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Sigurdsson AI, Louloudis I, Banasik K, Westergaard D, Winther O, Lund O, Ostrowski S, Erikstrup C, Pedersen O, Nyegaard M, Brunak S, Vilhjálmsson B, Rasmussen S. Deep integrative models for large-scale human genomics. Nucleic Acids Res 2023; 51:e67. [PMID: 37224538 PMCID: PMC10325897 DOI: 10.1093/nar/gkad373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 05/26/2023] Open
Abstract
Polygenic risk scores (PRSs) are expected to play a critical role in precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predictors mainly capture additive relationships and are limited in data modalities they can use. We developed a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), specifically designed for large-scale genomics data. The framework supports multi-task learning, automatic integration of other clinical and biochemical data, and model explainability. When applied to individual-level data from the UK Biobank, the GLN model demonstrated a competitive performance compared to established neural network architectures, particularly for certain traits, showcasing its potential in modeling complex genetic relationships. Furthermore, the GLN model outperformed linear PRS methods for Type 1 Diabetes, likely due to modeling non-additive genetic effects and epistasis. This was supported by our identification of widespread non-additive genetic effects and epistasis in the context of T1D. Finally, we constructed PRS models that integrated genotype, blood, urine, and anthropometric data and found that this improved performance for 93% of the 290 diseases and disorders considered. EIR is available at https://github.com/arnor-sigurdsson/EIR.
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Affiliation(s)
- Arnór I Sigurdsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Louloudis
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole Winther
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
| | - Ole Lund
- Danish National Genome Center, Ørestads Boulevard 5, 2300 Copenhagen S, Denmark
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, 8000 Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Immunology, Zealand University Hospital, 4600 Køge, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, DK- 9260 Gistrup, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research (NCRR), Aarhus University, 8000 Aarhus C, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), 8210 Aarhus V, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, 8000 Aarhus C, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Aytan-Aktug D, Grigorjev V, Szarvas J, Clausen PTLC, Munk P, Nguyen M, Davis JJ, Aarestrup FM, Lund O. SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies. Microbiol Spectr 2022; 10:e0264122. [PMID: 36377945 PMCID: PMC9769690 DOI: 10.1128/spectrum.02641-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Vladislav Grigorjev
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Janes VA, Matamoros S, Munk P, Clausen PTLC, Koekkoek SM, Koster LAM, Jakobs ME, de Wever B, Visser CE, Aarestrup FM, Lund O, de Jong MD, Bossuyt PMM, Mende DR, Schultsz C. Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study. The Lancet Microbe 2022; 3:e588-e597. [DOI: 10.1016/s2666-5247(22)00088-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/11/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022] Open
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Aytan-Aktug D, Clausen PTLC, Szarvas J, Munk P, Otani S, Nguyen M, Davis JJ, Lund O, Aarestrup FM. PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest. mSystems 2022; 7:e0118021. [PMID: 35382558 PMCID: PMC9040769 DOI: 10.1128/msystems.01180-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning-specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/). IMPORTANCE Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities to the host organisms through accessory genes that can encode antimicrobial resistance and virulence. In addition to lateral inheritance, plasmids can be transferred horizontally between bacterial taxa. Therefore, detection of the host range of plasmids is crucial for understanding and predicting the dissemination trajectories of extrachromosomal genes and bacterial evolution as well as taking effective countermeasures against antimicrobial resistance.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Nydahl TK, Ahorhorlu SY, Ndiaye M, Das MK, Hansson H, Bravo MC, Wang CW, Lusingu J, Theisen M, Singh SK, Singh S, Campino S, Lund O, Roper C, Alifrangis M. Identification of Single-Nucleotide Polymorphisms in the Mitochondrial Genome and Kelch 13 Gene of Plasmodium falciparum in Different Geographical Populations. Am J Trop Med Hyg 2021; 105:1085-1092. [PMID: 34270452 DOI: 10.4269/ajtmh.21-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/30/2021] [Indexed: 11/07/2022] Open
Abstract
The emergence of artemisinin-resistant Plasmodium falciparum parasites in Southeast Asia threatens malaria control and elimination. The interconnectedness of parasite populations may be essential to monitor the spread of resistance. Combining a published barcoding system of geographically restricted single-nucleotide polymorphisms (SNPs), mainly mitochondria of P. falciparum with SNPs in the K13 artemisinin resistance marker, could elucidate the parasite population structure and provide insight regarding the spread of drug resistance. We explored the diversity of mitochondrial SNPs (bp position 611-2825) and identified K13 SNPs from malaria patients in the districts of India (Ranchi), Tanzania (Korogwe), and Senegal (Podor, Richard Toll, Kaolack, and Ndoffane). DNA was amplified using a nested PCR and Sanger-sequenced. Overall, 199 K13 sequences (India: N = 92; Tanzania: N = 48; Senegal: N = 59) and 237 mitochondrial sequences (India: N = 93; Tanzania: N = 48; Senegal: N = 96) were generated. SNPs were identified by comparisons with reference genomes. We detected previously reported geographically restricted mitochondrial SNPs (T2175C and G1367A) as markers for parasites originating from the Indian subcontinent and several geographically unrestricted mitochondrial SNPs. Combining haplotypes with published P. falciparum mitochondrial genome data suggested possible regional differences within India. All three countries had G1692A, but Tanzanian and Senegalese SNPs were well-differentiated. Some mitochondrial SNPs are reported here for the first time. Four nonsynonymous K13 SNPs were detected: K189T (India, Tanzania, Senegal); A175T (Tanzania); and A174V and R255K (Senegal). This study supports the use of mitochondrial SNPs to determine the origin of the parasite and suggests that the P. falciparum populations studied were susceptible to artemisinin during sampling because all K13 SNPs observed were outside the propeller domain for artemisinin resistance.
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Affiliation(s)
- Tine Kliim Nydahl
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Samuel Yao Ahorhorlu
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana, Ghana
| | - Magatte Ndiaye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Senegal
| | - Manoj Kumar Das
- Field Unit, National Institute of Malaria Research, Ranchi, Jharkhand, India
| | - Helle Hansson
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marina Crespo Bravo
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christian William Wang
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - John Lusingu
- National Institute for Medical Research, Tanga Centre, Tanzania
| | - Michael Theisen
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Susheel Kumar Singh
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Subhash Singh
- Indian Institute of Integrative Medicine, Jammu, India
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ole Lund
- Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
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Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1285] [Impact Index Per Article: 428.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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Allesøe RL, Lemvigh CK, Phan MVT, Clausen PTLC, Florensa AF, Koopmans MPG, Lund O, Cotten M. Automated download and clean-up of family-specific databases for kmer-based virus identification. Bioinformatics 2021; 37:705-710. [PMID: 33031509 PMCID: PMC8097684 DOI: 10.1093/bioinformatics/btaa857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
SUMMARY Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistance genes that might be present in some GenBank viral entries, and could lead to false positives in virus identification. For utilizing the database, we present a useful opportunity for dealing with possible human contamination. We show the applicability of DONE by downloading a virus database comprising 37 virus families. We observed an average increase of 16 776 new entries downloaded per month for the 37 families. In addition, we demonstrate the utility of a custom database compared to a standard reference database for classifying both simulated and real sequence data. AVAILABILITYAND IMPLEMENTATION The DONE pipeline for downloading and cleaning is deposited in a publicly available repository (https://bitbucket.org/genomicepidemiology/done/src/master/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rosa L Allesøe
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Camilla K Lemvigh
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.,Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Alfred F Florensa
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands
| | - Ole Lund
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands.,MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, G61 1QH Scotland, UK
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8
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Hallgren MB, Overballe-Petersen S, Lund O, Hasman H, Clausen PTLC. MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads. Biol Methods Protoc 2021; 6:bpab008. [PMID: 33981853 PMCID: PMC8106442 DOI: 10.1093/biomethods/bpab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from the Illumina sequencing platforms and long reads from Oxford Nanopore Technologies’ (ONT) platforms as input. MINTyper performs automated reference identification, alignment, alignment trimming, optional methylation masking, and pairwise distance calculations. With this approach, we could rapidly and accurately cluster a set of DNA sequenced isolates, with a known epidemiological relationship to confirm the clustering. Functions were built to allow for both high-accuracy methylation-aware base-called MinION reads (hac_m Q10) and fast generated lower-quality reads (fast Q8) to be used, also in combination with Illumina data. With fast Q8 reads a higher number of base pairs were excluded from the calculated distance matrix, compared with the high-accuracy methylation-aware Q10 base-calling of ONT data. Nonetheless, when using different qualities of ONT data with corresponding input parameters, the clustering of isolates were nearly identical.
