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  • 1.
    Andersson, Madelen
    et al.
    Dept Infect Dis, Blekinge Hosp, Karlskrona, Sweden.
    Resman, Fredrik
    Dept Translat Med Med Microbiol, Lund Univ, Malmö, Sweden.
    Eitrem, Rickard
    Dept Communicable Dis Control, County Blekinge, Karlskrona, Sweden.
    Drobni, Peter
    Dept Clin Microbiol, County Kronoberg, Växjö, Sweden; Dept Clin Microbiol, County Kronoberg, Karlskrona, Sweden.
    Riesbeck, Kristian
    Dept Translat Med Med Microbiol, Lund Univ, Malmö, Sweden.
    Kahlmeter, Gunnar
    Dept Clin Microbiol, County Kronoberg, Växjö, Sweden; Dept Clin Microbiol, County Kronoberg, Karlskrona, Sweden; Dept Med Sci, Div Clin Bacteriol, Uppsala Univ, Uppsala, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för hälsovetenskap och medicin. Örebro universitet, Institutionen för medicinska vetenskaper. Dept Clin Microbiol, County Kronoberg, Växjö, Sweden; Dept Clin Microbiol, County Kronoberg, Karlskrona, Sweden; Dept Lab Med Clin Microbiol, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Outbreak of a beta-lactam resistant non-typeable Haemophilus influenzae sequence type 14 associated with severe clinical outcomes2015Inngår i: BMC Infectious Diseases, ISSN 1471-2334, E-ISSN 1471-2334, Vol. 15, artikkel-id 581Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: During October 2011 several residents and staff members at a long-term care facility (LTCF) for elderly fell ill with respiratory symptoms. Several of the residents required hospitalization and one died. Non-typeable Haemophilus influenzae (NTHi) was identified as the causative pathogen. Methods: A descriptive analysis of the outbreak and countermeasures was performed. For each identified bacterial isolate implied in the outbreak, standard laboratory resistance testing was performed, as well as molecular typing and phylogenetic analysis. Results: The identified H. influenzae was beta-lactamase negative but had strikingly high MIC-values of ampicillin, cefuroxime and cefotaxime. All isolates displayed the same mutation in the ftsI gene encoding penicillin-binding protein (PBP) 3, and all but one were identified as sequence type 14 by Multilocus Sequence Typing (MLST). In total 15 individuals in connection to the LTCF; 8 residents, 6 staff members and one partner to a staff member were colonized with the strain. Conclusion: This report illustrates the existence of non-typeable H. influenzae with high virulence, and furthermore emphasizes the importance of continuous surveillance of possible outbreaks in health care facilities and prompt measures when outbreaks occur.

  • 2.
    Björk, Helena
    et al.
    Dept Otorhinolaryngol, Cent Hosp Växjö, Växjö, Sweden.
    Bieber, Lena
    Dept Clin Microbiol, Cent Hosp Växjö, Växjö, Sweden.
    Hedin, Katarina
    Dept Clin Sci Family Med, Lund Univ, Malmö, Sweden; Unit Res & Dev, Kronoberg County Council, Växjö, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för hälsovetenskap och medicin. Region Örebro län. Dept Clin Microbiol, Cent Hosp Växjö, Växjö, Sweden.
    Tonsillar colonisation of Fusobacterium necrophorum in patients subjected to tonsillectomy2015Inngår i: BMC Infectious Diseases, ISSN 1471-2334, E-ISSN 1471-2334, Vol. 15, artikkel-id 264Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Fusobacterium necrophorum is a well-known cause of Lemirre's disease and accumulating evidence support its pathogenic role in peritonsillar abscess while its role in recurrent and chronic tonsillitis is uncertain. The objective of this study was to assess the prevalence of oropharyngeal colonisation with F. necrophorum and Beta-haemolytic streptococci in a cohort of patients scheduled for tonsillectomy due to recurrent or persistent throat pain, and to evaluate the dynamics of colonisation with repeated sampling during a follow-up time of 6 to 8 months. Methods: Fifty-seven (57) patients aged 15-52 years scheduled for tonsillectomy due to chronic/recurrent tonsillitis or recurrent peritonsillar abscess were included. Throat swabs for the detection of F. necrophorum and Beta-haemolytic streptococci and clinical data was collected at inclusion, at the time of surgery and 6 to 8 months after surgery. Statistical analysis was performed using the Chi-square, Fisher's exact and Mc Nemar tests. Results: Fusobacterium necrophorum was found in 28, 30 and 16 % of the patients at inclusion, surgery and follow up respectively. The corresponding results for beta-haemolytic streptococci were 5, 9 and 5 %. Patients colonised with F. necrophorum at follow-up, after tonsillectomy, were equally relieved from their previous throat pain as non-colonised patients. Looking at individual patients, the culture results for F. necrophorum varied over time, indicating a transient colonisation. Conclusion: Fusobacterium necrophorum was frequently found in throat cultures in this cohort of patients with recurrent or chronic throat pain leading to tonsillectomy. Colonisation was equally frequent in the asymptomatic cohort post-tonsillectomy, indicating that F. necrophorum is not alone causative of the symptoms. In an individual perspective, colonisation with F. necrophorum was transient over time.

  • 3.
    Fagerström, Anna
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine.
    Aspelin, Oscar
    1928 Diagnostics, Stena Center 1D, Gothenburg, Sweden.
    Söderquist, Bo
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine.
    Mölling, Paula
    Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Comparative analysis of blaCTX-M-15-IncI1 plasmids in clinical Escherichia coli isolated during a 5-year period in a low-endemic settingManuskript (preprint) (Annet vitenskapelig)
  • 4.
    Fagerström, Anna
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine.
    Mölling, Paula
    Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Khan, Faisal Ahmad
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine.
    Jass, Jana
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Söderquist, Bo
    Örebro universitet, Institutionen för medicinska vetenskaper.
    Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters2019Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, nr 11, artikkel-id e0224861Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790-0.953)) and the environmental isolates (DI 0.947 (0.920-0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svartån river and Hjälmaren lake, were indistinguishable or closely related (≤10 allele differences) to clinical isolates. Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.

