Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces

Global health perspectives on antibacterial drug discovery and the preclinical pipeline

Antibacterial resistance is a global challenge that requires a coordinated international response. The current clinical pipeline largely consists of derivatives of established antibiotic classes, whereas the discovery and preclinical pipeline is diverse and innovative including new direct-acting agents with no cross-resistance with existing antibiotics. These novel compounds target pathways such as lipoprotein synthesis, lipopolysaccharide biosynthesis and transport, outer membrane assembly, peptidoglycan biosynthesis, fatty acid biosynthesis and isoprenoid biosynthesis. If these agents can be developed into safe, effective and affordable drugs, they could address a broad range of infections worldwide, benefiting large patient populations without geographical limitations. However, strategies such as indirect-acting or pathogen-specific treatments are likely to benefit small patient groups, primarily in high-income countries that have advanced health-care systems and diagnostic infrastructure. Although encouraging, the discovery and preclinical pipeline remains insufficiently robust to offset the high attrition rates typical of early-stage drug innovation and to meet global health needs.

Insights of SEDRIC, the Surveillance and Epidemiology of Drug-Resistant Infections Consortium

The increasing threat from infection with drug-resistant pathogens is among the most serious public health challenges of our time. Formed by Wellcome in 2018, the Surveillance and Epidemiology of Drug-Resistant Infections Consortium (SEDRIC) is an international think tank whose aim is to inform policy and change the way countries track, share, and analyse data relating to drug-resistant infections, by defining knowledge gaps and identifying barriers to the delivery of global surveillance. SEDRIC delivers its aims through discussions and analyses by world-leading scientists that result in recommendations and advocacy to Wellcome and others. As a result, SEDRIC has made key contributions in furthering global and national actions. Here, we look back at the work of the consortium between 2018-2024, highlighting notable successes. We provide specific examples where technical analyses and recommendations have helped to inform policy and funding priorities that will have real-world impact on the surveillance and epidemiology of infections with drug-resistant pathogens.

One Health bottom-up analysis of the dissemination pathways concerning critical priority carbapenemase- and ESBL-producing Enterobacterales from storks and beyond

BACKGROUND

'One Health' initiatives to tackle the rising risk of antimicrobial resistance (AMR) have flourished due to increasing detection of Enterobacterales producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases (CPs).

OBJECTIVES

This study aimed to conduct an in-depth holistic analysis of Escherichia coli (Ec) and Klebsiella pneumoniae (Kp) isolates recovered from landfill-foraging white stork faecal samples and clinical isolates from a nearby hospital.

METHODS

Faecal samples (n = 211) were collected from storks foraging at two landfills in Spain. Ec/Kp stork isolates were recovered on selective media and whole-genome sequencing (WGS), together with isolates obtained from the nearby hospital. These genomic data were compared with public genomes from different contexts (clinical, environmental, or animal hubs) to understand global transmission dynamics.

RESULTS

A wide range of blaESBL/blapAmpC (blaCTX-M/blaSHV-12/blaDHA) were detected in 71 stork samples (33.6%), while blaCP (blaKPC/blaNDM/blaOXA-48/blaVIM) were identified in 28 (13.3%) samples. Clonal and plasmid transmissions were evidenced inside and between both landfills. Mapping against 10 624 public Ec/Kp genomes and from those of nearby hospital revealed that identical strains (<10 allelic differences with Ec-ST38/ST131 and Kp-ST512 lineages) and epidemic plasmids (full identity/coverage with IncN/blaKPC-2, IncF/blaKPC-3, IncX3/blaNDM-7, IncL/blaOXA-48) were found from clinical isolates in countries located along the storks' migration routes.

CONCLUSIONS

Storks may be contaminated by bacterial isolates from a likely human origin and become non-human reservoirs of critical genes, which can be dispersed over long distances. Identifying strains/plasmids along the stork's routes that are identical or closely related to those described here opens new perspectives for large-scale research to understand the AMR transmission dynamics.

Evaluation of Antibiotic Resistance Mechanisms in Gram-Positive Bacteria

The prevalence of resistance in Gram-positive bacterial infections is rapidly rising, presenting a pressing global challenge for both healthcare systems and economies. The WHO categorizes these bacteria into critical, high, and medium priority groups based on the urgency for developing new antibiotics. While the first priority pathogen list was issued in 2017, the 2024 list remains largely unchanged. Despite six years having passed, the progress that has been made in developing novel treatment approaches remains insufficient, allowing antimicrobial resistance to persist and worsen on a global scale. Various strategies have been implemented to address this growing threat by targeting specific resistance mechanisms. This review evaluates antimicrobial resistance (AMR) in Gram-positive bacteria, highlighting its critical impact on global health due to the rise of multidrug-resistant pathogens. It focuses on the unique cell wall structure of Gram-positive bacteria, which influences their identification and susceptibility to antibiotics. The review explores the mechanisms of AMR, including enzymatic inactivation, modification of drug targets, limiting drug uptake, and increased drug efflux. It also examines the resistance strategies employed by high-priority Gram-positive pathogens such as Staphylococcus aureus, Streptococcus pneumoniae, and Enterococcus faecium, as identified in the WHO's 2024 priority list.

