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  • 1.
    Berthenet, Elvire
    et al.
    Swansea University, United Kingdom.
    Yahara, Koji
    National Institute of Infectious Diseases, Toyama, Japan.
    Thorell, Kaisa
    Karolinska Institutet, Stockholm, Sweden.
    Pascoe, Ben
    University of Bath, United Kingdom.
    Meric, Guillaume
    University of Bath, United Kingdom.
    Mikhail, Jane M.
    Swansea University, United Kingdom / Cardiff University, United Kingdom.
    Engstrand, Lars
    Karolinska Institutet, Stockholm, Sweden.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Burette, Alain
    Centre Hospitalier Interrégional Edith Cavell/Site de la Basilique, Brussels, Belgium.
    Megraud, Francis
    Centre National de Référence des Campylobacters et des Hélicobacters, Bordeaux, France / University Bordeaux, France.
    Varon, Christine
    University Bordeaux, France.
    Atherton, John C.
    Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom.
    Smith, Sinead
    Trinity College Dublin, Ireland.
    Wilkinson, Thomas S.
    Swansea University Medical School, Swansea University, Microbiology and Infectious Disease Group, Swansea, United Kingdom.
    Hitchings, Matthew D.
    Swansea University, United Kingdom.
    Falush, Daniel
    University of Bath, United Kingdom.
    Sheppard, Samuel K.
    University of Bath, United Kingdom.
    A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk2018Ingår i: BMC Biology, E-ISSN 1741-7007, Vol. 16, nr 1, artikel-id 84Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND:

    Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gastric cancer. Epidemiological evidence shows that progression to cancer depends upon the host and pathogen factors, but questions remain about why cancer phenotypes develop in a minority of infected people. Here, we use comparative genomics approaches to understand how genetic variation amongst bacterial strains influences disease progression.

    RESULTS:

    We performed a genome-wide association study (GWAS) on 173 H. pylori isolates from the European population (hpEurope) with known disease aetiology, including 49 from individuals with gastric cancer. We identified SNPs and genes that differed in frequency between isolates from patients with gastric cancer and those with gastritis. The gastric cancer phenotype was associated with the presence of babA and genes in the cag pathogenicity island, one of the major virulence determinants of H. pylori, as well as non-synonymous variations in several less well-studied genes. We devised a simple risk score based on the risk level of associated elements present, which has the potential to identify strains that are likely to cause cancer but will require refinement and validation.

    CONCLUSION:

    There are a number of challenges to applying GWAS to bacterial infections, including the difficulty of obtaining matched controls, multiple strain colonization and the possibility that causative strains may not be present when disease is detected. Our results demonstrate that bacterial factors have a sufficiently strong influence on disease progression that even a small-scale GWAS can identify them. Therefore, H. pylori GWAS can elucidate mechanistic pathways to disease and guide clinical treatment options, including for asymptomatic carriers.

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  • 2.
    Enroth, Helena
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Unilabs AB.
    Engstrand, L.
    Karolinska Institute and Science for Life Laboratory.
    Infectious Diseases: Helicobacter pylori2015Ingår i: Reference Module in Biomedical Sciences, Elsevier, 2015Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    Abstract Helicobacter pylori infection is one of the most common human infections in the world. The bacteria cause peptic ulcer disease and their infection is an important factor for gastric cancer development. The bacteria are transmitted from person to person within families, with young children most often infected. The bacteria reside in the stomach for a lifetime if untreated by antimicrobial agents. Many virulence factors are known that contribute to the persistence of the bacteria in the stomach, and the bacteria harbors a pathogenicity island in its genome. The discovery of H. pylori as a cause of gastritis in the stomach led to the Nobel Prize in Physiology or Medicine 2005.

  • 3.
    Enroth, Helena
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Retz, Karolina
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Carl
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Svensson, Kristina
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection2019Ingår i: Infectious Diseases, ISSN 2374-4235, E-ISSN 2374-4243, Vol. 51, nr 4, s. 249-258Artikel i tidskrift (Refereegranskat)
    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.

