{"entity": "researcher", "timestamp": "2026-09-12T07:35:47.119Z", "family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498"}}, "publications": [{"entity": "publication", "iuid": "7d80eacd707b42e79fdec1d031200057", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7d80eacd707b42e79fdec1d031200057.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7d80eacd707b42e79fdec1d031200057"}}, "title": "Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol", "authors": [{"family": "Gschwind", "given": "Remi", "initials": "R", "orcid": "0000-0001-7741-9764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/287bf0d97cad4eb7b389fa0a8495e86b.json"}}, {"family": "Bonnet", "given": "Mehdi", "initials": "M"}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Jarqu\u00edn-D\u00edaz", "given": "Victor Hugo", "initials": "VH", "orcid": "0000-0003-3758-1091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d573d1cb515a4c75b3c8ff2f97be419a.json"}}, {"family": "Wenne", "given": "Marcus", "initials": "M", "orcid": "0009-0008-1941-4146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d60a98a3b54120b369ffe5dd29c854.json"}}, {"family": "L\u00f6ber", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-7468-9531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b71c22b8d28b46e490fa499603ada68d.json"}}, {"family": "Godron", "given": "Nicolas", "initials": "N", "orcid": "0009-0004-4143-5462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0285cb4da845488b97f091bc0d3acac5.json"}}, {"family": "Kampouris", "given": "Ioannis D", "initials": "ID", "orcid": "0000-0003-2093-5930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a58d348ca1f496d8c3915e23c411a6c.json"}}, {"family": "Tskhay", "given": "Faina", "initials": "F", "orcid": "0000-0001-8700-3279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66867423459544e7a72b0a9090a46cee.json"}}, {"family": "Naheed", "given": "Fouzia", "initials": "F"}, {"family": "Debroucker", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Bui-Hai", "given": "Maximilien", "initials": "M"}, {"family": "Aiba", "given": "In\u00e8s El", "initials": "IE"}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8605cdbfc14403b607a3b5ace7249d.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Forslund-Startceva", "given": "Sofia K", "initials": "SK", "orcid": "0000-0003-4285-6993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80bd453b4d084425948404417485140b.json"}}, {"family": "Zahra", "given": "Rabaab", "initials": "R", "orcid": "0000-0001-8784-0114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a678f0c2414244ac894b5f0540b5ef5f.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}, {"family": "Ruppe", "given": "Etienne", "initials": "E"}], "type": "posted-content", "published": "2025-05-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.26.656069", "pmid": null, "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-06-04T08:15:56.666Z", "modified": "2025-09-09T09:29:47.219Z"}, {"entity": "publication", "iuid": "889b1d49e4b64d8498be41da2c00fea8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/889b1d49e4b64d8498be41da2c00fea8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/889b1d49e4b64d8498be41da2c00fea8"}}, "title": "Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.", "authors": [{"family": "De Martinis", "given": "Elaine Cristina Pereira", "initials": "ECP"}, {"family": "Alves", "given": "Virg\u00ednia Farias", "initials": "VF"}, {"family": "Pereira", "given": "Marita Gimenez", "initials": "MG"}, {"family": "Andrade", "given": "Leonardo Neves", "initials": "LN"}, {"family": "Abichabki", "given": "Nath\u00e1lia", "initials": "N"}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Dannborg", "given": "Mirjam", "initials": "M", "orcid": "0000-0003-3171-9379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3379f6c1295741a9ba945f9e92a552eb.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1488699", "issn-l": "1664-3224"}, "abstract": "Recent advances in cell culturing and DNA sequencing have dramatically altered the field of human microbiome research. Three-dimensional (3D) cell culture is an important tool in cell biology, in cancer research, and for studying host-microbe interactions, as it mimics the in vivo characteristics of the host environment in an in vitro system, providing reliable and reproducible models. This work provides an overview of the main 3D culture techniques applied to study interactions between host cells and pathogenic microorganisms, how these systems can be integrated with high-throughput molecular methods, and how multi-species model systems may pave the way forward to pinpoint interactions among host, beneficial microbes and pathogens.", "doi": "10.3389/fimmu.2025.1488699", "pmid": "40051624", "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11882522"}], "notes": [], "created": "2025-06-04T08:12:47.630Z", "modified": "2025-11-04T14:26:49.910Z"}, {"entity": "publication", "iuid": "3f0b8d3a98de4d11803b835f00f67d49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f0b8d3a98de4d11803b835f00f67d49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f0b8d3a98de4d11803b835f00f67d49"}}, "title": "Strategies