Antimicrobial usage and resistance in beef production

Improving the detection of integrative conjugative elements in bovine nasopharyngeal swabs using multiplex recombinase polymerase amplification

Bovine respiratory disease (BRD) is an important health and economic burden to the cattle industry worldwide. Three bacterial pathogens frequently associated with BRD (Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) can possess integrative and conjugative elements (ICEs), a diverse group of mobile genetic elements that acquire antimicrobial resistance (AMR) genes (ARGs) and decrease the therapeutic efficacy of antimicrobial drugs. We developed a duplex recombinase polymerase amplification (RPA) assay to detect up to two variants of ICEs in these Pasteurellaceae. Whole genome sequence analysis of M. haemolytica, P. multocida, and H. somni isolates harbouring ICEs revealed the presence of tnpA or ebrB next to tet(H), a conserved ARG that is frequently detected in ICEs within BRD-associated bacteria. This real-time multiplex RPA assay targeted both ICE variants simultaneously, denoted as tetH_tnpA and tetH_ebrB, with a limit of detection (LOD) of 29 (95% CI [23, 46]) and 38 genome copies (95% CI [30, 59]), respectively. DNA was extracted from 100 deep nasopharyngeal swabs collected from feedlot cattle on arrival. Samples were tested for ICEs using a real-time multiplex RPA assay, and for M. haemolytica, P. multocida, H. somni, and Mycoplasma bovis using both culture methods and RPA. The assay provided sensitive and accurate identification of ICEs in extracted DNA, providing a useful molecular tool for timely detection of potential risk factors associated with the development of antimicrobial-resistant BRD in feedlot cattle.

Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features

The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.

Confronting the complexities of antimicrobial management for Staphyloccous aureus causing bovine mastitis: an innovative paradigm

Globally, Mastitis is a disease commonly affecting dairy cattle which leads to the use of antimicrobials. The majority of mastitis etiological agents are bacterial pathogens and Staphylococcus aureus is the predominant causative agent. Antimicrobial treatment is administered mainly via intramammary and intramuscular routes. Due to increasing antimicrobial resistance (AMR) often associated with antimicrobial misuse, the treatment of mastitis is becoming challenging with less alternative treatment options. Besides, biofilms formation and ability of mastitis-causing bacteria to enter and adhere within the cells of the mammary epithelium complicate the treatment of bovine mastitis. In this review article, we address the challenges in treating mastitis through conventional antibiotic treatment because of the rising AMR, biofilms formation, and the intracellular survival of bacteria. This review article describes different alternative treatments including phytochemical compounds, antimicrobial peptides (AMPs), phage therapy, and Graphene Nanomaterial-Based Therapy that can potentially be further developed to complement existing antimicrobial therapy and overcome the growing threat of AMR in etiologies of mastitis.

Diversity of antimicrobial-resistant bacteria isolated from Australian chicken and pork meat

Antimicrobial-resistant bacteria are frequently isolated from retail meat and may infect humans. To determine the diversity of antimicrobial-resistant bacteria in Australian retail meat, bacteria were cultured on selective media from raw chicken (n = 244) and pork (n = 160) meat samples obtained from all four major supermarket chains in the ACT/NSW, Australia, between March and June 2021. Antimicrobial susceptibility testing (AST) was performed for 13 critically and 4 highly important antibiotics as categorised by the World Health Organization (WHO) for a wide range of species detected in the meat samples. A total of 288 isolates underwent whole-genome sequencing (WGS) to identify the presence of antimicrobial resistance (AMR) genes, virulence genes, and plasmids. AST testing revealed that 35/288 (12%) of the isolates were found to be multidrug-resistant (MDR). Using WGS data, 232/288 (81%) of the isolates were found to harbour resistance genes for critically or highly important antibiotics. This study reveals a greater diversity of AMR genes in bacteria isolated from retail meat in Australia than previous studies have shown, emphasising the importance of monitoring AMR in not only foodborne pathogenic bacteria, but other species that are capable of transferring AMR genes to pathogenic bacteria.

Strategies for Bovine Respiratory Disease (BRD) Diagnosis and Prognosis: A Comprehensive Overview

Despite significant advances in vaccination strategies and antibiotic therapy, bovine respiratory disease (BRD) continues to be the leading disease affecting the global cattle industry. The etiology of BRD is complex, often involving multiple microbial agents, which lead to intricate interactions between the host immune system and pathogens during various beef production stages. These interactions present environmental, social, and geographical challenges. Accurate diagnosis is essential for effective disease management. Nevertheless, correct identification of BRD cases remains a daunting challenge for animal health technicians in feedlots. In response to current regulations, there is a growing interest in refining clinical diagnoses of BRD to curb the overuse of antimicrobials. This shift marks a pivotal first step toward establishing a structured diagnostic framework for this disease. This review article provides an update on recent developments and future perspectives in clinical diagnostics and prognostic techniques for BRD, assessing their benefits and limitations. The methods discussed include the evaluation of clinical signs and animal behavior, biomarker analysis, molecular diagnostics, ultrasound imaging, and prognostic modeling. While some techniques show promise as standalone diagnostics, it is likely that a multifaceted approach-leveraging a combination of these methods-will yield the most accurate diagnosis of BRD.

Antimicrobial use and resistance in food animal production: food safety and associated concerns in Sub-Saharan Africa

The use of antimicrobials in food animal (FA) production is a common practice all over the world, with even greater usage and dependence in the developing world, including Sub-Saharan Africa (SSA). However, this practice which serves obvious economic benefits to producers has raised public health concerns over the last decades, thus driving the selection and dissemination of antimicrobial resistance and adversely impacting food safety and environmental health. This review presents the current and comprehensive antimicrobial usage practices in food animal production across SSA. We further highlighted the overall regional drivers as well as the public health, environmental, and economic impact of antimicrobial use in the production of food animals. Antimicrobial use is likely to increase with even exacerbated outcomes unless cost-effective, safe, and sustainable alternatives to antibiotics, especially probiotics, prebiotics, bacteriocins, antimicrobial peptides, bacteriophages, vaccines, etc. are urgently advocated for and used in food animal production in SSA. These, in addition to the implementation of strong legislation on antimicrobial use, and improved hygiene will help mitigate the public health concerns associated with antimicrobial use in food animals and improve the well-being and safety of food animals and their products.

Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis

The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.

