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Fagerlind, Magnus
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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
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
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
Fagerlind, M., Stålhammar, H., Olsson, B. & Klinga-Levan, K. (2015). Expression of miRNAs in Bull Spermatozoa Correlates with Fertility Rates. Reproduction in domestic animals, 50(4), 587-594
Open this publication in new window or tab >>Expression of miRNAs in Bull Spermatozoa Correlates with Fertility Rates
2015 (English)In: Reproduction in domestic animals, ISSN 0936-6768, E-ISSN 1439-0531, Vol. 50, no 4, p. 587-594Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Blackwell Verlag, 2015
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology Genetics and Breeding
Research subject
Natural sciences; Bioinformatics
Identifiers
urn:nbn:se:his:diva-11552 (URN)10.1111/rda.12531 (DOI)000357976200009 ()25998690 (PubMedID)2-s2.0-84936986482 (Scopus ID)
Funder
Knowledge Foundation
Available from: 2015-09-24 Created: 2015-09-24 Last updated: 2018-08-23Bibliographically approved
Fagerlind, M. G., Webb, J. S., Barraud, N., McDougald, D., Jansson, A., Nilsson, P., . . . Rice, S. A. (2012). Dynamic modelling of cell death during biofilm development. Journal of Theoretical Biology, 295, 23-36
Open this publication in new window or tab >>Dynamic modelling of cell death during biofilm development
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2012 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 295, p. 23-36Article in journal (Refereed) Published
Abstract [en]

Biofilms are currently recognised as the predominant bacterial life-style and it has been suggested that biofilm development is influenced by a number of different processes such as adhesion, detachment, mass transport, quorum sensing, cell death and active dispersal. One of the least understood processes and its effects on biofilm development is cell death. However, experimental studies suggest that bacterial death is an important process during biofilm development and many studies show a relationship between cell death and dispersal in microbial biofilms. We present a model of the process of cell death during biofilm development, with a particular focus on the spatial localisation of cell death or cell damage. Three rules governing cell death or cell damage were evaluated which compared the effects of starvation, damage accumulation, and viability during biofilm development and were also used to design laboratory based experiments to test the model. Results from model simulations show that actively growing biofilms develop steep nutrient gradients within the interior of the biofilm that affect neighbouring microcolonies resulting in cell death and detachment. Two of the rules indicated that high substrate concentrations lead to accelerated cell death, in contrast to the third rule, based on the accumulation of damage, which predicted earlier cell death for biofilms grown with low substrate concentrations. Comparison of the modelling results with experimental results suggests that cell death is favoured under low nutrient conditions and that the accumulation of damage may be the main cause of cell death during biofilm development. (C) 2011 Elsevier Ltd. All rights reserved.

Place, publisher, year, edition, pages
Academic Press, 2012
Keywords
Biofilm, Individual based CA, Cell death
National Category
Natural Sciences Microbiology Microbiology in the medical area
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-5452 (URN)10.1016/j.jtbi.2011.10.007 (DOI)000299408500003 ()2-s2.0-82255169356 (Scopus ID)
Available from: 2012-02-23 Created: 2012-02-22 Last updated: 2021-08-31Bibliographically approved
Ericson, H. & Fagerlind, M. (2010). Incorporating Sunflower for Science in teacher education to increase the pedagogical information technology competence of teachers and teacher students in natural science. In: Gibson, D. & Dodge, B. (Ed.), Society for Information Technology & Teacher Education, 21st International Conference, March 29 - April 2, 2010, Sand Diego, California, USA: . Paper presented at Society for Information Technology & Teacher Education, 21st International Conference, March 29 - April 2, 2010, Sand Diego, California, USA (pp. 463-468). Association for the Advancement of Computing in Education
Open this publication in new window or tab >>Incorporating Sunflower for Science in teacher education to increase the pedagogical information technology competence of teachers and teacher students in natural science
2010 (English)In: Society for Information Technology & Teacher Education, 21st International Conference, March 29 - April 2, 2010, Sand Diego, California, USA / [ed] Gibson, D. & Dodge, B., Association for the Advancement of Computing in Education, 2010, p. 463-468Conference paper, Published paper (Refereed)
Abstract [en]

