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Paganini JA, Kerkvliet JJ, Vader L, Plantinga NL, Meneses R, Corander J, Willems RJL, Arredondo-Alonso S, Schürch AC. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microb Genom 2024; 10:001193. [PMID: 38376388 PMCID: PMC10926690 DOI: 10.1099/mgen.0.001193] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-based tool that bins plasmid-predicted contigs into distinct plasmid predictions. Gplas2 is more effective at recovering plasmids with large sequencing coverage variations and can be combined with the output of any binary classifier. The combination of plasmidEC with gplas2 showed a high completeness (median=0.818) and F1-Score (median=0.812) when reconstructing ARG plasmids and exceeded the binning capacity of the reference-based method MOB-suite. In the absence of long-read data, our method offers an excellent alternative to reconstruct ARG plasmids in E. coli.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jesse J. Kerkvliet
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lisa Vader
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Kerkvliet JJ, Bossers A, Kers JG, Meneses R, Willems R, Schürch AC. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements. PeerJ 2024; 12:e16695. [PMID: 38188174 PMCID: PMC10771768 DOI: 10.7717/peerj.16695] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.
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Affiliation(s)
- Jesse J. Kerkvliet
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Alex Bossers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
- Wageningen University, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jannigje G. Kers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Rob Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
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Boralli CMDS, Paganini JA, Meneses RS, Mata CPSMD, Leite EMM, Schürch AC, Paganelli FL, Willems RJL, Camargo ILBC. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone. Antibiotics (Basel) 2023; 12:antibiotics12050926. [PMID: 37237829 DOI: 10.3390/antibiotics12050926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.
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Affiliation(s)
- Camila Maria Dos Santos Boralli
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | | | - Rodrigo Silva Meneses
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | | | | | - Anita C Schürch
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Fernanda L Paganelli
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ilana Lopes Baratella Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
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Arredondo-Alonso S, Pöntinen AK, Cléon F, Gladstone RA, Schürch AC, Johnsen PJ, Samuelsen Ø, Corander J. A high-throughput multiplexing and selection strategy to complete bacterial genomes. Gigascience 2021; 10:giab079. [PMID: 34891160 PMCID: PMC8673558 DOI: 10.1093/gigascience/giab079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/14/2021] [Revised: 09/29/2021] [Accepted: 11/12/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. RESULTS Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. CONCLUSIONS The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridgeshire CB10 1RQ, UK
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Anita C Schürch
- Department of Medical Microbiology, UMC Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038, Tromsø, Norway
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridgeshire CB10 1RQ, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, 02130, Espoo, Helsinki, Finland
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Paganini JA, Plantinga NL, Arredondo-Alonso S, Willems RJL, Schürch AC. Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data. Microorganisms 2021; 9:1613. [PMID: 34442692 PMCID: PMC8400445 DOI: 10.3390/microorganisms9081613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/06/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
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Verschuuren TD, van Hout D, Arredondo-Alonso S, Fluit AC, Reuland EA, Top J, Schürch AC, Bosch T, Bonten MJM, Kluytmans JAJW, Willems RJL. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17). J Antimicrob Chemother 2021; 76:901-908. [PMID: 33428729 PMCID: PMC7953314 DOI: 10.1093/jac/dkaa534] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/03/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly. OBJECTIVES To evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community. METHODS WGS was performed on 451 Dutch ESBL-Ec isolates (2014-17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski's proportional similarity index (PSI). RESULTS Nine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P < 0.01). Within ST131, H30Rx (C2) subclade was more prevalent among clinical isolates (55% versus 26%, P < 0.01). The proportion of ESBL gene blaCTX-M-1 was lower in clinical isolates (5% versus 18%, P < 0.01). Czekanowski's PSI confirmed that the differences in ESBL-Ec from community faeces and clinical isolates were limited. CONCLUSIONS Distributions of the 10 most prevalent clones and ESBL genes from ESBL-Ec community gut colonization and extra-intestinal infection overlapped in majority, indicating that isolates from routine clinical practice could be used to monitor ESBL-Ec clones and ESBL genes in the community.
