A Review of Antimicrobial Resistance in Poultry Farming within Low-Resource Settings

The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.

A Review of the Varied Uses of Macroalgae as Dietary Supplements in Selected Poultry with Special Reference to Laying Hen and Broiler Chickens

Seaweeds comprise ca. 12,000 species. Global annual harvest is ca. 30.13 million metric tonnes, (valued ca. $11.7 billion USD in 2016) for various commercial applications. The growing scope of seaweed-based applications in food, agricultural fertilizers, animal feed additives, pharmaceuticals, cosmetics and personal care is expected to boost market demand. Agriculture and animal feed applications held the second largest seaweed market share in 2017, and the combined market is anticipated to reach much higher values by 2024 due to the impacts of current research and development targeting enhanced animal health and productivity. In general, seaweeds have been utilized in animal feed as a rich source of carbohydrates, protein, minerals, vitamins and dietary fibers with relatively well-balanced amino acid profiles and a unique blend of bioactive compounds. Worldwide, the animal nutrition market is largely driven by rising demand for poultry feeds, which represents ca. 47% of the total consumption for all animal nutrition. This review provides an overview of the utilization of specific seaweeds as sustainable feed sources for poultry production, including a detailed survey of seaweed-supplemented diets on growth, performance, gastrointestinal flora, disease, immunity and overall health of laying/broiler hens. Anti-microbial effects of seaweeds are also discussed.

Antimicrobial Effects of Selected, Cultivated Red Seaweeds and Their Components in Combination with Tetracycline, against Poultry Pathogen Salmonella Enteritidis

Poultry and its products are an economical source of high-quality protein for human consumption. In animal agriculture, antibiotics are used as therapeutic agents to treat disease in livestock, or as prophylactics to prevent disease and in so doing enhance production. However, the extensive use of antibiotics in livestock husbandry has come at the cost of increasingly drug-resistant bacterial pathogens. This highlights an urgent need to find effective alternatives to be used to treat infections, particularly in poultry and especially caused by drug-resistant Salmonella strains. In this study, we describe the combined effect of extracts of the red seaweeds Chondrus crispus (CC) and Sarcodiotheca gaudichaudii (SG) and compounds isolated from these in combinations with industry standard antibiotics (i.e., tetracycline and streptomycin) against Salmonella Enteritidis. Streptomycin exhibited the higher antimicrobial activity against S. Enteritidis, as compared to tetracycline with a MIC25 and MIC50 of 1.00 and 1.63 μg/mL, respectively. The addition of a water extract of CC at a concentration of 200 µg/mL in addition to tetracycline significantly enhanced the antibacterial activity (log CFU/mL 4.7 and 4.5 at MIC25 and MIC50, respectively). SG water extract, at 400 and 800 µg/mL (p = 0.05, n = 9), also in combination with tetracycline, showed complete inhibition of bacterial growth. Combinations of floridoside (a purified red seaweed component) and tetracycline (MIC25 and MIC50) in vitro revealed that only the lower concentration (i.e., 15 μg/mL) of floridoside potentiated the activity of tetracycline. Sub-lethal concentrations of tetracycline (MIC50 and MIC25), in combination with floridoside, exhibited antimicrobial activities that were comparable to full-strength tetracycline (23 μg/mL). Furthermore, the relative transcript levels of efflux-related genes of S. Enteritidis, namely marA, arcB and ramA, were significantly repressed by the combined treatment of floridoside and tetracycline, as compared to control MIC treatments (MIC25 and MIC50). Taken together, these findings demonstrated that the red seaweeds CC and SG and their selected, purified components can be used to increase the lifetime of existing, patented antibiotics and can also help to reduce costly (economic and environmental) therapeutic and prophylactic use of antibiotics in poultry. To our knowledge, this is the first report of antibiotic potentiation of existing industry standard antibiotics using red seaweeds and their selected extracts against S. Enteritidis.

