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Qvick, A., Bratulic, S., Carlsson, J., Stenmark, B., Karlsson, C., Nielsen, J., . . . Helenius, G. (2024). Discriminating Benign from Malignant Lung Diseases Using Plasma Glycosaminoglycans and Cell-Free DNA. International Journal of Molecular Sciences, 25(18), Article ID 9777.
Open this publication in new window or tab >>Discriminating Benign from Malignant Lung Diseases Using Plasma Glycosaminoglycans and Cell-Free DNA
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2024 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 25, no 18, article id 9777Article in journal (Refereed) Published
Abstract [en]

We aimed to investigate the use of free glycosaminoglycan profiles (GAGomes) and cfDNA in plasma to differentiate between lung cancer and benign lung disease, in a cohort of 113 patients initially suspected of lung cancer. GAGomes were analyzed in all samples using the MIRAM® Free Glycosaminoglycan Kit with ultra-high-performance liquid chromatography and electrospray ionization triple quadrupole mass spectrometry. In a subset of samples, cfDNA concentration and NGS-data was available. We detected two GAGome features, 0S chondroitin sulfate (CS), and 4S CS, with cancer-specific changes. Based on the observed GAGome changes, we devised a model to predict lung cancer. The model, named the GAGome score, could detect lung cancer with 41.2% sensitivity (95% CI: 9.2-54.2%) at 96.4% specificity (95% CI: 95.2-100.0%, n = 113). When we combined the GAGome score with a cfDNA-based model, the sensitivity increased from 42.6% (95% CI: 31.7-60.6%, cfDNA alone) to 70.5% (95% CI: 57.4-81.5%) at 95% specificity (95% CI: 75.1-100%, n = 74). Notably, the combined GAGome and cfDNA testing improved the sensitivity, compared to cfDNA alone, especially in ASCL stage I (55.6% vs 11.1%). Our findings show that plasma GAGome profiles can enhance cfDNA testing performance, highlighting the applicability of a multiomics approach in lung cancer diagnostics.

Place, publisher, year, edition, pages
MDPI, 2024
Keywords
GAGome, cfDNA, glycosaminoglycans, lung cancer, multiomics
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:oru:diva-116392 (URN)10.3390/ijms25189777 (DOI)001323972500001 ()39337265 (PubMedID)2-s2.0-85205260687 (Scopus ID)
Funder
NyckelfondenInsamlingsstiftelsen Lions Cancerforskningsfond Mellansverige Uppsala-Örebro
Note

Funding: This work was funded by the Nyckelfonden-Örebro University Hospital Research Foundation, the Lions Fund for Cancer Research Uppsala-Örebro, and the Uppsala-Örebro Regional Research Council.

Available from: 2024-09-30 Created: 2024-09-30 Last updated: 2024-11-06Bibliographically approved
Persson, A., Koivula, T., Jacobsson, S. & Stenmark, B. (2024). Diverse proinflammatory response in pharyngeal epithelial cells upon interaction with Neisseria meningitidis carriage and invasive isolates. BMC Infectious Diseases, 24(1), Article ID 286.
Open this publication in new window or tab >>Diverse proinflammatory response in pharyngeal epithelial cells upon interaction with Neisseria meningitidis carriage and invasive isolates
2024 (English)In: BMC Infectious Diseases, E-ISSN 1471-2334, Vol. 24, no 1, article id 286Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Invasive meningococcal disease (IMD), including sepsis and meningitis, can develop when Neisseria meningitidis bacteria breach the barrier and gain access to the circulation. While IMD is a rare outcome of bacterial exposure, colonization of the oropharynx is present in approximately 10% of the human population. This asymptomatic carriage can be long or short term, and it is unknown which determining factors regulate bacterial colonization. Despite descriptions of many bacterial virulence factors and recent advances in detailed genetic identification and characterization of bacteria, the factors mediating invasion and disease vs. asymptomatic carriage following bacterial colonization remain unknown. The pharyngeal epithelia play a role in the innate immune defense against pathogens, and the aim of this study was to investigate the proinflammatory response of pharyngeal epithelial cells following meningococcal exposure to describe the potential inflammatory mediation performed during the initial host‒pathogen interaction. Clinically relevant isolates of serogroups B, C, W and Y, derived from patients with meningococcal disease as well as asymptomatic carriers, were included in the study.

