Abstract
BackgroundEnvironmental 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).ResultsThe 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.ConclusionThis 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.
Highlights
Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health
The aim of this study was to apply a combination of long-read Nanopore and short-read Illumina-based sequencing to obtain high-quality complete genome sequences of the two Extended-spectrum β-lactamase (ESBL)-positive E. coli strains (631 and 1500) isolated from blue mussels (M. edulis) collected from coastal waters in Norway [27], in order to determine the genomic map of resistance genes and their potential for horizontal transfer
Complete genome sequences of the two CTX-Mproducing E. coli strains The Oxford Nanopore sequencing run generated 471,175 sequence reads for strain 631 and 576,474 sequence reads for strain 1500, with average read length of 7.7 kb and 6.7 kb, respectively
Summary
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). Extended-spectrum β-lactamases are a group of enzymes that hydrolyze β-lactam antibiotics, including 3rd generation cephalosporins [2]. These enzymes are divided into molecular class A, C and D, based on the protein sequences [3]. CTX-M-producing Escherichia coli are dominated by a few high-risk clones, such as sequence type (ST) 131 and ST38 [6, 7]. E. coli ST131 and ST38 are recognized as enteroaggregative E. coli (EAEC) that can cause extra-intestinal infections, including blood stream infection and urinary tract infection [8,9,10]
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