Antimicrobial resistance in Enterococcus isolated from western Canadian cow-calf herds

BACKGROUND

Data on antimicrobial resistance (AMR) in cow-calf herds is limited and there have been no Canadian studies examining AMR in Enterococcus in cow-calf herds. Enterococcus is a ubiquitous Gram-positive indicator of AMR for enteric organisms that is also important in human health. The objective of this study was to describe AMR in specific Enterococcus species of interest from cow-calf herds; highlighting differences in AMR among isolates from cows and calves and samples collected in the spring and fall. Isolates (n = 1505) were examined from 349 calves and 385 cows from 39 herds in the spring of 2021 and 413 calves from 39 herds and 358 cows from 36 herds in the fall of 2021. Enterococcus species were identified using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS) and antimicrobial susceptibility testing was completed based on a prioritization scheme for importance to human health and using the National Antimicrobial Resistance Monitoring System (NARMS) Gram positive Sensititre broth microdilution panel.

RESULTS

Resistance was observed to at least one antimicrobial in 86% (630/734) of isolates from the spring and 84% (644/771) of isolates from the fall. The most common types of resistance across all species were: lincomycin, quinupristin/dalfopristin, daptomycin, ciprofloxacin, and tetracycline. However, the proportion of isolates with AMR varied substantially based on species. Multiclass resistance, defined as resistance to ≥3 antimicrobial classes after excluding intrinsic resistance, was highest in isolates from calves in the spring (6.9%) (24/349) and cows in the fall (6.7%) (24/357). Differences in resistance were seen between cows and calves in the spring and fall as well as across seasons, with no differences seen between cows and calves in the fall.

CONCLUSIONS

While most Enterococcus isolates were resistant to at least one antimicrobial, questions remain regarding species differences in intrinsic resistance and the accuracy of certain antimicrobial breakpoints for specific Enterococcus spp. As a result, some species-specific AMR profiles should be interpreted with caution. Despite these constraints, Enterococcus species are important indicator organisms for AMR and resulting data can be used to inform stewardship initiatives.

Antimicrobial Effects of Plant-Based Supplements on Gut Microbial Diversity in Small Ruminants

Every year in the United States, approximately 48 million people are affected by bacterial illnesses that are transmitted through food, leading to 3000 fatalities. These illnesses typically stem from food animals and their by-products, which may harbor dangerous pathogens like Salmonella enterica, Listeria monocytogenes, enterohemorrhagic Escherichia coli O157:H7, and Campylobacter jejuni. Factors that contribute to contamination include manure used as a soil amendment, exposure to polluted irrigation water, and contact with animals. To improve food safety, researchers are studying pre-slaughter intervention methods to eliminate bacterial contamination in live animals. While small ruminants are vital to global agriculture and income generation for small farms, traditional feeding practices involve supplements and antibiotics to boost performance, which contributes to antibiotic resistance. Hence, researchers are looking for friendly bacterial strains that enhance both animal and human health without impacting livestock productivity. The global trend is to minimize the use of antibiotics as feed supplements, with many countries prohibiting or limiting their use. The aim of this review is to provide a comprehensive insight on the antioxidant capabilities, therapeutic attributes, and applications of bioactive compounds derived from sweet potato tops (SPTs), rice bran (RB) and radish tops (RTs). This overview provides an insight on plant parts that are abundant in antioxidant and prebiotic effects and could be used as value-added products in animal feed and pharmaceutical applications. This review was based on previous findings that supplementation of basal diets with natural supplements represents a multifaceted intervention that will become highly important over time. By remarkably reducing the burden of foodborne pathogens, they apply to multiple species, are cheap, do not require withdrawal periods, and can be applied at any time in food animal production.

A mapping review of methicillin-resistant Staphylococcus aureus proportions, genetic diversity, and antimicrobial resistance patterns in Cameroon

BACKGROUND

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has increased and poses a significant threat to human and animal health in Cameroon and the world at large. MRSA strains have infiltrated various settings, including hospitals, communities, and livestock, contributing to increased morbidity, treatment costs, and mortality. This evidence synthesis aims to understand MRSA prevalence, resistance patterns, and genetic characterization in Cameroon.

METHODS

The methodology was consistent with the PRISMA 2020 guidelines. Studies of any design containing scientific data on MRSA prevalence, genetic diversity, and antimicrobial resistance patterns in Cameroon were eligible for inclusion, with no restrictions on language or publication date. The search involved a comprehensive search strategy in several databases including Medline, Embase, Global Health, Web of Science, African Index Medicus, and African Journal Online. The risk of bias in the included studies was assessed using the Hoy et al tool, and the results were synthesized and presented in narrative synthesis and/or tables and graphs.

RESULTS

The systematic review analyzed 24 studies, mostly conducted after 2010, in various settings in Cameroon. The studies, characterized by moderate to low bias, revealed a wide prevalence of MRSA ranging from 1.9% to 46.8%, with considerable variation based on demographic and environmental factors. Animal (0.2%), food (3.2% to 15.4%), and environmental samples (0.0% to 34.6%) also showed a varied prevalence of MRSA. The genetic diversity of MRSA was heterogeneous, with different virulence gene profiles and clonal lineages identified in various populations and sample types. Antimicrobial resistance rates showed great variability in the different regions of Cameroon, with notable antibiotic resistance recorded for the beta-lactam, fluoroquinolone, glycopeptide, lincosamide, and macrolide families.

CONCLUSION

This study highlights the significant variability in MRSA prevalence, genetic diversity, and antimicrobial resistance patterns in Cameroon, and emphasizes the pressing need for comprehensive antimicrobial stewardship strategies in the country.

Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome

Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.

Sequencing and culture-based characterization of the vaginal and uterine microbiota in beef cattle that became pregnant or remained open following artificial insemination

IMPORTANCE

Emerging evidence suggests that microbiome-targeted approaches may provide a novel opportunity to reduce the incidence of reproductive failures in cattle. To develop such microbiome-based strategies, one of the first logical steps is to identify reproductive microbiome features related to fertility and to isolate the fertility-associated microbial species for developing a future bacterial consortium that could be administered before breeding to enhance pregnancy outcomes. Here, we characterized the vaginal and uterine microbiota in beef cattle that became pregnant or remained open via artificial insemination and identified microbiota features associated with fertility. We compared similarities between vaginal and uterine microbiota and between heifers and cows. Using culturing, we provided new insights into the culturable fraction of the vaginal and uterine microbiota and their antimicrobial resistance. Overall, our findings will serve as an important basis for future research aimed at harnessing the vaginal and uterine microbiome for improved cattle fertility.