RESULTS: The most potent cellular response with proinflammatory secretion of TNF, IL-6, CXCL8, CCL2, IL-1β and IL-18 was found in response to invasive serogroup B isolates. This potent response pattern was also mirrored by increased bacterial adhesion to cells as well as induced cell death. It was, however, only with serogroup B isolates where the most potent cellular response was toward the IMD isolates. In contrast, the most potent cellular response using serogroup Y isolates was directed toward the carriage isolates rather than the IMD isolates. In addition, by comparing isolates from outbreaks in Sweden (epidemiologically linked and highly genetically similar), we found the most potent proinflammatory response in cells exposed to carriage isolates rather than the IMD isolates.

CONCLUSION: Although certain expected correlations between host‒pathogen interactions and cellular proinflammatory responses were found using IMD serogroup B isolates, our data indicate that carriage isolates invoke stronger proinflammatory activation of the epithelial lining than IMD isolates.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2024
Keywords
Adhesion, Cell death, Chemokines, Cytokines, FaDu, Host pathogen interaction, IMD
National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-112128 (URN)10.1186/s12879-024-09186-3 (DOI)001180236300001 ()38443838 (PubMedID)2-s2.0-85186877260 (Scopus ID)
Funder
Örebro UniversityRegion Örebro County, OLL-929401; OLL-942196
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-03-21Bibliographically approved
Kekki, J., Thegel, A., Stenmark, B. & Söderquist, B. (2024). Evolution of community-associated MRSA: a 20-year genomic and epidemiological study in Region Örebro County, Sweden. Frontiers in Microbiology, 15, Article ID 1504860.
Open this publication in new window or tab >>Evolution of community-associated MRSA: a 20-year genomic and epidemiological study in Region Örebro County, Sweden
2024 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 15, article id 1504860Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) has been an issue in healthcare since the 1960s. It was initially found only in healthcare facilities, but in the late 1990s it began to be seen with no healthcare connexion. The mechanisms of intercontinental and national spread are not fully understood, as sometimes novel outbreaks occur without any identifiable source or connexion to locally dominant clonal clusters.

METHODS: This study investigated the epidemiology and genomics of community-associated MRSA in Region Örebro County, Sweden, through 330 isolates collected between 2000 and 2019.

RESULTS: A shift in the dominant sequence type (ST) from ST80 to ST22 occurred in 2011-2019, along with an increase in the prevalence of STs belonging to clonal complexes CC5 and CC22. Both ST8 and ST80 isolates seemed to give way to emerging ST22 isolates, also indicated by the declining presence of the USA300 clone. The staphylococcal chromosomal cassette mec (SCCmec) type IV Remained dominant.

CONCLUSIONS: The SCCmec type IV characteristic appears to be relatively geographically stable, possibly due to its low fitness cost and transductal capabilities. This warrants further studies of SCCmec type IV variant's survival mechanics as well as the effects of migratory flow on local epidemiology, in preparation for future possible outbreaks.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2024
Keywords
CA-MRSA, MLST, SCCmec, Staphylococcus aureus, clonal complex, epidemiology
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-118166 (URN)10.3389/fmicb.2024.1504860 (DOI)001390484300001 ()39764449 (PubMedID)2-s2.0-85214142219 (Scopus ID)
Available from: 2025-01-09 Created: 2025-01-09 Last updated: 2025-01-20Bibliographically approved
Qvick, A., Andersson, E., Oldaeus Almerén, A., Waenerlund, M., Stenmark, B., Karlsson, C., . . . Helenius, G. (2024). Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers. Molecular Diagnosis & Therapy, 28(6), 835-845
Open this publication in new window or tab >>Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers
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2024 (English)In: Molecular Diagnosis & Therapy, ISSN 1177-1062, E-ISSN 1179-2000, Vol. 28, no 6, p. 835-845Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Human papillomavirus (HPV) has emerged as a significant contributor to cancer incidence globally, particularly in the context of oropharyngeal squamous cell carcinoma (OPSCC) and cancer of unknown primary (HNCUP). This study aimed to develop and validate droplet digital PCR (ddPCR) assays for the detection of circulating tumor HPV DNA (ctHPV-DNA) in plasma, focusing on high-risk HPV genotypes associated with these cancers.

METHODS: ddPCR assays for HPV16, 18, 33, 35, 56, and 59 were developed and tested using gBlocks, HPV cell-free DNA, fragmented tumor HPV+ DNA, and plasma samples from patients with HPV+ OPSCC (n = 110) and HNCUP (n = 9).

