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1.	Andersson, Martin, et al. (författare) Seasonal variations in use and outcome of rapid antigen detection tests and cultures in pharyngotonsillitis : a register study in primary care 2021 Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 21:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Diagnosis and treatment of pharyngotonsillitis are commonly focused on group A streptococci (GAS), although the disease is often associated with other pathogens. While the incidence of pharyngotonsillitis is known to vary with season, seasonal variations in the prevalence of potential pathogens are sparsely explored. The aim of this study was to explore any seasonal variations in the use and outcome of rapid antigen detection tests (RADTs) for GAS and throat cultures among patients diagnosed with pharyngotonsillitis in primary care.METHODS: We retrieved and combined retrospective data from the electronic medical record system and the laboratory information system in Kronoberg County, Sweden. Primary care visits resulting in a diagnosis of tonsillitis or pharyngitis were included, covering the period 2013-2016. The monthly rate of visits was measured, along with the use and outcome of RADTs for GAS and throat cultures obtained on the date of diagnosis. The variations between calendar months were then analysed.RESULTS: We found variations between calendar months, not only in the mean rate of visits resulting in a diagnosis of pharyngotonsillitis (p < 0.001), but in the mean proportion of RADTs being positive for GAS among the diagnosed (p < 0.001), and in the mean proportion of visits associated with a throat culture (p < 0.001). A lower mean rate of visits in August and September coincided with a lower proportion of RADTs being positive for GAS among them, which correlated with a higher proportion of visits associated with a throat culture.CONCLUSIONS: This study suggests that the role of GAS in pharyngotonsillitis in Sweden is less prominent in August and September than during the rest of the year.
2.	Ingberg, Edvin, 1988-, et al. (författare) 16S metagenomics for bacterial identification versus cultures in acute pharyngotonsillitis patients and controls 2018 Konferensbidrag (refereegranskat)abstract 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.
3.	Ingberg, Edvin, 1988-, et al. (författare) RT-PCR cycle threshold value in combination with visual scoring of chest computed tomography at hospital admission predicts outcome in COVID-19 2022 Ingår i: Infectious Diseases. - : Taylor & Francis. - 2374-4235 .- 2374-4243. ; 54:6, s. 431-440 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: COVID-19 has a most variable prognosis. Several risk factors for an unfavourable outcome have been identified including extensive lung involvement on chest CT and high viral load estimated by RT-PCR cycle threshold (Ct) values. We investigated Ct value for outcome prediction, relation between Ct value and extent of lung involvement on chest CT and the combination of Ct value and chest CT lung involvement to predict outcome in COVID-19.METHODS: Population-based retrospective study on all patients (n = 286) hospitalised for COVID-19 in Örebro Region, Sweden, between 1 March and 31 August 2020. Nasopharyngeal samples and chest CT at hospital admission were evaluated in relation to outcome of COVID-19.RESULTS: Both Ct value and chest CT lung involvement were independently associated with risk for ICU admission or death. Lung involvement was superior as a single parameter, but addition of Ct value increased the prediction performance. Ct value was especially useful to identify patients with high risk for severe disease despite limited lung involvement.CONCLUSIONS: The addition of RT-PCR Ct value to the assessment of lung involvement on chest CT adds valuable prognostic information in COVID-19. We believe that this information can be used to support clinical decision-making when managing COVID-19 patients.
4.	Saarentausta, Katariina, et al. (författare) Potential impact of the COVID-19 pandemic on the national and regional incidence, epidemiology and diagnostic testing of chlamydia and gonorrhoea in Sweden, 2020 2022 Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : Munksgaard Forlag. - 0903-4641 .- 1600-0463. ; 130:1, s. 34-42 Tidskriftsartikel (refereegranskat)abstract The COVID-19 pandemic has challenged the societies and health care systems globally, and resulted in many social and physical distancing restrictions to limit the spread of SARS-CoV-2. These restrictions have also likely affected the frequency of intimate contacts and the spread of sexually transmitted infections (STIs). Compared to most other countries, Sweden especially in Spring-Autumn 2020 pursued mainly milder voluntary, i.e. not mandatory enforced by laws, recommended restrictions and the impacts of these on society and spread of STIs remain largely unknown. We describe the potential impact of the COVID-19 pandemic on the national and regional incidence, epidemiology and diagnostic testing of chlamydia and gonorrhoea in Sweden in 2020. Compared to 2019, we found a significant decrease in incidence of chlamydia (-4.5%) and gonorrhoea (-17.5%), and in diagnostic testing (-10.5% for chlamydia, -9.4% for gonorrhoea) in 2020. However, the decrease in chlamydia incidence, which has mainly been decreasing last 10 years, was not significant when compared with the average incidence in 2017-2019. The largest decrease in national incidence of both infections was observed among young and heterosexual patients, however some Swedish regions showed an increased incidence, particularly of chlamydia. Increased "internet-based self-sampling" testing approach partly compensated for a decreased attendance at STI clinics. Studies, including sexual behavior, prevention, reasons for attending STI health care, STIs in different anatomical sites, and management of STIs, are required to elucidate the impact of COVID-19-associated social and physical distancing restrictions on sexual activity and the incidence and epidemiology of chlamydia and gonorrhoea in Sweden.
5.	Säll, Olof, 1980-, et al. (författare) Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain 2021 Ingår i: Epidemiology and Infection. - : Cambridge University Press. - 0950-2688 .- 1469-4409. ; 149 Tidskriftsartikel (refereegranskat)abstract Since 2015, the incidence of invasive meningococcal disease (IMD) caused by serogroup W (MenW) has increased in Sweden, due to the introduction of the 2013 strain belonging to clonal complex 11. The aim of this study was to describe the clinical presentation of MenW infections, in particular the 2013 strain, including genetic associations. Medical records of confirmed MenW IMD cases in Sweden during the years 1995-2019 (n = 113) were retrospectively reviewed and the clinical data analysed according to strain. Of all MenW patients, bacteraemia without the focus of infection was seen in 44%, bacteraemic pneumonia in 26%, meningitis in 13% and epiglottitis in 8%, gastrointestinal symptoms in 48% and 4% presented with petechiae. Phylogenetic analysis was used for possible links between genetic relationship and clinical picture. The 2013 strain infections, particularly in one cluster, were associated with more severe disease compared with other MenW infections. The patients with 2013 strain infections (n = 68) were older (52 years vs. 25 years for other strains), presented more often with diarrhoea as an atypical presentation (P = 0.045) and were more frequently admitted for intensive care (P = 0.032). There is a risk that the atypical clinical presentation of MenW infections, with predominantly gastrointestinal or respiratory symptoms rather than neck stiffness or petechiae, may lead to delay in life-saving treatment.