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Affiliation(s)
- T D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - D van Hout
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - S Arredondo-Alonso
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E A Reuland
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Top
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Schürch
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - T Bosch
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M J M Bonten
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - R J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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Arredondo-Alonso S, Top J, Corander J, Willems RJL, Schürch AC. Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genome Med 2021; 13:9. [PMID: 33472670 PMCID: PMC7816424 DOI: 10.1186/s13073-020-00825-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 07/06/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or by Tn1546 transposition between different genomic locations. METHODS We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterization was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination. RESULTS On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant. In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination. CONCLUSIONS In related VRE cases, the dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway.,Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.,Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Helsinki, Finland
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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Arredondo-Alonso S, Bootsma M, Hein Y, Rogers MRC, Corander J, Willems RJL, Schürch AC. gplas: a comprehensive tool for plasmid analysis using short-read graphs. Bioinformatics 2020; 36:3874-3876. [PMID: 32271863 PMCID: PMC7320608 DOI: 10.1093/bioinformatics/btaa233] [Citation(s) in RCA: 16] [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: 11/11/2019] [Revised: 01/27/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
Summary Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data. Availability and implementation Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Martin Bootsma
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care of the UMC Utrecht.,Department of Mathematics, Faculty of Sciences, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Yaïr Hein
- Department of Mathematics, Faculty of Sciences, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Jukka Corander
- Department of Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Saffron Walden CB10 1RQ, UK.,Department of Biostatistics, University of Oslo, 0317 Oslo, Norway.,Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, FI-00014 Helsinki, Finland
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
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10
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Top J, Arredondo-Alonso S, Schürch AC, Puranen S, Pesonen M, Pensar J, Willems RJL, Corander J. Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium. Microb Genom 2020; 6:mgen000488. [PMID: 33253085 PMCID: PMC8116687 DOI: 10.1099/mgen.0.000488] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium. Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Santeri Puranen
- Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
| | - Maiju Pesonen
- Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Present address: Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Johan Pensar
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Present address: Department of Mathematics, University of Oslo, 0316 Oslo, Norway
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
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11
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van den Bunt G, van Pelt W, Hidalgo L, Scharringa J, de Greeff SC, Schürch AC, Mughini-Gras L, Bonten MJM, Fluit AC. Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 31615600 PMCID: PMC6794991 DOI: 10.2807/1560-7917.es.2019.24.41.1800594] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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] [Indexed: 11/24/2022]
Abstract
Background The epidemiology of carriage of extended-spectrum beta-lactamase-producing (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in the general population is unknown. Aim In this observational study, the prevalence and risk factors for intestinal ESBL-E and CPE carriage in the Dutch general population were determined. ESBL-E were characterised. Methods From 2014 to 2016, ca 2,000 residents were invited monthly to complete a questionnaire and provide a faecal sample, which was tested for ESBL-E. The first 1,758 samples were also tested for CPE. Risk factors for ESBL-E carriage were identified by multivariable logistic regression analysis. ESBL-E isolates underwent whole genome sequencing. Results Of 47,957 individuals invited, 4,177 (8.7%) completed the questionnaire and provided a faecal sample. ESBL-E were detected in 186 (4.5%) individuals, resulting in an adjusted prevalence of 5.0% (95% confidence interval (CI):3.4–6.6%). Risk factors were: born outside the Netherlands (odds ratio (OR): 1.99; 95% CI: 1.16−4.54), eating in restaurants > 20 times/year (OR: 1.70; 95% CI: 1.04−2.76), antibiotic use < 6 months ago (OR: 2.05; 95% CI: 1.05−4.03), swimming in sea/ocean < 12 months ago (OR: 1.63; 95% CI: 1.11−2.39), travelling to Africa (OR: 3.03; 95% CI: 1.23−7.46) or Asia (OR: 2.00; 95% CI: 1.02−3.90) < 12 months ago, and not changing kitchen towels daily (OR: 2.19; 95% CI: 1.24−3.87). The last had the largest population attributable risk (PAR) (47.5%). Eighty-four of 189 (44.4%) ESBL-E isolates carried blaCTX-M-15. Escherichia coli isolates belonged to 70 different sequence types (ST)s, of which ST131 (42/178 isolates; 23.6%) was most prevalent. Associations were observed between IncFIA plasmids and ST131 and blaCTX-M-27, and between IncI1 and ST88 and blaCTX-M-1. No CPE were detected. Conclusions The prevalence of ESBL-E carriage in the Netherlands’ community-dwelling population is 5.0%. Identified risk factors were mostly travelling (particularly to Asia and Africa) and kitchen hygiene. CPE were not detected.
