Publications
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Villamil-Alonso, Alejandra; Tortosa, Pablo; Moldal, Torfinn; Bøe, Cathrine Arnason; Bragason, Birkir Thor & Nilsen, Hanne
[Show all 13 contributors for this article]
(2026).
Whole-genome sequencing reveals a novel
<i>Renibacterium salmoninarum</i>
lineage and suggests geographic endemism combined with anthropogenic spread in the North-East Atlantic Area.
Applied and Environmental Microbiology.
ISSN 0099-2240.
doi:
10.1128/aem.00347-26.
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ABSTRACT Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD) and has been isolated from northern European salmonid farms since the 1960s. The bacterium has been detected only sporadically in Norway during the last few decades, but the country has experienced several geographically spread outbreaks since December 2022. The phylogenomic relationships of R. salmoninarum isolates associated with the epizootics ongoing on the West Coast and in Mid-Norway were explored using draft genomes generated by whole-genome sequencing. A broad overview of the phylogeography of this pathogen was gained through sequencing and analysis of a collection of isolates from Norway ( n = 67), Iceland ( n = 12), Denmark ( n = 12), and the Faroe Islands ( n = 1), along with a collection of 109 publicly available sequences. We identified two distinct contemporary clades of R. salmoninarum causing BKD in Norway in the period 2022–2024. Both clades belong to the expanding, aquaculture-associated Lineage 1. The epidemiological picture appears consistent with contemporary aquaculture operations, raising questions on the effectiveness or practice of current biosecurity practices toward R. salmoninarum . This work also describes a hitherto undescribed lineage (Lineage 3), predominantly from Iceland, where BKD is considered endemic. The detection of endemic reservoirs of R. salmoninarum in European water systems underscores the potential for ongoing pathogen circulation independent of acute outbreaks. This finding emphasizes the importance of further investigation of the mechanisms of pathogen persistence, particularly within environments related to aquaculture, where chronic infection reservoirs could compromise disease management and biosecurity. IMPORTANCE Renibacterium salmoninarum , the causative agent of bacterial kidney disease (BKD), is a salmonid pathogen that often presents as subclinical, chronic infections, complicating detection and control. Effective management of BKD is crucial for sustainable aquaculture and wild fish conservation. Recognizing the need for comprehensive sampling, previous studies have underscored the importance of a global isolate collection to better understand the pathogen’s epidemiology. While the slow genetic evolution and highly conserved genome of the bacterium have reduced the resolution of conventional typing methods in the past, applying whole-genome sequencing has enabled its molecular tracing at the outbreak level. Here, we present the largest phylogenomic analysis of R. salmoninarum to date, including sequences from Denmark, Iceland, and the Faroe Islands for the first time. This expanded data set elucidates past and present movements of the pathogen in European waters, providing actionable insights to support development of targeted BKD management and biosecurity strategies.
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Soltvedt, Eiril; Lagesen, Karin; Nørstebø, Simen Foyn; Rodriguez-Campos, Sabrina; Bergsjø, Bjarne A & Skancke, Ellen
[Show all 8 contributors for this article]
(2026).
Canine Providencia alcalifaciens: virulence factors and phylogenetic analysis of an emerging enteropathogen.
Microbial Genomics.
12(1).
doi:
10.1099/mgen.0.001628.
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In 2019, an outbreak of acute haemorrhagic diarrhoea (AHD) in dogs in Norway was linked to Providencia alcalifaciens . A marked increase in diarrhoeal cases in dogs during the autumn, along with the frequent identification of P. alcalifaciens in affected dogs, supports its role as a causative agent in seasonal diarrhoea in dogs in Norway. Previous phylogenetic studies have revealed two major genetic lineages of P. alcalifaciens , one of which is associated with diarrhoeal disease and carries a plasmid-borne type 3 transport system (T3SS 1a ). The aim of this study was to place Norwegian P. alcalifaciens isolates in a global phylogenetic context and to characterize the distribution of putative virulence-associated genes (VAGs) in isolates from dogs with AHD. Whole-genome sequencing was performed on 273 isolates, and 48 publicly available genomes were included for comparative analyses. Bioinformatic processing and phylogenetic analyses were conducted on the complete dataset of 321 P . alcalifaciens genomes. VAGs were identified using ABRicate and two virulence gene databases. Phylogenetic analyses revealed two main clusters, A and B. Most isolates from sick dogs belonged to cluster A, particularly to subcluster A-1 – the largest of five subclusters – which primarily contained isolates from sick dogs. All isolates in subclusters A-1 and A-4 harboured genes encoding T3SS 1a , a type II secretion system and the effector genes stcE , yopJ and cdtA-C . blast searches using closed reference genomes showed high sequence identity (>90%) to plasmid elements in 196 of 197 isolates from subclusters A-1 and A-4, suggesting plasmid-mediated acquisition of virulence factors. These findings support that specific genetic variants of P. alcalifaciens , particularly those in subclusters A-1 and A-4, exhibit increased virulence potential and are associated with AHD in dogs. The high proportion of isolates from clinically affected dogs, including many from the 2019 outbreak, further underscores the link between subcluster A-1 and disease.
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Frederiksen, Rikki Franklin; Urdahl, Anne Margrete; Slettemeås, Jannice Schau; Granstad, Silje; Simm, Roger & Lagesen, Karin
(2025).
Genomic characterization of vancomycin-resistant enterococci in Norwegian poultry.
PLOS ONE.
20(6).
doi:
10.1371/journal.pone.0324789.
