Antimicrobial resistance in livestock: advances and alternatives to antibiotics

Recombinant Sendai Virus Vectors as Novel Vaccine Candidates Against Animal Viruses

Vaccination plays a pivotal role in the control and prevention of animal infectious diseases. However, no efficient and safe universal vaccines are currently registered for major pathogens such as influenza A virus, foot-and-mouth disease virus (FMDV), simian immunodeficiency virus (SIV), and small ruminant lentiviruses (SRLV). Here, we review the development of Sendai virus (SeV) vectors as a promising vaccine platform for animal diseases. Recombinant SeV vectors (rSeVv) possess several key features that make them highly suitable for developing vaccination strategies: (1) SeV has exclusively cytoplasmic replication cycle, therefore incapable of transforming host cells by integrating into the cellular genome, (2) rSeVv can accommodate large foreign gene/s inserts (~5 kb) with strong but adjustable transgene expression, (3) can be propagated to high titers in both embryonated chicken eggs and mammalian cell lines, (4) exhibits potent infectivity across a broad range of mammalian cells from different animals species, (5) undergo transient replication in the upper and lower respiratory tracts of non-natural hosts, (6) has not been associated with disease in pigs, non-humans primates, and small ruminants, ensuring a favorable safety profile, and (7) induce a robust innate and cellular immune responses. Preclinical and clinical studies using rSeVv-based vaccines against influenza A virus, FMDV, SIV, and SRLV have yielded promising results. Therefore, this review highlights the potential of rSeVv-based vaccine platforms as a valuable strategy for combating animal viruses.

Effects of Diet Xylooligosaccharide Supplementation on Growth Performance, Carcass Characteristics, and Meat Quality of Hu Lambs

In this study, we examined the effect of xylooligosaccharide (XOS) supplementation on the growth performance, carcass characteristics, and meat quality of Hu lambs. In total, 60 Hu lambs (two months old and weighing 17.32 ± 0.81 kg) were randomly assigned to four treatment groups, each with three replicates and five lambs per replicate. The lambs were fed basal diets supplemented with 0, 1.5, 3, or 4.5 g/kg XOSs in a basal diet for 60 days, with the groups designated XOS0%, XOS1.5%, XOS3%, and XOS4.5%, respectively. The results revealed, compared to theXOS0% group, the XOS3% group presented a lower F:G during 31 to 45 d (p = 0.06). By the 60th day, the body length indices of groups XOS3% and XOS4.5% increased compared to the XOS0% group, with a significant increase observed in group XOS4.5% (p < 0.05). Additionally, the GR values of the XOS1.5%, XOS3%, and XOS4.5% groups increased significantly, and the rumen fluid pH values of the XOS3% and XOS4.5% groups increased significantly (p < 0.01). The crude fat content in the XOS1.5% and XOS4.5% groups were significantly lower (p < 0.05). The hardness, adhesiveness, elasticity, cohesiveness, and chewiness of the mutton in the XOS1.5%, XOS3%, and XOS4.5% groups were increased, although the differences were not statistically significant (p > 0.05). Correlation analysis indicates that there is a significant correlation between growth performance, carcass traits, and meat quality (p < 0.05). The factors influencing meat quality originate from the growth period and the slaughtering phase, which can be attributed to the effects of xylooligosaccharides. In conclusion, XOS had positive effects on the growth performance, carcass characteristics, and meat quality of Hu lambs. The comprehensive effect of group XOS3% was best. Considering the production cost, the 3 g/kg XOSs is identified as the optimal supplementation level for sheep.

Exploring Antibiotic Use in the Community: A Household-Based Survey Using the Drug Bag Method in Rural Burkina Faso

In Burkina Faso, there is lack of awareness of antibiotic use at the community level. This study aims to generate information on the commonly used antibiotics along with the reasons for which they have been used in rural Burkina Faso. The drug bag method was employed to collect information from 423 households in the health district of Nanoro. Descriptive analyses were performed using R software version 4.2.1. Of the 33 antibiotics inventoried, amoxicillin tablets and oxytetracycline were the most recognized and used antibiotics. This study indicated that antibiotics were used for a range of health problems in the community, some of which were administered as painkillers. While primary healthcare facilities constituted the primary source of drugs for households (76.8%), informal drug sellers constituted an additional option (61.5%) for community members. This is a significant concern, given that some antibiotics classified as "Watch"-such as norfloxacin-were readily available in these outlets, despite not being included on the country's Essential Medicines List. This study underscores the necessity of considering the role played by formal providers in the inappropriate use of antibiotics and the importance of understanding the circumstances and logical reasoning underlying communities' access to and use of antibiotics.

