Paul S Morley

Texas A&M University | TAMU · Large Animal Clinical Science

Introduction The gastrointestinal microbiota profoundly influences the health and productivity of animals. This study aimed to characterize microbial community structures of the mouth, gastrointestinal tract (GIT), and feces of cattle. Methods Samples were collected from 18 Akaushi crossbred steers at harvest from multiple locations, including the...

This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and met...

Bovine respiratory disease (BRD) is a multifactorial disease complex resulting from interactions among host immunologi­cal response, environmental conditions and polymicrobial components. Metaphylaxis, or the mass administration of an antimicrobial upon arrival to a stocker or feedlot facility, is the primary method of control for BRD. Our objectiv...

Bovine respiratory disease (BRD) is the main cause of morbidity and mortality in beef cattle. Four bacterial species (Mannheimia haemolytica, Histophilus somni, Pasteurella multocida and Myco­plasma bovis) are considered key pathogens in the development of BRD. To minimize the risk of developing BRD, beef cattle are often administered antibiotics a...

Previous research on stabilization methods for microbiome investigations has largely focused on human fecal samples. There are a few studies using feces from other species, but no published studies investigating preservation of samples collected from cattle. Given that microbial taxa are differentially impacted during storage it is warranted to stu...

Bovine respiratory disease (BRD) is a leading cause of disease in feedlot and stocker calves with Mannheimia haemolytica (MH) as one of the most common etiologies. One of the most effective means of controlling BRD is through metaphylaxis, which involves administering antimicrobials to all animals at high risk of developing BRD. However, increasing...

Background: Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs...

Liver abscesses (LAs) are a common and important problem in cattle because of their association with decreased growth and production, low carcass quality, and the significant economic losses associated with liver condemnation. Fusobacterium necrophorum has traditionally been considered the primary etiologic agent of LA formation in cattle, but rece...

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 fo...

Bovine respiratory disease (BRD) is commonly controlled by metaphylaxis, but increasing prevalence of antimicrobial re­sistant (AMR) Mannheimia haemolytica (MH) may decrease ef­ficacy. The objective of this study was to determine the effect of macrolide metaphylaxis on 1) morbidity and mortality in stocker cattle over a 21-day period and 2) isolati...

Mycoplasma bovis is a bacterium member of the family Myco­plasmataceae, characterized by a small genome, lack of cell wall, and high nutritional requirements for in vitro growth (Li et al., 2011; Parker et al., 2018; Dudek et al., 2020). Traditionally, M. bovis has been linked to chronic BRD cases and treatment failures (Booker et al., 2008; Hermey...

Introduction The objectives of this study were to evaluate the impacts of two modified-live virus (MLV) vaccination protocols and respiratory disease (BRD) occurrence on the microbial community composition of the nasopharynx in feedlot cattle. Methods The treatment groups included in this randomized controlled trial included: 1) no viral respirato...

Introduction Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Esche...

Objective Changes in the gut microbiome during early-stage development can be associated with lasting effects on the structure and function of microbial communities, which in turn can affect the health and performance of animals. The purpose of this study was to characterize changes in the fecal microbiome and resistome of calves during early life...

Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-thro...

Emerging evidence regarding the microbiome of liver abscesses and the GIT cattle suggests that a reexamination of the etiopathogenesis of LAs is warranted. Microbiome studies using 16S rRNA gene sequencing have demonstrated that LAs are highly polymicrobial, and hundreds of bacterial taxa are typically found in these lesions at slaughter. Fusobacte...

Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for...

Modified-live virus (MLV) respiratory vaccines are commonly administered to beef cattle upon arrival in feedlots to prevent bovine respiratory disease (BRD) but their impact on respiratory microbial communities is unknown. The objective of this study was to evaluate the impact of intranasal and parenteral MLV vaccination and health status on the re...

Background Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemol...

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...

Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with the complex and rich community of microorganism in the foregut to allow digestion of complex carbohydrates. This study used...

Liver abscesses (LAs) are extremely prevalent in cattle and result in significant economic losses due to liver condemnation, decreased growth and production, and lower carcass quality. LAs are commonly attributed to the transition to diets high in rapidly fermentable starch which results in rumen epithelial inflammation that allows pathogenic bacte...

Background: The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire population of bacteria (the microbiome) and entirety of all resistance genes (the resistome) that are found in this population. T...

Ruminants are a critical human food source and are a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with complex and rich microbial communities in the foregut to allow digestion of complex carbohydrates. This study used 16S rRNA gene sequencing to...