  • 5.
    Gaines, Hans
    et al.
    Public Health Agency of Sweden, Solna, Sweden; Dept Med, Infect Dis Unit, Karolinska Institute, Stockholm, Sweden; Dept Infect Dis, Karolinska Univ Hosp, Stockholm, Sweden.
    Albert, Jan
    Dept Microbiol Tumor & Cell Biol, Karolinska Institute, Stockholm, Sweden; Dept Clin Microbiol, Karolinska Univ Hosp, Stockholm, Sweden; Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden.
    Axelsson, Maria
    Public Health Agency of Sweden, Solna, Sweden.
    Berglund, Torsten
    Public Health Agency of Sweden, Solna, Sweden.
    Gisslen, Magnus
    Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden; Dept Infect Dis, Sahlgrenska Acad, Univ Gothenburg, Gothenburg, Sweden.
    Sonnerborg, Anders
    Dept Infect Dis, Karolinska Univ Hosp, Stockholm, Sweden; Dept Clin Microbiol, Karolinska Univ Hosp, Stockholm, Sweden; Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden; Div Clin Microbiol, Dept Lab Med, Karolinska Institute, Stockholm, Sweden.
    Blaxhult, Anders
    Dept Infect Dis, Södersjukhuset Venhälsan, Stockholm, Sweden.
    Bogdanovic, Gordana
    Dept Clin Microbiol, Karolinska Univ Hosp, Stockholm, Sweden.
    Brytting, Maria
    Public Health Agency of Sweden, Solna, Sweden.
    Carlander, Christina
    Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden; Clin Infect Dis, Cty Hosp Västmanland, Västerås, Sweden.
    Flamholc, Leo
    Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden; Dept Infect Dis, Skåne Univ Hosp, Lund Univ, Malmö, Sweden.
    Follin, Per
    Dept Communicable Dis Control & Prevent, Region Västra Götaland, Gothenburg, Sweden.
    Haggar, Axana
    Natl Board Hlth & Welf, Stockholm, Sweden.
    Hagstam, Per
    Dept Communicable Dis Control & Prevent, Malmö, Sweden.
    Johansson, Marcus
    Dept Clin Microbiol & Infect Dis, Kalmar Cty Hosp, Kalmar, Sweden.
    Naver, Lars
    Swedish Reference Grp Antiviral Therapy, Stockholm, Sweden; Dept Pediat, Karolinska Univ Hosp, Stockholm, Sweden; Dept Clin Sci Intervent & Technol, Karolinska Institute, Stockholm, Sweden.
    Blom, Jenny Persson
    Swedish Work Environment Authority, Stockholm, Sweden.
    Samuelson, Agneta
    Dept Clin Microbiol, Karolinska Univ Hosp, Stockholm, Sweden.
    Strom, Helena
    Natl Board Hlth & Welf, Stockholm, Sweden.
    Sundqvist, Martin
    Region Örebro län. Clin Microbiol, Örebro University Hospital, Örebro, Sweden.
    Johansson, Veronica Svedhem
    Dept Infect Dis, Karolinska Univ Hosp, Stockholm, Sweden.
    Wisell, Karin Tegmark
    Public Health Agency of Sweden, Solna, Sweden.
    Tegnell, Anders
    Public Health Agency of Sweden, Solna, Sweden.
    Thorstensson, Rigmor
    Public Health Agency of Sweden, Solna, Sweden.
    Six-week follow-up after HIV-1 exposure: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy2016Inngår i: INFECTIOUS DISEASES, ISSN 2374-4235, Vol. 48, nr 2, s. 93-98Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    In 2014 the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy (RAV) conducted a review and analysis of the state of knowledge on the duration of follow-up after exposure to human immunodeficiency virus (HIV). Up until then a follow-up of 12 weeks after exposure had been recommended, but improved tests and new information on early diagnosis motivated a re-evaluation of the national recommendations by experts representing infectious diseases and microbiology, county medical officers, the RAV, the Public Health Agency, and other national authorities. Based on the current state of knowledge the Public Health Agency of Sweden and the RAV recommend, starting in April 2015, a follow-up period of 6 weeks after possible HIV-1 exposure, if HIV testing is performed using laboratory-based combination tests detecting both HIV antibody and antigen. If point-of-care rapid HIV tests are used, a follow-up period of 8 weeks is recommended, because currently available rapid tests have insufficient sensitivity for detection of HIV-1 antigen. A follow-up period of 12 weeks is recommended after a possible exposure for HIV-2, since presently used assays do not include HIV-2 antigens and only limited information is available on the development of HIV antibodies during early HIV-2 infection. If pre- or post-exposure prophylaxis is administered, the follow-up period is recommended to begin after completion of prophylaxis. Even if infection cannot be reliably excluded before the end of the recommended follow-up period, HIV testing should be performed at first contact for persons who seek such testing.

  • 6.
    Golparian, Daniel
    et al.
    WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden.
    Boräng, Stina
    Department of Clinical Microbiology, Karolinska University Hospital Huddinge, Stockholm, Sweden .
    Sundqvist, Martin
    Örebro universitet, Institutionen för hälsovetenskap och medicin. WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Unemo, Magnus
    Örebro universitet, Institutionen för hälsovetenskap och medicin. WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Evaluation of the New BD Max GC Real-Time PCR Assay, Analytically and Clinically as a Supplementary Test for the BD ProbeTec GC Qx Amplified DNA Assay, for Molecular Detection of Neisseria gonorrhoeae2015Inngår i: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 53, nr 12, s. 3935-3937Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The new BD Max GC real-time PCR assay showed high clinical and analytical sensitivity and specificity. It can be an effective and accurate supplementary test for the BD ProbeTec GC Qx amplified DNA assay, which had suboptimal specificity, and might also be used for initial detection of Neisseria gonorrhoeae.

  • 7.
    Hedin, K.
    et al.
    Dept Clin Sci, Family Med, Lund Univ, Malmö, Sweden; Unit Res & Dev, Cent Hosp Växjö, Kronoberg Cty Council, Växjö, Sweden.
    Bieber, L.
    Dept Clin Microbiol, Cent Hosp Växjö, Växjö, Sweden.
    Lindh, M.
    Dept Clin Virol, Sahlgrens Univ Hosp, Gothenburg, Sweden.
    Sundqvist, Martin
    Region Örebro län. Dept Lab Med, Clin Microbiol, Örebro University Hospital, Örebro, Sweden.
    The aetiology of pharyngotonsillitis in adolescents and adults: Fusobacterium necrophorum is commonly found2015Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 21, nr 3Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sore throat is common in primary healthcare. Aetiological studies have focused on the presence of a limited number of pathogens. The aim of the present study was to investigate the presence of a wide range of bacteria and viruses, including Fusobacterium necrophorum, in patients with pharyngotonsillitis and in asymptomatic controls. A prospective case control study was performed in primary healthcare in Kronoberg County, Sweden. Patients (n = 220) aged 15 to 45 years with a suspected acute pharyngotonsillitis, and controls (n = 128), were included. Nasopharyngeal and throat swabs were analysed for beta-hemolytic streptococci, F. necrophorum, Mycoplasma pneumoniae, and Chlamydophila pneumoniae, and 13 respiratory viruses. Serum samples were analysed for antibodies to Epstein-Barr virus. The patient history and symptoms, including Centor score, were analysed in relation to pathogens. In 155/220 (70.5%) of the patients, as compared to 26/128 (20.3%) of the controls (p < 0.001), at least one microorganism was found. Group A streptococci, F. necrophorum, and influenza B virus were the three most common findings, and all significantly more common in patients than in controls (p < 0.001, p 0.001, and p 0.002, respectively). Patients with F. necrophorum only (n = 14) displayed a lower Centor score than patients with Group A streptococcus only (n = 46), but a higher score than patients with influenza B, other viruses, or no potential pathogen (Kruskal-Wallis p < 0.001). A pathogen was detected in 70% of the patients, displaying a wide range of pathogens contributing to the aetiology of pharyngotonsillitis. This study supports F. necrophorum as one of the pathogens to be considered in the aetiology of pharyngotonsillitis. Clinical Microbiology and Infection (C) 2014 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. Open access under CC BY-NC-ND license.

  • 8.
    Idelevich, E. A.
    et al.
    Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
    Seifert, H.
    Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology.
    Scudeller, L.
    Clinical Epidemiology Unit, Scientific Direction, Fondazione IRCCS, Policlinico San Matteo Pavia Fondazione IRCCS, Pavia, Italy.
    Amit, S.
    Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Centre, Jerusalem, Israel.
    Balode, A.
    Pauls Stradins Clinical University Hospital, Riga, Latvia.
    Bilozor, A.
    Microbiology Laboratory, Diagnostic Clinic, East-Tallinn Central Hospital, Tallinn, Estonia.
    Drevinek, P.
    Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic.
    Tufan, Z. Kocak
    Infectious Diseases and Clinical Microbiology Department, Medical School of Ankara Yildirim Beyazit University, Ankara, Turkey.
    Koraqi, A.
    Clinical Microbiology Laboratory, University Hospital Centre ‘Mother Theresa’, Tirana, Albania.
    Lamy, B.
    Laboratory of Clinical Microbiology, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, INSERM U1065 (C3M), Nice, France.
    Marekovic, I.
    Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia.
    Miciuleviciene, J.
    Vilnius City Clinical Hospital, Vilnius, Lithuania.
    Premru, M. Mueller
    Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
    Pascual, A.
    Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain.
    Pournaras, S.
    Laboratory of Clinical Microbiology, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece.
    Saegeman, V.
    Department of Infection Control and Epidemiology, University Hospitals Leuven, Leuven, Belgium.
    Schønheyder, H. C.
    Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
    Schrenzel, J.
    Bacteriology Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
    Strateva, T.
    Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria.
    Tilley, R.
    Department of Microbiology, University Hospitals Plymouth NHS Trust, Plymouth, UK.
    Wiersinga, W. J.
    Department of Infectious Diseases and Centre for Experimental Molecular Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
    Zabicka, D.
    National Medicines Institute, Warsaw, Poland.
    Carmeli, Y.
    Division of Epidemiology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel.
    Becker, K.
    Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
    Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey2019Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 25, nr 11, s. 1399-1407Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objectives: High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories.