Overcoming China's animal waste disposal challenge brought by elevated levels of veterinary antimicrobial residues and antimicrobial resistance

Direct application of animal waste on farmlands was banned in China recently, rendering organic fertilizer production a sound solution for disposing of animal manures and recycling their materials and nutrients. Due to the overuse of antimicrobials in livestock and poultry farms, manure-based organic fertilizers often contain elevated residues of antimicrobials and abundant antimicrobial resistance genes. Land application of such products has caused significant concerns on the environmental pollution of antimicrobials, and the transmission and development of antimicrobial resistance (AMR), which is a major global health challenge. China's recent attempt to restrict the contents of antimicrobial residues in organic fertilizers encountered strong resistance from the industry as it would hinder the utilization of animal manures as a raw material. Reducing and even eliminating the use of antimicrobials in animal farms is the ultimate solution to the challenge of manure disposal posed by the elevated levels of antimicrobial residues and AMR. Phasing out the non-therapeutic use of antimicrobials, developing substitutes of antimicrobials, enhancing animal welfare in farms, promoting diversification of animal farms, and developing antimicrobial removal and disinfection technologies for animal waste are recommended to improve the veterinary antimicrobial stewardship and manure management in China's animal agriculture. These concerted measures would enhance the sustainability of crop and animal farming systems in China and mitigate the impact of antimicrobials and AMR to agro-environmental quality and human health.

Screening and selection of eubiotic compounds possessing immunomodulatory and anti-Clostridium perfringens properties

Eubiotics are water and/or feed additives used in poultry to promote gut health and control enteric burden of pathogens, including Clostridium perfringens. While several eubiotic compounds (ECs) are being introduced commercially, it is essential to devise an in vitro model to screen these compounds to assess their immunomodulatory and antimicrobial properties prior to their testing in vivo. A chicken macrophage cell-line (MQ-NCSU) was used to develop an in vitro model to screen the immunological and anti-C. perfringens properties of 10 ECs: monobutyrin, monolaurin, calcium butyrate, tributyrin, carvacrol, curcumin, green tea extract, rosemary extract, monomyristate, and tartaric acid. An optimal concentration for each EC was selected by measuring the effect on viability of MQ-NCSU cells. Cells were then treated with ECs for 6, 12, and 24 h. and expression of interferon-gamma (IFNγ), interleukin (IL)-1β, IL-6, IL-10, transforming growth factor-beta (TGFβ) and cluster of differentiation (CD40) genes, as well as major histocompatibility complex (MHC)-II protein were evaluated. At 6 h post-stimulation, monobutyrin, calcium butyrate, and green tea extract treatments induced a significant downregulation of IFNγ, IL-6, or IL-1β gene transcription and MHC-II expression, while the IL-10 or TGFβ gene expression in these treatments as well as those receiving rosemary extract and tartaric acid was significantly upregulated, when compared to control, suggesting immunomodulatory properties of these ECs. Finally, pretreatment of macrophages with these selected 5 ECs for 24 h followed by C. perfringens infection showed that monobutyrin, green tea extract, rosemary extract, and calcium butyrate treatments can inhibit bacterial growth significantly at 12 and/or 24 h post-infection, when compared to the control. Collectively, our findings show that ECs possessing immunomodulatory and anti-C. perfringens properties can be selected using an in vitro avian macrophage cell-based model so that such ECs can further be tested in vivo for their disease prevention efficacy.

Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli

BACKGROUND

Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.

RESULTS

Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q < 0.2 and fold change > 2.0). In addition, pigs in antibiotic had a reduced (P < 0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P < 0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.

CONCLUSIONS

The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.