RESULTS: Assays demonstrated robust technical sensitivity across all tested HPV genotypes. Clinical application of the assays on a cohort of patients with HPV+ OPSCC and HNCUP revealed high sensitivity (91.6%) and wide variability in ctHPV-DNA levels. Analyses revealed correlations between ctHPV-DNA levels and TNM stage and tumor viral load. The association between ctHPV-DNA and tumor viral load persisted even after adjusting for TNM stage. At posttreatment, 72.5% of samples had reached undetectable ctHPV-DNA levels. Having detectable ctHPV-DNA posttreatment was associated with a higher ctHPV-DNA level at diagnosis and higher viral load at diagnosis.

CONCLUSION: The findings underscore the potential of ctHPV-DNA as a biomarker for monitoring HPV+ cancers and offer insights into tumor dynamics. Implementation of these assays in clinical practice could enhance no-invasive treatment monitoring and recurrence detection in HPV-associated cancers.

CLINICAL TRIALS: NCT05904327.

Place, publisher, year, edition, pages
Adis International Ltd., 2024
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:oru:diva-116394 (URN)10.1007/s40291-024-00743-9 (DOI)001321547500001 ()39325260 (PubMedID)2-s2.0-85204878050 (Scopus ID)
Funder
Örebro UniversityRegion Örebro CountyInsamlingsstiftelsen Lions Cancerforskningsfond Mellansverige Uppsala-Örebro
Note

Funding: Open access funding provided by Örebro University. This work was funded by the Örebro County Council Research committee, Nyckelfonden-Örebro University Hospital Research Foundation, Lions fund for cancer research Uppsala-Örebro, and Uppsala-Örebro Regional research council.

Available from: 2024-09-30 Created: 2024-09-30 Last updated: 2024-11-06Bibliographically approved
Koskela, A., Lindqvist, C. M., Asghar, N., Johansson, M., Sundqvist, M., Mölling, P. & Stenmark, B. (2023). Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. In: : . Paper presented at Smögen Virology Symposium 2023, Smögen, Sweden, August 24-26, 2023..
Open this publication in new window or tab >>Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
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2023 (English)Conference paper, Poster (with or without abstract) (Other academic)
Abstract [en]

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.

National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-108004 (URN)
Conference
Smögen Virology Symposium 2023, Smögen, Sweden, August 24-26, 2023.
Available from: 2023-09-01 Created: 2023-09-01 Last updated: 2023-09-05Bibliographically approved
Koskela, A., Lindqvist, C. M., Asghar, N., Johansson, M., Sundqvist, M., Mölling, P. & Stenmark, B. (2023). Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. Scientific Reports, 13(1), Article ID 6461.
Open this publication in new window or tab >>Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
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2023 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 6461Article in journal (Refereed) Published
Abstract [en]

The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) 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.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-105616 (URN)10.1038/s41598-023-33168-1 (DOI)001025198300001 ()37081087 (PubMedID)2-s2.0-85153442204 (Scopus ID)
Funder
Region Örebro CountyÖrebro University
Available from: 2023-04-21 Created: 2023-04-21 Last updated: 2023-09-05Bibliographically approved
Eriksson, L., Johannesen, T. B., Stenmark, B., Jacobsson, S., Säll, O., Hedberg, S. T., . . . Mölling, P. (2023). Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis. Microbial Genomics, 9(10), Article ID 001124.
Open this publication in new window or tab >>Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis
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2023 (English)In: Microbial Genomics, E-ISSN 2057-5858, Vol. 9, no 10, article id 001124Article in journal (Refereed) Published
Abstract [en]

Neisseria meningitidis can be a human commensal in the upper respiratory tract but is also capable of causing invasive diseases such as meningococcal meningitis and septicaemia. No specific genetic markers have been detected to distinguish carriage from disease isolates. The aim here was to find genetic traits that could be linked to phenotypic outcomes associated with carriage versus invasive N. meningitidis disease through a bacterial genome-wide association study (GWAS). In this study, invasive N. meningitidis isolates collected in Sweden (n=103) and carriage isolates collected at Örebro University, Sweden (n=213) 2018-2019 were analysed. The GWAS analysis, treeWAS, was applied to single-nucleotide polymorphisms (SNPs), genes and k-mers. One gene and one non-synonymous SNP were associated with invasive disease and seven genes and one non-synonymous SNP were associated with carriage isolates. The gene associated with invasive disease encodes a phage transposase (NEIS1048), and the associated invasive SNP glmU S373C encodes the enzyme N-acetylglucosamine 1-phosphate (GlcNAC 1-P) uridyltransferase. Of the genes associated with carriage isolates, a gene variant of porB encoding PorB class 3, the genes pilE/pilS and tspB have known functions. The SNP associated with carriage was fkbp D33N, encoding a FK506-binding protein (FKBP). K-mers from PilS, tbpB and tspB were found to be associated with carriage, while k-mers from mtrD and tbpA were associated with invasiveness. In the genes fkbp, glmU, PilC and pilE, k-mers were found that were associated with both carriage and invasive isolates, indicating that specific variations within these genes could play a role in invasiveness. The data presented here highlight genetic traits that are significantly associated with invasive or carriage N. meningitidis across the species population. These traits could prove essential to our understanding of the pathogenicity of N. meningitidis and could help to identify future vaccine targets.

