Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.

Scientific Reports
Bas BerbersSigrid C J De Keersmaecker

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 re...Continue Reading

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Citations

Sep 9, 2020·Emerging Microbes & Infections·Claudia E CoipanEelco Franz
Jan 24, 2021·Briefings in Bioinformatics·Dropen ShekaPaul M K Gordon
Oct 16, 2020·The Journal of Antimicrobial Chemotherapy·Tianwei ShenBrian J Werth
Mar 7, 2021·Antibiotics·Georgia D KaprouMiguel Prieto
Mar 23, 2021·Human Immunology·Taishan HuAnh Dinh

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Datasets Mentioned

BETA
2014-3557
CP041693.1
M77789.2
and
M19465.1
M29725.1
AY357120.1

Methods Mentioned

BETA
PCRs
PCR
genetic modifications

Software Mentioned

Samtools
tblastn
SeqBuilder
Berokka
Minimap2
Unicycler
Qualimap
Bandage
BLAST
ResFinder

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