Controlling Multi-Drug-Resistant Traits of Salmonella Obtained from Retail Poultry Shops Using Metal-Organic Framework (MOF) as a Novel Technique

Salmonella spp. is considered one of the most important causes of food-borne illness globally. Poultry and its products are usually incriminated in its spread. Treatment with antibiotics is the first choice to deal with such cases; however, multi-drug resistance and biofilm formation have been recorded in animals and humans. This study aimed to detect the antibiotic profile of isolated traits from different sources and to find innovative alternatives, such as MOFs. A total of 350 samples were collected from randomly selected retailed poultry shops in Beni-Suef Province, Egypt. Their antimicrobial susceptibility against eight different antibiotics was tested, and multi-drug resistance was found in most of them. Surprisingly, promising results toward MOF were detected. Cu/Ni/Co-MOF (MOF3) showed superior antibacterial efficiency to Cu/Ni-MOF (MOF2) and Cu-MOF (MOF1) at p value ≤ 0.01. These findings highlight the tendency of Salmonella spp. to develop MDR to most of the antibiotics used in the field and the need to find new alternatives to overcome it, as well as confirming the ability of the environment to act as a source of human and animal affection.

Detection of antimicrobial resistance genes in Lactobacillus spp. from poultry probiotic products and their horizontal transfer among Escherichia coli

The study was conducted to identify the antimicrobial resistance genes (ARGs) in Lactobacillus spp. from poultry probiotic products and their potential to spread among Escherichia coli. Lactobacillus spp. were isolated and identified from 35 poultry probiotic samples based on the cultural, biochemical, and molecular findings. All the isolates (n = 35) were screened for the presence of some ARGs such as β-lactamases encoding genes (blaTEM, blaCTXM-1, and blaCTXM-2), plasmid-mediated quinolone resistance gene (qnrA, qnrB, and qnrS), and tetracycline resistance genes (tetA and tetB). Five Lactobacillus spp. isolates from three brands were positive for one or more ARGs. The qnrS was detected in four isolates. The blaTEM and tetB were detected in two isolates. One isolate contained blaCTX-M-1, blaCTX-M-2, and tetA genes. Brand-wise analysis revealed that one isolate from Brand 4 contained blaTEM, blaCTX-M-1, blaCTX-M-2, qnrS, and tetA genes, one isolate from Brand 2 contained blaTEM gene, and three isolates from Brand 7 harbored qnrS gene. The co-culture of Lactobacillus spp. and E. coli resulted in the transmission of qnrS, CTX-M-1, and tetA from Lactobacillus spp. to E. coli. Results of antimicrobial susceptibility test revealed that the highest resistance was observed to cefepime and cefotaxime followed by penicillin G, oxacillin, cefuroxime, and ofloxacin. The findings of the present study indicate the potential risk of horizontal spread of antimicrobial resistance through probiotic bacteria among the poultry population. Therefore, it is very necessary to check for ARGs along with other attributes of probiotic bacteria to avoid the inclusion of resistant strains in probiotics.

Design and Synthesis of Novel Antimicrobial Agents

The necessity for the discovery of innovative antimicrobials to treat life-threatening diseases has increased as multidrug-resistant bacteria has spread. Due to antibiotics' availability over the counter in many nations, antibiotic resistance is linked to overuse, abuse, and misuse of these drugs. The World Health Organization (WHO) recognized 12 families of bacteria that present the greatest harm to human health, where options of antibiotic therapy are extremely limited. Therefore, this paper reviews possible new ways for the development of novel classes of antibiotics for which there is no pre-existing resistance in human bacterial pathogens. By utilizing research and technology such as nanotechnology and computational methods (such as in silico and Fragment-based drug design (FBDD)), there has been an improvement in antimicrobial actions and selectivity with target sites. Moreover, there are antibiotic alternatives, such as antimicrobial peptides, essential oils, anti-Quorum sensing agents, darobactins, vitamin B6, bacteriophages, odilorhabdins, 18β-glycyrrhetinic acid, and cannabinoids. Additionally, drug repurposing (such as with ticagrelor, mitomycin C, auranofin, pentamidine, and zidovudine) and synthesis of novel antibacterial agents (including lactones, piperidinol, sugar-based bactericides, isoxazole, carbazole, pyrimidine, and pyrazole derivatives) represent novel approaches to treating infectious diseases. Nonetheless, prodrugs (e.g., siderophores) have recently shown to be an excellent platform to design a new generation of antimicrobial agents with better efficacy against multidrug-resistant bacteria. Ultimately, to combat resistant bacteria and to stop the spread of resistant illnesses, regulations and public education regarding the use of antibiotics in hospitals and the agricultural sector should be combined with research and technological advancements.