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Affiliation(s)
- Malte B Hallgren
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
| | | | - Ole Lund
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
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9
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Szarvas J, Bartels MD, Westh H, Lund O. Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting. Front Microbiol 2021; 12:636608. [PMID: 33868194 PMCID: PMC8047125 DOI: 10.3389/fmicb.2021.636608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mette Damkjaer Bartels
- MRSA Knowledge Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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10
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Karlsen ST, Vesth TC, Oregaard G, Poulsen VK, Lund O, Henderson G, Bælum J. Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis. PLoS One 2021; 16:e0246287. [PMID: 33720959 PMCID: PMC7959382 DOI: 10.1371/journal.pone.0246287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/17/2021] [Indexed: 11/18/2022] Open
Abstract
Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to create systematic, high-throughput screening methods for these properties. Fast acidification of milk is such a strain-dependent property. To predict the maximum hourly acidification rate (Vmax), we trained Random Forest (RF) models on four different genomic representations: Presence/absence of gene families, counts of Pfam domains, the 8 nucleotide long subsequences of their DNA (8-mers), and the 9 nucleotide long subsequences of their DNA (9-mers). Vmax was measured at different temperatures, volumes, and in the presence or absence of yeast extract. These conditions were added as features in each RF model. The four models were trained on 257 strains, and the correlation between the measured Vmax and the predicted Vmax was evaluated with Pearson Correlation Coefficients (PC) on a separate dataset of 85 strains. The models all had high PC scores: 0.83 (gene presence/absence model), 0.84 (Pfam domain model), 0.76 (8-mer model), and 0.85 (9-mer model). The models all based their predictions on relevant genetic features and showed consensus on systems for lactose metabolism, degradation of casein, and pH stress response. Each model also predicted a set of features not found by the other models.
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Affiliation(s)
- Signe Tang Karlsen
- Chr. Hansen A/S, Hoersholm, Denmark
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| | | | | | | | - Ole Lund
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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11
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Pataki BÁ, Matamoros S, van der Putten BCL, Remondini D, Giampieri E, Aytan-Aktug D, Hendriksen RS, Lund O, Csabai I, Schultsz C. Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning. Sci Rep 2020; 10:15026. [PMID: 32929164 PMCID: PMC7490380 DOI: 10.1038/s41598-020-71693-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance of AMR. This work proposes a machine learning approach that can predict the minimum inhibitory concentration (MIC) for a given antibiotic, here ciprofloxacin, on the basis of both genome-wide mutation profiles and profiles of acquired antimicrobial resistance genes. We analysed 704 Escherichia coli genomes combined with their respective MIC measurements for ciprofloxacin originating from different countries. The four most important predictors found by the model, mutations in gyrA residues Ser83 and Asp87, a mutation in parC residue Ser80 and presence of the qnrS1 gene, have been experimentally validated before. Using only these four predictors in a linear regression model, 65% and 93% of the test samples’ MIC were correctly predicted within a two- and a four-fold dilution range, respectively. The presented work does not treat machine learning as a black box model concept, but also identifies the genomic features that determine susceptibility. The recent progress in WGS technology in combination with machine learning analysis approaches indicates that in the near future WGS of bacteria might become cheaper and faster than a MIC measurement.
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Affiliation(s)
- Bálint Ármin Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary. .,Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary.
| | - Sébastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Boas C L van der Putten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA), University of Bologna, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Department of Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.,Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary
| | - Constance Schultsz
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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12
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Hasman H, Clausen PTLC, Kaya H, Hansen F, Knudsen JD, Wang M, Holzknecht BJ, Samulioniené J, Røder BL, Frimodt-Møller N, Lund O, Hammerum AM. LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences. J Antimicrob Chemother 2020; 74:1473-1476. [PMID: 30863844 DOI: 10.1093/jac/dkz092] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES In enterococci, resistance to linezolid is often mediated by mutations in the V domain of the 23S rRNA gene (G2576T or G2505A). Furthermore, four genes [optrA, cfr, cfr(B) and poxtA] encode linezolid resistance in enterococci. We aimed to develop a Web tool for detection of the two mutations and the four genes encoding linezolid resistance in enterococci from whole-genome sequence data. METHODS LRE-Finder (where LRE stands for linezolid-resistant enterococci) detected the fraction of Ts in position 2576 and the fraction of As in position 2505 of the 23S rRNA and the cfr, cfr(B), optrA and poxtA genes by aligning raw sequencing reads (fastq format) with k-mer alignment. For evaluation, fastq files from 21 LRE isolates were submitted to LRE-Finder. As negative controls, fastq files from 1473 non-LRE isolates were submitted to LRE-Finder. The MICs of linezolid were determined for the 21 LRE isolates. As LRE-negative controls, 26 VRE isolates were additionally selected for linezolid MIC determination. RESULTS LRE-Finder was validated and showed 100% concordance with phenotypic susceptibility testing. A cut-off of 10% mutations in position 2576 and/or position 2505 was set in LRE-Finder for predicting a linezolid resistance phenotype. This cut-off allows for detection of a single mutated 23S allele in both Enterococcus faecalis and Enterococcus faecium, while ignoring low-level sequencing noise. CONCLUSIONS A Web tool for detection of the 23S rRNA mutations (G2576T and G2505A) and the optrA, cfr, cfr(B) and poxtA genes from whole-genome sequences from enterococci is now available online.
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Affiliation(s)
- Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Philip T L C Clausen
- Department of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Hansen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jenny Dahl Knudsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Jurgita Samulioniené
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Bent L Røder
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
| | | | - Ole Lund
- Department of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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13
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Kumburu HH, Sonda T, van Zwetselaar M, Leekitcharoenphon P, Lukjancenko O, Mmbaga BT, Alifrangis M, Lund O, Aarestrup FM, Kibiki GS. Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania. J Antimicrob Chemother 2020; 74:1484-1493. [PMID: 30843063 PMCID: PMC6524488 DOI: 10.1093/jac/dkz055] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 12/11/2018] [Accepted: 01/16/2019] [Indexed: 11/25/2022] Open
Abstract
Background Reliable phenotypic antimicrobial susceptibility testing can be a challenge in clinical settings in low- and middle-income countries. WGS is a promising approach to enhance current capabilities. Aim To study diversity and resistance determinants and to predict and compare resistance patterns from WGS data of Acinetobacter baumannii with phenotypic results from classical microbiological testing at a tertiary care hospital in Tanzania. Methods and results MLST using Pasteur/Oxford schemes yielded eight different STs from each scheme. Of the eight, two STs were identified to be global clones 1 (n = 4) and 2 (n = 1) as per the Pasteur scheme. Resistance testing using classical microbiology determined between 50% and 92.9% resistance across all drugs. Percentage agreement between phenotypic and genotypic prediction of resistance ranged between 57.1% and 100%, with coefficient of agreement (κ) between 0.05 and 1. Seven isolates harboured mutations at significant loci (S81L in gyrA and S84L in parC). A number of novel plasmids were detected, including pKCRI-309C-1 (219000 bp) carrying 10 resistance genes, pKCRI-43-1 (34935 bp) carrying two resistance genes and pKCRI-49-1 (11681 bp) and pKCRI-28-1 (29606 bp), each carrying three resistance genes. New ampC alleles detected included ampC-69, ampC-70 and ampC-71. Global clone 1 and 2 isolates were found to harbour ISAba1 directly upstream of the ampC gene. Finally, SNP-based phylogenetic analysis of the A. baumannii isolates revealed closely related isolates in three clusters. Conclusions The validity of the use of WGS in the prediction of phenotypic resistance can be appreciated, but at this stage is not sufficient for it to replace conventional antimicrobial susceptibility testing in our setting.
