| 1. |
- Beeton, Michael L., et al.
(författare)
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Mycoplasma pneumoniae infections, 11 countries in Europe and Israel, 2011 to 2016
- 2020
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Ingår i: Eurosurveillance. - : EUR CENTRE DIS PREVENTION & CONTROL. - 1025-496X .- 1560-7917. ; 25:2, s. 39-51
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia, with large epidemics previously described to occur every 4 to 7 years.Aim: To better understand the diagnostic methods used to detect M. pneumoniae; to better understand M. pneumoniae testing and surveillance in use; to identify epidemics; to determine detection number per age group, age demographics for positive detections, concurrence of epidemics and annual peaks across geographical areas; and to determine the effect of geographical location on the timing of epidemics.Methods: A questionnaire was sent in May 2016 to Mycoplasma experts with national or regional responsibility within the ESCMID Study Group for Mycoplasma and Chlamydia Infections in 17 countries across Europe and Israel, retrospectively requesting details on M. pneumoniae-positive samples from January 2011 to April 2016. The Moving Epidemic Method was used to determine epidemic periods and effect of country latitude across the countries for the five periods under investigation.Results: Representatives from 12 countries provided data on M. pneumoniae infections, accounting for 95,666 positive samples. Two laboratories initiated routine macrolide resistance testing since 2013. Between 2011 and 2016, three epidemics were identified: 2011/12, 2014/15 and 2015/16. The distribution of patient ages for M. pneumoniae-positive samples showed three patterns. During epidemic years, an association between country latitude and calendar week when epidemic periods began was noted.Conclusions: An association between epidemics and latitude was observed. Differences were noted in the age distribution of positive cases and detection methods used and practice. A lack of macrolide resistance monitoring was noted.
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| 2. |
- Beser, Jessica, et al.
(författare)
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Seroprevalence of SARS-CoV-2 in Sweden, April 26 to May 9, 2021
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- A national point seroprevalence study of SARS-CoV-2 was conducted in Sweden in April–May 2021. In total, 2860 individuals 3 to 90 years old from a probability-based web panel were included. Results showed that an estimated 32.6% of the population in Sweden had detectable levels of antibodies, and among non-vaccinated 20.1% had detectable levels of antibodies. We tested for differences in seroprevalence between age groups and by sex and estimated seroprevalence among previously infected participants by time since reporting.
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| 3. |
- Brolund, Alma, et al.
(författare)
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Development of a real-time SYBRGreen PCR assay for rapid detection of acquired AmpC in Enterobacteriaceae
- 2010
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 1872-8359 .- 0167-7012. ; 82:3, s. 229-233
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Acquired AmpC enzymes, classified as miscellaneous extended-spectrum beta-lactamase (ESBLM) enzymes according to a recently proposed beta-lactamase classification, are increasing according to several publications. Simple and rapid methods for detection of ESBLM are needed for appropriate infection control. A gel-based multiplex PCR method for acquired bla(AmpC) detection and subtype classification has been available for several years. Here, we describe a modification of the protocol to suit real-time PCR platforms and to include novel genotypes. Material and methods: Clinical isolates with clavulanic acid non-reversible non-susceptibility to extended-spectrum cephalosporins were subjected to combination disk testing with cefoxitin +/- cloxacillin at Malmo University Hospital. Phenotypical AmpC production was defined as cloxacillin reversible cefoxitin resistance. In this study 51 phenotypical AmpC-producing isolates, were subjected to the acquired bla(AmpC) real-time PCR assay. The acquired blaAmpC positive isolates were further characterized by DNA sequencing of the acquired AmpC encoding gene, Pulsed-Field Gel Electrophoresis (PFGE) and PCR-based replicon typing. Results and discussion: The real-time PCR assay was able to detect and sub-classify all acquired bla(AmpC) genes described to date. The assay can be performed in less than 3 h, including pre-PCR preparations. Analysis of the isolate collection resulted in 18 of 51 phenotypical AmpC-producing isolates being positive in the acquired bla(AmpC) real-time multiplex PCR assay; 17 of subtype CIT and one DHA. Sequence analysis identified 16 isolates as blaCMY-2, one as blaCMY-16 and one as blaDHA-1. Detected plasmid replicon types were I1 and B/O. Two of the E. coli isolates were identical according to PFGE and the others were unrelated. (C) 2010 Elsevier B.V. All rights reserved.
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| 4. |
- Brolund, Alma, et al.
(författare)
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Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:6, s. e65793-
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Tidskriftsartikel (refereegranskat)abstract
- Infections caused by Extended spectrum beta-lactamase (ESBL)-producing E. coli are an emerging global problem, threatening the effectiveness of the extensively used beta-lactam antibiotics. ESBL dissemination is facilitated by plasmids, transposons, and other mobile elements. We have characterized the plasmid content of ESBL-producing E. coli from human urinary tract infections. Ten diverse isolates were selected; they had unrelated pulsed-field gel electrophoresis (PFGE) types (<90% similarity), were from geographically dispersed locations and had diverging antibiotic resistance profiles. Three isolates belonged to the globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9 phylogroups were identified in all ten isolates. The plasmid content (plasmidome) of each strain was analyzed using a combination of molecular methods and high-throughput sequencing. Hidden Markov Model-based analysis of unassembled sequencing reads was used to analyze the genetic diversity of the plasmid samples and to detect resistance genes. Each isolate contained between two and eight distinct plasmids, and at least 22 large plasmids were identified overall. The plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM, pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small cryptic high copy-number plasmids were frequent, containing one to seven open reading frames per plasmid. Three clustered groups of such small cryptic plasmids could be distinguished based on sequence similarity. Extrachromosomal prophages were found in three isolates. Two of them resembled the E. coli P1 phage and one was previously unknown. The present study confirms plasmid multiplicity in multi-resistant E. coli. We conclude that high-throughput sequencing successfully provides information on the extrachromosomal gene content and can be used to generate a genetic fingerprint of possible use in epidemiology. This could be a valuable tool for tracing plasmids in outbreaks.