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Affiliation(s)
- Gerrita van den Bunt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laura Hidalgo
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Sabine C de Greeff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Lapo Mughini-Gras
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Ad C Fluit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
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12
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van Hout D, Verschuuren TD, Bruijning-Verhagen PCJ, Bosch T, Schürch AC, Willems RJL, Bonten MJM, Kluytmans JAJW. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content. PLoS One 2020; 15:e0227604. [PMID: 31935253 PMCID: PMC6959556 DOI: 10.1371/journal.pone.0227604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 10/28/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec isolates from ECB episodes with different epidemiological characteristics. METHODS A random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG. RESULTS ST73 was most prevalent among the 212 non-ESBL-Ec (N = 26, 12.3%) and ST131 among the 69 ESBL-Ec (N = 30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N = 22, P value < .001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1-6) and 7 (IQR 4-9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < .001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1-8). Median VG scores were 13 (IQR 9-20) and 12 (IQR 8-14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = .002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11-21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 5-13) or hepatic-biliary focus (median 11, IQR 5-18) (P values = .007 and .04, respectively). VG content varied between different E. coli STs. CONCLUSIONS Non-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.
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Affiliation(s)
- Denise van Hout
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- * E-mail:
| | - Tess D. Verschuuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Patricia C. J. Bruijning-Verhagen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thijs Bosch
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Marc J. M. Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Jan A. J. W. Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Microvida Laboratory for Medical Microbiology and Department of Infection Control, Amphia Hospital, Breda, The Netherlands
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13
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Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. Corrigendum: mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2019; 5. [PMID: 30714567 PMCID: PMC6412059 DOI: 10.1099/mgen.0.000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C. Braat
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tess D. Verschuuren
- 2Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- 5Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- 4Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- 3Faculty of Medicine, Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Rob J. L. Willems
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C. Schürch
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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14
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Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2018; 4. [PMID: 30383524 PMCID: PMC6321875 DOI: 10.1099/mgen.0.000224] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [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] [Indexed: 12/13/2022] Open
Abstract
Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E. faecium=0.92, F1-score K. pneumoniae=0.90, F1-score E. coli=0.76), which outperformed other existing plasmid prediction tools using a benchmarking set of isolates. We demonstrated the scalability of our models by accurately predicting the plasmidome of a large collection of 1644 E. faecium isolates and illustrate its applicability by predicting the location of antibiotic-resistance genes in all three species. The SVM classifiers are publicly available as an R package and graphical-user interface called 'mlplasmids'. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.