    Methods: We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.

    Results: Responses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC.

    Conclusions: Laboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.

  • 9.
    Ingberg, Edvin
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län.
    Mölling, P.
    Jacobsson, Susanne
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län.
    Alm, E.
    Hedin, K.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län.
    16S metagenomics for bacterial identification versus cultures in acute pharyngotonsillitis patients and controls2018Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Background: Sore throat/pharyngotonsillitis is a very common condition. While most cases are viral, the primary bacterial pathogen is group A beta-hemolytic streptococcus (Streptococcus pyogenes). Further, Fusobacterium necrophorum has over the last decade attracted attention. rnrnSequence-based techniques continue to gain ground in medical microbiology. To describe the microbiota in a sample, either the whole genomes (metagenomics) or marker genes/genomic regions (metataxonomics), such as the 16S rRNA gene, can be sequenced. Some studies have investigated how findings from these methods correspond to conventional microbiological methods for infectious diseases, such as cultures. However, no previous study has approached the condition acute pharyngotonsillitis this way.

    Methods: Throat samples from patients with acute sore throat (n=129) and controls (n=86), both groups aged 15-45, were collected. DNA was extracted and the V3-V4 regions of the 16S rRNA genes were amplified using PCR. After normalization based on fragment analysis, and size selection with Ampure beads and PCR against adapter sequences coupled to the V3-V4 fragments, clonal amplifiction was performed with isothermal PCR. Finally, sequencing was performed on the Ion Torrent S5 XL. The SILVA database was used for taxonomic classification and the results were compared to culture findings for S. pyogenes and F. necrophorum, using Mann Whitney U tests.

    Results: Among the 215 samples, 46 patients and 1 of the controls were culture-positive for S. pyogenes. For F. necrophorum, 20 patients and 3 controls were culture-positive. Seven of the samples were culture-positive for both S. pyogenes and F. necrophorum. rnrnIn the metataxonomic analysis, S. pyogenes were significantly more abundant among patients than controls (p=0.0046), and in samples culture-positive for S. pyogenes, compared to culture-negative (p<0.0001).

    The percent of reads representing F. necrophorum were significantly higher in patients compared to controls (p<0.001), as well as in culture-positive samples compared to culture-negative (p<0.0001). rnrnAlthough significant differences between culture-positive and culture-negative samples were seen, even among culture-positive samples the abundance of S. pyogenes or F. necrophorum were on average low (2,1% and 10,6%, respectively) and with large variation (0-49,8% and 0-76,1%, respectively).

    Conclusions: Findings from a metataxonomic 16S rRNA gene analysis differed regarding species of interest between groups based on symptoms of a sore throat or culture findings. However, the results were heterogeneous and difficult to interpret for a single sample.

  • 10.
    Johansson, Åsa
    et al.
    Department of Clinical Microbiology, Central Hospital, Växjö, Sweden.
    Ekelöf, Josefine
    Sch Nat Sci, Linnaeus Univ, Kalmar, Sweden.
    Giske, Christian G.
    Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden; Karolinska Univ Hosp, Stockholm, Sweden.
    Sundqvist, Martin
    Region Örebro län. Department of Clinical Microbiology, Central Hospital, Växjö, Sweden; Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    The detection and verification of carbapenemases using ertapenem and Matrix Assisted Laser Desorption Ionization-Time of Flight2014Inngår i: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 14, artikkel-id 89Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The increase in carbapenemase producing Enterobacteriaceae and Pseudomonas aeruginosa is a significant threat to modern medicine. A rapid detection of carbapenemase production in Klebsiella pneumoniae and Pseudomonas aeruginosa is of importance for the institution of correct antibiotic treatment and infection control measures.

    Results: Standardised inoculums of K. pneumoniae or P. aeruginosa were incubated at 37 degrees C with ertapenem in 15 and 120 min followed by centrifugation. The supernatant was applied on a steel target plate, covered with HCCA matrix and analysed using a Microflex(TM) (Bruker Daltonics) in the mass range of 4-600 Da. The assay detected and separated KPC from other carbapenemases in K. pneumoniae after only 15 min incubation. In P. aeruginosa, however, only 8/14 isolates of VIM-producing P. aeruginosa were detected. None of the tested carbapenemase negative isolates displayed a pattern of hydrolysis of ertapenem.

    Conclusions: This assay allows for a very rapid detection and verification of KPC (45 min including the preparation steps) and MBL production (150 min) in K. pneumoniae and can be performed using standard matrix. However, the study revealed the need for optimization of the substrate/species combination in assays for the detection of carbapenemases in P. aeruginosa using MALDI-TOF.

  • 11.
    Johansson, Åsa
    et al.
    Dept of Clinical Microbiology, Växjö Central Hospital, Växjö, Sweden.
    Larsen, Anders Rhod
    Natl Reference Lab Staphylococci, Statens Serum Inst, Copenhagen, Denmark.
    Skov, Robert
    Natl Reference Lab Staphylococci, Statens Serum Inst, Copenhagen, Denmark.
    Sundqvist, Martin
    Region Örebro län. v; Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Importance of a Diverse Isolate Collection When Defining Genotype-Specific Mass Spectra in Staphylococcus aureus2014Inngår i: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 52, nr 7, s. 2738-2739Artikkel i tidsskrift (Fagfellevurdert)
  • 12.
    Lamy, B.
    et al.
    Laboratoire de Bactériologie, Hôpital l’Archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre méditerranéen de médecine moléculaire, Nice, France; FacultédeMédecine, Université Côte d’Azur, Nice, France; ESCMID study group for bloodstream infection and sepsis (ESGBIS), Switzerland.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. ESCMID study group for bloodstream infection and sepsis (ESGBIS), Switzerland; Faculty of Medicine and Health, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Towards an improved diagnosis of bloodstream infection: promises and hurdles2018Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 24, nr 9, s. 933-934Artikkel i tidsskrift (Annet vitenskapelig)
  • 13.
    Lamy, Brigitte
    et al.
    Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France; Faculté de Médecine, Université Côte D’Azur, Nice, France.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology.
    Idelevich, Evgeny A.
    Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
    Bloodstream infections - Standard and progress in pathogen diagnostics2020Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 26, nr 2, s. 142-150Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Background: Bloodstream infection (BSI) is a major public health burden worldwide, with high mortality. Patient outcome is critically influenced by delayed therapy, and fast and accurate pathogen diagnostics decisively improves the care of patients. During the past two decades major improvements have been made in the diagnostic performance of blood culture diagnostics through actions on pre-analysis and time to result.

    Aims: To review and discuss the literature for standard procedures and the progress in BSI pathogen diagnostics, and to propose a new mindset to reach an improved diagnostic workflow.

    Sources: Scientific articles and reviews available through NCBI/Pubmed.