The use of information and communication technology in teaching is an excellent way to visualize processes as well as promote active learning in natural science, hence providing an additional dimension in teaching. KompLIT (Competence Enhancement of Teacher Education Information Technology) is a Swedish project that aims to increase the competence in pedagogical information technology for both teachers and teacher students. As part of this project the software Sunflower for Science has been tested and evaluated by both teachers and teacher students. Sunflower for Science consists of 26 programs in physics, chemistry and biology and uses an interactive approach that engages students with an activity-based learning. The outcome from the evaluation is that Sunflower for Science is very user-friendly, it promotes deeper learning as well as increases the students’ attitude towards chemistry.

Place, publisher, year, edition, pages
Association for the Advancement of Computing in Education, 2010
National Category
Natural Sciences
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-4510 (URN)
Conference
Society for Information Technology & Teacher Education, 21st International Conference, March 29 - April 2, 2010, Sand Diego, California, USA
Available from: 2010-12-29 Created: 2010-12-29 Last updated: 2017-11-27Bibliographically approved
Jansson, A., Fagerlind, M., Karlsson, D., Nilsson, P. & Cooley, M. (2006). In silico simulations suggest that Th-cell development is regulated by both selective and instructive mechanisms. Immunology and Cell Biology, 84(2), 218-226
Open this publication in new window or tab >>In silico simulations suggest that Th-cell development is regulated by both selective and instructive mechanisms
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2006 (English)In: Immunology and Cell Biology, ISSN 0818-9641, E-ISSN 1440-1711, Vol. 84, no 2, p. 218-226Article in journal (Refereed) Published
Abstract [en]

Th-cell differentiation is highly influenced by the local cytokine environment. Although cytokines such as IL-12 and IL-4 are known to polarize the Th-cell response towards Th1 or Th2, respectively, it is not known whether these cytokines instruct the developmental fate of uncommitted Th cells or select cells that have already been committed through a stochastic process. We present an individual based model that accommodates both stochastic and deterministic processes to simulate the dynamic behaviour of selective versus instructive Th-cell development. The predictions made by each model show distinct behaviours, which are compared with experimental observations. The simulations show that the instructive model generates an exclusive Th1 or Th2 response in the absence of an external cytokine source, whereas the selective model favours coexistence of the phenotypes. A hybrid model, including both instructive and selective development, shows behaviour similar to either the selective or the instructive model dependent on the strength of activation. The hybrid model shows the closest qualitative agreement with a number of well-established experimental observations. The predictions by each model suggest that neither pure selective nor instructive Th development is likely to be functional as exclusive mechanisms in Th1/Th2 development.

Place, publisher, year, edition, pages
Nature Publishing Group, 2006
Identifiers
urn:nbn:se:his:diva-1796 (URN)10.1111/j.1440-1711.2006.01425.x (DOI)000235590300012 ()16519740 (PubMedID)2-s2.0-33644766851 (Scopus ID)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2021-08-31Bibliographically approved
Fagerlind, M., Nilsson, P., Harlén, M., Karlsson, S., Rice, S. A. & Kjelleberg, S. (2005). Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa. Biosystems (Amsterdam. Print), 80(2), 201-213
Open this publication in new window or tab >>Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa
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2005 (English)In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 80, no 2, p. 201-213Article in journal (Refereed) Published
Abstract [en]

