{"entity": "researcher", "timestamp": "2026-09-25T18:00:31.774Z", "family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "affiliations": ["Section of Clinical Microbioloby, Department Medical Sciences, Uppsala University, Uppsala, Sweden.", "Department of Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden.", "Science for Life Laboratory, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786"}}, "publications": [{"entity": "publication", "iuid": "5ea1fb67bd15413aa48d51c8e80f6d99", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ea1fb67bd15413aa48d51c8e80f6d99.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ea1fb67bd15413aa48d51c8e80f6d99"}}, "title": "Genomic analysis of a Neisseria meningitidis patient isolate causing a false-positive result in the Abbott Alinity m STI, Sweden: a case report.", "authors": [{"family": "Herrmann", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-8729-2306", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1942e0a4b18472a82c1c17b5154ac89.json"}}, {"family": "S\u00e4ll\u00e9ber", "given": "Andreas", "initials": "A"}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786.json"}}], "type": "case reports", "published": "2025-11-00", "journal": {"title": "ASM Case Rep", "issn": "2996-2684", "volume": "1", "issue": "6", "issn-l": null}, "abstract": "Diagnostics of sexually transmitted infections, such as Neisseria gonorrhoeae (NG), are often performed using high-volume test systems, often in combination with other targets. This report examines the occurrence of two false-positive NG results from pharyngeal samples in the Abbott Alinity m STI assay, cleared by the Food and Drug Administration.\n\nAnalysis of pharyngeal samples from two men who have sex with men was positive for NG in the Abbott Alinity m STI assay, but negative upon confirmation testing with the Cepheid Xpert CT/NG assay. A pharyngeal culture isolate was obtained from one of the two men. The isolate tested negative for being NG in four different commercial nucleic acid amplification tests. A laboratory-developed PCR based on two targets gave inconclusive results, with positive detection for the opa gene but no detection for the porA gene. The isolate was identified as Neisseria meningitidis (NM) in MALDI-TOF analysis. Whole-genome sequencing revealed 322 diverse virulence genes, of which 314 were typical for NM and 8 for NG. Phylogenetic analysis showed a taxonomic delineation for NM.\n\nConfirmatory tests with alternative targets are essential for accurate analysis of NG, especially in low-prevalence settings. Evaluation of diagnostic tools to ensure accurate detection of NG is also needed.", "doi": "10.1128/asmcr.00143-25", "pmid": "41244285", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12584176"}, {"db": "pii", "key": "asmcr00143-25"}], "notes": [], "created": "2026-09-23T12:35:51.395Z", "modified": "2026-09-23T12:35:51.543Z"}, {"entity": "publication", "iuid": "57080e32c6004f3fb0352b5bb7b83c2d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57080e32c6004f3fb0352b5bb7b83c2d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57080e32c6004f3fb0352b5bb7b83c2d"}}, "title": "From SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance.", "authors": [{"family": "Cumlin", "given": "Tomas", "initials": "T"}, {"family": "Karlsson", "given": "Ida", "initials": "I", "orcid": "0000-0002-5598-1200", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0886d94fdde24c8aaaa3bbc2369e605b.json"}}, {"family": "Haars", "given": "Jonathan", "initials": "J", "orcid": "0009-0003-8735-4097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/366865f87201405b93e8c51c268f1d44.json"}}, {"family": "Rosengren", "given": "Maria", "initials": "M"}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}, {"family": "Pimushyna", "given": "Maryna", "initials": "M", "orcid": "0009-0001-7730-0584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5358506ed4514a39b2ca804e2f4d4056.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cfe5cbb5d454552bdcbc464238f88fb.json"}}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786.json"}}], "type": "journal article", "published": "2024-06-17", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "12", "issn-l": null}, "abstract": "The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer automation for SARS-CoV-2 Oxford Nanopore Technology sequencing data analysis, they are inapplicable to users with limited programming skills. A solution is to establish such automated workflows within a graphical user interface software. We developed two workflows in the software Geneious Prime 2022.1.1, adapted for data obtained from the Midnight and Artic's nCoV-2019 sequencing protocols. Both workflows perform trimming, read mapping, consensus generation, and annotation on SARS-CoV-2 Nanopore sequencing data. Additionally, one workflow includes phylogenetic assignment using the bioinformatic tools pangolin and Nextclade as plugins. The basic workflow was validated in 2020, adhering to the requirements of the European Centre for Disease Prevention and Control for SARS-CoV-2 sequencing and analysis. The enhanced workflow, providing phylogenetic assignment, underwent validation at Uppsala University Hospital by analysing 96 clinical samples. It provided accurate diagnoses matching the original results of the basic workflow while also reducing manual clicks and analysis time. These bioinformatic workflows streamline SARS-CoV-2 Nanopore data analysis in Geneious Prime, saving time and manual work for operators lacking programming knowledge.", "doi": "10.3390/ijms25126645", "pmid": "38928350", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11204113"}, {"db": "pii", "key": "ijms25126645"}], "notes": [], "created": "2026-09-23T13:17:32.119Z", "modified": "2026-09-23T13:17:32.235Z"}, {"entity": "publication", "iuid": "a49ac8a0ccf64443a86dd650c3f1a821", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a49ac8a0ccf64443a86dd650c3f1a821.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a49ac8a0ccf64443a86dd650c3f1a821"}}, "title": "Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022-2023.", "authors": [{"family": "Haars", "given": "Jonathan", "initials": "J", "orcid": "0009-0003-8735-4097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/366865f87201405b93e8c51c268f1d44.json"}}, {"family": "Palanisamy", "given": "Navaneethan", "initials": "N", "orcid": "0000-0003-0369-2316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee609f9e97a4445aa3c20dbfaed5a8bf.json"}}, {"family": "Wallin", "given": "Frans", "initials": "F"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Lindh", "given": "Johan", "initials": "J"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Ellstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786.json"}}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "11", "issue": "10", "issn-l": "2076-2607"}, "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 \u00d6rebro 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.", "doi": "10.3390/microorganisms11102417", "pmid": "37894075", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10609123"}, {"db": "pii", "key": "microorganisms11102417"}], "notes": [], "created": "2026-09-23T12:59:34.179Z", "modified": "2026-09-23T12:59:34.345Z"}, {"entity": "publication", "iuid": "5081484cebce47d7b04b75199c663a20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5081484cebce47d7b04b75199c663a20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5081484cebce47d7b04b75199c663a20"}}, "title": "In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation.", "authors": [{"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Andersson", "given": "Tanja", "initials": "T"}, {"family": "Mannsverk", "given": "Steinar Sm\u00f8rholm", "initials": "SS"}, {"family": "Bergholm", "given": "Julia", "initials": "J"}, {"family": "Ellstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Hill", "given": "Anna", "initials": "A"}, {"family": "Lindh", "given": "Johan", "initials": "J"}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf620e34cca4df88309d96bf8cd0786.json"}}], "type": "journal article", "published": "2022-02-28", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "14", "issue": "3", "issn-l": "1999-4915"}, "abstract": "We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher.", "doi": "10.3390/v14030504", "pmid": "35336908", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8953675"}, {"db": "pii", "key": "v14030504"}], "notes": [], "created": "2026-09-23T13:09:27.495Z", "modified": "2026-09-23T13:09:27.512Z"}]}