICPW) logistic regression models to investigate potential effects ofM. bovispresence on arrival (d0), day seven (d7) and day 14 (d14) post-arrival onM. haemolyticaprevalence on day 28 (d28) post-arrival, adjusting for the previous history ofP. multocida, H. somni, BRSV, BRD morbidity, and body weight. The potential association between time-to-BRD detection andM. bovispresence on d0, d7, and d14 post-arrival, was inferredviaan ICPW time-to-event model. The presence ofM. bovisin nasal swabs collected on d7 post-arrival was significantly associated with an increase in the prevalence ofM. haemolyticaon d28 (prevalence difference: 45%; 95% Confidence Interval: 31%, 60%;P-value < 0.001). Significant time-varying coefficients forM. bovispresence 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 wereM. bovispositive 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 thatM. bovismay be influencing the respiratory environment during the acute phase of BRD, increasing the abundance ofM. haemolytica, which could have important impacts on the occurrence of BRD.

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.

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.

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.

Bovine respiratory disease (BRD) is a major economic and animal welfare issue in the beef industry. Mycoplasma bovis is one of the main causal organisms, particularly in chronic cases. Due to the difficulty of isolating M. bovis from clinical isolates, there is a lack of information on the genetic diversity of this pathogen in the Texas panhandle region of the United States. Therefore, our objective was to provide genome-level characterization of M. bovis isolated from the lung lesions of beef and dairy cattle in the Texas panhandle. Fifty-four isolates displaying mycoplasma-like growth were recovered from bovine lung lesions by the Texas Veterinary Medical Diagnostic Laboratory in 2021 and 2022. Of these isolates, 32 were determined to be M. bovis via species-specific qPCR using the uvrC gene. Long-read whole-genome sequencing was used to identify key virulence factors, antimicrobial resistance genes, and to assess the genetic diversity of these isolates. Fisher’s exact tests were used to identify associations between isolate characteristics and host metadata, including the state of origin, type of operation, animal age, and animal sex. Our results indicate that there is considerable genetic diversity among the M. bovis isolates, despite their shared geography in the Texas panhandle, though significant clustering based on host metadata was observed. Analysis of the pangenome showed that the M. bovis isolates in this study also harbor a diverse array of virulence genes, but no antimicrobial resistance genes were identified in this study.

Cattle marketed through auction market systems and/or that remain unvaccinated are considered higher risk for BRD, but impacts on host response remain unclear. We sought to identify specific genomic patterns of beef calves vaccinated against BRD viruses or not and commercially marketed or directly transported in a split-plot randomized controlled trial. Forty-one calves who remained clinically healthy from birth through backgrounding were selected (randomly stratified) from a larger cohort of cattle (n = 81). Treatment groups included VAX/DIRECT (n = 12), VAX/AUCTION (n = 11), NOVAX/DIRECT (n = 7), and NOVAX/AUCTION (n = 11). Blood RNA was acquired across five time points, sequenced, and bioinformatically processed via HISAT2 and StringTie2. Significant transcriptional changes (FDR < 0.05) were observed at backgrounding entry (T5) in NOVAX/AUCTION cattle exhibiting 2809 uniquely differentially expressed genes and relative activation of immune, inflammatory, and metabolic pathways with upregulation of interferon-stimulated genes (e.g., IFIT3, MX2, and TRIM25) and downregulation of specialized proresolving mediator (SPM) enzymes (ALOX5 and ALOX15). VAX/AUCTION cattle exhibited modulated immune activation and preserved expression of SPM-associated genes when compared to NOVAX/AUCTION cattle. Both marketing route and vaccination shape the molecular immune landscape during high-stress transitions, with preweaning vaccination potentially modulating this response. This study provides mechanistic insight into how management practices influence immunological resilience and highlights the value of integrating transcriptomics into BRD risk mitigation.