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Microbiome Profiling by Whole Genome Sequencing During Acute and Chronic Lung Transplant Rejection
Abstracts S183 matching; however, donor tobacco abuse, recipient on life support, and transplant era were significantly different. Overall survival (OS) was significantly worse in the HCV+D group (median survival: 1.3 vs. 5.1 years; p= 0.002; Figure A). Results were confirmed in the matched cohort. After inclusion criteria were met, 289 (1.7%) of lung transplant recipients were HCV+R. These patients appeared similar to their HCV -R counterparts, except they were older and had lower functional status. OS was significantly lower in HCV positive individuals (median survival: 3.8 vs. 5.1 years; p= 0.005; Figure B). Again, results were confirmed by adjusted analysis. Conclusion: HCV positive status is a rare problem when considering both lung recipients and donors. Current data demonstrate significantly worse outcomes for both HCV- patients receiving a HCV+ lung and HCV+ patients receiving a HCV- lung. Caution must be used when offering a transplant lung in these cases.
(n= 19) ExtraCorporeal Membrane Oxygenation support. The actuarial survival rates were respectively 89% (n= 162), 85,4% (n= 90), and 85,4% (n= 24) at 1, 2 and 3 years. Concerning High Emergency transplanted patients, the actuarial survival rates were respectively 80,5% (n= 34), 75,5% (n= 20), and 75,5% (n= 11) at 1, 2 and 3 years. Evolution of mean FEV1 was 76+/-19%, 81+/-22% and 69+/-26% at 1, 2 and 3 years. Conclusion: COLT is the largest study in Europe with such biocollection and prospective database. It allows establishing multicentric connections between European transplant centers, in order to identify a biological marker of CLAD. First clinical analysis of CF patients outcomes after bilateral lung transplantation are encouraging in term of morbi-mortality, even in the High Emergency LTR subgroup. 4( 90) Microbiome Profiling by Whole Genome Sequencing During Acute and Chronic Lung Transplant Rejection B.C. Keller ,1 D.E. Byers,1 S.A. Handley,2 G. Zhao,2 C.A. Witt,1 R.D. Yusen,1 E.P. Trulock,1 R.R. Hachem,1 D. Wang,3 H.W. Virgin.2 1Medicine, Washington University, Saint Louis, MO; 2Pathology & Immunology, Washington University, Saint Louis, MO; 3Molecular Microbiology and Pathology & Immunology, Washington University, Saint Louis, MO.
4( 89) Clinical Outcome of Bilateral Lung Transplantation for Cystic Fibrosis in the Frame of the European Multicentric COLT Study P. Lacoste ,1 A. Tissot,1 P.J. Royer,2 M. Pain,2 K. Botturi-Cavaillès,2 A. Magnan,1 Colt consortium.1 1CHU Nantes, Nantes, France; 2Institut du Thorax, Inserm UMR 1087, Nantes, France. Purpose: Bilateral lung transplantation is considered as a therapeutic option for patients with end-stage cystic fibrosis (CF). The main long term complication of lung transplantation is CLAD (Chronic Lung Allograft Dysfunction). COLT (COhort in Lung Transplantation) is the largest biocollection in Europe set up in order to identify biological markers of CLAD. The objective of the study is to describe clinical outcomes of CF, with at least one year follow up post transplantation. Methods: COLT consists in sharing clinical, biological, functional and radiological data of included patients in each center. Clinical data are collected prospectively in an online database processing « integralis », dedicated to COLT. From October 2009 to june 2012, 156 CF patients underwent bilateral lung transplantation. 48% were men, mean age 27.5 ± 7.6 years and 18 ± 1,9 IMC. The mean follow-up is of 2 years ± 0,96. Results: 65% (n= 102) lung transplant recipients (LTR) with CF were infected with Pseudomonas aeruginosa, 33% (n= 52) with Staphylococcus Aureus, 1,92%, (n= 3) with Burkholderia Cepacia. Before transplantation, 38% (n= 59) patients were colonized with Aspergillus Fumigatus, 32,7% (n= 51) with Candida Albicans. The mean time on waiting list was 123 ± 418 days with 27% (n= 42) High Emergency transplanted patients (waiting time: 7 ± 5 days). 38% (n= 60) were transplanted with a miss-match of Cytomegalovirus, 12% (n= 19) for Epstein Barr Virus. The post-transplantation morbidity was: 12,8% (n= 20) tracheotomy, 12% (n= 19) dialysis, 12%
