Introductory paragraph Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern in clinical settings worldwide. Two fundamentally different processes shape the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to patient (between-patient transfer), and the transfer of carbapenemase-encoding plasmids between enterobacteria in the gut microbiota of individual patients (within-patient transfer). The relative contribution of each process to the overall dissemination of carbapenem resistance in hospitals remains poorly understood. Here, we used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterise the dissemination routes of a pOXA-48-like carbapenemase-encoding plasmid in a hospital setting over a two-year period. Our results revealed frequent between-patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella pneumoniae and sporadically Escherichia coli . The results also identified pOXA-48 dissemination hotspots within the hospital, such as specific wards and individual rooms within wards. Using high-resolution plasmid sequence analysis, we uncovered the pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid transfer occurs in the gut of virtually every colonised patient. The complex and multifaceted epidemiological scenario exposed by this study provides insights for the development of intervention strategies to control the in-hospital spread of CPE.

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.

Introductory paragraph 28 Infections caused by carbapenemase-producing enterobacteria (CPE) are a major 29 concern in clinical settings worldwide. Two fundamentally different processes shape 30 the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to 31 patient (between-patient transfer), and the transfer of carbapenemase-encoding 32 plasmids between enterobacteria in the gut microbiota of individual patients (within-33 patient transfer). The relative contribution of each process to the overall dissemination 34 of carbapenem resistance in hospitals remains poorly understood. Here, we used 35 mechanistic models combining epidemiological data from more than 9,000 patients 36 with whole genome sequence information from 250 enterobacteria clones to 37 characterise the dissemination routes of the carbapenemase-encoding plasmid pOXA-38 48 in a hospital setting over a two-year period. Our results revealed frequent between-39 patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella 40 pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 41 dissemination hotspots within the hospital, such as specific wards and individual rooms 42 within wards. Using high-resolution plasmid sequence analysis, we uncovered the 43 pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid 44 transfer occurs in the gut of virtually every colonised patient. The complex and 45 multifaceted epidemiological scenario exposed by this study provides new insights for 46 the development of intervention strategies to control the in-hospital spread of CPE. 47 48 frequency with which this occurs in the clinical settings and its importance for the 56 dissemination of resistance at a local level remain poorly defined. 57 One of the most clinically relevant groups of nosocomial pathogens are enterobacteria 58 that produce carbapenemases (ß-lactamase enzymes able to degrade carbapenem 59 antibiotics). Among carbapenemase-producing enterobacteria (CPE), clones of 60 Klebsiella pneumoniae and Escherichia coli carrying plasmid-encoded 61 carbapenemases pose the highest clinical threat 5 . Despite their clinical relevance, 62 major gaps remain in our understanding of the epidemiology of CPE and of 63 carbapenemase-encoding plasmids. Previous work has highlighted the importance of 64 in-hospital CPE transmission from patient to patient 6,7 (between-patient transfer). 65 However, the dissemination and evolution of CPE in hospitals present an additional 66 layer of complexity: the transfer of carbapenemase-encoding plasmids between 67 enterobacteria clones in the gut microbiota of individual patients (within-patient 68 transfer) 8,9 . Understanding the relative importance of between-patient and within-69 patient transfer is of central importance for understanding the epidemiology of CPE 70 and informing intervention strategies to control the spread of carbapenem resistance 71 in clinical settings. 72One of the most frequent carbapenemases in enterobacteria is O...