Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin

Velez, Leandro da Silva; Aburjaile, Flávia Figueira; Farias, Antônio Roberto Gomes de; Baia, Ana Dulce Botelho; Oliveira, Willams José de; Silva, Adriano Márcio Freire; Benko‐Iseppon, Ana Maria; Azevedo, Vasco; Brenig, Bertram; Ham, Jong Hyun; Souza, Elineide Barbosa de; Gama, Marco Aurélio Siqueira da

doi:10.1016/j.syapm.2023.126415

Cited by 11 publications

(5 citation statements)

References 39 publications

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“…Similarly, we have previously shown that the Bcc strains AZ4-2-10-S1D7 and XXVI belonged to new species, which we had called BCC03 ( Bach et al, 2022b ). More recently, two novel Bcc species were described isolated from the semi-arid north-east Brazilian region causing onion sour skin: “ Burkholderia sola ” and “ Burkholderia semiarida ” ( Velez et al, 2023 ). The latter groups with the BCC03 strains in ANI and phylogenetic analyses ( Figures 3 and S5 ).…”

Section: Resultsmentioning

confidence: 99%

“…However, different thresholds are suggested and might be accepted to delineate species that show diagnostic distinct phenotypic traits as is the case of closely related Paraburkholderia species ( Mullins and Mahenthiralingam, 2021 ). Moreover, genome metrics are increasingly being used to split known species into novel ones ( Velez et al, 2023 ) and detect the presence of synonyms, which are species described with different names that belong to the same species ( Madhaiyan et al, 2022 ). These peculiarities and updates complicate the correct species assignment for those unfamiliar with the taxonomy of the group.…”

Section: Introductionmentioning

confidence: 99%

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Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Bach,

Volpiano,

Sant’Anna

et al. 2023

Genet. Mol. Biol.

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The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Bach,

Volpiano,

Sant’Anna

et al. 2023

Genet. Mol. Biol.

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“…alliicola (Bga) causes slippery skin (Burkholder, 1950). In addition to the common onion pathogenic members B. cepacia, B. cenocepacia, and B. ambifaria , three new onion pathogenic species B. orbicola, B. semiarida, and B. sola were recently described asmembers of the Bcc complex (Morales-Ruíz et al, 2022; Velez et al, 2023). While all described onion pathogenic members in Burkholderia infect bulbs and are storage pathogens, Bga is also associated with foliar necrosis (Kawamoto and Lorbeer, 1974; Lee et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Thiosulfinate tolerance gene clusters are common features ofBurkholderiaonion pathogens

Paudel,

Zhao,

Stice

et al. 2024

Preprint

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Burkholderia gladioli pv. alliicola, B.cepacia, and B. orbicola are common bacterial pathogens of onion. Onions produce organosulfur thiosulfinate defensive compounds after cellular decompartmentalization. Using whole genome sequencing and in silico analysis, we identified putative thiosulfinate tolerance gene (TTG) clusters in multiple onion-associated Burkholderia species similar to those characterized in other Allium-associated bacterial endophytes and pathogens. Sequence analysis revealed the presence of three Burkholderia TTG cluster types with both Type A and Type B being broadly distributed in B. gladioli, B. cepacia, and B. orbicola in both the chromosome and plasmids. Based on isolate natural variation and generation of isogenic strains, we determined the in vitro and in vivo contribution of TTG clusters in B. gladioli, B. cepacia, and B. orbicola. The Burkholderia TTG clusters contributed to enhanced allicin tolerance and improved growth in filtered onion extract by all three species. TTG clusters also made clear contributions to B gladioli foliar necrosis symptoms and bacterial populations. Surprisingly, the TTG cluster did not contribute to bacterial populations in onion bulb scales by these three species. Based on our findings, we hypothesize onion-associated Burkholderia may evade or inhibit the production of thiosulfinates in onion bulb tissues.

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“…The Bcc comprises 27 closely related and distinct bacterial species that are found widely in nature and artificial habitats [ 12 ]. They are human opportunistic pathogens that can cause severe infection in immunocompromised and critically ill individuals [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

A culture-independent nucleic acid diagnostics method for use in the detection and quantification of Burkholderia cepacia complex contamination in aqueous finished pharmaceutical products

Duong,

Minogue,

Fullbrook

et al. 2024

PLoS ONE

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The Burkholderia cepacia complex (Bcc) is the number one bacterial complex associated with contaminated Finished Pharmaceutical Products (FPPs). This has resulted in multiple healthcare related infection morbidity and mortality events in conjunction with significant FPP recalls globally. Current microbiological quality control of FPPs before release for distribution depends on lengthy, laborious, non-specific, traditional culture-dependent methods which lack sensitivity. Here, we present the development of a culture-independent Bcc Nucleic Acid Diagnostic (NAD) method for detecting Bcc contaminants associated with Over-The-Counter aqueous FPPs. The culture-independent Bcc NAD method was validated to be specific for detecting Bcc at different contamination levels from spiked aqueous FPPs. The accuracy in Bcc quantitative measurements was achieved by the high degree of Bcc recovery from aqueous FPPs. The low variation observed between several repeated Bcc quantitative measurements further demonstrated the precision of Bcc quantification in FPPs. The robustness of the culture-independent Bcc NAD method was determined when its accuracy and precision were not significantly affected during testing of numerous aqueous FPP types with different ingredient matrices, antimicrobial preservative components and routes of administration. The culture-independent Bcc NAD method showed an ability to detect Bcc in spiked aqueous FPPs at a concentration of 20 Bcc CFU/mL. The rapid (≤ 4 hours from sample in to result out), robust, culture-independent Bcc NAD method presented provides rigorous test specificity, accuracy, precision, and sensitivity. This method, validated with equivalence to ISO standard ISO/TS 12869:2019, can be a valuable diagnostic tool in supporting microbiological quality control procedures to aid the pharmaceutical industry in preventing Bcc contamination of aqueous FPPs for consumer safety.

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Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin

Cited by 11 publications

References 39 publications

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Thiosulfinate tolerance gene clusters are common features ofBurkholderiaonion pathogens

A culture-independent nucleic acid diagnostics method for use in the detection and quantification of Burkholderia cepacia complex contamination in aqueous finished pharmaceutical products

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