Purpose: Prior studies have reported an association between microbes and chronic allograft dysfunction after lung transplantation. However, these studies were limited by microbe-specific detection methods. The development of next-generation sequencing technology now allows for the unbiased characterization of the complete lung microbiome. Methods: We performed whole genome shotgun (WGS) sequencing on 18 bronchoalveolar lavage (BAL) samples collected serially from 9 lung transplant recipients with acute rejection (A2 or higher, n = 4) or chronic rejection (BOS1 or higher, n = 5). Total nucleic acid was extracted from BAL supernatant, reverse-transcribed, and PCR-amplified before library construction and sequencing with Illumina HiSeq. Sequence analysis was performed using a custom bioinformatics pipeline. Briefly, reads were quality-controlled and clustered to identify unique reads. Human reads were subtracted by BLAST search against the human genome. Remaining reads were assembled into contigs, clustered to remove duplicates and assigned to taxa after BLASTx or BLASTn against the NCBI nr and nt databases. Results: After quality control and removal of host reads, one-third of reads remained (4.4 million out of 12.9 million reads/sample). Contig assembly and clustering reduced the number of unique reads to ~5800/sample. Of these only 0.3% (range 0.04% to 1.58%) and 0.25% (range 0.02% to 0.79%) were assignable to fungi or virus, respectively, and a large proportion of the viral reads were bacteriophage. Inter-subject variability as well as variability between sequential samples from the same subject was clearly evident. Importantly, more than 50% of unique reads were unassignable after comparison to current databases. Conclusion: Significant variability exists in the lung microbiome after lung transplantation, even within a single person. Levels of unique fungi or viruses appear to be relatively low compared to bacteria, but given that more than 50% of reads are unassignable, this may represent a significant under-estimation of the total diversity of the lung microbiome. More complete fungal and viral reference databases are needed to better define these parts of the lung microbiome. Nevertheless, we demonstrate the feasibility of WGS sequencing as a platform for performing an unbiased analysis of the complete lung microbiome. 4( 91) Community Acquired Respiratory Viral Infection after Lung Transplantation: BOS Risk and Risks of Specific Viruses M. Benzimra , H.W. Ainge-Allen, A.L. Rigby, M.A. Malouf, A.P. Havryk, M. Plit, A.R. Glanville. Lung Transplant Unit, St Vincent’s Hospital, Sydney, Australia. Purpose: Community acquired respiratory viral (CARV) infections are a reported risk factor for bronchiolitis obliterans syndrome (BOS) after lung transplantation (LTx) but the risk of specific viral infections is unknown. We assessed the risk of specific CARV for BOS and death after LTx.
(n= 19) ExtraCorporeal Membrane Oxygenation support. The actuarial survival rates were respectively 89% (n= 162), 85,4% (n= 90), and 85,4% (n= 24) at 1, 2 and 3 years. Concerning High Emergency transplanted patients, the actuarial survival rates were respectively 80,5% (n= 34), 75,5% (n= 20), and 75,5% (n= 11) at 1, 2 and 3 years. Evolution of mean FEV1 was 76+/-19%, 81+/-22% and 69+/-26% at 1, 2 and 3 years. Conclusion: COLT is the largest study in Europe with such biocollection and prospective database. It allows establishing multicentric connections between European transplant centers, in order to identify a biological marker of CLAD. First clinical analysis of CF patients outcomes after bilateral lung transplantation are encouraging in term of morbi-mortality, even in the High Emergency LTR subgroup. 4( 90) Microbiome Profiling by Whole Genome Sequencing During Acute and Chronic Lung Transplant Rejection B.C. Keller ,1 D.E. Byers,1 S.A. Handley,2 G. Zhao,2 C.A. Witt,1 R.D. Yusen,1 E.P. Trulock,1 R.R. Hachem,1 D. Wang,3 H.W. Virgin.2 1Medicine, Washington University, Saint Louis, MO; 2Pathology & Immunology, Washington University, Saint Louis, MO; 3Molecular Microbiology and Pathology & Immunology, Washington University, Saint Louis, MO.