Antimicrobials Used in Backyard and Commercial Poultry and Swine Farms in the Philippines: A Qualitative Pilot Study

Chicken and pork are the most frequently consumed meat products in the Philippines. Swine and poultry are reared in either commercial farms (CMf) or backyard farms (BYf); the latter production system is relatively common and essential to food security in low- and middle-income countries (LMICs) such as the Philippines. Similar to resource-limited LMICs, antimicrobial use (AMU) surveillance has not yet been established; thus, AMU in food animals is a knowledge gap in understanding the emergence of antimicrobial resistance (AMR) in zoonotic foodborne bacteria in the country. This qualitative AMU pilot study aims to describe the antimicrobial active ingredients (AAIs) used and associated AMU practices (e.g., source of AAIs and informed AMU decisions) by poultry and swine CMf and BYf in the Philippines. Ninety-three farms across four regions in the Philippines voluntarily provided AMU information as part of a larger biosecurity and good practices study. The percentage of farms using AAI over the total number of farms was the metric used to describe AMU. In total, there were 30 AAIs used (CMf: n =27 and BYf: n = 13); per farm, the number of AAIs used ranged from 1 to 7. The spectrum of AAIs was more diverse in swine (n = 24) compared to poultry (n = 18). Enrofloxacin was the most frequently reported AAI in poultry (33%) and swine (36%) farms. Respiratory diseases were the most frequently reported reason for AMU in both species. Between production systems, significant differences were observed in the percentage of farms using amoxicillin (27% CMf vs. 3% BYf), colistin (17% CMf vs. 3% BYf), and oxytetracycline (12% CMf vs. 39% BYf). In terms of AMU practices, of important concern was the over-the-counter access of AAIs at retail outlets and the limited veterinary oversight in BYf. Our data indicated that antimicrobials critically important for human medicine are frequently used in poultry and swine farms in the Philippines. This study can inform the development of guidelines for curbing AMR through prudent AMU and serves as a reference point for AMU surveillance capacity development in the Philippines.

Overall assessment of antimicrobial peptides in piglets: a set of meta-analyses

Developing alternatives to antibiotics is an urgent need in livestock production. Antimicrobial peptides (AMPs) are regarded as powerful antibiotic substitutes (ASs) because AMPs have broad-spectrum antimicrobial activities and growth-promoting ability. Here, we aimed to comprehensively assess the effects of AMPs on the growth performance, diarrhea rate, intestinal morphology and immunity of healthy or challenged piglets, compared with an antibiotics group or negative control group. We performed a set of meta-analyses of feeding trials from database inception to 27 May 2019. Among the 1379 identified studies, 20 were included in our meta-analyses (56 arms and 4067 piglets). The meta-analyses revealed that (1) compared with the negative control group, AMPs significantly improved the healthy piglets' average daily gain (ADG), average daily feed intake (ADFI), gain : feed ratio (G/F), levels of immune globulin (Ig) IgM and IgG, and intestinal villus height : crypt depth ratio (V/C) (P < 0.05). Meanwhile, AMPs significantly increased the challenged piglets' ADG, ADFI, G/F and V/C of the jejunum and ileum, and notably deceased the diarrhea rate (P < 0.05); (2) compared with antibiotics group, the effects of AMPs were slightly weaker than those of antibiotics in the healthy piglets, but AMPs have similar effects to those of antibiotics in challenged piglets. In a higher purity, the optimal dose of AMPs may be approximately 0.01%. Our findings indicate that AMPs can improve piglet growth performance, enhance immunity, benefit intestinal morphology and decrease the diarrheal rate. AMPs could be great ASs especially under infection conditions.

National action to combat AMR: a One-Health approach to assess policy priorities in action plans

Little is known about the overall trend and prioritisations of past and current antimicrobial resistance (AMR) policies. Here we introduce a quantitative method to analyse AMR policies. The AMR-Policy Analysis Coding Toolkit (AMR-PACT) uses several categorical variables. Thirteen AMR action plans from five countries (China, Japan, Norway, the UK and the USA) were used to develop the tool and identify possible values for each variable. The scope and capability of AMR-PACT is demonstrated through the 2015 WHO's Global Action Plan and 2017 Hong Kong AMR Action Plan (HKAP). Majority of policies were aimed at either human or animal sector with less attention given to the environment, plant or food sector. Both plans shared the same two strategic focus areas, namely the conservation of antibiotics and the improved surveillance of resistance. There were no policies dedicated to improving access to antibiotics in the HKAP. These empirical results provide useful insights into the priorities and gaps of AMR policies. The method proposed here can help understand countries' priorities regarding AMR, support the creation of AMR policy database and foster innovative policymaking.