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Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R C Rogers
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C Braat
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tess D Verschuuren
- 2Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- 3Faculty of Medicine, Department of Biostatistics, University of Oslo, Oslo, Norway.,4Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,5Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rob J L Willems
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C Schürch
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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15
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Arredondo-Alonso S, Willems RJ, van Schaik W, Schürch AC. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microb Genom 2017; 3:e000128. [PMID: 29177087 PMCID: PMC5695206 DOI: 10.1099/mgen.0.000128] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [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: 05/17/2017] [Accepted: 07/18/2017] [Indexed: 01/26/2023] Open
Abstract
To benchmark algorithms for automated plasmid sequence reconstruction from short-read sequencing data, we selected 42 publicly available complete bacterial genome sequences spanning 12 genera, containing 148 plasmids. We predicted plasmids from short-read data with four programs (PlasmidSPAdes, Recycler, cBar and PlasmidFinder) and compared the outcome to the reference sequences. PlasmidSPAdes reconstructs plasmids based on coverage differences in the assembly graph. It reconstructed most of the reference plasmids (recall=0.82), but approximately a quarter of the predicted plasmid contigs were false positives (precision=0.75). PlasmidSPAdes merged 84 % of the predictions from genomes with multiple plasmids into a single bin. Recycler searches the assembly graph for sub-graphs corresponding to circular sequences and correctly predicted small plasmids, but failed with long plasmids (recall=0.12, precision=0.30). cBar, which applies pentamer frequency analysis to detect plasmid-derived contigs, showed a recall and precision of 0.76 and 0.62, respectively. However, cBar categorizes contigs as plasmid-derived and does not bin the different plasmids. PlasmidFinder, which searches for replicons, had the highest precision (1.0), but was restricted by the contents of its database and the contig length obtained from de novo assembly (recall=0.36). PlasmidSPAdes and Recycler detected putative small plasmids (<10 kbp), which were also predicted as plasmids by cBar, but were absent in the original assembly. This study shows that it is possible to automatically predict small plasmids. Prediction of large plasmids (>50 kbp) containing repeated sequences remains challenging and limits the high-throughput analysis of plasmids from short-read whole-genome sequencing data.
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Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Rob J Willems
- 1Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Willem van Schaik
- 1Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands.,2Institute of Microbiology and Infection, University of Birmingham, Birmingham, England, UK
| | - Anita C Schürch
- 1Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
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16
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Schürch AC, van Schaik W. Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance. Ann N Y Acad Sci 2017; 1388:108-120. [PMID: 28134443 DOI: 10.1111/nyas.13310] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [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: 09/30/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022]
Abstract
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore). The challenges posed by the analysis of sequencing data sets for antimicrobial-resistance determinants and the solutions offered by modern bioinformatics tools are discussed. Finally, we illustrate the power of WGS-based surveillance of antimicrobial resistance by summarizing recent studies on the spread of the multidrug-resistant opportunistic pathogen Klebsiella pneumoniae and the transferable colistin-resistance gene mcr-1, in which high-throughput WGS analyses played essential roles. The implementation of WGS for surveillance of antibiotic-resistant bacteria is technically feasible and cost effective and provides actionable results with reference to infection control. Consequently, the time has come for laboratories to implement routine genome sequencing as part of their surveillance programs for antibiotic-resistant bacteria.
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Affiliation(s)
- Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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17
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Raj VS, Hundie GB, Schürch AC, Smits SL, Pas SD, Le Pogam S, Janssen HLA, de Knegt RJ, Osterhaus ADME, Najera I, Boucher CA, Haagmans BL. Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients. Sci Rep 2017; 7:4688. [PMID: 28680115 PMCID: PMC5498547 DOI: 10.1038/s41598-017-04931-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Current standard-of-care treatment of chronically infected hepatitis C virus (HCV) patients involves direct-acting antivirals (DAA). However, concerns exist regarding the emergence of drug -resistant variants and subsequent treatment failure. In this study, we investigate potential natural drug-resistance mutations in the NS5B gene of HCV genotype 1b from treatment-naïve patients. Population-based sequencing and 454 deep sequencing of NS5B gene were performed on plasma and liver samples obtained from 18 treatment- naïve patients. The quasispecies distribution in plasma and liver samples showed a remarkable overlap in each patient. Although unique sequences in plasma or liver were observed, in the majority of cases the most dominant sequences were shown to be identical in both compartments. Neither in plasma nor in the liver codon changes were detected at position 282 that cause resistance to nucleos(t)ide analogues. However, in 10 patients the V321I change conferring resistance to nucleos(t)ide NS5B polymerase inhibitors and in 16 patients the C316N/Y/H non-nucleoside inhibitors were found mainly in liver samples. In conclusion, 454-deep sequencing of liver and plasma compartments in treatment naïve patients provides insight into viral quasispecies and the pre-existence of some drug-resistant variants in the liver, which are not necessarily present in plasma.
