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Schütz SD, Liechti N, Altpeter E, Labutin A, Wütrich T, Schmidt KM, Buettcher M, Moser M, Bruggmann R, Wittwer M. Phylogeography of Francisella tularensis subspecies holarctica and epidemiology of tularemia in Switzerland. Front Microbiol 2023; 14:1151049. [PMID: 37113234 PMCID: PMC10126411 DOI: 10.3389/fmicb.2023.1151049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Tularemia, an endemic disease that mainly affects wild animals and humans, is caused by Francisella tularensis subsp. holarctica (Fth) in Switzerland. The Swiss Fth population consist of multiple different subclades which are distributed throughout the country. The aim of this study is to characterize the genetic diversity of Fth in Switzerland and to describe the phylogeographic relationship of isolates by single nucleotide polymorphism (SNP) analysis. This analysis is combined with human surveillance data from reported cases over the last 10 years and in vitro and in silico antibiotic resistance tests to provide insight into the epidemiology of tularemia in Switzerland. We sequenced the whole genomes of 52 Fth strains of human or tick origin collected in Switzerland between 2009 and 2022 and analyzed together with all publicly available sequencing data of Swiss and European Fth. Next, we performed a preliminary classification with the established canonical single nucleotide polymorphism nomenclature. Furthermore, we tested 20 isolates from all main Swiss clades for antimicrobial susceptibility against a panel of antimicrobial agents. All 52 sequenced isolates from Switzerland belong to major clade B.6, specifically subclades B.45 and B.46, previously described in Western Europe. We were able to accurately reconstruct the population structure according to the global phylogenetic framework. No resistance to clinically recommended antibiotics could be identified in vitro or in silico in the western B.6 strains.
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Affiliation(s)
- Sara Doina Schütz
- Interfaculty Bioinformatics Unit, University of Bern and Swiss Institute of Bioinformatics, Bern, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Nicole Liechti
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
| | | | - Anton Labutin
- Swiss Federal Office of Public Health, Bern, Switzerland
| | - Tsering Wütrich
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
| | - Kristina Maria Schmidt
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
| | - Michael Buettcher
- Paediatric Infectious Diseases Unit, Children’s Hospital Lucerne, Lucerne Cantonal Hospital, Lucerne, Switzerland
- Faculty of Health Sciences and Medicine, University of Lucerne, Lucerne, Switzerland
- Paediatric Pharmacology and Pharmacometrics Research Center, University Children’s Hospital Basel, Basel, Switzerland
| | - Michel Moser
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern and Swiss Institute of Bioinformatics, Bern, Switzerland
| | - Matthias Wittwer
- Spiez Laboratory, Federal Office for Civil Protection and Swiss National Reference Center for Highly Pathogenic Bacteria (NABA), Spiez, Switzerland
- *Correspondence: Matthias Wittwer,
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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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