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Affiliation(s)
- Happiness H Kumburu
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | | | | | - Blandina T Mmbaga
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- DTU-Bioinformatics, Technical University of Denmark, Copenhagen, Denmark
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14
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Krause KE, Jenkins TP, Skaarup C, Engmark M, Casewell NR, Ainsworth S, Lomonte B, Fernández J, Gutiérrez JM, Lund O, Laustsen AH. An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity. PLoS Negl Trop Dis 2020; 14:e0008366. [PMID: 32579606 PMCID: PMC7313730 DOI: 10.1371/journal.pntd.0008366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022] Open
Abstract
Snakebite envenoming is a major neglected tropical disease that affects millions of people every year. The only effective treatment against snakebite envenoming consists of unspecified cocktails of polyclonal antibodies purified from the plasma of immunized production animals. Currently, little data exists on the molecular interactions between venom-toxin epitopes and antivenom-antibody paratopes. To address this issue, high-density peptide microarray (hdpm) technology has recently been adapted to the field of toxinology. However, analysis of such valuable datasets requires expert understanding and, thus, complicates its broad application within the field. In the present study, we developed a user-friendly, and high-throughput web application named “Snake Toxin and Antivenom Binding Profiles” (STAB Profiles), to allow straight-forward analysis of hdpm datasets. To test our tool and evaluate its performance with a large dataset, we conducted hdpm assays using all African snake toxin protein sequences available in the UniProt database at the time of study design, together with eight commercial antivenoms in clinical use in Africa, thus representing the largest venom-antivenom dataset to date. Furthermore, we introduced a novel method for evaluating raw signals from a peptide microarray experiment and a data normalization protocol enabling intra-microarray and even inter-microarray chip comparisons. Finally, these data, alongside all the data from previous similar studies by Engmark et al., were preprocessed according to our newly developed protocol and made publicly available for download through the STAB Profiles web application (http://tropicalpharmacology.com/tools/stab-profiles/). With these data and our tool, we were able to gain key insights into toxin-antivenom interactions and were able to differentiate the ability of different antivenoms to interact with certain toxins of interest. The data, as well as the web application, we present in this article should be of significant value to the venom-antivenom research community. Knowledge gained from our current and future analyses of this dataset carry the potential to guide the improvement and optimization of current antivenoms for maximum patient benefit, as well as aid the development of next-generation antivenoms. Millions of people are bitten by venomous snakes each year, resulting in over 100,000 deaths. Currently, such envenomings are treated with animal derived antivenoms that contain undefined antibodies against snake venom toxins that have been raised by the production animal’s immune system. To date, our understanding of these antibody toxin interactions is sparse, but with the help of high-density peptide microarray (hdpm) technology this is starting to change. Whilst this technology is very powerful, analysis of the output data is complex and requires expert training. Therefore, in this study, we developed a user-friendly, and high-throughput web application named “Snake Toxin and Antivenom Binding Profiles” (STAB Profiles). Furthermore, we ensured our tool was functional and able to handle large amounts of data by creating an entirely novel and larger than ever hdpm dataset based on all African snake toxin proteins together with eight commercial antivenoms. With these data and our tool, we were able to further our understanding on toxin-antivenom interactions and were able to differentiate the ability of different antivenoms to interact with certain toxins of interest. Ideally, these and future insights can help guide the improvement and optimization of current antivenoms, as well as aid the informed development of next-generation antivenoms.
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Affiliation(s)
- Kamille E. Krause
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail: (TPJ); (AHL)
| | - Carina Skaarup
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mikael Engmark
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Stuart Ainsworth
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Julián Fernández
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - José M. Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail: (TPJ); (AHL)
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15
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Matamoros S, Hendriksen RS, Pataki BÁ, Pakseresht N, Rossello M, Silvester N, Amid C, Aarestrup FM, Koopmans M, Cochrane G, Csabai I, Lund O, Schultsz C. Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences. Microb Genom 2020; 6:e000342. [PMID: 32255760 PMCID: PMC7371118 DOI: 10.1099/mgen.0.000342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/31/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collaboration between international partners. Here, we present the 'AMR Data Hub', an online infrastructure for storage and sharing of structured phenotypic AMR data linked to bacterial whole-genome sequences. Leveraging infrastructure built by the European COMPARE Consortium and structured around the European Nucleotide Archive (ENA), the AMR Data Hub already provides an extensive data collection of more than 2500 isolates with linked genome and AMR data. Representing these data in standardized formats, we provide tools for the validation and submission of new data and services supporting search, browse and retrieval. The current collection was created through a collaboration by several partners from the European COMPARE Consortium, demonstrating the capacities and utility of the AMR Data Hub and its associated tools. We anticipate growth of content and offer the hub as a basis for future research into methods to explore and predict AMR.
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Affiliation(s)
- Sébastien Matamoros
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands
| | - Rene S. Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Bálint Ármin Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary
| | - Nima Pakseresht
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marc Rossello
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Clara Amid
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guy Cochrane
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Constance Schultsz
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
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Marcelino VR, Clausen PTLC, Buchmann JP, Wille M, Iredell JR, Meyer W, Lund O, Sorrell TC, Holmes EC. CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biol 2020; 21:103. [PMID: 32345331 PMCID: PMC7189439 DOI: 10.1186/s13059-020-02014-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/13/2020] [Indexed: 01/19/2023] Open
Abstract
There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly, and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
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Affiliation(s)
- Vanessa R Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia.
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Jan P Buchmann
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, 2145, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, 2145, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Ole Lund
- National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
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18
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Szarvas J, Ahrenfeldt J, Cisneros JLB, Thomsen MCF, Aarestrup FM, Lund O. Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform. Commun Biol 2020; 3:137. [PMID: 32198478 PMCID: PMC7083913 DOI: 10.1038/s42003-020-0869-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/03/2020] [Indexed: 11/09/2022] Open
Abstract
Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance. The data is divided into sets by mapping to reference genomes, then consensus sequences are generated. Nucleotide based genetic distance is calculated between the sequences in each set, and isolates are clustered together at 10 single-nucleotide polymorphisms. Phylogenetic trees are inferred from the non-redundant sequences and the clustered isolates are added back. The method is accurate at grouping outbreak strains together, while discriminating them from non-outbreak strains. The pipeline is applied in Evergreen Online, which processes publicly available sequencing data from foodborne bacterial pathogens on a daily basis, updating phylogenetic trees as needed.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Johanne Ahrenfeldt
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jose Luis Bellod Cisneros
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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19
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Johnsen CH, Clausen PTLC, Aarestrup FM, Lund O. Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites. Front Microbiol 2019; 10:2464. [PMID: 31736907 PMCID: PMC6834686 DOI: 10.3389/fmicb.2019.02464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 10/15/2019] [Indexed: 11/21/2022] Open
Abstract
Resistance in Mycobacterium tuberculosis is a major obstacle for effective treatment of tuberculosis. Multiple studies have shown promising results for predicting drug resistance in M. tuberculosis based on whole genome sequencing (WGS) data, however, these tools are often limited to this single species. We have previously developed a common platform for resistance prediction in multiple species. This platform detects acquired resistance genes (ResFinder) and species-specific chromosomal mutations (PointFinder) associated with resistance, all based on WGS data. In this study, we present a new version of PointFinder together with an updated M. tuberculosis database. PointFinder now includes predictions based on insertions and deletions, and it explicitly reports frameshift mutations and premature stop codons. We found that premature stop codons in four resistance-associated genes (katG, ethA, pncA, and gidB) were over-represented in resistant strains, and we saw an increased prediction performance when including premature stop codons in these genes as resistance markers. Different M. tuberculosis resistance prediction tools vary in performance mostly due to the mutation library used. We found that a well-established mutation library included non-predictive linage markers, and through forward feature selection we eliminated those from the mutation library. Compared to other similar web-based tools, PointFinder performs equally good. The advantages of PointFinder is that together with ResFinder it serves as a common web-based and downloadable platform for resistance detection in multiple species. It is easy to use for clinicians and already widely used in the research community.
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Affiliation(s)
- Camilla Hundahl Johnsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Philip T L C Clausen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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20
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Ingham AC, Kielsen K, Cilieborg MS, Lund O, Holmes S, Aarestrup FM, Müller KG, Pamp SJ. Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation. Microbiome 2019; 7:131. [PMID: 31519210 PMCID: PMC6744702 DOI: 10.1186/s40168-019-0745-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/29/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including cancers such as acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g., at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. RESULTS In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) high concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state. CONCLUSIONS We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution, and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine.
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Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Kielsen
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Malene Skovsted Cilieborg
- Comparative Pediatrics and Nutrition, Department of Clinical Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, USA
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Gottlob Müller
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.