Prevalence and resistance to antibacterial agents in Salmonella enterica strains isolated from poultry products in Northern Kazakhstan

Background and Aim: Salmonella is one of the main causative agents of foodborne infections. The source of the pathogen, in most cases, is poultry products. The intensification of poultry farming and the constant and uncontrolled use of antimicrobials has led to an increase in the level of antibiotic resistance, especially in developing countries. This study aimed to determine the level of sensitivity to antimicrobial agents in Salmonella enterica strains isolated from poultry products in Northern Kazakhstan, as well as to determine the genetic mechanisms of resistance and the presence of integrons. Materials and Methods: In total, 398 samples of poultry products sold in Northern Kazakhstan were selected. Salmonella strains were isolated from product samples using microbiological methods. Salmonella was identified based on morphological, biochemical, and serological methods, as well as polymerase chain reaction (PCR). Sensitivity testing for antimicrobial agents was performed using the disk diffusion method. The detection of resistance genes was performed using PCR and gel electrophoresis. Results: Out of 398 samples of poultry products, a total of 46 Salmonella isolates were obtained. Most of the isolates belong to the serovar Salmonella Enteritidis (80.4%). The assessment of sensitivity to antibacterial agents showed that Salmonella was mainly resistant to nalidixic acid (63%), furadonin (60.9%), ofloxacin (45.6%), and tetracycline (39.1%). In 64.3% of cases, Salmonella was resistant to three or more groups of antibacterial agents. Resistance genes such as tetA, tetB, blaTEM, aadA, sul3, and catII, as well as integrons of two classes (teg1 and teg2), were identified. Conclusion: Poultry products contain antimicrobial-resistant strains of Salmonella, as well as genes encoding resistance mechanisms. The results emphasize the need for constant monitoring of not only pathogenic microorganisms but also their sensitivity to antimicrobial agents. The potential threat to human health requires a unified approach to the problem of antibiotic resistance from representatives of both public health and the agroindustrial complex. Keywords: antibiotic resistance, food safety, poultry, resistance genes, Salmonella.

Health horizons: Future trends and technologies from the European Medicines Agency's horizon scanning collaborations

In medicines development, the progress in science and technology is accelerating. Awareness of these developments and their associated challenges and opportunities is essential for medicines regulators and others to translate them into benefits for society. In this context, the European Medicines Agency uses horizon scanning to shine a light on early signals of relevant innovation and technological trends with impact on medicinal products. This article provides the results of systematic horizon scanning exercises conducted by the Agency, in collaboration with the World Health Organization (WHO) and the European Commission's Joint Research Centre's (DG JRC). These collaborative exercises aim to inform policy-makers of new trends and increase preparedness in responding to them. A subset of 25 technological trends, divided into three clusters were selected and reviewed from the perspective of medicines regulators. For each of these trends, the expected impact and challenges for their adoption are discussed, along with recommendations for developers, regulators and policy makers.