    Content: Blood culture performance relies largely on the quality of its pre-analytical phase that is improved with educational actions monitored by using key performance indicators, and external quality assessment. Advanced blood culture systems now provide tools for an automated estimation of bottle filling. These proved efficient to facilitate effective training for improving blood collection. On analytic aspects, rapid methods for pathogen identification, among which matrix-assisted laser desorption/ ionization time of flight mass spectrometry dominates, and rapid antimicrobial susceptibility testing are reviewed. These technical developments call for improvements in all other steps, especially in pre- and post-analytic logistics to give the full reciprocation of these techniques on patient management. This aspect is summarized by the term 'microbiologistics', which covers all possible improvements in the logistic chain from sampling to report.

  • 14.
    Malm, Kerstin
    et al.
    Örebro universitet, Institutionen för hälsovetenskaper. Department of Laboratory Medicine, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Andersson, Sören
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Sundqvist, Martin
    Department of Laboratory Medicine, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Evaluation of the Veris MDx (TM) system for quantification of Hepatitis B DNA and Hepatitis C and HIV-1 RNA in a medium sized University Hospital2016Inngår i: Journal of Clinical Virology, ISSN 1386-6532, E-ISSN 1873-5967, Vol. 82, s. S27-S27Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Introduction: In the diagnosis and treatment of Hepatitis B (HBV), Hepatitis C (HCV) and HIV, it is crucial to detect and quantify viral nucleic acid. Patients on therapy are monitored continuously to out-rule relapses or reinfections (HCV) while for patients with HIV these tests are important to early on detect potential break-throughs due to resistance development. Quantification methods are today more standardized and fast but still with no opportunity to analyze the samples with full random access. Recently the VERIS MDxTMplatform from Beckman Coulter with this possibility was launched.

    Objectives: To evaluate a new, random access laboratory instrument for the simultaneous detection and quantification of HBV, HCV and HIV-1.

    Methods: WHO standards for HBV-DNA, HCV-RNA and HIV-1-RNA provided from the National Institute for Biological Standards and Control (NIBSC) were diluted down to the designated lowest level of detection and analyzed in triplicates on the Veris MDxTM(Beckman Coulter Inc. 250 S. Kraemer Blvd. Brea, CA U.S.A.) instrument. Plasma samples from routine laboratory testing were analyzed and compared to the routine methods used at our hospital or the referral hospital, for HBV; COBAS®AmpliPrep/COBAS® TaqMan®HBV Test, v2.0 (Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA, USA) (Karolinska University Hospital Huddinge), for HCV; COBAS® TaqMan®HCV Test v2.0 for use with the High Pure System (Roche) (Örebro) and for HIV; Aptima HIV-1 Quant Dx Assay (Hologic Inc. 250 Campus Drive Marlborough, MA, USA) (Örebro). 55 samples for HBV, 120 samples for HCV and 60 samples for HIV have been analyzed so far. The absolute majority of samples for HCV and HIV analysis were from patients on treatment. All viral load data were analyzed as log10-transformed values.

    Results: The Veris MDxTMshowed good compatibility to the designated quantities of the WHO standards (except for HIV-1 where a slight over-quantification could be observed for dilutions in the higher range, i.e. >1000 copies/mL). The limits of detection assigned by the manufacturer could be confirmed. In clinical samples the Veris MDxTM showed similar results to the comparators with a correlation for quantifiable samples of 0.94 (HBV), 0.98 (HCV) and 0.98 (HIV). The Veris MDxTMshowed a slightly higher sensitivity though as DNA/RNA was detected in 4 samples for HBV, 8 for HCV and 7 for HIV when the comparator method did not. The opposite was seen in 0, 0 and 6 samples respectively.

    Conclusion: The Veris MDxTMfor quantitative analysis of HBV, HCV and HIV nucleic acids showed good correlation to the comparator methods used in this study with a tendency of higher sensitivity for the detection of HBV and HCV. The Instrument provides an easy, fast and flexible method for quantification of RNA and DNA in plasma samples.

  • 15.
    Muhammad, Ibrahim
    et al.
    Department of Laboratory Medicine, WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Microbiology, Örebro Univ. Hospital, Örebro, Sweden.
    Golparian, Daniel
    Department of Laboratory Medicine, WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Microbiology, Örebro Univ. Hospital, Örebro, Sweden.
    Dillon, Jo-Anne R
    Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
    Johansson, Åsa
    Department of Clinical Microbiology, Central Hospital, Växjö, Sweden.
    Ohnishi, Makoto
    National Institute of Infectious Diseases, Tokyo, Japan.
    Sethi, Sunil
    Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India.
    Chen, Shao-chun
    National Center for STD Control, Chinese Centers for Disease Control and Prevention, Nanjing, China.
    Nakayama, Shu-ichi
    National Institute of Infectious Diseases, Tokyo, Japan.
    Sundqvist, Martin
    Region Örebro län. Department of Laboratory Medicine, WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Bala, Manju
    Apex Regional STD Teaching, Training and Research Centre, VMMC and Safdarjang Hospital, New Delhi, India.
    Unemo, Magnus
    Region Örebro län. Department of Laboratory Medicine, WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Characterisation of blaTEM genes and types of β-lactamase plasmids in Neisseria gonorrhoeae - the prevalent and conserved blaTEM-135 has not recently evolved and existed in the Toronto plasmid from the origin2014Inngår i: BMC Infectious Diseases, ISSN 1471-2334, E-ISSN 1471-2334, Vol. 14, nr 1, artikkel-id 454Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major concern worldwide. It has been recently feared that the blaTEM-1 gene is, via blaTEM-135, evolving into an extended-spectrum β-lactamase (ESBL), which could degrade all cephalosporins including ceftriaxone. The aims of the present study were to characterize the blaTEM genes, types of β-lactamase plasmids, the degradation of ampicillin by TEM-135 compared to TEM-1, and to perform molecular epidemiological typing of β-lactamase-producing N. gonorrhoeae strains internationally.

    METHODS: β-lactamase producing N. gonorrhoeae isolates (n = 139) cultured from 2000 to 2011 in 15 countries were examined using antibiograms, blaTEM gene sequencing, β-lactamase plasmid typing, and N. gonorrhoeae multiantigen sequence typing (NG-MAST). Furthermore, the blaTEM gene was sequenced in the first described Toronto plasmid (pJD7), one of the first Asian plasmids (pJD4) and African plasmids (pJD5) isolated in Canada. The degradation of ampicillin by TEM-135 compared to TEM-1 was examined using a MALDI-TOF MS hydrolysis assay.

    RESULTS: Six different blaTEM sequences were identified (among isolates with 125 different NG-MAST STs), i.e. blaTEM-1 (in 104 isolates), blaTEM-135 (in 30 isolates), and four novel blaTEM sequences (in 5 isolates). The blaTEM-1 allele was only found in the African and Asian plasmids, while all Rio/Toronto plasmids possessed the blaTEM-135 allele. Most interesting, the first described gonococcal Toronto plasmid (pJD7), identified in 1984, also possessed the highly conserved blaTEM-135 allele. The degradation of ampicillin by TEM-135 compared to TEM-1 was indistinguishable in the MALDI-TOF MS hydrolysis assay.

    CONCLUSIONS: blaTEM-135, encoding TEM-135, is predominantly and originally associated with the Rio/Toronto plasmid and prevalent among the β-lactamase producing gonococcal strains circulating globally. blaTEM-135 does not appear, as previously hypothesized, to have recently evolved due to some evolutionary selective pressure, for example, by the extensive use of extended-spectrum cephalosporins worldwide. On the contrary, the present study shows that blaTEM-135 existed in the Toronto plasmid from its discovery and that blaTEM-135 is highly conserved (not further evolved in the past >30 years). Nevertheless, international studies for monitoring the presence of different blaTEM alleles, the possible evolution of the blaTEM-135 allele, and the types of β-lactamase producing plasmids, remain imperative.

