Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli

PloS One
Narjol Gonzalez-EscalonaMaria Hoffmann

Abstract

Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete Shiga toxin-producing Escherichia coli (STEC) O26:H11/H- genomes from two different sequence types (ST21 and 29), each acquired using the Nextera XT MiSeq, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read whole genome sequencing (WGS) using Nextera XT MiSeq failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobi...Continue Reading

References

Jan 1, 1983·Journal of Molecular Evolution·M NeiY Tateno
Feb 11, 1998·Clinical Microbiology Reviews·J P Nataro, J B Kaper
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Oct 14, 2004·Bioinformatics·Paul Stothard, David S Wishart
Nov 8, 2005·Journal of Clinical Microbiology·Junkal GarmendiaGad Frankel
May 13, 2006·Molecular Microbiology·Thierry WirthMark Achtman
Feb 21, 2007·Bioinformatics·Jan KrumsiekThomas Rattei
Feb 12, 2008·BMC Genomics·Ramy K AzizOlga Zagnitko
Mar 2, 2012·Emerging Infectious Diseases·Margo E Chase-ToppingDavid L Gally
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Feb 5, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Martina BielaszewskaHelge Karch
Apr 30, 2013·Virulence·Analía Inés Etcheverría, Nora Lía Padola
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Oct 10, 2013·Genome Biology and Evolution·Stefan BletzAlexander Mellmann
Feb 28, 2014·Journal of Clinical Microbiology·Katrine Grimstrup JoensenFrank M Aarestrup
Aug 22, 2014·Bioinformatics·Nicholas J Loman, Aaron R Quinlan
Apr 1, 2015·Nature Methods·Nicholas J Loman, Mick Watson
Apr 29, 2015·Nucleic Acids Research·Bhavjinder K DhillonFiona S L Brinkman
May 15, 2015·Journal of Clinical Microbiology·Katrine G JoensenFlemming Scheutz
May 23, 2015·The Journal of Infectious Diseases·Maria HoffmannEric W Brown
Jun 16, 2015·Nature Methods·Nicholas J LomanJared T Simpson
Jul 30, 2015·The Journal of Antimicrobial Chemotherapy·Kim JudgeSharon J Peacock
Nov 7, 2015·Genomics, Proteomics & Bioinformatics·Anthony Rhoads, Kin Fai Au
Jan 21, 2016·Cancer Biology & Therapy·Alexis L NorrisWinston Timp
Jan 27, 2016·Emerging Infectious Diseases·Thomas HoenenHeinz Feldmann
Feb 4, 2016·Nature·Joshua QuickMiles W Carroll
May 5, 2016·Nucleic Acids Research·David ArndtDavid S Wishart
Jun 18, 2016·Emerging Infectious Diseases·Narjol Gonzalez-EscalonaJaime Martinez-Urtaza
Jul 28, 2016·Nature Methods·Matthew LooseMichael Stout
Oct 31, 2016·Genomics, Proteomics & Bioinformatics·Hengyun LuZemin Ning
Jan 8, 2017·Nucleic Acids Research·Eric van der HelmMorten O A Sommer
Feb 22, 2017·Nature Methods·Jared T SimpsonWinston Timp

❮ Previous
Next ❯

Citations

Mar 11, 2020·Frontiers in Microbiology·Narjol Gonzalez-Escalona, Shashi K Sharma
Aug 14, 2020·Scientific Reports·Adriel Latorre-PérezCristina Vilanova
Jan 26, 2021·The Canadian Journal of Infectious Diseases & Medical Microbiology = Journal Canadien Des Maladies Infectieuses Et De La Microbiologie Médicale·Xiaojian ZhuShaogui Wan
Feb 5, 2021·Nature Communications·Leonardos MageirosSamuel K Sheppard
Dec 5, 2020·International Journal of Molecular Sciences·Zhao ChenJianghong Meng
Mar 7, 2021·Antibiotics·Georgia D KaprouMiguel Prieto
Jun 15, 2021·EcoSal Plus·Eric W BrownMarc W Allard
Oct 5, 2020·Infectious Disease Clinics of North America·Andrea EndimianiMichael R Jacobs

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP027334.1
SRR8333590
SRR8335317
CP037944
CFSAN027346
CP037947
CP037942

Software Mentioned

PHASTER
Resfinder
Ridom SeqSphere +
PacBio Hierarchical Genome Assembly Process ( HGAP3 . 0 )
Quiver
Ridom
MiSeq
HGAP
SerotypeFinder
Pacbio

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.