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  • 4.
    Enroth, Helena
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Unilabs AB.
    Wefer, Hugo
    Clinical genomics, Science for Life Laboratories.
    Ljungström, Lars
    Dept. of Infectious Diseases, Skaraborg Hospital Skövde.
    Tilevik, Diana
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    NGS pilot study of E. coli ESBL from patients with suspected sepsis2015Konferensbidrag (Refereegranskat)
  • 5.
    Gustafsson, Erik
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Jacobsson, Gunnar
    Department of Infectious Diseases, Skaraborg Hospital, Skövde.
    Nilsson, Patric
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Enroth, Helena
    Department of Clinical Microbiology, Skaraborg Hospital, Capio Diagnostic AB, Skövde.
    Beronius, Marie Kia
    Centre for General Medicine, Kungsbacka.
    Andersson, Rune
    6Research and Development Centre, Skaraborg Hospital, Skövde, Sweden.
    Arvidson, Staffan
    Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Stockholm.
    Invasive Staphylococcus aureus strains are highly variable in PFGE patterns, agr group and exoprotein production2009Ingår i: Scandinavian Journal of Infectious Diseases, ISSN 0036-5548, E-ISSN 1651-1980, Vol. 41, nr 8, s. 577-583Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present study, we have investigated 37 invasive Staphylococcus aureus strains (collected between 1997 and 2005) from 33 human episodes of septicaemia causing either endocarditis or vertebral osteomyelitis. All S. aureus strains were typed using pulsed field gel electrophoresis (PFGE), and most strains belonged to any of 4 different PFGE clusters. There was no correlation between any of the PFGE clusters with site of infection. All strains showed highly different expression patterns of extracellular proteins, i.e. we found a vast variation in the number of proteins and amount of individual proteins expressed by the different strains. There was no correlation between any cluster of exoprotein patterns with endocarditis or with vertebral osteomyelitis. We did not find any correlation between agr group and endocarditis, as previously reported. On the other hand, a correlation between some of the PFGE clusters with a certain agr group was found. Known risk factors for S. aureus infections were observed in a majority of the patients.

  • 6.
    Irani Shemirani, Mahnaz
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Göteborg Universitet.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde.
    Comparison of Whole Genome Sequencing Pipelines for Analysis of Staphylococcus aureus Isolates from Sepsis Patients2019Konferensbidrag (Refereegranskat)
  • 7.
    Kokkonen, Alexander
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Unilabs AB.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Fagerlind, Magnus
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde.
    Clinical use of 16SrRNA Ion TorrentNext-generation sequencing and bioinformatics pipeline2019Konferensbidrag (Övrigt vetenskapligt)
  • 8.
    Ljungström, Lars
    et al.
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Enroth, Helena
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Claesson, Berndt E. B.
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Ovemyr, Ida
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Karlsson, Jesper
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Fröberg, Berit
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Brodin, Anna-Karin
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Jacobsson, Gunnar
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Andersson, Rune
    Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden..
    Karlsson, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Clinical evaluation of commercial nucleic acid amplification tests in patients with suspected sepsis2015Ingår i: BMC Infectious Diseases, E-ISSN 1471-2334, Vol. 15, nr 1, artikel-id 199Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND: Sepsis is a serious medical condition requiring timely administered, appropriate antibiotic therapy. Blood culture is regarded as the gold standard for aetiological diagnosis of sepsis, but it suffers from low sensitivity and long turnaround time. Thus, nucleic acid amplification tests (NAATs) have emerged to shorten the time to identification of causative microbes. The aim of the present study was to evaluate the clinical utility in everyday practice in the emergency department of two commercial NAATs in patients suspected with sepsis.

    METHODS: During a six-week period, blood samples were collected consecutively from all adult patients admitted to the general emergency department for suspicion of a community-onset sepsis and treated with intravenous antibiotics. Along with conventional blood cultures, multiplex PCR (Magicplex™) was performed on whole blood specimens whereas portions from blood culture bottles were used for analysis by microarray-based assay (Prove-it™). The aetiological significance of identified organisms was determined by two infectious disease physicians based on clinical presentation and expected pathogenicity.

    RESULTS: Among 382 episodes of suspected sepsis, clinically relevant microbes were detected by blood culture in 42 episodes (11%), by multiplex PCR in 37 episodes (9.7%), and by microarray in 32 episodes (8.4%). Although moderate agreement with blood culture (kappa 0.50), the multiplex PCR added diagnostic value by timely detection of 15 clinically relevant findings in blood culture-negative specimens. Results of the microarray corresponded very well to those of blood culture (kappa 0.90), but were available just marginally prior to blood culture results.