Practices and drivers for antibiotic use in cattle production systems in Kenya

Understanding antibiotic use in livestock systems is key in combating antimicrobial resistance (AMR) and developing effective interventions. Using a standardised questionnaire, we investigated the patterns and drivers of antibiotic use in 165 cattle farms across the three major cattle production systems in Kenya: intensive, extensive, and semi-intensive systems across in three counties: Machakos, Makueni and Narok in Kenya. We used a causal diagram to inform regression models to explore the drivers of antibiotic use in the study farms. Antibiotic use was reported in 92.7% of farms, primarily for prophylactic purposes. Oxytetracycline, penicillin, and streptomycin were the most used antibiotics to treat and control the most reported diseases including mastitis, diarrhoea and East Coast fever (ECF). Regression analysis indicated a positive association between the frequency of antibiotic use at the farm level and both disease incidence and herd size. Conversely, farms that provided cattle with appropriate housing were less likely to use antibiotics, and there was no difference in antibiotic use between those who consulted with veterinarians or sourced antibiotics directly from animal health providers. Our study highlights the complexities around understanding the interplay between practices and drivers of antibiotic use. It also underscores the necessity to enhance education regarding the appropriate usage of antibiotics among cattle farmers, encourage the adoption of proper herd management practices which may reduce disease burden, and reinforce veterinary services and supportive legislation to promote the prudent use of antimicrobials.

Viability and Virulence of Listeria monocytogenes in Poultry

The prevalence of Listeria monocytogenes in 30 samples of poultry was determined using culture-dependent (isolation on OCLA and confirmation by conventional polymerase chain reaction -PCR-, OCLA&PCR) and culture-independent (real-time polymerase chain reaction, q-PCR) methods. L. monocytogenes was detected in 15 samples (50.0%) by OCLA&PCR and in 20 (66.7%) by q-PCR. The concentrations (log10 cfu/g) of L. monocytogenes (q-PCR) ranged from 2.40 to 5.22 (total cells) and from <2.15 to 3.93 (viable cells). The two methods, q-PCR using a viability marker (v-PCR) and OCLA&PCR (gold standard), were compared for their capacity to detect viable cells of L. monocytogenes, with the potential to cause human disease. The values for sensitivity, specificity and efficiency of the v-PCR were 100%, 66.7% and 83.3%, respectively. The agreement between the two methods (kappa coefficient) was 0.67. The presence of nine virulence genes (hlyA, actA, inlB, inlA, inlC, inlJ, prfA, plcA and iap) was studied in 45 L. monocytogenes isolates (three from each positive sample) using PCR. All the strains harbored between six and nine virulence genes. Fifteen isolates (33.3% of the total) did not show the potential to form biofilm on a polystyrene surface, as determined by a crystal violet assay. The remaining strains were classified as weak (23 isolates, 51.1% of the total), moderate (one isolate, 2.2%) or strong (six isolates, 13.3%) biofilm producers. The strains were tested for susceptibility to a panel of 15 antibiotics. An average of 5.11 ± 1.30 resistances per isolate was observed. When the values for resistance and for reduced susceptibility were taken jointly, this figure rose to 6.91 ± 1.59. There was a prevalence of resistance or reduced susceptibility of more than 50.0% for oxacillin, cefoxitin, cefotaxime, cefepime ciprofloxacin, enrofloxacin and nitrofurantoin. For the remaining antibiotics tested, the corresponding values ranged from 0.0% for chloramphenicol to 48.9% for rifampicin. The high prevalence and level of L. monocytogenes with numerous virulence factors in poultry underline how crucial it is to follow correct hygiene procedures during the processing of this foodstuff in order to reduce the risk of human listeriosis.

Longitudinal Assessment of Prevalence and Incidence of Salmonella and Escherichia coli O157 Resistance to Antimicrobials in Feedlot Cattle Sourced and Finished in Two Different Regions of the United States

The objective was to investigate the influence of cattle origin and region of finishing on the prevalence of Salmonella, Escherichia coli O157:H7, and select antimicrobial resistance in E. coli populations. Yearling heifers (n = 190) were utilized in a 2 × 2 factorial arrangement. After determining fecal Salmonella prevalence, heifers were sorted into one of four treatments: heifers originating from South Dakota (SD) and finished in SD (SD-SD); heifers originating from SD and finished in Texas (SD-TX); heifers originating from TX and finished in SD (TX-SD); and heifers originating from TX and finished in TX (TX-TX). Fecal, pen, and water scum line samples were collected longitudinally throughout the study; hide swab and subiliac lymph node (SLN) samples were collected at study end. A treatment × time interaction was observed (p ≤ 0.01) for fecal Salmonella prevalence, with prevalence being greatest for TX-TX and TX-SD heifers before transport. From day (d) 14 through study end, prevalence was greatest for TX-TX and SD-TX heifers compared with SD-SD and TX-SD heifers. Salmonella prevalence on hides were greater (p ≤ 0.01) for heifers finished in TX compared with SD. Salmonella prevalence in SLN tended (p = 0.06) to be greater in TX-TX and SD-TX heifers compared with TX-SD and SD-SD. Fecal E. coli O157:H7 prevalence had a treatment × time interaction (p = 0.04), with SD-TX prevalence being greater than TX-SD on d 56 and SD-SD and TX-TX being intermediate. A treatment × time interaction was observed for fecal trimethoprim-sulfamethoxazole-resistant and cefotaxime-resistant E. coli O157:H7 prevalence (p ≤ 0.01). Overall, these data suggest that the region of finishing influences pathogenic bacterial shedding patterns, with the initial 14 d after feedlot arrival being critical for pathogen carriage.

Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter

Background

Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes.

Objective

This study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland.

Methods

A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS).

Results

Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium.

Conclusion

Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.

Bovine Airway Models: Approaches for Investigating Bovine Respiratory Disease

Bovine respiratory disease (BRD) is a multifactorial condition where different genera of bacteria, such as Mannheimia haemolytica, Histophilus somni, Pasteurella multocida, and Mycoplasma bovis, and viruses, like bovine respiratory syncytial virus, bovine viral diarrhea virus, and bovine herpes virus-1, infect the lower respiratory tract of cattle. These pathogens can co-infect cells in the respiratory system, thereby making specific treatment very difficult. Currently, the most common models for studying BRD include a submerged tissue culture (STC), where monolayers of epithelial cells are typically covered either in cellular or spent biofilm culture medium. Another model is an air-liquid interface (ALI), where epithelial cells are exposed on their apical side and allowed to differentiate. However, limited work has been reported on the study of three-dimensional (3D) bovine models that incorporate multiple cell types to represent the architecture of the respiratory tract. The roles of different defense mechanisms in an infected bovine respiratory system, such as mucin production, tight junction barriers, and the production of antimicrobial peptides in in vitro cultures require further investigation in order to provide a comprehensive understanding of the disease pathogenesis. In this report, we describe the different aspects of BRD, including the most implicated pathogens and the respiratory tract, which are important to incorporate in disease models assembled in vitro. Although current advancements of bovine respiratory cultures have led to knowledge of the disease, 3D multicellular organoids that better recapitulate the in vivo environment exhibit potential for future investigations.

