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Sepsis: Genotypic analysis of clinical Klebsiella spp. using next-generation sequencing
University of Skövde, School of Bioscience. (Forskningscentrum i Systembiologi (Infektionsbiologi))
2018 (English)Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
Abstract [en]

Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response system and can occur when the immune system over- or under- reacts to an infection. Klebsiella spp. has been found to be one of the leading causes of sepsis, and the increasing occurrence of antibiotic resistance observed has become a major concern in clinical care. To study the genome and increase knowledge of the biodiversity of K. pneumoniae, K. variicola, and K. oxytoca, bacterial isolates were collected from blood, urine, nasopharynx, and wounds of patients with suspected sepsis. Next-generation sequencing was performed, and the presence of antibiotic resistance genes and plasmids were studied. Furthermore, a prediction of traits for each phylogroup was performed and the results from whole-genome sequencing were compared to phenotypic results. Among the K. pneumoniae isolates obtained, almost half had been misidentified by standard phenotypic methods and were found to be K. variicola, K. quasipneumoniae, and K. quasivariicola. A significant difference in the number of antibiotic resistance genes were observed between K. pneumoniae and K. variicola compared to K. oxytoca, however no significant difference was observed between K. pneumoniae and K. variicola, suggesting the underestimated pathogenicity of K. variicola. A genetic agreement was observed between the type of beta-lactamase harboured and presence or absence of nitrogen-fixation genes to the phylogroup, providing a way of species identification. Further studies should be conducted on the pathogenicity and virulence of K. variicola and K. quasipneumoniae to avoid misidentification, find organism-specific treatments, and narrow down the antibiotic prescription.

Place, publisher, year, edition, pages
2018. , p. 50
Keywords [en]
Sepsis, Klebsiella, systems biology, next-generation sequencing, NGS
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-15842OAI: oai:DiVA.org:his-15842DiVA, id: diva2:1225335
External cooperation
Unilabs, Skövde (Klinisk mikrobiologi och klinisk bakteriologi); SciLifeLab, Solna; Skaraborgs sjukhus, Skövde (Infektionsmottagningen)
Subject / course
Systems Biology
Educational program
Tumor Biology - Master’s Programme
Presentation
2018-05-30, G106, Högskolevägen 1, Skövde, 08:15 (English)
Supervisors
Examiners
Projects
Biodiversitet vid SepsisAvailable from: 2018-06-28 Created: 2018-06-26 Last updated: 2018-06-28Bibliographically approved

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Master thesis(2297 kB)33 downloads
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CiteExportLink to record
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Citation style
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