6.	Säll, Olof, 1980-, et al. (författare) Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students Annan publikation (övrigt vetenskapligt/konstnärligt)
7.	Säll, Olof, 1980-, et al. (författare) Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students 2023 Ingår i: Epidemiology and Infection. - : Cambridge University Press. - 0950-2688 .- 1469-4409. ; 151 Tidskriftsartikel (refereegranskat)abstract The bacterium Neisseria meningitidis causes life-threatening disease worldwide, typically with a clinical presentation of sepsis or meningitis, but can be carried asymptomatically as part of the normal human oropharyngeal microbiota. The aim of this study was to examine N. meningitidis carriage with regard to prevalence, risk factors for carriage, distribution of meningococcal lineages and persistence of meningococcal carriage. Throat samples and data from a self-reported questionnaire were obtained from 2744 university students (median age: 23 years) at a university in Sweden on four occasions during a 12-month period. Meningococcal isolates were characterised using whole-genome sequencing. The carriage rate among the students was 9.1% (319/3488; 95% CI 8.2-10.1). Factors associated with higher carriage rate were age ≤22 years, previous tonsillectomy, cigarette smoking, drinking alcohol and attending parties, pubs and clubs. Female gender and sharing a household with children aged 0-9 years were associated with lower carriage. The most frequent genogroups were capsule null locus (cnl), group B and group Y and the most commonly identified clonal complexes (cc) were cc198 and cc23. Persistent carriage with the same meningococcal strain for 12 months was observed in two students. Follow-up times exceeding 12 months are recommended for future studies investigating long-term carriage of N. meningitidis.
8.	Thulin Hedberg, Sara, et al. (författare) Invasive meningococcal disease in Sweden 2016 2017 Ingår i: 14th Congress of the EMGM, European Meningococcal and Haemophilus Disease Society. - Prague : The European Meningococcal and Haemophilus Disease Society EMGM. - 9788090666238 ; , s. 69-69 Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract 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.
9.	Andersson, Madelen, et al. (författare) Outbreak of a beta-lactam resistant non-typeable Haemophilus influenzae sequence type 14 associated with severe clinical outcomes 2015 Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 15 Tidskriftsartikel (refereegranskat)abstract 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.
10.	Campillay Lagos, Amaya, 1989-, et al. (författare) Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches 2022 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12:1 Tidskriftsartikel (refereegranskat)abstract Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.
11.	Fagerström, Anna, 1980-, et al. (författare) Comparative analysis of blaCTX-M-15-IncI1 plasmids in clinical Escherichia coli isolated during a 5-year period in a low-endemic setting Annan publikation (övrigt vetenskapligt/konstnärligt)
12.	Fagerström, Anna, 1980-, et al. (författare) Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters 2019 Ingår i: PLOS ONE. - : PLOS. - 1932-6203. ; 14:11 Tidskriftsartikel (refereegranskat)abstract 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.
13.	Fagerström, Anna, 1980- (författare) Long-term molecular epidemiology of extended-spectrum β-lactamase producing Escherichia coli in a low-endemic setting 2020 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Escherichia coli is a commensal inhabitant in the gastro-intestinal tract of humans and animals but it is also the most common bacterial species causing urinary tract infection, which ranges in severity from distal cystitis to urosepsis and septic shock. During the past decades, the prevalence of antibiotic resistant E. coli has increased worldwide. Extended-spectrum β-lactamases (ESBL) causes resistance to β-lactam antibiotics, the most widely used class of antibiotics. The genes encoding ESBL, bla, are usually carried on conjugative plasmids, which can be transferred between different bacterial lineages and different species. These plasmids frequently also carry resistance genes to additional antibiotic classes, and ESBL-producing E. coli are therefore often multidrug-resistant. The aim of this thesis was to describe the long-term molecular epidemiology of ESBL-producing E. coli in Örebro County during the time when they first started to emerge. In addition, potential transmission to the environment was investigated by performing a comparative analysis on ESBL-producing E. coli isolated from patients and from the aquatic environment in Örebro city. In general, the E. coli population was genetically diverse, but the pandemic lineage ST131, first identified in 2004, appears to have been responsible for the dramatic increase of CTX-M-15-producing E.coli observed during the late 2000s. CTX-M-15 was the most prevalent ESBL-type followed by CTX-M-14 and these genes were mainly found on plasmids belonging to the IncF or IncI1 families. Continuous horizontal transmission of IncI1 ST31 and ST37 plasmids between diverse E. coli lineages have also contributed to the dissemination of blaCTX-M-15 in Örebro County. Extended spectrum β-lactamase-producing E. coli were found to be common in the aquatic environment in Örebro city and E. coli lineages genetically similar to those causing infections in humans were present in environmental waters indicating that transmission of ESBL-producing E. colifrom humans to the aquatic environment likely has occurred.