Dietary and Sexual Correlates of Gut Microbiota in the Japanese Gecko, Gekko japonicus (Schlegel, 1836)

Numerous studies have demonstrated that multiple intrinsic and extrinsic factors shape the structure and composition of gut microbiota in a host. The disorder of the gut microbiota may trigger various host diseases. Here, we collected fecal samples from wild-caught Japanese geckos (Gekko japonicus) and captive conspecifics fed with mealworms (mealworm-fed geckos) and fruit flies (fly-fed geckos), aiming to examine the dietary and sexual correlates of the gut microbiota. We used 16S rRNA gene sequencing technology to determine the composition of the gut microbiota. The dominant phyla with a mean relative abundance higher than 10% were Verrucomicrobiota, Bacteroidota, and Firmicutes. Gut microbial community richness and diversity were higher in mealworm-fed geckos than in wild geckos. Neither community evenness nor beta diversity of gut microbiota differed among wild, mealworm-fed, and fly-fed geckos. The beta rather than alpha diversity of gut microbiota was sex dependent. Based on the relative abundance of gut bacteria and their gene functions, we concluded that gut microbiota contributed more significantly to the host's metabolic and immune functions. A higher diversity of gut microbiota in mealworm-fed geckos could result from higher chitin content in insects of the order Coleoptera. This study not only provides basic information about the gut microbiota of G. japonicus but also shows that gut microbiota correlates with dietary habits and sex in the species.

A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota: a Pilot Study

Bovine respiratory disease (BRD) remains the most significant health challenge affecting the North American beef cattle industry and results in $3 billion in economic losses yearly. Current BRD control strategies mainly rely on antibiotics, with metaphylaxis commonly employed to mitigate BRD incidence in commercial feedlots.

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain

In this study, we evaluated the seminal and fecal microbiota in yearling beef bulls fed a common diet to achieve moderate (1.13 kg/day) or high (1.80 kg/day) rates of weight gain. Semen samples were collected on days 0 and 112 of dietary intervention (n = 19/group) as well as postbreeding (n = 6/group) using electroejaculation, and the microbiota was assessed using 16S rRNA gene sequencing, quantitative PCR (qPCR), and culturing. The fecal microbiota was also evaluated, and its similarity with seminal microbiota was assessed. A subset of seminal bacterial isolates (n = 33) was screened for resistance against 28 antibiotics. A complex and dynamic microbiota was detected in bovine semen, and the community structure was affected by sampling time (R2 = 0.16, P < 0.001). Microbial richness increased significantly from day 0 to day 112, and diversity increased after breeding (P > 0.05). Seminal microbiota remained unaffected by the differential rates of gain, and its overall composition was distinct from fecal microbiota, with only 6% of the taxa shared between them. A total of 364 isolates from 49 different genera were recovered under aerobic and anaerobic culturing. Among these seminal isolates were pathogenic species and those resistant to several antibiotics. Overall, our results suggest that bovine semen harbors a rich and complex microbiota which changes over time and during the breeding season but appears to be resilient to differential gains achieved via a common diet. Seminal microbiota is distinct from the fecal microbiota and harbors potentially pathogenic and antibiotic-resistant bacterial species. IMPORTANCE Increasing evidence from human and other animal species supports the existence of a commensal microbiota in semen and that this seminal microbiota may influence not only sperm quality and fertility but also female reproduction. Seminal microbiota in bulls and its evolution and factors shaping this community, however, remain largely underexplored. In this study, we characterized the seminal microbiota of yearling beef bulls and its response to the bull age, different weight gains, and mating activity. We compared bacterial composition between seminal and fecal microbiota and evaluated the diversity of culturable seminal bacteria and their antimicrobial resistance. Our results obtained from sequencing, culturing, and antibiotic susceptibility testing provide novel information on the taxonomic composition, evolution, and factors shaping the seminal microbiota of yearling beef bulls. This information will serve as an important basis for further understanding of the seminal microbiome and its involvement in reproductive health and fertility in cattle.

Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multidrug resistance in Histophilus somni

Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).

Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle

Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.

Soil antibiotic resistance genes accumulate at different rates over four decades of manure application

Manure can be a source of antibiotic resistance genes (ARGs) that enter the soil. However, previous studies assessing ARG persistence in soil have generally lacked continuity over sampling times, consistency of location, and assessing the impact of discontinuing manure application. We evaluated both short- and long-term ARG accumulation dynamics in soil with a 40-year known history of manure use. Manure application caused a greater abundance of tetracycline, macrolide, and sulfonamide ARGs in the soil. There was an initial spike in ARG abundance resulting from manure bacteria harboring ARGs being introduced to soil, followed by resident soil bacteria out-competing them, which led to ARG dissipation within a year. However, over four decades, annual manure application caused linear or exponential ARG accumulation, and bacteria associated with ARGs differed compared to those in the short term. Eleven years after discontinuing manure application, most soil ARG levels declined but remained elevated. We systematically explored the historical accumulation of ARGs in manured soil, and provide insight into factors that affect their persistence.

Molecular and Antimicrobial Susceptibility Characterization of Escherichia coli Isolates from Bovine Slaughterhouse Process

Antimicrobials are routinely used in human and veterinary medicine. With repeated exposure, antimicrobials promote antibiotic resistance, which poses a threat to public health. In this study, we aimed to determine the susceptibility patterns, virulence factors, and phylogroups of E. coli isolates during the killing process in a bovine slaughterhouse. We analyzed 336 samples (from water, surfaces, carcasses, and feces), and 83.3% (280/336) were positive for E. coli. The most common phenotypic resistances that we detected were 50.7% (142/280) for tetracycline, 44.2% (124/280) for cephalothin, 34.6% (97/280) for streptomycin, and 36.7% (103/280) for ampicillin. A total of 82.4% of the isolates had resistance for at least one antimicrobial, and 37.5% presented multiresistance. We detected a total of 69 different phenotypic resistance patterns. We detected six other resistance-related genes, the most prevalent being tetA (22.5%) and strB (15.7%). The prevalence values of the virulence genes were 5.4% in hlyA, 1.4% in stx1, and 0.7% in stx2. The frequencies of the pathogenic strains (B2 and D) were 32.8% (92/280) and 67.1% (188/280) as commensals A and B1, respectively. E. coli isolates with pathogenic potential and multiresistance may represent an important source of dissemination and a risk to consumers.

MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology

The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.

Prevalence of antimicrobial resistance in fecal Escherichia coli and Enterococcus spp. isolates from beef cow-calf operations in northern California and associations with farm practices

Antimicrobials are necessary for the treatment of bacterial infections in animals, but increased antimicrobial resistance (AMR) is becoming a concern for veterinarians and livestock producers. This cross-sectional study was conducted on cow-calf operations in northern California to assess prevalence of AMR in Escherichia coli and Enterococcus spp. shed in feces of beef cattle of different life stages, breeds, and past antimicrobial exposures and to evaluate if any significant factors could be identified that are associated with AMR status of the isolates. A total of 244 E. coli and 238 Enterococcus isolates were obtained from cow and calf fecal samples, tested for susceptibility to 19 antimicrobials, and classified as resistant or non-susceptible to the antimicrobials for which breakpoints were available. For E. coli, percent of resistant isolates by antimicrobial were as follows: ampicillin 100% (244/244), sulfadimethoxine 25.4% (62/244), trimethoprim-sulfamethoxazole 4.9% (12/244), and ceftiofur 0.4% (1/244) while percent of non-susceptible isolates by antimicrobial were: tetracycline 13.1% (32/244), and florfenicol 19.3% (47/244). For Enterococcus spp., percent of resistant isolates by antimicrobial were as follows: ampicillin 0.4% (1/238) while percent of non-susceptible isolates by antimicrobial were tetracycline 12.6% (30/238) and penicillin 1.7% (4/238). No animal level or farm level management practices, including antimicrobial exposures, were significantly associated with differences in isolate resistant or non-susceptible status for either E. coli or Enterococcus isolates. This is contrary to the suggestion that administration of antibiotics is solely responsible for development of AMR in exposed bacteria and demonstrates that there are other factors involved, either not captured in this study or not currently well understood. In addition, the overall use of antimicrobials in this cow-calf study was lower than other sectors of the livestock industry. Limited information is available on cow-calf AMR from fecal bacteria, and the results of this study serve as a reference for future studies to support a better understanding and estimation of drivers and trends for AMR in cow-calf operations.

Antimicrobial usage and associated residues and resistance emergence in smallholder beef cattle production systems in Nigeria: A One Health challenge

Livestock intensification has facilitated antimicrobial use (AMU) with consequent antimicrobial resistance (AMR) development. We assessed AMU in beef farms, pathways for residues and resistance dissemination to humans, risk status, residues identification, and drivers for antimicrobial residues and resistance emergence in beef cattle production systems. A cross-sectional survey was conducted in randomly selected beef farms of Northern Nigeria, between 2018 and 2019. Traffic Light model and Disc Diffusion Test were used to assess risk status and determined residues, respectively. Data was analyzed using descriptive statistics and logistic regression models at 95% confidence level. About 92% (n = 608) farmers participated. The majority of farmers managing intensive (78.9%) and semi-intensive (76.6%) farms did not follow antimicrobial dosage instructions. Also, 72.4% and 83.9% of the farmers on intensive and semi-intensive systems, respectively, did not observed withdrawal periods after AMU. Furthermore, 71.5% farmers in intensive and 53.2% in semi-intensive farms used antimicrobials as growth promoters. Antimicrobials frequently used include tetracyclines, sulfonamides and penicillin. Antimicrobial residues and resistance dissemination pathways from beef herds were: consumption of contaminated meat with residues (p = 0.007); contacts with contaminated cattle and fomites (p < 0.001); and contaminated manure and aerosols in farm environment (p = 0.003). Significant drivers of residues and resistance emergence were antimicrobial misuse and overuse (OR = 2.72; 95% CI:1.93-3.83), non-enforcement of laws (OR = 2.98; 95% CI:2.11-4.21), poor education and expertise (OR = 1.52; 95% CI:1.09-2.12), and husbandry management system (OR = 10.24; 95% CI:6.75-15.54). The majority of intensive (63.6%) and semi-intensive (57.63%) farm systems belonged to Class 3 (Red risk) status. Antimicrobial residues were detected in 48.4% intensively and 34.4% semi-intensively managed farms. The study revealed poor practices of AMU in beef cattle production. Many factors were found to influenced antimicrobial residues and resistance occurrence and dissemination. A 'One Health' approach mitigation with adequate sanitation, hygiene, and good biosecurity measures will assure food safety, public and environmental health.

Factors associated with antimicrobial resistant enterococci in Canadian beef cattle: A scoping review

Introduction

Antimicrobial resistance (AMR) is a global health concern, occurring when bacteria evolve to render antimicrobials no longer effective. Antimicrobials have important roles in beef production; however, the potential to introduce AMR to people through beef products is a concern. This scoping review identifies factors associated with changes in the prevalence of antimicrobial-resistant Enterococcus spp. applicable to the Canadian farm-to-fork beef continuum.

Methods

Five databases (MEDLINE, BIOSIS, Web of Science, Embase, and CAB Abstracts) were searched for articles published from January 1984 to March 2022, using a priori inclusion criteria. Peer-reviewed articles were included if they met all the following criteria: written in English, applicable to the Canadian beef production context, primary research, in vivo research, describing an intervention or exposure, and specific to Enterococcus spp.

Results

Out of 804 screened articles, 26 were selected for inclusion. The included articles discussed 37 factors potentially associated with AMR in enterococci, with multiple articles discussing at least two of the same factors. Factors discussed included antimicrobial administration (n = 16), raised without antimicrobials (n = 6), metal supplementation (n = 4), probiotics supplementation (n = 3), pen environment (n = 2), essential oil supplementation (n = 1), grass feeding (n = 1), therapeutic versus subtherapeutic antimicrobial use (n = 1), feeding wet distiller grains with solubles (n = 1), nutritional supplementation (n = 1) and processing plant type (n = 1). Results were included irrespective of their quality of evidence.

Discussion

Comparability issues arising throughout the review process were related to data aggregation, hierarchical structures, study design, and inconsistent data reporting. Findings from articles were often temporally specific in that resistance was associated with AMR outcomes at sampling times closer to exposure compared to studies that sampled at longer intervals after exposure. Resistance was often nuanced to unique gene and phenotypic resistance patterns that varied with species of enterococci. Intrinsic resistance and interpretation of minimum inhibitory concentration varied greatly among enterococcal species, highlighting the importance of caution when comparing articles and generalizing findings.

