Henrik Westh’s research while affiliated with University of Copenhagen and other places

Background We aimed to describe the genomic epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) in Eastern Denmark from 2020 to 2022, identify and characterise the vanB Transposon 1549 (Tn1549) insertion sites among vanB VREfm clones and identify emerging VREfm clones. Methods We analysed all VREfm from our routine diagnostic sequencing during the study period. Using the Seqsphere + v.8.2.0 software (Ridom GmbH, Münster, Germany, (http://www.ridom.de/seqsphere), minimum spanning trees were created to visualise clusters. Tn1549 insertion sites were determined by in silico PCR. Nanopore sequencing was performed to assemble the regions surrounding Tn1549, which helped determine the insertion site locations. Results We included 2,437 isolates in the study. A total of 463 isolates carried vanA, 1,963 isolates carried vanB, and 11 isolates carried both genes. Of all isolates carrying vanB, 254 isolates had the Tn1549 inserted in the araA2 gene, 1,604 in the sir2 gene, and 116 in neither the araA2 nor sir2 genes. We identified eight chromosomal insertion sites other than in the araA2 and sir2 genes. Three isolates carried the Tn1549 on plasmids. No emerging clones were found. Results We have described the genomic epidemiology during the study period and identified ten chromosomal Tn1549 insertion sites.

Passive maternal-fetal transfer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies has been demonstrated, whilst the degree of transfer depending on the trimester of infection is lacking. Due to neonates’ immature immune systems, this knowledge could be of interest when investigating the degree of early-life protection against SARS-CoV-2. For perinatal infections such as Rubella and Toxoplasmosis, the timing of infection related to gestational age is crucial for the severity of maternal-fetal outcomes; hence, the trimester of SARS-CoV-2 infection could potentially be crucial. So far, there is no stratification on all three trimesters of SARS-CoV-2 infection in relation to maternal antibody levels in SARS-CoV-2 positive women, and the degree of transfer of SARS-CoV-2 antibodies to the newborn nor on obstetric and neonatal outcomes, which we examined in this study. Eleven departments in Denmark invited women who tested SARS-CoV-2 positive during pregnancy to participate with a blood sample and a cord blood sample at delivery. 459 SARS-CoV-2 positive women and 2567 SARS-CoV-2 negative women were included. A percentage of 87.5%, 95.3%, and 60.3% of newborns of women who tested positive in their first, second, and third trimester, respectively, had a significantly higher immunoglobin G (IgG) antibody level than their mother at delivery, indicating that the fetus is able to concentrate antibody levels or maintain the level of IgG antibodies transferred. None of the examined maternal-fetal outcomes were increased in women infected with SARS-CoV-2.

Background WGS can potentially be routinely used in clinical microbiology settings, especially with the increase in sequencing accuracy and decrease in cost. Escherichia coli is the most common bacterial species analysed in those settings, thus fast and accurate diagnostics can lead to reductions in morbidity, mortality and healthcare costs. Objectives To evaluate WGS for diagnostics and surveillance in a collection of clinical E. coli; to examine the pool of antimicrobial resistance (AMR) determinants circulating in Denmark and the most frequent STs; and to evaluate core-genome MLST (cgMLST) and SNP-based clustering approaches for detecting genetically related isolates. Methods We analysed the genomes of 699 E. coli isolates collected throughout all Danish Clinical Microbiology Laboratories. We used rMLST and KmerFinder for species identification, ResFinder for prediction of AMR, and PlasmidFinder for plasmid identification. We used Center for Genomic Epidemiology MLST, cgMLSTFinder and CSI Phylogeny to perform typing and clustering analysis. Results Genetic AMR determinants were detected in 56.2% of isolates. We identified 182 MLSTs, most frequently ST-69, ST-73, ST-95 and ST-131. Using a maximum 15-allele difference as the threshold for genetic relatedness, we identified 23 clusters. SNP-based phylogenetic analysis within clusters revealed from 0 to 13 SNPs, except two cases with 111 and 461 SNPs. Conclusions WGS data are useful to characterize clinical E. coli isolates, including predicting AMR profiles and subtyping in concordance with surveillance data. We have shown that it is possible to adequately cluster isolates through a cgMLST approach, but it remains necessary to define proper interpretative criteria.