14.	Göransson, J., et al. (författare) Performance of a System for Rapid Phenotypic Antimicrobial Susceptibility Testing of Gram-Negative Bacteria Directly from Positive Blood Culture Bottles 2023 Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 61:3 Tidskriftsartikel (refereegranskat)abstract The rapid administration of optimal antimicrobial treatment is paramount for the treatment of bloodstream infections (BSIs), and rapid antimicrobial susceptibility testing (AST) results are essential. Q-linea has developed the ASTar system, a rapid phenotypic AST device. Here, we report the performance of the ASTar BC G- (Gram-negative) kit when assessed according to the ISO 20776-2:2007 standard for performance evaluation of in vitro diagnostic AST devices. The evaluated ASTar BC G- kit uses a broad panel of 23 antimicrobials for the treatment of BSIs caused by Gram-negative fastidious and nonfastidious bacteria across a range of 6 to 14 2-fold dilutions, including cefoxitin as a screening agent for AmpC-producing Enterobacterales. The ASTar system processes blood culture samples to generate data on MICs and susceptible, intermediate, or resistant (SIR) category. The automated protocol includes concentration determination and concentration adjustment to enable a controlled inoculum, followed by broth microdilution (BMD) and microscopy performed continuously to generate MIC values within approximately 6 h once the test is run on the ASTar system. The performance of the ASTar system was assessed against the ISO 20776-2:2007 standard BMD reference method. Testing was performed across three sites, with results from 412 contrived blood cultures and 74 fresh clinical blood cultures. The ASTar system was also tested for reproducibility, with triplicate testing of 11 strains. The accuracy study comprised 8,650 data points of bacterium-antimicrobial tests. The ASTar system demonstrated an overall essential agreement (EA) of 95.8% (8,283/8,650) and a categorical agreement (CA) of 97.6% (8,433/8,639) compared to the reference BMD method. The overall rate of major discrepancies (MDs) was 0.9% (62/6,845), and that of very major discrepancies (VMDs) was 2.4% (30/1,239). This study shows that the ASTar system delivers reproducible results with overall EA and CA of >95%.
15.	Haars, Jonathan, et al. (författare) Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023 2023 Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 11:10 Tidskriftsartikel (refereegranskat)abstract Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.
16.	Haglund, Sofie, 1975-, et al. (författare) CXCL13 in laboratory diagnosis of Lyme neuroborreliosis-the performance of the recomBead and ReaScan CXCL13 assays in human cerebrospinal fluid samples 2022 Ingår i: European Journal of Clinical Microbiology and Infectious Diseases. - : Springer. - 0934-9723 .- 1435-4373. ; 41:1, s. 175-179 Tidskriftsartikel (refereegranskat)abstract The chemokine CXCL13 is used as complement to serology in the diagnostics of Lyme neuroborreliosis (LNB). We evaluated and compared the semi-quantitative, cassette-based ReaScan CXCL13 assay with the quantitative recomBead CXCL13 assay using a collection of 209 cerebrospinal fluid samples. The categorical agreement between results interpreted as negative, grey zone, and positive by the two methods was 87%. The diagnostic sensitivity was higher using the recomBead assay, whereas specificity was higher using ReaScan. Few manual steps, and a short turn-around time with no batching of samples makes the ReaScan CXCL13 assay an attractive complement to serology in the diagnostics of LNB.
17.	Idelevich, E. A., et al. (författare) Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey 2019 Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 25:11, s. 1399-1407 Tidskriftsartikel (refereegranskat)abstract 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.
18.	Johansson, Åsa, et al. (författare) Importance of a Diverse Isolate Collection When Defining Genotype-Specific Mass Spectra in Staphylococcus aureus 2014 Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 52:7, s. 2738-2739 Tidskriftsartikel (refereegranskat)
19.	Johansson, Åsa, et al. (författare) The detection and verification of carbapenemases using ertapenem and Matrix Assisted Laser Desorption Ionization-Time of Flight 2014 Ingår i: BMC Microbiology. - : BioMed Central. - 1471-2180. ; 14 Tidskriftsartikel (refereegranskat)abstract 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.
20.	Koskela, Anita, 1979-, et al. (författare) Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization 2023 Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1 Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) worldwide pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14–30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
21.	Lamy, Brigitte, et al. (författare) Bloodstream infections - Standard and progress in pathogen diagnostics 2020 Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 26:2, s. 142-150 Forskningsöversikt (refereegranskat)abstract 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.
22.	Lamy, B., et al. (författare) Towards an improved diagnosis of bloodstream infection : promises and hurdles 2018 Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 24:9, s. 933-934 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
23.	Liljedahl Prytz, Karolina, 1976-, et al. (författare) Antibiotic treatment with one single dose of gentamicin at admittance in addition to a beta-lactam antibiotic in the treatment of community-acquired bloodstream infection with sepsis 2020 Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 15:7 Tidskriftsartikel (refereegranskat)abstract Background: Combination therapy in the treatment of sepsis, especially the value of combining a beta-Lactam antibiotic with an aminoglycoside, has been discussed. This retrospective cohort study including patients with sepsis or septic shock aimed to investigate whether one single dose of gentamicin at admittance (SGA) added to beta-Lactam antibiotic could result in a lower risk of mortality than beta-Lactam monotherapy, without exposing the patient to the risk of nephrotoxicity.Methods and findings: All patients with positive blood cultures were evaluated for participation (n = 1318). After retrospective medical chart review, a group of patients with community-acquired sepsis with positive blood cultures who received beta-Lactam antibiotic with or without the addition of SGA (n = 399) were included for the analysis. Mean age was 74.6 yrs. (range 19-98) with 216 (54%) males. Sequential Organ Failure Assessment score (SOFA score) median was 3 (interquartile range [IQR] 2-5) and the median Charlson Comorbidity Index for the whole group was 2 (IQR 1-3). Sixty-seven (67) patients (17%) had septic shock. The 28-day mortality in the combination therapy group was 10% (20 of 197) and in the monotherapy group 22% (45 of 202), adjusted HR 3.5 (95% CI (1.9-6.2),p= < 0.001. No significant difference in incidence of acute kidney injury (AKI) was detected.Conclusion: This retrospective observational study including patients with community-acquired sepsis or septic shock and positive blood cultures, who meet Sepsis-3 criteria, shows that the addition of one single dose of gentamicin to beta-lactam treatment at admittance was associated with a decreased risk of mortality and was not associated with AKI. This antibiotic regime may be an alternative to broad-spectrum antibiotic treatment of community-acquired sepsis. Further prospective studies are warranted to confirm these results.
