To Örebro University

There is evidence that persistent dysregulation of the immune system caused by SARS-CoV-2 infection may increase susceptibility to other infections. Here, we assessed whether it is associated with subsequent diagnoses of infectious mononucleosis due to Epstein-Barr virus (EBV-IM). Residents of Sweden aged 3-100 years without a prior diagnosis of EBV-IM were followed between January 1, 2020, and November 30, 2022, comprising a total of 9 978 860 participants. Individuals were categorized into those without a COVID-19 diagnosis, those with a positive SARS-CoV-2 polymerase chain reaction (PCR) test only - less severe exposure, and those admitted to hospital with COVID-19 - more severe exposure. Cox regression was used to estimate hazard ratios (HR) with 95% confidence intervals (95% CI) for the association between the exposure, modeled as a time-varying covariate, and EBV-IM occurrence. EBV-IM rates per 100 000 person-years and 95% CIs were 4.6 (4.4-4.9) for individuals not diagnosed with COVID-19, 7.8 (6.9-8.9) for those with a positive SARS-CoV-2 test only, and 10.5 (6.2-17.6) for patients admitted to hospital with COVID-19. HR and 95% CI were 1.61 (1.39-1.88) for people with a positive PCR test only and 5.71 (3.33-9.79) for those admitted to hospital with COVID-19 compared with people without a COVID-19 diagnosis, after adjustment for birth year, sex, Swedish healthcare region, region of birth, and Charlson comorbidity index. SARS-CoV-2 infection was associated with a subsequent raised risk of EBV-IM, including among those with less severe acute infection, signaling immune perturbation and the possibility of further delayed sequelae linked with EBV-IM.

OBJECTIVES: Optimal antibiotic treatment is important in the treatment of sepsis. However, patients with sepsis are at risk of suboptimal antibiotic concentrations. This study aimed to evaluate β-lactam antibiotic concentrations during the first 48 h in patients with community-acquired sepsis admitted to the ICU, and to identify variables associated with antibiotic concentrations that were too low or too high.

METHODS: This prospective, observational, single-centre study included patients aged ≥18 years with a high likelihood of infection, a SOFA score of ≥2p, planned β-lactam antibiotic treatment, and ICU admission. The exclusion criteria were ongoing antibiotic treatment and/or nosocomial infections. β-Lactam concentrations were measured up to seven times during the first 48 h. The estimated trough concentrations were divided by the predetermined MIC to generate MIC-multiples for comparison. Patients were allocated to three groups based on the MIC-multiple (MIC× < 1, 1-8 or >8).

RESULTS: Fifty patients were included, with a median of seven samples per patient (257 samples). The group with MIC-multiples of <1 (n = 16) was associated with younger age, lower Charlson comorbidity index, Simplified Acute Physiology Score 3, creatinine concentration, and need for noradrenaline. The group with MIC-multiples of >8 (n = 15) had higher creatinine and noradrenaline levels.

CONCLUSIONS: ICU patients with sepsis are at risk of either too low or too high antibiotic concentrations, and specific patient characteristics may be predictable. Therapeutic drug monitoring in combination with model-informed precision dosing may also help to optimize antibiotic dosing in the early phase of community-acquired sepsis to prevent treatment failure and toxicity.

BACKGROUND: Escherichia coli, the most common bacterium causing urinary tract infections (UTIs), is increasingly reported as resistant to multiple antibiotics. Swedish surveillance data from hospital and primary health care (PHC) report a 17%-19% prevalence of resistance to ciprofloxacin in E. coli from urine cultures in men over 20 years of age. Surveillance data may include nosocomial infections. However, few studies have described resistance in E. coli in men with community-acquired UTI in PHC. We aimed to describe the microbiological results, including antibiotic resistance in E. coli, in men with lower UTI (LUTI) attending PHC.

METHODS: In this retrospective study based on information from electronic medical records, we included patients from 289 PHC centres. For all men aged 18-79 years diagnosed with LUTI in PHC from January 2012 to December 2015, we extracted data on age, UTI diagnosis and results from urine cultures. RESULTS: A total of 17 987 episodes of lower UTI were identified. E. coli was detected in 62% of positive cultures and 63% of detected E. coli isolates were susceptible to all tested antimicrobials. Resistance in E. coli to the first-choice antibiotics pivmecillinam and nitrofurantoin were 2% and 1%, respectively. Resistance to ciprofloxacin was 9%, and to trimethoprim it was 17%.