Drivers of Antibiotic Resistance Transmissionin Low- and Middle-Income Countriesfrom a "One Health" Perspective-A Review

Antibiotic resistance is an ecosystem problem threatening the interrelated human-animalenvironmenthealth under the "One Health" framework. Resistant bacteria arising in onegeographical area can spread via cross-reservoir transmission to other areas worldwide either bydirect exposure or through the food chain and the environment. Drivers of antibiotic resistance arecomplex and multi-sectoral particularly in Lower- and Middle-income countries. These includeinappropriate socio-ecological behaviors; poverty; overcrowding; lack of surveillance systems; foodsupply chain safety issues; highly contaminated waste effluents; and loose rules and regulations. Inorder to examine the drivers of antibiotic resistance from a "one health" perspective, a literaturereview was conducted on three databases including PubMed, Medline and Google Scholar. A totalof 485 studies of potential relevance were selected, out of which 182 were included in this review.Results have shown that the aforementioned market failures are the leading cause for the negativeexternality of antibiotic resistance that extends in scope from the individual to the global ecosystem.Incremental and sustainable global actions can make the change, however, the problem willcontinue to prevail if governments do not prioritize the "One health" approach and if individual'saccountability is still denied in a world struggling with profound socio-economic problems.

The War against Tuberculosis: A Review of Natural Compounds and Their Derivatives

Tuberculosis (TB), caused by the bacterial organism Mycobacterium tuberculosis, pose a major threat to public health, especially in middle and low-income countries. Worldwide in 2018, approximately 10 million new cases of TB were reported to the World Health Organization (WHO). There are a limited number of medications available to treat TB; additionally, multi-drug resistant TB and extensively-drug resistant TB strains are becoming more prevalent. As a result of various factors, such as increased costs of developing new medications and adverse side effects from current medications, researchers continue to evaluate natural compounds for additional treatment options. These substances have the potential to target bacterial cell structures and may contribute to successful treatment. For example, a study reported that green and black tea, which contains epigallocatechin gallate (a phenolic antioxidant), may decrease the risk of contracting TB in experimental subjects; cumin (a seed from the parsley plant) has been demonstrated to improve the bioavailability of rifampicin, an important anti-TB medication, and propolis (a natural substance produced by honeybees) has been shown to improve the binding affinity of anti-TB medications to bacterial cell structures. In this article, we review the opportunistic pathogen M. tuberculosis, various potential therapeutic targets, available therapies, and natural compounds that may have anti-TB properties. In conclusion, different natural compounds alone as well as in combination with already approved medication regimens should continue to be investigated as treatment options for TB.

The application of machine learning techniques to innovative antibacterial discovery and development

INTRODUCTION

After the initial wave of antibiotic discovery, few novel classes of antibiotics have emerged, with the latest dating back to the 1980's. Furthermore, the pace of antibiotic drug discovery is unable to keep up with the increasing prevalence of antibiotic drug resistance. However, the increasing amount of available data promotes the use of machine learning techniques (MLT) in drug discovery projects (e.g. construction of regression/classification models and ranking/virtual screening of compounds).

AREAS COVERED

In this review, the authors cover some of the applications of MLT in medicinal chemistry, focusing on the development of new antibiotics, the prediction of resistance and its mechanisms. The aim of this review is to illustrate the main advantages and disadvantages and the major trends from studies over the past 5 years.

EXPERT OPINION

The application of MLT to antibacterial drug discovery can aid the selection of new and potent lead compounds, with desirable pharmacokinetic and toxic profiles for further optimization. The increasing volume of available data along with the constant improvement in computational power and algorithms has meant that we are experiencing a transition in the way we face modern issues such as drug resistance, where our decisions are data-driven and experiments can be focused by data-suggested hypotheses.

Growing Trend of Fighting Infections in Aquaculture Environment-Opportunities and Challenges of Phage Therapy

Phage therapy, a promising alternative to antimicrobial treatment of bacterial diseases, is getting more and more popular, especially due to the rising awareness of antibiotic resistance and restrictions in antibiotics' use. During recent years, we observed a growing trend of bacteriophages' application in aquaculture, which in each year reports high losses due to bacterial diseases. This review provides an update of the status of bacteriophage therapy for the treatment and prevention of infections in the aquatic environment. As it is still mostly in the scientific stage, there are a few constraints that may prevent effective therapy. Therefore, specific characteristics of bacteriophages, that can act in favor or against their successful use in treatment, were described. We underlined aspects that need to be considered: specificity of phages, bacterial resistance, safety, immune response of the host organism, formulation, administration and stability of phage preparations as well as bacteriophages' influence on the environment. The biggest challenge to overcome is finding the right balance between the desired and problematic characteristics of bacteriophages. Finally, regulatory approval challenges may be encountered by bacteriophage manufacturers. Even though there are still some technical constraints connected with the global use of bacteriophage therapy, it was concluded that it can be successfully applied in aquaculture.