4( 89) Clinical Outcome of Bilateral Lung Transplantation for Cystic Fibrosis in the Frame of the European Multicentric COLT Study P. Lacoste ,1 A. Tissot,1 P.J. Royer,2 M. Pain,2 K. Botturi-Cavaillès,2 A. Magnan,1 Colt consortium.1 1CHU Nantes, Nantes, France; 2Institut du Thorax, Inserm UMR 1087, Nantes, France. Purpose: Bilateral lung transplantation is considered as a therapeutic option for patients with end-stage cystic fibrosis (CF). The main long term complication of lung transplantation is CLAD (Chronic Lung Allograft Dysfunction). COLT (COhort in Lung Transplantation) is the largest biocollection in Europe set up in order to identify biological markers of CLAD. The objective of the study is to describe clinical outcomes of CF, with at least one year follow up post transplantation. Methods: COLT consists in sharing clinical, biological, functional and radiological data of included patients in each center. Clinical data are collected prospectively in an online database processing « integralis », dedicated to COLT. From October 2009 to june 2012, 156 CF patients underwent bilateral lung transplantation. 48% were men, mean age 27.5 ± 7.6 years and 18 ± 1,9 IMC. The mean follow-up is of 2 years ± 0,96. Results: 65% (n= 102) lung transplant recipients (LTR) with CF were infected with Pseudomonas aeruginosa, 33% (n= 52) with Staphylococcus Aureus, 1,92%, (n= 3) with Burkholderia Cepacia. Before transplantation, 38% (n= 59) patients were colonized with Aspergillus Fumigatus, 32,7% (n= 51) with Candida Albicans. The mean time on waiting list was 123 ± 418 days with 27% (n= 42) High Emergency transplanted patients (waiting time: 7 ± 5 days). 38% (n= 60) were transplanted with a miss-match of Cytomegalovirus, 12% (n= 19) for Epstein Barr Virus. The post-transplantation morbidity was: 12,8% (n= 20) tracheotomy, 12% (n= 19) dialysis, 12%
Purpose: Prior studies have reported an association between microbes and chronic allograft dysfunction after lung transplantation. However, these studies were limited by microbe-specific detection methods. The development of next-generation sequencing technology now allows for the unbiased characterization of the complete lung microbiome. Methods: We performed whole genome shotgun (WGS) sequencing on 18 bronchoalveolar lavage (BAL) samples collected serially from 9 lung transplant recipients with acute rejection (A2 or higher, n = 4) or chronic rejection (BOS1 or higher, n = 5). Total nucleic acid was extracted from BAL supernatant, reverse-transcribed, and PCR-amplified before library construction and sequencing with Illumina HiSeq. Sequence analysis was performed using a custom bioinformatics pipeline. Briefly, reads were quality-controlled and clustered to identify unique reads. Human reads were subtracted by BLAST search against the human genome. Remaining reads were assembled into contigs, clustered to remove duplicates and assigned to taxa after BLASTx or BLASTn against the NCBI nr and nt databases. Results: After quality control and removal of host reads, one-third of reads remained (4.4 million out of 12.9 million reads/sample). Contig assembly and clustering reduced the number of unique reads to ~5800/sample. Of these only 0.3% (range 0.04% to 1.58%) and 0.25% (range 0.02% to 0.79%) were assignable to fungi or virus, respectively, and a large proportion of the viral reads were bacteriophage. Inter-subject variability as well as variability between sequential samples from the same subject was clearly evident. Importantly, more than 50% of unique reads were unassignable after comparison to current databases. Conclusion: Significant variability exists in the lung microbiome after lung transplantation, even within a single person. Levels of unique fungi or viruses appear to be relatively low compared to bacteria, but given that more than 50% of reads are unassignable, this may represent a significant under-estimation of the total diversity of the lung microbiome. More complete fungal and viral reference databases are needed to better define these parts of the lung microbiome. Nevertheless, we demonstrate the feasibility of WGS sequencing as a platform for performing an unbiased analysis of the complete lung microbiome. 4( 91) Community Acquired Respiratory Viral Infection after Lung Transplantation: BOS Risk and Risks of Specific Viruses M. Benzimra , H.W. Ainge-Allen, A.L. Rigby, M.A. Malouf, A.P. Havryk, M. Plit, A.R. Glanville. Lung Transplant Unit, St Vincent’s Hospital, Sydney, Australia. Purpose: Community acquired respiratory viral (CARV) infections are a reported risk factor for bronchiolitis obliterans syndrome (BOS) after lung transplantation (LTx) but the risk of specific viral infections is unknown. We assessed the risk of specific CARV for BOS and death after LTx.