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Affiliation(s)
- V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Viroclinics Biosciences BV, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sophie Le Pogam
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Gastroenterology, University Health Network, Toronto, Canada
| | - Rob J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Isabel Najera
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Charles A Boucher
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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18
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van Diemen FR, Kruse EM, Hooykaas MJG, Bruggeling CE, Schürch AC, van Ham PM, Imhof SM, Nijhuis M, Wiertz EJHJ, Lebbink RJ. CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections. PLoS Pathog 2016; 12:e1005701. [PMID: 27362483 PMCID: PMC4928872 DOI: 10.1371/journal.ppat.1005701] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
Herpesviruses infect the majority of the human population and can cause significant morbidity and mortality. Herpes simplex virus (HSV) type 1 causes cold sores and herpes simplex keratitis, whereas HSV-2 is responsible for genital herpes. Human cytomegalovirus (HCMV) is the most common viral cause of congenital defects and is responsible for serious disease in immuno-compromised individuals. Epstein-Barr virus (EBV) is associated with infectious mononucleosis and a broad range of malignancies, including Burkitt’s lymphoma, nasopharyngeal carcinoma, Hodgkin’s disease, and post-transplant lymphomas. Herpesviruses persist in their host for life by establishing a latent infection that is interrupted by periodic reactivation events during which replication occurs. Current antiviral drug treatments target the clinical manifestations of this productive stage, but they are ineffective at eliminating these viruses from the infected host. Here, we set out to combat both productive and latent herpesvirus infections by exploiting the CRISPR/Cas9 system to target viral genetic elements important for virus fitness. We show effective abrogation of HCMV and HSV-1 replication by targeting gRNAs to essential viral genes. Simultaneous targeting of HSV-1 with multiple gRNAs completely abolished the production of infectious particles from human cells. Using the same approach, EBV can be almost completely cleared from latently infected EBV-transformed human tumor cells. Our studies indicate that the CRISPR/Cas9 system can be effectively targeted to herpesvirus genomes as a potent prophylactic and therapeutic anti-viral strategy that may be used to impair viral replication and clear latent virus infection. Herpesviruses are large DNA viruses that are carried by almost 100% of the adult human population. Herpesviruses include several important human pathogens, such as herpes simplex viruses (HSV) type 1 and 2 (causing cold sores and genital herpes, respectively), human cytomegalovirus (HCMV; the most common viral cause of congenital defects, and responsible for serious disease in immuno-compromised individuals), and Epstein-Barr virus (EBV; associated with infectious mononucleosis and a wide range of malignancies). Current antiviral drug treatments are not effective in clearing herpesviruses from infected individuals. Therefore, there is a need for alternative strategies to combat these pathogenic viruses and prevent or cure herpesvirus-associated diseases. Here, we have assessed whether a direct attack of herpesvirus genomes within virus-infected cells can inactivate these viruses. For this, we have made use of the recently developed CRISPR/Cas9 genome-engineering system to target and alter specific regions within the genome of these viruses. By targeting sites in the genomes of three different herpesviruses (HSV-1, HCMV, and EBV), we show complete inhibition of viral replication and in some cases even eradication of the viral genomes from infected cells. The findings presented in this study open new avenues for the development of therapeutic strategies to combat pathogenic human herpesviruses using novel genome-engineering technologies.