  • 16.
    Månsson, Emeli
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Centre for Clinical Research, Hospital of Västmanland Västerås, Västerås, Sweden.
    Hellmark, Bengt
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine.
    Stegger, Marc
    Statens Serum Institut, Copenhagen, Denmark.
    Andersen, Paal Skytt
    Statens Serum Institut, Copenhagen, Denmark.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine.
    Söderquist, Bo
    Örebro universitet, Institutionen för medicinska vetenskaper.
    Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins2017Inngår i: Journal of Medical Microbiology, ISSN 0022-2615, E-ISSN 1473-5644, Vol. 66, nr 5, s. 601-608Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Purpose: The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.

    Methodology: Phylogenetic relationships between 25 S. pettenkoferi isolates collected from blood cultures and intra-operative air sampling were determined by repetitive-sequence-based PCR typing and analysis of similar to 157 000 SNPs identified in the core genome after WGS. Antibiotic susceptibility testing and tests for biofilm production (microtitre plate assay) were performed.

    Results: Repetitive-sequence-based PCR as well as WGS data demonstrated the close relatedness of clinically significant blood culture isolates to probable contaminants, as well as to environmental isolates. Antibiotic-susceptibility testing demonstrated a low level of antimicrobial resistance. The mecA gene was present in two cefoxitin-resistant isolates. No isolates were found to produce biofilm.

    Conclusion: Close genomic relatedness of S. pettenkoferi isolates from different geographical locations and origins were found within clades, but with substantial genomic difference between the two major clades. The ecological niche of S. pettenkoferi remains unconfirmed, but the presence of S. pettenkoferi in the air of the operating field favours the suggestion of a role in skin flora. Identification of S. pettenkoferi in clinical samples should, in a majority of cases, most likely be regarded as a probable contamination, and its role as a possible pathogen in immunocompromised hosts remains to be clarified.

  • 17.
    Månsson, Emeli
    et al.
    Örebro universitet, Institutionen för hälsovetenskap och medicin. Centre for Clinical Research, Uppsala University, Uppsala, Sweden; County Hospital, Västerås, Sweden.
    Hellmark, Bengt
    Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för hälsovetenskap och medicin.
    Söderquist, Bo
    Örebro universitet, Institutionen för läkarutbildning.
    Sequence types of Staphylococcus epidermidis associated with prosthetic joint infections are not present in the laminar airflow during prosthetic joint surgery2015Inngår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 123, nr 7, s. 589-595Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular characterization of Staphylococcus epidermidis isolates from prosthetic joint infections (PJIs) has demonstrated a predominance of healthcare-associated multi-drug resistant sequence types (ST2 and ST215). How, and when, patients acquire these nosocomial STs is not known. The aim was to investigate if sequence types of S. epidermidis associated with PJIs are found in the air during prosthetic joint surgery. Air sampling was undertaken during 17 hip/knee arthroplasties performed in operating theaters equipped with mobile laminar airflow units in a 500-bed hospital in central Sweden. Species identification was performed using MALDI-TOF MS and 16S rRNA gene analysis. Isolates identified as S. epidermidis were further characterized by MLST and antibiotic susceptibility testing. Seven hundred and thirty-five isolates were available for species identification. Micrococcus spp. (n = 303) and coagulase-negative staphylococci (n = 217) constituted the majority of the isolates. Thirty-two isolates of S. epidermidis were found. S. epidermidis isolates demonstrated a high level of allelic diversity with 18 different sequence types, but neither ST2 nor ST215 was found. Commensals with low pathogenic potential dominated among the airborne microorganisms in the operating field during prosthetic joint surgery. Nosocomial sequence types of S. epidermidis associated with PJIs were not found, and other routes of inoculation are therefore of interest in future studies.

  • 18.
    Nestor, David
    et al.
    Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro University, Örebro, Sweden; School of Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Malmvall, Bo-Eric
    Futurum - Academy for Health and Care, Jönköping County Council, Jönköping, Sweden.
    Masonda, Yohana Paul
    Department of Laboratory Medicine, Nkinga Referral Hospital Laboratory, Nkinga, Tanzania.
    Msafiri, John
    Department of Laboratory Medicine, Nkinga Referral Hospital Laboratory, Nkinga, Tanzania.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology.
    Detection of extended-spectrum beta-lactamase production in Enterobacteriales from patients with suspected urinary tract infections, Tabora region, Rural Tanzania2018Inngår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 126, nr 8, s. 700-702Artikkel i tidsskrift (Fagfellevurdert)
  • 19.
    Rapp, Ellionor
    et al.
    Department of Laboratory Medicine, Clinical Microbiology, University Hospital, Örebro, Sweden.
    Samuelsen, Ørjan
    Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, The Arctic University of Norway (UiT), Tromsø, Norway.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight2018Inngår i: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 146, s. 37-39Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study evaluated the performance of the MBT STAR-Carba kit (Bruker Daltonics), to detect carbapenemase producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter spp. in comparison with the RAPIDEC® CARBA NP test (BioMerieux). MBT STAR-Carba allowed the detection of carbapenemases in Enterobacteriaceae and P. aeruginosa.

  • 20.
    Rondahl, Elin
    et al.
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    Gruber, Maria
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    Joelsson, Sandra
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    Sundqvist, Martin
    Region Örebro län. Division Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Akerlind, Britt
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    Cardell, Kristina
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    Lindh, Magnus
    Dept Clin Microbiol, Gothenburg Univ, Gothenburg, Sweden.
    Serrander, Lena
    Dept Clin & Expt Med, Div Infect Dis, Linköping Univ, Linköping, Sweden.
    The risk of HCV RNA contamination in serology screening instruments with a fixed needle for sample transfer2014Inngår i: Journal of Clinical Virology, ISSN 1386-6532, E-ISSN 1873-5967, Vol. 60, nr 2, s. 172-173Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Hepatitis C diagnostics involve antibody screening and confirmation of current infection by detection of HCV RNA positivity. In screening instruments with fixed pipetting needle, there is a risk of sample carry-over contamination.

    Objectives: The aim of this study was to evaluate the risk of such contamination in a proposed clinical setting. Study design: In the present study, known HCV RNA positive (n = 149) and negative (n = 149) samples were analysed by anti-HCV Abbott in an Architect instrument in an alternating fashion in order to test for contamination.

    Results: In subsequent retesting of the previously HCV RNA-negative samples, six samples (4%) were positive by the Cobas Taqman assay with a maximum level of 33 IU/mL. The results show that there is a risk for transfer of HCV in the Architect instrument but they also show that the levels of HCV RNA observed are low.

    Conclusions: We conclude that complementary HCV RNA testing on samples identified as anti-HCV positive by screening can be recommended because the complementary results are reliable in the majority of cases when either HCV RNA is negative or HCV RNA is positive with a level > 1000 IU/mL. In a minority of cases, with low HCV RNA after anti-HCV antibody screening, cross-contamination should be suspected and a new sample requested for HCV RNA testing. This strategy would reduce the need for obtaining a new sample from the vast majority of patients with a newly discovered HCV antibody positivity. (C) 2014 The Authors. Published by Elsevier B.V

  • 21.
    Sundqvist, Martin
    Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Reversibility of antibiotic resistance2014Inngår i: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 119, nr 2, s. 142-148Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Although theoretically attractive, the reversibility of resistance has proven difficult in practice, even though antibiotic resistance mechanisms induce a fitness cost to the bacterium. Associated resistance to other antibiotics and compensatory mutations seem to ameliorate the effect of antibiotic interventions in the community. In this paper the current understanding of the concepts of reversibility of antibiotic resistance and the interventions performed in hospitals and in the community are reviewed.