High prevalence of antimicrobial resistance and multidrug resistance among bacterial isolates from diseased pets: Retrospective laboratory data (2015-2017)

Laboratory surveillance and the monitoring of antimicrobial resistance (AMR) trends and patterns among local isolates have been highly effective in providing comprehensive information for public health decision-making. A total of 396 cases along with 449 specimens were received for antibiotic susceptibility testing at a public university veterinary diagnostic laboratory in Malaysia between 2015 and 2017. Escherichia coli was the most frequently isolated (n = 101, 13%) bacteria, followed by Staphylococcus pseudintermedius (n = 97, 12%) and Streptococcus canis (n = 62, 8%). In cats, S. pseudintermedius isolates were highly resistant to azithromycin (90%), while the E. coli isolates were highly resistant to doxycycline (90%), tetracycline (81%), and cephalexin (75%). About 55% of S. pseudintermedius and 82% of E. coli were multi-drug resistant (MDR). In dogs, S. intermedius isolates were highly resistant to aminoglycosides neomycin (90.9%) and gentamicin (84.6%), and tetracycline (75%). Whereas the E. coli isolates were highly resistant to cephalexin (82.1%) and amoxicillin/clavulanic acid (76.5%). MDR was observed in 60% of S. intermedius and 72% of E. coli from dogs. Generally, the bacterial isolates from cats demonstrated higher levels of resistance to multiple antibiotics compared to those from dogs.

Formulating Diets for Improved Health Status of Pigs: Current Knowledge and Perspectives

Our understanding of nutrition has been evolving to support both performance and immune status of pigs, particularly in disease-challenged animals which experience repartitioning of nutrients from growth towards the immune response. In this sense, it is critical to understand how stress may impact nutrient metabolism and the effects of nutritional interventions able to modulate organ (e.g., gastrointestinal tract) functionality and health. This will be pivotal in the development of effective diet formulation strategies in the context of improved animal performance and health. Therefore, this review will address qualitative and quantitative effects of immune system stimulation on voluntary feed intake and growth performance measurements in pigs. Due to the known repartitioning of nutrients, the effects of stimulating the immune system on nutrient requirements, stratified according to different challenge models, will be explored. Finally, different nutritional strategies (i.e., low protein, amino acid-supplemented diets; functional amino acid supplementation; dietary fiber level and source; diet complexity; organic acids; plant secondary metabolites) will be presented and discussed in the context of their possible role in enhancing the immune response and animal performance.

High-Throughput Identification of Epigenetic Compounds to Enhance Chicken Host Defense Peptide Gene Expression

Enhancing the synthesis of endogenous host defense peptides (HDPs) has emerged as a novel antibiotic-free approach to infectious disease control and prevention. A number of epigenetic compounds have been identified as HDP inducers and several have proved beneficial in antimicrobial therapy. However, species-specific regulation of HDP synthesis is evident. In attempt to identify epigenetic compounds with potent HDP-inducing activity for poultry-specific application, we developed a stable luciferase reporter cell line, known as HTC/AvBD10-luc, following our earlier construction of HTC/AvBD9-luc. HTC/AvBD10-luc was developed through permanent integration of a chicken macrophage cell line, HTC, with a lentiviral luciferase reporter vector driven by a 4-Kb AvBD10 gene promoter. Using a high throughput screening assay based on the two stable cell lines, we identified 33 hits, mostly being histone deacetylase (HDAC) inhibitors, from a library of 148 epigenetic compounds. Among them, entinostat and its structural analog, tucidinostat, were particularly effective in promoting multiple HDP gene expression in chicken macrophages and jejunal explants. Desirably, neither compounds triggered an inflammatory response. Moreover, oral gavage of entinostat significantly enhanced HDP gene expression in the chicken intestinal tract. Collectively, the high throughput assay proves to be effective in identifying HDP inducers, and both entinostat and tucidinostat could be potentially useful as alternatives to antibiotics to enhance intestinal immunity and disease resistance.

Ionizing Radiation Technologies for Vaccine Development - A Mini Review

Given the current pandemic the world is struggling with, there is an urgent need to continually improve vaccine technologies. Ionizing radiation technology has a long history in the development of vaccines, dating back to the mid-20th century. Ionizing radiation technology is a highly versatile technology that has a variety of commercial applications around the world. This brief review summarizes the core technology, the overall effects of ionizing radiation on bacterial cells and reviews vaccine development efforts using ionizing technologies, namely gamma radiation, electron beam, and X-rays.

