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Wagner DM, Birdsell DN, McDonough RF, Nottingham R, Kocos K, Celona K, Özsürekci Y, Öhrman C, Karlsson L, Myrtennäs K, Sjödin A, Johansson A, Keim PS, Forsman M, Sahl JW. Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples. PLoS One 2022; 17:e0273273. [PMID: 36223396 PMCID: PMC9555625 DOI: 10.1371/journal.pone.0273273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.
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Affiliation(s)
- David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Dawn N. Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Ryelan F. McDonough
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nottingham
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karisma Kocos
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kimberly Celona
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Yasemin Özsürekci
- Department of Pediatric Infectious Diseases, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Linda Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Paul S. Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Ramirez-Paredes JG, Larsson P, Thompson KD, Penman DJ, Busse HJ, Öhrman C, Sjödin A, Soto E, Richards RH, Adams A, Colquhoun DJ. Reclassification of Francisella noatunensis subsp. orientalis Ottem et al. 2009 as Francisella orientalis sp. nov., Francisella noatunensis subsp. chilensis subsp. nov. and emended description of Francisella noatunensis. Int J Syst Evol Microbiol 2020; 70:2034-2048. [PMID: 32160147 DOI: 10.1099/ijsem.0.004009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Francisella noatunensis is a fastidious facultative intracellular bacterial pathogen that causes 'piscine francisellosis', a serious disease affecting both marine and fresh water farmed and wild fish worldwide. Currently two F. noatunensis subspecies are recognized, i.e. F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis. In the present study, the taxonomy of F. noatunensis was revisited using a polyphasic approach, including whole genome derived parameters such as digital DNA-DNA hybridization, whole genome average nucleotide identity (wg-ANIm), whole genome phylogenetic analysis, whole genome G+C content, metabolic fingerprinting and chemotaxonomic analyses. The results indicated that isolates belonging to F. noatunensis subsp. orientalis represent a phenotypically and genetically homogenous taxon, clearly distinguishable from F. noatunensis subsp. noatunensis that fulfils requirements for separate species status. We propose, therefore, elevation of F. noatunensis subsp. orientalis to the species rank as Francisella orientalis sp. nov. with the type strain remaining as Ehime-1T (DSM 21254T=LMG 24544T). Furthermore, we identified sufficient phenotypic and genetic differences between F. noatunensis subsp. noatunensis recovered from diseased farmed Atlantic salmon in Chile and those isolated from wild and farmed Atlantic cod in Northern Europe to warrant proposal of the Chilean as a novel F. noatunensis subspecies, i.e. Francisella noatunensis subsp. chilensis subsp. nov. with strain PQ1106T (CECT 9798T=NCTC14375T) as the type strain. Finally, we emend the description of F. noatunensis by including further metabolic information and the description of atypical strains.
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Affiliation(s)
- Jose Gustavo Ramirez-Paredes
- Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
- Present address: Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
| | - Pär Larsson
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
- Department of Medical Biosciences, Umea University, Umeå, Sweden
| | - Kim D Thompson
- Aquaculture Research Group, Moredun Research Institute, Edinburgh, Scotland, EH26 0PZ, UK
| | - David J Penman
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Hans-Jürgen Busse
- Institute of Microbiology, Veterinary University, Vienna, A-1160 Wien, Austria
| | - Caroline Öhrman
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Andreas Sjödin
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Esteban Soto
- Department of Medicine and Epidemiology, University of California Davis, School of Veterinary Medicine, Davis, California, 95616, USA
| | - Randolph H Richards
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Duncan J Colquhoun
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, N-0106 Oslo, Norway
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