Isolation and characterization of bacteriophages against virulent Aeromonas hydrophila

Background

Aeromonas hydrophila is an important water-borne pathogen that leads to a great economic loss in aquaculture. Along with the abuse of antibiotics, drug-resistant strains rise rapidly. In addition, the biofilms formed by this bacterium limited the antibacterial effect of antibiotics. Bacteriophages have been attracting increasing attention as a potential alternative to antibiotics against bacterial infections.

Results

Five phages against pathogenic A. hydrophila, named N21, W3, G65, Y71 and Y81, were isolated. Morphological analysis by transmission electron microscopy revealed that phages N21, W3 and G65 belong to the family Myoviridae, while Y71 and Y81 belong to the Podoviridae. These phages were found to have broad host spectra, short latent periods and normal burst sizes. They were sensitive to high temperature but had a wide adaptability to the pH. In addition, the phages G65 and Y81 showed considerable bacterial killing effect and potential in preventing formation of A. hydrophila biofilm; and the phages G65, W3 and N21 were able to scavenge mature biofilm effectively. Phage treatments applied to the pathogenic A. hydrophila in mice model resulted in a significantly decreased bacterial loads in tissues.

Conclusions

Five A. hydrophila phages were isolated with broad host ranges, low latent periods, and wide pH and thermal tolerance. And the phages exhibited varying abilities in controlling A. hydrophila infection. This work presents promising data supporting the future use of phage therapy.

Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission

Antimicrobial resistance (AMR) is a growing public health challenge that is expected to disproportionately burden lower- and middle-income countries (LMICs) in the coming decades. Although the contributions of human and veterinary antibiotic misuse to this crisis are well-recognized, environmental transmission (via water, soil or food contaminated with human and animal faeces) has been given less attention as a global driver of AMR, especially in urban informal settlements in LMICs-commonly known as 'shanty towns' or 'slums'. These settlements may be unique hotspots for environmental AMR transmission given: (1) the high density of humans, livestock and vermin living in close proximity; (2) frequent antibiotic misuse; and (3) insufficient drinking water, drainage and sanitation infrastructure. Here, we highlight the need for strategies to disrupt environmental AMR transmission in urban informal settlements. We propose that water and waste infrastructure improvements tailored to these settings should be evaluated for their effectiveness in limiting environmental AMR dissemination, lowering the community-level burden of antimicrobial-resistant infections and preventing antibiotic misuse. We also suggest that additional research is directed towards developing economic and legal incentives for evaluating and implementing water and waste infrastructure in these settings. Given that almost 90% of urban population growth will occur in regions predicted to be most burdened by the AMR crisis, there is an urgent need to build effective, evidence-based policies that could influence massive investments in the built urban environment in LMICs over the next few decades.

Raising awareness of antimicrobial resistance in rural aquaculture practice in Bangladesh through digital communications: a pilot study

One of the key strategic objectives of the World Health Organisation’s global antimicrobial resistance (AMR) action plan is to improve public awareness and understanding of this issue. Very few AMR awareness campaigns have targeted the animal production sector, particularly in low- and middle-income countries (LMICs) where rural communities can be geographically difficult to access via traditional face-to-face community engagement methods. Aquaculture is a major food production industry in Bangladesh and across Asia, an area which poses a significant risk to global AMR dissemination. In this pilot study, we sought to investigate the potential for digital communication materials to rapidly and effectively communicate AMR messages to rural aquaculture farmers in Bangladesh. Working with stakeholders from the Bangladesh aquaculture industry, we developed a 4-minute digital animation designed specifically for this audience and assessed its capacity to engage and communicate AMR messages to farmers. We then conducted a small-scale social media campaign, to determine the potential for rapidly disseminating AMR awareness materials to a large audience across Bangladesh, where there is an extensive 4 G internet network and an ever-increasing proportion of the population (57% as of December 2019) have mobile internet access. Thirty-six farmers were surveyed: all of them liked this method of communication and 97% said it would change the way they use antibiotics in the future. Through the social media campaign, the animation received 9,100 views in the first 2 weeks alone. Although preliminary, these results demonstrate the huge potential for digital communication methods for the rapid and widespread communication of AMR awareness materials to rural aquaculture communities in Bangladesh and across Asia. Our results support the need for more research into the most appropriate and effective content of AMR awareness campaigns for aquaculture communities and question the need for explaining the science underlying AMR in such communication materials.

Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes

Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.

Aquaculture at the crossroads of global warming and antimicrobial resistance

In many developing countries, aquaculture is key to ensuring food security for millions of people. It is thus important to measure the full implications of environmental changes on the sustainability of aquaculture. We conduct a double meta-analysis (460 articles) to explore how global warming and antimicrobial resistance (AMR) impact aquaculture. We calculate a Multi-Antibiotic Resistance index (MAR) of aquaculture-related bacteria (11,274 isolates) for 40 countries, of which mostly low- and middle-income countries present high AMR levels. Here we show that aquaculture MAR indices correlate with MAR indices from human clinical bacteria, temperature and countries’ climate vulnerability. We also find that infected aquatic animals present higher mortalities at warmer temperatures. Countries most vulnerable to climate change will probably face the highest AMR risks, impacting human health beyond the aquaculture sector, highlighting the need for urgent action. Sustainable solutions to minimise antibiotic use and increase system resilience are therefore needed.

Global environmental changes threaten many food-producing sectors, including aquaculture. Here the authors show that countries most vulnerable to climate change will probably face the highest antimicrobial resistance in aquaculture-related bacteria, and that infected aquatic animals have higher mortality at warmer temperatures.

Retrospective suspect screening reveals previously ignored antibiotics, antifungal compounds, and metabolites in Bangladesh surface waters

Densely populated countries in Asia, such as Bangladesh, are considered to be major contributors to the increased occurrence of global antimicrobial resistance (AMR). Several factors make low-and middle-income countries vulnerable to increased emergence and spread of AMR in the environment including limited regulations on antimicrobial drug use, high volume of antimicrobials used in human medicine and agricultural production, and poor wastewater management. Previous monitoring campaigns to investigate the presence of antibiotics in the aquatic environment have employed targeted analysis in which selected antibiotics are measured using liquid chromatography with tandem mass spectrometry (LC/MS/MS). However, this approach can miss several important contaminants that can contribute to the selective pressure that promotes maintenance and dissemination of antibiotic resistance genes (ARGs) in the environment. Nontarget analysis by suspect screening and reanalysis of stored digital data of previously ran samples can provide information on analytes that were formerly uncharacterized and may be chemicals of emerging concern (CECs). In this study, surface waters in both urban and rural sites in Bangladesh were collected and analyzed for the presence of antibiotic residues and other pharmaceuticals. Utilizing targeted analysis, the antibiotics with the highest concentrations detected were ciprofloxacin (1407 ng/L) and clarithromycin (909 ng/L). In addition, using high-resolution LC/MS/MS in the first ever application of retrospective analysis in samples from Bangladesh, additional antibiotics clindamycin, lincomycin, linezolid, metronidazole, moxifloxacin, nalidixic acid, and sulfapyridine were detected. Prevalence of amoxicillin transformation products in surface waters was also confirmed. In addition, medicinal and agricultural antifungal compounds were frequently found in Bangladeshi surface waters. This later finding - the near ubiquity of antifungal agents in environmental samples - is of particular concern, as it may be contributing to the alarming rise of multi-drug resistant fungal (e.g. Candida auris) disease recently seen in humans throughout the world.

Integrating evolution into medical education for women's health care practitioners

Evolution is a fundamental principle in biology; however, it has been neglected in medical education. We argue that an evolutionary perspective is especially important for women's health care providers, as selection will act strongly on reproductive parameters, and the biological costs of female reproduction are generally more resource expensive than for men (e.g. due to gestation and lactation) with greater effects on health and wellbeing. An evolutionary perspective is needed to understand antibiotic resistance, disease and health risks associated with mismatches between our evolved adaptations and current conditions, the importance of the microbiome and the maternal role in how infants acquire and develop their early-life microbiome (vaginal birth, lactation), and the importance of breastmilk as a biochemical signal from mothers to their babies. We present data that obstetrician-gynecologists' views regarding the inclusion of evolution within their training is generally positive, but many barriers are perceived. Requiring coursework in evolutionary biology with an emphasis on evolutionary medicine prior to enrollment in medical school may be a solution.

Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea

The spread of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) has posed a critical health risk to both humans and animals, because resistance to beta-lactam antibiotics makes treatment for commonly infectious diseases more complicated. In this study, we report the prevalence and genetic characteristics of ESBL-ECs isolated from retail meat samples in Korea. A total of 1205 E. coli strains were isolated from 3234 raw meat samples, purchased from nationwide retail stores between 2015 and 2018. Antimicrobial susceptibility testing was performed for all isolates by a broth microdilution method, and the ESBL phenotype was determined according to the Clinical and Laboratory Standards Institute (CLSI) confirmatory method. All ESBL-EC isolates (n = 29) were subjected to whole-genome sequencing (WGS). The antimicrobial resistance genes, plasmid incompatibility types, E. coli phylogroups, and phylogenetic relations were investigated based on the WGS data. The prevalence of ESBL-ECs in chicken was significantly higher than that in other meat samples. The results in this study demonstrate that clonally diverse ESBL-ECs with a multidrug resistance phenotype were distributed nationwide, although their prevalence from retail meat was 0.9%. The dissemination of ESBL-ECs from retail meat poses a potential risk to consumers and food-handlers, suggesting that the continuous surveillance of ESBL-ECs in retail meat should be conducted at the national level.

Bonelli R, A. Penna B, P. Albuquerque J, M. Souza R, M. F. Cerqueira A. Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview

In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.

Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview

In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.

Efficient isolation of Campylobacter bacteriophages from chicken skin, analysis of several isolation protocols

The application of Campylobacter specific bacteriophages appears as a promising food safety tool for the biocontrol of this pathogen in the poultry meat production chain. However, their isolation is a complicated challenge since their occurrence appears to be low. This work assessed the efficiency of seven protocols for recovering Campylobacter phages from chicken skin samples inoculated at phage loads from 5.0 × 10¹ to 5.0 × 10⁶ PFU/g. The enrichment of chicken skin in selective Bolton broth containing target isolates was the most efficient procedure, showing a low detection limit of 5.0 × 10¹ PFU/g and high recovery rates of up to 560%. This method's effectiveness increased as phage concentration decreased, showing its suitability for phage isolation. When this method was applied to isolate new Campylobacter phages from retail chicken skin, a total of 280 phages were recovered achieving an isolation success rate of 257%. From the 109 samples 68 resulted phage positive (62%). Chicken skin could be, therefore, considered a rich source in Campylobacter phages. This method is a simple, reproducible and efficient approach for the successful isolation of both group II and III Campylobacter specific bacteriophages, which could be helpful for the enhancement of food safety by reducing this pathogen contamination in broiler meat.

The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later

In 2013, a Lancet Infectious Diseases Commission described the state of antimicrobial resistance worldwide. Since then, greater awareness of the public health ramifications of antimicrobial resistance has led to national actions and global initiatives, including a resolution at the high-level meeting of the UN General Assembly in 2016. Progress in addressing this issue has ranged from a ban on irrational drug combinations in India to commitments to ban colistin as a growth promoter in animals, improve hospital infection control, and implement better antimicrobial stewardship. Funds have been mobilised, and regulatory barriers to new antibiotic development have been relaxed. These efforts have been episodic and uneven across countries, however. Sustained funding for antimicrobial resistance and globally harmonised targets to monitor progress are still urgently needed. Except for in a few leading countries, antimicrobial resistance has not captured the sustained focus of national leaders and country-level actors, including care providers.

Microbiome studies in the medical sciences and the need for closer multidisciplinary interplay

Next-generation sequencing techniques have enabled identification of the microorganisms colonizing mucosal tissues. The International Congress "MicrobiotaMi 2020" (Milan, February 2020) will focus on the mechanisms of microbiota-related functions in health and disease and their clinical application.

The afterlife of antibiotics

Antibiotics have an afterlife. They remain biologically active and affect microbial ecosystems in and outside the body. Antibiotics used by humans and animals are excreted and reach the environment through multiple pathways causing widespread contamination of soil and water globally. Wastewater treatment plants to not eliminate all antibiotic residues and resistance genes.