Essential oils and their nanoemulsions as green alternatives to antibiotics in poultry nutrition: a comprehensive review

Increasing market pressure to reduce the use of antibiotics and the Veterinary Feed Directive of 2019 have led to expanded research on alternate antibiotic solutions. This review aimed to assess the benefits of using essential oils (EOs) and their nanoemulsions (NEs) as feed supplements for poultry and their potential use as antibiotic alternatives in organic poultry production. Antibiotics are commonly used to enhance the growth and prevent diseases in poultry animals due to their antimicrobial activities. EOs are a complex mixture of volatile compounds derived from plants and manufactured via various fermentation, extraction, and steam distillation methods. EOs are categorized into 2 groups of compounds: terpenes and phenylpropenes. Differences among various EOs depend on the source plant type, physical and chemical soil conditions, harvest time, plant maturity, drying technology used, storage conditions, and extraction time. EOs can be used for therapeutic purposes in various situations in broiler production as they possess antibacterial, antifungal, antiparasitic, and antiviral activities. Several studies have been conducted using various combinations of EOs or crude extracts of their bioactive compounds to investigate their complexity and applications in organic poultry production. NEs are carrier systems that can be used to overcome the volatile nature of EOs, which is a major factor limiting their application. NEs are being progressively used to improve the bioavailability of the volatile lipophilic components of EOs. This review discusses the use of these nonantibiotic alternatives as antibiotics for poultry feed in organic poultry production.

Evaluation of Activated Charcoal as an Alternative to Antimicrobials for the Treatment of Neonatal Calf Diarrhea

PURPOSE

Neonatal calf diarrhea (NCD) is a major cause of death and economic loss in the cattle industry. Although NCD is caused by a variety of nutritional factors and non-bacterial pathogens, treatment typically includes systemic antimicrobial therapy, even for non-severe cases that are more likely to have non-bacterial causes. Novel, non-antimicrobial therapies are needed to reduce antimicrobial use and optimize production efficiency.

METHODS

This production-level study compared the efficacy of activated charcoal to that of an antimicrobial regimen for treating mild-to-moderate cases of NCD, and identified the most common etiological agents. Calves diagnosed with non-severe diarrhea were randomly allocated into 3 treatment groups (n = 86 per group): group A received a standard antimicrobial regimen, B received both antimicrobials and activated charcoal, and C received activated charcoal only. Animals were monitored over the course of 7 days for mortality and recovery from diarrhea. Fecal samples were collected upon enrollment (day 0) and on day 7 to assess the presence of major NCD-causing pathogens.

RESULTS

Mortality was higher for groups B and C relative to A, although this difference was only statistically significant for group B vs A. No significant difference in the number of recovered animals was observed among the treatment groups, although group C was significantly slower to recover than A or B. The vast majority of day 0 samples were positive for non-bacterial organisms (mainly rotavirus and Cryptosporidium parvum), which decreased significantly by day 7 regardless of treatment group.

CONCLUSION

Antimicrobials only moderately improved outcomes for non-severe diarrhea cases relative to activated charcoal. Thus, systemic antimicrobial treatment is likely unnecessary for the majority of NCD cases and should be limited to severe cases.

Probiotics as Therapeutic Tools against Pathogenic Biofilms: Have We Found the Perfect Weapon?

Bacterial populations inhabiting a variety of natural and human-associated niches have the ability to grow in the form of biofilms. A large part of pathological chronic conditions, and essentially all the bacterial infections associated with implanted medical devices or prosthetics, are caused by microorganisms embedded in a matrix made of polysaccharides, proteins, and nucleic acids. Biofilm infections are generally characterized by a slow onset, mild symptoms, tendency to chronicity, and refractory response to antibiotic therapy. Even though the molecular mechanisms responsible for resistance to antimicrobial agents and host defenses have been deeply clarified, effective means to fight biofilms are still required. Lactic acid bacteria (LAB), used as probiotics, are emerging as powerful weapons to prevent adhesion, biofilm formation, and control overgrowth of pathogens. Hence, using probiotics or their metabolites to quench and interrupt bacterial communication and aggregation, and to interfere with biofilm formation and stability, might represent a new frontier in clinical microbiology and a valid alternative to antibiotic therapies. This review summarizes the current knowledge on the experimental and therapeutic applications of LAB to interfere with biofilm formation or disrupt the stability of pathogenic biofilms.