24.	Lind, Alexander, et al. (författare) Anxiety, depression and quality of life in relation to SARS-CoV-2 antibodies in individuals living with diabetes during the second wave of COVID-19 2024 Ingår i: Diabetes epidemiology and management. - : Elsevier. - 2666-9706. ; 13 Tidskriftsartikel (refereegranskat)abstract Aims: The objective was to compare anxiety, depression, and quality of life (QoL) in individuals living with type 1 (T1D) and type 2 (T2D) diabetes with matched controls during the second wave of the COVID-19 pandemic.Methods: Via randomization, individuals living with diabetes T1D (n = 203) and T2D (n = 413), were identified during February-July 2021 through health-care registers. Population controls (n = 282) were matched for age, gender, and residential area. Questionnaires included self-assessment of anxiety, depression, QoL, and demographics in relation to SARS-CoV-2 exposure. Blood was collected through home-capillary sampling, and SARS-CoV-2 Nucleocapsid (NCP) and Spike antibodies (SC2_S1) were determined by multiplex Antibody Detection by Agglutination-PCR (ADAP) assays.Results: Younger age and health issues were related to anxiety, depression, and QoL, with no differences between the study groups. Female gender was associated with anxiety, while obesity was associated with lower QoL. The SARS-CoV-2 NCP seroprevalence was higher in T1D (8.9 %) compared to T2D (3.9 %) and controls (4.0 %), while the SARS-CoV-2 SC2_S1 seroprevalence was higher for controls (25.5 %) compared to T1D (16.8 %) and T2D (14.0 %).Conclusions: A higher SARS-CoV-2 infection rate in T1D may be explained by younger age and higher employment rate, and the associated increased risk for viral exposure.
25.	Malm, Kerstin, 1960-, et al. (författare) 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 Hospital 2016 Ingår i: Journal of Clinical Virology. - : Elsevier. - 1386-6532 .- 1873-5967. ; 82, s. S27-S27 Tidskriftsartikel (refereegranskat)abstract 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.
26.	Metcalfe, Daniel B., et al. (författare) Patchy field sampling biases understanding of climate change impacts across the Arctic 2018 Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:9, s. 1443-1448 Tidskriftsartikel (refereegranskat)abstract Effective societal responses to rapid climate change in the Arctic rely on an accurate representation of region-specific ecosystem properties and processes. However, this is limited by the scarcity and patchy distribution of field measurements. Here, we use a comprehensive, geo-referenced database of primary field measurements in 1,840 published studies across the Arctic to identify statistically significant spatial biases in field sampling and study citation across this globally important region. We find that 31% of all study citations are derived from sites located within 50 km of just two research sites: Toolik Lake in the USA and Abisko in Sweden. Furthermore, relatively colder, more rapidly warming and sparsely vegetated sites are under-sampled and under-recognized in terms of citations, particularly among microbiology-related studies. The poorly sampled and cited areas, mainly in the Canadian high-Arctic archipelago and the Arctic coastline of Russia, constitute a large fraction of the Arctic ice-free land area. Our results suggest that the current pattern of sampling and citation may bias the scientific consensuses that underpin attempts to accurately predict and effectively mitigate climate change in the region. Further work is required to increase both the quality and quantity of sampling, and incorporate existing literature from poorly cited areas to generate a more representative picture of Arctic climate change and its environmental impacts.
27.	Muhammad, Ibrahim, et al. (författare) 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 origin 2014 Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 14:1 Tidskriftsartikel (refereegranskat)abstract 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.
28.	Månsson, Emeli, 1978-, et al. (författare) Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins 2017 Ingår i: Journal of Medical Microbiology. - : Microbiology Society. - 0022-2615 .- 1473-5644. ; 66:5, s. 601-608 Tidskriftsartikel (refereegranskat)abstract 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.
29.	Månsson, Emeli, 1978-, et al. (författare) Methicillin-Resistant Staphylococcus epidermidis Lineages in the Nasal and Skin Microbiota of Patients Planned for Arthroplasty Surgery 2021 Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 9:2 Tidskriftsartikel (refereegranskat)abstract Staphylococcus epidermidis, ubiquitous in the human nasal and skin microbiota, is a common causative microorganism in prosthetic joint infections (PJIs). A high proportion of PJI isolates have been shown to harbor genetic traits associated with resistance to/tolerance of agents used for antimicrobial prophylaxis in joint arthroplasties. These traits were found within multidrug-resistant S. epidermidis (MDRSE) lineages of multiple genetic backgrounds. In this study, the aim was to study whether MDRSE lineages previously associated with PJIs are present in the nasal and skin microbiota of patients planned for arthroplasty surgery but before hospitalization. We cultured samples from nares, inguinal creases, and skin over the hip or knee (dependent on the planned procedure) taken two weeks (median) prior to admittance to the hospital for total joint arthroplasty from 66 patients on agar plates selecting for methicillin resistance. S. epidermidis colonies were identified and tested for the presence of mecA. Methicillin-resistant S. epidermidis (MRSE) were characterized by Illumina-based whole-genome sequencing. Using this method, we found that 30/66 (45%) of patients were colonized with MRSE at 1-3 body sites. A subset of patients, 10/66 (15%), were colonized with MDRSE lineages associated with PJIs. The qacA gene was identified in MRSE isolates from 19/30 (63%) of MRSE colonized patients, whereas genes associated with aminoglycoside resistance were less common, found in 11/30 (37%). We found that MDRSE lineages previously associated with PJIs were present in a subset of patients' pre-admission microbiota, plausibly in low relative abundance, and may be selected for by the current prophylaxis regimen comprising whole-body cleansing with chlorhexidine-gluconate containing soap. To further lower the rate of S. epidermidis PJIs, the current prophylaxis may need to be modified, but it is important for possible perioperative MDRSE transmission events and specific risk factors for MDRSE PJIs to be investigated before reevaluating antimicrobial prophylaxis.
