Characterization of clinical Ralstonia strains and their taxonomic position

Ad C. Fluit*, Jumamurat R. Bayjanov, María Díez Aguilar, Rafael Cantón, Michael M. Tunney, J. Stuart Elborn, Mireille van Westreenen, Miquel B. Ekkelenkamp

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.

Original languageEnglish
Pages (from-to)1721-1733
Number of pages13
JournalAntonie van Leeuwenhoek, International Journal of General and Molecular Microbiology
Volume114
Issue number10
DOIs
Publication statusPublished - 31 Aug 2021

Bibliographical note

Funding Information:
The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement number [115721-2], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies in kind contribution. MD-A was partially supported by the Innovative Medicines Initiative (IMI), European Commission-funded project [iABC grant 115721-2]. Research activities of RC are supported by Plan Nacional de I+D+i 2013–2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economía, Industria y Competitividad, Spanish Network for Research in Infectious Diseases [REIPI RD16/0016/0011] and projects PI12-00734, PI PI15/00466 and PIPI19/01043, co-financed by the European Regional Development Fund ‘A way to achieve Europe’ (ERDF), Operative program Intelligent Growth 2014–2020.

Publisher Copyright:
© 2021, The Author(s).

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