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21
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Sonda TB, Horumpende PG, Kumburu HH, van Zwetselaar M, Mshana SE, Alifrangis M, Lund O, Aarestrup FM, Chilongola JO, Mmbaga BT, Kibiki GS. Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme. PLoS One 2019; 14:e0220261. [PMID: 31381579 PMCID: PMC6681960 DOI: 10.1371/journal.pone.0220261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Excessive use of antibiotics, especially watch group antibiotics such as ceftriaxone leads to emergence and spread of antimicrobial resistance (AMR). In low and middle-income countries (LMICs), antibiotics are overused but data on consumption is scarcely available. We aimed at determining the extent and predictors of ceftriaxone use in a tertiary care university teaching hospital in Kilimanjaro, Tanzania. A hospital-based cross-sectional study was conducted from August 2013 through August 2015. Patients admitted in the medical, surgical wards and their respective intensive care units, receiving antimicrobials and other medications for various ailments were enrolled. Socio-demographic and clinical data were recorded in a structured questionnaire from patients' files and logistic regression was performed to determine the predictors for ceftriaxone use. Out of the 630 patients included in this study, 322 (51.1%) patients were on ceftriaxone during their time of hospitalization. Twenty-two patients out of 320 (6.9%) had been on ceftriaxone treatment without evidence of infection. Ceftriaxone use for surgical prophylaxis was 44 (40.7%), of which 32 (72.7%) and 9 (20.5%) received ceftriaxone prophylaxis before and after surgery, respectively. Three (6.8%) received ceftriaxone prophylaxis during surgery. Predicting factors for that the health facility administered ceftriaxone were identified as history of any medication use before referral to hospital [OR = 3.4, 95% CI (1.0-11.4), p = 0.047], bacterial infection [OR = 18.0, 95% CI (1.4-225.7, p = 0.025)], surgical ward [OR = 2.9, 95% CI (0.9-9.4), p = 0.078] and medical wards [OR = 5.0, 95% CI (0.9-28.3), p = 0.070]. Overall, a high ceftriaxone use at KCMC hospital was observed. Antimicrobial stewardship programs are highly needed to monitor and regulate hospital antimicrobial consumption, which in turn could help in halting the rising crisis of antimicrobial resistance.
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Affiliation(s)
- Tolbert B. Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Pius G. Horumpende
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Lugalo General Military Hospital, Military College of Medical Sciences, Dar es Salaam, Tanzania
| | - Happiness H. Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Michael Alifrangis
- Centre for Medical Parasitology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark; Copenhagen, Denmark
| | - Frank M. Aarestrup
- Centre for Genomic Epidemiology, Technical University of Denmark; Copenhagen, Denmark
| | - Jaffu O. Chilongola
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
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22
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Asplund M, Kjartansdóttir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ. Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. Clin Microbiol Infect 2019; 25:1277-1285. [PMID: 31059795 DOI: 10.1016/j.cmi.2019.04.028] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Sample preparation for high-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences. METHODS A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed using different protocols. In total, 712 sequencing libraries were investigated for viral sequence contamination. RESULTS Among sequences showing similarity to viruses, 493 were significantly associated with the use of laboratory components. Each of these viral sequences had sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components. CONCLUSIONS We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover, we show that detection can be problematic due to stochastic appearance and limited non-template controls. Although the exact origin of these viral sequences requires further research, our results support laboratory-component-linked viral sequence contamination of both biological and synthetic origin.
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Affiliation(s)
- M Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - K R Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - H Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J A R Herrera
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - J Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T A Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - R H Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - I B Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S R Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - A Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M L Matey-Hernandez
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - D E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - P V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Sicheritz-Pontén
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - E Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - O Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - S Brunak
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L P Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - A J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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23
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Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun 2019; 10:1124. [PMID: 30850636 PMCID: PMC6408512 DOI: 10.1038/s41467-019-08853-3] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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Affiliation(s)
- Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Njage
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bram van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK
| | - Oksana Lukjancenko
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rolf S Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Josef Korbinian Vogt
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Tina Zuidema
- RIKILT Wageningen University and Research, Wageningen, 6708, The Netherlands
| | - Ana Maria de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, 08100, Malaysia
| | - Heike Schmitt
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | | | | | - Sünje J Pamp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Marion P Koopmans
- Viroscience, Erasmus Medical Center, Rotterdam, 3015, The Netherlands
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
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Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G. The COMPARE Data Hubs. Database (Oxford) 2019; 2019:baz136. [PMID: 31868882 PMCID: PMC6927095 DOI: 10.1093/database/baz136] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022]
Abstract
Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.
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Affiliation(s)
- Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Lukasz D Dynovski
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bálint Á Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ariane Belka
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Jose L B Cisneros
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - George B Haringhuizen
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Camilla Hundahl
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Abdulrahman Hussein
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf S Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | | | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carolina dos S Ribeiro
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Jeffrey E Skiby
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - János M Szalai-Gindl
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Martin C F Thomsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Simone M Cacciò
- European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità (ISS), Rome 00161, Italy
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Annelies Kroneman
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - Frank Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307. [PMID: 30157759 PMCID: PMC6116485 DOI: 10.1186/s12859-018-2336-6] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates. RESULTS The functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory. CONCLUSION With KMA, it was possible map raw reads directly against redundant databases with high accuracy, speed and memory efficiency.
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Affiliation(s)
- Philip T L C Clausen
- Department of Bioinformatics, Technical University of Denmark, 2800, Kgs Lyngby, Denmark. .,Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark.
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ole Lund
- Department of Bioinformatics, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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Thomsen MCF, Hasman H, Westh H, Kaya H, Lund O. RUCS: rapid identification of PCR primers for unique core sequences. Bioinformatics 2018; 33:3917-3921. [PMID: 28968748 PMCID: PMC5860091 DOI: 10.1093/bioinformatics/btx526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/29/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. Results Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. Availability and implementation Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. Contact mcft@cbs.dtu.dk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin Christen Frølund Thomsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
- To whom correspondence should be addressed.
| | - Henrik Hasman
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
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27
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Kibiki GS, Aarestrup FM. Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis 2018; 37:1901-1914. [PMID: 30030694 DOI: 10.1007/s10096-018-3324-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Gibson S Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
| | - Frank M Aarestrup
- DTU-Food, Centre for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
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28
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Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup FM. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother 2018; 72:2764-2768. [PMID: 29091202 PMCID: PMC5890747 DOI: 10.1093/jac/dkx217] [Citation(s) in RCA: 429] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/07/2017] [Indexed: 11/23/2022] Open
Abstract
Background Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Methods Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations. Results were compared with phenotypic antimicrobial susceptibility testing results. Results A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between tested and predicted susceptibility were observed: two C. jejuni isolates with phenotypic fluoroquinolone resistance and two with phenotypic erythromycin resistance and five colistin-susceptible E. coli isolates with a detected pmrB V161G mutation when assembled with Velvet, but not when using SPAdes or when mapping the reads. Conclusions PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
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Affiliation(s)
- Ea Zankari
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.,Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Rosa Allesøe
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Katrine G Joensen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lina M Cavaco
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Aarestrup FM, Kibiki G, Lund O. Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania. Antimicrob Resist Infect Control 2018; 7:72. [PMID: 29977533 PMCID: PMC5992844 DOI: 10.1186/s13756-018-0361-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Background Limited information regarding the clonality of circulating E. coli strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of E. coli isolated from patients in a tertiary care hospital in Tanzania. Methods E. coli isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain E. coli relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance. Results Out of 38 E. coli isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes. On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and p = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and p = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote E. coli immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs. Conclusion There is a high diversity of E. coli isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.
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Affiliation(s)
- Tolbert Sonda
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Happiness Kumburu
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | | | - Gibson Kibiki
- 2Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
| | - Ole Lund
- 5Centre for Biological Sequence Analysis, Technical University of Denmark, Copenhagen, Denmark
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30
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Christensen MK, Lykkegaard E, Lund O, O'Neill LD. Qualitative analysis of MMI raters' scorings of medical school candidates: A matter of taste? Adv Health Sci Educ Theory Pract 2018; 23:289-310. [PMID: 28956195 DOI: 10.1007/s10459-017-9794-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/20/2017] [Indexed: 05/25/2023]
Abstract
Recent years have seen leading medical educationalists repeatedly call for a paradigm shift in the way we view, value and use subjectivity in assessment. The argument is that subjective expert raters generally bring desired quality, not just noise, to performance evaluations. While several reviews document the psychometric qualities of the Multiple Mini-Interview (MMI), we currently lack qualitative studies examining what we can learn from MMI raters' subjectivity. The present qualitative study therefore investigates rater subjectivity or taste in MMI selection interview. Taste (Bourdieu 1984) is a practical sense, which makes it possible at a pre-reflective level to apply 'invisible' or 'tacit' categories of perception for distinguishing between good and bad. The study draws on data from explorative in-depth interviews with 12 purposefully selected MMI raters. We find that MMI raters spontaneously applied subjective criteria-their taste-enabling them to assess the candidates' interpersonal attributes and to predict the candidates' potential. In addition, MMI raters seemed to share a taste for certain qualities in the candidates (e.g. reflectivity, resilience, empathy, contact, alikeness, 'the good colleague'); hence, taste may be the result of an ongoing enculturation in medical education and healthcare systems. This study suggests that taste is an inevitable condition in the assessment of students' performance. The MMI set-up should therefore make room for MMI raters' taste and their connoisseurship, i.e. their ability to taste, to improve the quality of their assessment of medical school candidates.
