Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia

Salloum, Tamara; Nassour, Elie; Araj, George F.; Abboud, Edmond; Tokajian, Sima

doi:10.1099/jmm.0.000759

Cited by 4 publications

(5 citation statements)

References 56 publications

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“…Resistance genes were observed against meropenem, trimethoprim/sulfamethoxazole, levofloxacin, and cefepime, despite the susceptibility described according to the disk diffusion test (DDT), considered as multidrug-susceptible, corroborating previous studies that revealed no direct correlation of gene expression with phenotype [25].…”

Section: Discussionsupporting

confidence: 84%

Genomic analysis of Burkholderia cenocepacia isolated from a liver abscess in a patient with cystic fibrosis

Vianna

Menezes

Almeida

et al. 2021

APMIS

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Burkholderia cenocepacia complex is associated with high transmissibility, virulence, and poor prognosis in cystic fibrosis (CF) patients. However, extrapulmonary infections are rare. We investigated the genome of a B. cenocepacia IIIA isolated from a liver abscess in a Brazilian CF patient and compared it to strain J2315. The whole genome was sequenced, and contigs were annotated by Rapid Annotation using Subsystem Technology. The Pathosystems Resource Integration Center was used to map antimicrobial and virulence genes. The genomic island (GIs) analysis was performed using two prediction methods, and the presence of putative plasmids and insertion sequences (ISs) was investigated. The isolate was confirmed as B. cenocepacia IIIA to ST-28 (ET12 lineage). A total of 64 genes for antimicrobial resistance and 47 genes related to virulence were identified. Among the virulence factors, there was a predominance of factors related to the invasion mechanism, to the flagellar biosynthesis protein, and to the RNA polymerase sigma factor for flagellar operon (cdpA). Two IS families (IS3 and IS5) and only one plasmid were found. On average 56 GIs were predicted by at least one of the methods applied. Comparative analysis showed resistance mechanisms and virulence factors revealing invasive determinants used by B. cenocepacia IIIA (ET12) in the process of disease spread to other infection sites (extrapulmonary) of highly virulent strains in CF patients.

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Section: Discussionsupporting

confidence: 84%

Genomic analysis of Burkholderia cenocepacia isolated from a liver abscess in a patient with cystic fibrosis

Vianna

Menezes

Almeida

et al. 2021

APMIS

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“…3 and 5). Specifically, BCC08 and BCC05 should represent B. cenocepacia genomovars IIIA and IIIB, respectively [23,56,57]. The dDDH and Fig.…”

Section: Reclassification Of the Bcc Based On Species Tree And Dddh/animentioning

confidence: 99%

“…At present, with the advent of next-generation sequencing technologies, an increasing number of complete genome sequences of the bacteria in the BCC have been published [21][22][23][24]. This provides an ideal opportunity for re-examining the taxonomy of BCC by traditional molecular methods.…”

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confidence: 99%

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Yuan¹,

Zhou²,

Zhou³

et al. 2020

Biol Direct

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Background: Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods: We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results: We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions: This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer: This article was reviewed by Dr. Xianwen Ren.

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“…Confirmation of HGT was performed by a combination of BLAST screening and largescale phylogenetic trees. BLAST screening was performed based on our previous study [42]. In brief, candidate sequences in B. glumae were compared against sequences in the NCBI (National Center for Biotechnology Information) reference genome using BLASTp [43] followed by extracting the sequences with highest similarity for further study.…”

Section: Horizontal Gene Transfer (Hgt) Analysismentioning

confidence: 99%

“…These sequences were aligned using MAFFT [45], and the conserved region of each alignment was trimmed using TrimAI [46] with stringent settings. Maximum likelihood and Bayesian phylogenies were generated based on our previous study [42].…”

Section: Horizontal Gene Transfer (Hgt) Analysismentioning

confidence: 99%

Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208

et al. 2021

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Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.

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Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia

Abstract: This study mapped existing genetic variations in B. cenocepacia associated with notorious outcomes in CF patients, and the data obtained provide comprehensive, genome-inferred insights and multifactorial examination of an important human pathogen.

Cited by 4 publications

References 56 publications

Genomic analysis of Burkholderia cenocepacia isolated from a liver abscess in a patient with cystic fibrosis

Genomic analysis of Burkholderia cenocepacia isolated from a liver abscess in a patient with cystic fibrosis

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208

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