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| 5. |
- Gaines, Hans, et al.
(författare)
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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 Therapy
- 2016
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Ingår i: Infectious Diseases. - : Informa UK Limited. - 2374-4235 .- 2374-4243. ; 48:2, s. 93-98
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 6. |
- Tegmark Wisell, Karin
(författare)
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Regulation of virulence gene expression in Staphylococcus aureus
- 2000
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The pathogenic bacterium Staphylococcus aureus has the ability to cause a wide variety of human diseases, ranging from superficial abscesses and wound infections to deep and systemic infections such as osteomyelitis, endocarditis and septicaemia. The ability to cause disease has been attributed to a large number of toxins and digesting enzymes as well as to proteins at the bacterial surface that bind various host molecules. These so-called virulence factors are accessory, and are supposed to be synthesised in response to the specific needs during the course of the infectious process. The work described in this thesis aims at a better understanding of the mechanisms that regulate the expression of virulence factors. Two interacting regulatory systems, agr (accessory gene regulator) and sar (staphylococcal accessory regulator), are involved in this regulation. The agr locus, which encodes a two-component signal transduction system responding to cell density, controls the expression of at least 25 different virulence factors. The effector molecule of the agr system is a regulatory RNA molecule, named RNAIII. The sar locus has been shown to regulate several staphylococcal virulence genes by modulating the activity of agr, but also via agr-independent mechanisms. The effector of the sar locus is a 14.7 kDa DNA binding protein, SarA. In animal models of infection both agr and sarA have been shown to affect virulence. How RNAIII and sarA function at the molecular level is, however, poorly understood. The structure and function of the RNAIII promoter have been studied in detail showing that SarA, which regulates the synthesis of RNAIII under certain growth conditions, binds to multiple sites within the RNAIII promoter region. It has also been shown that a region of 93 bp upstream of the transcription start point is sufficient for agr-dependent regulation of RNAIII synthesis. The RNAIII genes of several coagulase negative staphylococcal species S. epidermidis, S. simulans and S. warneri have been identified and analysed. The RNAIII molecules from the coagulase negative staphylococci were able to partially complement an RNAIII deficient S. aureus mutant. By the construction of hybrid RNAIII molecules it has also been demonstrated that highly conserved primary and secondary structures in both the 5´- and the 3´-half of the RNAIII molecule are required for regulation of virulence genes, and that separate parts of the molecule were involved in regulation of different target genes. Several genes known to be regulated by RNAIII have been demonstrated to be regulated by the sarA locus, independent of its effect on expression of RNAIII. By electrophoresis mobility shift experiments and DNase footprinting, SarA has been found to bind in a very similar way to the promoter regions of genes that are either activated or repressed by sarA. SarA does not appear to recognise a conserved DNA sequence motif but rather binds to AT-rich sequences. New potential regulators of agr (RNAIII), hla (alpha-hemolysin), ssp (serine protease) and spa (protein A) have been searched for using specific promoter DNA linked to magnetic beads. Of several new candidate regulators, one protein with a high degree of similarity to SarA, named SarH1 (Sar Homologue 1) has been characterised and found to be part of the agr-sarA regulatory network controlling virulence gene expression. By computer searches in the unfinished S. aureus genome databases four additional Sar homologues have been found, some of which may also be involved in this regulatory network.
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| 7. |
- Wisell, Karin Tegmark, et al.
(författare)
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Trimethoprim and enterococci in urinary tract infections : new perspectives on an old issue
- 2008
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Ingår i: The Journal of antimicrobial chemotherapy. - : Oxford University Press (OUP). - 1460-2091 .- 0305-7453. ; 62:1, s. 35-40
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Tidskriftsartikel (refereegranskat)abstract
- The lack of oral treatment alternatives for enterococcal urinary tract infections (UTIs) has led to a renewed interest in trimethoprim. Enterococci can incorporate exogenously produced folates and thereby reverse the effect of trimethoprim. Although a large proportion of enterococci appear susceptible to trimethoprim in vitro using standard media devoid of folates, a 360-fold increase in the MIC can be seen when susceptibility testing is performed in media containing fresh urine. Even if trimethoprim has a favourable pharmacokinetic profile, with high serum and very high urine concentrations, pharmacodynamic (PD) estimates show that a large proportion of the apparent wild-type isolates (as categorized by standard susceptibility testing) have unfavourable PD indices. The clinical efficacy of trimethoprim in enterococcal UTI is debated. We could identify not more than 38 evaluable cases of enterococcal UTI in the literature. The eradication rate was 82%. Case reports where patients on co-trimoxazole for UTI have developed bacteraemia with enterococci susceptible to trimethoprim seem to support experimental findings that standard antimicrobial susceptibility testing poorly predicts the clinical outcome of trimethoprim therapy. The European Committee on Antimicrobial Susceptibility Testing and the national breakpoint committees in Europe have recently debated the role of trimethoprim in the treatment of enterococcal UTI and agreed to categorize wild-type enterococci as intermediate to trimethoprim and trimethoprim/sulfamethoxazole. This allows the distinction between enterococci with and without acquired resistance mechanisms to trimethoprim. This review discusses the microbiological, experimental, clinical and PD aspects of the usage of trimethoprim for enterococcal UTI.
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| 8. |
- Woksepp, Hanna, et al.
(författare)
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High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli
- 2011
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Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 49:12, s. 4032-4039
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Tidskriftsartikel (refereegranskat)abstract
- Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.
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