Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels ( Mytilus edulis ) in Norway

BMC Microbiology

article

Grevskott, Didrik H.¹  Salvà-Serra, Francisco²  Moore, Edward R. B.²  Marathe, Nachiket P.¹ 

[1] Department of Contaminants and Biohazards, Institute of Marine Research (IMR);Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg;Culture Collection University of Gothenburg (CCUG);Centre for Antibiotic Resistance Research (CARe), University of Gothenburg;Department of Clinical Microbiology, Sahlgrenska University Hospital;Department of Biology, University of the Balearic Islands

关键词: Norway;    Escherichia coli;    ESBL;    Nanopore;    Genome sequence;    MinION;    Long-read sequencing;    Antibiotic resistance;   

DOI  :  10.1186/s12866-020-01821-8

学科分类：放射科、核医学、医学影像

来源: BioMed Central

【 摘 要 】

Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health. This study applied a combination of long-read Oxford Nanopore MinION and short-read Illumina MiSeq-based sequencing to obtain closed complete genome sequences of two CTX-M-producing multidrug-resistant Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway, in order to understand the potential for mobility of the detected antibiotic resistance genes (ARGs). The complete genome sequence of strain 631 (E. coli sequence type 38) was assembled into a circular chromosome of 5.19 Mb and five plasmids (between 98 kb and 5 kb). The majority of ARGs cluster in close proximity to each other on the chromosome within two separate multidrug-resistance determining regions (MDRs), each flanked by IS26 transposases. MDR-1 carries blaTEM-1, tmrB, aac(3)-IId, aadA5, mph(A), mrx, sul1, qacEΔ1 and dfrA17; while MDR-2 harbors aph(3″)-Ib, aph(6)-Id, blaTEM-1, catA1, tet(D) and sul2. Four identical chromosomal copies of blaCTX-M-14 are located outside these regions, flanked by ISEc9 transposases. Strain 1500 (E. coli sequence type 191) exhibited a circular chromosome of 4.73 Mb and two plasmids (91 kb and 4 kb). The 91 kb conjugative plasmid belonging to IncI1 group carries blaCTX-M-15 and blaTEM-1 genes. This study confirms the efficacy of combining Nanopore long-read and Illumina short-read sequencing for determining complete bacterial genome sequences, enabling detection and characterization of clinically important ARGs in the marine environment in Norway, with potential for further dissemination. It also highlights the need for environmental surveillance of antibiotic resistance in low prevalence settings like Norway.

【 授权许可】

CC BY|CC0