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Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis.
PLoS Negl Trop Dis. 2017 Sep; 11(9):e0005928.PN

Abstract

The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc) species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.

Authors+Show Affiliations

Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia. Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia. Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia. Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America. Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28910350

Citation

Price, Erin P., et al. "Phylogeographic, Genomic, and Meropenem Susceptibility Analysis of Burkholderia Ubonensis." PLoS Neglected Tropical Diseases, vol. 11, no. 9, 2017, pp. e0005928.
Price EP, Sarovich DS, Webb JR, et al. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Negl Trop Dis. 2017;11(9):e0005928.
Price, E. P., Sarovich, D. S., Webb, J. R., Hall, C. M., Jaramillo, S. A., Sahl, J. W., Kaestli, M., Mayo, M., Harrington, G., Baker, A. L., Sidak-Loftis, L. C., Settles, E. W., Lummis, M., Schupp, J. M., Gillece, J. D., Tuanyok, A., Warner, J., Busch, J. D., Keim, P., ... Wagner, D. M. (2017). Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Neglected Tropical Diseases, 11(9), e0005928. https://doi.org/10.1371/journal.pntd.0005928
Price EP, et al. Phylogeographic, Genomic, and Meropenem Susceptibility Analysis of Burkholderia Ubonensis. PLoS Negl Trop Dis. 2017;11(9):e0005928. PubMed PMID: 28910350.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. AU - Price,Erin P, AU - Sarovich,Derek S, AU - Webb,Jessica R, AU - Hall,Carina M, AU - Jaramillo,Sierra A, AU - Sahl,Jason W, AU - Kaestli,Mirjam, AU - Mayo,Mark, AU - Harrington,Glenda, AU - Baker,Anthony L, AU - Sidak-Loftis,Lindsay C, AU - Settles,Erik W, AU - Lummis,Madeline, AU - Schupp,James M, AU - Gillece,John D, AU - Tuanyok,Apichai, AU - Warner,Jeffrey, AU - Busch,Joseph D, AU - Keim,Paul, AU - Currie,Bart J, AU - Wagner,David M, Y1 - 2017/09/14/ PY - 2017/02/26/received PY - 2017/09/03/accepted PY - 2017/09/26/revised PY - 2017/9/15/pubmed PY - 2017/10/3/medline PY - 2017/9/15/entrez SP - e0005928 EP - e0005928 JF - PLoS neglected tropical diseases JO - PLoS Negl Trop Dis VL - 11 IS - 9 N2 - The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc) species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species. SN - 1935-2735 UR - https://www.unboundmedicine.com/medline/citation/28910350/Phylogeographic_genomic_and_meropenem_susceptibility_analysis_of_Burkholderia_ubonensis_ L2 - http://dx.plos.org/10.1371/journal.pntd.0005928 DB - PRIME DP - Unbound Medicine ER -