for taxonomic and functional annotation of metagenomes", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "book-chapter", "published": "2025-00-00", "journal": {"pages": "57-81", "issn-l": null}, "abstract": null, "doi": "10.1016/b978-0-323-91631-8.00002-0", "pmid": null, "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [], "notes": [], "created": "2024-11-18T11:46:26.151Z", "modified": "2025-03-26T11:39:35.922Z"}, {"entity": "publication", "iuid": "8dfc8924633947c19ceaad89e691e329", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8dfc8924633947c19ceaad89e691e329.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8dfc8924633947c19ceaad89e691e329"}}, "title": "Limited Effects of Tetracycline and Ciprofloxacin on Soil Bacterial Communities", "authors": [{"family": "Wenne", "given": "Marcus", "initials": "M", "orcid": "0009-0008-1941-4146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d60a98a3b54120b369ffe5dd29c854.json"}}, {"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2025-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.5249550", "pmid": null, "labels": {"Johan Bengtsson-Palme": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-06-04T08:16:02.193Z", "modified": "2025-12-05T10:15:22.934Z"}, {"entity": "publication", "iuid": "07bb5f0d9127493089db67eec353c920", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07bb5f0d9127493089db67eec353c920.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07bb5f0d9127493089db67eec353c920"}}, "title": "Metagenomic assemblies tend to break around antibiotic resistance genes.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Karkman", "given": "Antti", "initials": "A", "orcid": "0000-0003-0983-3319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ba670092f8496d8ebedcb07d0b6e62.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "959", "issn-l": "1471-2164"}, "abstract": "Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.\n\nThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.\n\nOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.", "doi": "10.1186/s12864-024-10876-0", "pmid": "39402510", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC11479545"}, {"db": "pii", "key": "10.1186/s12864-024-10876-0"}], "notes": [], "created": "2024-11-18T11:43:50.298Z", "modified": "2024-11-19T07:23:23.086Z"}, {"entity": "publication", "iuid": "2d3fe81551fa4460aa2a48d466dba3e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d3fe81551fa4460aa2a48d466dba3e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d3fe81551fa4460aa2a48d466dba3e2"}}, "title": "Metagenomic assemblies tend to break around antibiotic resistance genes", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Karkman", "given": "Antti", "initials": "A", "orcid": "0000-0003-0983-3319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ba670092f8496d8ebedcb07d0b6e62.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2023-12-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.13.571436", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:51:00.058Z", "modified": "2026-08-20T10:51:00.117Z"}, {"entity": "publication", "iuid": "1dd5448da4264efab44a0f27d42fad69", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dd5448da4264efab44a0f27d42fad69.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dd5448da4264efab44a0f27d42fad69"}}, "title": "A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "review", "published": "2023-08-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "issn-l": "0160-4120", "volume": "178", "issue": null, "pages": "108084"}, "abstract": "The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.", "doi": "10.1016/j.envint.2023.108084", "pmid": "37421899", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(23)00357-4"}], "notes": [], "created": "2022-11-08T09:31:13.181Z", "modified": "2024-11-18T11:42:53.864Z"}, {"entity": "publication", "iuid": "06666b5ae8b94390ab6c73ad20a7942f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/06666b5ae8b94390ab6c73ad20a7942f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/06666b5ae8b94390ab6c73ad20a7942f"}}, "title": "A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A", "orcid": "0000-0002-0493-7808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd75cbcc659c4ca398eb678fad1dc498.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU", "orcid": "0000-0002-9301-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c66286f83a8430f954fbc5c52db10c5.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "posted-content", "published": "2022-01-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.01.29.478248", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:22.646Z", "modified": "2026-08-20T10:09:22.715Z"}]}