Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

Abstract

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...

The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities

“…The presence of the entire pOXA-48 plasmid was confirmed by sequencing the complete genomes of the 50 transconjugant clones, which also revealed the genetic relatedness of the isolates (Figure 1b). In line with previous studies 31,40 , the sequencing results revealed that a subset of isolates initially identified as K. pneumoniae in fact belonged to the species Klebsiella quasipneumoniae (n= 4) and Klebsiella variicola (n= 1). These species are also pOXA-48 hosts in our hospital 31 and so were maintained in the study (Figure 1b).…”

“…In line with previous studies 31,40 , the sequencing results revealed that a subset of isolates initially identified as K. pneumoniae in fact belonged to the species Klebsiella quasipneumoniae (n= 4) and Klebsiella variicola (n= 1). These species are also pOXA-48 hosts in our hospital 31 and so were maintained in the study (Figure 1b). distance (a measure of k-mer similarity).…”

“…These results suggest that the high cost associated with plasmid acquisition in this clade may limit in-hospital spread of pOXA-48-carrying K. pneumoniae ST1427. Conversely, pOXA-48 is commonly associated with K. pneumoniae ST11 in our hospital 31,36 , and in the four ST11 clones tested in this study, pOXA-48 produced neutral (Kpn07, Kpn20, Kpn23) or even beneficial fitness effects (Kpn22, Figure 4A)…”

“…Our experimental system is in fact inspired by the dynamics of pOXA-48 in the gut microbiota of hospitalised patients. In a recent study, we observed that once patients are colonised by a pOXA-48-carrying clone, the plasmid spreads through conjugation to other resident enterobacteria present in the gut microbiota 31 . Crucially, pOXA-48 usually persists in the gut of patients throughout the hospital stay and can be detected in subsequent hospital admissions months or years later, and not necessarily in the original colonizing strain 31 .…”

“…Third, most mathematical models of plasmid population biology study clonal or near-clonal populations. However, bacteria usually live in complex communities in which conjugative plasmids can spread between different bacterial hosts [30][31][32] . To fully understand plasmid persistence in natural bacterial populations, it will be necessary to address these limitations.…”