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Affiliation(s)
- Ferdy R. van Diemen
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth M. Kruse
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Anita C. Schürch
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Petra M. van Ham
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Saskia M. Imhof
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique Nijhuis
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Robert Jan Lebbink
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol 2015; 6:1069. [PMID: 26483782 PMCID: PMC4589665 DOI: 10.3389/fmicb.2015.01069] [Citation(s) in RCA: 21] [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: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
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Smits SL, Schapendonk CME, van Beek J, Vennema H, Schürch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus ADME, Koopmans MP. New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg Infect Dis 2015; 20:1218-22. [PMID: 24964003 PMCID: PMC4073879 DOI: 10.3201/eid2007.140190] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Emerging viral infections can be identified by using a viral metagenomics approach for clinical human material. Diarrhea samples of patients with unexplained gastroenteritis from the Netherlands were analyzed by using viral metagenomics. Novel circular DNA viruses, bufaviruses, and genogroup III picobirnaviruses were identified. These data expand our knowledge of the human virome.
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Siegers JY, van de Bildt MWG, van Elk CE, Schürch AC, Tordo N, Kuiken T, Bodewes R, Osterhaus ADME. Genetic relatedness of dolphin rhabdovirus with fish rhabdoviruses. Emerg Infect Dis 2015; 20:1081-2. [PMID: 24857764 PMCID: PMC4036773 DOI: 10.3201/eid2006.131880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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23
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Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Assembly of viral genomes from metagenomes. Front Microbiol 2014; 5:714. [PMID: 25566226 PMCID: PMC4270193 DOI: 10.3389/fmicb.2014.00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 09/17/2014] [Accepted: 11/30/2014] [Indexed: 11/20/2022] Open
Abstract
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
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Affiliation(s)
- Saskia L. Smits
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
| | - Aritz Ruiz-Gonzalez
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA)Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine HannoverHannover, Germany
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
- Center for Infection Medicine and Zoonoses ResearchHannover, Germany
| | - Anita C. Schürch
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
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Bodewes R, Ruiz-Gonzalez A, Schürch AC, Osterhaus AD, Smits SL. Novel Divergent Rhabdovirus in Feces of Red Fox, Spain. Emerg Infect Dis 2014. [DOI: 10.3201/eid2013.140236] [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: 11/19/2022] Open
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Schürch AC, Schipper D, Bijl MA, Dau J, Beckmen KB, Schapendonk CME, Raj VS, Osterhaus ADME, Haagmans BL, Tryland M, Smits SL. Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. PLoS One 2014; 9:e105227. [PMID: 25140520 PMCID: PMC4139337 DOI: 10.1371/journal.pone.0105227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 04/18/2014] [Accepted: 07/18/2014] [Indexed: 12/16/2022] Open
Abstract
Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.
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Affiliation(s)
- Anita C. Schürch
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Debby Schipper
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maarten A. Bijl
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jim Dau
- Alaska Department of Fish and Game, Kotzebue, Alaska, United States of America
| | - Kimberlee B. Beckmen
- Alaska Department of Fish and Game, Division of Wildlife Conservation, Fairbanks, Alaska, United States of America
| | | | - V. Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- Viroclinics Biosciences, Rotterdam, The Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Morten Tryland
- Research Group for Arctic Infection Biology, Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø, Norway
- Genøk - Centre for Biosafety, Tromsø, Norway
| | - Saskia L. Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- Viroclinics Biosciences, Rotterdam, The Netherlands
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Bodewes R, Lempp C, Schürch AC, Habierski A, Hahn K, Lamers M, von Dörnberg K, Wohlsein P, Drexler JF, Haagmans BL, Smits SL, Baumgärtner W, Osterhaus ADME. Novel divergent nidovirus in a python with pneumonia. J Gen Virol 2014; 95:2480-2485. [PMID: 25063552 DOI: 10.1099/vir.0.068700-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Charlotte Lempp
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Andre Habierski
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Kerstin Hahn
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Mart Lamers
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany.,Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Saskia L Smits
- Viroclinics Biosciences BV, Rotterdam, The Netherlands.,Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Albert D M E Osterhaus
- Artemis Research Institute for Wildlife Health, Utrecht, The Netherlands.,Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.,Viroclinics Biosciences BV, Rotterdam, The Netherlands.,Centre for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
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27
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Smits SL, Zijlstra EE, van Hellemond JJ, Schapendonk CME, Bodewes R, Schürch AC, Haagmans BL, Osterhaus ADME. Novel cyclovirus in human cerebrospinal fluid, Malawi, 2010-2011. Emerg Infect Dis 2014; 19. [PMID: 23968557 PMCID: PMC3810929 DOI: 10.3201/eid1909.130404] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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] [Indexed: 01/29/2023] Open
Abstract
To identify unknown human viruses, we analyzed serum and cerebrospinal fluid samples from patients with unexplained paraplegia from Malawi by using viral metagenomics. A novel cyclovirus species was identified and subsequently found in 15% and 10% of serum and cerebrospinal fluid samples, respectively. These data expand our knowledge of cyclovirus diversity and tropism.