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Affiliation(s)
| | - Eva Lykkegaard
- Centre for Health Sciences Education, Aarhus University, Aarhus, Denmark
| | - Ole Lund
- Centre for Health Sciences Education, Aarhus University, Aarhus, Denmark
| | - Lotte D O'Neill
- SDU Centre for Teaching and Learning, University of Southern Denmark, Odense, Denmark
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Terkelsen D, Tolstrup J, Johnsen CH, Lund O, Larsen HK, Worning P, Unemo M, Westh H. Multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and intermediate resistance to azithromycin, Denmark, 2017. ACTA ACUST UNITED AC 2018; 22. [PMID: 29067905 PMCID: PMC5710115 DOI: 10.2807/1560-7917.es.2017.22.42.17-00659] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe a multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and azithromycin intermediate resistance in a heterosexual man in Denmark, 2017. Whole genome sequencing of the strain GK124 identified MSLT ST1903, NG-MAST ST1614 and all relevant resistance determinants including similar penA resistance mutations previously described in ceftriaxone-resistant gonococcal strains. Although treatment with ceftriaxone 0.5 g plus azithromycin 2 g was successful, increased awareness of spread of gonococcal strains threatening the recommended dual therapy is crucial.
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Affiliation(s)
- David Terkelsen
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen, Denmark.,These authors contributed equally to the work
| | - Jacob Tolstrup
- These authors contributed equally to the work.,Department of Dermatovenerology, Bispebjerg Hospital, Copenhagen, Denmark
| | | | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Peder Worning
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen, Denmark
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,These authors share last authorship
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,These authors share last authorship
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32
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Nag S, Kofoed PE, Ursing J, Lemvigh CK, Allesøe RL, Rodrigues A, Svendsen CA, Jensen JD, Alifrangis M, Lund O, Aarestrup FM. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots. Malar J 2018; 17:91. [PMID: 29471822 PMCID: PMC5824530 DOI: 10.1186/s12936-018-2232-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria remains a major health burden and genomic research represents one of the necessary approaches for continued progress towards malaria control and elimination. Sample acquisition for this purpose is troublesome, with the majority of malaria-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. METHODS Venous blood samples were collected from malaria patients in Bandim, Guinea-Bissau and leukocyte-depleted using Plasmodipur filters, the enriched parasite sample was spotted on Whatman paper and dried. The samples were stored at ambient temperatures and subsequently used for DNA-extraction. Ratios of parasite:human content of the extracted DNA was assessed by qPCR, and five samples with varying parasitaemia, were sequenced. Sequencing data were used to analyse the sample content, as well as sample coverage and depth as compared to the 3d7 reference genome. RESULTS qPCR revealed that 73% of the 199 samples were applicable for WGS, as defined by a minimum ratio of parasite:human DNA of 2:1. WGS revealed an even distribution of sequence data across the 3d7 reference genome, regardless of parasitaemia. The acquired read depths varied from 16 to 99×, and coverage varied from 87.5 to 98.9% of the 3d7 reference genome. SNP-analysis of six genes, for which amplicon sequencing has been performed previously, confirmed the reliability of the WGS-data. CONCLUSION This study describes a simple filter paper based protocol for sampling P. falciparum from malaria patients for subsequent direct WGS, enabling acquisition of samples in remote settings with no access to electricity.
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Affiliation(s)
- Sidsel Nag
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.
| | - Poul-Erik Kofoed
- Department of Paediatrics, Kolding Hospital, Kolding, Denmark.,Bandim Health Project, Bissau, Guinea-Bissau
| | - Johan Ursing
- Bandim Health Project, Bissau, Guinea-Bissau.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Danderyds Hospital, Danderyd, Sweden
| | | | | | | | - Christina Aaby Svendsen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jacob Dyring Jensen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Alifrangis
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Ole Lund
- DTU Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Aarestrup FM, Kibiki G. Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis 2018; 37:897-906. [PMID: 29464424 PMCID: PMC5917002 DOI: 10.1007/s10096-018-3196-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/18/2018] [Indexed: 12/19/2022]
Abstract
Emergence and spread of extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria, mainly due to CTX-M, is a major global public health problem. Patients infected with ESBL-producing gram-negative bacteria have an increased risk of treatment failure and death. We investigated the prevalence and risk factors for CTX-M gram-negative bacteria isolated from clinical specimens of patients hospitalized at a tertiary care hospital in Kilimanjaro, Tanzania. Isolated gram-negative bacteria from inpatients admitted at Kilimanjaro Christian Medical Centre (KCMC) between August 2013 and August 2015 were fully genome sequenced. The prevalence of ESBL-producing gram-negative bacteria was determined based on the presence of blaCTX-M. The odds ratio (OR) and risk factors for ESBL-producing gram-negative bacteria due to CTX-M were assessed using logistic regression models. The overall CTX-M prevalence (95% CI) was 13.6% (10.1–18.1). Adjusted for other factors, the OR of CTX-M gram-negative bacteria for patients previously hospitalized was 0.26 (0.08–0.88), p = 0.031; the OR for patients currently on antibiotics was 4.02 (1.29–12.58), p = 0.017; the OR for patients currently on ceftriaxone was 0.14 (0.04–0.46), p = 0.001; and the OR for patients with wound infections was 0.24 (0.09–0.61), p = 0.003. The prevalence of ESBL-producing gram-negative bacteria due to CTX-M in this setting is relatively low compared to other previous reports in similar settings. However, to properly stop further spread in the hospital, we recommend setting up a hospital surveillance system that takes full advantage of the available next-generation sequencing facility to routinely screen for all types of bacterial resistance genes.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Happiness Kumburu
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- DTU-Food, Centre for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
| | - Gibson Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
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Kaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Allesøe RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR. SCC mecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data. mSphere 2018; 3:e00612-17. [PMID: 29468193 PMCID: PMC5812897 DOI: 10.1128/msphere.00612-17] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 01/05/2023] Open
Abstract
Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.
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Affiliation(s)
- Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rosa Lundbye Allesøe
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Camilla Koldbæk Lemvigh
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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35
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Engmark M, Jespersen MC, Lomonte B, Lund O, Laustsen AH. High-density peptide microarray exploration of the antibody response in a rabbit immunized with a neurotoxic venom fraction. Toxicon 2017; 138:151-158. [PMID: 28867663 DOI: 10.1016/j.toxicon.2017.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022]
Abstract
Polyvalent snakebite antivenoms derive their therapeutic success from the ability of their antibodies to neutralize venom toxins across multiple snake species. This ability results from a production process involving immunization of large mammals with a broad suite of toxins present in venoms. As a result of immunization with this wide range of toxins, many polyvalent antivenoms have a high degree of cross-reactivity to similar toxins in other snake venoms - a cross-reactivity which cannot easily be deconvoluted. As a proof of concept, we aimed at exploring the opposite scenario by performing a high-throughput evaluation of the extent of cross-reactivity of a polyclonal mixture of antibodies that was raised against only a single snake venom fraction. For this purpose, a venom fraction containing short neurotoxin 1 (SN-1; Uniprot accession number P01416, three-finger toxin (3FTx) family), which is the medically most important toxin from the notorious black mamba (Dendroaspis polylepis), was employed. Following immunization of a rabbit, a specific polyclonal antibody response was confirmed by ELISA and immunodiffusion. Subsequently, these antibodies were investigated by high-density peptide microarray to reveal linear elements of recognized epitopes across 742 3FTxs and 10 dendrotoxins. This exploratory study demonstrates in a single immunized animal that cross-reactivity between toxins of high similarity may be difficult to obtain when immunizing with a single 3FTx containing venom fraction. Additionally, this study explored the influence of employing different lengths of peptides in high-density peptide microarray experiments for identification of toxin epitopes. Using 8-mer, 12-mer, and 15-mer peptides, a single linear epitope element was identified in SN-1 with high precision.