30.	Månsson, Emeli, 1978- (författare) Molecular epidemiology of Staphylococcus epidermidis in prosthetic joint infections 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Staphylococcus epidermidis is ubiquitous in the human microbiota, but also an important pathogen in healthcare-associated infections, such as prosthetic joint infections (PJIs). In this thesis, aspects of the molecular epidemiology of S. epidermidis in PJIs were investigated with the aim of improving our understanding of the pre- and perioperative measures required to reduce the incidence of S. epidermidis PJIs.In Paper I, S. epidermidis retrieved from air sampling in the operating field during arthroplasty was characterized by multilocus sequence typing and antibiotic susceptibility testing. No isolates belonging to sequence types (STs) 2 and 215, previously associated with PJIs, were found in the air of the operating field. During air sampling, several Staphylococcus pettenkoferi isolates were identified, and as a spin-off of Paper I, the genomic relatedness of these isolates to S. pettenkoferi isolates from blood cultures was described in Paper II.In Paper III, genetic traits distinguishing S. epidermidis isolated from PJIs were determined using genome-wide association study accounting for population effects after whole-genome sequencing (WGS) of a population- based 10-year collection of S. epidermidis isolates from PJIs and of nasal isolates retrieved from patients scheduled for arthroplasty. Genes associated with antimicrobial agents used for prophylaxis in arthroplasty, i.e., beta-lactam antibiotics, aminoglycosides, and chlorhexidine, were associated with PJI origin. S. epidermidis from PJIs were dominated by the ST2a, ST2b, ST5, and ST215 lineages.In Paper IV, selective agar plates were used to investigate colonization with methicillin resistant S. epidermidis (MRSE) in patients scheduled for arthroplasty. MRSE were further characterized by WGS. A subset of patients was found to harbour PJI-associated S. epidermidis lineages in their microbiota before hospitalization, but no isolates belonging to the ST2a lineage nor any rifampicin-resistant isolates were retrieved.
31.	Månsson, Emeli, 1978-, et al. (författare) Sequence types of Staphylococcus epidermidis associated with prosthetic joint infections are not present in the laminar airflow during prosthetic joint surgery 2015 Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - Hoboken, USA : Wiley-Blackwell. - 0903-4641 .- 1600-0463. ; 123:7, s. 589-595 Tidskriftsartikel (refereegranskat)abstract 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.
32.	Nestor, David, 1992-, et al. (författare) Detection of extended-spectrum beta-lactamase production in Enterobacteriales from patients with suspected urinary tract infections, Tabora region, Rural Tanzania 2018 Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : Wiley-Blackwell Publishing Inc.. - 0903-4641 .- 1600-0463. ; 126:8, s. 700-702 Tidskriftsartikel (refereegranskat)
33.	Nestor, David, 1992-, et al. (författare) Early prediction of blood stream infection in a prospectively collected cohort 2021 Ingår i: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Blood stream infection (BSI) and sepsis are serious clinical conditions and identification of the disease-causing pathogen is important for patient management. The RISE (Rapid Identification of SEpsis) study was carried out to collect a cohort allowing high-quality studies on different aspects of BSI and sepsis. The aim of this study was to identify patients at high risk for BSI who might benefit most from new, faster, etiological testing using neutrophil to lymphocyte count ratio (NLCR) and Shapiro score.METHODS: Adult patients (≥ 18 years) presenting at the emergency department (ED) with suspected BSI were prospectively included between 2014 and 2016 at Örebro University Hospital. Besides extra blood sampling, all study patients were treated according to ED routines. Electronic patient charts were retrospectively reviewed. A modified Shapiro score (MSS) and NLCR were extracted and compiled. Continuous score variables were analysed with area under receiver operator characteristics curves (AUC) to evaluate the ability of BSI prediction.RESULTS: The final cohort consisted of 484 patients where 84 (17%) had positive blood culture judged clinically significant. At optimal cut-offs, MSS (≥3 points) and NLCR (> 12) showed equal ability to predict BSI in the whole cohort (AUC 0.71/0.74; sensitivity 69%/67%; specificity 64%/68% respectively) and in a subgroup of 155 patients fulfilling Sepsis-3 criteria (AUC 0.71/0.66; sensitivity 81%/65%; specificity 46%/57% respectively). In BSI cases only predicted by NLCR> 12 the abundance of Gram-negative to Gram-positive pathogens (n = 13 to n = 4) differed significantly from those only predicted by MSS ≥3 p (n = 7 to n = 12 respectively) (p < 0.05).CONCLUSIONS: MSS and NLCR predicted BSI in the RISE cohort with similar cut-offs as shown in previous studies. Combining the MSS and NLCR did not increase the predictive performance. Differences in BSI prediction between MSS and NLCR regarding etiology need further evaluation.
34.	Nestor, David, 1992-, et al. (författare) Evaluation of the FilmArray (TM) Meningitis/Encephalitis panel with focus on bacteria and Cryptococcus spp 2019 Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 157, s. 113-116 Tidskriftsartikel (refereegranskat)abstract Purpose: Molecular methods provide fast and accurate detection of both bacteria and viruses in the cerebrospinal fluid (CSF) causing infection in the central nervous system (CNS). In the present study we evaluated the bacterial detection performance of the fully automated FilmArray (TM) Meningitis/Encephalitis (ME) panel (bioMerieux) by comparing it with culture and multiplexed in-house PCR. Methods: Three sample types were analysed; Contrived samples with known bacterial/fungal concentration (n = 29), clinical samples from patients with verified cause of CNS infection (n = 17) and external quality assessment (EQA) samples (n = 11). Another six samples were purposely prepared with multiple targets to evaluate multiplex capacity. Results: The FilmArray (TM) had a slightly higher limit of detection for Streptococcus pneumoniae, Neisseria meningitidis, Listeria monocytogenes and Streptococcus agalactiae compared to in-house PCR methods but performed equal or better when compared to culture. The FilmArray (TM) ME panel detected the expected pathogen in 17 of 17 clinical samples and yielded detection of three additional viruses of which one was confirmed with comparator techniques. All but one of the EQA samples were correctly detected. Conclusions: The results of this study are promising and the FilmArray (TM) ME panel could add to the diagnostic algorithm in CNS-infections. However, the limit of detection for the important pathogens N. meningitidis and S. pneumoniae could be improved.