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.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.

Antimicrobial peptides used as growth promoters in livestock production

Antibiotic growth promoters (AGPs) have been administered in livestock for decades to improve food digestion in growing animals, while also contributing to the control of microbial pathogens. The long-term and indiscrimate use of AGPs has generated genetic modifications in bacteria, leading to antimicrobial resistance (AMR), which can be disseminated to commensal and pathogenic bacteria. Thus, antimicrobial peptides (AMPs) are used to replaced AGPs. AMPs are found in all domains of life, and their cationic characteristics can establish electrostatic interactions with the bacterial membrane. These molecules used as growth promoters can present benefits for nutrient digestibility, intestinal microbiota, intestinal morphology, and immune function activities. Therefore, this review focuses on the application of AMPs with growth promoting potential in livestock, as an alternative to conventional antibiotic growth promoters, in an attempt to control AMR. KEY POINTS: • The long-term and indiscriminate use of AGPs in animal food can cause AMR. • AMPs can be used as substitute of antibiotics in animal food suplementation. • Animal food suplementated with AMPs can provied economic efficiency and sustainable livestock production.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Friend or Foe? Impacts of Dietary Xylans, Xylooligosaccharides, and Xylanases on Intestinal Health and Growth Performance of Monogastric Animals

This paper discusses the structural difference and role of xylan, procedures involved in the production of xylooligosaccharides (XOS), and their implementation into animal feeds. Xylan is non-starch polysaccharides that share a β-(1-4)-linked xylopyranose backbone as a common feature. Due to the myriad of residues that can be substituted on the polymers within the xylan family, more anti-nutritional factors are associated with certain types of xylan than others. XOS are sugar oligomers extracted from xylan-containing lignocellulosic materials, such as crop residues, wood, and herbaceous biomass, that possess prebiotic effects. XOS can also be produced in the intestine of monogastric animals to some extent when exogenous enzymes, such as xylanase, are added to the feed. Xylanase supplementation is a common practice within both swine and poultry production to reduce intestinal viscosity and improve digestive utilization of nutrients. The efficacy of xylanase supplementation varies widely due a number of factors, one of which being the presence of xylanase inhibitors present in common feedstuffs. The use of prebiotics in animal feeding is gaining popularity as producers look to accelerate growth rate, enhance intestinal health, and improve other production parameters in an attempt to provide a safe and sustainable food product. Available research on the impact of xylan, XOS, as well as xylanase on the growth and health of swine and poultry, is also summarized. The response to xylanase supplementation in swine and poultry feeds is highly variable and whether the benefits are a result of nutrient release from NSP, reduction in digesta viscosity, production of short chain xylooligosaccharides or a combination of these is still in question. XOS supplementation seems to benefit both swine and poultry at various stages of production, as well as varying levels of XOS purity and degree of polymerization; however, further research is needed to elucidate the ideal dosage, purity, and degree of polymerization needed to confer benefits on intestinal health and performance in each respective species.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

Antibiotic resistance in Salmonella spp. isolated from poultry: A global overview

Salmonella enterica is the most important foodborne pathogen, and it is often associated with the contamination of poultry products. Annually, Salmonella causes around 93 million cases of gastroenteritis and 155,000 deaths worldwide. Antimicrobial therapy is the first choice of treatment for this bacterial infection; however, antimicrobial resistance has become a problem due to the misuse of antibiotics both in human medicine and animal production. It has been predicted that by 2050, antibiotic-resistant pathogens will cause around 10 million deaths worldwide, and the WHO has suggested the need to usher in the post-antibiotic era. The purpose of this review is to discuss and update the status of Salmonella antibiotic resistance, in particular, its prevalence, serotypes, and antibiotic resistance patterns in response to critical antimicrobials used in human medicine and the poultry industry. Based on our review, the median prevalence values of Salmonella in broiler chickens, raw chicken meat, and in eggs and egg-laying hens were 40.5% ( interquartile range [IQR] 11.5-58.2%), 30% (IQR 20-43.5%), and 40% (IQR 14.2-51.5%), respectively. The most common serotype was Salmonella Enteritidis, followed by Salmonella Typhimurium. The highest antibiotic resistance levels within the poultry production chain were found for nalidixic acid and ampicillin. These findings highlight the need for government entities, poultry researchers, and producers to find ways to reduce the impact of antibiotic use in poultry, focusing especially on active surveillance and finding alternatives to antibiotics.