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Affiliation(s)
- Mikael Engmark
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Martin C Jespersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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36
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Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 2017; 548:87-91. [PMID: 28746312 DOI: 10.1038/nature23264] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/04/2017] [Indexed: 12/17/2022]
Abstract
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
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Affiliation(s)
- Lasse Maretty
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jacob Malte Jensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jonas Andreas Sibbesen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Siyang Liu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.,BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Palle Villesen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Kirstine Belling
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Christian Theil Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jose M G Izarzugaza
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Marie Grosjean
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Grove
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Thomas D Als
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shujia Huang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Ruiqi Xu
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Weijian Ye
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Junhua Rao
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jihua Sun
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Chen Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Johan van Beusekom
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Espeseth
- Department of Psychology, University of Oslo, 0317 Oslo, Norway.,NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Esben Flindt
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rune M Friborg
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Anders E Halager
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Stephanie Le Hellard
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Dr E. Martens Research Group of Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5021, Norway
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Francesco Lescai
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shengting Li
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Ole Lund
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Peter Løngren
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Maria Luisa Matey-Hernandez
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ole Mors
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Christian N S Pedersen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Patrick Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Ali Syed
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - David Westergaard
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Rachita Yadav
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ning Li
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Krogh
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark.,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, 2000 Frederiksberg, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ramneek Gupta
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Søren Besenbacher
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Anders D Børglum
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Jun Wang
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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37
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Engmark M, Lomonte B, Gutiérrez JM, Laustsen AH, De Masi F, Andersen MR, Lund O. Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping. PLoS Negl Trop Dis 2017; 11:e0005768. [PMID: 28708892 PMCID: PMC5529020 DOI: 10.1371/journal.pntd.0005768] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/26/2017] [Accepted: 07/03/2017] [Indexed: 11/22/2022] Open
Abstract
Snakebite antivenom is a 120 years old invention based on polyclonal mixtures of antibodies purified from the blood of hyper-immunized animals. Knowledge on antibody recognition sites (epitopes) on snake venom proteins is limited, but may be used to provide molecular level explanations for antivenom cross-reactivity. In turn, this may help guide antivenom development by elucidating immunological biases in existing antivenoms. In this study, we have identified and characterized linear elements of B-cell epitopes from 870 pit viper venom protein sequences by employing a high-throughput methodology based on custom designed high-density peptide microarrays. By combining data on antibody-peptide interactions with multiple sequence alignments of homologous toxin sequences and protein modelling, we have determined linear elements of antibody binding sites for snake venom metalloproteases (SVMPs), phospholipases A2s (PLA2s), and snake venom serine proteases (SVSPs). The studied antivenom antibodies were found to recognize linear elements in each of the three enzymatic toxin families. In contrast to a similar study of elapid (non-enzymatic) neurotoxins, these enzymatic toxins were generally not recognized at the catalytic active site responsible for toxicity, but instead at other sites, of which some are known for allosteric inhibition or for interaction with the tissue target. Antibody recognition was found to be preserved for several minor variations in the protein sequences, although the antibody-toxin interactions could often be eliminated completely by substitution of a single residue. This finding is likely to have large implications for the cross-reactivity of the antivenom and indicate that multiple different antibodies are likely to be needed for targeting an entire group of toxins in these recognized sites. Although snakebite antivenom is a 120-year-old invention, saving lives and limbs of thousands of snakebite victims every year, little is known about the mechanisms and molecular interactions of how antivenoms neutralize snake toxins. Antivenoms are produced by immunizing large animals with cocktails of snake venoms resulting in antibodies recognizing toxic as well as non-toxic venom proteins to variable degrees. As a result, high doses of antivenom are needed for treating a snakebite victim, causing more severe adverse reactions due to a high burden of heterologous antivenom proteins. For the first time, we have characterized the antibody recognition sites on hundreds of pit viper toxins using high-throughput peptide microarray technology and an antivenom specific for three pit vipers inflicting a high number of bites in Central America. Most pit viper toxins are enzymes known to have a catalytic site important for toxicity. However, our results suggest that the employed antivenom generally does not target such sites, but instead inhibits toxicity by binding to alternative sites, possibly causing conformational shifts in the toxin structures or interference with toxin-target recognition. The identification of these toxin-specific recognition sites may explain why the antivenom is effective against certain snakebites from pit vipers whose venoms are not part of the immunization mixture.
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Affiliation(s)
- Mikael Engmark
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- * E-mail:
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Federico De Masi
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
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Joensen KG, Engsbro ALØ, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM. Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease. Eur J Clin Microbiol Infect Dis 2017; 36:1339-1342. [DOI: 10.1007/s10096-017-2993-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T. Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS One 2017; 12:e0179778. [PMID: 28604817 PMCID: PMC5467888 DOI: 10.1371/journal.pone.0179778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Nag S, Dalgaard MD, Kofoed PE, Ursing J, Crespo M, Andersen LO, Aarestrup FM, Lund O, Alifrangis M. High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology. Sci Rep 2017; 7:2398. [PMID: 28546554 PMCID: PMC5445084 DOI: 10.1038/s41598-017-02724-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/18/2017] [Indexed: 01/10/2023] Open
Abstract
Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8-100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.
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Affiliation(s)
- Sidsel Nag
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen, 1356, Copenhagen K, Denmark.
- Department of Infectious Diseases, Copenhagen University Hospital, 2200, Copenhagen N, Denmark.
| | - Marlene D Dalgaard
- Department of Systems Biology, Technical University of Denmark, Kemitorvet Building 208, 2800, Kgs. Lyngby, Denmark
| | - Poul-Erik Kofoed
- Department of Paediatrics, Kolding Hospital, University of Southern Denmark, 6000, Kolding, Denmark
- Bandim Health Project, Bissau, Guinea-Bissau
| | - Johan Ursing
- Bandim Health Project, Bissau, Guinea-Bissau
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marina Crespo
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen, 1356, Copenhagen K, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, 2200, Copenhagen N, Denmark
| | - Lee O'Brien Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | | | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Kemitorvet Building 208, 2800, Kgs. Lyngby, Denmark
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen, 1356, Copenhagen K, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, 2200, Copenhagen N, Denmark
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Scharf L, Tauriainen J, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, Lund O, Reyes-Terán G, Hecht FM, Deeks SG, Betts MR, Buggert M, Karlsson AC. HIV-induced modifications of TIGIT expression impair CD8 T cell polyfunctionality. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.78.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
HIV-specific CD8 T cells display an accumulation of inhibitory receptors that are associated with poor effector functions. Expression of the inhibitory receptor, T cell immunoglobulin and ITIM domain (TIGIT), its co-stimulatory receptor CD226 and their ligand poliovirus receptor (PVR) are altered during chronic viral infections and cancer. Here we show that the TIGIT/CD226/PVR axis is dysregulated during HIV infection and linked to poor polyfunctional activity, increased expression of inhibitory receptors and an altered effector transcriptional programming. We report that TIGIT expression is increased on CD8 T cells in untreated HIV infection. Additionally, a longitudinal increase in TIGIT expression was demonstrated despite early initiation of antiretroviral therapy during acute HIV infection. The HIV-specific TIGIT+ CD8 T cells co-expressed PD-1, CD160 and 2B4 and had an inverse expression profile of the T-box transcription factors T-bet and Eomes. The HIV-specific CD8 T cells were almost exclusively TIGIThiCD226neg/dim and the frequency of TIGIThi cells was inversely correlated with polyfunctionality. Furthermore, the TIGIT/CD226 ligand PVR was increased on CD4 T cells, especially T follicular helper (Tfh) cells in HIV-infected lymph nodes. These results demonstrate a preferential skewing of the TIGIT/CD226 axis towards the inhibitory receptor TIGIT on CD8 T cells during HIV-1 infection, which is linked to severe T cell dysfunction. The findings highlight the importance of the TIGIT/CD226/PVR axis as an immune checkpoint barrier that potentially could hinder future therapeutic “cure” strategies that require potent HIV-specific CD8 T cells and/or the clearance of HIV-1 infected Tfh cells.