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Vancomycin resistant enterococci (VRE) are a globally leading cause of nosocomial infections in humans, and a potential animal VRE reservoir, especially in poultry, is of concern. It has been suggested that the presence of VRE in broilers has been prolonged due to co-selection of narasin resistance (narAB genes) and vancomycin resistance (vanA genes), and that these genes may be present on the same plasmids. The aim of this study was to use whole genome sequencing to characterize and compare both the chromosomes and plasmids of VRE isolates from poultry in Norway, and to elucidate whether co-localisation of narAB and vanA genes on the same genetic elements, or clonal spread, could explain the persistence of VRE. A total of 30 VRE isolates from the years 2002–2013 were included, 23 from broiler flocks and seven from turkey flocks. WGS analyses showed that the isolates were genetically diverse with the number of SNPs ranging from 10 to 2807. The isolates belonged to 15 different sequence types, though all carried a plasmid similar to pVEF plasmids, and contained both vanA and narAB. A comparative gene analysis indicated that narAB is carried on a composite transposon, and that interspecies transfer of the plasmid between Enterococcus faecium and Enterococcus hirae may occur. The absence of transfer genes on the pVEF-like plasmids and their presence on a megaplasmid suggest that the megaplasmid probably act as a helper plasmid. Overall, the results support that the use of narasin in broilers may be a risk factor for a persistent reservoir of VRE in broilers.
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Slettemeås, Jannice Schau; Sekse, Camilla; Sunde, Marianne; Norström, Madelaine; Wester, Astrid Louise & Naseer, Mohammed Umaer
[Show all 10 contributors for this article]
(2024).
Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway.
BMC Microbiology.
24(1).
doi:
10.1186/s12866-024-03412-3.
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Background
The usage of fluoroquinolones in Norwegian livestock production is very low, including in broiler production. Historically, quinolone-resistant Escherichia coli (QREC) isolated from Norwegian production animals rarely occur. However, with the introduction of a selective screening method for QREC in the Norwegian monitoring programme for antimicrobial resistance in the veterinary sector in 2014; 89.5% of broiler caecal samples and 70.7% of broiler meat samples were positive. This triggered the concern if there could be possible links between broiler and human reservoirs of QREC. We are addressing this by characterizing genomes of QREC from humans (healthy carriers and patients) and broiler isolates (meat and caecum).
Results
The most frequent mechanism for quinolone resistance in both broiler and human E. coli isolates were mutations in the chromosomally located gyrA and parC genes, although plasmid mediated quinolone resistance (PMQR) was also identified. There was some relatedness of the isolates within human and broiler groups, but little between these two groups. Further, some overlap was seen for isolates with the same sequence type isolated from broiler and humans, but overall, the SNP distance was high.
Conclusion
Based on data from this study, QREC from broiler makes a limited contribution to the incidence of QREC in humans in Norway.
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Frederiksen, Rikki Franklin; Slettemeås, Jannice Schau; Granstad, Silje; Lagesen, Karin; Pikkemaat, Mariel G. & Urdahl, Anne Margrete
[Show all 7 contributors for this article]
(2024).
Polyether ionophore resistance in a one health perspective.
Frontiers in Microbiology.
15(1347490),
p. 1–11.
doi:
10.3389/fmicb.2024.1347490.
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Antimicrobial resistance is a major threat to human health and must be approached from a One Health perspective. Use of antimicrobials in animal husbandry can lead to dissemination and persistence of resistance in human pathogens. Polyether ionophores (PIs) have antimicrobial activities and are among the most extensively used feed additives for major production animals. Recent discoveries of genetically encoded PI resistance mechanisms and co-localization of resistance mechanisms against PIs and antimicrobials used in human medicine on transferrable plasmids, have raised concerns that use of PIs as feed additives bear potential risks for human health. This review summarizes the current knowledge on PI resistance and discusses the potential consequences of PI-usage as feed additives in a One Health perspective.
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Gulla, Snorre; Colquhoun, Duncan John; Olsen, Anne Berit; Spilsberg, Bjørn; Lagesen, Karin & Åkesson, Caroline Piercey
[Show all 10 contributors for this article]
(2023).
Phylogeography and host specificity of Pasteurellaceae pathogenic to sea-farmed fish in the north-east Atlantic.
Frontiers in Microbiology.
14.
doi:
10.3389/fmicb.2023.1236290.
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The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named “Pasteurella atlantica”. Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved “P. atlantica gv. cyclopteri” (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by “P. atlantica gv. salmonicida” (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and “P. atlantica” from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and “P. atlantica” should be moved to the genus Phocoenobacter.
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Haverkamp, Thomas Hendricus Augustus; Kaspersen, Håkon; Øines, Øivind; Spilsberg, Bjørn; Telke, Amar & Lagesen, Karin
[Show all 10 contributors for this article]
(2022).
Closed Genome Sequences of Providencia alcalifaciens Isolates from Dogs.
Microbiology Resource Announcements (MRA).
11(2).
doi:
10.1128/mra.00955-21.
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Eight Providencia alcalifaciens isolates from eight different dogs in Norway with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technologies sequencing, all of the genomes were complete and closed after hybrid assembly
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Spilsberg, Bjørn; Nilsen, Hanne Katrine; Tavornpanich, Saraya; Gulla, Snorre; Jansen, Mona Dverdal & Lagesen, Karin
[Show all 8 contributors for this article]
(2022).
Tenacibaculosis in Norwegian Atlantic salmon (Salmo salar) cage-farmed in cold sea water is primarily associated with Tenacibaculum finnmarkense genomovar finnmarkense.
Journal of Fish Diseases.
ISSN 0140-7775.
45(4).
doi:
10.1111/jfd.13577.
