Abstract:
:Antimicrobial resistance (AMR) is a major public health threat. Plasmids are able to transfer AMR genes among bacterial isolates. Whole genome sequencing (WGS) is a powerful tool to monitor AMR determinants. However, plasmids are difficult to reconstruct from WGS data. This study aimed to improve the characterization, including the localization of AMR genes using short and long read WGS strategies. We used a genetically modified (GM) Bacillus subtilis isolated as unexpected contamination in a feed additive, and therefore considered unauthorized (RASFF 2014.1249), as a case study. In GM organisms, AMR genes are used as selection markers. Because of the concern of spread of these AMR genes when present on mobile genetic elements, it is crucial to characterize their location. Our approach resulted in an assembly of one chromosome and one plasmid, each with several AMR determinants of which five are against critically important antibiotics. Interestingly, we found several plasmids, containing AMR genes, integrated in the chromosome in a repetitive region of at least 53 kb. Our findings would have been impossible using short reads only. We illustrated the added value of long read sequencing in addressing the challenges of plasmid reconstruction within the context of evaluating the risk of AMR spread.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Berbers B,Saltykova A,Garcia-Graells C,Philipp P,Arella F,Marchal K,Winand R,Vanneste K,Roosens NHC,De Keersmaecker SCJdoi
10.1038/s41598-020-61158-0subject
Has Abstractpub_date
2020-03-09 00:00:00pages
4310issue
1issn
2045-2322pii
10.1038/s41598-020-61158-0journal_volume
10pub_type
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