The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance

Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics

Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.

Biosecurity Practices to Enhance Responsible Antimicrobial Use and Reduce the Burden of Antimicrobial Resistance

The article shows the case for using biosecurity measures to mitigate antimicrobial resistance (AMR) in beef and dairy production through actions of veterinarians and animal caretakers. The impact of biosecurity on the prevention of bacterial infections is discussed, with the goal being to reduce the need for antimicrobial drugs. This is expected to reduce the selection for AMR in pathogens and commensal bacterial organisms in beef and dairy animals. The potential impact of biosecurity on the prevention of dissemination of antimicrobial resistant bacteria and AMR genes in the environment is also described.

Modelling Interventions to Combat Antibacterial Resistance in East Africa Using Causal Bayesian Networks

Antibacterial resistance (ABR) poses significant challenges to combating infections worldwide. ABR drivers are interconnected, complicating identification of intervention points. Researchers need a systems-based perspective that considers interrelated drivers collectively. We focus on urinary tract infections (UTIs), which are increasingly impacted by emergence of multi-drug resistant (MDR) bacteria. We analysed 2,007 adult outpatients with UTIs in Kenya, Tanzania, and Uganda in 2019-2020. We applied structure learning in Bayesian networks, a graphical probabilistic model, alongside expert knowledge to construct a causal diagram of drivers of prevalence of MDR UTI. MDR prevalence was influenced more by demographic, socioeconomic and environmental conditions than recent antibiotic use. We conducted hypothetical interventions to estimate drivers' causal effects, revealing that improving education access, providing protected drinking water and flush toilets, and reducing overcrowding would decrease MDR prevalence. A systems-based approach identified underlying causal patterns contributing to prevalence of MDR, and could guide the development of complexity-aware targeted interventions.

Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.

Effects of Antimicrobial Agents Used for Dental Treatments: Impacts on the Human Oral Ecosystem and the Resistome

Antimicrobial resistance (AMR) is a major public health concern, especially with regard to bacterial resistance to antibiotics. Dentists are responsible for approximately 10% of all antibiotic prescriptions. In addition, there seems to be a lack of awareness of potential resistance toward antiseptics and biocides such as chlorhexidine digluconate (CHX) or cetylpyridinium chloride (CPC), which are commonly used in dental practice but also included in over-the-counter products. In comparison to the gut microbiome, only a small number of studies have investigated the impact of antibiotics on the oral microbiome. Amoxicillin is a commonly prescribed antibiotic in dentistry, often used in combination with metronidazole. Several studies have addressed its impact on the oral microbiome. Similarly, the effects of ciprofloxacin, clindamycin, cephazolin, and benzylpenicillin have also been examined in various studies. However, due to variations in study designs, it is difficult to compare the effects of antibiotics on the oral microbiota, and conclusions can only be drawn at the phyla level. In contrast, studies on CPC and CHX have also focused on the genus level. The oral resistome mainly contains genes involved in resistance to macrolides, MLSB (macrolide, lincosamide, and streptogramin B), lincosamide and streptogramin A, fluoroquinolone, tetracycline, or penicillin. The oral cavity therefore serves as a reservoir for antibiotic resistance genes (ARGs), which are of crucial importance both for inflammations in the oral cavity and for the treatment of the entire human organism. Therefore, dentists must weigh up the benefits and risks of using antibiotics very carefully.

Catastrophic floods and antimicrobial resistance: Interconnected threats with wide-ranging impacts

•Climate change and AMR combined worsen vulnerabilities, accelerating AMR spread.•Floods can spread AMR-related pathogens, impacting health, agriculture, and ecosystems.•Integrated strategies are needed to address climate change and AMR, enhancing sanitation.

Launching Austria's One Health network: paving the way for transdisciplinary collaborations

In the post-COVID-19 era, stakeholders, including policymakers, funders, and the public, are increasingly seeking for a cross-sectoral systems-based approach to health risks extending beyond conventional measures. Anchored on three health pillars -human, animal, and environmental- One Health offers a promising framework to effectively address this demand. While some nations have already implemented national One Health strategic plans, European countries, in general, are lagging behind the global agenda. On 22 February 2024, an initiative was launched in Austria toward addressing this gap, bringing together multiple sectors and disciplines, marking the initial step in creating a national One Health network. The workshop emphasized the importance of enhancing One Health education and addressed key topics, such as incorporating the environmental pillar of One Health as well as socio-economic and cultural drivers to further our understanding of outbreaks, and establishing trusted communication channels, including data sharing, between disciplines and sectors. Identified challenges encompassed the need for more funding of transdisciplinary research. Opportunities for advancement include initiating local One Health projects and showcasing their positive impacts. Moving forward, efforts will focus on establishing a mature and globally connected One Health framework in Austria and supporting the integration of One Health aspects into education curricula, research programs, and policies.

Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms

Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.

