Antimicrobial consumption and resistance in bacteria from humans and food-producing animals: Fourth joint inter-agency report on integrated analysis of antimicrobial agent consumption and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU/EEA JIACRA IV - 2019-2021

Consumption of antimicrobials for use in food-producing animals in New Zealand, a measure of progress in reduction from 2015 to 2022

AIMS

To describe progress in the reduction of the consumption of antimicrobial drugs by food-producing animals in New Zealand to 2022 and to identify the animal production sectors where progress has been greatest, and those where opportunities remain.

METHODS

Data were sourced from official government and industry reports to update previous estimates of consumption (as sales) of antimicrobial products applied to food-producing animals in New Zealand, European countries and the USA. Antimicrobial consumption (AMC) was estimated based on the amount of active ingredient sold, per kg of animal biomass standardised to the probable weight at time of treatment or lifetime mean weight but not slaughter weight (population correction unit; PCU). This methodology is widely used for international comparisons.

RESULTS

The estimated gross consumption of antimicrobials in food-producing animals in New Zealand increased steadily from 2005 to 2013 (from 7.54 to 11.28 mg/PCU). From 2014 to 2018 the estimate flattened to a 5-year rolling mean of 10.40 mg/PCU. In 2019-2021 the consumption dropped. The NZ consumption in 2022 was substantially lower, estimated at 5.84 mg/PCU, 29% less than in 2005 and 45% less than the peak that occurred in 2017.

CONCLUSIONS

The use of antimicrobials in food-producing animals in New Zealand is at the lowest rate for nearly 20 years, at 5.8 mg/PCU. Key progress has been made particularly by the poultry industry. Clear future areas to be targeted include prophylactic use of intramammary products applied when drying off dairy cows and a more widespread strategic use in treatment of clinical mastitis.

CLINICAL RELEVANCE

Veterinarians in New Zealand should leverage the significant reduction achieved in AMC by food-producing animals by continuing to improve strategies for antimicrobial use to further reduce the risk of antimicrobial resistance.

Identifying AWaRe indicators for appropriate antibiotic use: a narrative review

INTRODUCTION

Quality indicators (QIs) are widely used tools for antibiotic stewardship programmes. The Access, Watch, Reserve (AWaRe) system has been developed by the WHO to classify antibiotics based on their spectrum of activity and potential selection of antibiotic resistance. This review aimed to identify existing indicators for optimal antibiotic use to inform the development of future AWaRe QIs.

METHODS

A literature search was performed in PubMed. We included articles describing QIs for hospital and primary healthcare antibiotic use. We extracted information about (i) the type of infection; (ii) setting; (iii) target for quality assessment; and (iv) methodology used for the development. We then identified the indicators that reflected the guidance provided in the AWaRe system.

RESULTS

A total of 773 indicators for antibiotic use were identified. The management of health services and/or workers, the consumption of antibiotics, and antibiotic prescribing/dispensing were the principal targets for quality assessment. There was a similar distribution of indicators across primary and secondary care. For infection-specific indicators, about 50% focused on respiratory tract infections. Only a few QIs included information on review treatment or microbiological investigations. Although only 8 (1%) indicators directly cited the AWaRe system in the wording of the indicators, 445 (57.6%) indicators reflected the guidance provided in the AWaRe book.

CONCLUSIONS

A high number of indicators for appropriate antibiotic use have been developed. However, few are currently based directly on the WHO AWaRe system. There is a clear need to develop globally applicable AWaRe based indicators that can be integrated into antibiotic stewardship programmes.

Ten-Year Antimicrobial Resistance Trend in Uropathogenic Escherichia coli (UPEC) Isolated from Dogs and Cats Admitted to a Veterinary Teaching Hospital in Italy

Urinary tract infections (UTIs) are a common occurrence in cats and dogs. Surveillance of antibiotic resistance trends helps in the prudent selection of suitable antimicrobial agents. However, there are limited available data on this matter in Italy. This retrospective study aimed to investigate the trends of antimicrobial resistance in uropathogenic Escherichia coli (UPEC) isolated from cats and dogs over ten years (January 2014 to October 2023). Three hundred thirty-nine UPEC strains were isolated from urine samples submitted to the Veterinary Teaching Hospital of Torino (Italy). Antimicrobial susceptibility testing was conducted for up to 11 classes of antibacterials, categorized into four categories (A, B, C, and D) following the European Medicine Agency guidelines for prudent antimicrobial use in animals. The results reveal a higher resistance towards compounds in categories C and D, while fewer isolates were resistant to antibacterials in categories B and A. Resistance has steadily increased from 2014 to 2019. Starting from 2020, a decline in resistance is evident in all four categories. The reduction is more pronounced for the categories subject to the greatest restrictions under European and national legislation. The change in resistance trend is in line with findings from other European countries and food-production animals in Italy.

