Abstract Background Klebsiella pneumoniae (Kp) is an important pathogen of humans and animals, and recent reports of ‘convergent’ strains that carry both virulence and antimicrobial resistance genes (ARGs) have raised serious public health concern. The plasmid-borne iuc locus, encoding the siderophore aerobactin, is a key virulence factor in this species. The variant iuc 3 is associated with porcine and human clinical isolates and is carried by mostly uncharacterised IncF plasmids. Methods We used a combination of short-read and long-read sequencing to characterise IncFIB(K)/IncFII iuc 3-carrying plasmids harboured by 79 Kp isolates and one K. oxytoca isolate recovered as part of two large ‘One-Health’ studies in Italy (SpARK) and Thailand (OH-DART). Adding data from public repositories gave a combined dataset of 517 iuc 3 isolates, and the plasmids were analysed using both clustering and phylogenetic methods. Findings We note seven large, convergent, plasmids from Thailand that have emerged through the hybridisation of co-circulating plasmids harbouring iuc 3 and antimicrobial resistance genes (ARGs) encoding extended-spectrum beta-lactamases (ESBLs). We were also able to identify putative parental plasmids which were mostly associated with two neighbouring meat markets, as were the hybrid plasmids. Clustering and global phylogenetic analyses resolved an iuc 3 plasmid sub-group circulating throughout Asia, with occasional examples in Europe and elsewhere. This variant carries multiple ARGs and is commonly harboured by clinical isolates, thus warranting targeted plasmid surveillance. Interpretation Our study reveals that plasmid hybridisation leading to the convergence of resistance and virulence traits may be very common, even in non-clinical (‘One-Health’) settings. Population-scale plasmid genomics makes it possible to identify putative parental plasmids, which will help to identify plasmid types that are most likely to hybridise, and what the selective consequences may be for the plasmid and host. A distinct iuc 3 plasmid sub-variant is associated with clinical isolates in Asia which requires close monitoring. Research In Context Multiple reports of ‘convergent’ clones of Klebsiella pneumoniae that combine both hypervirulence and multidrug resistance (MDR-hvKp) have been published recently; a PubMed search in November 2023 using the key words ‘convergence Klebsiella pneumoniae ’ returned 143 papers, 99 of which were published from 2020 onwards. Our study demonstrates that the hybridisation of plasmids carrying AMR and virulence genes is a frequent, ongoing, process in natural populations. The subsequent transfer of plasmids conferring both traits is thus likely to be a key driver behind the spread of convergent strains. Our study also provides an exemplar of how hybrid assemblies can facilitate large-scale global genomic plasmid epidemiology. Evidence before the study Although multiple recent reports highlight the emergence and spread of convergent Kp strains, the confluence of resistance and virulence genes within the same plasmid has not been studied at a population level, and putative parental plasmids are rarely identified. Moreover, there have been few high-resolution genomic epidemiology studies on closely related plasmids using both long and short-read data on a global scale. Added value We more than double the number of complete sequences available for plasmids harbouring iuc 3 from 58 to 139 and provide evidence on the host lineages most likely to harbour these plasmids (e.g., ST35), and epidemiological source (e.g., pig, wild animal, human). Our comparative analysis of phylogenetic and clustering approaches will help to inform future plasmid epidemiological studies. Implications The hybridisation of plasmids harbouring virulence and resistance genes occurs frequently in natural populations, even within ‘One-Health’ settings. However, the selective drivers (if any) and evolutionary consequences of this phenomenon are unclear. There is clear utility in generating closed plasmid genomes on a population scale, and targeted plasmid surveillance on a clinical sub-variant of iuc 3 plasmids is warranted.

Convergence and global epidemiology ofKlebsiella pneumoniaeplasmids harbouring theiuc3 virulence locus