Burkholderia pulmonis sp. nov. and Burkholderia torrens sp. nov.: novel Burkholderia cepacia complex species from human clinical and environmental sources

Twenty-four Burkholderia arboris -like isolates obtained from samples of persons with cystic fibrosis and environmental sources were analysed using genomic approaches to clarify their taxonomic positions. Phylogenomic and overall genome relatedness index analyses revealed three distinct clusters. One cluster comprised the B. arboris type strain and thus corresponded to B. arboris , while the other two represented novel species within the Burkholderia cepacia complex, for which the names Burkholderia pulmonis sp. nov. (with LMG 33096ᵀ=CCUG 77266ᵀ as type strain) and Burkholderia torrens sp. nov. (with LMG 34232 T =TSD-620 T as type strain) are proposed. Closed genomes were obtained for all 24 isolates through hybrid assembly of Illumina data and Oxford Nanopore Technologies long-read sequencing data. The genome sizes ranged from 7.05 to 8.64 Mbp and exhibited the characteristic multi-replicon structure of Burkholderia , comprising two major replicons and a third, smaller, replicon (~0.96–1.27 Mbp) called pC3, except in B. pulmonis strains R-18413 and R-72673 and B. arboris strains R-132 and R-16920, which lost the third replicon. One or two small plasmids (24–355 kbp) were detected in several B. pulmonis and B. arboris strains. Several pairs or clusters of clonally related isolates were detected and included isolates with and without pC3.