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Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SAFT, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 2013; 13:110. [PMID: 23446317 PMCID: PMC3599118 DOI: 10.1186/1471-2334-13-110] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [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: 01/31/2013] [Accepted: 02/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required. METHODS We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. RESULTS Multiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links. CONCLUSIONS This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
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Affiliation(s)
- Josephine M Bryant
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anita C Schürch
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henk van Deutekom
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jessica L de Beer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Victor de Jager
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Kristin Kremer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Sacha A F T van Hijum
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
- NIZO food research, P.O. Box 206710 BA, Ede, The Netherlands
| | - Roland J Siezen
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Martien Borgdorff
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dick van Soolingen
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Department of Clinical Microbiology and department of Lung Disease, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Smits SL, van Leeuwen M, Schapendonk CME, Schürch AC, Bodewes R, Haagmans BL, Osterhaus ADME. Picobirnaviruses in the human respiratory tract. Emerg Infect Dis 2013; 18:1539-40. [PMID: 22932227 PMCID: PMC3437736 DOI: 10.3201/eid1809.120507] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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30
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McEvoy CRE, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, Warren RM, Gey van Pittius NC. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS One 2012; 7:e30593. [PMID: 22496726 PMCID: PMC3319526 DOI: 10.1371/journal.pone.0030593] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [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: 09/14/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of "classical" antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design.
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Affiliation(s)
- Christopher R E McEvoy
- Department of Science and Technology, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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Schürch AC, Kremer K, Hendriks ACA, Freyee B, McEvoy CRE, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D. SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS One 2011; 6:e28365. [PMID: 22162765 PMCID: PMC3230589 DOI: 10.1371/journal.pone.0028365] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [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: 07/05/2011] [Accepted: 11/07/2011] [Indexed: 02/04/2023] Open
Abstract
The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains.
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Affiliation(s)
- Anita C. Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Amber C. A. Hendriks
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Benthe Freyee
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Christopher R. E. McEvoy
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Reinout van Crevel
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Martin J. Boeree
- Department of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
| | - Paul van Helden
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Robin M. Warren
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Roland J. Siezen
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
- Department of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
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Schürch AC, van Soolingen D. DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing. Infect Genet Evol 2011; 12:602-9. [PMID: 22067515 DOI: 10.1016/j.meegid.2011.08.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/12/2011] [Accepted: 08/19/2011] [Indexed: 11/26/2022]
Abstract
Current typing methods for Mycobacterium tuberculosis complex evolved from simple phenotypic approaches like phage typing and drug susceptibility profiling to DNA-based strain typing methods, such as IS6110-restriction fragment length polymorphisms (RFLP) and variable number of tandem repeats (VNTR) typing. Examples of the usefulness of molecular typing are source case finding and epidemiological linkage of tuberculosis (TB) cases, international transmission of MDR/XDR-TB, the discrimination between endogenous reactivation and exogenous re-infection as a cause of relapses after curative treatment of tuberculosis, the evidence of multiple M. tuberculosis infections, and the disclosure of laboratory cross-contaminations. Simultaneously, phylogenetic analyses were developed based on single nucleotide polymorphisms (SNPs), genomic deletions usually referred to as regions of difference (RDs) and spoligotyping which served both strain typing and phylogenetic analysis. National and international initiatives that rely on the application of these typing methods have brought significant insight into the molecular epidemiology of tuberculosis. However, current DNA fingerprinting methods have important limitations. They can often not distinguish between genetically closely related strains and the turn-over of these markers is variable. Moreover, the suitability of most DNA typing methods for phylogenetic reconstruction is limited as they show a high propensity of convergent evolution or misinfer genetic distances. In order to fully explore the possibilities of genotyping in the molecular epidemiology of tuberculosis and to study the phylogeny of the causative bacteria reliably, the application of whole-genome sequencing (WGS) analysis for all M. tuberculosis isolates is the optimal, although currently still a costly solution. In the last years WGS for typing of pathogens has been explored and yielded important additional information on strain diversity in comparison to the classical DNA typing methods. With the ongoing cost reduction of DNA sequencing it is possible that WGS will become the sole diagnostic tool in the secondary laboratory diagnosis of tuberculosis for identification, drug susceptibility testing and genetic characterization.
