Carbapenems are broad-spectrum beta (β)-lactam antimicrobials that are considered last-resort agents for the treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. The expanded use of carbapenems in clinical settings has contributed to the global emergence of carbapenem-resistant Enterobacteriaceae, which pose a major public health challenge due to limited therapeutic options and high associated morbidity and mortality (Paul et al., 2022). Although carbapenem resistance has traditionally been linked to healthcare environments, increasing evidence indicates that resistant bacteria and resistance determinants are now disseminated across diverse ecological niches beyond hospitals.

Food-producing animals have gained attention as potential reservoirs and transmission pathways for clinically relevant antimicrobial-resistant bacteria. Carbapenem-resistant and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli have been detected in livestock, companion animals, wildlife, and food products, raising concerns regarding zoonotic transmission and environmental dissemination (Köck et al., 2018). Given that carbapenems are not approved for use in animal agriculture, carbapenem resistance in food animals is thought to result from indirect selection pressure, co-selection with other antimicrobials, and horizontal gene transfer mediated by mobile genetic elements (European Food Safety Authority & European Center for Disease Prevention and Control (EFSA & ECDC, 2023).

Among antimicrobial-resistant organisms, ESBL-producing E. coli has been designated by the World Health Organization as a critical priority pathogen due to its widespread distribution, genetic plasticity, and ability to cause both intestinal and extraintestinal infections. ESBL-producing E. coli are commonly reported in food-animal reservoirs and retail meat products, and several studies have demonstrated genetic relatedness between animal-derived isolates and human clinical strains, underscoring the public health importance of the food chain as a potential route of transmission (Kanokudom et al., 2021).

In Malaysia, antimicrobial-resistant E. coli in poultry has been documented, including reports of carbapenem-resistant E. coli in live chickens and ESBL-producing strains in poultry products (Aklilu et al., 2021); (Aklilu et al., 2018). However, information remains limited regarding isolates that simultaneously exhibit carbapenem resistance and ESBL production, particularly those characterized using whole-genome sequencing. Moreover, data on the genetic backgrounds, resistance gene profiles, and virulence potential of such isolates from food animals in Malaysia are scarce.

Within a One Health framework that recognizes the interconnectedness of human, animal, and environmental health, genomic surveillance of antimicrobial-resistant bacteria in food-animal production systems is essential for early detection of high-risk lineages and mitigation of their spread. Whole-genome sequencing enables comprehensive characterization of resistance and virulence determinants and supports high-resolution tracking of globally disseminated clones. This study aimed to characterize the genome, antimicrobial resistance determinants, and virulence-associated genes of a novel carbapenem-resistant ESBL-producing E. coli ST410 isolate from poultry in Malaysia.

The genome annotation service in PATRIC uses a k-mer-based AMR gene detection method that leverages PATRIC’s curated collection of representative AMR gene sequence variants and assigns functional annotations, broad mechanisms of antibiotic resistance, drug classes, and, in some cases, the specific antibiotic to which each AMR confers resistance. A summary of the AMR and virulence genes annotated in this genome, along with the corresponding AMR mechanisms, is shown in Tables 1 and 2. Multilocus sequence typing (MLST) of the isolate, performed using MLST 2.0 (https://cge.cbs.dtu.dk/services/MLST/), showed that PR24.ERK-UMK belongs to a globally disseminated antimicrobial-resistant E. coli, ST410.

Phylogenetic analyses showed that E. coli PR24.ERK-UMK was closely related to E. coli O104:H4 str.2011-3493. The isolate also shares about 72% similarity with Shigella sp. (Shigella flexneri 2a str. 301 and Shigella boydii sb227) based on whole-genome single-nucleotide polymorphism (SNP) analysis (Figure 1). Several antibiotic resistance-conferring genes were identified, providing resistance against extended-spectrum β-lactams, carbapenems, fluoroquinolones, macrolides, and tetracyclines (Table 1).

Among the several resistance encoding genes identified are fim (Fimbrin-like protein FimI), ompF (Outer membrane porin OmpF), SbcD (Exonuclease SbcD), recD (Exodeoxyribonuclease V alpha chain (EC 3.1.11.5)), fur (Ferric uptake regulation protein), soxS (DNA-binding transcriptional dual regulator SoxS), cadB (Lysine/cadaverine antiporter membrane protein CadB), fimB (Type 1 fimbriae regulatory protein FimB), hrpA (ATP-dependent helicase HrpA) and speA (Biosynthetic arginine decarboxylase (EC 4.1.1.19)) (Figure 2).