1.1 Background:Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. The current standard for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia h...

Professionals in animal agriculture promote prudent use of antimicrobials to address public and animal health concerns, such as reduction of antimicrobial residues and antimicrobial resistance (AMR) in products. Few studies evaluate the effect of selective dry-cow therapy on preservation of the milk microbiome or the profile of AMR genes (the resis...

Background Antimicrobial drugs (AMDs) are used in beef production to treat clinical disease and to prevent or control infections in groups of cattle. Use of AMDs in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR ha...

Bulk tank milk (BTM) is regularly used for surveillance on dairy farms for disease conditions such as mastitis and Johne's disease. In this study, we used 16S rRNA sequencing and bait-capture enrichment to characterize the microbiota and resistome of BTM, and investigate potential differences between the cream or pellet fractions. A total of 12 BTM...

Introduction Multidrug resistance (MDR) is a serious issue prevalent in various agriculture-related foodborne pathogens including Salmonella enterica (S. enterica) Typhimurium. Class I integrons have been detected in Salmonella spp. strains isolated from food producing animals and humans and likely play a critical role in transmitting antimicrobial...

Antibiotics used during food animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail g...

Liver abscess syndrome (LAS) is a well-recognized and important problem for beef production in all types of cattle. LAS has been shown to be associated with decreased growth efficiency and lower carcass quality, in addition to losses associated with carcass trimming and condemnation of materials at slaughter. The etiopathogenesis of LAS has traditi...

Antimicrobial drugs are important tools for maintaining human and animal health. Globally, antimicrobial use (AMU) in food-producing animals is under increasing scrutiny due to its potential to promote antimicrobial resistance (AMR). Historically, comprehensive Canadian data related to the types of antimicrobial drugs used, extent of use, common in...

Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bact...

Restricting antibiotic use in food production animals is a target for reducing antimicrobial drug–resistant infections in humans. To estimate the probability of antibiotic-resistant nontyphoidal salmonellosis per meal made with beef during 2002–2010, we used US surveillance data. Applying data for nontyphoidal Salmonella in raised-without-antibioti...

Culled beef cows (cows that have reached the end of their productive life span in cow-calf operations) and culled dairy cows represent approximately 18% of the cattle harvested in the United States annually, but data on antimicrobial resistance (AMR) in these cull cattle are extremely limited. To address this data gap, colon contents were obtained...

Background Equid herpesvirus type 1 (EHV‐1) is ubiquitous in equine populations causing respiratory disease, and complications including late‐term abortion and neurological disease. Eradication of EHV‐1 from housing environments that typically contain unsealed wood and porous bedding materials can be challenging. However, consideration should be gi...

Objective: To assess production animal medicine veterinarians' prescription practices and identify factors influencing their use of antimicrobial drugs (AMDs) and their perceptions of and attitudes toward antimicrobial resistance (AMR). Sample: 157 production animal veterinarians in the United States. Procedures: An online cross-sectional survey...

Abstract Background: Plague caused by Yersinia pestis is a highly infectious and potentially fatal zoonotic disease that can be spread by wild and domestic animals. In endemic areas of the northern hemisphere plague typically cycles from March to October, when flea vectors are active. Clinical forms of disease include bubonic, septicemic, and pneum...

Background Differentiation of lymphocytic‐plasmacytic enteropathy (LPE) from small cell lymphoma (SCL) in cats can be challenging. Hypothesis/Objective Histology‐guided mass spectrometry (HGMS) is a suitable method for the differentiation of LPE from SCL in cats. Animals Forty‐one cats with LPE and 52 cats with SCL. Methods This is a retrospecti...

The true etiology of liver abscesses is not well known. Therefore, the objective of this study was to characterize the microbial communities in the rumen lining, digesta, and rumen fluid from beef cattle consuming a high energy diet, using 16S rRNA gene amplicon sequencing. Twelve crossbred feedlot steers (450 ±10 kg; ~ 3.0 years of age) fitted wit...

Objectives The occurrences of human bacterial infections complicated by antimicrobial resistance (AMR) have increased in recent decades. Concerns have been raised that food-animal production practices that incorporate antimicrobials contribute significantly to human AMR exposures since food-animal production accounts for approximately 81% of U.S. a...

In the United States, ~1.4 million sporadic human Salmonella enterica infections occur annually, with an estimated 6% attributable to reptile exposure. Detection of Salmonella in reptiles can be challenging given the limitations among detection methods. We evaluated sampling and detection methods for S. enterica in a cross-sectional study of reptil...

Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequenc-ing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented...

This study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100% concordant and indicat...

The accurate quantification of antimicrobial use (AMU) in production animals is critical for monitoring trends in exposure to antimicrobial drugs (AMD) over time and examining potential associations with antimicrobial resistance in bacteria. In this study, a census sample of cattle was used to quantify individually-dosed and in-feed AMU as both num...

The potential for antimicrobial use (AMU) to lead to the development of antimicrobial resistant bacteria is an increasingly important priority in human and veterinary medicine. Accurate AMU quantification is essential to assessing the risk of antimicrobial resistance due to AMU. The quantification of AMU in production animals can be difficult, and...

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition be...

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces,...

Background: Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage. Results:...

Background Transmission of Salmonella in veterinary hospitals is typically associated with environmental contamination. Links between isolates recovered from hospitalized large animals and environment suggest animals as the likely source. Therefore, understanding factors influencing shedding is key in control. Shedding in hospitalized animals has b...

The characterization of antimicrobial resistance genes from high-throughput sequencing data has become foundational in public health research and regulation. This requires mapping sequence reads to databases of known antimicrobial resistance genes to determine the genes present in the sample. Mapping sequence reads to known genes is traditionally a...

This chapter focuses on the understanding and application of metagenomics as it applies to meat and poultry research. Key concepts for understanding metagenomics include how to conduct a metagenomic study from experimental design to analysis, the difference between shotgun metagenomics and 16S rRNA amplicon studies, and data visualization. Special...

In December 2017, a dog that had pneumonic plague was brought to a veterinary teaching hospital in northern Colorado, USA. Several factors, including signalment, season, imaging, and laboratory findings, contributed to delayed diagnosis and resulted in potential exposure of >116 persons and 46 concurrently hospitalized animals to Yersinia pestis.

Antimicrobial resistance (AMR) is a significant threat to both human and animal health. The spread of AMR bacteria and genes across systems can occur through a myriad of pathways, both related and unrelated to agriculture, including via wastewater, soils, manure applications, direct exchange between humans and animals, and food exposure. Tracing or...

Globally, increasing acquired antimicrobial resistance among pathogenic bacteria presents an urgent challenge to human and animal health. As a result, significant efforts, such as the One Health Initiative, are underway to curtail and optimize the use of critically important antimicrobials for human medicine in all applications, including food anim...

n December 2017, a dog that had pneumonic plague was brought to a veterinary teaching hospital in northern Colorado, USA. Several factors, including signalment, season, imaging, and laboratory findings, contributed to delayed diagnosis and resulted in potential exposure of >116 persons and 46 concurrently hospitalized animals to Yersinia pestis.

Liver abscesses in feedlot cattle form secondary to high concentrate feeds and rumen acidosis. Antimicrobial drugs are commonly included in cattle feed for prevention of liver abscesses, but concerns regarding antimicrobial resistance have increased the need for alternative treatments. A block randomized clinical trial was conducted to evaluate the...

Background T‐zone lymphoma (TZL), an indolent disease in older dogs, comprises approximately 12% of lymphomas in dogs. TZL cells exhibit an activated phenotype, indicating the disease may be antigen‐driven. Prior research found that asymptomatic aged Golden Retrievers (GLDRs) commonly have populations of T‐zone‐like cells (phenotypically identical...

Suppl. Table 1 Antibody panels used for immunophenotyping. Suppl. Table 2. Modeling results for case versus control sensitivity analyses. Final model indicates the model reported as our main results (n = 140 cases, n = 147 controls). Age sensitivity analysis removed 20 cases that were < 9 years of age (n = 120 cases, n = 147 controls). Cancer sensi...

Suppl. Figure 3 Flow chart of variable selection for multivariable modeling. All variables selected to be included in best subsets were evaluated for collinearity before proceeding with best subsets regression.

Abstract ObjectivesThe occurrences of human bacterial infections complicated by antimicrobial resistance (AMR) have increased in recent decades. Concerns have been raised that food-animal production practices that incorporate antimicrobials contribute significantly to human AMR exposures since food-animal production accounts for approximately 81%...

Infections caused by Coxiella burnetii, commonly referred to as coxiellosis when occurring in animals and Query fever when occurring in humans, are an important cause of abortions, decreased reproductive efficiency, and subclinical infections in ruminants. The organism also represents an important zoonotic concern associated with its ability to aer...