Antimicrobial resistance in humans, livestock and the wider environment

Occurrence, identification, and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa

The increasing occurrence of multidrug-resistant Enterobacteriaceae in clinical and environmental settings has been seen globally as a complex public health challenge, mostly in the developing nations where they significantly impact freshwater used for a variety of domestic purposes and irrigation. This paper detail the occurrence and antibiogram signatures of the Enterobacteriaceae community in Tsomo and Tyhume rivers within the Eastern Cape Province, the Republic of South Africa, using standard methods. The average distribution of the presumptive Enterobacteriaceae in the rivers ranged from 1 × 102 CFU/100ml to 1.95 × 104 CFU/100ml. We confirmed 56 (70.8%) out of 79 presumptive Enterobacteriaceae isolated being species within the family Enterobacteriaceae through the Matrix-Assisted Laser Desorption Ionization Time of Flight technique. Citrobacter-, Enterobacter-, Klebsiella species, and Escherichia coli were selected (n = 40) due to their pathogenic potentials for antibiogram profiling. The results of the antibiotic susceptibility testing gave a revelation that all the isolates were phenotypically multidrug-resistant. The resistance against ampicillin (95%), tetracycline and doxycycline (88%), and trimethoprim-sulfamethoxazole (85%) antibiotics were most prevalent. The Multiple Antibiotic Resistance indices stretched from 0.22 to 0.94, with the highest index observed in a C. freundii isolate. Molecular characterisation using the PCR technique revealed the dominance of blaTEM (30%; 12/40) among the eight groups of β-lactams resistance determinants assayed. The prevalence of others was blaCTX-M genes including group 1, 2 and 9 (27.5%), blaSHV (20%), blaOXA-1-like (10%), blaPER (2.5%), and blaVEB (0%). The frequencies of the resistance determinants for the carbapenems were blaKPC (17.6%), blaGES (11.8%), blaIMP (11.8%), blaVIM (11.8%), and blaOXA-48-like (5.9%). Out of the six plasmid-mediated AmpC (pAmpC) genes investigated blaACC, blaEBC, blaFOX, blaCIT, blaDHA, and blaMOX, only the first four were detected. In this category, the most dominant was blaEBC, with 18.4% (7/38). The prevalence of the non-β-lactamases include tetA (33.3%), tetB (30.5%), tetC (2.8%), tetD (11.1%), tetK (0%), tetM (13.9%), catI (12%), catII (68%), sulI (14.3%), sulII (22.9%) and aadA (8.3%). Notably, a C. koseri harboured 42.8% (12/28) of the genes assayed for which includes five of the ESBL genes (including the only blaPER detected in this study), two of the pAmpC resistance genes (blaACC and blaCIT), and five of the non-β-lactamase genes. This study gives the first report on C. koseri exhibiting the co-occurrence of ESBL/AmpC β-lactamase genes from the environment to the best of our knowledge. The detection of a blaPER producing Citrobacter spp. in this study is remarkable. These findings provide evidence that freshwater serves as reservoirs of antimicrobial resistance determinants, which can then be easily transferred to human beings via the food chain and water.

The challenges and applications of nanotechnology against bacterial resistance

Bacterial resistance to the antibiotics develops rapidly and is increasingly serious health concern in the world. It is an insoluble topic due to the multiple resistant mechanisms. The overexpression of relative activities of the efflux pump has proven to be a frequent and important source of bacterial resistance. Efflux transporters in the membrane from the resistant bacteria could play a key role to inhibit the intracellular drug intake and impede the drug activities. However, nanoparticles (NPs), one of the most frequently used encapsulation materials, could increase the intracellular accumulation of the drug and inhibit the transporter activity effectively. The rational and successful application of nanotechnology is a key factor in overcoming bacterial resistance. Furthermore, nanoparticles such as metallic, carbon nanotubes and so on, may prevent the development of drug resistance and be associated with antibiotic agents, inhibiting biofilm formation or increasing the access into the target cell and exterminating the bacteria eventually. In the current study, the mechanisms of bacterial resistance are discussed and summarized. Additionally, the opportunities and challenges in the use of nanoparticles against bacterial resistance are also illuminated. At the same time, the use of nanoparticles to combat multidrug-resistant bacteria is also investigated by coupling natural antimicrobials or other alternatives. In short, we have provided a new perspective for the application of nanoparticles against multidrug-resistant bacteria.

Temporal and geographical research trends of antimicrobial resistance in wildlife - A bibliometric analysis

Antimicrobial resistance (AMR) is a complex and global problem. Despite the growing literature on AMR in the medical and veterinary settings, there is still a lack of knowledge on the wildlife compartment. The main aim of this study was to report the global trends in AMR research in wildlife, through a bibliometric study of articles found in the Web of Science database. Search terms were "ANTIMICROBIAL" OR "ANTIBIOTIC" AND "RESISTANT" OR "RESISTANCE" and "WILDLIFE" "MAMMAL" "BIRD" "REPTILE" "FERAL" "FREE RANGE". A total of 219 articles were obtained, published between 1979 and 2019. A rising interest in the last decades towards this topic becomes evident. During this period, the scientific literature was distributed among several scientific areas, however it became more multidisciplinary in the last years, focusing on the "One Health" paradigm. There was a geographical bias in the research outputs: most published documents were from the United States, followed by Spain, Portugal and the United Kingdom. The most productive institutions in terms of publication number were located in Portugal and Spain. An important level of international collaboration was identified. An analysis of the main keywords showed an overall dominance of "AMR", "E. coli", "genes", "prevalence", "bacteria", "Salmonella spp." and "wild birds". This is the first study providing a global overview of the spatial and temporal trends of research related to AMR in wildlife. Given the growth tendency over the last years, it is envisaged that scientific production will expand in the future. In addition to offering a broad view of the existing research trends, this study identifies research gaps both in terms of geographical incidence and in relation to unexplored subtopics. Unearthing scientific areas that should be explored in the future is key to designing new strategic research agendas in AMR research in wildlife and to inform funding programs.

Towards the Prediction of Antimicrobial Efficacy for Hydrogen Bonded, Self-Associating Amphiphiles

Herein we report 50 structurally related supramolecular self-associating amphiphilic (SSA) salts and related compounds. These SSAs are shown to act as antimicrobial agents, active against model Gram-positive (methicillin-resistant Staphylococcus aureus) and/or Gram-negative (Escherichia coli) bacteria of clinical interest. Through a combination of solution-state, gas-phase, solid-state and in silico measurements, we determine 14 different physicochemical parameters for each of these 50 structurally related compounds. These parameter sets are then used to identify molecular structure-physicochemical property-antimicrobial activity relationships for our model Gram-negative and Gram-positive bacteria, while simultaneously providing insight towards the elucidation of SSA mode of antimicrobial action.

