{"entity": "journal", "iuid": "beede5f958ad4004baeefe6f120bf2a8", "timestamp": "2026-07-17T09:04:56.204Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Microb%20Genom.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Microb%20Genom"}}, "title": "Microb Genom", "issn": "2057-5858", "issn-l": null, "publications_count": 6, "publications": [{"entity": "publication", "iuid": "bdd145617e0c401ea708379b0493f458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458"}}, "title": "Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.", "authors": [{"family": "T\u00e5ng Hallb\u00e4ck", "given": "Erika", "initials": "E"}, {"family": "Bj\u00f6rkman", "given": "Jonas T", "initials": "JT"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Fang", "given": "Hong", "initials": "H"}, {"family": "Sylvin", "given": "Isak", "initials": "I"}, {"family": "Kaden", "given": "Ren", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "S\u00f6derlund Strand", "given": "Anna", "initials": "A"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Campillay Lagos", "given": "Amaya", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "11", "issue": "1", "issn-l": null}, "abstract": "Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances.Results. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison.Conclusions. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.", "doi": "10.1099/mgen.0.001331", "pmid": "39869391", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11893271"}], "notes": [], "created": "2025-03-19T04:58:38.247Z", "modified": "2025-11-19T15:18:20.002Z"}, {"entity": "publication", "iuid": "51ce186df53f47eabfec4017dff0ed47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ce186df53f47eabfec4017dff0ed47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ce186df53f47eabfec4017dff0ed47"}}, "title": "pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.", "authors": [{"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "S\u00e1nchez-Serrano", "given": "Andrea", "initials": "A"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.", "doi": "10.1099/mgen.0.001189", "pmid": "38288762", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10868605"}], "notes": [], "created": "2024-11-20T14:53:37.991Z", "modified": "2024-11-20T14:53:38.117Z"}, {"entity": "publication", "iuid": "5b3508419d454b42ad2e8e5537ee4608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b3508419d454b42ad2e8e5537ee4608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b3508419d454b42ad2e8e5537ee4608"}}, "title": "Rapid adaptations of Legionella pneumophila to the human host.", "authors": [{"family": "Leenheer", "given": "Dani\u00ebl", "initials": "D"}, {"family": "Moreno", "given": "Ana\u00edsa B", "initials": "AB"}, {"family": "Paranjape", "given": "Kiran", "initials": "K"}, {"family": "Murray", "given": "Susan", "initials": "S"}, {"family": "Jarraud", "given": "Sophie", "initials": "S"}, {"family": "Ginevra", "given": "Christophe", "initials": "C"}, {"family": "Guy", "given": "Lionel", "initials": "L"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "9", "issue": "3", "issn-l": null}, "abstract": "Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires' disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite the similarities in infection mechanisms, the hosts are different enough that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The other is a gene coding for an EAL-domain-containing protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. The clinical strain, carrying the mutated EAL-domain-containing homologue, grows faster in macrophages than the wild-type strain, and thus appears to be better adapted to the human host. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, parallel evolution - here mutations in the same genes observed in independent human infections - could point to adaptations to the accidental human host. These results suggest that despite the ability of L. pneumophila to infect, replicate in and exit from macrophages, its human-specific adaptations are unlikely to be fixed in the population.", "doi": "10.1099/mgen.0.000958", "pmid": "36947445", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10132064"}], "notes": [], "created": "2023-10-04T12:58:47.617Z", "modified": "2024-01-16T13:48:33.890Z"}, {"entity": "publication", "iuid": "430cf56e0f614f9ea751fe8a8820bc64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/430cf56e0f614f9ea751fe8a8820bc64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/430cf56e0f614f9ea751fe8a8820bc64"}}, "title": "Genomic differentiation within East Asian Helicobacter pylori.", "authors": [{"family": "You", "given": "Yuanhai", "initials": "Y"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "He", "given": "Lihua", "initials": "L"}, {"family": "Yahara", "given": "Koji", "initials": "K"}, {"family": "Yamaoka", "given": "Yoshio", "initials": "Y"}, {"family": "Cha", "given": "Jeong-Heon", "initials": "JH"}, {"family": "Murakami", "given": "Kazunari", "initials": "K"}, {"family": "Katsura", "given": "Yukako", "initials": "Y"}, {"family": "Kobayashi", "given": "Ichizo", "initials": "I"}, {"family": "Falush", "given": "Daniel", "initials": "D"}, {"family": "Zhang", "given": "Jianzhong", "initials": "J"}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "8", "issue": "2", "issn-l": null}, "abstract": "The East Asian region, including China, Japan and Korea, accounts for half of gastric cancer deaths. However, different areas have contrasting gastric cancer incidences and the population structure of Helicobacter pylori in this ethnically diverse region is yet unknown. We aimed to investigate genomic differences in H. pylori between these areas to identify sequence polymorphisms associated with increased cancer risk. We analysed 381 H. pylori genomes collected from different areas of the three countries using phylogenetic and population genetic tools to characterize population differentiation. The functional consequences of SNPs with a highest fixation index (Fst) between subpopulations were