Interaction Between Peroxisome Proliferator-Activated Receptors and Cannabidiol in the Gut of Chickens Applied to Different Challenge Conditions

Peroxisome proliferator-activated receptors (PPARs) are important targets for cannabidiol (CBD), which mediate many of its biological actions. The hypothesis of the present research assumed that PPARs affect the gut response to different challenge factors in chickens (C. perfringens vs. lipopolysaccharides (LPS) from E. coli), and that CBD can mediate the pathways of this response. The study proved that CBD and the challenge factors significantly affect the expression level of PPARα (p = 0.001) and selected genes determining gut barrier function. A positive correlation was demonstrated between PPARs and genes involved in the formation of tight junctions, immune, and oxidative stress responses in chickens. Dietary supplementation with CBD actively mediated the expression rate of PPARs, but the mechanism of interaction between CBD and PPARs was different depending on the stress factor used. The addition of CBD to the birds' diets did not contribute to reducing intestinal permeability under induced stress conditions nor cause stress, as indicated by the absence of elevated blood cortisol and endotoxin levels. CBD also supported the mechanisms of protecting intestinal cells from the cytotoxic effects in a C. perfringens challenge through the levels of genes involved in oxidative stress. This study indicates the importance of research toward understanding the mechanisms of PPARs as a target for enhancing intestinal barrier function, provides new results on the biological action of CBD in chickens, and shows a constant PPAR association with the jejunum mucosa of birds.

UROPOT: study protocol for a randomized, double-blind phase I/II trial for metabolism-based potentiation of antimicrobial prophylaxis in the urological tract

BACKGROUND

Urinary tract catheters, including Double-J or ureteral stents, are prone to bacterial colonization forming biofilms and leading to asymptomatic bacteriuria. In the context of asymptomatic bacteriuria, endourological procedures causing mucosa-inducing lesions can lead to severe infections. Antibiotic prophylaxis is warranted, yet its efficacy is limited by biofilm formation on stents. Biofilms promote antibiotic tolerance, the capacity of genetically susceptible bacteria to survive a normally lethal dose of antimicrobial therapy. The UROPOT study evaluates the effectiveness of a first-in-type metabolism-based aminoglycoside potentiation for (i) preventing infectious complications of asymptomatic bacteriuria during mucosa lesion-inducing endourological procedures and (ii) assessing its anti-tolerance efficacy.

METHODS

The UROPOT trial is a phase I/II single-center (Lausanne University Hospital (CHUV), Switzerland) randomized double-blinded trial. Over 2 years, patients with asymptomatic Escherichia coli and/or Klebsiella pneumoniae bacteriuria, undergoing endourological procedures, will be randomly allocated to one of three treatment arms (1:1:1 randomization ratio, 30 patients per group) to evaluate the efficacy of mannitol-potentiated low-dose amikacin compared to established standard treatments (ceftriaxone or amikacin standard dose). Patients will be recruited at the CHUV Urology Outpatient Clinic. The primary outcome is the comparative incidence of postoperative urinary tract infections (assessed at 48 h) between the investigational amikacin/mannitol therapy and standard (ceftriaxone or amikacin) antibiotic prophylaxis, defined by specific systemic symptoms and/or positive blood and/or urine culture. Secondary outcomes include assessing microbiological eradication through anti-biofilm activity, sustained microbiological eradication, and mannitol and antibiotics pharmacokinetics in blood and urine. Safety outcomes will evaluate the incidence of adverse events following amikacin/mannitol therapy and postoperative surgical complications at postoperative day 14.

DISCUSSION

UROPOT tests a novel antimicrobial strategy based on "metabolic potentiation" for prophylaxis enabling aminoglycoside dose reduction and targeting biofilm activity. The anti-biofilm effect may prove beneficial, particularly in patients who have a permanent stent in situ needing recurrent endourological manipulations strategies in preventing infections and achieving sustained microbiological eradication in pre-stented patients.