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Affiliation(s)
- Anita C Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb/LIS, pb 22), P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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Affiliation(s)
- Anita C Schürch
- RIVM, National Institute for Public Health and the Environment, 3730BA Bilthoven, the Netherlands
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Schürch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D. Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis. J Clin Microbiol 2011; 49:1318-22. [PMID: 21325559 PMCID: PMC3122804 DOI: 10.1128/jcm.01848-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 02/04/2011] [Indexed: 11/20/2022] Open
Abstract
The "Harlingen" IS6110 restriction fragment length polymorphism (RFLP) cluster has linked over 100 tuberculosis cases in The Netherlands since 1993. Four Mycobacterium tuberculosis isolates that were epidemiologically linked to this cluster had different spoligotype patterns, as well as slightly divergent IS6110 profiles, compared to the majority of the isolates. Sequencing of the direct repeat (DR) locus revealed sequence polymorphisms at the putative deletion sites. These deletion footprints provided evidence for independent deletions of the central region of the DR locus in three isolates, while the different genotype of the fourth isolate was explained by transmission. Our finding suggests that convergent deletions in the DR locus occur frequently. However, deletion footprints are not suitable to detect convergent deletions in the DR because they seem to be exceptional. Deletion footprints in the DR were not described previously, and we did not observe them in any public M. tuberculosis complex sequences. We conclude that preferential deletions in the DR loci of closely related strains are usually an unnoted event that interferes with clustering of closely related strains.
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Affiliation(s)
- Anita C. Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
| | - Albert Kiers
- Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden
| | - Martin J. Boeree
- University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Roland J. Siezen
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
- University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
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de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen H, McEvoy CRE, van Soolingen D, Thiede B, Warren RM, Wiker HG. Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol Cell Proteomics 2010; 10:M110.002527. [PMID: 21030493 PMCID: PMC3013451 DOI: 10.1074/mcp.m110.002527] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [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] [Indexed: 01/04/2023] Open
Abstract
Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains.
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Affiliation(s)
- Gustavo A de Souza
- The Gade Institute, Section for Microbiology and Immunology, University of Bergen, N-5021 Bergen, Norway
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Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D. High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster. J Clin Microbiol 2010; 48:3403-6. [PMID: 20592143 PMCID: PMC2937716 DOI: 10.1128/jcm.00370-10] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/19/2010] [Accepted: 06/22/2010] [Indexed: 01/20/2023] Open
Abstract
To investigate whether genome sequencing yields more useful markers than those currently used to study the epidemiology of tuberculosis, it was applied to three Mycobacterium tuberculosis isolates of the Harlingen outbreak. Our findings suggest that single nucleotide polymorphisms can be used to identify transmission chains in restriction fragment length polymorphism clusters.
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Affiliation(s)
- Anita C. Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Olaf Daviena
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Albert Kiers
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Martin J. Boeree
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Roland J. Siezen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
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Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D. The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale. Infection, Genetics and Evolution 2010; 10:108-14. [DOI: 10.1016/j.meegid.2009.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 11/24/2022]
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