examined by mapping amino acid changes on 3D protein structure, solved or modelled. Overall, 329/381 genomes belonged to the previously identified hspEAsia population indicating that import of bacteria from other regions of the world has been uncommon. Seven subregional clusters were found within hspEAsia, related to subpopulations with various ethnicities, geographies and gastric cancer risks. Subpopulation-specific amino acid changes were found in multidrug exporters (hefC), transporters (frpB-4), outer membrane proteins (hopI) and several genes involved in host interaction, such as a catalase site, involved in H2O2 entrance, and a flagellin site mimicking host glycosylation. Several of the top hits, including frpB-4, hefC, alpB/hopB and hofC, have been found to be differentiated within the Americas in previous studies, indicating that a handful of genes may be key to local geographic adaptation. H. pylori within East Asia are not homogeneous but have become differentiated geographically at multiple loci that might have facilitated adaptation to local conditions and hosts. This has important implications for further evaluation of these changes in relation to the varying gastric cancer incidence between geographical areas in this region.", "doi": "10.1099/mgen.0.000676", "pmid": "35188454", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8942036"}], "notes": [], "created": "2022-11-09T15:46:27.181Z", "modified": "2024-01-16T13:48:37.642Z"}, {"entity": "publication", "iuid": "7f473288e3b642c59aced9e1c0a27093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f473288e3b642c59aced9e1c0a27093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f473288e3b642c59aced9e1c0a27093"}}, "title": "Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.", "authors": [{"family": "W\u00e4neskog", "given": "Marcus", "initials": "M", "orcid": "0000-0003-2480-5631", "researcher": {"href": "https://publications.scilifelab.se/researcher/061c0a9720bc4c12936ae06e4cc34448.json"}}, {"family": "Halvorsen", "given": "Tiffany", "initials": "T", "orcid": "0000-0001-9845-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c43bcbbe9e440078b97b0a839ae8933.json"}}, {"family": "Filek", "given": "Klara", "initials": "K", "orcid": "0000-0003-2518-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/27050310845f4590bdcb3ba86ca0a8f2.json"}}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Hammarl\u00f6f", "given": "Disa L", "initials": "DL", "orcid": "0000-0002-8077-7615", "researcher": {"href": "https://publications.scilifelab.se/researcher/88cfbc6e22a64030bd973295f6cd5972.json"}}, {"family": "Hayes", "given": "Christopher S", "initials": "CS", "orcid": "0000-0002-2216-6445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8098c48713b64fc1ab2ac333111af518.json"}}, {"family": "Braaten", "given": "Bruce A", "initials": "BA"}, {"family": "Low", "given": "David A", "initials": "DA"}, {"family": "Poole", "given": "Stephen J", "initials": "SJ", "orcid": "0000-0002-5504-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa971b41ea8f47bc8895654c8cd7cfd6.json"}}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S", "orcid": "0000-0002-3275-0936", "researcher": {"href": "https://publications.scilifelab.se/researcher/622e0bb6cb184df9b8788aa218174dac.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "7", "issue": "3", "pages": null, "issn-l": null}, "abstract": "The phenomenon of contact-dependent growth inhibition (CDI) and the genes required for CDI (cdiBAI) were identified and isolated in 2005 from an Escherichia coli isolate (EC93) from rats. Although the cdiBAI EC93 locus has been the focus of extensive research during the past 15 years, little is known about the EC93 isolate from which it originates. Here we sequenced the EC93 genome and find two complete and functional cdiBAI loci (including the previously identified cdi locus), both carried on a large 127 kb plasmid. These cdiBAI systems are differentially expressed in laboratory media, enabling EC93 to outcompete E. coli cells lacking cognate cdiI immunity genes. The two CDI systems deliver distinct effector peptides that each dissipate the membrane potential of target cells, although the two toxins display different toxic potencies. Despite the differential expression and toxic potencies of these CDI systems, both yielded similar competitive advantages against E. coli cells lacking immunity. This can be explained by the fact that the less expressed cdiBAI system (cdiBAIEC93-2) delivers a more potent toxin than the highly expressed cdiBAIEC93-1 system. Moreover, our results indicate that unlike most sequenced CDI+ bacterial isolates, the two cdi loci of E. coli EC93 are located on a plasmid and are expressed in laboratory media.", "doi": "10.1099/mgen.0.000534", "pmid": "33646095", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8190604"}], "notes": [], "created": "2021-03-13T09:59:02.922Z", "modified": "2024-01-16T13:48:40.610Z"}, {"entity": "publication", "iuid": "ba8e61b15fdf4091b7ee12bca3608e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26"}}, "title": "The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Einarsson", "given": "Elin", "initials": "E", "orcid": "0000-0002-1242-5263", "researcher": {"href": "https://publications.scilifelab.se/researcher/be89fa4c7f9d484c858a0bf385f06c61.json"}}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Peirasmaki", "given": "Dimitra", "initials": "D", "orcid": "0000-0001-5376-626X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94231cbd0cab4644b42c3fab58cea9aa.json"}}, {"family": "Eckmann", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "6", "issue": "8", "issn-l": null}, "abstract": "Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris-mouse pathosystem.", "doi": "10.1099/mgen.0.000402", "pmid": "32618561", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7641422"}], "notes": [], "created": "2021-01-08T16:29:45.383Z", "modified": "2021-11-10T12:48:32.906Z"}], "created": "2021-01-08T16:29:45.397Z", "modified": "2021-01-08T16:29:45.397Z"}