35.	Pallon, Jon, et al. (författare) Association between bacterial finding, antibiotic treatment and clinical course in patients with pharyngotonsillitis : a registry-based study in primary healthcare in Sweden 2021 Ingår i: BMC Infectious Diseases. - : BioMed Central. - 1471-2334. ; 21:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: The role of non-group A streptococci and Fusobacterium necrophorum in pharyngotonsillitis has been disputed and few prospective studies have evaluated the effect of antibiotic treatment. This study uses registry data to investigate the relation between antibiotic prescription for pharyngotonsillitis in primary healthcare and return visits for pharyngotonsillitis, complications, and tonsillectomy.METHODS: Retrospective data were extracted from the regional electronic medical record system in Kronoberg County, Sweden, for all patients diagnosed with pharyngotonsillitis between 2012 and 2016. From these data, two cohorts were formed: one based on rapid antigen detection tests (RADT) for group A streptococci (GAS) and one based on routine throat cultures for β-haemolytic streptococci and F. necrophorum. The 90 days following the inclusion visit were assessed for new visits for pharyngotonsillitis, complications, and tonsillectomy, and related to bacterial aetiology and antibiotic prescriptions given at inclusion.RESULTS: In the RADT cohort (n = 13,781), antibiotic prescription for patients with a positive RADT for GAS was associated with fewer return visits for pharyngotonsillitis within 30 days compared with no prescription (8.7% vs. 12%; p = 0.02), but not with the complication rate within 30 days (1.5% vs. 1.8%; p = 0.7) or with the tonsillectomy rate within 90 days (0.27% vs. 0.26%; p = 1). In contrast, antibiotic prescription for patients with a negative RADT was associated with more return visits for pharyngotonsillitis within 30 days (9.7% vs. 7.0%; p = 0.01). In the culture cohort (n = 1 370), antibiotic prescription for patients with Streptococcus dysgalactiae ssp. equisimilis was associated with fewer return visits for pharyngotonsillitis within 30 days compared with no prescription (15% vs. 29%; p = 0.03).CONCLUSIONS: Antibiotic prescription was associated with fewer return visits for pharyngotonsillitis in patients with a positive RADT for GAS but with more return visits in patients with a negative RADT for GAS. There were no differences in purulent complications related to antibiotic prescription.
36.	Pallon, Jon, et al. (författare) Presence of microorganisms in children with pharyngotonsillitis and healthy controls: a prospective study in primary healthcare 2021 Ingår i: Infection. - : Springer Science and Business Media LLC. - 0300-8126 .- 1439-0973. ; 49:4, s. 715-724 Tidskriftsartikel (refereegranskat)abstract Purpose Most studies on paediatric pharyngotonsillitis focus on group A streptococci. This study, however, analyses a broad spectrum of bacteria and viruses related to paediatric pharyngotonsillitis and evaluates their associated clinical symptoms and courses. Methods This observational prospective study in primary healthcare includes 77 children aged < 15 with a sore throat and 34 asymptomatic children, all of whom were sampled from the tonsils with an E-swab(R) for analysis with culture and PCR for 14 bacteria and 15 viruses. Patients were evaluated clinically, and their symptoms recorded in diaries for 10 days. Participants were followed up for 3 months by reviewing medical records. Results A pathogen was detected in 86% of patients and in 71% of controls (P = 0.06). Bacteria were found in 69% of patients and 59% of controls (P = 0.3), and viruses in 36% and 26%, respectively (P = 0.3). Group A streptococci was the most common finding, with a prevalence of 49% and 32%, respectively (P = 0.1). Clinical signs were not useful for distinguishing pathogens. None of the controls and 16% of the patients reconsulted for a sore throat within 3 months. Conclusion Bacteria were more common than viruses in both study groups. The high rate of pathogens in asymptomatic children interferes with diagnoses based on aetiology.
37.	Pallon, Jon, et al. (författare) The aetiology of pharyngotonsillitis in primary health care : a prospective observational study 2021 Ingår i: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Few studies on pharyngotonsillitis have examined the clinical presentation of different aetiologies where pathogens have been detected using molecular methods. We aimed to assess how well clinical signs and symptoms can predict (1) the presence or absence of a broad range of viruses and bacteria, and (2) reconsultations for a sore throat or a complication.METHODS: In this descriptive observational prospective study in primary health care 220 patients aged 15-45 with suspected pharyngotonsillitis were sampled from nose, throat and blood and screened for 20 bacteria and viruses using polymerase chain reaction (PCR), culture and serology. Odds ratios (OR) and predictive values with 95% confidence intervals (CI) were used to show association between microbiological findings and clinical signs and symptoms. Patients were followed up after 3 months by reviewing electronic medical records.RESULTS: Both cough and coryza were more common in patients with only viruses (67%) than in patients with only bacteria (21%) (p < 0.001), whereas tonsillar coating was more common in patients with only bacteria (53%) than in patients with only viruses (29%) (p = 0.006). Tonsillar coating (adjusted OR 6.0; 95% CI 2.5-14) and a lack of cough (adjusted OR 3.5; 95% CI 1.5-8.0) were significantly associated with Streptococcus pyogenes (group A streptococci; GAS) and with any bacterial finding. A Centor score of 3-4 had a positive predictive value of 49% (95% CI 42-57) for GAS and 66% (95% CI 57-74) for any bacterial findings. The use of rapid antigen detection test for GAS increased the positive predictive value for this group to 93%.CONCLUSIONS: Signs and symptoms, both single and combined, were insufficient to rule in GAS or other pathogens. However, both cough and coryza were useful to rule out GAS. The results support the clinical approach of restricting rapid antigen detection testing to patients with 3-4 Centor criteria. The low carriage rate of bacteria among asymptomatic controls implied that most detections in patients represented a true infection.