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Affiliation(s)
| | | | | | | | | | | | - Ole Lund
- 2Technical University of Denmark, Denmark
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Kumburu HH, Sonda T, Mmbaga BT, Alifrangis M, Lund O, Kibiki G, Aarestrup FM. Patterns of infections, aetiological agents and antimicrobial resistance at a tertiary care hospital in northern Tanzania. Trop Med Int Health 2017; 22:454-464. [PMID: 28072493 DOI: 10.1111/tmi.12836] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To determine the causative agents of infections and their antimicrobial susceptibility at a tertiary care hospital in Moshi, Tanzania, to guide optimal treatment. METHODS A total of 590 specimens (stool (56), sputum (122), blood (126) and wound swabs (286)) were collected from 575 patients admitted in the medical and surgical departments. The bacterial species were determined by conventional methods, and disc diffusion was used to determine the antimicrobial susceptibility pattern of the bacterial isolates. RESULTS A total of 249 (42.2%) specimens were culture-positive yielding a total of 377 isolates. A wide range of bacteria was isolated, the most predominant being Gram-negative bacteria: Proteus spp. (n = 48, 12.7%), Escherichia coli (n = 44, 11.7%), Pseudomonas spp. (n = 40, 10.6%) and Klebsiella spp (n = 38, 10.1%). Wound infections were characterised by multiple isolates (n = 293, 77.7%), with the most frequent being Proteus spp. (n = 44, 15%), Pseudomonas (n = 37, 12.6%), Staphylococcus (n = 29, 9.9%) and Klebsiella spp. (n = 28, 9.6%). All Staphylococcus aureus tested were resistant to penicillin (n = 22, 100%) and susceptible to vancomycin. Significant resistance to cephalosporins such as cefazolin (n = 62, 72.9%), ceftriaxone (n = 44, 51.8%) and ceftazidime (n = 40, 37.4%) was observed in Gram-negative bacteria, as well as resistance to cefoxitin (n = 6, 27.3%) in S. aureus. CONCLUSION The study has revealed a wide range of causative agents, with an alarming rate of resistance to the commonly used antimicrobial agents. Furthermore, the bacterial spectrum differs from those often observed in high-income countries. This highlights the imperative of regular generation of data on aetiological agents and their antimicrobial susceptibility patterns especially in infectious disease endemic settings. The key steps would be to ensure the diagnostic capacity at a sufficient number of sites and implement structures to routinely exchange, compare, analyse and report data. Sentinel sites (hospitals) across the country (and region) should report on a representative subset of bacterial species and their susceptibility to drugs at least annually. A central organising body should collate the data and report to relevant national and international stakeholders.
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Affiliation(s)
- Happiness Houka Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina Theophil Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Centre for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Copenhagen, Denmark
| | - Gibson Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
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Hansen CS, Østerbye T, Marcatili P, Lund O, Buus S, Nielsen M. ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping. PLoS One 2017; 12:e0168453. [PMID: 28095436 PMCID: PMC5240915 DOI: 10.1371/journal.pone.0168453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes. Using exhaustive amino acid substitution analysis of peptides originating from target antigens, these microarrays can be used to address the specificity of polyclonal antibodies raised against such antigens containing hundreds of epitopes. However, the interpretation of the data provided in such large-scale screenings is far from trivial and in most cases it requires advanced computational and statistical skills. Here, we present an online application for automated identification of linear B cell epitopes, allowing the non-expert user to analyse peptide microarray data. The application takes as input quantitative peptide data of fully or partially substituted overlapping peptides from a given antigen sequence and identifies epitope residues (residues that are significantly affected by substitutions) and visualize the selectivity towards each residue by sequence logo plots. Demonstrating utility, the application was used to identify and address the antibody specificity of 18 linear epitope regions in Human Serum Albumin (HSA), using peptide microarray data consisting of fully substituted peptides spanning the entire sequence of HSA and incubated with polyclonal rabbit anti-HSA (and mouse anti-rabbit-Cy3). The application is made available at: www.cbs.dtu.dk/services/ArrayPitope.
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Affiliation(s)
- Christian Skjødt Hansen
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Thomas Østerbye
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
- * E-mail:
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Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, Lund O, Reyes-Terán G, Hecht FM, Deeks SG, Betts MR, Buggert M, Karlsson AC. Perturbed CD8 + T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals. Sci Rep 2017; 7:40354. [PMID: 28084312 PMCID: PMC5233961 DOI: 10.1038/srep40354] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/05/2016] [Indexed: 12/05/2022] Open
Abstract
HIV-specific CD8+ T cells demonstrate an exhausted phenotype associated with increased expression of inhibitory receptors, decreased functional capacity, and a skewed transcriptional profile, which are only partially restored by antiretroviral treatment (ART). Expression levels of the inhibitory receptor, T cell immunoglobulin and ITIM domain (TIGIT), the co-stimulatory receptor CD226 and their ligand PVR are altered in viral infections and cancer. However, the extent to which the TIGIT/CD226/PVR-axis is affected by HIV-infection has not been characterized. Here, we report that TIGIT expression increased over time despite early initiation of ART. HIV-specific CD8+ T cells were almost exclusively TIGIT+, had an inverse expression of the transcription factors T-bet and Eomes and co-expressed PD-1, CD160 and 2B4. HIV-specific TIGIThi cells were negatively correlated with polyfunctionality and displayed a diminished expression of CD226. Furthermore, expression of PVR was increased on CD4+ T cells, especially T follicular helper (Tfh) cells, in HIV-infected lymph nodes. These results depict a skewing of the TIGIT/CD226 axis from CD226 co-stimulation towards TIGIT-mediated inhibition of CD8+ T cells, despite early ART. These findings highlight the importance of the TIGIT/CD226/PVR axis as an immune checkpoint barrier that could hinder future “cure” strategies requiring potent HIV-specific CD8+ T cells.
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Affiliation(s)
- Johanna Tauriainen
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lydia Scharf
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Juliet Frederiksen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ali Naji
- Division of Transplantation, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Gustavo Reyes-Terán
- Centre for Infectious Diseases Research, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Frederick M Hecht
- Department of Medicine, University of California, San Francisco Positive Health Program, San Francisco General Hospital, San Francisco, CA, United States of America
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco Positive Health Program, San Francisco General Hospital, San Francisco, CA, United States of America
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Annika C Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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Berg ES, Wester AL, Ahrenfeldt J, Mo SS, Slettemeås JS, Steinbakk M, Samuelsen Ø, Grude N, Simonsen GS, Løhr IH, Jørgensen SB, Tofteland S, Lund O, Dahle UR, Sunde M. Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/bla CMY-2 resistance plasmids. Clin Microbiol Infect 2017; 23:407.e9-407.e15. [PMID: 28082191 DOI: 10.1016/j.cmi.2016.12.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/11/2016] [Accepted: 12/28/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVES In 2012 and 2014 the Norwegian monitoring programme for antimicrobial resistance in the veterinary and food production sectors (NORM-VET) showed that 124 of a total of 406 samples (31%) of Norwegian retail chicken meat were contaminated with extended-spectrum cephalosporin-resistant Escherichia coli. The aim of this study was to compare selected cephalosporin-resistant E. coli from humans and poultry to determine their genetic relatedness based on whole genome sequencing (WGS). METHODS Escherichia coli representing three prevalent cephalosporin-resistant multi-locus sequence types (STs) isolated from poultry (n=17) were selected from the NORM-VET strain collections. All strains carried an IncK plasmid with a blaCMY-2 gene. Clinical E. coli isolates (n=284) with AmpC-mediated resistance were collected at Norwegian microbiology laboratories from 2010 to 2014. PCR screening showed that 29 of the clinical isolates harboured both IncK and blaCMY-2. All IncK/blaCMY-2-positive isolates were analysed with WGS-based bioinformatics tools. RESULTS Analysis of single nucleotide polymorphisms (SNP) in 2.5 Mbp of shared genome sequences showed close relationship, with fewer than 15 SNP differences between five clinical isolates from urinary tract infections (UTIs) and the ST38 isolates from poultry. Furthermore, all of the 29 clinical isolates harboured IncK/blaCMY-2 plasmid variants highly similar to the IncK/blaCMY-2 plasmid present in the poultry isolates. CONCLUSIONS Our results provide support for the hypothesis that clonal transfer of cephalosporin-resistant E. coli from chicken meat to humans may occur, and may cause difficult-to-treat infections. Furthermore, these E. coli can be a source of AmpC-resistance plasmids for opportunistic pathogens in the human microbiota.
