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2019-12-16Zeitschriftenartikel DOI: 10.25646/6557
Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430
dc.contributor.authorEpping, Lennard
dc.contributor.authorGolz, Julia C.
dc.contributor.authorKnüver, Marie-Theres
dc.contributor.authorHuber, Charlotte
dc.contributor.authorThürmer, Andrea
dc.contributor.authorWieler, Lothar H.
dc.contributor.authorStingl, Kerstin
dc.contributor.authorSemmler, Torsten
dc.date.accessioned2020-03-18T08:50:22Z
dc.date.available2020-03-18T08:50:22Z
dc.date.issued2019-12-16none
dc.identifier.other10.1186/s13099-019-0340-7
dc.identifier.urihttp://edoc.rki.de/176904/6525
dc.description.abstractBackground Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION. Results In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones. Conclusion The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectCampylobacter jejunieng
dc.subjectLong read sequencingeng
dc.subjectHybrid assemblieseng
dc.subjectAssembler comparisoneng
dc.subjectAntibiotic resistanceeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleComparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430none
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/6525-7
dc.identifier.doihttp://dx.doi.org/10.25646/6557
dc.type.versionpublishedVersionnone
local.edoc.container-titleGut Pathogensnone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://link.springer.com/article/10.1186/s13099-019-0340-7none
local.edoc.container-publisher-nameBioMed Centralnone
local.edoc.container-volume11none
local.edoc.container-issue59none
local.edoc.container-year2019none
local.edoc.container-firstpage1none
local.edoc.container-lastpage8none
local.edoc.rki-departmentProjektgruppen/Nachwuchsgruppennone
dc.description.versionPeer Reviewednone

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