  • 22.
    Sundqvist, Martin
    et al.
    Region Örebro län. Department of Clinical Microbiology, Central Hospital, Växjö, Sweden; Department of Medical Sciences, Division of Infectious Diseases, Uppsala University, Uppsala, Uppsala, Sweden; Department of Laboratory Medicine, Clinical Microbiology, University Hospital, Örebro, Sweden.
    Granholm, Susanne
    Dept Clin Microbiol, Lab Mol Infect Med Sweden, Umeå Univ, Umeå, Sweden.
    Naseer, Umaer
    Dept Microbiol & Infect Control, Reference Ctr Detect Antimicrobial Resistance, Univ Hosp North Norway, Tromsø, Norway; Dept Med Biol, Res Grp Host Microbe Interact, Univ Tromsø, Tromsø, Norway.
    Ryden, Patrik
    Dept Math & Math Stat, Umeå Univ, Umeå, Sweden.
    Brolund, Alma
    Publ Hlth Agcy Sweden, Solna, Sweden; Dept Microbiol Tumor & Cell Biol, Karolinska Inst, Stockholm, Sweden.
    Sundsfjord, Arnfinn
    Dept Microbiol & Infect Control, Reference Ctr Detect Antimicrobial Resistance, Univ Hosp North Norway, Tromsø, Norway; Dept Med Biol, Res Grp Host Microbe Interact, Univ Tromsø, Tromsø, Norway.
    Kahlmeter, Gunnar
    Dept Clin Microbiol, Cent Hosp Växjö, Växjö, Sweden; Div Clin Bacteriol, Dept Med Sci, Uppsala Univ, Uppsala, Sweden.
    Johansson, Anders
    Dept Clin Microbiol, Lab Mol Infect Med Sweden, Umeå Univ, Umeå, Sweden.
    Within-Population Distribution of Trimethoprim Resistance in Escherichia coli before and after a Community-Wide Intervention on Trimethoprim Use2014Inngår i: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 58, nr 12, s. 7492-7500Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A 2-year prospective intervention on the prescription of trimethoprim reduced the use by 85% in a health care region with 178,000 inhabitants. Here, we performed before-and-after analyses of the within-population distribution of trimethoprim resistance in Escherichia coli. Phylogenetic and population genetic methods were applied to multilocus sequence typing data of 548 consecutively collected E. coli isolates from clinical urinary specimens. Results were analyzed in relation to antibiotic susceptibility and the presence and genomic location of different trimethoprim resistance gene classes. A total of 163 E. coli sequence types (STs) were identified, of which 68 were previously undescribed. The isolates fell into one of three distinct genetic clusters designated BAPS 1 (E. coli phylogroup B2), BAPS 2 (phylogroup A and B1), and BAPS 3 (phylogroup D), each with a similar frequency before and after the intervention. BAPS 2 and BAPS 3 were positively and BAPS 1 was negatively associated with trimethoprim resistance (odds ratios of 1.97, 3.17, and 0.26, respectively). In before-and-after analyses, trimethoprim resistance frequency increased in BAPS 1 and decreased in BAPS 2. Resistance to antibiotics other than trimethoprim increased in BAPS 2. Analysis of the genomic location of different trimethoprim resistance genes in isolates of ST69, ST58, and ST73 identified multiple independent acquisition events in isolates of the same ST. The results show that despite a stable overall resistance frequency in E. coli before and after the intervention, marked within-population changes occurred. A decrease of resistance in one major genetic cluster was masked by a reciprocal increase in another major cluster.

  • 23.
    Sundqvist, Martin
    et al.
    Region Örebro län. Dept Lab Med Clin Microbiol, Örebro University Hospital, Örebro, Sweden.
    Olafsson, Jonas
    Dept Clin Microbiol, Kalmar Cty Hosp, Kalmar, Sweden.
    Matuschek, Erika
    EUCAST Dev Lab, Cent Hosp Växjö, Växjö, Sweden.
    EUCAST breakpoints can be used to interpret direct susceptibility testing of Enterobacteriaceae from urine samples2015Inngår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 123, nr 2, s. 152-155Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Increasing resistance calls for rapid antibiotic susceptibility testing (AST). This study validated the use of EUCAST breakpoints for AST using disk diffusion directly from urine samples. Two hundred and thirty-three urine samples with growth of varying amounts of Enterobacteriaceae were included and susceptibility testing (disk diffusion) was performed on Mueller-Hinton agar with overnight incubation directly from urine samples in parallel with disk diffusion according to EUCAST methodology. Confluent growth was obtained in 188 of 233 urine samples and used as criteria for zone measurements. Only 15 discrepancies (3 very major errors, 5 major errors and 7 minor errors) were observed in a total of 855 tests showing the safety of this approach. Direct susceptibility testing from urine samples can be interpreted using EUCAST clinical breakpoints and can thus safely be used to achieve more rapid AST result.

  • 24.
    Säll, Olof
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Infectious Diseases.
    Thulin Hedberg, Sara
    Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Neander, Marita
    Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Tiwari, Sabina
    United Mission Hospital Tansen, Tansen, Nepal.
    Dornon, Lester
    United Mission Hospital Tansen, Tansen, Nepal.
    Bom, Rabin
    United Mission Hospital Tansen, Tansen, Nepal.
    Lagerqvist, Nina
    Public Health Agency of Sweden, Solna, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Clinical Microbiology.
    Mölling, Paula
    Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches2019Inngår i: American Journal of Tropical Medicine and Hygiene, ISSN 0002-9637, E-ISSN 1476-1645, Vol. 101, nr 1, s. 253-259Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein-Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.

  • 25.
    Säll, Olof
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Dept. of Infectious Diseases, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Thulin-Hedberg, Sara
    Dept. of Laboratory Medicine, School of Medical Sciences, Örebro University, Örebro, Sweden.
    Bom, Rabin
    United Mission Hospital Tansen, Tansen, Nepal.
    Dornon, Les
    United Mission Hospital Tansen, Tansen, Nepal.
    Tiwari, Sabina
    United Mission Hospital Tansen, Tansen, Nepal.
    Neander, Marita
    Dept. of Laboratory Medicine, School of Medical Sciences, Örebro University, Örebro, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Dept. of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden.
    Mölling, Paula
    Dept. of Laboratory Medicine, School of Medical Sciences, Örebro University, Örebro, Sweden.
    Etiology of CNS infections in Nepal using the FilmArray meningitis/encephalitis panel2017Inngår i: International Journal of Antimicrobial Agents, ISSN 0924-8579, E-ISSN 1872-7913, Vol. 50, nr Suppl. 2, s. S66-S66Artikkel i tidsskrift (Annet vitenskapelig)
  • 26.
    Thulin, Elisabeth
    et al.
    Dept Med Biochem & Microbiol, Uppsala Univ, Uppsala, Sweden.
    Sundqvist, Martin
    Region Örebro län. Lab Med, Clin Microbiol, Örebro University Hospital, Örebro, Sweden.
    Andersson, Dan I.
    Dept Med Biochem & Microbiol, Uppsala Univ, Uppsala, Sweden.
    Amdinocillin (Mecillinam) Resistance Mutations in Clinical Isolates and Laboratory-Selected Mutants of Escherichia coli2015Inngår i: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 59, nr 3, s. 1723-1732Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amdinocillin (mecillinam) is a beta-lactam antibiotic that is used mainly for the treatment of uncomplicated urinary tract infections. The objectives of this study were to identify mutations that confer amdinocillin resistance on laboratory-isolated mutants and clinical isolates of Escherichia coli and to determine why amdinocillin resistance remains rare clinically even though resistance is easily selected in the laboratory. Under laboratory selection, frequencies of mutation to amdinocillin resistance varied from 8 x 10(-8) to 2 x 10(-5) per cell, depending on the concentration of amdinocillin used during selection. Several genes have been demonstrated to give amdinocillin resistance, but here eight novel genes previously unknown to be involved in amdinocillin resistance were identified. These genes encode functions involved in the respiratory chain, the ribosome, cysteine biosynthesis, tRNA synthesis, and pyrophosphate metabolism. The clinical isolates exhibited significantly greater fitness than the laboratory-isolated mutants and a different mutation spectrum. The cysB gene was mutated (inactivated) in all of the clinical isolates, in contrast to the laboratory-isolated mutants, where mainly other types of more costly mutations were found. Our results suggest that the frequency of mutation to amdinocillin resistance is high because of the large mutational target (at least 38 genes). However, the majority of these resistant mutants have a low growth rate, reducing the probability that they are stably maintained in the bladder. Inactivation of the cysB gene and a resulting loss of cysteine biosynthesis are the major mechanism of amdinocillin resistance in clinical isolates of E. coli.

