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Pernestig, Anna-KarinORCID iD iconorcid.org/0000-0003-4221-6013
Publications (10 of 24) Show all publications
Tilevik, D., Pernestig, A.-K. & Ljungström, L. (2019). Clinical routine biomarkers in combination for early identification of patients with bacterial sepsis. In: : . Paper presented at 29th European Congress of Clinical Microbiology and Infectious Diseases, ECCMID, Amsterdam, Netherlands, 13-16 April, 2019.
Open this publication in new window or tab >>Clinical routine biomarkers in combination for early identification of patients with bacterial sepsis
2019 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Medical and Health Sciences Infectious Medicine
Research subject
Infection Biology; INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-18199 (URN)
Conference
29th European Congress of Clinical Microbiology and Infectious Diseases, ECCMID, Amsterdam, Netherlands, 13-16 April, 2019
Available from: 2020-02-07 Created: 2020-02-07 Last updated: 2020-03-13Bibliographically approved
Kokkonen, A., Tilevik, D., Pernestig, A.-K., Tilevik, A., Fagerlind, M. & Enroth, H. (2019). Clinical use of 16SrRNA Ion TorrentNext-generation sequencing and bioinformatics pipeline. In: : . Paper presented at 14th Annual Workshop in Systems Biology, University of Skövde, Sweden, 21 November 2019.
Open this publication in new window or tab >>Clinical use of 16SrRNA Ion TorrentNext-generation sequencing and bioinformatics pipeline
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2019 (English)Conference paper, Poster (with or without abstract) (Other academic)
National Category
Medical and Health Sciences Infectious Medicine
Research subject
INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-18275 (URN)
Conference
14th Annual Workshop in Systems Biology, University of Skövde, Sweden, 21 November 2019
Projects
BioMine
Funder
Knowledge Foundation
Available from: 2020-03-03 Created: 2020-03-03 Last updated: 2020-03-13Bibliographically approved
Irani Shemirani, M., Tilevik, A., Tilevik, D., Pernestig, A.-K. & Enroth, H. (2019). Comparison of Whole Genome Sequencing Pipelines for Analysis of Staphylococcus aureus Isolates from Sepsis Patients. In: : . Paper presented at 14th Annual Workshop in Systems Biology, University of Skövde, Sweden, 21 November 2019.
Open this publication in new window or tab >>Comparison of Whole Genome Sequencing Pipelines for Analysis of Staphylococcus aureus Isolates from Sepsis Patients
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2019 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Medical and Health Sciences Infectious Medicine
Research subject
INF502 Biomarkers; Infection Biology
Identifiers
urn:nbn:se:his:diva-18274 (URN)
Conference
14th Annual Workshop in Systems Biology, University of Skövde, Sweden, 21 November 2019
Projects
BioMine - Data-mining för identifiering, selektion och validering av biomarkörer
Funder
Knowledge Foundation, 20160330
Available from: 2020-03-03 Created: 2020-03-03 Last updated: 2020-03-13Bibliographically approved
Enroth, H., Retz, K., Andersson, S., Andersson, C., Svensson, K., Ljungström, L., . . . Pernestig, A.-K. (2019). Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection. Infectious Diseases, 51(4), 249-258
Open this publication in new window or tab >>Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection
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2019 (English)In: Infectious Diseases, ISSN 2374-4235, E-ISSN 2374-4243, Vol. 51, no 4, p. 249-258Article in journal (Refereed) Published
Abstract [en]

Background: Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures.

Materials and methods: During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden.

Results: The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH®assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4–98.3), when the causative agent was covered by the QuickFISH® assay.

Conclusions: The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents.

Place, publisher, year, edition, pages
Taylor & Francis, 2019
Keywords
MALDI-TOF MS analysis, QuickFISH®, sepsis diagnostics, blood culture, Maldi Sepsityper™
National Category
Other Medical Engineering Microbiology in the medical area Infectious Medicine Biomedical Laboratory Science/Technology
Research subject
Infection Biology
Identifiers
urn:nbn:se:his:diva-16603 (URN)10.1080/23744235.2018.1554258 (DOI)000465440800002 ()30729840 (PubMedID)2-s2.0-85061188564 (Scopus ID)
Funder
Knowledge Foundation
Available from: 2019-02-07 Created: 2019-02-07 Last updated: 2020-02-14Bibliographically approved
Tilevik, D., Saxenborn, P., Tilevik, A., Fagerlind, M., Lubovac-Pilav, Z., Pernestig, A.-K. & Enroth, H. (2019). Using next-generation sequencing to study biodiversity in Klebsiella spp. isolated from patients with suspected sepsis. In: : . Paper presented at 29th European Congress of Clinical Microbiology and Infectious Diseases, ECCMID, Amsterdam, Netherlands, 13-16 April, 2019.
Open this publication in new window or tab >>Using next-generation sequencing to study biodiversity in Klebsiella spp. isolated from patients with suspected sepsis
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2019 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Medical and Health Sciences Infectious Medicine Microbiology
Research subject
Infection Biology; Bioinformatics
Identifiers
urn:nbn:se:his:diva-18200 (URN)
Conference
29th European Congress of Clinical Microbiology and Infectious Diseases, ECCMID, Amsterdam, Netherlands, 13-16 April, 2019
Available from: 2020-02-07 Created: 2020-02-07 Last updated: 2020-03-12Bibliographically approved
Dave, V. P., Ngo, T. A., Pernestig, A.-K., Tilevik, D., Kanit, K., Nguyen, T., . . . Bang, D. D. (2018). MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics. Laboratory Investigation, 99(4), 452-469
Open this publication in new window or tab >>MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics
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2018 (English)In: Laboratory Investigation, ISSN 0023-6837, E-ISSN 1530-0307, Vol. 99, no 4, p. 452-469Article, review/survey (Refereed) Published
Abstract [en]

