Identification of Shiga Toxin-Producing Escherichia coli Outbreaks Using Whole Genome Sequencing.
Outbreak
STEC
Shiga toxin-producing Escherichia coli
Subtyping
WGS
Whole genome sequencing
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
11
3
2021
pubmed:
12
3
2021
medline:
2
4
2021
Statut:
ppublish
Résumé
Today, whole genome sequencing (WGS)-based typing is the gold standard approach to detect outbreaks of Shiga toxin-producing Escherichia coli (STEC) and to differentiate them from sporadic cases. Here, we describe an optimized protocol to efficiently determine the genome sequences of STEC using short read Illumina technology and provide information on helpful tools for the subsequent bioinformatic analysis.
Identifiants
pubmed: 33704749
doi: 10.1007/978-1-0716-1339-9_3
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
87-97Références
Karch H, Tarr PI, Bielaszewska M (2005) Enterohaemorrhagic Escherichia coli in human medicine. Int J Med Microbiol 295(6-7):405–418. https://doi.org/10.1016/j.ijmm.2005.06.009
doi: 10.1016/j.ijmm.2005.06.009
pubmed: 16238016
Epidemiologisches Bulletin 31/2011 (2011) Informationen zum EHEC-/HUS-Ausbruchsgeschehen von Mai bis Juli 2011 in Deutschland – Ende des Ausbruchs Robert Koch-Institut, Epidemiologie und Gesundheitsberichterstattung. doi: https://doi.org/10.25646/4517
Centers for Disease Control and Prevention (CDC). (2006). Multistate outbreak of E. coli O157:H7 infections linked to fresh spinach (FINAL UPDATE). https://www.cdc.gov/ecoli/2006/spinach-10-2006.html . Accessed 25 Jan 2020
National Institute of Health and Infectious Diseases Control Division MoHaWoJ (1998) Enterohemorrhagic Escherichia coli (verocytotoxin-producing E. coli) infection, 1996—April 1998. Infect Agents Surveill Rep 19:122–123
National Institute of Health and Infectious Diseases Control Division MoHaWoJ (1997) Verocytotoxin-producing Escherichia coli (enterohemorrhagic E. coli) infections, Japan, 1996-June 1997. Infect Agents Surveill Rep 18:153–154
Salipante SJ, SenGupta DJ, Cummings LA et al (2015) Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 53(4):1072–1079. https://doi.org/10.1128/JCM.03385-14
doi: 10.1128/JCM.03385-14
pubmed: 25631811
pmcid: 4365209
ECDC EFSA, Van Walle I et al (2019) EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food-borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC-EFSA molecular typing database. EFSA Support Publ 16(5):1337E. https://doi.org/10.2903/sp.efsa.2019.EN-1337
doi: 10.2903/sp.efsa.2019.EN-1337
Kohl TA, Harmsen D, Rothganger J et al (2018) Harmonized genome wide typing of tubercle bacilli using a web-based gene-by-gene nomenclature system. EBioMedicine 34:131–138. https://doi.org/10.1016/j.ebiom.2018.07.030
doi: 10.1016/j.ebiom.2018.07.030
pubmed: 30115606
pmcid: 6116475
Illumina, Inc. (2019) Nextera XT DNA library prep reference guide. https://support.illumina.com/sequencing/sequencing_kits/nextera_xt_dna_kit/documentation.html . Accessed 25 Jan 2020
Koser CU, Fraser LJ, Ioannou A et al (2014) Rapid single-colony whole-genome sequencing of bacterial pathogens. J Antimicrob Chemother 69(5):1275–1281. https://doi.org/10.1093/jac/dkt494
doi: 10.1093/jac/dkt494
pubmed: 24370932
Mellmann A, Bletz S, Boking T et al (2016) Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. J Clin Microbiol 54(12):2874–2881. https://doi.org/10.1128/JCM.00790-16
doi: 10.1128/JCM.00790-16
pubmed: 27558178
pmcid: 5121374
Illumina, Inc. (2019) MiSeq system guide. https://support.illumina.com/sequencing/sequencing_instruments/miseq/documentation.html . Accessed 9 Jun 2020
Babraham Institute. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ . Accessed 25 Jan 2020
Souvorov A, Agarwala R, Lipman DJ (2018) SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 19(1):153. https://doi.org/10.1186/s13059-018-1540-z
doi: 10.1186/s13059-018-1540-z
pubmed: 30286803
pmcid: 6172800
Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. https://doi.org/10.1186/1471-2105-11-595
doi: 10.1186/1471-2105-11-595
pubmed: 21143983
pmcid: 3004885
Gati NS, Middendorf-Bauchart B, Bletz S et al (2019) Origin and evolution of hybrid Shiga toxin-producing and uropathogenic Escherichia coli strains of sequence type 141. J Clin Microbiol 58(1). https://doi.org/10.1128/JCM.01309-19
Kossow A, Zhang W, Bielaszewska M et al (2016) Molecular characterization of human atypical sorbitol-fermenting enteropathogenic Escherichia coli O157 reveals high diversity. J Clin Microbiol 54(5):1357–1363. https://doi.org/10.1128/JCM.02897-15
doi: 10.1128/JCM.02897-15
pubmed: 26984976
pmcid: 4844722
Feldgarden M, Brover V, Haft DH et al (2019) Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 63(11). https://doi.org/10.1128/AAC.00483-19