Systematic Review Registration

[http://hdl.handle.net/1880/113592].

Quantification of Total and Viable Cells and Determination of Serogroups and Antibiotic Resistance Patterns of Listeria monocytogenes in Chicken Meat from the North-Western Iberian Peninsula

Twenty samples of minced chicken meat procured from butcher’s shops in León (Spain; 10 samples) and Vila Real (Portugal; 10 samples) were analyzed. Microbial concentrations (log10 cfu/g) of 7.53 ± 1.02 (viable aerobic microbiota), 7.13 ± 1.07 (psychrotrophic microorganisms), and 4.23 ± 0.88 (enterobacteria) were found. The detection method described in the UNE-EN ISO 11290-1 standard (based on isolation from the chromogenic medium OCLA) with confirmation by the polymerase chain reaction (PCR; lmo1030) (OCLA−PCR), revealed Listeria monocytogenes in 14 samples (70.0% of the total), nine of Spanish origin and five of Portuguese (p > 0.05). The levels of viable and inactivated L. monocytogenes in the samples were determined with a q-PCR using propidium monoazide (PMAxx) as a viability marker. Seven samples tested positive both with the OCLA−PCR and with the q-PCR, with estimated concentrations of viable cells varying between 2.15 log10 cfu/g (detection limit) and 2.94 log10 cfu/g. Three samples tested negative both with the OCLA−PCR and with the q-PCR. Seven samples were positive with the OCLA−PCR, but negative with the q-PCR, and three samples tested negative with the OCLA−PCR and positive with the q-PCR. The percentage of viable cells relative to the total ranged between 2.4% and 86.0%. Seventy isolates of L. monocytogenes (five from each positive sample) were classified in PCR serogroups with a multiplex PCR assay. L. monocytogenes isolates belonged to serogroups IIa (52 isolates; 74.3%), IIc (7; 10.0%), IVa (2; 2.9%), and IVb (9; 12.9%). The susceptibility of the 70 isolates to 15 antibiotics of clinical interest was tested. The strains presented resistance to between three and eight antibiotics. The average number of resistances was greater (p < 0.001) among strains isolated from Spanish samples (6.20 ± 1.08), than in those from Portugal (5.00 ± 1.08). In both groups of strains, a prevalence of resistance higher than 95% was observed for oxacillin, cefoxitin, cefotaxime, and cefepime. The need to handle minced chicken meat correctly, taking care to cook it sufficiently and to avoid cross-contamination, so as to reduce the danger of listeriosis, is emphasized. A combination of culture-dependent and culture-independent methods offers complementary routes for the detection in food of the cells of L. monocytogenes in various different physiological states.

Prevalence and Implications of Shiga Toxin-Producing E. coli in Farm and Wild Ruminants

Shiga-toxin-producing Escherichia coli (STEC) is a food-borne pathogen that causes human gastrointestinal infections across the globe, leading to kidney failure or even death in severe cases. E. coli are commensal members of humans and animals' (cattle, bison, and pigs) guts, however, may acquire Shiga-toxin-encoded phages. This acquisition or colonization by STEC may lead to dysbiosis in the intestinal microbial community of the host. Wildlife and livestock animals can be asymptomatically colonized by STEC, leading to pathogen shedding and transmission. Furthermore, there has been a steady uptick in new STEC variants representing various serotypes. These, along with hybrids of other pathogenic E. coli (UPEC and ExPEC), are of serious concern, especially when they possess enhanced antimicrobial resistance, biofilm formation, etc. Recent studies have reported these in the livestock and food industry with minimal focus on wildlife. Disturbed natural habitats and changing climates are increasingly creating wildlife reservoirs of these pathogens, leading to a rise in zoonotic infections. Therefore, this review comprehensively surveyed studies on STEC prevalence in livestock and wildlife hosts. We further present important microbial and environmental factors contributing to STEC spread as well as infections. Finally, we delve into potential strategies for limiting STEC shedding and transmission.

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants

BACKGROUND

Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi.

RESULTS

Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins.

CONCLUSIONS

There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.

Association between Tulathromycin Treatment for Bovine Respiratory Disease and Antimicrobial Resistance Profiles among Gut Commensals and Foodborne Bacterial Pathogens Isolated from Feces of Beef Steers

ABSTRACT

This study was conducted to evaluate the association between a therapeutic dose of tulathromycin for bovine respiratory disease in beef steers and the antimicrobial and multidrug resistance profiles of the gastrointestinal tract commensals Escherichia coli and Enterococcus spp. and the foodborne pathogens Salmonella enterica and Campylobacter spp. isolated from fecal samples. Individual fecal samples were collected on days 0, 14, and 28 from 70 beef steers that were housed in a single pen and had been treated or not treated with tulathromycin. Samples were cultured for bacterial isolation, and isolates were tested for antimicrobial susceptibility with the broth microdilution method to determine the MICs of clinically relevant antimicrobials used in both human and veterinary medicine. Generalized linear mixed effects models were fitted to estimate the prevalence of the bacterial species and the prevalence of resistant isolates over time and between treated and nontreated cattle and of multidrug-resistant isolates. Model-adjusted mean prevalences of E. coli, Enterococcus spp., S. enterica, and Campylobacter spp. were 99.5, 85.9, 1.5, and 17.7%, respectively. The prevalence of erythromycin-resistant Enterococcus spp. was significantly higher on day 14 (59.7%) than on day 28 (22.2%). A higher prevalence of erythromycin-resistant Enterococcus spp. was found in samples from treated (59.3%) than in samples from nontreated (27.6%) animals. Multidrug resistance (three or more antimicrobial classes) was observed in 8.4% of E. coli isolates and 62.7% of Enterococcus isolates. The administration of tulathromycin was significantly associated with an increased prevalence of erythromycin-resistant Enterococcus spp. isolates.

HIGHLIGHTS

Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

Transmission of antibiotic resistance at the wildlife-livestock interface

Antibiotic-resistant microorganisms (ARMs) are widespread in natural environments, animals (wildlife and livestock), and humans, which has reduced our capacity to control life threatening infectious disease. Yet, little is known about their transmission pathways, especially at the wildlife-livestock interface. This study investigated the potential transmission of ARMs and antibiotic resistance genes (ARGs) between cattle and wildlife by comparing gut microbiota and ARG profiles of feral swine (Sus scrofa), coyotes (Canis latrans), cattle (Bos taurus), and environmental microbiota. Unexpectedly, wild animals harbored more abundant ARMs and ARGs compared to grazing cattle. Gut microbiota of cattle was significantly more similar to that of feral swine captured within the cattle grazing area where the home range of both species overlapped substantially. In addition, ARMs against medically important antibiotics were more prevalent in wildlife than grazing cattle, suggesting that wildlife could be a source of ARMs colonization in livestock.