The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering

Households provide a habitat for bacteria originating from humans, animals, foods, contaminated clothes, or other sources. Thus, bacteria carrying antibiotic resistance genes (ARGs) may be introduced via household members, animals, or the water supply from external habitats into private households and vice versa. Since data on antibiotic resistance (ABR) in the domestic environment are limited, this study aimed to determine the abundance of β-lactamase, mobile colistin resistance, and class 1 integron genes and the correlation of their presence and to characterize phenotypically resistant strains in 54 private households in Germany. Additionally, the persistence of antibiotic-resistant bacteria during automated dishwashing compared to that during laundering was assessed. Shower drains, washing machines, and dishwashers were sampled and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using a Vitek 2 system. The results showed a significantly higher relative ARG abundance of 0.2367 ARG copies/16S rRNA gene copies in shower drains than in dishwashers (0.1329 ARG copies/16S rRNA gene copies) and washing machines (0.0006 ARG copies/16S rRNA gene copies). bla _CMY-2, bla _ACT/MIR, and bla _OXA-48 were the most prevalent ARG, and intI1 occurred in 96.3% of the households, while no mcr genes were detected. Several β-lactamase genes co-occurred, and the resistance of bacterial isolates correlated positively with genotypic resistance, with carbapenemase genes dominating across isolates. Antibiotic-resistant bacteria were significantly reduced during automated dishwashing as well as laundering tests and did not differ from susceptible strains. Overall, the domestic environment may represent a potential reservoir of β-lactamase genes and β-lactam-resistant bacteria, with shower drains being the dominant source of ABR.IMPORTANCE The abundance of antibiotic-resistant bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods, and wastewater treatment plants. In this respect, β-lactams and colistin are of particular interest due to the emergence of multidrug-resistant Gram-negative bacteria. Despite the connection of private households to these environments, only a few studies have focused on the domestic environment so far. Therefore, the present study further investigated the occurrence of ARGs and antibiotic-resistant bacteria in shower drains, washing machines, and dishwashers. The analysis of the domestic environment as a potential reservoir of resistant bacteria is crucial to determine whether households contribute to the spread of ABR or may be a habitat where resistant bacteria from the natural environment, humans, food, or water are selected due to the use of detergents, antimicrobial products, and antibiotics. Furthermore, ABR could limit the options for the treatment of infections arising in the domestic environment.

Isolation and Characterization of Multidrug-Resistant Escherichia coli and Salmonella spp. from Healthy and Diseased Turkeys

Diseases caused by Escherichia coli (E. coli) and Salmonella spp. can negatively impact turkey farming. The aim of this study was to isolate and characterize multidrug-resistant (MDR) E. coli and Salmonella spp. in healthy and diseased turkeys. A total of 30 fecal samples from healthy turkeys and 25 intestinal samples from diseased turkeys that died of enteritis were collected. Bacterial isolation and identification were based on biochemical properties and polymerase chain reaction (PCR). Antibiogram profiles were determined by disk diffusion. The tetracycline-resistance gene tetA was detected by PCR. All samples were positive for E. coli. Only 11 samples (11/30; 36.67%) were positive for Salmonella spp. from healthy turkeys, whereas 16 (16/25; 64%) samples were positive for Salmonella spp. from diseased turkeys. E. coli isolated from diseased turkeys showed higher resistance to levofloxacin, gentamicin, chloramphenicol, ciprofloxacin, streptomycin, and tetracycline. Salmonella spp. isolated from healthy turkeys exhibited higher resistance to gentamicin, chloramphenicol, ciprofloxacin, streptomycin, imipenem, and meropenem. All E. coli and Salmonella spp. from both healthy and diseased turkeys were resistant to erythromycin. Salmonella spp. from both healthy and diseased turkeys were resistant to tetracycline. Multidrug resistance was observed in both E. coli and Salmonella spp. from diseased turkeys. Finally, the tetA gene was detected in 93.1% of the E. coli isolates and in 92.59% of the Salmonella spp. isolates. To the best of our knowledge, this is the first study to isolate and characterize tetA-gene-containing MDR E. coli and Salmonella spp. from healthy and diseased turkeys in Bangladesh. Both microorganisms are of zoonotic significance and represent a significant public health challenge.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Antibiotic Use in Organic and Non-organic Swedish Dairy Farms: A Comparison of Three Recording Methods

Biases of antimicrobial use (AMU) reporting systems pose a challenge to monitoring of AMU. Our study aimed to cross-compare three data sources of AMU in Swedish dairy herds to provide an account of the validity of AMU reports. We studied AMU differences between two production systems, to investigate how the reporting system affected this comparison. On-farm quantification of AMU via a manual collection of empty drug containers (BIN) took place in organic (n = 30) and conventional (n = 30) dairy herds during two periods between February 2016 and March 2017. A data extract mirroring these periods was obtained from two linked datasets that contain AMU data as reported by the prescribing veterinarians. These included data from the Swedish Board of Agriculture system (SBA) and Växa milk recording system (VXA). Using the European Medicines Agency technical units, the total number of defined daily doses (DDD_vet), and defined course doses (DCD_vet) per animal/year were calculated for each herd/period/dataset. Descriptive statistics and Bland–Altman plots were used to evaluate the agreement and systematic bias between the datasets. Mixed models for repeated measures were used to assess AMU differences between production systems. We found consistent numerical differences for the calculated AMU metrics, with BIN presenting higher usage compared to the SBA and VXA. This was driven by a disparity in intramammary tubes (IMt) which appear to be underreported in the national datasets. A statistically significant interaction (BIN dataset) between the production system and drug administration form was found, where AMU for injectable and lactating cow IMt drug forms differed by the production system, but no difference was found for dry-cow IMt. We conclude that calculating AMU using DDD_vet and DCD_vet metrics at a herd level based on Swedish national datasets is useful, with the caveat of IMt potentially being misrepresented. The BIN method offers an alternative to monitoring AMU, but scaling up requires considerations. The lower disease caseload in organic herds partly explains the lower AMU in particular drug forms. The fact that organic and conventional herds' had equally low AMU for dry-cow IMt, coupled with mismatches in IMt report across herds indicated an area of further research.

Health care, overconsumption and uneconomic growth: A conceptual framework

Concerns have grown in recent decades that economic growth in many rich countries may, in fact, be uneconomic. Uneconomic growth occurs when expansion in economic activity causes environmental and social costs that are greater than the benefits of that additional activity. Health care has enjoyed a close historical relationship with economic growth, with health care spending consistently growing faster than GDP over the long term. This paper explores the possible relationship between health care and uneconomic growth. It summarises the rapidly growing evidence on the harms caused by poor quality health care and by the overuse of health care, and on the environmental harms caused by health care systems. Further, it develops a conceptual framework for considering the overconsumption of health care and the joint harms to human health and the natural environment that ensue. This framework illustrates how health-damaging overconsumption in the wider economy combines with unnecessary or low-quality health care to create a cycle of "failure demand" and defensive expenditure on health care services. Health care therefore provides important sectoral insights on the phenomenon of uneconomic growth. There are rich opportunities for interdisciplinary research to quantify the joint harms of overconsumption in health and health care, and to estimate the optimal scale of the health sector from novel perspectives that prioritise human and planetary health and well-being over GDP and profit.

Antibiotic exposure perturbs the bacterial community in the small brown planthopper Laodelphax striatellus

Bacteria symbionts in herbivores play an important role in host biology and ecology, and are affected by environmental factors such as temperature, diet, habitat, antibiotics and so on. However, the effects of antibiotics on the microbiome of the small brown planthopper Laodelphax striatellus (SBPH) remain unclear. Here, we studied the effects of tetracycline on the diversity and composition of bacterial colonies in different tissues of SBPH using high throughput sequencing of 16S ribosomal RNA amplicons. Our results show that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria were most abundant in SBPH, and the genera Asaia and Wolbachia were most abundant in all body parts of SBPH. Antibiotic treatment had persistent effects on the composition of the SBPH microbiome. Tetracycline depleted the population of Firmicutes, Bacteroidetes, Tenericutes and Fusobacteria, and nearly 100% eliminated Wolbachia, Bacteroides and Abiotrophia in SBPH. Together, these results suggest that antibiotic exposure affects the bacteria symbionts of different body parts in SBPH and will facilitate future studies of the bacterial symbionts of arthropod hosts.

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms

BACKGROUND

Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust.

OBJECTIVES

We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored.

METHODS

In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool.

RESULTS

The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study.

CONCLUSION

Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.

Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) in drinking water fountains in urban parks

The presence of Staphylococcus aureus in drinking water is a concern because of its potential to cause human infection and also because of its multiple antimicrobial resistance. This study evaluated the water quality of drinking water fountains and mist makers in four municipal parks of São Paulo for 13 months. Although all samples met bacteriological water quality criteria according to Brazilian regulations, the absence of residual chlorine (<0.1 mg/L) was observed. These data were significantly correlated with the frequency of S. aureus that was found in 25.2% of the samples. The mecA gene was detected in 36.7% of the isolates demonstrating its potential for resistance to several antimicrobials. Furthermore, 27.3% isolates carrying the mecA gene had methicillin-resistant Staphylococcus aureus (MRSA) phenotypic potential. The presence of S. aureus with characteristics of microbial resistance in water for human consumption is an unprecedented finding. Hence, conducting surveillance for opportunistic bacteria, such as staphylococci in drinking water, is reasonable to take control measures and to protect human health, especially in public places with high attendance.

Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics

BACKGROUND

Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur.

OBJECTIVES

To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR.

SOURCES

Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli.

CONTENT

We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface.

IMPLICATIONS

A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.

Construction of generic roadmaps for the strategic coordination of global research into infectious diseases of animals and zoonoses

The Strategic Alliance for Research into Infectious Diseases of Animals and Zoonoses (STAR-IDAZ) International Research Consortium (IRC) coordinates global animal health research to accelerate delivery of disease control tools and strategies. With this vision, STAR-IDAZ IRC has constructed four generic research roadmaps for the development of candidate vaccines, diagnostic tests, therapeutics and control strategies for animal diseases. The roadmaps for vaccines, diagnostic tests and therapeutics lead towards a desired target product profile (TPP). These interactive roadmaps describe the building blocks and for each the key research questions, dependencies, challenges and possible solution routes to identify the basic research needed for translation to the TPP. The control strategies roadmap encompasses the vaccine, diagnostic tests, and therapeutic roadmaps within a wider framework focusing on the inter-dependence of multiple tools and knowledge to control diseases for the benefit of animal and human health. The roadmaps are now being completed for specific diseases and complemented by state-of-the-art information on relevant projects and publications to ensure that the necessary research gaps are addressed for selected priority diseases.

Chemical composition, antioxidant capacity and antibacterial action of five Moroccan essential oils against Listeria monocytogenes and different serotypes of Salmonella enterica

Essential oils (EOs) obtained from aromatic plants are rich in natural components with interesting antimicrobial effects. The aim of this study was to evaluate the chemical composition of EOs extracted from Origanum majorana (OM-EO), Mentha suaveolens (MS-EO), Rosmarinus officinalis (RO-EO), Salvia officinalis (SO-EO) and Mentha pulegium (MP-EO). Their antioxidant properties and antibacterial activity against Listeria monocytogenes and different serotypes of Salmonella enterica subsp. enterica were also studied. The EOs were extracted from plants by hydro-distillation and their chemical composition was determined by GC-MS. Terpinen-4-ol, 1,8-Cineole, Camphor, Limonene and Cinerone were the main chemical components found in OM-EO, RO-EO, SO-EO, MP-EO and MS-EO, respectively. To the best of our knowledge, Limonene and Cinerone were reported, for the first time, as the major components of MP-EO and MS-EO. Moreover, our results showed that MS-EO had the best antioxidant activity with an IC₅₀ of 0.78 ± 0.05 mg/mL, EC₅₀ of 1.53 ± 0.07 mg/mL, and RC₅₀ of 0.98 ± 0.04 mg/mL, and the higher antibacterial activity using microdilution broth method with MIC of 0.5% for Salmonella and 0.25% for L. monocytogenes, while OM-EO had the best antibacterial activity using disc diffusion method (inhibition diameters ranged between 15.3 ± 0.3 mm and 18.5 ± 0.3 mm for Salmonella and between 20.1 ± 0.2 mm and 25.4 ± 0.4 mm for L. monocytogenes). However, OM-EO and MS-EO present the higher percentage of sub-lethally injured cells against S. enterica (5.50 ± 0.11%) and L. monocytogenes (5.23 ± 0.07%), respectively. From this study, we can conclude that the investigated EOs are rich in components with interesting antibacterial activity and they could be applied in food preparations as natural preservatives to extend the shelf life of food products and to inhibit the growth of food-borne pathogens.

Multidrug-Resistant Bacteria Isolated from Different Aquatic Environments in the North of Spain and South of France

Due to the global progress of antimicrobial resistance, the World Health Organization (WHO) published the list of the antibiotic-resistant "priority pathogens" in order to promote research and development of new antibiotics to the families of bacteria that cause severe and often deadly infections. In the framework of the One Health approach, the surveillance of these pathogens in different environments should be implemented in order to analyze their spread and the potential risk of transmission of antibiotic resistances by food and water. Therefore, the objective of this work was to determine the presence of high and critical priority pathogens included in the aforementioned list in different aquatic environments in the POCTEFA area (North Spain-South France). In addition to these pathogens, detection of colistin-resistant Enterobacteriaceae was included due its relevance as being the antibiotic of choice to treat infections caused by multidrug resistant bacteria (MDR). From the total of 80 analyzed samples, 100% of the wastewater treatment plants (WWTPs) and collectors (from hospitals and slaughterhouses) and 96.4% of the rivers, carried antibiotic resistant bacteria (ARB) against the tested antibiotics. Fifty-five (17.7%) of the isolates were identified as target microorganisms (high and critical priority pathogens of WHO list) and 58.2% (n = 32) of them came from WWTPs and collectors. Phenotypic and genotypic characterization showed that 96.4% were MDR and resistance to penicillins/cephalosporins was the most widespread. The presence of bla genes, KPC-type carbapenemases, mcr-1 and vanB genes has been confirmed. In summary, the presence of clinically relevant MDR bacteria in the studied aquatic environments demonstrates the need to improve surveillance and treatments of wastewaters from slaughterhouses, hospitals and WWTPs, in order to minimize the dispersion of resistance through the effluents of these areas.

Can the One Health Approach Save Us from the Emergence and Reemergence of Infectious Pathogens in the Era of Climate Change: Implications for Antimicrobial Resistance?

Climate change has become a controversial topic in today’s media despite decades of warnings from climate scientists and has influenced human health significantly with the increasing prevalence of infectious pathogens and contribution to antimicrobial resistance. Elevated temperatures lead to rising sea and carbon dioxide levels, changing environments and interactions between humans and other species. These changes have led to the emergence and reemergence of infectious pathogens that have already developed significant antimicrobial resistance. Although these new infectious pathogens are alarming, we can still reduce the burden of infectious diseases in the era of climate change if we focus on One Health strategies. This approach aims at the simultaneous protection of humans, animals and environment from climate change and antimicrobial impacts. Once these relationships are better understood, these models can be created, but the support of our legislative and health system partnerships are critical to helping with strengthening education and awareness.

Impedimetric Determination of Kanamycin in Milk with Aptasensor Based on Carbon Black-Oligolactide Composite

The determination of antibiotics in food is important due to their negative effect on human health related to antimicrobial resistance problem, renal toxicity, and allergic effects. We propose an impedimetric aptasensor for the determination of kanamycin A (KANA), which was assembled on the glassy carbon electrode by the deposition of carbon black in a chitosan matrix followed by carbodiimide binding of aminated aptamer mixed with oligolactide derivative of thiacalix[4]arene in a cone configuration. The assembling was monitored by cyclic voltammetry, electrochemical impedance spectroscopy, and scanning electron microscopy. In the presence of the KANA, the charge transfer resistance of the inner interface surprisingly decreased with the analyte concentration within 0.7 and 50 nM (limit of detection 0.3 nM). This was attributed to the partial shielding of the negative charge of the aptamer and of its support, a highly porous 3D structure of the surface layer caused by a macrocyclic core of the carrier. The use of electrostatic assembling in the presence of cationic polyelectrolyte decreased tenfold the detectable concentration of KANA. The aptasensor was successfully tested in the determination of KANA in spiked milk and yogurt with recoveries within 95% and 115%.