38.	Pallon, Jon, et al. (författare) The use and usefulness of point-of-care tests in patients with pharyngotonsillitis - an observational study in primary health care 2024 Ingår i: BMC Primary Care. - : BioMed Central (BMC). - 2731-4553. ; 25:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Rapid antigen detection tests (RADT) for Group A streptococci (GAS) and point-of-care tests for C-reactive protein (CRP) are commonly used in patients with pharyngotonsillitis in Sweden and Denmark although CRP testing is not supported by guidelines. We aimed to describe (1) the proportion of patients tested with RADT and/or CRP, (2) the relation between test results and antibiotic prescribing, and (3) the association between CRP level and microbial aetiology.METHODS: We used a post-hoc-analysis of data collected in primary health care in a prospective aetiological study of 220 patients 15-45 years old diagnosed with pharyngotonsillitis. The outcomes of RADTs and CRP tests were related to antibiotic prescribing and microbial aetiology.RESULTS: A RADT was used in 94% of the patients. A CRP test was used in 50% of the patients but more commonly in those with a negative RADT (59%) than in those with a positive RADT (38%) (p = 0.005). Most (74%) CRP tests were used in patients with a negative RADT. Antibiotic prescribing differed greatly between patients with a positive RADT (96%) and patients with a negative RADT (17%) (p < 0.001). In patients with a negative RADT, there was a positive association between CRP value and antibiotic prescribing (OR 1.05; 95% CI 1.02-1.07; p < 0.001). Patients with CRP values ≤ 30 mg/l were seldomly prescribed antibiotics. Patients with GAS in culture had the highest median CRP (46 mg/l), which was higher than in patients without GAS (8 mg/l; p < 0.001). However, the positive predictive value for GAS never exceeded 0.60 (95% CI 0.31-0.83) at the investigated CRP levels.CONCLUSIONS: The widespread use of tests is a major deviation from national guidelines. Most CRP tests were used in patients with a negative RADT, suggesting a belief in the added value of a CRP test, and the CRP result seemed to influence antibiotic prescribing. However, as an aetiological test, CRP is not useful for predicting GAS.
39.	Rapp, Ellionor, et al. (författare) Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight 2018 Ingår i: Journal of Microbiological Methods. - : Elsevier. - 0167-7012 .- 1872-8359. ; 146, s. 37-39 Tidskriftsartikel (refereegranskat)abstract 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.
40.	Rondahl, E., et al. (författare) The risk of HCV RNA contamination in serology screening instruments with a fixed needle for sample transfer 2014 Ingår i: Journal of Clinical Virology. - : Elsevier BV. - 1386-6532 .- 1873-5967. ; 60:2, s. 172-173 Tidskriftsartikel (refereegranskat)abstract 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. © 2014 The Authors.
41.	Sagerfors, Susanna, 1977-, et al. (författare) Corneal Culture in Infectious Keratitis : Effect of the Inoculation Method and Media on the Corneal Culture Outcome 2021 Ingår i: Journal of Clinical Medicine. - : MDPI. - 2077-0383. ; 10:9 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: To compare two different methods of corneal culture in infectious keratitis: multiple sampling for direct inoculation and enrichment (standard method) and a single sample via transport medium for indirect inoculation (indirect inoculation method).METHODS: Prospective inclusion of patients fulfilling predefined criteria of infectious keratitis undergoing corneal culture according to both studied methods in a randomized order.RESULTS: = 0.002) and a significantly higher proportion of microorganisms than the indirect inoculation method, with a Cohen's kappa of 0.38 (95% CI: 0.28-0.49) for agreement between the methods. Subanalysis of culture results showed that direct inoculation on gonococcal agar only combined with the indirect inoculation method resulted in a similar rate of culture positive patients and proportion of detected microorganisms to the standard method.CONCLUSION: Indirect inoculation of one corneal sample cannot replace direct inoculation of multiple corneal samples without loss of information. A combination of directly and indirectly inoculated samples can reduce the number of corneal samples by four without statistically significant differences in culture outcome or in the proportion of detected microorganisms.
42.	Strålin, Kristoffer, et al. (författare) Performance of PCR/electrospray ionization-mass spectrometry on whole blood for detection of bloodstream microorganisms in patients with suspected sepsis 2020 Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 58:9, s. e01860-19 Tidskriftsartikel (refereegranskat)abstract Blood culture (BC) often fails to detect bloodstream microorganisms in sepsis. However, molecular diagnostics hold great potential. The molecular method PCR/electrospray ionization-mass spectrometry (PCR/ESI-MS) can detect DNA from hundreds of different microorganisms in whole blood. The aim of the present study was to evaluate the performance of this method in a multicenter study including 16 teaching hospitals in the USA (n=13) and Europe (n=3). First, on 2,754 contrived whole blood samples, with or without spiked microorganisms, PCR/ESI-MS produced 99.1% true positive and 97.2% true negative results. Secondly, among 1,460 patients with suspected sepsis (sepsis-2 definition), BC and PCR/ESI-MS on whole blood were positive in 14.6% and 25.6% of cases, respectively, with the following result combinations: BC+/PCR/ESI-MS-, 4.3%; BC+/PCR/ESI-MS+, 10.3%; BC-/PCR/ESI-MS+, 15.3%; and BC-/PCR/ESI-MS-, 70.1%. Compared with BC, PCR/ESI-MS showed the following sensitivities (coagulase-negative staphylococci not included): Gram-positive bacteria, 58%; Gram-negative bacteria, 78%; and Candida species, 83%. The specificities were > 94% for all individual species. Patients treated with prior antimicrobial medications (n=603) had significantly increased PCR/ESI-MS positivity rates compared with patients without prior antimicrobial treatment, 31% vs 22% (p<0.0001), with pronounced differences for Gram-negative bacteria and Candida species. In conclusion, PCR/ESI-MS showed excellent performance on contrived samples. On clinical samples, it showed high specificities, moderately high sensitivities for Gram-negative bacteria and Candida species, and elevated positivity rates during antimicrobial treatment. These promising results encourage further development of molecular diagnostics on whole blood for detection of bloodstream microorganisms in sepsis.