    CONCLUSIONS: The use of NAATs on whole blood specimens in adjunct to current culture-based methods provides a clinical add-on value by allowing for detection of organisms missed by blood culture. However, the aetiological significance of findings detected by NAATs should be interpreted with caution as the high analytical sensitivity may add findings that do not necessarily corroborate with the clinical diagnosis.

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  • 9.
    Ljungström, Lars R.
    et al.
    Department of Infectious Diseases, Skaraborg Hospital / CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg.
    Jacobsson, Gunnar
    Department of Infectious Diseases, Skaraborg Hospital, Skövde / CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg.
    Claesson, Berndt E. B.
    Department of Clinical Microbiology, Unilabs, Skaraborg Hospital, Skövde.
    Andersson, Rune
    CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Molecular Microbiology, Unilabs, Skaraborg Hospital, Skövde.
    Respiratory viral infections are underdiagnosed in patients with suspected sepsis2017Ingår i: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 36, nr 10, s. 1767-1776Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The study aim was to investigate the prevalence and clinical relevance of viral findings by multiplex PCR from the nasopharynx of clinically septic patients during a winter season. During 11 weeks of the influenza epidemic period in January-March 2012, consecutive adult patients suspected to be septic (n = 432) were analyzed with cultures from blood and nasopharynx plus multiplex PCR for respiratory viruses on the nasopharyngeal specimen. The results were compared with those from microbiology analyses ordered as part of standard care. During the winter season, viral respiratory pathogens, mainly influenza A virus, human metapneumovirus, coronavirus, and respiratory syncytial virus were clinically underdiagnosed in 70% of patients positive by the multiplex PCR assay. During the first four weeks of the influenza epidemic, few tests for influenza were ordered by clinicians, indicating low awareness that the epidemic had started. Nasopharyngeal findings of Streptococcus pneumoniae and Haemophilus influenzae by culture correlated to pneumonia diagnosis, and in those patients laboratory signs of viral co-infections were common but rarely suspected by clinicians. The role of respiratory viral infections in patients presenting with a clinical picture of sepsis is underestimated. Specific antiviral treatment might be beneficial in some cases and may reduce spread in a hospital setting. Diagnosing viral infections may promote reduction of unnecessary antibiotic use. It can also be a tool for decisions concerning patient logistics, in order to minimize exposure of susceptible patients and personnel.

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  • 10.
    Nolskog, Peter
    et al.
    Department of Communicable Disease Control and Prevention, Region of Västra Götaland, Skaraborg Hospital, Skövde, Sweden.
    Backhaus, Erik
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Nasic, Salmir
    Research and Development Centre, Skaraborg Hospital, Skövde, Sweden.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Clinical molecular microbiology, Laboratory Medicine, Unilabs, Skövde, Sweden.
    STI with Mycoplasma genitalium: More common than Chlamydia trachomatis in patients attending youth clinics in Sweden2019Ingår i: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 38, nr 1, s. 81-86Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The prevalence of Chlamydia trachomatis in Sweden is well known, whereas the prevalence of Mycoplasma genitalium is less well documented. Youth clinics offer free contraception advice, sexually transmitted infection (STI) testing and/or contact tracing for the age group 15–25 years. The main objective of this study was to determine the prevalence of STIs, the presence of symptoms and the role of contact tracing. From July 2013 to March 2014, 1001 persons, 509 women and 492 men, were included in this study of six youth clinics in the Region of Västra Götaland. Symptoms were registered and whether the patient was tested because of contract tracing. Collection of urine samples, testing, treatment and disease registration were performed according to clinical routines. Urine samples were analysed for C. trachomatis/N. gonorrhoeae on the Cobas 4800 system (Roche). M. genitalium was analysed by lab-developed PCR. Genital infection was present in 16.8%. The prevalence of M. genitalium was higher than for C. trachomatis (9.6% and 7.1%). Men with symptoms have a significantly higher relative risk for infection with M. genitalium or C. trachomatis compared to asymptomatic men, while there is no increase for women. Contact tracing is important since positive outcome has a high relative risk for both infections. The prevalence of M. genitalium was higher than C. trachomatis in this study population. Initial testing for both C. trachomatis and M. genitalium should at least be considered for young men presenting with symptoms of genital infection. In finding positive cases, contact tracing is of great importance. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.

