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Shemirani, M. I., Tilevik, D., Tilevik, A., Jurcevic, S., Arnellos, D., Enroth, H. & Pernestig, A.-K. (2023). Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis. BMC Infectious Diseases, 23(1), 39, Article ID 39.
Open this publication in new window or tab >>Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis
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2023 (English)In: BMC Infectious Diseases, E-ISSN 1471-2334, Vol. 23, no 1, p. 39-, article id 39Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory.

METHODS: Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement.

RESULTS: There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates.

CONCLUSIONS: Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Antimicrobial susceptibility, Benchmarking, Clinical microbiology, Illumina sequencing, S. aureus, Species identification, Virulence genes, Whole-genome sequencing
National Category
Microbiology Bioinformatics and Systems Biology Infectious Medicine Microbiology in the medical area Genetics
Research subject
Infection Biology
Identifiers
urn:nbn:se:his:diva-22199 (URN)10.1186/s12879-022-07977-0 (DOI)000921125300004 ()36670352 (PubMedID)2-s2.0-85146795212 (Scopus ID)
Funder
Knowledge Foundation, 206/0330Knowledge Foundation, 2017/14
Note

CC BY 4.0

The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Correspondence: Anna‑Karin Pernestig anna‑karin.pernestig@his.se

Open access funding provided by University of Skövde. Swedish Knowledge Foundation BioMine Grant No. 206/0330, Swedish Knowledge Foundation Associate Senior Lecturer in Systems biology, Grant No. 2017/14, Stiftelsen Tornspiran, Internal research fund, Unilabs AB.

The datasets generated and/or analysed during the current study are available in the online NCBI repository, https://www.ncbi.nlm.nih.gov/, BioProject PRJNA606666, http://www.ncbi.nlm.nih.gov/bioproject/606666

Available from: 2023-01-23 Created: 2023-01-23 Last updated: 2024-01-17Bibliographically approved
Tilevik, D., Pernestig, A.-K., Fagerlind, M., Tilevik, A., Ljungström, L., Johansson, M. & Enroth, H. (2022). Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden. Microbial Pathogenesis, 173(Part A), Article ID 105836.
Open this publication in new window or tab >>Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden
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2022 (English)In: Microbial Pathogenesis, ISSN 0882-4010, E-ISSN 1096-1208, Vol. 173, no Part A, article id 105836Article in journal (Refereed) Published
Abstract [en]

Extra-intestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a large number of human infections globally. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance, most importantly the increasing recognition of isolates producing extended-spectrum β-lactamases (ESBL). Herein, we used whole-genome sequencing (WGS) on ExPEC isolates for a comprehensive genotypic characterization. Twenty-one ExPEC isolates, nine with and 12 without ESBL-production, from 16 patients with suspected sepsis were sequenced on an Illumina MiSeq platform. Analysis of WGS data was performed with widely used bioinformatics software and tools for genotypic characterization of the isolates. A higher number of plasmids, virulence and resistance genes were observed in the ESBL-producing isolates than the non-ESBL-producing, although not statistically significant due to the low sample size. All nine ESBL-producing ExPEC isolates presented with at least one bla gene, as did three of the 12 without ESBL-production. Multi-locus sequence typing analysis revealed a diversity of sequence types whereas phylogroup A prevailed among isolates both with and without ESBL-production. In conclusion, this limited study shows that analysis of WGS data can be used for genotypic characterization of ExPEC isolates to obtain in-depth information of clinical relevance.

Place, publisher, year, edition, pages
Elsevier, 2022
Keywords
Escherichia coli isolates, Whole-genome sequencing, ESBL, Virulence, Plasmid, Resistance genes, Phylogenetic groups
National Category
Microbiology in the medical area Microbiology Infectious Medicine Genetics Medical Genetics Bioinformatics and Systems Biology
Research subject
Infection Biology
Identifiers
urn:nbn:se:his:diva-21968 (URN)10.1016/j.micpath.2022.105836 (DOI)000891651100007 ()36265734 (PubMedID)2-s2.0-85140323332 (Scopus ID)
Note

CC BY 4.0

Available online 17 October 2022

Corresponding author: Diana Tilevik

This research received no external financial support.

Available from: 2022-10-18 Created: 2022-10-18 Last updated: 2023-01-17Bibliographically approved
Saxenborn, P., Baxter, J., Tilevik, A., Fagerlind, M., Dyrkell, F., Pernestig, A.-K., . . . Tilevik, D. (2021). Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden. Frontiers in Microbiology, 12, Article ID 640408.
Open this publication in new window or tab >>Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden
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2021 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, article id 640408Article in journal (Refereed) Published
Abstract [en]

Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2021
Keywords
Klebsiella, whole-genome sequencing, antimicrobial susceptibility, clinical microbiology, multidrug resistance, nanopore-based sequencing, Illumina sequencing
National Category
Medical and Health Sciences Microbiology in the medical area
Research subject
Infection Biology
Identifiers
urn:nbn:se:his:diva-19688 (URN)10.3389/fmicb.2021.640408 (DOI)000650016100001 ()33995300 (PubMedID)2-s2.0-85105914228 (Scopus ID)
Funder
Knowledge Foundation, 206/0330
Note

CC BY 4.0

Correspondence: Diana Tilevik diana.tilevik@his.se

Available from: 2021-05-06 Created: 2021-05-06 Last updated: 2024-01-17Bibliographically approved
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; Infection Biology
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: 2021-08-31Bibliographically 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: 2022-12-29Bibliographically 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: 2021-08-31Bibliographically 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
Note

© United States & Canadian Academy of Pathology 2018. The RightsLink Digital Licensing and Rights Management Service (including RightsLink for Open Access) is available (A) to users of copyrighted works found at the websites of participating publishers who are seeking permissions or licenses to use those works, and (B) to authors of articles and other manuscripts who are seeking to pay author publication charges in connection with the submission of their works to publishers.

Available from: 2018-12-18 Created: 2018-12-18 Last updated: 2021-01-07Bibliographically 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, 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: 2021-06-14Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-8181-4131

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