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Skin conditions associated with Tenacibaculum spp. constitute a significant threat to the health and welfare of sea-farmed Atlantic salmon (Salmo salar L.) in Norway. Fifteen presumptive tenacibaculosis outbreaks distributed along the Norwegian coast during the late winter and spring of 2018 were investigated. Bacteriological culture confirmed the presence of Tenacibaculum spp. Seventy-six isolates cultured from individual fish were selected and subjected to whole-genome sequencing and MALDI-TOF MS analysis. Average nucleotide identity and MALDI-TOF analyses confirmed the presence of T. finnmarkense and T. dicentrarchi, with further division of T. finnmarkense into genomovars (gv.) finnmarkense and ulcerans. Core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses identified the presence of a genetically conserved cluster of gv. finnmarkense isolates against a background of relatively genetically diverse gv. finnmarkense and gv. ulcerans isolates in 13 of the 15 studied cases. This clustering strongly suggests a link between T. finnmarkense gv. finnmarkense and development of clinical tenacibaculosis in sea-farmed Norwegian salmon in the late winter and spring. Analysis of 25 Tenacibaculum isolates collected during the spring of 2019 from similar cases identified a similar distribution of genotypes. Low water temperatures were common to all cases, and most incidences involved relatively small fish shortly after sea transfer, suggesting that these fish are particularly predisposed to Tenacibaculum infection.
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Kaspersen, Håkon; Sekse, Camilla; Fiskebeck, Eve Marie Louise Zeyl; Slettemeås, Jannice Schau; Simm, Roger & Norström, Madelaine
[Show all 8 contributors for this article]
(2020).
Dissemination of Quinolone-Resistant Escherichia coli in the Norwegian Broiler and Pig Production Chains and Possible Persistence in the Broiler Production Environment.
Applied and Environmental Microbiology.
ISSN 0099-2240.
doi:
10.1128/AEM.02769-19.
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In Norway, the use of quinolones in livestock populations is very low, and prophylactic use is prohibited. Despite this, quinolone-resistant Escherichia coli (QREC) isolates are present at low levels in several animal species. The source of these QREC isolates is unknown. The aim of this study was to characterize and compare QREC isolates from different animal species to identify putative factors that may promote the occurrence of QREC. A total of 280 QREC isolates, from broilers, pigs, red foxes, and wild birds, were whole-genome sequenced and analyzed. Well-known chromosomal and plasmid-mediated resistance mechanisms were identified. In addition, mutations in marR, marA, and rpoB causing novel amino acid substitutions in their respective proteins were detected. Phylogenetic analyses were used to determine the relationships between the isolates. Quinolone resistance mechanism patterns appeared to follow sequence type groups. Similar QREC isolates with similar resistance mechanism patterns were detected from the samples, and further phylogenetic analysis indicated close evolutionary relationships between specific isolates from different sources. This suggests the dissemination of highly similar QREC isolates between animal species and also the persistence of QREC strains within the broiler production chain. This highlights the importance of both control measures at the top of the production chain as well as biosecurity measures to avoid the further dissemination and persistence of QREC in these environments.
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Olsen, Anne Berit; Spilsberg, Bjørn; Nilsen, Hanne Katrine; Lagesen, Karin; Gulla, Snorre & Avendano-herrera, Ruben
[Show all 9 contributors for this article]
(2020).
Tenacibaculum piscium sp. nov., isolated from skin ulcers of sea-farmed fish, and description of Tenacibaculum finnmarkense sp. nov. with subdivision into genomovars finnmarkense and ulcerans.
International Journal of Systematic and Evolutionary Microbiology.
ISSN 1466-5026.
doi:
10.1099/ijsem.0.004501.
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Mable, Barbara K.; Brysting, Anne Krag; Jørgensen, Marte Holten; Carbonell, Anna K.Z.; Kiefer, Christiane & Ruiz-Duarte, Paola
[Show all 8 contributors for this article]
(2018).
Adding Complexity to Complexity: Gene Family Evolution in Polyploids.
Frontiers in Ecology and Evolution.
6,
p. 1–20.
doi:
10.3389/fevo.2018.00114.
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Comparative genomics of non-model organisms has resurrected whole genome duplication (WGD) from being viewed as a somewhat obscure process that happens in plants to a primary driver of eukaryotic diversification. The shadow of past ploidy increases has left a strong signature of duplicated genes organized into gene families, even in small genomes that have undergone effectively complete rediploidization. Nevertheless, despite continually advancing technologies and bioinformatics pipelines, resolving the fate of duplicate genes remains a substantial challenge. For example, many important recognition processes are driven not only by allelic expansion through retention of duplicates but also by diversification and copy number variation. This creates technical difficulties with assembly to reference genomes and accurate interpretation of homology. Thus, relatively little is known about the impacts of recent polyploidization and hybridization on the evolution of gene families under selective forces that maintain diversity, such as balancing selection. Here we use a complex of species and ploidy levels in the genus Arabidopsis (A. lyrata and A. arenosa) as a model to investigate the evolutionary dynamics of a large and complicated gene family known to be under strong balancing selection: the receptor-like kinases, which include the female component of genetically controlled self-incompatibility. Specifically, we question: (1) How does diversity of S-receptor kinase (SRK) alleles in tetraploids compare to that in their close diploid relatives? (2) Is there increased trans-specific polymorphism (i.e., sharing of alleles that transcend speciation, characteristic of balancing selection) in tetraploids compared to diploids due to the higher number of copies they carry? (3) Do these highly variable loci show evidence of introgression among extant species/ploidy levels within or outside known zones of hybridization? (4) Is there evidence for copy number variation among paralogs? We use this example to highlight specific issues to consider when interpreting gene family evolution, particularly in relation to polyploids but also more generally in diploids. We conclude with recommendations for strategies to address the challenges of resolving such complex loci in the future, using advances in deep sequencing approaches.
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Kaspersen, Håkon; Urdahl, Anne Margrete; Simm, Roger; Slettemeås, Jannice Schau; Lagesen, Karin & Norström, Madelaine
(2018).
Occurrence of quinolone resistant E. coli originating from different animal species in Norway.
Veterinary Microbiology.
ISSN 0378-1135.
217,
p. 25–31.
doi:
10.1016/j.vetmic.2018.02.022.