TRIAL REGISTRATION

The protocol is approved by the local ethics committee (CER-VD, 2023-01369, protocole 2.0) and the Swiss Agency for Therapeutic Products (Swissmedic, 701,676) and is registered on the NIH's ClinicalTrials.gov (trial registration number: NCT05761405). Registered on March 07, 2023.

Prevalence, Characterization, and Epidemiological Relationships between ESBL and Carbapenemase-Producing Escherichia coli, Klebsiella pneumoniae, and Acinetobacter spp. Isolated from Humans and the Kitchen Environment of Two Greek Hospitals

BACKGROUND

Extended-spectrum-β-lactamase (ESBL) and carbapenemase-producing Enterobacterales and Acinetobacter spp. pose significant challenges as nosocomial pathogens, demonstrating resistance against various antimicrobials. Their presence in food suggests that hospital kitchens could serve as antibiotic resistance reservoirs leading to patients' infection.

OBJECTIVES

The aim of this study was to assess the prevalence and characteristics of β-lactam-resistant strains of Escherichia coli, Klebsiella pneumoniae, and Acinetobacter spp. isolated from the kitchen environment and from the staff of two Greek hospitals.

METHODS

Strains were recovered after selective isolation with β-lactams and were identified with MALDI-TOF MS. Antimicrobial susceptibility and presence of common β-lactamase genes were evaluated. Protein profiles were examined to analyze potential relationships of the strain with those from hospital patients. E. coli strains were further categorized into phylogenetic groups.

RESULTS

The overall prevalence in the kitchen environment was 4.5%, 1.5%, and 15.0% for E. coli, K. pneumoniae, and Acinetobacter spp., respectively, whereas the prevalence of Acinetobacter spp. in human skin was 4.0%. Almost all strains were multidrug-resistant. All E. coli strains were ESBL producers and belonged to phylogroups A and B1. All K. pneumoniae and seven Acinetobacter strains were carbapenemase-producers. A protein profile analysis showed relatedness between chicken and kitchen environment strains, as well as between kitchen environment and patient strains originated either from the same or from different hospitals.

CONCLUSIONS

The results suggest that hospital kitchens may act as important pathogen hotspots contributing to the circulation of resistant strains in the hospital environment.

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

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

Phylogenetics and Mobilization of Genomic Traits of Cephalosporin-Resistant Escherichia coli Originated from Retail Meat

Contaminations with cephalosporin-resistant Escherichia coli across the food chain may pose a significant threat to public health because those antimicrobials are critically important in human medicine. The impact of the presented data is especially significant concerning Poland's role as one of the leading food producers in the EU. This work aimed to characterize the genomic contents of cephalosporin-resistant Escherichia coli (n = 36) isolated from retail meat to expand the official AMR monitoring reported by EFSA. The ESBL mechanism was predominant (via blaCTX-M-1 and blaSHV-12), with the AmpC-type represented by the blaCMY-2 variant. The strains harbored multiple resistance genes, mainly conferring resistance to aminoglycosides, sulfonamides, trimethoprim, tetracyclines. In some isolates, virulence factors-including intimin (eae) and its receptor (tir) were detected, indicating significant pathogenic potential. Resistance genes showed a link with IncI1 and IncB/O/K/Z plasmids. Cephalosporinases were particularly linked to ISEc9/ISEc1 (blaCTX-M-1 and blaCMY-2). The association of virulence with mobile elements was less common-mostly with IncF plasmids. The analysis of E. coli isolated from retail meat indicates accumulation of ARGs and their association with various mobile genetic elements, thus increasing the potential for the transmission of resistance across the food chain.

Genetic Diversity in Salmonella enterica in Outbreaks of Foodborne and Zoonotic Origin in the USA in 2006-2017