Genomics and Bioinformatics in One Health: Transdisciplinary Approaches for Health Promotion and Disease Prevention

The One Health concept underscores the interconnectedness of human, animal, and environmental health, necessitating an integrated, transdisciplinary approach to tackle contemporary health challenges. This perspective paper explores the pivotal role of genomics and bioinformatics in advancing One Health initiatives. By leveraging genomic technologies and bioinformatics tools, researchers can decode complex biological data, enabling comprehensive insights into pathogen evolution, transmission dynamics, and host-pathogen interactions across species and environments (or ecosystems). These insights are crucial for predicting and mitigating zoonotic disease outbreaks, understanding antimicrobial resistance patterns, and developing targeted interventions for health promotion and disease prevention. Furthermore, integrating genomic data with environmental and epidemiological information enhances the precision of public health responses. Here we discuss case studies demonstrating successful applications of genomics and bioinformatics in One Health contexts, such as including data integration, standardization, and ethical considerations in genomic research. By fostering collaboration among geneticists, bioinformaticians, epidemiologists, zoologists, and data scientists, the One Health approach can harness the full potential of genomics and bioinformatics to safeguard global health. This perspective underscores the necessity of continued investment in interdisciplinary education, research infrastructure, and policy frameworks to effectively employ these technologies in the service of a healthier planet.

Drivers of virulence and antimicrobial resistance in Gram-negative bacteria in different settings: A genomic perspective

The human gut presents a complex ecosystem harboring trillions of microorganisms living in close association with each other and the host body. Any perturbation or imbalance of the normal gut microbiota may prove detrimental to human health. Enteric infections and treatment with antibiotics pose major threats to gut microbiota health. Recent genomics-driven research has provided insights into the transmission and evolutionary dynamics of major enteric pathogens such as Escherichia coli, Klebsiella pneumoniae, Vibrio cholerae, Helicobacter pylori and Salmonella spp. Studies entailing the identification of various dominant lineages of some of these organisms based on artificial intelligence and machine learning point to the possibility of a system for prediction of antimicrobial resistance (AMR) as some lineages have a higher propensity to acquire virulence and fitness advantages. This is pertinent in the light of emerging AMR being one of the immediate threats posed by pathogenic bacteria in the form of a multi-layered fitness manifesting as phenotypic drug resistance at the level of clinics and field settings. To develop a holistic or systems-level understanding of such devastating traits, present methodologies need to be advanced with the high throughput techniques integrating community and ecosystem/niche level data across different omics platforms. The next major challenge for public health epidemiologists is understanding the interactions and functioning of these pathogens at the community level, both in the gut and outside. This would provide new insights into the dimensions of enteric bacteria in different environments and niches and would have a plausible impact on infection control strategies in terms of tackling AMR. Hence, the aim of this review is to discuss virulence and AMR in Gram-negative pathogens, the spillover of AMR and methodological advancements aimed at addressing it through a unified One Health framework applicable to the farms, the environment, different clinical settings and the human gut.

Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children

Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.

Leftover of Amoxicillin Suspension After Use by Children in the Netherlands

PURPOSE

In clinical practice, a discrepancy may exist between the prescribed amount of a drug and the commercially available pack sizes in the pharmacy, potentially contributing to drug waste. This study aimed-as an example of this phenomena-to quantify leftover of amoxicillin suspension prescribed to children, due to discrepancies between physician-prescribed and pharmacy-dispensed amounts.

METHODS

We performed a retrospective cohort study including amoxicillin suspension dispensations for patients aged 0-12 years between 2017 and 2019 utilizing the Dutch PHARMO database. Leftover amount of amoxicillin was estimated by assessing the discrepancy between the prescribed and dispensed amounts. Extrapolated amoxicillin weight and economic spillage estimates for the Netherlands were determined. The impact of two theoretical interventions on leftover amount was assessed: (1) introducing vials with half the volume of the current 100 and 30 mL vials and (2) a combination of the first intervention with a maximum of 10% round-down by the dispensing pharmacy of the prescribed dose.

RESULTS

We included 79 512 amoxicillin suspension dispensations for 62 252 patients. The mean leftover amount of amoxicillin suspension per dispensing was 27%. The yearly amount of amoxicillin leftover was 49.8 kg in the study cohort, equivalent to yearly 633 kg and €621 000 when extrapolated to the Netherlands. Employing the first theoretical intervention reduced the mean leftover per dispensing to 20%, reducing the yearly leftover to 31.6 kg amoxicillin in the study cohort, and to 400 kg and €400 000 extrapolated. The second theoretical intervention further reduced leftover to 17%, reducing the yearly leftover to 24.3 kg amoxicillin in the study cohort, and to 300 kg and €300 000 extrapolated.

CONCLUSION

Approximately a quarter of amoxicillin suspension remains as leftover per dispensing. Applying different theoretical intervention shows the potential for a significant reduction of amoxicillin leftover.

Antibiotic resistance: A key microbial survival mechanism that threatens public health

Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.