Pseudomonas aeruginosa is a gram-negative bacterium that causes serious illnesses, particularly in immunocompromised individuals, often with a fatal outcome. The finding that the acylated homoserine lactone quorum sensing (QS) system controls the production of virulence factors in P. aeruginosa makes this system a possible target for antimicrobial therapy. It has been suggested that an N-(3-oxododecanoyl)-homoserine lactone (3O-C12-HSL) antagonist, a QS blocker (QSB), would interfere efficiently with the quorum sensing system in P. aeruginosa and thus reduce the virulence of this pathogen. In this work, a mathematical model of the QS system in P. aeruginosa has been developed. The model was used to virtually add 3O-C12-HSL antagonists that differed in their affinity for the receptor protein and for their ability to mediate degradation of the receptor. The model suggests that very small differences in these parameters for different 3O-C12-HSL antagonists can greatly affect the success of QSB based inhibition of the QS system in P. aeruginosa. Most importantly, it is proposed that the ability of the 3O-C12-HSL antagonist to mediate degradation of LasR is the core parameter for successful QSB based inhibition of the QS system in P. aeruginosa. Finally, this study demonstrates that QSBs can shift the system to a low steady state, corresponding to an uninduced state and thus, suggests that the use of 3O-C12-HSL antagonists may constitute a promising therapeutic approach against P. aeruginosa involved infections.

Place, publisher, year, edition, pages
Elsevier, 2005
National Category
Medical and Health Sciences
Research subject
Medical sciences
Identifiers
urn:nbn:se:his:diva-1573 (URN)10.1016/j.biosystems.2004.11.008 (DOI)000228697100010 ()15823419 (PubMedID)2-s2.0-17044367383 (Scopus ID)
Available from: 2007-07-23 Created: 2007-07-23 Last updated: 2017-12-12Bibliographically approved
Fagerlind, M., Rice, S. A., Nilsson, P., Harlén, M., James, S., Charlton, T. & Kjelleberg, S. (2003). The Role of Regulators in the Expression of Quorum-Sensing Signals in Pseudomonas aeruginosa. Journal of Molecular Microbiology and Biotechnology, 6(2), 88-100
Open this publication in new window or tab >>The Role of Regulators in the Expression of Quorum-Sensing Signals in Pseudomonas aeruginosa
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2003 (English)In: Journal of Molecular Microbiology and Biotechnology, ISSN 1464-1801, Vol. 6, no 2, p. 88-100Article in journal (Refereed) Published
Abstract [en]

Quorum-sensing systems provide Pseudomonas aeruginosa with a sensitive regulatory mechanism that allows for the induction of several phenotypic genes in a cell density fashion. In this work, a mathematical model of the acylated homoserine lactones regulatory network system in P. aeruginosa has been developed. It is the first integrated model to consider both quorum-sensing systems. The model has allowed us to disentangle the complex behavior exhibited by the system as the concentration of extracellular OdDHL is increased. At either low or high levels of extracellular OdDHL, the bacterium remains in an uninduced or induced state, respectively. At moderate levels, the behavior is characterized by several states. Here, the bacteria can switch suddenly from an uninduced to an induced phenotype in response to small changes in the concentration of extracellular OdDHL. Additionally, we have been able to address the roles of RsaL and Vfr as regulators of the quorum-sensing system. An important result from this analysis suggests that RsaL will increase the concentration of extracellular OdDHL required to induce the system, and it is a key regulator of the inhibition of the quorum-sensing system under low cell densities. Most importantly, our results suggest that Vfr has strong regulatory effects on the system as an increased affinity between the LasR/OdDHL complex, and the lasR promoter leads to significant qualitative changes in induction patterns. We also show experimental data that demonstrate that Vfr is required for signal production in the early phase of growth, but that in the latter stages of growth, the vfr mutant is able to synthesize wild-type levels of signal.

Place, publisher, year, edition, pages
S. Karger, 2003
Identifiers
urn:nbn:se:his:diva-1966 (URN)10.1159/000076739 (DOI)000220720100003 ()15044827 (PubMedID)2-s2.0-1642588338 (Scopus ID)
Available from: 2007-10-10 Created: 2007-10-10 Last updated: 2017-11-27Bibliographically approved
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