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

Abstract

Background: 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). Results: 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 bla TEM-1 , tmrB, aac(3)-IId, aadA5, mph(A), mrx, sul1, qacEΔ1 and dfrA17; while MDR-2 harbors aph(3″)-Ib, aph(6)-Id, bla TEM-1 , catA1, tet(D) and sul2. Four identical chromosomal copies of bla CTX-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 bla CTX-M-15 and bla TEM-1 genes. Conclusion: 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.

Antibiotic Sensitivity Screening of Klebsiella spp. and Raoultella spp. Isolated from Marine Bivalve Molluscs Reveal Presence of CTX-M-Producing K. pneumoniae

“…The overall results from our study are in accordance with previous studies on AMR in bacteria from the Norwegian marine environment, where low prevalence of acquired resistance was found in E. coli and Vibrio spp. [22,60,61]. In the present study, acquired resistance was only found in few K. pneumoniae isolates and in none of the other isolated species.…”

Genomic characteristics of mcr-1 and blaCTX-M-type in a single multidrug-resistant Escherichia coli ST93 from chicken in China

“…Similarly, many conjugative plasmids, such as IncF, IncI, IncK, and IncHI2, play important roles in the global dissemination of extended-spectrum β-lactamase ( ESBL ) genes, which confers resistance to most β-lactam antimicrobials, especially to third-generation cephalosporins ( Wang et al., 2018b ; Irrgang et al., 2018 ; Furlan et al., 2020 ; Grevskott et al., 2020 ). Studies over the last decade have shown that class A β-lactamases belonging to the CTX-M-type have become the predominant ESBL in many parts of the world, and have spread rapidly among clinical populations of Enterobacterales ( D'Andrea et al., 2013 ; Furlan et al., 2020 ).…”

Novel Plasmid Carrying Mobile Colistin Resistance Gene mcr-4.3 and Mercury Resistance Genes in Shewanella baltica: Insights into Mobilization of mcr-4.3 in Shewanella Species

“…In order to understand the genetic context of the mcr-4.3 gene, we determined the complete, closed genome sequence of S. baltica strain 11FHM2 (carrying mcr-4.3 and a novel catB variant), using an Oxford Nanopore MinION instrument, as described previously ( 12 ). The complete genome of strain 11FHM2 was determined to be 5,406,724 bp, with one contig representing a chromosome of 5,068,880 bp and three contigs representing novel plasmids (pSBP1, 194,145 bp; pSBP2_mcr4, 86,727 bp; and pSBP3, 56,972 bp).…”