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Salloum T, Nassour E, Araj GF, Abboud E, Tokajian S. Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia. J Med Microbiol 2018; 67:1157-1167. [PMID: 29897328 DOI: 10.1099/jmm.0.000759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
PURPOSE Burkholderia cenocepacia is among the most common members of the Burkholderia cepacia complex (Bcc) isolated from patients with cystic fibrosis (CF). The factors triggering the high rates of morbidity and mortality in CF patients are not well elucidated. In this study, we aim to highlight the genome diversity of two clinical isolates of B. cenocepacia through comparative genome analysis. METHODOLOGY The repertoire of virulence factors and resistance genes compared to reference strains J2315 and K56-2 was elucidated. The isolates were screened for the presence of phages and insertion sequences. Two methods were combined to obtain an accurate prediction of genomic islands (GIs): the cumulative GC profile and the IslandViewer web tool. To study evolutionary relatedness, whole genome-based single-nucleotide polymorphism (wgSNP) analysis was also performed with 43 publically available strains of the Bcc of various sequence types.Results/Key findings. Genome-based species identification of the two isolates BC-AUH and BC-BMEH confirmed the species as B. cenocepacia. Both belonged to ST-602, a double-locus variant of ST-32 (CC31), genomovar IIIA, and carried a large number of antibiotic resistance genes. Eighteen GIs were predicted in BC-AUH and BC-BMEH, occupying 9.3 and 6.1 % of the respective genomes. Comparison to J2315 revealed 89 and 85 genes unique to BC-BMEH and BC-AUH, respectively. Additionally, 1823 intergenic SNPs were detected between BC-BMEH and BC-AUH. CONCLUSION 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.
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Affiliation(s)
- Tamara Salloum
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Elie Nassour
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - George F Araj
- 2Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Edmond Abboud
- 3Laboratory Department, the Middle East Institute of Health University Center, Bsalim, Lebanon
| | - Sima Tokajian
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
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Guo FB, Xiong L, Zhang KY, Dong C, Zhang FZ, Woo PCY. Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands. BMC Microbiol 2017; 17:73. [PMID: 28347342 PMCID: PMC5369199 DOI: 10.1186/s12866-017-0986-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium's adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline. RESULTS In this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection. CONCLUSIONS This approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.
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Affiliation(s)
- Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Lifeng Xiong
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Kai-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Fa-Zhan Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
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Lee AHY, Flibotte S, Sinha S, Paiero A, Ehrlich RL, Balashov S, Ehrlich GD, Zlosnik JEA, Mell JC, Nislow C. Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs. Genome Res 2017; 27:650-662. [PMID: 28325850 PMCID: PMC5378182 DOI: 10.1101/gr.213363.116] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/16/2017] [Indexed: 11/24/2022]
Abstract
Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures—including immune responses and therapeutic interventions—shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2–20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.
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Affiliation(s)
- Amy Huei-Yi Lee
- Department of Microbiology and Immunology.,Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Stephane Flibotte
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Adrianna Paiero
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Genomics Core Facility, Clinical and Translational Research Institute, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infection Diseases, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
| | - Sergey Balashov
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Genomics Core Facility, Clinical and Translational Research Institute, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infection Diseases, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Genomics Core Facility, Clinical and Translational Research Institute, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infection Diseases, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
| | - James E A Zlosnik
- Centre for Preventing and Understanding Infection in Children, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Genomics Core Facility, Clinical and Translational Research Institute, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infection Diseases, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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