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The aim of this study was to describe and compare the occurrence of quinolone resistant Escherichia coli (QREC) in various animal species in relation to human population density. Data from the Norwegian monitoring programme for antimicrobial resistance in feed, food and animals from 2006 to 2016 was compiled and analysed. In total, 4568 E. coli isolates were included in this study. The isolates originated from broilers, layers, cattle, turkeys, dogs, wild birds, red foxes, reindeer, sheep, horses and pigs. Data regarding the geographical location of sampling was obtained for 4050 of these isolates and used to categorize the isolates depending on the human population density of the area. In total, 1.4% of the isolates were categorized as quinolone resistant. Compared to most European countries, there was an overall low occurrence of QREC in various animal species in Norway, though with an interspecies variation with the highest occurrence in broilers and wild birds (p < 0.05). Human population density was not associated with the occurrence of QREC. Since fluoroquinolones are not used prophylactically and in almost negligent amounts in various species in Norway, the interspecies variation in the occurrence of QREC suggests that other factors than fluoroquinolone use may be important in the development of QREC.
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Gulla, Snorre; Barnes, Andrew C.; Welch, Timothy J.; Romalde, Jesús L.; Ryder, David & Ormsby, Michael J.
[Show all 11 contributors for this article]
(2018).
Multilocus variable-number tandem-repeat analysis of Yersinia ruckeri confirms the existence of host specificity, geographic endemism, and anthropogenic dissemination of virulent clones.
Applied and Environmental Microbiology.
ISSN 0099-2240.
84:e00730-18(16),
p. 1–13.
doi:
10.1128/aem.00730-18.
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A multilocus variable-number tandem-repeat analysis (MLVA) assay was developed for epizootiological study of the internationally significant fish pathogen Yersinia ruckeri, which causes yersiniosis in salmonids. The assay involves amplification of 10 variable-number tandem-repeat (VNTR) loci in two five-plex PCRs, followed by capillary electrophoresis. A collection of 484 Y. ruckeri isolates, originating from various biological sources and collected from four continents over 7 decades, was analyzed. Minimum-spanning-tree cluster analysis of MLVA profiles separated the studied population into nine major clonal complexes and a number of minor clusters and singletons. The major clonal complexes could be associated with host species, geographic origin, and serotype. A single large clonal complex of serotype O1 isolates dominating the yersiniosis situation in international rainbow trout farming suggests anthropogenic spread of this clone, possibly related to transport of fish. Moreover, subclustering within this clonal complex indicates putative transmission routes and multiple biotype shift events. In contrast to the situation in rainbow trout, Y. ruckeri strains associated with disease in Atlantic salmon appear as more or less geographically isolated clonal complexes. A single complex of serotype O1 exclusive to Norway was found to be responsible for almost all major yersiniosis outbreaks in modern Norwegian salmon farming, and site-specific subclustering further indicates persistent colonization of freshwater farms in Norway. Identification of genetically diverse Y. ruckeri isolates from clinically healthy fish and environmental sources also suggests the widespread existence of less-virulent or avirulent strains.
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Khelik, Ksenia; Lagesen, Karin; Sandve, Geir Kjetil; Rognes, Torbjørn & Nederbragt, Alexander Johan
(2017).
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.
BMC Bioinformatics.
18(1),
p. 1–14.
doi:
10.1186/s12859-017-1748-z.
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Background Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration. Results We here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff. Conclusions We have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on https://github.com/uio-cels/NucDiff under the MPL license.
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Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Eri, Lars Magne; Jeansson, Stig & Jakobsen, Kjetill Sigurd
(2014).
Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-Independent High Throughput Sequencing: A Case Report.
Open Microbiology Journal.
8,
p. 148–153.
doi:
10.2174/1874285801408010148.
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Xiao, Xi; Sogge, Hanne; Lagesen, Karin; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd & Rohrlack, Thomas
(2014).
Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment.
PLOS ONE.
9(8).
doi:
10.1371/journal.pone.0106510.
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Assessing phytoplankton diversity is of primary importance for both basic and applied ecological studies. Following the advances in molecular methods, phytoplankton studies are switching from using classical microscopy to high throughput sequencing approaches. However, methodological comparisons of these approaches have rarely been reported. In this study, we compared the two methods, using a unique dataset of multiple water samples taken from a natural freshwater environment. Environmental DNA was extracted from 300 water samples collected weekly during 20 years, followed by high throughput sequencing of amplicons from the 16S and 18S rRNA hypervariable regions. For each water sample, phytoplankton diversity was also estimated using light microscopy. Our study indicates that species compositions detected by light microscopy and 454 high throughput sequencing do not always match. High throughput sequencing detected more rare species and picoplankton than light microscopy, and thus gave a better assessment of phytoplankton diversity. However, when compared to light microscopy, high throughput sequencing of 16S and 18S rRNA amplicons did not adequately identify phytoplankton at the species level. In summary, our study recommends a combined strategy using both morphological and molecular techniques.
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Tooming-Klunderud, Ave; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin & Glöckner, Gernot
[Show all 9 contributors for this article]
(2013).
From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains.
Applied and Environmental Microbiology.
ISSN 0099-2240.
79(21),
p. 6803–6812.
doi:
10.1128/AEM.01455-13.
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Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related Planktothrix strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight Planktothrix strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.
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Booth, James A.; Thomassen, Gard O Sundby; Rowe, Alexander D.; Weel-Sneve, Ragnhild; Lagesen, Karin & Kristiansen, Knut Ivan
[Show all 9 contributors for this article]
(2013).
Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response.
Scientific Reports.
3.
doi:
10.1038/srep03053.
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The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.
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Vesth, Tammi; Lagesen, Karin; Acar, Öncel & Ussery, David
(2013).
CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics.
PLOS ONE.
8(4),
p. 1–16.
doi:
10.1371/journal.pone.0060120.
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Background: Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. Results: The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Conclusion: This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.
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Muinck, Eric De; Lagesen, Karin; Afset, Jan Egil; Didelot, Xavier; Rønningen, Kjersti Skjold & Rudi, Knut
[Show all 8 contributors for this article]
(2013).
Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche.
BMC Genomics.
14.
doi:
10.1186/1471-2164-14-81.
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Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche. Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles. Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.
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Jørgensen, Marte Holten; Lagesen, Karin; Mable, Barbara & Brysting, Anne Krag
(2012).
Using high-throughput sequencing to investigate the evolution of self-incompatibility genes in the Brassicaceae: strategies and challenges.
Plant Ecology & Diversity.
ISSN 1755-0874.
5(4),
p. 473–484.
doi:
10.1080/17550874.2012.748098.
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Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Jeansson, Stig & Jakobsen, Kjetill Sigurd
(2012).
Alterations of microbiota in urine from women with interstitial cystitis.
BMC Microbiology.
12(205).
doi:
10.1186/1471-2180-12-205.
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Background Interstitial Cystitis (IC) is a chronic inflammatory condition of the bladder with unknown etiology. The aim of this study was to characterize the microbial community present in the urine from IC female patients by 454 high throughput sequencing of the 16S variable regions V1V2 and V6. The taxonomical composition, richness and diversity of the IC microbiota were determined and compared to the microbial profile of asymptomatic healthy female (HF) urine. Results The composition and distribution of bacterial sequences differed between the urine microbiota of IC patients and HFs. Reduced sequence richness and diversity were found in IC patient urine, and a significant difference in the community structure of IC urine in relation to HF urine was observed. More than 90% of the IC sequence reads were identified as belonging to the bacterial genus Lactobacillus, a marked increase compared to 60% in HF urine. Conclusion The 16S rDNA sequence data demonstrates a shift in the composition of the bacterial community in IC urine. The reduced microbial diversity and richness is accompanied by a higher abundance of the bacterial genus Lactobacillus, compared to HF urine. This study demonstrates that high throughput sequencing analysis of urine microbiota in IC patients is a powerful tool towards a better understanding of this enigmatic disease.
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Siddiqui, Huma; Nederbragt, Alexander Johan; Lagesen, Karin; Jeansson, Stig & Jakobsen, Kjetill Sigurd
(2011).
Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons.
BMC Microbiology.
11.
doi:
10.1186/1471-2180-11-244.
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Background Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques. Results Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500. Conclusions Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.
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Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik
[Show all 42 contributors for this article]
(2011).
The genome sequence of Atlantic cod reveals a unique immune system.
Nature.
ISSN 0028-0836.
477(7363),
p. 207–210.
doi:
10.1038/nature10342.
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Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
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Bohlin, Jon; Snipen, Lars-Gustav; Hardy, Simon P.; Kristoffersen, Anja Bråthen; Lagesen, Karin & Dønvik, Torunn
[Show all 8 contributors for this article]
(2010).
Analysis of intra-genomic GC content homogeneity within prokaryotes.
BMC Genomics.
11.
doi:
10.1186/1471-2164-11-464.
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Background Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity. Results The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content was also found but appears to be non-linear and varies greatly among phyla. Conclusions Our findings show that GCVAR is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that GCVAR should be used as a complement to mean GC content.
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Friis, C; Wassenaar, TM; Javed, MA; Snipen, Lars-Gustav; Lagesen, Karin & Hallin, PF
[Show all 11 contributors for this article]
(2010).
Genomic Characterization of Campylobacter jejuni Strain M1.
PLOS ONE.
5(8).
doi:
10.1371/journal.pone.0012253.
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Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C. jejuni strain M1, and compared this to 12 other C. jejuni sequenced genomes currently publicly available. Compared to these, M1 is closest to strain 81116. Based on the 13 genome sequences, we have identified the C. jejuni pan-genome, as well as the core genome, the auxiliary genes, and genes unique between strains M1 and 81116. The pan-genome contains 2,427 gene families, whilst the core genome comprised 1,295 gene families, or about two-thirds of the gene content of the average of the sequenced C. jejuni genomes. Various comparison and visualization tools were applied to the 13 C. jejuni genome sequences, including a species pan- and core genome plot, a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1.
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Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M. & Lagesen, Karin
[Show all 9 contributors for this article]
(2010).
Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides.
PLOS ONE.
5(12).
doi:
10.1371/journal.pone.0015356.
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Background
Despite comprehensive investigation, the Escherichia coli SOS response system is not yet fully understood. We have applied custom designed whole genome tiling arrays to measure UV invoked transcriptional changes in E. coli. This study provides a more complete insight into the transcriptome and the UV irradiation response of this microorganism.
Results
We detected a number of novel differentially expressed transcripts in addition to the expected SOS response genes (such as sulA, recN, uvrA, lexA, umuC and umuD) in the UV treated cells. Several of the differentially expressed transcripts might play important roles in regulation of the cellular response to UV damage. We have predicted 23 novel small peptides from our set of detected non-gene transcripts. Further, three of the predicted peptides were cloned into protein expression vectors to test the biological activity. All three constructs expressed the predicted peptides, in which two of them were highly toxic to the cell. Additionally, a remarkably high overlap with previously in-silico predicted non-coding RNAs (ncRNAs) was detected. Generally we detected a far higher transcriptional activity than the annotation suggests, and these findings correspond with previous transcription mappings from E. coli and other organisms.
Conclusions
Here we demonstrate that the E. coli transcriptome consists of far more transcripts than the present annotation suggests, of which many transcripts seem important to the bacterial stress response. Sequence alignment of promoter regions suggest novel regulatory consensus sequences for some of the upregulated genes. Finally, several of the novel transcripts identified in this study encode putative small peptides, which are biologically active.
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Ussery, DW; Kiil, K; Lagesen, Karin; Sicheritz-Pontén, T; bohlin, jon & Wassenaar, TM
(2009).
The Genus Burkholderia: Analysis of 56 Genomic Sequences.
In Reuse, H de & Bereswill, S (Ed.),
Microbial Pathogenomics.