The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signaling-based, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018
Keywords
IN-SITU HYBRIDIZATION, ELECTROCHEMICAL BIOSENSORS, CIRCULATING MICRORNAS, MICROFLUIDIC PLATFORM, CANCER DIAGNOSTICS, EXPRESSION, BIOMARKERS, ACID, PROBES, RNA
National Category
Biochemistry and Molecular Biology Medical Biotechnology
Research subject
Infection Biology; INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-16509 (URN)10.1038/s41374-018-0143-3 (DOI)000462161500002 ()30542067 (PubMedID)2-s2.0-85058447908 (Scopus ID)
Projects
SMARTDIAGNOS
Funder
EU, Horizon 2020, 68797
Available from: 2018-12-18 Created: 2018-12-18 Last updated: 2020-02-14Bibliographically approved
Ljungström, L., Pernestig, A.-K., Jacobsson, G., Andersson, R., Usener, B. & Tilevik, D. (2017). Diagnostic accuracy of procalcitonin, neutrophil-lymphocyte count ratio, C-reactive protein, and lactate in patients with suspected bacterial sepsis. PLoS ONE, 12(7), Article ID e018704.
Open this publication in new window or tab >>Diagnostic accuracy of procalcitonin, neutrophil-lymphocyte count ratio, C-reactive protein, and lactate in patients with suspected bacterial sepsis
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2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 7, article id e018704Article in journal (Refereed) Published
Abstract [en]

BACKGROUND:

Early recognition is a key factor to achieve improved outcomes for septic patients. Combinations of biomarkers, as opposed to single ones, may improve timely diagnosis and survival. We investigated the performance characteristics of sepsis biomarkers, alone and in combination, for diagnosis of verified bacterial sepsis using Sepsis-2 and Sepsis-3 criteria, respectively.

METHODS:

Procalcitonin (PCT), neutrophil-lymphocyte count ratio (NLCR), C-reactive protein (CRP), and lactate were determined in a total of 1,572 episodes of adult patients admitted to the emergency department on suspicion of sepsis. All sampling were performed prior to antibiotic administration. Discriminant analysis was used to construct two composite biomarkers consisting of linear combinations of the investigated biomarkers, one including three selected biomarkers (i.e., NLCR, CRP, and lactate), and another including all four (i.e., PCT, NLCR, CRP, and lactate). The diagnostic performances of the composite biomarkers as well as the individual biomarkers were compared using the area under the receiver operating characteristic curve (AUC).

RESULTS:

For diagnosis of bacterial sepsis based on Sepsis-3 criteria, the AUC for PCT (0.68; 95% CI 0.65-0.71) was comparable to the AUCs for the both composite biomarkers. Using the Sepsis-2 criteria for bacterial sepsis diagnosis, the AUC for the NLCR (0.68; 95% CI 0.65-0.71) but not for the other single biomarkers, was equal to the AUCs for the both composite biomarkers. For diagnosis of severe bacterial sepsis or septic shock based on the Sepsis-2 criteria, the AUCs for both composite biomarkers were significantly greater than those of the single biomarkers (0.85; 95% CI 0.82-0.88 for the composite three-biomarker, and 0.86; 95% CI 0.83-0.89 for the composite four-biomarker).

CONCLUSIONS:

Combinations of biomarkers can improve the diagnosis of verified bacterial sepsis in the most critically ill patients, but in less severe septic conditions either the NLCR or PCT alone exhibit equivalent performance.