  • 11.
    Owemyr, Ida
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Enroth, Helena
    Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Skaraborg Hospital, Skövde, Sweden.
    Jacobsson, Gunnar
    Skaraborgs Sjukhus, Skövde, Sweden.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Karlsson, Diana
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Evaluation of microarray-based assay for identification of bloodstream bacteria in patients with suspected sepsis2013Konferensbidrag (Refereegranskat)
  • 12.
    Owemyr, Ida
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Enroth, Helena
    Unilabs AB, Skövde.
    Ljungström, Lars
    Kärnsjukhuset, Skövde.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Karlsson, Diana
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Utvärdering av microarray-baserad plattform för snabb identifiering av patogener hos patienter med misstänkt sepsis2012Konferensbidrag (Refereegranskat)
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  • 13.
    Retz, Carolina
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Enroth, Helena
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital.
    Karlsson, Diana
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    Quicker identification of Gram-positive cocci in clusters in patients with suspected sepsis2014Konferensbidrag (Refereegranskat)
    Abstract [en]

    Sepsis is the primary cause of death from infection. Globally, an estimated 18 million people die from sepsis annually, exceeding deaths caused by HIV/AIDS, breast cancer, and prostate cancer combined1. Early sepsis diagnosis and targeted antimicrobial (AM) therapy reduce the length of intensive care for patients and cost by 30%2. The current gold standard, using blood cultures (BC), takes 12-72 h to detect pathogens in the blood and even longer to identify the exact pathogen and its AM susceptibility for optimal therapy. The aim of this study was to determine whether the QuickFISHTMBC test (AdvanDx, Woburn, MA) could be robust, timesaving and specific in the clinical microbiology laboratory setting, for identification of the pathogens causing life-threatening bloodstream infections.

  • 14.
    Retz, Karolina
    et al.
    Department of Clinical Microbiology, Unilabs AB, Skövde.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde .
    Andersson, Carl
    Högskolan i Skövde.
    Svensson, Kristina
    Department of Clinical Microbiology, Unilabs AB, Skövde .
    Ljungström, Lars
    The Skaraborg Hospital, Skövde, Sweden .
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Clinical Microbiology, Unilabs AB, Skövde .
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Evaluation of the QuickFISH and the Sepsityper assays for early identification of etiological agents in bloodstream infection in a clinical routine setting2017Konferensbidrag (Refereegranskat)
  • 15.
    Saxenborn, Patricia
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Baxter, John
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Fagerlind, Magnus
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Dyrkell, Fredrik
    1928 Diagnostics, Gothenburg, Sweden.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden2021Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, artikel-id 640408Artikel i tidskrift (Refereegranskat)
    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.

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  • 16.
    Shemirani, Mahnaz Irani
    et al.
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Tilevik, Diana
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Jurcevic, Sanja
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Arnellos, Dimitrios
    1928 Diagnostics, Gothenburg, Sweden.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis2023Ingår i: BMC Infectious Diseases, E-ISSN 1471-2334, Vol. 23, nr 1, s. 39-, artikel-id 39Artikel i tidskrift (Refereegranskat)
    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.

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  • 17.
    Tilevik, Diana
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Fagerlind, Magnus
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Johansson, Markus
    1928 Diagnostics, Arvid Hedvalls backe, Gothenburg, Sweden.
    Enroth, Helena
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi. Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skaraborg Hospital, Skövde.
    Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden2022Ingår i: Microbial Pathogenesis, ISSN 0882-4010, E-ISSN 1096-1208, Vol. 173, nr Part A, artikel-id 105836Artikel i tidskrift (Refereegranskat)
    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.

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  • 18.
    Tilevik, Diana
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Saxenborn, Patricia
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Tilevik, Andreas
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Fagerlind, Magnus
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Lubovac-Pilav, Zelmina
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Pernestig, Anna-Karin
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningsmiljön Systembiologi.
    Enroth, Helena
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Using next-generation sequencing to study biodiversity in Klebsiella spp. isolated from patients with suspected sepsis2019Konferensbidrag (Refereegranskat)
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