43.	Sundqvist, Kyle, 1978, et al. (författare) The pumpistor: A linearized model of a flux-pumped superconducting quantum interference device for use as a negative-resistance parametric amplifier 2013 Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 103:102603 Tidskriftsartikel (refereegranskat)abstract We describe a circuit model for a flux-driven Superconducting QUantum Interference Device (SQUID). This is useful for developing insight into how these devices perform as active elements in parametric amplifiers. The key concept is that frequency mixing in a flux-pumped SQUID allows for the appearance of an effective negative resistance. In the three-wave, degenerate case treated here, a negative resistance appears only over a certain range of allowed input signal phase. This model readily lends itself to testable predictions of more complicated circuits.
44.	Sundqvist, Martin, 1974- (författare) Antibiotic Resistance and Population Dynamics of Escherichia coli in Relation to a Large Scale Antibiotic Consumption Intervention 2010 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Antibiotic resistance challenges the practice and development of modern medicine. The aim of this thesis was to test the hypothesis that antibiotic resistance is reversible once the selection pressure of an antibiotic is removed. A decisive reduction (85%) in trimethoprim and trimethoprim-sulfamethoxazole over 24 months in Kronoberg County, Sweden, is described. The resistance baseline prior to the intervention and the effects of the intervention on resistance levels, trimethoprim resistance genes (dfr-genes) and population structure in Escherichia coli were studied. The effects of different algorithms for excluding patient duplicate isolates were small but systematic. An identical algorithm was used throughout. The drastic decrease in the use of trimethoprim containing drugs did not result in a corresponding decrease in trimethoprim resistance. This was true both for total trimethoprim resistance and for trimethoprim mono-resistance. The distributions of E. coli phenotypes, dfr-genes and E. coli sequence types were stable. The marginal effect on resistance rates was explained by a low fitness cost of trimethoprim resistance observed in vitro and the high levels of associated resistance in trimethoprim resistant isolates. Trimethoprim resistance was, although widespread in the E. coli population, more common in certain E. coli sequence types. The distributions of dfr-genes were different in E. coli and K. pneumoniae and between different E. coli sequence types. These results indicate mechanisms related to the genetic back-bone of E coli to be important for the acquisition and persistence of antibiotic resistance. The findings of this thesis indicates that, at least for some classes of antibiotics, we may have overestimated the usefulness of a strategy for reversing antimicrobial resistance based on the fitness cost of resistance. We have equally underestimated the conserving effects of associated resistance. The stability of the dfr-genes and E. coli sequence types underlines the importance of associated resistance and successful lineages in the spread and maintenance of antibiotic resistance in E. coli.
45.	Sundqvist, Martin, 1974- (författare) Reversibility of antibiotic resistance 2014 Ingår i: Upsala Journal of Medical Sciences. - : Informa Healthcare. - 0300-9734 .- 2000-1967. ; 119:2, s. 142-148 Forskningsöversikt (refereegranskat)abstract 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.
46.	Sundqvist, Martin, 1974-, et al. (författare) Within-Population Distribution of Trimethoprim Resistance in Escherichia coli before and after a Community-Wide Intervention on Trimethoprim Use 2014 Ingår i: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 58:12, s. 7492-7500 Tidskriftsartikel (refereegranskat)abstract 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.
47.	Säll, Olof, 1980-, et al. (författare) Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches 2019 Ingår i: American Journal of Tropical Medicine and Hygiene. - : HighWire Press. - 0002-9637 .- 1476-1645. ; 101:1, s. 253-259 Tidskriftsartikel (refereegranskat)abstract 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.
48.	Säll, Olof, 1980-, et al. (författare) Etiology of CNS infections in Nepal using the FilmArray meningitis/encephalitis panel 2017 Ingår i: International Journal of Antimicrobial Agents. - : Elsevier. - 0924-8579 .- 1872-7913. ; 50:Suppl. 2, s. S66-S66 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
49.	Säll, Olof, 1980- (författare) Infections in the central nervous system with focus on meningococcal disease : clinical and epidemiological aspects 2022 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Infections in the central nervous system (CNS) include meningitis and encephalitis and are associated with high mortality and morbidity. A large number of different pathogens can cause these infections, including Neisseria meningitidis. It’s crucial to find the causative pathogen in order to provide the best treatment to the patient and for disease surveillance. In Paper I, molecular methods were used to investigate the microbial etiology in patients presenting with CNS infections at United Mission Hospital in Tansen, Nepal. Although the cerebrospinal fluid samples were analyzed for a large number of microbes using two commercial multiplex PCR panels and additional in-house real-time PCR, the etiology of the infections was still unknown in a large number of patients. This calls for further development of diagnostic methods for CNS infections.Neisseria meningitidis, the meningococcus, is a strictly human commensal but also capable to cause severe disease, typically in the form of sepsis and meningitis. The aim of Paper II and III was to study the clinical presentation of N. meningitidis serogroup Y and W infections, which increased unexpectedlyin Sweden from 2007 and 2014, respectively. By reviewing medical records of these infection episodes, the conclusion was drawn that atypical presentations with respiratory and gastrointestinal symptoms were common, rather than meningitis and petechiae.In Paper IV, meningococcal carriage was studied among students at Örebro University. Age ≤22 years, smoking, previous tonsillectomy, frequent partying and male gender were associated with higher carrier rates. The so far longest observation of carriage of the same meningococcal strain was presented, with a duration of at least one year.In conclusion, the results from these studies highlight the importance of early detection of meningococcal infections with atypical presentations and the need of improved diagnostics for CNS infections
50.	Thulin Hedberg, Sara, 1980-, et al. (författare) Droplet digital PCR for absolute quantification of proviral load of human T-cell lymphotropic virus (HTLV) types 1 and 2 2018 Ingår i: Journal of Virological Methods. - : Elsevier. - 0166-0934 .- 1879-0984. ; 260, s. 70-74 Tidskriftsartikel (refereegranskat)abstract 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.

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