Antimicrobial resistance in Escherichia coli and Staphylococcus aureus at human-animal interfaces on Chongming Island, Shanghai: A One Health perspective

Antimicrobial resistance (AMR) is a significant concern within the One Health framework due to its ability to spread across multiple interfaces. Phenotypic data remains the primary type for AMR surveillance, but exploring association across multiple interfaces poses certain challenges. In this study, AMR phenotypic data of clinical and food animal E. coli and S. aureus from Chongming Island over the past five years were analyzed to determine key characteristics of AMR and explore its association at the human-animal interface. The clinical E. coli isolates showed significant resistance to penicillins (83.92 %), cephems (63.05 %), fluoroquinolones (62.21 %), and tetracyclines (57.77 %), while S. aureus exhibited high resistance to penicillinase-labile penicillins (90.89 %), macrolides (51.51 %), penicillinase-stable penicillins (43.96 %), and lincosamides (43.55 %). Extended-spectrum β-lactamase (ESBL)-producing E. coli isolates accounted for 53.26 % (1398/2526), while methicillin-resistant Staphylococcus aureus (MRSA) prevalence was 43.81 % (435/993). Notably, there has been an increase in the proportion of E. coli isolates resistant to 8 to 12 antimicrobial classes, and in the proportion of S. aureus isolates resistant to 5 to 9 classes. Certain multi-drug resistance (MDR) phenotypes were first identified in food animal isolates and later emerged in clinical settings. Meanwhile, several MDR phenotypes were shared between the two interfaces, with 44 identified in E. coli and 12 in S. aureus. Further co-occurrence analysis in E. coli and S. aureus identified several co-occurrence phenotypic pairs or clusters, potentially mediated by a single plasmid or multiple plasmids within a bacterium, indicating potential associations at the human-animal interface. To summarize, a heightened prevalence of MDR in clinical E. coli and S. aureus has been observed, with some MDR profiles appearing in food animals before emerging in clinical settings. The co-occurrence of phenotypic pairs or clusters underscores the potential for AMR association and transmission between humans and food animals. Within the One Health framework, integrating genomic data into AMR monitoring is a crucial next step.

Metagenomic profiling of raw wastewater in Portugal highlights microbiota and resistome signatures of public health interest beyond the usual suspects

In response to the rapid emergence and dissemination of antimicrobial resistant bacteria (ARB) and genes (ARGs), integrated surveillance systems are needed to address antimicrobial resistance (AMR) within the One Health Era. Wastewater analyses enable biomarker monitoring at the sewershed level, offering timely insights into pathogen circulation and ARB/ARGs trends originating from different compartments. During two consecutive epidemic waves of the COVID-19 pandemic in Portugal, taxonomic and functional composition of raw urban wastewater from two wastewater treatment plants (WWTPs) representing one million in equivalent population, located in the main urban areas of the country, were profiled by shotgun metagenomics. Hospital wastewater from two central hospitals located in the WWTPs catchment areas were also sequenced. The resistome and virulome were profiled using metagenomic assemblies without taxonomic constraint, and then specifically characterized for ESKAPE pathogens. Urban and hospital wastewater exhibited specific microbiota signatures, Pseudomonadota dominated in the first and Bacteroidota in the latter. Correlation network analyses highlighted 85 (out of top 100) genera co-occurring across samples. The most frequent ARGs were classified in the multidrug, tetracyclines, and Macrolides, Lincosamides, Streptogramins (MLS) classes. Links established between AMR determinants and bacterial hosts evidenced that the diversity and abundance of ARGs is not restricted to ESKAPE, being also highly predominant among emergent enteropathogens, like Aeromonas and Aliarcobacter, or in the iron (II) oxidizer Acidovorax. The Aliarcobacter genus accumulated high abundance of sulphonamides and polymyxins ARGs, while Acinetobacter and Aeromonas hosted the highest abundance of ARGs against beta-lactams. Other bacteria (e.g. Clostridioides, Francisella, Vibrio cholerae) and genes (e.g. vanA-type vancomycin resistance) of public health interest were detected, with targeted monitoring efforts being needed to establish informative baseline data. Altogether, results highlight that wastewater monitoring is a valuable component of pathogen and AMR surveillance in healthy populations, providing a community-representative snapshot of public health trends beyond priority pathogens.

A bibliometric analysis of One Health approach in research on antimicrobial resistance

Background

Antimicrobial resistance (AMR) is a global public health threat that requires actions through One Health intervention. This study aims to trace the historical development of One Health research on AMR to provide evidence supporting future research and actions.

Methods

A bibliometric analysis is conducted with One Health articles in the field of antimicrobial resistance (AMR-OH articles) retrieved from the Web of Science Core Collection (WoSCC). AMR-OH articles refer to articles in the field of AMR that simultaneously involve elements from human health and at least one other domain, including animals, environment, or plants. Three research periods were identified based on the development of global actions in combating AMR. Descriptive analysis of publications, keyword cluster analysis, annual trending topic analysis, and co-authorship analysis were conducted using R software, V OSV iewer, and Pajek.

Results

The results indicated that the percentage of AMR-OH articles among all AMR articles increased from 5.21% in 1990 to 20.01% in 2023. Key topics in the current AMR-OH articles included the mechanism of AMR, AMR epidemiology, and public health control strategies. Epidemiological research initially focused on human and animal health and then shifted to environmental factors in the third period. Research at the molecular level focused on the mechanisms of AMR transmission in various domains, along with the dynamics and diversity of antibiotic resistance genes (ARGs). The co-authorship analysis suggested a significant increase in cooperation among low- and middle-income countries in the third period.

Conclusion

The scope of epidemiological research on AMR has expanded by including human, animal, and environmental areas. Moreover, genetic and molecular level research represents the forefront of this field, offering innovative tools to combat AMR in the future. This study suggests further research to translate existing findings into practical implementation of the One Health strategy, and to support globally consistent action in combating AMR.

Innovations in genomic antimicrobial resistance surveillance

Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.

Genomics for public health and international surveillance of antimicrobial resistance

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.