Background Staphylococcus saprophyticus is the second most common bacteria causing uncomplicated urinary tract infections (UTI). It is considered non-susceptible to mecillinam, with no defined breakpoint and only few available minimal inhibitory concentration (MIC) observations. However, this consideration does not correlate with clinical outcome. With this study, we aimed to provide a comprehensive MIC distribution analysis of mecillinam for S. saprophyticus, which could be useful for determining potential breakpoints. Materials/methods We studied 112 isolates of S. saprophyticus from human urine samples from four European countries. The broth microdilution and MIC test strip methods were used to determine mecillinam MIC. Results Broth microdilution MICs ranged from 4 to ≥ 256 mg/L, with a binary clustering at 32–64 and ≥256 mg/L. The MIC were duplicated for each isolate with similar results. The MIC distribution from the test strip method aligned well with the results from the broth microdilution method. Disc diffusion test yielded an 8 mm inhibitory zone in three isolates with MIC of 32 mg/L. Conclusions Considering mecillinam concentration in the urine usually reach 200 mg/L in conventional treatment, the clinical success frequently seen with pivmecillinam treatment for UTI caused by S. saprophyticus may be explained by the MIC cluster of 32–64 mg/L. This cluster might be identified by an 8 mm inhibitory zone in disc diffusion tests. Clinical studies with MIC data are needed to examine potential breakpoints. As of now, clinicians should not switch empirical pivmecillinam treatment to other antibiotics based solely on the presence of S. saprophyticus.

Background Pregnancy is a complex biological process and serious complications can arise when the delicate balance between the maternal and semi-allogeneic fetal immune systems is disrupted or challenged. Gestational diabetes mellitus (GDM), pre-eclampsia, preterm birth, and low birth weight pose serious threats to maternal and fetal health. Identification of early biomarkers through an in-depth understanding of molecular mechanisms is critical for early intervention. Methods We analyzed the associations between 47 proteins involved in inflammation, chemotaxis, angiogenesis, and immune system regulation, maternal and neonatal health outcomes, and the baseline characteristics and pre-existing conditions of the mother in a prospective cohort of 1049 pregnant women around the 20th gestational week. We used Bayesian linear regression models to examine the impact of risk factors on biomarker levels and Bayesian cause-specific parametric proportional hazards models to analyze the effect of biomarkers on maternal and neonatal outcomes. We evaluated the predictive value of baseline characteristics and 47 proteins using machine-learning models and identified the most predictive biomarkers using Shapley additive explanation scores. Results Associations were identified between specific inflammatory markers and several conditions, including maternal age and pre-pregnancy body mass index, chronic diseases, complications from prior pregnancies, and COVID-19 exposure. Smoking during pregnancy affected GM-CSF and 9 other biomarkers. Distinct biomarker patterns were observed for different ethnicities. Within obstetric complications, IL-6 inversely correlated with pre-eclampsia risk, while birth weight to gestational age ratio was linked to markers including VEGF and PlGF. GDM was associated with IL-1RA, IL-17D, and eotaxin-3. Severe postpartum hemorrhage correlated with CRP, IL-13, and proteins of the IL-17 family. Predictive modeling yielded area under the receiver operating characteristic curve values of 0.708 and 0.672 for GDM and pre-eclampsia, respectively. Significant predictive biomarkers for GDM included IL-1RA and eotaxin-3, while pre-eclampsia prediction yielded the highest predictions when including MIP-1β, IL-1RA, and IL-12p70. Conclusions Our study provides novel insights into the interplay between preexisting conditions and immune dysregulation in pregnancy. These findings contribute to our understanding of the pathophysiology of obstetric complications and the identification of novel biomarkers for early intervention(s) to improve maternal and fetal health.

Objective The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10 mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at – 80 °C was up to 24 h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity. Results Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.

Objectives To develop and validate a real-time PCR assay detecting the sequence bridging Tn1549 and the Enterococcus faecium chromosome in the emerging vanB vancomycin-resistant E. faecium (VREfm) clone (ST80/CT2406). Methods The Tn1549 insertion site was determined on routinely sequenced VREfm isolates. The outer boundaries of Tn1549 and adjoining host bacterial sequences were determined using a BLAST search in the silent information regulator gene sir2. Next, the primers and probe were developed, targeting the sequence bridging Tn1549 and the E. faecium chromosome. Finally, the PCR assay was validated on well-characterized strains and prospectively performed on rectal screening samples submitted to our laboratory. Results and conclusions The PCR assay proved to be accurate and provide rapid diagnosis of the emerging vanB VREfm in rectal screening samples.

Here we describe the first double-blinded, randomized, placebo-controlled trial (RCT) on vaginal microbiota transplantation (VMT) without antibiotics in women with both symptomatic and asymptomatic vaginal dysbiosis. Forty-nine women were randomly assigned to VMT or placebo. The trial did not show a significant conversion to our predefined Lactobacillus -dominated microbiome. However, in participants not initially converting, antiseptic pretreatment before a subsequent VMT led to a 50% conversion rate, associated with an anti-inflammatory shift in gene expression. Metagenomic sequencing and strain-level genetic analysis confirmed donor engraftment in five of 10 women who showed microbiome conversion. Extensive exploration of the microbiome, immune response and metadata revealed differences in baseline energy metabolism in participants who later experienced donor engraftment. Treatments for vaginal dysbiosis are urgently needed and given that VMT can lead to donor engraftment and change the vaginal immune profile, future studies should focus on optimizing this treatment for various women’s health diseases.