CONCLUSIONS: Resistance levels for ciprofloxacin in E. coli among men with LUTI in PHC were lower than in surveillance data. The results of this study point to the importance of surveillance of resistance in urine samples from patients with LUTI in PHC in order to choose the right empirical antibiotic treatment.

Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for Staphylococcus aureus and Streptococcus pneumoniae were more pronounced compared to Escherichia coli. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.

OBJECTIVES: We aimed to 1) detect tick-borne encephalitis virus (TBEV) RNA in clinical samples from patients with TBE, 2) characterise the detected RNA using Sanger sequencing, and 3) examine whether RNA detection was associated with disease severity.

METHODS: We studied 137 patients infected and diagnosed with TBE between 2016 and 2021 in Region Örebro County and Region Värmland. Biobanked serum (n = 129) and cerebrospinal fluid (CSF; n = 110) samples were analysed. Serum was tested for TBEV-specific antibodies, and both serum and CSF for TBEV RNA using PCR. Following nested PCR, the 5' non-coding region (5'NCR) of five samples underwent Sanger sequencing. Disease severity was assessed based on intensive care unit (ICU) admission, duration of ICU stay and need for mechanical ventilation.

RESULTS: TBEV RNA was detected in 5 serum samples (3.9 %) and 7 CSF samples (6.4 %), representing 10 patients (7.3 %). Patients with detectable RNA were older, more frequently admitted to an ICU (p = 0.04), and more often required mechanical ventilation (p = 0.01) compared to those without detectable TBEV RNA. Sequencing of the 5'NCR in four patients revealed differences from the 5 ´NCR of the Swedish reference strain Torö-2003. The Örebro sequences were identical but differed from the Värmland sequences at two nucleotide positions.

CONCLUSIONS: TBEV RNA was detectable in both serum and CSF of TBE patients, and its presence was associated with more frequent ICU admission and need for mechanical ventilation. Sequencing of the 5'NCR revealed genetic variation between TBEV sequences from patients in Örebro and Värmland.

Background: Monoclonal antibodies (mAbs) are an important option against SARS-CoV-2, especially as pre-exposure prophylaxis (PrEP) for patients with immune system impairment. PrEP mAbs like sipavibart and pemivibart have been approved for limited use in several countries. Certain SARS-CoV-2 variants carry mutations in the spike (S) protein, conferring resistance to these mAbs.

Objectives: We aimed to examine the relative abundance of different circulating SARS-CoV-2 variants/mutations in central Sweden between 2023 and 2024, and to predict the effectiveness of sipavibart and pemivibart.

Methods: An amplicon-based Nanopore sequencing method was used for sequencing SARS-CoV-2 samples. Coronapp was used to identify mutations in these sequences. Using the published in vitro resistance data for sipavibart and pemivibart, the effectiveness of these mAbs was inferred.

Results: We have observed that the relative abundance of the KP.3.1.1 variant and the Q493E mutation started to increase in the later part of 2024 in the region. Also, since April 2024, the relative abundance of the F456L mutation reached 100% during many weeks until the end of the study period. The KP.3.1.1 variant is significantly resistant to pemivibart. Further, the presence of the F456L mutation in the Omicron subvariants confers high fold resistance towards sipavibart.

Conclusion: The use of sipavibart or pemivibart as PrEP for COVID-19 in the region may currently not be effective unless new SARS-CoV-2 variants appear not containing these resistance mutations. Further, new mAbs under development as PrEP for COVID-19 can be effectively used by routinely sequencing SARS-CoV-2 in patients to identify variants and resistance mutations.