Antimicrobial Resistance and Food Animals: Influence of Livestock Environment on the Emergence and Dissemination of Antimicrobial Resistance

The emergence and dissemination of antimicrobial resistance among human, animal and zoonotic pathogens pose an enormous threat to human health worldwide. The use of antibiotics in human and veterinary medicine, and especially the use of large quantities of antibiotics in livestock for the purpose of growth promotion of food animals is believed to be contributing to the modern trend of the emergence and spread of bacteria with antibiotic resistant traits. To better control the emergence and spread of antimicrobial resistance several countries from Western Europe implemented a ban for antibiotic use in livestock, specifically the use of antibiotics for growth promotion of food animals. This review article summarizes the recent knowledge of molecular acquisition of antimicrobial resistance and the effects of implementation of antibiotic growth promoter bans on the spread of antimicrobial resistant bacteria in animals and humans. In this article, we also discuss the main zoonotic transmission routes of antimicrobial resistance and novel approaches designed to prevent or slow down the emergence and spread of antimicrobial resistance worldwide. Finally, we provide future perspectives associated with the control and management of the emergence and spread of antimicrobial resistant bacteria.

A Fast and Easily Parallelizable Biosensor Method for Measuring Extractable Tetracyclines in Soils

Quantification of extractable antibiotics in soils is important to assessing their bioavailability and mobility, and ultimately their ecotoxicological and health risks. This study aimed to establish a biosensor method for detecting extractable tetracyclines in soils (Alfisol, Mollisol, and Ultisol) using whole-cell biosensors containing a reporter plasmid (pMTGFP or pMTmCherry) carrying fluorescent protein genes tightly controlled by tetracyclines-responsive control region (tetRO). This whole-cell biosensor method can simultaneously measure 96 or more samples within 6 h and is easily parallelizable, whereas a typical high-performance liquid chromatography (HPLC) method may require 7 times more of analysis time and much greater cost to achieve similar analytical throughput. The biosensor method had a detection limit for each of six tetracyclines between 5.32-10.2 μg/kg soil, which is considered adequate for detecting tetracyclines in ethylenediaminetetraacetic acid (EDTA) extracts of soils. Relative standard deviation was between 19.8-51.2% for the biosensor Escherichia coli DH5α/pMTGFP and 2.98-25.8% for E. coli DH5α/pMTmCherry, respectively, suggesting that E. coli DH5α/pMTmCherry was superior to E. coli DH5α/pMTGFP for detecting extractable tetracyclines in soils. This new, fast, easily parallelizable, and cost-effective biosensor method has the potential for measuring extractable concentrations of tetracyclines for a large number of soil samples in large-scale monitoring studies.

A novel fluorescent "turn-on" aptasensor based on nitrogen-doped graphene quantum dots and hexagonal cobalt oxyhydroxide nanoflakes to detect tetracycline

In this study, a novel fluorescent "turn-on" aptasensor was developed for sensitive and rapid detection of tetracycline (TC) in animal-derived food. It is based on aptamer-functionalized nitrogen-doped graphene quantum dots (N-GQDs-aptamer) coupled with cobalt oxyhydroxide (CoOOH) nanoflakes. The CoOOH nanoflakes are efficient fluorescence quenchers in homogeneous solutions, and this is due to their advantages of excellent optical properties, superior flexibility, and water dispersibility. The proposed method's mechanism is driven by quenching based on the fluorescence resonance energy transfer (FRET) between the donor (N-GQDs) and the acceptor (CoOOH nanoflakes). On the other hand, fluorescence recovery is caused by the structure switching behavior of the aptamer. Compared with previous methods, our developed method exhibits better behavior in terms of being easy to fabricate and being simple in detection procedure and maintains the detection limit low enough in TC determination: a linear range from 1 to 100 ng mL^-1 and a detection limit of 0.95 ng mL^-1 (S/N = 3). Furthermore, the proposed method was applied to five animal-derived food samples (milk, honey, fish, eggs, and chicken muscle) and demonstrated practical applicability. As well, the method has the advantages of simplicity in pre-treatment and convenience in instruments, saves times, and is cost-effective. Finally, the proposed method demonstrates significant potential for sensitive and rapid detection of specific components in real samples. Graphical abstract.

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.

