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 sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.

Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.

The epidemic of antimicrobial resistant infections continues to challenge, compromising animal care, complicating food animal production and posing zoonotic disease risks. While the overall role of therapeutic antimicrobial use in animals in the development AMR in animal and human pathogens is poorly defined, veterinarians must consider the impacts of antimicrobial use in animal and take steps to optimize antimicrobial use, so as to maximize the health benefits to animals while minimizing the likelihood of antimicrobial resistance and other adverse effects. This consensus statement aims to provide guidance on the therapeutic use of antimicrobials in animals, balancing the need for effective therapy with minimizing development of antimicrobial resistance in bacteria from animals and humans.

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

The purpose of this study was to use meta-analytic methods to estimate the effect of a commercially available yeast culture product on milk production and other production measures in lactating dairy cows using a meta-analysis of randomized controlled trials. Sixty-one research publications (published journal articles, published abstracts, and technical reports) were identified through a review of literature provided by the manufacturer and a search of published literature using 6 search engines. Thirty-six separate studies with 69 comparisons met the criteria for inclusion in the meta-analysis. The fixed-effect meta-analysis showed substantial heterogeneity for milk yield, energy-corrected milk, 3.5% fat-corrected milk, milk fat yield, and milk protein yield. Sub-group analysis of the data showed much less heterogeneity in peer-reviewed studies versus non-peer-reviewed abstracts and technical reports, and tended to show higher, but not significantly different, treatment effects. A random-effects meta-analysis showed estimated raw mean differences between treated and untreated cattle reported in peer-reviewed publications of 1.18 kg/d [95% confidence interval (CI): 0.55 to 1.81], 1.61 kg/d (95% CI: 0.92 to 2.29), and 1.65 kg/d (95% CI: 0.97 to 2.34) for milk yield, 3.5% fat-corrected milk, and energy-corrected milk, respectively. Milk fat yield and milk protein yield for peer-reviewed studies showed an increase in the raw mean difference of 0.06 kg/d (95% CI: 0.01 to 0.10) and 0.03 kg/d (95% CI: 0.00 to 0.05), respectively. Estimated raw mean dry matter intake of the peer-reviewed studies during early lactation (<70 d in milk) and not-early lactation were 0.62 kg/d (95% CI: 0.21 to 1.02) and a decrease of 0.78 kg/d (95% CI: -1.36 to -0.21), respectively. These findings provide strong evidence that this commercially available yeast culture product provides significant improvement in several important milk production outcomes as evaluated in production settings typical for commercial dairies in North America. Utilizing meta-analytic methods to study the complete breadth of information relating to a specific treatment by studying multiple overcomes of all eligible studies can reduce the uncertainty often seen in small individual studies designed without sufficient power to detect differences in treatments.

Objective—To evaluate trends in feedlot cattle mortality ratios over time, by primary body system affected, and by type of animal. Design—Retrospective cohort study. Animals—Approximately 21.8 million cattle entering 121 feedlots in the United States during 1994 through 1999. Procedures—Yearly and monthly mortality ratios were calculated. Numbers of deaths were modeled by use of Poisson regression methods for repeated measures. Relative risks of death over time and by animal type were estimated. Results—Averaged over time, the mortality ratio was 12.6 deaths/1,000 cattle entering the feedlots. The mortality ratio increased from 10.3 deaths/1,000 cattle in 1994 to 14.2 deaths/1,000 cattle in 1999, but this difference was not statistically significant (P = 0.09). Cattle entering the feedlots during 1999 had a significantly increased risk (relative risk, 1.46) of dying of respiratory tract disorders, compared with cattle that entered during 1994, and respiratory tract disorders accounted for 57.1% of all deaths. Dairy cattle had a significantly increased risk of death of any cause, compared with beef steers. Beef heifers had a significantly increased risk of dying of respiratory tract disorders, compared with beef steers. Conclusions and Clinical Relevance—Results suggested that although overall yearly mortality ratio did not significantly increase during the study, the risk of death attributable to respiratory tract disorders was increased during most years, compared with risk of death during 1994. The increased rates of fatal respiratory tract disorders may also reflect increased rates of non-fatal respiratory tract disorders, which would be expected to have adverse production effects in surviving animals. (J Am Vet Med Assoc 2001;219:1122–1127)