First complete genome sequences ofStreptococcus pyogenesNCTC 8198Tand CCUG 4207T, the type strain of the type species of the genusStreptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies

Salvà‐Serra, Francisco; Jaén‐Luchoro, Daniel; He, Jakobsson; Gonzales-Silès, Lucia; Karlsson, Roger; Busquets, Antonio; Gomila, Margarita; Bennasar, Antonio; Je, Russell; Fazal, Muhammad; Alexander, Sarah; Erb, Moore

doi:10.1101/2020.03.10.985267

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“…To the best of our knowledge this is the first study reporting closed complete genome sequences of CTX-M-producing E. coli strains (631 and 1500) isolated from blue mussels (Mytilus edulis) in Norway. In accordance with previous studies, we used a combination of Nanopore and Illumina sequencing and hybrid de novo assembly combining Nanopore long-reads with the accuracy of Illumina reads, for obtaining closed complete genome sequences [37][38][39][40][41].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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First complete genome sequences ofStreptococcus pyogenesNCTC 8198^Tand CCUG 4207^T, the type strain of the type species of the genusStreptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies

Abstract: First complete genome sequences of Streptococcus pyogenes NCTC 8198 T 1 and CCUG 4207 T , the type strain of the type species of the genus 2 Streptococcus: 100% match in length and sequence identity between PacBio 3 solo and Illumina plus Oxford Nanopore hybrid assemblies 4 5

Cited by 1 publication

References 94 publications

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

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

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