S. Karger.
ISSN 9783805591928.
p. 140–157.
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Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta & Rognes, Torbjørn
(2009).
Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays.
PLOS ONE.
4(6).
doi:
10.1371/journal.pone.0005943.
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Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome's complexity and sequence composition, need to be considered in the design to ensure a high quality microarray. Secondly, since tiling projects today very often exceed the limits of conventional array-experiments, researchers cannot use established computer tools designed for commercial arrays, and instead have to redesign previous methods or create novel tools. Principal Findings Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, respectively, as well as the use of multiple copies of control probe-sets on tiling microarrays. Furthermore, a novel normalisation and background estimation procedure for tiling arrays is presented along with a method for array analysis focused on detection of short transcripts. The design, normalisation and analysis methods have been applied in various experiments and several of the detected novel short transcripts have been biologically confirmed by Northern blot tests. Conclusions Tiling-arrays are becoming increasingly applicable in genomic research, but researchers still lack both the tools for custom design of arrays, as well as the systems and procedures for analysis of the vast amount of data resulting from such experiments. We believe that the methods described herein will be a useful contribution and resource for researchers designing and analysing custom tiling arrays for both bacteria and higher organisms. © 2009 Thomassen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Lagesen, Karin & Rognes, Torbjørn
[Show all 7 contributors for this article]
(2009).
Genome dynamics in major bacterial pathogens.
FEMS Microbiology Reviews.
ISSN 0168-6445.
33(3),
p. 453–470.
doi:
10.1111/j.1574-6976.2009.00173.x.
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Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content encoding proteins provides clues toward understanding the microbial lifestyle related to habitat and niche. Campylobacter jejuni, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, the pathogenic Neisseria, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus are major human pathogens causing detrimental morbidity and mortality at a global scale. An algorithm for the clustering of orthologs was established in order to identify whether orthologs of selected genes were present or absent in the genomes of the pathogenic bacteria under study. Based on the known genes for the various functions and their orthologs in selected pathogenic bacteria, an overview of the presence of the different types of genes was created. In this context, we focus on selected processes enabling genome dynamics in these particular pathogens, namely DNA repair, recombination and horizontal gene transfer. An understanding of the precise molecular functions of the enzymes participating in DNA metabolism and their importance in the maintenance of bacterial genome integrity has also, in recent years, indicated a future role for these enzymes as targets for therapeutic intervention.
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Lagesen, K; Hallin, P; Rødland, Einar Andreas; Staerfeldt, HH; Rognes, T & Ussery, DW
(2007).
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Nucleic Acids Research (NAR).
ISSN 0305-1048.
35.
doi:
10.1093/nar/gkm160.
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The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.
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Ussery, DW; Hallin, PF; Lagesen, Karin & Wassenaar, TM
(2005).
Genome update: tRNAs in sequenced microbial genomes.
Microbiology (Reading).
ISSN 1350-0872.
150,
p. 1603–1606.
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Ussery, DW; Hallin, PF; Lagesen, Karin & Coenye, T
(2004).
Genome update: rRNAs in sequenced microbial genomes.
Microbiology (Reading).
ISSN 1350-0872.
150,
p. 1113–1115.
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Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Seeberg, Erling Christen; Rognes, Torbjørn & Tønjum, Tone
(2004).
Biased distribution of DNA uptake sequences towards genome maintenance genes.
Nucleic Acids Research (NAR).
ISSN 0305-1048.
32(3),
p. 1050–1058.
doi:
10.1093/nar/gkh255.
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Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseriameningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9–10mers residing within coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction‐modification and replication than in any other annotated gene group in these organisms. Pasteurella multocida also displayed high frequencies of a putative DUS identical to that previously identified in H.influenzae and with a skewed distribution towards genome maintenance genes, indicating that this bacterium might be transformation competent under certain conditions. These results imply that the high frequency of DUS in genome maintenance genes is conserved among phylogenetically divergent species and thus are of significant biological importance. Increased DUS density is expected to enhance DNA uptake and the over‐representation of DUS in genome maintenance genes might reflect facilitated recovery of genome preserving functions. For example, transient and beneficial increase in genome instability can be allowed during pathogenesis simply through loss of antimutator genes, since these DUS‐containing sequences will be preferentially recovered. Furthermore, uptake of such genes could provide a mechanism for facilitated recovery from DNA damage after genotoxic stress. © The Author 2004. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model.
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Spilsberg, Bjørn; Nilsen, Hanne Katrine; Gulla, Snorre; Lagesen, Karin; Colquhoun, Duncan John & Olsen, Anne Berit
(2024).
Draft genome sequences of 13 Tenacibaculum maritimum isolates from farmed Norwegian Cyclopterus lumpus (lumpfish) and Scophthalmus maximus (turbot).
Microbiology Resource Announcements (MRA).
13(6).
doi:
10.1128/mra.00165-24.
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Thirteen bacterial isolates of Tenacibaculum maritimum were sequenced and assembled. The strains were isolated from four disease outbreaks in farmed marine fish in Norway. Eight isolates were from Cyclopterus lumpus (lumpfish), and five were from Scophthalmus maximus (turbot). Overall, sequence similarity did not correlate with host species or geographic location.
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Spilsberg, Bjørn; Nilsen, Hanne Katrine; Gulla, Snorre; Lagesen, Karin; Olsen, Anne Berit & Colquhoun, Duncan John
(2022).
Draft Genome Sequences of 23 Tenacibaculum Isolates from Farmed Norwegian Lumpfish, Cyclopterus lumpus.
Microbiology Resource Announcements (MRA).
11(4).
doi:
10.1128/mra.01249-21.
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Draft genome sequences of 23 Tenacibaculum sp. strains that were isolated
from Cyclopterus lumpus (lumpfish) were investigated to elucidate possible routes
of transmission between Salmo salar (Atlantic salmon) and lumpfish.
