97 Limited genetic diversity of blaCMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae Introduction Antimicrobial resistance in Gram-negative bacteria is a worldwide growing public health problem (Davies and Davies 2010; Premanandh, Samara, and Mazen 2016). The gut is an important reservoir for resistant Gram-negative bacteria, both in humans and livestock (Carlet 2012; A. Carattoli 2008). Antimicrobial resistance in livestock has been suggested as a potential source for resistance in humans, with a growing number of studies published on this potential transmission route for antimicrobial resistance mechanisms in Gram-negative bacteria (C. Dierikx et al. 2013; Ewers et al. 2012; Berg et al. 2017). AmpC beta-lactamase-production is an example of these mechanisms as a potential source for 3rd generation cephalosporin resistance in Gram-negative bacteria (Jacoby 2009). Plasmids are an important vector for antimicrobial resistance dissemination with genes for various resistance mechanisms (e.g., AmpC beta-lactamase genes) being located on these mobile genetic elements. Incompatibility group I1 (IncI1) plasmids of the plasmid sequence type (pST) 12 have been associated with the spread of blaCMY-2, which is the most common AmpC beta-lactamase gene (Accogli et al. 2013; Alessandra Carattoli et al. 2018; Hansen et al. 2016). Recent studies show that the sequence of IncI1 plasmids is highly conserved (Pietsch et al. 2018; Roer et al. 2019; Castellanos et al. 2019; Valcek et al. 2019; Shirakawa et al. 2020). Most studies to date are based on short-read sequence mechanisms (Pietsch et al. 2018; Castellanos et al. 2019; Shirakawa et al. 2020). However, it remains challenging to study plasmid transmission using shortread sequencing data alone. Repeated sequences, often shared between plasmid and chromosomal DNA, hinder the assembly of the bacterial genome from short-read data, often resulting in contigs of which the origin, either plasmid or chromosomal, cannot be resolved (Stohr et al. 2020). This limits the interpretation of plasmid transmission by not providing accurate prediction of the total plasmid sequence. Recently, a combination of short- and long-read sequence data provided an accurate analysis, such as shown in a recent study on IncI1 plasmids of pST3 and pST7 (Valcek et al. 2019). Everything considered, the number of studies using combined short- and long-read sequencing data of IncI1-pST12 plasmids from human and livestock origin is still limited. The transmission of antimicrobial resistant bacteria within and between domains is predominantly based on the comparison of bacterial chromosome. However, when only typing the bacterial chromosome, the transmission of resistance gene-containing plasmids can go undetected. Although plasmid replicon typing combined with pMLST data can be useful to monitor the spread of plasmids through populations, more accurate 6
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