Prevention of antibiotic resistance - an epidemiological scoping review to identify research categories and knowledge gaps

BACKGROUND

Antibiotics have become the cornerstone for the treatment of infectious diseases and contributed significantly to the dramatic global health development during the last 70 years. Millions of people now survive what were previously life-threatening infections. But antibiotics are finite resources and misuse has led to antibiotic resistance and reduced efficacy within just a few years of introduction of each new antibiotic. The World Health Organization rates antibiotic resistance as a 'global security threat' impacting on global health, food security and development and as important as terrorism and climate change.

OBJECTIVES

This paper explores, through a scoping review of the literature published during the past 20 years, the magnitude of peer-reviewed and grey literature that addresses antibiotic resistance and specifically the extent to which "prevention" has been at the core. The ultimate aim is to identify know-do gaps and strategies to prevent ABR.

METHODS

The review covers four main data bases, Web of Science, Medline, Scopus and Ebsco searched for 2000-17. The broader research field "antibiotic OR antimicrobial resistance" gave 431,335 hits. Narrowing the search criteria to "Prevention of antibiotic OR antimicrobial resistance" resulted in 1062 remaining titles. Of these, 622 were unique titles. After screening of the 622 titles for relevance, 420 abstracts were read, and of these 282 papers were read in full. An additional 53 references were identified from these papers, and 64 published during 2018 and 2019 were also included. The final scoping review database thus consisted of 399 papers.

RESULTS

A thematic structure emerged when categorizing articles in different subject areas, serving as a proxy for interest expressed from the research community. The research area has been an evolving one with about half of the 399 papers published during the past four years of the study period. Epidemiological modelling needs strengthening and there is a need for more and better surveillance systems, especially in lower- and middle-income countries. There is a wealth of information on the local and national uses and misuses of antibiotics. Educational and stewardship programmes basically lack evidence. Several studies address knowledge of the public and prescribers. The lessons for policy are conveyed in many alarming reports from national and international organizations.

CONCLUSIONS

Descriptive rather than theoretical ambitions have characterized the literature. If we want to better understand and explain the antibiotic situation from a behavioural perspective, the required approaches are lacking. A framework for an epidemiological causal web behind ABR is suggested and may serve to identify entry points for potential interventions.

Effects of Different Probiotics on Laying Performance, Egg Quality, Oxidative Status, and Gut Health in Laying Hens

With recent bans on the growth-promoting use of antibiotics, alternative strategies are needed to improve the performance of agricultural animals. Here, the effects of dietary supplementation with Clostridium butyricum and a combination of Saccharomyces boulardii and Pediococcus acidilactici were assessed on laying performance, egg quality, oxidative status, and gut health in laying hens. A total of 8208 Lohmann pink laying hens were divided into 3 treatment groups, with each group replicated 12 times (n = 228). Hens in the control group (CON) were provided a basic diet devoid of added antibiotics and probiotics. Treatment group 1 (T1) received the same base diet supplemented with 0.5 g/kg C. butyricum, and the diets of treatment group 2 (T2) supplemented with S. boulardii (0.05 g/kg) and P. acidilactici (0.1 g/kg) for the entirety of the 5-week trial. The data indicated that C. butyricum supplementation resulted in a significant reduction in ADFI, a significant increase in feed conversion, eggshell strength, and the CP% of albumen (dry matter, DM) relative to CON. The probiotic-treated hens exhibited decreased reactive oxygen species (ROS) levels in ileum and cecum, and reduced malondialdehyde (MDA) in serum. In conclusion, dietary supplementation with C. butyricum may be beneficial with respect to hen performance, egg quality, and gut health.

Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

Global trends in antimicrobial resistance in animals in low- and middle-income countries

The global scale-up in demand for animal protein is the most notable dietary trend of our time. Antimicrobial consumption in animals is threefold that of humans and has enabled large-scale animal protein production. The consequences for the development of antimicrobial resistance in animals have received comparatively less attention than in humans. We analyzed 901 point prevalence surveys of pathogens in developing countries to map resistance in animals. China and India represented the largest hotspots of resistance, with new hotspots emerging in Brazil and Kenya. From 2000 to 2018, the proportion of antimicrobials showing resistance above 50% increased from 0.15 to 0.41 in chickens and from 0.13 to 0.34 in pigs. Escalating resistance in animals is anticipated to have important consequences for animal health and, eventually, for human health.