Comparative structural analyses of the Class A beta-lactamase (EC 3.5.2.6), CTX-M family, and extended-spectrum beta-lactamase show the unique features of the isolate, implying the possible novelty of the beta-lactamase gene in this isolate (Figure 3). The whole-genome sequence was submitted to GenBank. Biosample metadata are available in the NCBI BioSample database (http://www.ncbi.nlm.nih.gov/biosample/) under accession number SAMN22160936.

Extended-spectrum β-lactamase-producing and carbapenem-resistant E. coli have become emerging problems in food animals and are a potential source of human infection and/or colonization. Although extended-spectrum β-lactam antibiotics and carbapenems are not used in poultry production in Malaysia, reports have documented the prevalence of these pathogens in chickens (Aklilu et al., 2021). This might be attributed to the fact that genes encoding carbapenemases and extended-spectrum β-lactamases are mostly plasmid-mediated, and that co-resistance may play a role in the spread of such plasmid-mediated resistance mechanisms (European Food Safety Authority & European Center for Disease Prevention and Control (EFSA & ECDC, 2023).

The identification of a carbapenem-resistant and ESBL-producing Escherichia coli ST410 isolate from poultry highlights the expanding ecological distribution of this globally disseminated high-risk clone. Although carbapenems are not used in poultry production, the presence of carbapenem-associated resistance determinants likely reflects indirect selection pressure and horizontal gene transfer mediated by plasmid-encoded co-resistance mechanisms (European Food Safety Authority & European Center for Disease Prevention and Control (EFSA & ECDC, 2023); (Paul et al., 2022). Similar observations have been reported among livestock-associated Enterobacteriaceae, suggesting that food animals may act as reservoirs for clinically relevant antimicrobial resistance genes (Kanokudom et al., 2021).

The assignment of this isolate to sequence type ST410 is notable, as this lineage has been increasingly associated with multidrug resistance and ESBL production in both human and animal sources worldwide (Paul et al., 2022); (Köck et al., 2018). This resistance profile is consistent with previously reported ST410 isolates from human and animal sources, which frequently co-harbor these mechanisms of resistance. The detection of blaCTX-M-55 and blaTEM-176, together with regulatory and efflux-related genes (acrAB-TolC, marA, soxS), supports the classification of this isolate as a multidrug-resistant lineage with enhanced adaptive potential (Alcock et al., 2023).

In addition to antimicrobial resistance, the genome harbored several virulence-associated genes consistent with extraintestinal pathogenic E. coli. Genes involved in adhesion, iron acquisition, serum survival, and stress adaptation (fimB, fyuA, irp2, iss, gad) may enhance colonization and persistence in host environments (Liu et al., 2022); (Sayers et al., 2022). The co-occurrence of resistance and virulence determinants raises concerns about zoonotic potential and underscores the value of whole-genome sequencing for the surveillance of food-animal-associated AMR pathogens.

The detection of a multidrug-resistant ExPEC ST410 strain in poultry has important public health implications, as food animals may serve as reservoirs for high-risk E. coli lineages that can be transmitted to humans through the food chain or environmental exposure. Genomically similar resistant strains have been reported across animal, food, and clinical sectors, reinforcing the need for integrated One Health surveillance approaches (Paul et al., 2022); (Kanokudom et al., 2021). Early genomic detection of such lineages in food production systems may facilitate targeted interventions to limit dissemination.

This study is limited by the analysis of a single isolate, preventing the assessment of prevalence or transmission dynamics within poultry populations. In addition, reliance on short-read sequencing limited our ability to fully resolve plasmid structures and the mobile genetic elements that mediate resistance transfer. Functional validation of resistance and virulence genes was beyond the scope of this work. Future studies incorporating larger collections of isolates, long-read sequences, and comparative analyses across animal, human, and environmental sources are warranted.

This study reports the draft genome of a carbapenem-resistant, ESBL-producing E. coli ST410 isolate from poultry in Malaysia, providing genomic evidence for the presence of a globally disseminated high-risk clone in food animal production. Despite methodological limitations, the co-occurrence of multidrug resistance and ExPEC-associated virulence determinants highlights the public health relevance of this finding. These results support the use of whole-genome sequencing as a critical tool for early detection and surveillance of priority antimicrobial-resistant lineages within a One Health framework.

The authors declare no conflict of interest.

The authors would like to express their appreciation to the Ministry of Higher Education, Malaysia (MOHE), for supporting this research. We would also like to thank the laboratory assistants at the Bacteriology, Mycology, and Virology Laboratories for their help in facilitating the research. We also extend our thanks to the Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, and the Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, for their support of this research.

During the preparation of this work, the author(s) used the built-in Microsoft Word Copilot to facilitate formatting and editing. After using this tool/service, the author(s) reviewed and edited the content as needed and take full responsibility for the content of the publication.