Analysis of microbiome data from feral swine, coyotes, domesticated cattle, and the surrounding environment reveals that wild animals harbor more abundant antibiotic-resistant organisms than livestock, and might act as a source of antibiotic-resistant microbes in outbreaks.

Comparative study on gut microbiota in three Anura frogs from a mountain stream

Composition and diversity in gut microbiota are impacted by a wide variety of factors. The similarity of gut microbiota in related or sympatric species has been gaining recent traction. Here, 16S rRNA gene sequencing technology was employed to study the gut microbiota of three sympatric frog species, namely Odorrana tormota, O. graminea, and Amolops wuyiensis. In these three frog species, the most abundant phylum was Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, and Firmicutes. The most abundant family was Burkholderiaceae in three species. The most dominant genera were Burkholderia, Caballeronia, and Paraburkholderia with the highest relative abundance in O. tormota, O. graminea, and A. wuyiensis, respectively. No differences were observed in alpha diversity indexes among the three frog species. However, bacterial similarity of gut microbiota was significantly different between O. tormota and A. wuyiensis and between O. graminea and A. wuyiensis. Metabolism‐related gene function was predominantly enriched in the gut microbiota of the three evaluated frog species. From these findings, that the relative abundance of the gut microbiota and predicted gene functions differed in three species, we conclude that there were significant differences in the gut microbiota of the three species. Similar alpha diversity and interspecific bacterial similarity in the gut might be related to bacterial transmission among the three Anura frogs evaluated in this study.

Bovine Respiratory Disease: Conventional to Culture-Independent Approaches to Studying Antimicrobial Resistance in North America

Numerous antimicrobial resistance (AMR) surveillance studies have been conducted in North American feedlot cattle to investigate the major bacterial pathogens of the bovine respiratory disease (BRD) complex, specifically: Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. While most bacterial isolates recovered from healthy cattle are susceptible to a repertoire of antimicrobials, multidrug resistance is common in isolates recovered from cattle suffering from BRD. Integrative and conjugative elements (ICE) have gained increasing notoriety in BRD-Pasteurellaceae as they appear to play a key role in the concentration and dissemination of antimicrobial resistant genes. Likewise, low macrolide susceptibility has been described in feedlot isolates of M. bovis. Horizontal gene transfer has also been implicated in the spread of AMR within mycoplasmas, and in-vitro experiments have shown that exposure to antimicrobials can generate high levels of resistance in mycoplasmas via a single conjugative event. Consequently, antimicrobial use (AMU) could be accelerating AMR horizontal transfer within all members of the bacterial BRD complex. While metagenomics has been applied to the study of AMR in the microbiota of the respiratory tract, the potential role of the respiratory tract microbiome as an AMR reservoir remains uncertain. Current and prospective molecular tools to survey and characterize AMR need to be adapted as point-of-care technologies to enhance prudent AMU in the beef industry.

Phenotypic and Genotypic Assessment of Antimicrobial Resistance in Escherichia coli from Australian Cattle Populations at Slaughter

ABSTRACT

Australia relies on periodic antimicrobial resistance (AMR) surveys to determine trends and changes in AMR in animal production systems. This study is a follow-up to a survey of Escherichia coli from healthy cattle at slaughter conducted in 2013, which provided baseline data on AMR prevalence across cattle groups and production practices. In this study, 591 beef cattle, 194 dairy cattle, and 216 veal calf fecal samples were collected from 25 beef and veal processing establishments in Australia, representing approximately 77% of total export volume. A total of 969 matrix-assisted laser desorption-ionization results confirmed commensal E. coli isolates from 574 beef cattle, 186 dairy cattle, and 209 veal calves were recovered, and antimicrobial susceptibility testing was carried out by microbroth dilution to 16 drugs from 10 classes interpreted against epidemiological cutoff breakpoints. Overall, a high proportion of E. coli isolates (83.8%) were wild type for all antimicrobials assessed. In addition, isolates that were non-wild type (NWT) for three or more classes of antimicrobial did not exceed 4% for any of the cattle groups. The prevalence of E. coli that were NWT for antimicrobials that are critical or of high importance to human health was very low, with 1.4% of all isolates tested determined to be NWT for fluoroquinolones, third-generation cephalosporins, or polymyxins. Genomic analysis of NWT isolates identified one beef cattle isolate (ST-10) harboring blaCMY-2 and a dairy isolate (ST-58) and two veal calf isolates (ST-58 and ST-394) that had qnrS1, which confer resistance to extended-spectrum cephalosporins and fluoroquinolones, respectively. The low levels of AMR reported in this study confirm previous Australian studies, which indicated that there is minimal evidence that specific production practices lead to widespread disproportionate development of NWT isolates.

HIGHLIGHTS

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

Galyean Appreciation Club Review: Revisiting nutrition and health of newly received cattle - What have we learned in the last 15 years?

Our objective was to review the literature related to the health and management of newly received cattle published since a previous review by Duff and Galyean (2007). Bovine respiratory disease (BRD) continues to be a major challenge for the beef industry. Depending on disease severity, animals treated for BRD have decreased performance and lowered carcass value. Diagnosis of BRD is less effective than desired, and progress on developing real-time, chute-side methods to diagnose BRD has been limited. Systems that combine lung auscultation with temperature and BW data show promise. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Vaccination and metaphylaxis continue to be important tools for prevention and control of BRD, but antimicrobial resistance is a concern with antibiotic use. Dietary energy concentration and roughage source/level continue to be important topics. Mineral supplementation has received considerable attention, particularly the use of organic vs. inorganic sources and injectable minerals or drenches given on arrival. Use of probiotics and prebiotics for newly received cattle has shown variable results, but further research is warranted. Health and nutrition of newly received cattle will continue to be an important research area in the years to come.