Mapping knowledge and comprehension of antimicrobial stewardship and biosecurity among veterinary students

OBJECTIVES

As an important public health concern, antimicrobial resistance (AMR) is related to lack of knowledge among healthcare professionals. Since the Global Action Plan on AMR highlights the importance of training all healthcare professionals, it is essential to focus our attention on the education related to judicious antimicrobial use. The current study was the first attempt in southeastern Europe to quantify the knowledge about antimicrobial usage and biosecurity measure among veterinary students.

METHODS

This questionnaire-based study was performed between April and May of 2019 on 213 veterinary students of the University of Novi Sad, Serbia and the University of Zagreb, Croatia.

RESULTS

Veterinary students appeared to be little aware of antimicrobial use in veterinary medicine contribution to overall AMR since only 56.8% have chosen strong contribution as the answer. Of the students surveyed, only 22.1%/35.7% of them strongly agreed/agreed that the amount of teaching time for pharmacology was about right. Students who denied having good knowledge of the pharmacology of antimicrobials showed higher knowledge about systemic use of antimicrobials in different clinical scenarios (p = 0.002). High importance of some antimicrobials for human medicine was not recognized by surveyed students. Only 8.5% of them identified gentamicin correctly, as first-line therapy. Students expected to graduate later were more likely to identify the importance of rating antimicrobials correctly than those who thought they would graduate earlier (p = 0.002). More than half of students gave correct answer at scenario regarding a dog with recurrent pyoderma by choosing culture and susceptibility (C & S) testing. Our students who think they will graduate sooner have higher knowledge level on C & S testing sample submission for range of clinical scenarios (p = 0.004). Moreover, appropriate use of PPE (personal protective equipment) procedure and biosecurity measure were reported for two thirds of our students in case of only for two clinical scenarios.

CONCLUSION

This study reveals that among veterinary students from Croatia and Serbia improved undergraduate education is needed on the AMR with emphasis on antimicrobial stewardship (AMS) and appropriate biosecurity.

Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times

Mass production and use of antibiotics has led to the rise of resistant bacteria, a problem possibly exacerbated by inappropriate and non-optimal application. Antibiotic treatment often follows fixed-dose regimens, with a standard dose of antibiotic administered equally spaced in time. But are such fixed-dose regimens optimal or can alternative regimens be designed to increase efficacy? Yet, few mathematical models have aimed to identify optimal treatments based on biological data of infections inside a living host. In addition, assumptions to make the mathematical models analytically tractable limit the search space of possible treatment regimens (e.g. to fixed-dose treatments). Here, we aimed to address these limitations by using experiments in a Galleria mellonella (insect) model of bacterial infection to create a fully parametrised mathematical model of a systemic Vibrio infection. We successfully validated this model with biological experiments, including treatments unseen by the mathematical model. Then, by applying artificial intelligence, this model was used to determine optimal antibiotic dosage regimens to treat the host to maximise survival while minimising total antibiotic used. As expected, host survival increased as total quantity of antibiotic applied during the course of treatment increased. However, many of the optimal regimens tended to follow a large initial ‘loading’ dose followed by doses of incremental reductions in antibiotic quantity (dose ‘tapering’). Moreover, application of the entire antibiotic in a single dose at the start of treatment was never optimal, except when the total quantity of antibiotic was very low. Importantly, the range of optimal regimens identified was broad enough to allow the antibiotic prescriber to choose a regimen based on additional criteria or preferences. Our findings demonstrate the utility of an insect host to model antibiotic therapies in vivo and the approach lays a foundation for future regimen optimisation for patient and societal benefits.

Research into optimal antibiotic use to improve efficacy is far behind that of cancer care, where personalised treatment is common. The integration of mathematical models with biological observations offers hope to optimise antibiotic use, and in this present study an in vivo insect model of systemic Vibrio infection was used for the first time to determine critical model parameters for optimal antibiotic treatment. By this approach, the optimal regimens tended to result from a large initial ‘loading’ dose followed by subsequent doses of incremental reductions in antibiotic quantity (dose ‘tapering’). The approach and findings of this study opens a new avenue towards optimal application of our precious antibiotic arsenal and may lead to more effective treatment regimens for patients, thus reducing the health and economic burdens associated with bacterial infections. Importantly, it can be argued that until we understand how to use a single antibiotic optimally, it is unlikely we will identify optimal ways to use multiple antibiotics simultaneously.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding

Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.

The Effects of Urbanization on the Infant Gut Microbiota and Health Outcomes

Humans and their gut microbiota have co-evolved over thousands of years, resulting in the establishment of a complex host-microbiota ecosystem. Early life environmental factors, such as delivery mode, nutrition, and medication use, have been shown to substantially affect both host-microbiota interactions and health outcomes. However, the effects of urbanization (characterized by the spectrum of rural and urban populations) on these early life events have been overlooked. A deeper understanding of the relationship between urbanization and microbiota development will allow for the identification of novel biological and social approaches that can be implemented to prevent and treat disease and promote maternal and infant/child health. The aim of this narrative review is to summarize how factors associated with urbanization differentially impact delivery mode, nutrition, and medication use, and how these changes subsequently affect the gut microbiota and health outcomes of infants. This narrative review also describes the important evidence gaps associated with these relationships and recommends actions that can be taken to improve the health of mothers and infants worldwide.

Substandard Quality of the Antimicrobials Sold in the Street Markets in Haiti

This pilot study was conducted to analyze the quality of the antimicrobials sold in the street markets in Port-au-Prince, Haiti. A total of 258 packs containing antimicrobials were bought in 28 street markets in Port-au-Prince (Haiti). Tablets and contents of capsules included in 196 packs were analyzed using a Raman handheld spectrometer (NanoRAM of BWTEK, Model: BWS456-785) during the first quarter of 2019. Three out of 11 antimicrobials (Amoxicillin, Metronidazole, and Cotrimoxazole) had a high spectral match with an HQI ≥ 90 to the respective authentic medicine for more than 95% of their tablets/capsules. For six antimicrobials (Tetracycline, Erythromycin, Cloxacillin, Azithromycin, Clarithromycin, and the combination Amoxicillin + Clavulanic Acid) none of their tablets/capsules showed a sufficient spectral match with the authentic medicine. This finding indicates that these products sold in the markets did not contain the labeled drug and/or contained a degraded drug. In addition to the fact that prescription antimicrobials can be purchased in street markets, the present field study found that for most of them (including "Watch" antimicrobials according to the AWaRe classification) were substandard, which contributes to the present antimicrobials resistance epidemic.

Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems

Antimicrobial use in agricultural animals is known to be associated with increases in antimicrobial resistance. Most prior studies have utilized culture and susceptibility testing of select organisms to document these phenomena. In this study we aimed to detect 66 antimicrobial resistance (AMR) genes for 10 antimicrobial agent classes directly in swine fecal samples using our previously developed antimicrobial resistance TaqMan array card (AMR-TAC) across three different swine farm management systems. This included 38 extensive antimicrobial use (both in treatment and feed), 30 limited antimicrobial use (treatment only), and 30 no antimicrobial use farms. The number of resistance genes detected in extensive antimicrobial use farms was higher than in limited and no antimicrobial use farms (28.2 genes ± 4.2 vs. 24.0 genes ± 4.1 and 22.8 genes ± 3.6, respectively, p < 0.05). A principal component analysis and hierarchical clustering of the AMR gene data showed the extensive use farm samples were disparate from the limited and no antimicrobial use farms. The prevalence of resistance genes in extensive use farms was significantly higher than the other farm categories for 18 resistance genes including bla SHV, bla CTX-M1 group, bla CTX-M9 group, bla VEB, bla CMY2-LAT, aac(6')-lb-cr, qnrB1, gyrA83L-E. coli, armA, rmtB, aac(3)-IIa, mphA, 23S rRNA 2075G-Campylobacter spp., mcr-1, catA1, floR, dfrA5-14, and dfrA17. These genotypic findings were supported by phenotypic susceptibility results on fecal E. coli isolates. To examine the timing of AMR gene abundance in swine farms, we also performed a longitudinal study in pigs. The results showed that AMR prevalence occurred both early, presumably from mothers, as well as after weaning, presumably from the environment. In summary, detection of AMR genes directly in fecal samples can be used to qualitatively and quantitatively monitor AMR in swine farms.

