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 been investigated, but many studies focused on subsets of animals limiting generalizability.
Objective
(1) Investigate factors associated with fecal shedding of Salmonella among hospitalized large animals at a veterinary hospital. (2) Compare results obtained using 2 comparison groups for risk factor analysis—large animals with high confidence in negative shedding status and those with potential for misclassification of shedding status.
Animals
Large animals admitted from March 2002 through December 2012.
Methods
A case‐control study was conducted among all hospitalized large animals that were routinely cultured as part of infection control efforts. Animal and hospital factors were evaluated. Data on factors of interest were collected retrospectively from electronic medical records. Multivariable conditional logistic regression was used to evaluate associations between animal factors and fecal shedding of Salmonella enterica.
Results
During the study period, 5.9% (648/11 061) of hospitalized large animals were culture positive for Salmonella, with the majority being cattle (72%; 467/648) and horses (22%; 143/648). Although the odds of shedding varied by comparison group, overall, 69.4% of animal shedding could be attributed to systemic illness (population attributable fraction) in this study.
Conclusions and Clinical Importance
Findings of this study inform our understanding of factors affecting Salmonella shedding in hospitalized large animals, thus improving our ability for implementation of evidence‐based control measures.
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 study impacts of preservation methods on microbial communities found in samples outside of human fecal samples. Here we tested methods of preserving bovine fecal respiratory specimens for up to 2 weeks at four temperatures (room temperature, 4°C, -20°C, and -80°C) by comparing microbial diversity and community composition to samples extracted immediately after collection. Importantly, fecal specimens preserved and analyzed were technical replicates, providing a look at the effects of preservation method in the absence of biological variation. We found that preservation with the OMNIgene®•GUT kit resulted in community structure most like that of fresh samples extracted immediately, even when stored at room temperature (~20°C). Samples that were flash-frozen without added preservation solution were the next most representative of original communities, while samples preserved with ethanol were the least representative. These results contradict previous reports that ethanol is effective in preserving fecal communities and suggest for studies investigating cattle either flash-freezing of samples without preservative or preservation with OMNIgene®•GUT will yield more representative microbial communities.
Abbreviations ACVIM American College of Veterinary Internal Medicine AES ACVIM-Endorsed Statement BoR Board of Regents COI conflict of interest ERC Education and Research Committee GRADE Grading of ...Recommendations, Assessment, Development, and Evaluation PRISMA Preferred Reporting Items for Systematic Reviews and Meta-Analyses The American College of Veterinary Internal Medicine (ACVIM) has commissioned groups of experts to produce “Consensus Statements” since 2000 to provide veterinarians with information about topics important to ACVIM Diplomates and the veterinary profession. The medical and veterinary communities increasingly rely on evidence-based statements on a particular topic for guidance and counsel on decisions relating to management of diseases. 1,2 There are several conventional formats for these statements, including consensus statements, practice guidelines, systematic reviews and position statements. 3-8 Recently, scoping reviews have become more common and are gaining some traction in the veterinary literature. 9 The methodology underlying each of these types of statements differs, but what all have in common is a well-described and accepted methodology for objectively considering and reporting the amount and quality of evidence. ...the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach is now widely used for developing practice (and other) guidelines, Cochrane prescribes a particular methodology for undertaking evidence-based reviews, Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) defines how systematic reviews should be carried out, and the Delphi method is widely accepted for development of consensus statements. 4,5,7,8,10-15 Scoping reviews are not designed or intended to produce a critically appraised and synthesized result/answer to a particular question and are therefore not included as an ACVIM-Endorsed Statement (AES). Consensus is tested and demonstrated using prescribed methodology to identify areas of agreement and disagreement within the group of experts. 14,18 Consensus statements are applicable to situations where evidence is limited or lacking, but where there is the opportunity to reduce uncertainty and improve quality of care. 6,14 Consensus statements take advantage of the collective wisdom of a group of experienced clinicians and researchers, substituting expert opinion for objective fact.
Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food ...and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.
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 origins and drivers of AMR bacteria and genes is challenging due to the array of contexts and the complexity of interactions overlapping health practice, microbiology, genetics, applied science and engineering, as well as social and human factors. Critically assessing the diverse and sometimes contradictory AMR literature is a valuable step in identifying tractable mitigation options to stem AMR spread. In this article we review research on the nonfoodborne spread of AMR, with a focus on domesticated animals and the environment and possible exposures to humans. Attention is especially placed on delineating possible sources and causes of AMR bacterial phenotypes, including underpinning the genetics important to human and animal health.
Antimicrobial resistance (AMR) is a significant threat to both human and animal health. Our article reviews research on the nonfoodborne spread of AMR with a focus on domesticated animals and the environment, and possible exposure risks to humans. Attention is especially placed on delineating possible sources and causes of AMR bacterial phenotypes, including underpinning genetics important to human and animal health.
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.
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 animal production. This review discusses the rationale behind multiple and competing “critically important antimicrobial” lists and their contexts as created by international, regional, and national organizations; identifies discrepancies among these lists; and describes issues surrounding risk management recommendations that have been made by regulatory organizations on the use of antibiotics in food animal production. A more harmonized approach to defining criticality in its various contexts (e.g., for human versus animal health, enteric diseases versus other systemic infections, and direct versus indirect selection of resistance) is needed in order to identify shared contextual features, aid in their translation into risk management, and identify the best ways to maintain the health of food animals, all while keeping in mind the wider risks of antimicrobial resistance, environmental impacts, and animal welfare considerations.
Most of the antibiotics sold for animal use in the US are either not considered medically important by the FDA (e.g., ionophores) or else are not included in the list of critically important antimicrobials for human medicine by the WHO (e.g., tetracyclines). Most of the highest priority critically important antimicrobials (HPCIA) have relatively low sales volumes (e.g., fluoroquinolones and cephalosporins), the exception to this being the macrolide class.
Highlights • Roughly 3% of those with alcohol dependence in Australia receive pharmacotherapy. • Of those, only 15–25% receive the recommended 3 months of treatment. • Treatment adherence is ...significantly higher for naltrexone relative to acamprosate. • Treatment adherence increases with age.
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