Current guidelines recommend the use of a two-step algorithm for the laboratory diagnosis of Clostridioides difficile infection (CDI). Several commercial rapid immunoassays that detect both GDH and toxin A/B in stool samples are available and could be used for both steps of the diagnostic algorithm. We aimed to evaluate the performance of three of these rapid immunoassays and study pathogen characteristics that might affect the sensitivity of toxin A/B detection. Leftover material from routinely collected stool samples from patients suspected of CDI was analyzed with the three immunoassays, nucleic acid amplification test (NAAT), and culture. Whole-genome sequencing was then used to evaluate C. difficile isolates recovered from the samples. The positive percent agreement between GDH detection and detection of tcdA by NAAT was 100% with all three immunoassays. The positive percent agreement for the detection of toxin A/B, however, was considerably lower (50.0%, 51.7%, and 71.4%), and freezing stool samples seemed to negatively affect the detection of both GDH and toxins. The isolates included in the study belonged to 23 different sequence types (ST) and all carried the tcdA and tcdB genes. The C. diff Quik Chek Complete performed the best of the three immunoassays, and when used in combination with NAAT, is a viable option for the laboratory diagnosis of CDI.

IMPORTANCE: Laboratory diagnosis of Clostridioides difficile infection is complex, and current guidelines recommend a two-step diagnostic algorithm with a sensitive screening test and a more specific confirmatory test. The study aimed to evaluate three commercial rapid immunoassays that detect both glutamate dehydrogenase (GDH) and toxins A and B. These tests could be used for both steps of the two-step diagnostic algorithm and facilitate rapid laboratory confirmation of CDI, which is important for clinical decision-making and infection control measures.

BACKGROUND: The role of Helicobacter pylori (H. pylori) screening and eradication on reducing upper gastrointestinal bleeding (UGIB) complications after acute myocardial infarction (MI) is uncertain. The HELicobacter Pylori screening to prevent gastrointestinal bleeding in patients with acute MI (HELP-MI SWEDEHEART) trial aims to determine whether systematic H. pylori screening compared to usual care reduces UGIB, mortality, and cardiovascular outcomes after MI.

METHODS: A cluster randomized, crossover, registry-based clinical trial using SWEDEHEART as trial platform for study population definition and source for data collection in combination with nationwide Swedish health data registries. Thirty-five Swedish hospitals, organized into 18 clusters based on percutaneous coronary intervention networks, were randomized to either routine H. pylori screening for adults with acute type-1 MI or usual care. After one year, a 2-month blanking period was followed by a crossover to the alternate allocation for one year. The trial enrolment was concluded after one additional year of registry-based follow-up. The primary endpoint is UGIB. Secondary endpoints include all-cause death, cardiovascular death, readmission for MI, stroke, or heart failure. Endpoints will be reported combined (Net Adverse Clinical Events; Major Adverse Cardiac or Cerebrovascular Events) and separately. The primary analysis will include all available follow-up time corresponding to a maximum follow-up time of 3 years and 2 months.

CONCLUSION: HELP-MI SWEDEHEART aims to determine the utility of routine H. pylori screening to reduce UGIB and improve cardiovascular outcomes after MI. By integrating national registry follow-up data with a pragmatic trial design, it has the potential to provide evidence for the effect of the implementation of routine H. pylori screening as part of acute MI care.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT05024864.

Bloodstream infections (BSI) are common, and identifying the causative organism is crucial for effective patient management. Shotgun metagenomics (SMg) has emerged as a promising diagnostic tool; however, standardized protocols are lacking. This study aimed to evaluate the use of SMg for diagnosing BSI in patients with confirmed or suspected infections, using stored samples collected at the time of blood culture (BC). DNA extraction was performed with Add-on 10 complement and SelectNA Blood Pathogen kit (Molzym) and SMg sequencing was performed on an Illumina MiSeq instrument (Illumina). The outputs from five taxonomic classification tools were compared with routine blood culture. Of the initial 51 samples (36 BCE-positive and 15 BCE-negative), 36 (71 %) were included in the taxonomic classification analysis. Fifteen samples were excluded due to a low DNA library yield (n = 8) or low sequencing output (n = 7). In two cases, SMg results matched BC findings involving one Cutibacterium acnes and one Staphylococcus aureus. These organisms could be clearly distinguished from the background level of bacterial DNA. Aside from these, SMg identified additional bacterial findings that overlapped with BC results but at low abundance making interpretation more difficult. Most SMg reads were suspected to represent contaminations, originating either from the patient or the laboratory. The output from the different taxonomic classification tools were overall similar but displayed notable differences related to their strategies for identifying bacterial findings. Based on these results, we discuss the challenges associated with SMg-based diagnosis of BSI and highlight key areas requiring further research to improve its clinical utility.