  • 27.
    Thulin Hedberg, Sara
    et al.
    Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Eriksson, Lorraine
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine.
    Demontis, Maria A.
    Imperial College, St Mary’s Hospital, London, UK.
    Mölling, Paula
    Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden.
    Taylor, Graham
    Imperial College, St Mary’s Hospital, London, UK.
    Malm, Kerstin
    Örebro universitet, Institutionen för hälsovetenskaper. Region Örebro län. Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden.
    Andersson, Sören
    Örebro universitet, Institutionen för medicinska vetenskaper. Department of Laboratory Medicine.
    Droplet digital PCR for absolute quantification of proviral load of human T-cell lymphotropic virus (HTLV) types 1 and 22018Inngår i: Journal of Virological Methods, ISSN 0166-0934, E-ISSN 1879-0984, Vol. 260, s. 70-74Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Human T-lymphotrophic virus (HTLV) types 1 and 2 cause lifelong infection whereby most infected individuals are asymptomatic whilst a minority develop infection-related disease. These latter patients invariably have been found to have high proviral load (PVL). Therefore, infected patients are monitored by determining the proportion of lymphocytes that are infected with HTLV-1/2. An increase in PVL has been shown to represent an increasing risk of developing HTLV-associated diseases. Monitoring of PVL requires a reliable and sensitive method. In this study assays based on droplet digital PCR (ddPCR) were established and evaluated for detection and quantification of HTLV-1/2.

    OBJECTIVES: To develop two parallel assays to detect the tax genes and determine the PVL of HTLV-1 and -2.

    STUDY DESIGN: Sixty-seven clinical samples from patients infected with HTLV-1 or HTLV-2 were analysed. The samples had previously been analysed with a qPCR and a comparison between ddPCR and qPCR was performed. The specificity of the assays were determined by analyzing samples from 20 healthy blood donors.

    RESULTS: The ddPCR was a stable and sensitive method for detection and quantification of HTLV-1 and -2. When comparing the qPCR and ddPCR the correlation was high (Pearsons correlation coefficient 0.96). The variability of the ddPCR was very low with intra-assay coefficient of variation (CV) of 0.97-3.3% (HTLV-1) and 1.7-8.2% (HTLV-2) and inter-assay CV of 1.8-6.1% (HTLV-1) and 1.2-12.9% (HTLV-2).

    CONCLUSIONS: The ddPCR reliably quantified HTLV DNA in clinical samples and could be a useful tool for monitoring of PVLs in HTLV-infected individuals.

  • 28.
    Thulin Hedberg, Sara
    et al.
    WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Mölling, Paula
    WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Stenmark, Bianca
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Unemo, Magnus
    WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Lepp, Tiia
    The Public Health Agency of Sweden, Stockholm, Sweden.
    Fredlund, Hans
    WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Jacobsson, Susanne
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Invasive meningococcal disease in Sweden 20162017Inngår i: 14th Congress of the EMGM, European Meningococcal and Haemophilus Disease Society: Book of Abstracts, Prague: The European Meningococcal and Haemophilus Disease Society EMGM , 2017, s. 69-69Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Invasive meningococcal disease (IMD) is notifiable in Sweden. The reporting system comprises of mandatory notification of cases and mandatory laboratory notification of samples to the Public Health Agency of Sweden, Stockholm. All samples are sent to the National Reference Laboratory for Pathogenic Neisseria, Örebro for further typing and surveillance.

    In 2016, 62 cases of IMD (incidence 0.6/100 000 population) were reported in Sweden. Among the patients 58 % were females and 42 % males, aged from 1 month to95 years with mean age of 42 years. The incidence was highest, as in previous years, in the age group 15-19 years (2.1/100 000 population) followed by elderly ≥80 years (1.8/100 000 population) and infants ≤1 year (1.7/100 000 population). The case fatality rate increased in 2016 to 12.9 % compared with 7.5 % in 2015, eight people died from the disease (MenW, n=3; MenY, n=2; MenB, n=2 and MenC n=1). None of the IMD cases in 2016 had any epidemiological linkage.

    All 62 cases of IMD were laboratory confirmed: 54 were culture-confirmed, three PCR-confirmed and in five cases further typing data are missing because no samples were sent to the National Reference Laboratory for Pathogenic Neisseria. The serogroup distribution was MenW (n=18, 31.5 %), MenY (n=18, 31.5 %), MenB (n=10, 17.5 %), MenC (n=10, 17.5 %) and one non-groupable isolate. The W:P1.5,2:F1-1:ST11 (cc11) (n=15) were predominant among the culture-confirmed meningococci during 2016 followed by Y:P1.5-2,10-1:F4-1:ST23 (cc23) (n=7) och Y:P1.5-1,2-2:F5-8:ST23 (cc23) (n=6). Antibiotic susceptibility testing was performed with Gradient test (Etest, BioMerieux). Decreased susceptibility to penicillin was seen in 30 % of the isolates (MIC >0,064 mg/L) of which one was resistant (MIC=0.5 mg/L). One of the isolates with decreased susceptibility to penicillin was also resistant to ciprofloxacin (MIC=0.125 mg/L). All other isolates were susceptible to cefotaxime, chloramphenicol, ciprofloxacin, rifampicin and meropenem. No β-lactamase producing isolates has so far been found in Sweden.

    To conclude, the incidence of IMD continues to be relatively low in Sweden, however, a shift in the serogroup distribution of N. meningitidisin Sweden is ongoing; the previously dominating disease-causing MenB and MenC have been replaced, first by MenY which emerged in 2009 and since 2015 also by MenW. MenW has gone from only causing invasive disease in a few, 0-6 cases per year from 1990 onwards, to now being the dominating serogroup together with MenY in Sweden 2016.

  • 29.
    Unemo, Magnus
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine.
    Hansen, Marit
    World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Hadad, Ronza
    World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Lindroth, Ylva
    Department of Laboratory Medicine, Medical Microbiology, Lund University, Skåne Laboratory Medicine, Lund, Sweden.
    Fredlund, Hans
    World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Puolakkainen, Mirja
    Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine.
    Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Orebro County, Sweden, May 20192019Inngår i: Eurosurveillance, ISSN 1025-496X, E-ISSN 1560-7917, Vol. 24, nr 26, s. 10-14, artikkel-id 1900370Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We identified the first two cases of the Finnish new variant of Chlamydia trachomatis (F-nvCT) beyond Finland in two clinical urogenital specimens in Orebro County, Sweden. These Aptima Combo 2 assay-negative specimens were Aptima Chlamydia trachomatis (CT) assay positive and had the characteristic C1515T mutation in the 23S rRNA gene. From 22 March to 31 May 2019, 1.3% (2/158) of the CT-positive cases in Orebro County were missed because of the F-nvCT. International awareness, investigations and actions are essential.

