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

Abstract

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.