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Olsen, Anne Berit; Spilsberg, Bjørn; Nilsen, Hanne Katrine; Gulla, Snorre; Lagesen, Karin & Colquhoun, Duncan John
(2021).
Tenacibaculosis in recently sea-transferred Norwegian Atlantic salmon (Salmo salar) is primarly associated with Tenacibaculum finnmarkense gv. finnmarkennse.
Full text in Research Archive
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Samy, Jeevan Karloss Antony; Marselis, Georgios; Fiskebeck, Eve Marie Louise Zeyl; Sekse, Camilla; Skjerdal, Olaug Taran & Lagesen, Karin
(2021).
The Why and the How of DNA sequencing for One Health – setting up a bioinformatics platform.
Full text in Research Archive
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Samy, Jeevan Karloss Antony; Marselis, Georgios; Fiskebeck, Eve Marie Louise Zeyl; Sekse, Camilla; Skjerdal, Olaug Taran & Lagesen, Karin
(2021).
Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses.
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Samy, Jeevan Karloss Antony; Marselis, Georgios; Fiskebeck, Eve Marie Louise Zeyl; Skjerdal, Olaug Taran; Sekse, Camilla & Lagesen, Karin
(2021).
Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses.
Full text in Research Archive
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Slettemeås, Jannice Schau; Sekse, Camilla; Kaspersen, Håkon; Sunde, Marianne; Norström, Madelaine & Wester, Astrid Louise
[Show all 10 contributors for this article]
(2021).
Quinolone resistant Escherichia coli from Norwegian livestock, wild animals and humans.
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Objectives
WHO have classified fluoroquinolones as a critically important antimicrobial for treatment in humans. The occurrence of quinolone resistance among E. coli (QREC) has been low in Norwegian poultry, but has increased in recent years. Characterization of the quinolone resistance mechanism in animal isolates, comparison to human isolates and the population structure of QREC have been studied through several projects at the Norwegian Veterinary Institute. The aim of the current study was to combine results from these previous studies to investigate if the QREC population found in animals could in any way contribute to the occurrence of QREC in humans.
Methods
A selection of QREC isolates from poultry, pig, red fox and wild birds collected in NORM-VET and human isolates collected through NORM and Ahus were subjected for Illumina sequencing. Strains harbouring plasmid resistant quinolone resistance (PMQR) genes were subjected to long read sequencing on a MinION device (ONT).
Results
Several unique sequence types (ST) were detected. Some were shared between human and animal QREC isolates. Point mutations were the main resistance mechanism identified, but PMQR genes were detected on plasmids of different incompatibility groups from both human and animal isolates.
Conclusions
There was little overlap of QREC isolates with same STs isolated from poultry and humans, and very few PMQR genes were detected.
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Spilsberg, Bjørn; Lagesen, Karin; Nilsen, Hanne Katrine; Olsen, Anne Berit & Colquhoun, Duncan John
(2019).
Elucidation of the role of Tenacibaculum spp. in atypical winter-ulcer in sea-farmed Atlantic salmon in Norway.
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Kaspersen, Håkon; Sekse, Camilla; Slettemeås, Jannice Schau; Simm, Roger; Norström, Madelaine & Urdahl, Anne Margrete
[Show all 7 contributors for this article]
(2019).
Low-resolution MLST as an initial analysis for deep characterization of quinolone resistant Escherichia coli.
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We are currently investigating the presence of putative antimicrobial resistance genes (ARG) and population structure in a set of quinolone resistant E. coli (QREC) from Norway, and as part of that study we are further investigating specific sequence types (ST). The goal of this study was to analyse clustering of isolates from selected STs, by utilizing whole genome MLST in addition to ARGs, virulence genes, and serotypes, to investigate the similarity between isolates from different animal species.
A total of 285 QREC isolates originating from broilers, pigs, red foxes and wild birds were subjected to whole genome sequencing. ARGs were identified with ARIBA, with the MegaRes (intrinsic genes) and ResFinder (acquired genes) databases. Core genome multi locus sequence typing (cgMLST) with chewBBACA using the Enterobase scheme for E. coli was used for distance calculation and tree generation, and the regular sequence types (ST) were determined by the Escherichia coli #1 Enterobase scheme. STs which are represented with at least 10 isolates and that are present in at least three animal species was selected for serotyping, virulence gene identification and whole genome MLST (wgMLST) by using SeroTypeFinder, VirulenceFinder, and chewBBACA, respectively. Based on this, sequence types 10, 58, 155 and 162 were selected for further analyses.
Some sequence types had a more homogenous distribution of ARGs than others. In regard to ARGs, serotypes, virulence genes and the wgMLST results, a higher diversity was seen in ST10 isolates. Serotypes clustered in concordance with wgMLST results, especially in ST162 and ST155.
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Spilsberg, Bjørn; Lagesen, Karin; Kristoffersen, Anja Bråthen & Holst-Jensen, Arne
(2017).
Identification and quantification of genetically modified organisms (GMO) from high throughput sequencing data.
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Slettemeås, Jannice Schau; Norström, Madelaine; Sunde, Marianne; Urdahl, Anne Margrete; Wester, Astrid Lousie & Lagesen, Karin
[Show all 9 contributors for this article]
(2017).
Quinolone resistant Escherichia coli from broiler in Norway - characterization, comparison to human isolates and molecular risk assessment.
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Background and objectives: Usage of fluoroquinolones (FQ) in Norwegian livestock production is negligible. Historically the occurrence of quinolone resistant Escherichia coli (QREC) in the Norwegian monitoring program for antimicrobial resistance in the veterinary sector (NORM-VET) has been rare. However, in NORM-VET 2014 a selective method was implemented for screening of QREC in broilers and QREC was found in 89.5% of caecal samples and in 70.7% of meat samples. In this study we aim to characterize and compare QREC from broilers and humans in Norway in order to investigate possible links between isolates of the two reservoirs.