Whole genome sequencing is replacing traditional laboratory surveillance methods as the primary tool to track and characterize clusters and outbreaks of the foodborne and zoonotic pathogen Salmonella enterica (S. enterica). In this study, 438 S. enterica isolates representing 35 serovars and 13 broad vehicle categories from one hundred epidemiologically confirmed outbreaks were evaluated for genetic variation to develop epidemiologically relevant interpretation guidelines for Salmonella disease cluster detection. The Illumina sequences were analyzed by core genome multi-locus sequence typing (cgMLST) and screened for antimicrobial resistance (AR) determinants and plasmids. Ninety-three of the one hundred outbreaks exhibited a close allele range (less than 10 allele differences with a subset closer than 5). The remaining seven outbreaks showed increased variation, of which three were considered polyclonal. A total of 16 and 28 outbreaks, respectively, showed variations in the AR and plasmid profiles. The serovars Newport and I 4,[5],12:i:-, as well as the zoonotic and poultry product vehicles, were overrepresented among the outbreaks, showing increased variation. A close allele range in cgMLST profiles can be considered a reliable proxy for epidemiological relatedness for the vast majority of S. enterica outbreak investigations. Variations associated with mobile elements happen relatively frequently during outbreaks and could be reflective of changing selective pressures.

First Data on WGS-Based Typing and Antimicrobial Resistance of Human Salmonella Enteritidis Isolates in Greece

Salmonella enterica subsp. enterica serotype Enteritidis (S. Enteritidis) is one of the major causes of foodborne infections and is responsible for many national and multi-country foodborne outbreaks worldwide. In Greece, human salmonellosis is a mandatory notifiable disease, with laboratory surveillance being on a voluntary basis. This study aims to provide the first insights into the genetic characteristics and antimicrobial resistance profiles of 47 S. Enteritidis human isolates using whole-genome sequencing (WGS) technology. The S. Enteritidis population was mainly resistant to fluoroquinolones due to gyrA point mutations, whereas one isolate presented a multi-resistant plasmid-mediated phenotype. ST11 was the most frequent sequence type, and phylogenetic analysis through the cgMLST and SNP methods revealed considerable genetic diversity. Regarding virulence factors, 8 out of the 24 known SPIs and C63PI were detected. Due to the observed variability between countries, it is of utmost importance to record the circulating S. Enteritidis strains' structure and genomic epidemiology at the national level. WGS is a valuable tool that is revolutionizing our approach to Salmonella by providing a deeper understanding of these pathogens and their impact on human health.

From Herd Health to Public Health: Digital Tools for Combating Antibiotic Resistance in Dairy Farms

The emergence of antimicrobial resistance (AMR) is a significant threat to global food security, human health, and the future of livestock production. Higher rates of antimicrobial use in dairy farming and the sheer lack of new antimicrobials available for use focused attention on the question of how the dairy production sector contributed to the development of AMR and paved the path toward taking action to curtail it on the targeted type of farms. This paper aims to provide an introduction to a phenomenon that has gained considerable attention in the recent past due to its ever-increasing impact, the use of antimicrobial drugs, the emergence of antimicrobial resistance (AMR) on dairy farms, and seeks to discuss the possibilities of approaches such as digital health monitoring and precision livestock farming. Using sensors, data, knowledge, automation, etc., digital health monitoring, as well as Precision Livestock Farming (PLF), is expected to enhance health control and minimize disease and antimicrobial usage. The work presents a literature review on the current status and trends of AMR in dairy farms, an understanding of the concept of digital health monitoring and PLF, and the presentation and usefulness of digital health monitoring and PLF in preventing AMR. The study also analyses the strengths and weaknesses of adopting and incorporating digital technologies and artificial intelligence for dairy farming and presents areas for further study and level of use.

Advantages and drawbacks of life cycle assessment application to the pharmaceuticals: a short critical literature review

Pharmaceuticals are among the most challenging products to assess by life cycle assessment (LCA). The main drawback highlighted by LCA practitioners is the lack of inventory data, both regarding the synthesis of active pharmaceutical ingredient (API) precursors (upstream) and the details concerning the downstream phases (use and end of life). A short critical review of pharma-LCAs found in the literature is here proposed, with discussion of several tools and models used to predict the environmental impacts derived from the life cycle of pharmaceuticals, emphasizing current strengths and weaknesses, and exploring the possibilities for improvements. The case of antibiotics is selected as a representative class of pharmaceuticals, due to their massive use worldwide and the growing related issue of antimicrobial resistance enrichment, which is generally not included in most of LCAs. Also, we comment on drafting product category rules (PCRs) in the relevant field to develop standard methodologies and enhance the comparability of the studies, ultimately advocating collaboration with companies and improving inventory data quality and availability for the whole value chain of products.

Antibiotic Residues, Antimicrobial Resistance and Intervention Strategies of Foodborne Pathogens

The primary determinant of human health is undoubtedly safe food [...].