  • 30.
    Unemo, Mats
    et al.
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Salado-Rasmussen, K.
    Department of Dermatovenereology, Bispebjerg University Hospital, Copenhagen, Denmark.
    Hansen, M.
    World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden.
    Olsen, A. O.
    Olafia Clinic and National Advisory Unit for Sexually Transmitted Infections, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
    Falk, M.
    Department of Dermatovenereology, Örebro University Hospital, Örebro, Sweden.
    Golparian, Daniel
    Örebro universitet, Institutionen för medicinska vetenskaper. World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Aasterød, M.
    Olafia Clinic and National Advisory Unit for Sexually Transmitted Infections, Oslo University Hospital, Oslo, Norway.
    Ringlander, J.
    World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Nilsson, C. Stezckó
    Department of Dermatovenereology, Örebro University Hospital, Örebro, Sweden.
    Sundqvist, Martin
    Örebro universitet, Institutionen för medicinska vetenskaper. Region Örebro län. World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden.
    Schønning, K.
    Department of Clinical Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
    Moi, H.
    Olafia Clinic and National Advisory Unit for Sexually Transmitted Infections, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
    Westh, H.
    Department of Clinical Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
    Jensen, J. S.
    Infection Preparedness, Research Unit for Reproductive Tract Microbiology, Statens Serum Institut, Copenhagen, Denmark.
    Clinical and analytical evaluation of the new Aptima Mycoplasma genitalium assay, with data on M. genitalium prevalence and antimicrobial resistance in M. genitalium in Denmark, Norway and Sweden in 20162018Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 24, nr 5, s. 533-539Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objectives: Mycoplasma genitalium (MG) causes urethritis and cervicitis, potentially causing reproductive complications. Resistance in MG to first-line (azithromycin) and second-line (moxifloxacin) treatment has increased. We examined the clinical and analytical performance of the new Conformite Europeene (CE)/in vitro diagnostics (IVD) Aptima Mycoplasma genitalium assay (CE/IVD AMG; Hologic); the prevalence of MG, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG); and MG resistance to azithromycin and moxifloxacin in Denmark, Norway and Sweden in 2016.

    Methods: From February 2016 to February 2017, urogenital and extragenital (only in Denmark) specimens from consecutive attendees at three sexually transmitted disease clinics were tested with the CE/ IVD AMG, the research-use-only MG Alt TMA-1 assay (Hologic), Aptima Combo 2 (CT/NG) assay and a laboratory-developed TaqMan real-time mgpB quantitative real-time PCR (qPCR). Resistance-associated mutations were determined by sequencing. Strains of MG and other mycoplasma species in different concentrations were also tested.

    Results: In total 5269 patients were included. The prevalence of MG was 7.2% (382/5269; 4.9-9.8% in the countries). The sensitivity of the CE/IVD AMG, MG Alt TMA-1 and mgpB qPCR ranged 99.13-100%, 99.13 -100% and 73.24-81.60%, respectively, in the countries. The specificity ranged 99.57-99.96%, 100% and 99.69-100%, respectively. The prevalence of resistance-associated mutations for azithromycin and moxifloxacin was 41.4% (120/290; 17.7-56.6%) and 6.6% (18/274; 4.1-10.2%), respectively. Multidrug resistance was found in all countries (2.7%; 1.1-4.2%).

    Conclusions: Both transcription-mediated amplification (TMA)-based MG assays had a highly superior sensitivity compared to the mgpB qPCR. The prevalence of MG and azithromycin resistance was high. Validated and quality-assured molecular tests for MG, routine resistance testing of MG-positive samples and antimicrobial resistance surveillance are crucial.

  • 31.
    Vennberg, Lisa
    et al.
    Department of Laboratory Medicine, Faculty of Medicine and Health, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Forsstrom, Katrin
    Department of Laboratory Medicine, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Rova, Lena
    Department of Clinical Microbiology Kronoberg County, Karlskrona, Sweden.
    Ekelund, Oskar
    Department of Clinical Microbiology Kronoberg County, Karlskrona, Sweden.
    Sundqvist, Martin
    Department of Laboratory Medicine, Faculty of Medicine & Health, Örebro, Sweden.
    Evaluation of a rapid test for the detection of Tick Borne Encephalitis (TBE) IgM in serum and CSF2016Inngår i: Journal of Clinical Virology, ISSN 1386-6532, E-ISSN 1873-5967, Vol. 82, s. S29-S30Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Introduction: The incidence of Tick-borne encephalitis (TBE) is increasing with 150–300 cases reported in Sweden annually. The clinical picture can be hard to differentiate from other causes of encephalitis and a rapid reliable diagnosis is therefore important. The laboratory diagnosis of TBE relies on ELISA-based testing to determine specific anti-TBE IgM and IgG in serum and in CSF. The aim of this study was to evaluate the ReaScan TBE IgM rapid test (Reagena, Toivala, Finland), a qualitative immune-chromatographic lateral flow assay for the rapid detection of TBE IgM in serum and CSF.

    Materials and methods: The material consisted of two blinded panels of serum and CSF. (1) 16 serum samples previously analyzed for TBE IgM and IgG using ELISA (Euroimmun) at the department of Clinical Microbiology Kronoberg County. Six of these were positive for TBE IgM, three of which had a matching CSF sample. (2) Seven (7) serum samples (6 with matching CSF samples) from patients diagnosed with TBE in Örebro County during 2015 based on IgM positivity (Immunozym) performed at the Dept of Clinical Virology, Karolinska University Hospital. All samples were analyzed using the ReaScan TBE IgM rapid test according to the manufacturer’s instructions.

    Results: The results obtained using ReaScan were in full concordance with the Euroimmun IgM assay for all 16 serum-samples from Kronoberg County. Of the 7 serum samples from Örebro 5 were positive for IgM with both ReaScan and Euroimmun with the remaining 2 samples being classified as Equivocal with Reascan and negative with Euroimmun. Of the 9 CSF samples tested, 2 were positive, 2 equivocal and 5 negative. The two CSF-samples with equivocal result and three of the negative CSF samples had corresponding serum samples that were positive for TBE IgM using Reascan.

    Conclusions: According to this small evaluation the ReaScan IgM rapid test seems to have a comparable performance to two commercially available ELISA assays (Euroimmun and Immunozym) for the detection of TBE IgM in serum. The two samples with equivocal Reascan-result originated from one patient on immunosuppression and one who acquired TBE despite vaccination. As others have shown the additive value of testing for IgM in CSF might be limited as only two out of nine samples here tested were positive. The Reascan TBE IgM assay seems as a valid diagnostic option for a rapid diagnosis of TBE. Additional ELISA with analysis of both IgM and IgG as well as molecular detection of TBE might be performed as confirmatory tests.

  • 32. Åkerlund, Anna
    et al.
    Sundqvist, Martin
    Region Örebro län. Klinisk mikrobiologi, Laboratoriemedicinska Länskliniken, Örebro, Sweden.
    Hanberger, Håkan
    Åhrén, Christina
    Serrander, Lena
    Giske, Christian G.
    Svarstiderna kan kortas vid mikrobiologisk diagnostik av sepsis [Response times can be shortened in microbiological diagnosis of sepsis]: Bättre öppettider på laboratorier och aktiv rådgivning ger snabbare terapi [Better opening hours in laboratories and active advice enables faster therapy]2015Inngår i: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 112, artikkel-id C73SArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [sv]

    Early and adequate antimicrobial therapy is lifesaving in patients with bloodstream infections (BSI). Continuous incubation and 24h availability of microbial pathogen identification in clinical microbiology laboratories shortens the time to report. To describe the current status in Swedish clinical microbiology laboratories, a web-based survey was performed. The survey showed major differences in availability both regarding laboratory opening hours and ability to incubate blood culture bottles outside working hours. It also showed differences in what was conveyed verbally to the clinician and in time to report of the bacterial species. Based on this survey, we debate how Swedish healthcare can improve the care of patients with BSI by offering a more rapid diagnostic process. This could be achieved through longer opening hours of the laboratory, better transport systems and blood culture cabinets positioned closer to the patient.

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