Gut carriage of antimicrobial resistance genes in women exposed to small-scale poultry farms in rural Uganda: A feasibility study

Background

Antibiotic use for livestock is presumed to be a contributor to the acquisition of antimicrobial resistance (AMR) genes in humans, yet studies do not capture AMR data before and after livestock introduction.

Methods

We performed a feasibility study by recruiting a subset of women in a delayed-start randomized controlled trial of small-scale chicken farming to examine the prevalence of clinically-relevant AMR genes. Stool samples were obtained at baseline and one year post-randomization from five intervention women who received chickens at the start of the study, six control women who did not receive chickens until the end of the study, and from chickens provided to the control group at the end of the study. Stool was screened for 87 clinically significant AMR genes using a commercially available qPCR array (Qiagen).

Results

Chickens harbored 23 AMR genes from classes found in humans as well as additional vancomycin and β-lactamase resistance genes. AMR patterns between intervention and control women appeared more similar at baseline than one year post randomization (PERMANOVA R² = 0.081, p = 0.61 at baseline, R² = 0.186, p = 0.09 at 12 months) Women in the control group who had direct contact with the chickens sampled in the study had greater similarities in AMR gene patterns to chickens than those in the intervention group who did not have direct contact with chickens sampled (p = 0.01). However, at one year there was a trend towards increased similarity in AMR patterns between humans in both groups and the chickens sampled (p = 0.06).

Conclusions

Studies designed to evaluate human AMR genes in the setting of animal exposure should account for high baseline AMR rates. Concomitant collection of animal, human, and environmental samples over time is recommended to determine the directionality and source of AMR genes.

Trial registration

ClinicalTrials.gov Identifier NCT02619227.

Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes

BACKGROUND

The crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.

METHODS

This was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistant E. coli isolated from stool samples from both humans (n = 30) and cattle (n = 12) in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/30 from human and 8/12 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes.

RESULTS

At household level, the genomes from both human and animals clustered away from one another except for one instance where two human isolates from the same household clustered together. However, 67% of the E. coli isolated from cattle were closely related to those found in humans. The E. coli isolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from the E. coli population from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump. A high variation of virulence genes was registered among the E. coli genomes from humans than those of cattle origin.

CONCLUSION

From the analysis of the core genome and phenotypic resistance, this study has demonstrated that the E. coli of human origin and those of cattle origin may have a common ancestry. Limited sharing of virulence genes presents a challenge to the notion that AMR in humans is as a result of antibiotic use in the farm and distorts the picture of the directionality of transmission of AMR at a human-animal interface and presents a task of exploring alternative routes of transmission of AMR.

Effects of essential oils and(or) benzoic acid in beef finishing cattle diets on the fatty acid profile and shelf life stability of ribeye steaks and ground beef

The effects of feeding essential oils and(or) benzoic acid to finishing steers on fatty acid profile and oxidative stability (color and lipid oxidation) of beef longissimus thoracis steaks and ground beef was determined in this study. Beef was procured from crossbred beef steers (n = 63) fed one of five dietary treatments: (1) control (no antibiotics fed); (2) monensin/tylosin (monensin supplemented at 33 mg/kg [DM basis]; tylosin supplemented at 11 mg/kg [DM basis]); (3) essential oils (supplemented at 1.0 g/steer/day); (4) benzoic acid (supplemented at 0.5% [DM basis]); and (5) combination (essential oils supplemented at 1.0 g/steer/day and benzoic acid supplemented at 0.5% [DM basis]). Although no improvements in shelf life stability were observed, feeding finishing cattle essential oils and(or) benzoic acid did not have detrimental impacts on beef color stability and lipid oxidation over a simulated retail display period.

Wild boar as a reservoir of antimicrobial resistance

Antimicrobial resistance (AMR) has been recognized as an emerging and growing problem worldwide. Knowledge concerning AMR bacteria circulating in wildlife is currently limited, although it could provide important insights into AMR emergence and persistence. Across Europe, wild boar (Sus scrofa) populations have dramatically increased their distribution and number over the last decades. In the context of AMR dynamics, wild boar is a perfect model species to unveil the emergence, spread and persistence of AMR at the human-livestock-wildlife interface. Here, we summarize the current knowledge on the importance of wild boar as a reservoir of antimicrobial resistant bacteria, and its possible use as sentinel species for surveillance. Analyses of available data showed a rising interest on this topic in the last years, highlighting the growing concern on wild boar potential role as AMR facilitator and it is foreseen that the importance of antimicrobial resistance research in wild boar will continue to increase in years to come. Available studieshave been focused on specific bacterial species, particularlyE. coli, Salmonellaspp. andEnterococcusspp., bioindicators of AMR, and have been mainly conducted in three countries: Spain, Portugal and Germany.Strikingly, AMR surveillance in wild boar is uneven and still poorly allocated as many wild boar high-density countries do not yet have publications on the topic.Overall, accumulated data showed thatwild boar are carriers of antimicrobial resistant bacteria, withvariation in the prevalence of bacterial species and thepercentage of resistance to different antibiotics. Thelack of harmonized sampling and testing protocols makes it difficult to compare AMR in wild boar.The need for the establishment of standardised protocols keen to provide quantitative comparable data is highlighted. We finally suggest the long-term monitoring of wild boar as a sentinel species for AMR surveillance in order to inform public policies on this topic.

One model to rule them all? Modelling approaches across OneHealth for human, animal and plant epidemics

One hundred years after the 1918 influenza outbreak, are we ready for the next pandemic? This paper addresses the need to identify and develop collaborative, interdisciplinary and cross-sectoral approaches to modelling of infectious diseases including the fields of not only human and veterinary medicine, but also plant epidemiology. Firstly, the paper explains the concepts on which the most common epidemiological modelling approaches are based, namely the division of a host population into susceptible, infected and removed (SIR) classes and the proportionality of the infection rate to the size of the susceptible and infected populations. It then demonstrates how these simple concepts have been developed into a vast and successful modelling framework that has been used in predicting and controlling disease outbreaks for over 100 years. Secondly, it considers the compartmental models based on the SIR paradigm within the broader concept of a 'disease tetrahedron' (comprising host, pathogen, environment and man) and uses it to review the similarities and differences among the fields comprising the 'OneHealth' approach. Finally, the paper advocates interactions between all fields and explores the future challenges facing modellers. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.

Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient

BACKGROUND

Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause.

RESULTS

The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing bla_CTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies.

CONCLUSIONS

Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.

Winter is coming - Impact of temperature on the variation of beta-lactamase and mcr genes in a wastewater treatment plant

Wastewater treatment plants (WWTP) play a key role in the dissemination of antibiotic resistance and analyzing the abundance of antibiotic resistance genes (ARGs) and resistant bacteria is necessary to evaluate the risk of proliferation caused by WWTPs. Since few studies investigated the seasonal variation of antibiotic resistance, this study aimed to determine the abundance of beta-lactamase and mcr genes and to characterize phenotypic resistant strains in a WWTP in Germany over the seasons. Wastewater, sewage sludge and effluent samples were collected over a one year period and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of nearly all investigated ARGs in the wastewater compared to sewage sludge and effluent. ARG abundance and temperature showed a negative correlation in wastewater and significant differences between ARG abundance during warmer and colder seasons were determined, indicating a seasonal effect. Co-occurrence of mcr-1 and carbapenemase genes in a multi-drug resistant Enterobacter cloacae and Escherichia coli producing extended-spectrum beta-lactamase (ESBL) was determined. To the best of our knowledge, this is the first detection of mcr-1, bla_VIM and bla_OXA-48 in an ESBL-producing E. coli. Although wastewater treatment reduced the abundance of ARGs and resistant strains, a dissemination into the river might be possible because carbapenemase-, CTX-M- and mcr-1-gene harboring strains were still present in the effluent.