Promoting Judicious Antimicrobial Use in Beef Production: The Role of Quarantine

Judicious antimicrobial stewardship in livestock industry is needed to reduce the use of antimicrobials (AMU) and the associated risk of antimicrobial resistance. Biosecurity measures are acknowledged for their role against the spread of diseases and the importance in reducing AMU in different species. However, their effectiveness in beef production has been scarcely considered. The aim of this study was to investigate the effect of the quarantine strategy on AMU in beef cattle. A total of 1206 Charolaise animals in five farms were included in the trial. Roughly half of the animals followed the standard procedure of the fattening cycle (no-quarantine; NO-QUA group) and half followed a 30-day period of quarantine (QUA group) since their arrival. Performance and antimicrobial data were recorded and a treatment incidence 100 (TI100it) per animal was calculated. Penicillins was the most used class of antimicrobials. Differences between groups were significant for males only, with NO-QUA group having greater TI100it (3.76 vs. 3.24; p < 0.05) and lower body weight at slaughter (713.4 vs. 723.7 kg; p < 0.05) than QUA group. Results suggest that quarantine strategy can reduce AMU in males without compromising their performance, whereas further investigation is needed for females.

Antimicrobial susceptibility screening test of Mannheimia haemolytica and Pasteurella multocida (serogroup A) Moroccan strains isolated from ruminants

The present study is the first report aimed to determine the antibiotic susceptibility profiles of Mannheimia haemolytica and Pasteurella multocida serogroup A Moroccan isolates. Each isolate was tested for sensitivity to amoxicillin (A), amoxicillin/clavulanic acid (AMC), gentamicin (CN), streptomycin (STR), florfenicol (FFC), doxycycline (DO), erythromycin (E), spiramycin (SP), nalidixic acid (NA), flumequine (UB), enrofloxacin (ENF) and sulfamethoxazole (SXT). All isolates showed resistance to the antibiotics tested at a rate greater than 14%, except for one P. multocida isolate which had no resistance profile against AMC. The highest level of resistance was found against NA for P. multocida (100%) and against UB (82.4%) for M. haemolytica. The sensitivity rates for P. multocida were between 0 (against NA) and 85.7% (against STR, AMC, FFC), whereas sensitivity of M. haemolytica isolates ranged from 17.6% against UB and 79.4% against AMC. For both Pasteurellaceae species, the AMC was the most effective antimicrobial agent, however multi-drug resistance was observed in all isolates raising the interest to monitor the antimicrobial susceptibility of Pasteurellaceae species to determine appropriate antibiotic for treatment of pasteurellosis.

Effect of Protracted Free-Choice Chlortetracycline-Medicated Mineral for Anaplasmosis Control on Escherichia coli Chlortetracycline Resistance Profile from Pastured Beef Cattle

Anaplasmosis is an economically-significant, hemolytic, tick-borne disease of cattle caused by Anaplasma marginale which can cause clinical anemia and death. Current control options are limited, and FDA-approved antimicrobial control options do not have a defined duration of use. A practical and routinely used anaplasmosis control method involves feeding free-choice chlortetracycline (CTC)-medicated mineral to pastured cattle for several months. Constant antimicrobial use poses the risk of expediting the development and dissemination of antimicrobial resistance in off-target commensal bacteria in the bovine gastrointestinal tract. The objective of this study was to determine the CTC-susceptibility of Escherichia coli isolated from anaplasmosis endemic beef cattle herds provided different FDA-approved free-choice CTC-medicated mineral formulations, all intended to provide cattle a dosage of 0.5 to 2.0 mg CTC/lb bodyweight per day. A closed-herd, comprised of Hereford-Angus cows, naturally endemic for anaplasmosis, were grazed in five different pastures with one herd serving as an untreated control group. The other cattle herds were randomly assigned one of four FDA-approved CTC-medicated mineral formulations (700, 5000, 6000, and 8000 g CTC/ton) labeled for “the control of active anaplasmosis” and provided their respective CTC-medicated mineral formulation for five consecutive months. Fecal samples were collected monthly from a subset of cows (n = 6 or 10) per pasture. Fecal samples were cultured for E. coli isolates and the minimal inhibitory concentration of CTC was determined. Baseline CTC-susceptibility of E. coli was variable among all treatment and control groups. The susceptibility of E. coli isolates was significantly different between study herds over the treatment period (p = 0.0037 across time and 0.009 at the final sampling time). The interaction between study herds and treatment period was not significant (p = 0.075).

A Review of UK-Registered and Candidate Vaccines for Bovine Respiratory Disease

Vaccination is widely regarded as a cornerstone in animal or herd health and infectious disease management. Nineteen vaccines against the major pathogens implicated in bovine respiratory disease are registered for use in the UK by the Veterinary Medicines Directorate (VMD). However, despite annual prophylactic vaccination, bovine respiratory disease is still conservatively estimated to cost the UK economy approximately £80 million per annum. This review examines the vaccine types available, discusses the surrounding literature and scientific rationale of the limitations and assesses the potential of novel vaccine technologies.

Antimicrobial Resistance in Enterococcus Spp. Isolated from a Beef Processing Plant and Retail Ground Beef

Antimicrobial use in food-producing animals has come under increasing scrutiny due to its potential association with antimicrobial resistance (AMR). Monitoring of AMR in indicator microorganisms such as Enterococcus spp. in meat production facilities and retail meat products can provide important information on the dynamics and prevalence of AMR in these environments. In this study, swabs or samples were obtained from various locations in a commercial beef packing operation (n = 600) and from retail ground beef (n = 60) over a 19-month period. All samples/swabs were enriched for Enterococcus spp., and suspected enterococci isolates were identified using species-specific PCR primers. Enterococcus faecalis was the most frequently isolated species, followed by Enterococcus hirae, which was found mostly on post-hide removal carcasses and in ground beef. Enterococcus faecium (n = 9) and E. faecalis (n = 120) isolates were further characterized for AMR. Twenty-one unique AMR profiles were identified, with 90% of isolates resistant to at least two antimicrobials and two that were resistant to nine antimicrobials. Tetracycline resistance was observed most often in E. faecalis (28.8%) and was likely mediated by tet(M). Genomic analysis of selected E. faecalis and E. faecium isolates revealed that many of the isolates in this study clustered with other publicly available genomes from ground beef, suggesting that these strains are well adapted to the beef processing environment.

IMPORTANCE Antimicrobial resistance (AMR) is a serious challenge facing the agricultural industry. Understanding the flow of antimicrobial-resistant bacteria through the beef fabrication process and into ground beef is an important step in identifying intervention points for reducing AMR. In this study, we used enterococci as indicator bacteria for monitoring AMR in a commercial beef packaging facility and in retail ground beef over a 19-month period. Although washing of carcasses post-hide removal reduced the isolation frequency of Enterococcus spp., a number of antimicrobial-resistant Enterococcus faecalis isolates were recovered from ground beef produced in the packaging plant. Genome analysis showed that several E. faecalis isolates were genetically similar to publicly available isolates recovered from retail ground beef in the United States.

A review of the resistome within the digestive tract of livestock

Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.