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Affiliation(s)
- E S Berg
- Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.
| | - A L Wester
- Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - J Ahrenfeldt
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - S S Mo
- Department of Diagnostic Services, Norwegian Veterinary Institute, Oslo, Norway
| | - J S Slettemeås
- Department of Diagnostic Services, Norwegian Veterinary Institute, Oslo, Norway
| | - M Steinbakk
- Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group for Microbial Pharmacology and Population Biology, Department of Pharmacy, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - N Grude
- Department of Clinical Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - G S Simonsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group for Host-Microbe Interactions, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - I H Løhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - S B Jørgensen
- Department of Clinical Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - S Tofteland
- Department of Clinical Microbiology, Sørlandet Hospital, Kristiansand, Norway
| | - O Lund
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - U R Dahle
- Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - M Sunde
- Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Diagnostic Services, Norwegian Veterinary Institute, Oslo, Norway
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Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O. Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. BMC Genomics 2017; 18:19. [PMID: 28056767 PMCID: PMC5217230 DOI: 10.1186/s12864-016-3407-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 12/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods. RESULTS Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator strain grow in the lab for 8 consecutive days, each day splitting the culture in two while also collecting samples for sequencing. The result is a data set consisting of 101 whole genome sequences with known phylogenetic relationship. Among the sequenced samples 51 correspond to internal nodes in the phylogeny because they are ancestral, while the remaining 50 correspond to leaves. We also used the newly created data set to compare three different online available methods that infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and REALPHY. One complication when comparing the output of these methods with the known phylogeny is that phylogenetic methods typically build trees where all observed sequences are placed as leafs, even though some of them are in fact ancestral. We therefore devised a method for post processing the inferred trees by collapsing short branches (thus relocating some leafs to internal nodes), and also present two new measures of tree similarity that takes into account the identity of both internal and leaf nodes. CONCLUSIONS Based on this analysis we find that, among the investigated methods, CSI Phylogeny had the best performance, correctly identifying 73% of all branches in the tree and 71% of all clades. We have made all data from this experiment (raw sequencing reads, consensus whole-genome sequences, as well as descriptions of the known phylogeny in a variety of formats) publicly available, with the hope that other groups may find this data useful for benchmarking and exploring the performance of epidemiological methods. All data is freely available at: https://cge.cbs.dtu.dk/services/evolution_data.php .
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Affiliation(s)
- Johanne Ahrenfeldt
- Center for Biological Sequence Analysis, DTU Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Carina Skaarup
- Center for Biological Sequence Analysis, DTU Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Henrik Hasman
- Department of Microbiology and Infection Control, Statens Serum Institute, Copenhagen, Denmark
| | - Anders Gorm Pedersen
- Center for Biological Sequence Analysis, DTU Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, DTU FOOD, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, DTU Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
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Coppola M, van Meijgaarden KE, Franken KLMC, Commandeur S, Dolganov G, Kramnik I, Schoolnik GK, Comas I, Lund O, Prins C, van den Eeden SJF, Korsvold GE, Oftung F, Geluk A, Ottenhoff THM. New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles. Sci Rep 2016; 6:37793. [PMID: 27892960 PMCID: PMC5125271 DOI: 10.1038/srep37793] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/03/2016] [Indexed: 12/16/2022] Open
Abstract
New strategies are needed to develop better tools to control TB, including identification of novel antigens for vaccination. Such Mtb antigens must be expressed during Mtb infection in the major target organ, the lung, and must be capable of eliciting human immune responses. Using genome-wide transcriptomics of Mtb infected lungs we developed data sets and methods to identify IVE-TB (in-vivo expressed Mtb) antigens expressed in the lung. Quantitative expression analysis of 2,068 Mtb genes from the predicted first operons identified the most upregulated IVE-TB genes during in-vivo pulmonary infection. By further analysing high-level conservation among whole-genome sequenced Mtb-complex strains (n = 219) and algorithms predicting HLA-class-Ia and II presented epitopes, we selected the most promising IVE-TB candidate antigens. Several of these were recognized by T-cells from in-vitro Mtb-PPD and ESAT6/CFP10-positive donors by proliferation and multi-cytokine production. This was validated in an independent cohort of latently Mtb-infected individuals. Significant T-cell responses were observed in the absence of IFN-γ-production. Collectively, the results underscore the power of our novel antigen discovery approach in identifying Mtb antigens, including those that induce unconventional T-cell responses, which may provide important novel tools for TB vaccination and biomarker profiling. Our generic approach is applicable to other infectious diseases.
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Affiliation(s)
- Mariateresa Coppola
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Susanna Commandeur
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregory Dolganov
- Department Microbiology Immunology, Stanford Univ. School of Medicine, Stanford, USA
| | - Igor Kramnik
- Department Immunology Infectious Diseases, Harvard School of Public Health, Boston, USA
| | - Gary K Schoolnik
- Department Microbiology Immunology, Stanford Univ. School of Medicine, Stanford, USA
| | - Inaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain.,CIBER in Epidemiology and Public Health, Madrid, Spain
| | - Ole Lund
- Dept. Systems Biology, Technical Univ., Denmark
| | - Corine Prins
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan J F van den Eeden
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Gro E Korsvold
- Department of Infectious Disease Immunology, Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Fredrik Oftung
- Department of Infectious Disease Immunology, Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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48
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Engmark M, Andersen MR, Laustsen AH, Patel J, Sullivan E, de Masi F, Hansen CS, Kringelum JV, Lomonte B, Gutiérrez JM, Lund O. High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays. Sci Rep 2016; 6:36629. [PMID: 27824133 PMCID: PMC5100549 DOI: 10.1038/srep36629] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
Snakebite envenoming is a serious condition requiring medical attention and administration of antivenom. Current antivenoms are antibody preparations obtained from the plasma of animals immunised with whole venom(s) and contain antibodies against snake venom toxins, but also against other antigens. In order to better understand the molecular interactions between antivenom antibodies and epitopes on snake venom toxins, a high-throughput immuno-profiling study on all manually curated toxins from Dendroaspis species and selected African Naja species was performed based on custom-made high-density peptide microarrays displaying linear toxin fragments. By detection of binding for three different antivenoms and performing an alanine scan, linear elements of epitopes and the positions important for binding were identified. A strong tendency of antivenom antibodies recognizing and binding to epitopes at the functional sites of toxins was observed. With these results, high-density peptide microarray technology is for the first time introduced in the field of toxinology and molecular details of the evolution of antibody-toxin interactions based on molecular recognition of distinctive toxic motifs are elucidated.
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Affiliation(s)
- Mikael Engmark
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark.,Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark
| | - Mikael R Andersen
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark
| | - Andreas H Laustsen
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark.,University of Copenhagen, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Copenhagen East, 2100, Denmark
| | - Jigar Patel
- Roche NimbleGen, Madison, Wisconsin 53719, USA
| | | | - Federico de Masi
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Christian S Hansen
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Jens V Kringelum
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Ole Lund
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
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49
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Sun H, Y.K. Yue P, Wang SR, Huo L, Zhao Y, Xie S, V. Kringelum J, Lund O, Taboureau O, Zhou J, N. S. Wong R, Fang WS. Synthesis and Biological Evaluations of Cytotoxic and Antiangiogenic Triterpenoids-Jacaranone Conjugates. Med Chem 2016; 12:775-785. [DOI: 10.2174/1573406412666160502153930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 03/29/2016] [Accepted: 04/27/2016] [Indexed: 11/22/2022]
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50
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Jurtz VI, Villarroel J, Lund O, Voldby Larsen M, Nielsen M. MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLoS One 2016; 11:e0163111. [PMID: 27684958 PMCID: PMC5042410 DOI: 10.1371/journal.pone.0163111] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/04/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are the most abundant biological entity on the planet, but at the same time do not account for much of the genetic material isolated from most environments due to their small genome sizes. They also show great genetic diversity and mosaic genomes making it challenging to analyze and understand them. Here we present MetaPhinder, a method to identify assembled genomic fragments (i.e.contigs) of phage origin in metagenomic data sets. The method is based on a comparison to a database of whole genome bacteriophage sequences, integrating hits to multiple genomes to accomodate for the mosaic genome structure of many bacteriophages. The method is demonstrated to out-perform both BLAST methods based on single hits and methods based on k-mer comparisons. MetaPhinder is available as a web service at the Center for Genomic Epidemiology https://cge.cbs.dtu.dk/services/MetaPhinder/, while the source code can be downloaded from https://bitbucket.org/genomicepidemiology/metaphinder or https://github.com/vanessajurtz/MetaPhinder.
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Affiliation(s)
| | - Julia Villarroel
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mette Voldby Larsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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