Antibiotic Activity of a Paraphaeosphaeria sporulosa-Produced Diketopiperazine against Salmonella enterica

A diketopiperazine has been purified from a culture filtrate of the endophytic fungus Paraphaeosphaeria sporulosa, isolated from healthy tissues of strawberry plants in a survey of microbes as sources of anti-bacterial metabolites. Its structure has been determined by nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS) analyses and was found to be identical to cyclo(L-Pro-L-Phe) purified from species of other fungal genera. This secondary metabolite has been selected following bioguided-assay fractionation against two strains of Salmonella enterica, the causal agent of bovine gastroenteritis. The diketopiperazine cyclo(L-Pro-L-Phe), isolated for the first time from Paraphaeosphaeria species, showed minimum inhibitory concentration (MIC) values of 71.3 and 78.6 μg/mL against the two S. enterica strains. This finding may be significant in limiting the use of synthetic antibiotics in animal husbandry and reducing the emergence of bacterial multidrug resistance. Further in vivo experiments of P. sporulosa diketopiperazines are important for the future application of these metabolites.

From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture

To reduce the use of antibiotics in animal agriculture, a number of effective or commercially viable alternatives have been implemented by food animal producers or are under development. Perhaps the most well-established strategies are flock and herd management practices to mitigate disease introduction and spread, and, subsequently, reduce the need for antibiotic use. While vaccines in food animal production have been used to prevent both bacterial and viral diseases, but historically, most vaccines have targeted viral diseases. Though vaccines against viral diseases can help reduce the need for antibiotic use by controlling the spread of secondary bacterial infections, more recent vaccines under development specifically target bacteria. New developments in selecting and potentially tailoring bacteriophages provide a promising avenue for controlling pathogenic bacteria without the need for traditional small-molecule antibiotics. In this article we discuss these established and emerging strategies, which are anticipated to reduce the reliance on antibiotics in food animal production and should reduce the prevalence and transmission to humans of antimicrobial resistant bacteria from these systems.

Antibiotics utilization and farmers' knowledge of its effects on soil ecosystem in the coastal drylands of Ghana

Background

There is paucity of information on antibiotics utilization amongst farmers, factors associated with administration of antibiotics and farmers’ knowledge of the effects of antibiotics on the soil ecosystem in Ghana.

Methods

A cross sectional quantitative survey across three coastal regions of Ghana was undertaken amongst poultry and livestock farmers. Six hundred respondents were selected from five districts each across the three regions. Pretested and structured questionnaire were used to collect data through face to face interview. Data were summarized using descriptive statistics and regression analysis. Factors associated with antibiotic administration were determined using binary multiple logistic regression at p ≤ 0.05.

Results

Out of the 600 farmers, 95% administered antibiotics and 84% bought antibiotics over-the-counter without prescription. Approximately 9% of antibiotic administration was carried out by veterinary officers, and the remaining, 91% based on farmer’s experience. Approximately 93% had access to antibiotics without any difficulty. Withdrawal period was always observed by only 16% of farmers. Majority (74%) of farmers never had education on antibiotics and none of the farmers screened manure for the antibiotic residuals. Years of farming, income status, level of education of farmers, type of animal kept, access to extension services, registration with farmers’ association, employing veterinary services, location of farm, system of production, education on antibiotics and access to antibiotics positively and significantly predicted the administration of antibiotics by farmers. Majority of farmers had inadequate knowledge of the effects of antibiotics on soil ecosystem with mean score ranging between 2.87±0.60 and 2.98 ± 0.7 on a scale of 5.0.

Conclusion

The study exposed the poor practices regarding antibiotic use and also inadequate knowledge on its effect on the soil ecosystem amongst farmers in Ghana. This calls for development of strategies to increase awareness on antibiotics because its misuse can negatively impact human, animals, environment and impact food security.