Place, publisher, year, edition, pages
Public Library of Science, 2017
National Category
Clinical Medicine
Research subject
Infection Biology; INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-14004 (URN)10.1371/journal.pone.0181704 (DOI)000406634500106 ()28727802 (PubMedID)2-s2.0-85024853446 (Scopus ID)
Available from: 2017-08-18 Created: 2017-08-18 Last updated: 2020-02-14Bibliographically approved
Retz, K., Andersson, S., Andersson, C., Svensson, K., Ljungström, L., Enroth, H., . . . Pernestig, A.-K. (2017). Evaluation of the QuickFISH and the Sepsityper assays for early identification of etiological agents in bloodstream infection in a clinical routine setting. In: : . Paper presented at 27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria, 22 – 25 April 2017.
Open this publication in new window or tab >>Evaluation of the QuickFISH and the Sepsityper assays for early identification of etiological agents in bloodstream infection in a clinical routine setting
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2017 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Clinical Medicine Microbiology in the medical area
Research subject
Infection Biology; INF000
Identifiers
urn:nbn:se:his:diva-13599 (URN)
Conference
27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria, 22 – 25 April 2017
Projects
Future sepsis diagnostics
Funder
Knowledge Foundation
Available from: 2017-06-02 Created: 2017-06-02 Last updated: 2020-02-14Bibliographically approved
Ljungström, L., Jacobsson, G., Pernestig, A.-K. & Tilevik, D. (2017). The diagnostic value of PCT as biomarker in patients suspected with community-onset bacterial sepsis. In: : . Paper presented at European Congress of Clinical Microbiology and Infectious Diseases. ECCMID
Open this publication in new window or tab >>The diagnostic value of PCT as biomarker in patients suspected with community-onset bacterial sepsis
2017 (English)Conference paper, Poster (with or without abstract) (Refereed)
Place, publisher, year, edition, pages
ECCMID, 2017
Keywords
severe sepsis, sepsis definition, biomarkers, bacteraemia
National Category
Medical Biotechnology Clinical Laboratory Medicine Infectious Medicine
Research subject
Infection Biology; INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-13550 (URN)
Conference
European Congress of Clinical Microbiology and Infectious Diseases
Funder
Knowledge Foundation
Available from: 2017-05-05 Created: 2017-05-05 Last updated: 2020-02-14Bibliographically approved
Helldin, T., Pernestig, A.-K. & Tilevik, D. (2017). Towards a Clinical Support System for the Early Diagnosis of Sepsis. In: Vincent G. Duffy (Ed.), Digital Human Modeling - Applications in Health, Safety, Ergonomics, and Risk Management: Health and Safety: 8th International Conference, DHM 2017 Held as Part of HCI International 2017 Vancouver, BC, Canada, July 9–14, 2017, Proceedings, Part II. Paper presented at 8th International Conference on Digital Human Modeling and Applications in Health, Safety, Ergonomics, and Risk Management, DHM 2017, held as part of 19th International Conference on Human-Computer Interaction, HCI 2017, Vancouver, Canada, July 9–14, 2017 (pp. 23-35). Springer
Open this publication in new window or tab >>Towards a Clinical Support System for the Early Diagnosis of Sepsis
2017 (English)In: Digital Human Modeling - Applications in Health, Safety, Ergonomics, and Risk Management: Health and Safety: 8th International Conference, DHM 2017 Held as Part of HCI International 2017 Vancouver, BC, Canada, July 9–14, 2017, Proceedings, Part II / [ed] Vincent G. Duffy, Springer, 2017, p. 23-35Conference paper, Published paper (Refereed)
Abstract [en]

Early and accurate diagnosis of sepsis is critical for patientsafety. However, this is a challenging task due to the very general symptomsassociated with sepsis, the immaturity of the tools used by theclinicians as well as the time-delays associated with the diagnostic methodsused today. This paper explores current literature regarding guidelinesfor clinical decision support, and support for sepsis diagnosis inparticular, together with guidelines extracted from interviews with fourclinicians and one biomedical analyst working at a hospital and clinicallaboratory in Sweden. The results indicate the need for the developmentof visual and interactive aids for enabling early and accurate diagnosisof sepsis.

Place, publisher, year, edition, pages
Springer, 2017
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 10287
Keywords
Clinical decision support, sepsis, guidelines, system transparency, electronic health record
National Category
Computer Sciences
Research subject
Skövde Artificial Intelligence Lab (SAIL); Infection Biology; INF301 Data Science; INF502 Biomarkers
Identifiers
urn:nbn:se:his:diva-13975 (URN)10.1007/978-3-319-58466-9_3 (DOI)2-s2.0-85025140829 (Scopus ID)978-3-319-58466-9 (ISBN)978-3-319-58465-2 (ISBN)
Conference
8th International Conference on Digital Human Modeling and Applications in Health, Safety, Ergonomics, and Risk Management, DHM 2017, held as part of 19th International Conference on Human-Computer Interaction, HCI 2017, Vancouver, Canada, July 9–14, 2017
Projects
SepsIT
Available from: 2017-08-11 Created: 2017-08-11 Last updated: 2020-02-14Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-4221-6013

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