Identification of risk factors associated with antimicrobial resistance in equine fecal Escherichia coli isolates

Antimicrobial resistance is a growing global problem that will need a multinational collaborative effort to overcome this serious challenge. The aim of the study is to investigate the potential risk factors associated with the prevalence and distribution of antimicrobial-resistance genes (ARGs) of Escherichia coli isolates obtained from equine fecal samples. One hundred and eighteen horses from different geographical locations and management systems were enrolled in the study and a questionnaire containing information about each individual horse was designed and filled. The enrolled horses belonged to 2 main categories (Hospitalized horses (n = 31), and Non hospitalized horses (n = 87)). In total, 103 E. coli isolates were collected from the 118 horse fecal samples. Genes that are responsible for resistance to β-lactams, tetracyclines, aminoglycosides, and trimethoprim were detected using uniplex and multiplex polymerase chain reaction (PCR). The prevalence of antimicrobial resistance was significantly higher in hospitalized horses compared to non-hospitalized ones (p ≤ .05), particularly against (trimethoprim, doxycycline, oxytetracycline, and amoxicillin-clavulanic acid). The most prevalent antimicrobial-resistant genes were aminoglycoside resistant genes (strA, strB, and aadA) in percentages; 89%, 85%, and 84%, respectively. Statistical analysis revealed a significant association between risk factors and occurrence of ARGs (p ≤ .05). Significant risk factors include the last treatment and history of antimicrobial administration, breed of horses, use of horses, type of diet fed for horses, practice management and history of last illness. Tetracycline-resistance gene (tetA) was 23 times more likely to be found in the Arabian and local breeds of horses compared to English and warmblood breed. TetA is also 8 times more likely to be found in horses that were fed a natural diet compared to other horses that were fed manufactured/ processed feed. In conclusion, E. coli bacterium can harbor high resistance to different classes of antimicrobials which increases the risk of potential uncontrolled transmission of the multi-drug resistant E. coli bacterium to veterinarians and horse handlers, as well as to the equine population itself.

Effects of Alternative Administration Programs of a Synbiotic Supplement on Broiler Performance, Foot Pad Dermatitis, Caecal Microbiota, and Blood Metabolites

This research investigated the effects of different synbiotic administration programs on broiler productive performance and foot pad dermatitis (FPD). Molecular insights on caecal microbiota and plasma metabolomics were also performed. - A total of 1000 one-day-old male chicks were grouped by the synbiotic treatment. The synbiotic was either sprayed as gel droplets onto newly hatched chicks at the hatchery (100 g/10,000 birds) or supplemented in-feed during the entire rearing period (1000, 500, and 250 g/ton according to feeding phase), or both. Only the treatments' combination produced significant results in comparison with the control group (untreated), improving feed conversion ratio from 14 to 29 d and in the overall period of the trial (1.570 vs. 1.509 and 1.643 vs. 1.596, respectively; p < 0.05) while lowering FPD occurrence at slaughter (17% vs. 5%; p < 0.05). These findings can be related to significant variations of caecal microbiota, like higher Firmicutes to Bacteroidetes ratio (with favorable implications for host's energy-harvesting potential from the diet) and more beneficial microbial consortium presumably sustaining eubiosis. Overall, these results indicate that administering synbiotics through gel droplets at the hatchery combined to in-feed supplementation for the whole growing cycle positively affects broiler feed efficiency and welfare.

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

Antimicrobial resistance (AMR) is a major public health threat. Plasmids are able to transfer AMR genes among bacterial isolates. Whole genome sequencing (WGS) is a powerful tool to monitor AMR determinants. However, plasmids are difficult to reconstruct from WGS data. This study aimed to improve the characterization, including the localization of AMR genes using short and long read WGS strategies. We used a genetically modified (GM) Bacillus subtilis isolated as unexpected contamination in a feed additive, and therefore considered unauthorized (RASFF 2014.1249), as a case study. In GM organisms, AMR genes are used as selection markers. Because of the concern of spread of these AMR genes when present on mobile genetic elements, it is crucial to characterize their location. Our approach resulted in an assembly of one chromosome and one plasmid, each with several AMR determinants of which five are against critically important antibiotics. Interestingly, we found several plasmids, containing AMR genes, integrated in the chromosome in a repetitive region of at least 53 kb. Our findings would have been impossible using short reads only. We illustrated the added value of long read sequencing in addressing the challenges of plasmid reconstruction within the context of evaluating the risk of AMR spread.

Cross-sectional study to identify risk factors associated with the occurrence of antimicrobial resistance genes in honey bees Apis mellifera) in Umbria, Central Italy

The use antimicrobials for therapeutic and metaphylactic purpose in humans and agriculture exerts selective pressure on animal and environmental microbiota resulting in the survival and spread of antimicrobial resistance genes among bacteria and subsequent development of resistance in bacteria. Previous studies have shown that honey bees' microbiota (Apis mellifera) can accumulate antimicrobial resistance genes in their microbiome and act as collectors and disseminators of resistance genes. The aim of this study was to investigate to what extent honey bees act as reservoir of select antimicrobial resistance genes. This study was conducted on 35 groups of bees. Bees were collected from 35 sites in Umbria, Italy. PCR was used to screen pooled ground bees' specimens for genes that code for resistance against antimicrobials that are commonly used in humans and in veterinary medicine including aminoglycosides (aph), beta-lactams (blaZ), tetracycline (tetM) and sulphonamides (sul1 and sul2). Twenty-four samples out of 35 (68.57%) were positive for at least one antimicrobial resistance gene. Two samples were positive for the aph, 5.71%; eight for blaZ, 22.86%; three for tetM, 8.57%; ten for sul1, 28.57% and eighteen for sul2, 51.43%. Positivity to more than one antimicrobial resistance gene was observed in nine samples, 25.71%. The multivariate analysis identified "presence of farms nearby" as the factor most closely related to PCR positivity. Honey bees (Apis mellifera) from Umbria, Italy, carry antimicrobial resistance genes and can be used as indicators of the presence of resistance genes in the environment.

The First blaKPC Harboring Klebsiella pneumoniae ST258 Strain Isolated in Pakistan

Klebsiella pneumoniae is an important pathogen that causes pneumonia and bloodstream infections, especially in neonates and intensive care patients. The carbapenems remain an important therapeutic option for clinicians, particularly against cephalosporin-resistant Gram-negative pathogens. This increased use of carbapenems at clinics has resulted in the evolution and spread of carbapenem-resistant K. pneumoniae. In this study, we isolated six bla K. pneumoniae carbapenemase (KPC)-producing strains belonging to sequence type 258 (ST258) from clinical, environmental, and veterinary sources. Antibiotic susceptibility was performed on these isolates and the genes responsible for extended-spectrum beta-lactamases and metallo-beta-lactamase production were screened. The molecular typing was done using multilocus sequence typing. Isolated strains were resistant to various antibiotic classes, including carbapenems, and carried the carbapenem-resistant gene, blaKPC. All strains were susceptible to tigecycline and colistin. This is the first report detecting K. pneumoniae ST258 strains in Pakistan.

