Closing Clostridium botulinum Group I Genomes Using a Combination of Short- and Long-Reads

Frontiers in Microbiology
Narjol Gonzalez-Escalona, Shashi K Sharma

Abstract

Clostridium botulinum is a Gram-positive, spore-forming anaerobic bacterium that produces botulinum neurotoxin (BoNT). Closing their genomes provides information about their neurotoxin clusters' arrangement(s) and their location (e.g., chromosome or plasmid) which cannot be assessed using draft genomes. Therefore, we tested the use of long-read sequencing (nanopore sequencing) in combination with short-read sequencing to close two toxin-producing strains. These genomes could be used by the Public Health Emergency Preparedness and Response staff during botulism outbreaks. The genomes of two toxin-producing C. botulinum strains, one from an environmental sample (83F_CFSAN034202) and the other from a clinical sample (CDC51232_CFSAN034200) were sequenced using MinION and MiSeq devices. The genomes, including the chromosomes and the plasmids, were closed by a combination of long-read and short-read sequencing. They belonged to different C. botulinum sequence types (STs), with 83F belonging to ST4 and CDC51232 to ST7. A whole genome single nucleotide polymorphism (SNP) analysis clustered these two strains with strains in lineage 2 (e.g., 6CDC297) and 4 (e.g., NCTC2916) from Group I, respectively. These two strains were also bivalent ...Continue Reading

References

Jan 1, 1983·Journal of Molecular Evolution·M NeiY Tateno
Aug 8, 1998·Annals of Internal Medicine·R L ShapiroD L Swerdlow
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Nov 23, 2006·Journal of Bacteriology·K K HillJ D Marks
Jan 2, 2007·Neurotoxicity Research·Juan Segura-Aguilar, Richard M Kostrzewa
Mar 11, 2008·Applied and Environmental Microbiology·Mark J JacobsonEric A Johnson
Mar 26, 2008·Journal of Neural Transmission·D Dressler
May 27, 2008·Applied and Environmental Microbiology·Brian H RaphaelJoanne D Andreadis
Jul 18, 2008·Handbook of Clinical Neurology·Eric A Johnson, Cesare Montecucco
Oct 5, 2010·Applied and Environmental Microbiology·Amita SachdevaShashi K Sharma
Dec 15, 2010·The New England Journal of Medicine·Chen-Shan ChinMatthew K Waldor
Mar 8, 2011·Journal of Bacteriology·Andrew T CarterMichael W Peck
Jul 29, 2011·The New England Journal of Medicine·David A RaskoMatthew K Waldor
Oct 20, 2011·BMC Microbiology·Rebecca R TerilliJohn R Barr
Nov 10, 2011·Toxins·Andy Pickett, Karen Perrow
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Dec 25, 2012·Genome Biology·Xavier DidelotRosalind M Harding
Sep 27, 2013·The New England Journal of Medicine·David W EyreA Sarah Walker
Oct 10, 2013·The Journal of Infectious Diseases·Nir DoverStephen S Arnon
Jan 28, 2014·Applied and Environmental Microbiology·Narjol Gonzalez-EscalonaShashi K Sharma
Jul 18, 2014·BMC Microbiology·Brian H RaphaelSusan E Maslanka
Dec 10, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Theresa J SmithLeonard A Smith
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
May 1, 2016·The Journal of Antimicrobial Chemotherapy·Daniel R Knight, Thomas V Riley
Jun 28, 2016·Nucleic Acids Research·Tatiana TatusovaJames Ostell
Oct 26, 2018·MSphere·Molly S MoritzSabine Pellett
Dec 12, 2018·Microbiology Resource Announcements·Narjol Gonzalez-EscalonaShashi K Sharma
Apr 2, 2019·Foodborne Pathogens and Disease·Jessica L HalpinCarolina Lúquez

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP031095
SRR7532470

Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

Mauve
Albacore
MiSeq
cgMLST
MinION
Mega
SPAdes
Epi2me
PacBio
MinKNOW

Related Concepts

Related Feeds

Botulism (ASM)

Botulism is a rare but serious paralytic illness caused by a nerve toxin that is produced by the bacterium clostridium botulinum. Discover the latest research on botulism here.

Botulism

Botulism is a rare but serious paralytic illness caused by a nerve toxin that is produced by the bacterium clostridium botulinum. Discover the latest research on botulism here.

Related Papers

Microbiology Resource Announcements
Narjol Gonzalez-EscalonaShashi K Sharma
Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Francesco GiordaniFlorigio Lista
© 2021 Meta ULC. All rights reserved