Improvement in detecting cytomegalovirus drug resistance mutations in solid organ transplant recipients with suspected resistance using next generation sequencing

• Published in: PloS one Vol. 14; no. 7; p. e0219701
• Main Authors: López-Aladid, Rubén, Guiu, Alba, Mosquera, Maria Mar, López-Medrano, Francisco, Cofán, Frederic, Linares, Laura, Torre-Cisneros, Julián, Vidal, Elisa, Moreno, Asunción, Aguado, Jose María, Cordero, Elisa, Martin-Gandul, Cecilia, Carratalá, Jordi, Sabé, Nuria, Niubó, Jordi, Cervera, Carlos, Capón, Alicia, Cervilla, Anna, Santos, Marta, Bodro, Marta, Muñoz, Patricia, Fariñas, Maria Carmen, Antón, Andrés, Aranzamendi, Maitane, Montejo, Miguel, Pérez-Romero, Pilar, Len, Oscar, Marcos, Maria Ángeles
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.07.2019; Public Library of Science (PLoS)
• Subjects: Antiviral agents; Bioinformatics; Biology and Life Sciences; Citomegalovirus; Cytomegalovirus; Cytomegalovirus - genetics; Cytomegalovirus - isolation & purification; Cytomegalovirus infections; Cytomegaloviruses; Deoxyribonucleic acid; Digital rights (Intellectual property); Diseases and pests; DNA; DNA polymerase; DNA sequencing; Drug resistance; Drug Resistance, Viral - genetics; Female; Ganciclovir; Genes, Viral; Genetic aspects; Genomes; Hepatic transplantation; High-Throughput Nucleotide Sequencing - methods; Hospitals; Humans; Impact resistance; Infections; Infectious diseases; Kinases; Lung transplantation; Male; Medical research; Medicine and Health Sciences; Microbial drug resistance; Middle Aged; Multivariate analysis; Mutation; Mutation - genetics; Next-generation sequencing; Organ transplant recipients; Organ transplantation; Patients; Prophylaxis; Research and analysis methods; Risk analysis; Risk factors; Transplant Recipients; Transplantation; Transplants & implants; Trasplantament hepàtic; Spain
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0219701

The aim of this study was to identify CMV drug resistance mutations (DRM) in solid organ transplant (SOT) recipients with suspected resistance comparing next-generation sequencing (NGS) with Sanger sequencing and assessing risk factors and the clinical impact of resistance. Using Sanger sequencing as the reference method, we prospectively assessed the ability of NGS to detect CMV DRM in the UL97 and UL54 genes in a nationwide observational study from September 2013 to August 2016. Among 44 patients recruited, 14 DRM were detected by Sanger in 12 patients (27%) and 20 DRM were detected by NGS, in 16 (36%). NGS confirmed all the DRM detected by Sanger. The additional six mutations detected by NGS were present in <20% of the sequenced population, being located in the UL97 gene and conferring high-level resistance to ganciclovir. The presence of DRM by NGS was associated with lung transplantation (p = 0.050), the administration of prophylaxis (p = 0.039), a higher mean time between transplantation and suspicion of resistance (p = 0.038) and longer antiviral treatment duration before suspicion (p = 0.024). However, the latter was the only factor independently associated with the presence of DRM by NGS in the multivariate analysis (OR 2.24, 95% CI 1.03 to 4.87). NGS showed a higher yield than Sanger sequencing for detecting CMV resistance mutations in SOT recipients. The presence of DRM detected by NGS was independently associated with longer antiviral treatment.