The Contribution of Wastewater to the Transmission of Antimicrobial Resistance in the Environment: Implications of Mass Gathering Settings

Antimicrobial resistance (AMR) is the major issue posing a serious global health threat. Low- and middle-income countries are likely to be the most affected, both in terms of impact on public health and economic burden. Recent studies highlighted the role of resistance networks on the transmission of AMR organisms, with this network being driven by complex interactions between clinical (e.g., human health, animal husbandry and veterinary medicine) and other components, including environmental factors (e.g., persistence of AMR in wastewater). Many studies have highlighted the role of wastewater as a significant environmental reservoir of AMR as it represents an ideal environment for AMR bacteria (ARB) and antimicrobial resistant genes (ARGs) to persist. Although the treatment process can help in removing or reducing the ARB load, it has limited impact on ARGs. ARGs are not degradable; therefore, they can be spread among microbial communities in the environment through horizontal gene transfer, which is the main resistance mechanism in most Gram-negative bacteria. Here we analysed the recent literature to highlight the contribution of wastewater to the emergence, persistence and transmission of AMR under different settings, particularly those associated with mass gathering events (e.g., Hajj and Kumbh Mela).

Manure Compost Is a Potential Source of Tetracycline-Resistant Escherichia coli and Tetracycline Resistance Genes in Japanese Farms

Manure compost has been thought of as a potential important route of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) from livestock to humans. To clarify the abundance of ARB and ARGs, ARB and ARGs were quantitatively determined in tetracycline-resistant Escherichia coli (harboring the tetA gene)-spiked feces in simulated composts. In the simulated composts, the concentration of spiked E. coli decreased below the detection limit at day 7. The tetA gene remained in manure compost for 20 days, although the levels of the gene decreased. Next, to clarify the field conditions of manure compost in Japan, the quantities of tetracycline-resistant bacteria, tetracycline resistance genes, and residual tetracyclines were determined using field-manure-matured composts in livestock farms. Tetracycline-resistant bacteria were detected in 54.5% of tested matured compost (6/11 farms). The copy number of the tetA gene and the concentrations of residual tetracyclines in field manure compost were significantly correlated. These results suggest that the use of antimicrobials in livestock constitutes a selective pressure, not only in livestock feces but also in manure compost. The appropriate use of antimicrobials in livestock and treatment of manure compost are important for avoiding the spread of ARB and ARGs.

European perspectives on efforts to reduce antimicrobial usage in food animal production

New regulations on veterinary medicines and medicated feed will substantially influence antimicrobial prescribing and usage throughout Europe into the future. These regulations have been informed by a very large body of work, including the substantial progress towards reduced antimicrobial usage in food animal production in a number of member states of the European Union (EU). This paper seeks to summarise European perspectives on efforts to reduce antimicrobial usage in food animal production. Work within the EU is informed by the global action plan of the World Health Organization, which includes a strategic objective to optimise the use of antimicrobial medicines in human and animal health. There is ongoing measurement of trends in antimicrobial usage and resistance throughout the EU, and detailed information on strategies to reduce the need to use antimicrobials in food animal production. Substantial scientific progress has been made on the measurement of antimicrobial usage, including at herd-level, and on the objective assessment of farm biosecurity. In a number of EU member states, monitoring systems for usage are well-established, allowing benchmarking for veterinarians and farms, and monitoring of national and industry-level trends. Several countries have introduced restrictions on antimicrobial prescribing and usage, including strategies to limit conflicts of interest around antimicrobial prescribing and usage. Further, a broad range of measures are being used across member states to reduce the need for antimicrobial usage in food animal production, focusing both at farm level and nationally. Veterinarians play a central role in the reduction of antimicrobial usage in farm animals. Ireland's National Action Plan on Antimicrobial Resistance 2017-20 (iNAP) provides an overview of Ireland's commitment to the development and implementation of a holistic, cross-sectoral 'One Health' approach to the problem of antimicrobial resistance. The new regulations offer an important springboard for further progress, in order to preserve the efficacy of existing antimicrobials, which are a critical international resource.

Control of Growth and Persistence of Listeria monocytogenes and β-Lactam-Resistant Escherichia coli by Thymol in Food Processing Settings

The main objective of this study was to evaluate the efficacy of thymol in controlling environmental contamination in food processing facilities. The effect of thymol was tested as an agent to prevent planktonic and bacterial biofilm growth of twenty-five Listeria monocytogenes isolates from a variety of foods and five Escherichia coli isolates from a farm. The E. coli isolates were positive for extended spectrum β-lactamase (ESBL) genes. All isolates and reference strains were susceptible to thymol at Minimum inhibitory concentration (MIC) values ranging from 250 to 800 μg/mL. An interesting activity of interference with biofilm formation of L. monocytogenes and E. coli was found for thymol at sub-MIC concentrations of 200, 100, 75, and 50 μg/mL. Anti-biofilm activity ranging from 59.71% to 66.90% against pre-formed 24-h-old L. monocytogenes biofilms at concentrations of 500 or 800 µg/mL, corresponding to 2× MIC, was determined against free-living forms of six isolates chosen as the best or moderate biofilm producers among the tested strains. The property of thymol to attack L. monocytogenes biofilm formation was also observed at a concentration of 100 µg/mL, corresponding to 1/4 MIC, by using a stainless-steel model to simulate the surfaces in food industries. This study gives information on the use of thymol in food processing setting.

Ethnoveterinary knowledge of farmers in bilingual regions of Switzerland - is there potential to extend veterinary options to reduce antimicrobial use?

ETHNOPHARMACOLOGICAL RELEVANCE

In the pre-antibiotic era, a broad spectrum of medicinal plants was used to treat livestock. This knowledge was neglected in European veterinary medicine for decades but kept alive by farmers. Emergence of multidrug resistant bacterial strains requires a severely restricted use of antibiotics in veterinary medicine. We conducted a survey on the ethnoveterinary knowledge of farmers in the bilingual (French and German speaking) Western region of Switzerland, namely the cantons of Fribourg, Neuchâtel and Jura, and in the French speaking part of the canton of Bern.

AIM OF THE STUDY

To find out whether differences exist in plants used by farmers in French speaking and bilingual regions of Switzerland as compared to our earlier studies conducted in Switzerland. Additional focus was on plants that are used in diseases which commonly are treated with antimicrobials, on plants used in skin afflictions, and on plants used in animal species such as horses, for which the range of veterinary medicinal products is limited.

MATERIAL AND METHODS

We conducted in 2015 semistructured interviews with 62 dialog partners, mainly cattle keeping farmers but also 18 horse keeping farmers. Of these, 41 were native French (FNS) and 21 native German speakers (GNS). Detailed information about homemade herbal remedies (plant species, plant part, manufacturing process) and the corresponding use reports (target animal species, category of use, route of administration, dosage, source of knowledge, frequency of use, last time of use and farmers satisfaction) were collected.

RESULTS

A total of 345 homemade remedies were reported, of which 240 contained only one plant species (Homemade Single Species Herbal Remedy Reports; HSHR). A total of 289 use reports (UR) were mentioned for the 240 HSHR, and they comprised 77 plant species belonging to 41 botanical families. Of these, 35 plant species were solely reported from FNS, 20 from GNS, and 22 from both. Taking into account earlier ethnoveterinary studies conducted in Switzerland only 10 (FNS) and 6 (GNS) plant species connected with 7% of FNS and GNS UR respectively were "unique" to the respective language group. The majority of the UR (219) was for treatment of cattle, while 38 UR were intended to treat horses. The most UR were for treatment of gastrointestinal and skin diseases. The most frequently mentioned plants were Linum usitatissimum L., Coffea L., Matricaria chamomilla L., Camellia sinensis (L.) Kuntze, and Quercus robur L. for gastrointestinal diseases, and Calendula officinalis L., Hypericum perforatum L. and Sanicula europaea L. for skin afflictions.

