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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
Scientific Reports, Volume 10, No. 1, Article 4310, Year 2020
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Description
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. © 2020, The Author(s).
Authors & Co-Authors
Berbers, Bas
Belgium, Brussels
Transversal Activities in Applied Genomics
Belgium, Leuven
Interuniversity Microelectronics Centre
Saltykova, Assia
Belgium, Brussels
Transversal Activities in Applied Genomics
Belgium, Leuven
Interuniversity Microelectronics Centre
Marchal, Kathleen
Belgium, Leuven
Interuniversity Microelectronics Centre
Belgium, Ghent
Universiteit Gent
Winand, Raf
Belgium, Brussels
Transversal Activities in Applied Genomics
Vanneste, Kevin
Belgium, Brussels
Transversal Activities in Applied Genomics
Roosens, Nancy H.C.
Belgium, Brussels
Transversal Activities in Applied Genomics
De Keersmaecker, Sigrid C.J.
Belgium, Brussels
Transversal Activities in Applied Genomics
Statistics
Citations: 47
Authors: 7
Affiliations: 3
Identifiers
Doi:
10.1038/s41598-020-61158-0
ISSN:
20452322
Research Areas
Genetics And Genomics
Study Design
Case Study
Study Approach
Qualitative