Material and methods: NORM-VET 2014 isolates from chicken meat (n=47) and caecal samples (n=53) resistant to nalidixic acid (NAL) and/or ciprofloxacin (CIP) were selected for sequencing. Human QREC isolates were collected via the Norwegian surveillance program for antimicrobial resistance (NORM) from urinary tract infections and bacteraemia (n=77), and from screening healthy carriers for QREC (n=23). Data regarding antimicrobial resistance were extracted from the monitoring programs (NORM-VET and NORM) and compared between isolates. The 200 isolates were sequenced using Nextera XT library prep on HiSeq 2500 with Rapid Run. The sequence data were trimmed using Trimmomatic, and assembled using SPAdes. We are currently analysing the sequence data for presence of resistance- and virulence genes, plasmids, MLST and SNP analysis.
Results: NORM-VET 2014 resistance data showed that the majority of the broiler isolates exhibited high level resistance to NAL (MICs >128 mg/L), but low level tolerance to CIP (MICs 0.12-0.5). Mutations in the gyrA gene were identified in most isolates, and a few exhibited the plasmid mediated resistance gene qnrS1. Data from the NORM program showed that the human isolates had a different MIC distribution with the largest proportion of isolates exhibiting high level CIP resistance (MICs >0.25), indicative of more mutations in the gyrA/parC genes. However, a considerable proportion of human isolates exhibited a quinolone resistance MIC profile corresponding to the most common profile found among the broiler isolates.
Conclusions: Preliminary results indicate that the main mechanism behind quinolone resistance in this study is mutations in gyrA, but plasmid mediated resistance were also identified. Further, the human isolates exhibit high level CIP resistance compared to low tolerance in the broiler isolates.
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Slettemeås, Jannice Schau; Sekse, Camilla & Lagesen, Karin
(2017).
Quinolone resistant Escherichia coli in Norwegian poultry and their impact on humans.
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Lagesen, Karin; Kaspersen, Håkon; Slettemeås, Jannice Schau; Sekse, Camilla & Urdahl, Anne Margrete
(2017).
BIFROST: A flexible and portable genomic read set characterization pipeline.
Full text in Research Archive
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Holst-Jensen, Arne; Spilsberg, Bjørn; Kristoffersen, Anja Bråthen & Lagesen, Karin
(2016).
Detection and quantification of genetically modified organisms by use of shotgun whole genome sequencing.
Full text in Research Archive
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Slettemeås, Jannice Schau; Norström, Madelaine; Sunde, Marianne; Urdahl, Anne Margrete; Wester, Astrid Lousie & Simonsen, Gunnar Skov
[Show all 9 contributors for this article]
(2016).
Quinolone resistant Escherichia coli from broiler in Norway - characterization, comparison to human isolates and molecular risk assessment.
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Background: The usage of fluoroquinolones (FQ) in the Norwegian livestock production is nearly negligible and findings of quinolone resistant Escherichia coli (QREC) in the Norwegian monitoring program for antimicrobial resistance in the veterinary sector (NORM-VET) has been rare. However, in NORM-VET 2014 a selective method was implemented for screening of QREC in poultry and QREC was found in 89.5% of caecal samples and in 70.7% of meat samples. It is unknown if humans have acquired QREC from a poultry reservoir. In this study we aimed to characterize QREC from poultry and humans in Norway. Furthermore comparison studies were carried out in order to investigate possible overlap between isolates of the two reservoirs.
Material/methods: Isolates from poultry meat and caecal samples defined as resistant to nalidixic acid and/or ciprofloxacin in NORM-VET 2014 were included in the present study. These isolates (n=336) were subjected to PCR-based phylotyping and a subset were screened for gyrA mutations by PCR and sequencing. Isolates from human origin resistant to fluoroquinolones were collected via the Norwegian monitoring program for human pathogens (NORM) from urinary tract infections and sepsis, and from a study screening of healthy carriers of QREC. Resistance data was extracted from the monitoring programs (NORM-VET and NORM) and compared between isolates of poultry and human origin. A subset of 192 isolates, 96 from each category will be subjected to whole-genome-sequencing (WGS) using Nextera XT library prep and a HiSeq 250 bp PE rapid run on a HiSeq 2500.
Results: Resistance data from NORM-VET 2014 showed that the majority of the broiler isolates exhibit high level resistance to nalidixic acid (> 128 mg/L), but low level tolerance to ciprofloxacin (MICs 0.12-0.5). Mutation in the gyrA gene was identified at position Ser83→Leu in a subset of relevant isolates. Furthermore the isolates grouped in the following phylogroups; 44.1% B2, 23.7% D, 18% B, 13% A, and 1.2% were non-typeable. Data from the NORM program showed that the human isolates had a different MIC distribution with the largest proportion of isolates exhibiting high level ciprofloxacin resistance (MICs > 0.25), indicative of more mutations in the gyrA/parC genes. However, a considerable proportion of human isolates exhibited a quinolone resistance MIC profile corresponding to the most common profile found among the broiler isolates. Half of the selected poultry isolates (n=48), from both poultry meat and poultry caecal samples has been subjected to WGS. These isolates were chosen on the background of their MIC profiles.
Conclusions: The preliminary data indicates that the main mechanism behind quinolone resistance in the broiler isolates is somewhat different than the mechanism responsible in the majority of human isolates. Human isolates with a typical “broiler MIC profile” was detected; genetic relationship among the isolates will be investigated.
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Colquhoun, Duncan John; Lagesen, Karin; Vestby, Lene Karine & Gulla, Snorre
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A time and economically effecient protocol using high throughput sequencing to create large sequence datasets for population genetics.
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Davidsen, L.; Lagesen, Karin; Rødland, A. E.; Rognes, Torbjørn & Tønjum, Tone
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Biased distribution of bacterial DNA uptake sequences.
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Published
Nov. 3, 2010 3:29 PM
- Last modified
Jan. 27, 2011 11:22 AM