CONCLUSION

No clear differences were found between the medicinal plants used by French native speakers and German native speakers. Several of the reported plants seem to be justified to widen the spectrum of veterinary therapeutic options in gastrointestinal and dermatological disorders in cattle and horses, and to reduce, at least to a certain degree, the need for antibiotic treatments. Our findings may help to strengthen the role of medicinal plants in veterinary research and practice, and to consider them as a further measure in official strategies for lowering the use of antibiotics.

Knowledge, Attitudes, and Perceptions Associated With Antimicrobial Stewardship Among Veterinary Students: A Multi-Country Survey From Nigeria, South Africa, and Sudan

In African countries, antimicrobial resistance (AMR) issue remains pertinent. Despite this, little efforts have been made to assess the future veterinary prescribers on their knowledge, attitudes and practices (KAP) related to antimicrobial usage. This multi-country survey attempts to explore the KAP of future veterinarians on stewardship of antimicrobial and identify knowledge gaps. Eight veterinary schools participated from Nigeria, Sudan and South Africa. Data regarding perceptions and knowledge were analyzed using Chi-square χ² test, Spearman's (Rho) Rank order correlation and factor analysis using principal component factoring extraction method. Fifty-two percent of the study participants were final year veterinary students, respectively, and majority (77.2%) had no previous knowledge of biomedical sciences. Majority age were 22-27 years (24.7 ± 2.8) 79% and multiple career fields post-graduation were preferred. Overall, poor perceptions and knowledge of antimicrobial stewardship were observed with variations among countries and only 36.3% (n = 123) of the students were confident in their ability to choose the ideal antimicrobial agents for a specific patient/group of animals. The majority of the final year students were confident of their knowledge regarding AMR (68%), making of Gram staining (69.2%) and in choosing the most ideal route for administering a specific antimicrobial (74.7%). The final year students had significantly (p < 0.05) higher confidence level for knowledge compared with the pre-final year students. Tetracyclines, penicillins, and sulphonamides represent the three most abused veterinary antimicrobials with similar ranking across countries. South African (69.7 ± 20.5) and Sudanese (68.1 ± 15.4) had significantly (p < 0.0001) higher mean scores compared to the Nigerian students (44.3 ± 6.8) in the student's ability to correctly match some specific antimicrobials against their classes but Nigerian students performed better in ranking antimicrobials. This survey revealed poor to average knowledge of antimicrobial stewardship among veterinary students with significant knowledge gaps across the countries. It is recommended that the relevant regulatory and standardization authorities should make concerted efforts and interventions to regularly review curricula to ensure the delivery of targeted formative and normative training, and improved lectures on antimicrobial usage and stewardship in order to improve the awareness and behaviors of future prescribers. The identified knowledge gaps of veterinary medical students on antimicrobial stewardship must be bridge to safeguard the future.

Effect of the Addition of Humic Substances as Growth Promoter in Broiler Chickens Under Two Feeding Regimens

Simple Summary

The rapid spread of antimicrobial-resistant genes in bacterial communities is a threat to human, animal, and environmental health that continues to progress inflexibly. Humic substances (HS) are promising complex molecules as an alternative to reduce the use of growth promoter antibiotics (GPA) in animal feeds. Improvements in productivity, intestinal health, immune response, and antioxidant status have been reported in broilers supplemented with HS. In the present study, broilers fed with an extract of HS (EHS) from a worm compost had similar carcass yield and excretion of coccidian oocysts but increased Clostridium perfringens and lactic acid bacteria (LAB) compared to broilers fed diets added with GPA. Broilers subjected to feed restriction had reduced growth performance and meat quality. These results confirm the growth-promoting effect of ESH, which could be explained by higher abundance of the beneficial LAB and by reducing the multiplication of harmful parasites in the gut of broilers.

Abstract

Humic substances (HS) from different sources have been evaluated to replace or reduce the use of growth promoter antibiotics (GPA) in the feeds of broiler chickens. The objective was to evaluate the growth performance, tibia measurements, nutrient balance, meat quality, and microbiological status of broiler fed with an HS extract (EHS) under ad libitum (ADLIB) or feed restriction (REST). Individually caged broilers (n = 180, 14–35 day of age) were assigned to a factorial arrangement of three dietary treatments: (1) positive control with bacitracin methylene disalicylate (BMD) and salinomycin; (2) negative control without BMD nor salinomycin, and (3) same as negative control with 0.25% EHS, and two feeding regimens 1) ADLIB or REST for 24 h on d 1, 7, and 14. Results were subjected to ANOVA. Positive control and EHS-fed broilers showed higher carcass yield (p < 0.05) and lower oocyst excretion (p < 0.01) compared to negative control birds. Lactic acid bacteria (LAB) and Clostridium perfringens (C. perfringens) were higher in negative control and EHS-broilers compared to positive control (p < 0.01). In conclusion, higher carcass yield, lower C. perfringens and oocyst excretion were found in positive control and higher carcass yield, higher LAB and lower oocyst excretion were found in EHS-fed broilers. Broilers subjected to REST had reduced growth performance and meat quality. In conclusion, EHS could be used to increase the carcass yield and beneficial LAB in broilers.

Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers

BACKGROUND

Point sources such as wastewater treatment plants (WWTPs) commonly discharge their effluent into rivers. Their waste may include antibiotic residues, disinfectants, antibiotic resistant bacteria (ARB), and Antimicrobial Resistance Genes (ARG). There is evidence that ARG can be found in the natural environment, but attribution to specific point sources is lacking.

OBJECTIVES

The goal of this study was to assess the release and dissemination of ARG from three WWTPs in southern Chile via two pathways: through the river systems, and through wild birds.

METHODS

A longitudinal study was conducted, collecting river sediment samples at different distances both upstream and downstream from each WWTP. Wild birds were sampled from around one of the WWTPs once a month for 13 months. A microfluidic q-PCR approach was used to quantify 48 genes covering different molecular mechanisms of resistance, and data was analyzed using ordination methods and linear mixed regression models.

RESULTS

There was a statistically significant increase downstream from the WWTPs (p < 0.05) for 17 ARG, but the downstream dissemination through the rivers was not clear. Beta-lactamase genes bla_KPC, bla_TEM, and bla_SHV were the most abundant in birds, with higher abundance of bla_SHV in migratory species compared to resident species (p < 0.05). The gene profile was more similar between the migratory and resident bird groups compared to the WWTP gene profile.

CONCLUSIONS

While results from this study indicate an influence of WWTPs on ARG abundance in the rivers, the biological significance of this increase and the extent of the WWTPs influence are unclear. In addition, wild birds were found to play a role in disseminating ARG, although association to the specific WWTP could not be ascertained.

Perspectives From the Science-Policy Interface in Animal Health and Welfare

The aim of this paper is to present scientific perspectives from the science-policy interface in animal health and welfare, with an emphasis on factors critical to scientific effectiveness. While there is broad acceptance of the value of scientific information to inform policy-making, interactions at the science-policy interface are not without difficulties. The literature highlights the need for scientists to build policy relevance to the research focus from the outset, to engage with policy-makers and other stakeholders throughout, to use platforms to facilitate science-policy dialogue, and to disseminate research findings appropriately. In the author's experience, there are a range of factors linked with effectiveness at the science-policy interface in animal health and welfare including a passion for public interest research, scientific independence, a commitment to scientific quality and openness, the opportunities afforded from partnership and collaboration, and an interest in strategic thinking and systems change. In an increasingly complex and rapidly changing world, an objective evidence base for policy decision-making is more important than ever. There is a need for particular attention to the value of collaboration between the natural and social sciences, a recognition among scientists and policy-makers that science is not value-free, the importance of effective communications, and the need to assess and communicate uncertainty. Further, there are particular challenges with science conducted in support of policy development for industry. It is hoped that this paper will stimulate and contribute to discussion and debate, both among scientists and between scientists and policy-makers, to increase scientific effectiveness at the science-policy interface in animal health and welfare.