Place, publisher, year, edition, pages
Microbiology Society, 2023
Keywords
Carriage, Genome-wide association study, Invasive meningococcal disease, Neisseria meningitidis
National Category
Medical Genetics and Genomics
Identifiers
urn:nbn:se:oru:diva-109425 (URN)10.1099/mgen.0.001124 (DOI)001107086200005 ()37874326 (PubMedID)2-s2.0-85175126623 (Scopus ID)
Funder
Region Örebro County, OLL-967424
Available from: 2023-10-25 Created: 2023-10-25 Last updated: 2025-02-10Bibliographically approved
Säll, O., Eriksson, L., Idosa Berhane, A., Persson, A., Magnuson, A., Thulin Hedberg, S., . . . Jacobsson, S. (2023). Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students. Epidemiology and Infection, 151, Article ID e25.
Open this publication in new window or tab >>Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students
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2023 (English)In: Epidemiology and Infection, ISSN 0950-2688, E-ISSN 1469-4409, Vol. 151, article id e25Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Cambridge University Press, 2023
Keywords
Carriage, Neisseria meningitidis, Swedish snus, university students, whole genome sequencing
National Category
Public Health, Global Health, Social Medicine and Epidemiology
Identifiers
urn:nbn:se:oru:diva-104135 (URN)10.1017/S0950268823000018 (DOI)000930011500001 ()36775828 (PubMedID)2-s2.0-85147835011 (Scopus ID)
Available from: 2023-02-13 Created: 2023-02-13 Last updated: 2023-03-16Bibliographically approved
Fioretos, T., Wirta, V., Cavelier, L., Berglund, E., Friedman, M., Akhras, M., . . . Rosenquist, R. (2022). Implementing precision medicine in a regionally organized healthcare system in Sweden [Letter to the editor]. Nature Medicine, 28(10), 1980-1982
Open this publication in new window or tab >>Implementing precision medicine in a regionally organized healthcare system in Sweden
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2022 (English)In: Nature Medicine, ISSN 1078-8956, E-ISSN 1546-170X, Vol. 28, no 10, p. 1980-1982Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
Nature Publishing Group, 2022
National Category
Health Care Service and Management, Health Policy and Services and Health Economy
Identifiers
urn:nbn:se:oru:diva-101431 (URN)10.1038/s41591-022-01963-4 (DOI)000857867600001 ()36123428 (PubMedID)2-s2.0-85138201780 (Scopus ID)
Note

Funding agencies:

SciLifeLab 

Medical faculty at Gothenburg University

Medical faculty at Linköping University

Medical faculty at Lund University

Medical faculty at Karolinska Institutet 

Available from: 2022-09-23 Created: 2022-09-23 Last updated: 2022-10-26Bibliographically approved
Säll, O., Stenmark, B., Jacobsson, S., Eriksson, L., Thulin Hedberg, S., Hertting, O., . . . Mölling, P. (2021). Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain. Epidemiology and Infection, 149, Article ID e126.
Open this publication in new window or tab >>Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain
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2021 (English)In: Epidemiology and Infection, ISSN 0950-2688, E-ISSN 1469-4409, Vol. 149, article id e126Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Cambridge University Press, 2021
Keywords
Invasive meningococcal disease, meningococcal disease, Neisseria meningitidis, serogroup W, Sweden
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-91688 (URN)10.1017/S0950268821001035 (DOI)000652182800001 ()33910672 (PubMedID)
Note

Funding Agency:

Swedish state under the ALF  

Available from: 2021-05-10 Created: 2021-05-10 Last updated: 2023-06-30Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-4637-8626

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