The airway microbiome of persons with cystic fibrosis correlates with acquisition and microbiological outcomes of incident Stenotrophomonas maltophilia infection

• Published in: Frontiers in microbiology 2024-04, Vol.15, p.1353145-1353145
• Main Authors: Bowron, Lauren A, Acosta, Nicole, Thornton, Christina S, Carpentero, Jennifer, Waddell, Barbara-Jean M, Bharadwaj, Lalit, Ebbert, Kirsten, Castañeda-Mogollón, Daniel, Conly, John M, Rabin, Harvey R, Surette, Michael G, Parkins, Michael D
• Format: Article
• Language: English
• Subjects: bronchiectasis; cystic fibrosis; emerging infections; incident; Microbiology; microbiome; Stenotrophomonas maltophilia
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2024.1353145

Chronic infection with in persons with cystic fibrosis (pwCF) has been linked to an increased risk of pulmonary exacerbations and lung function decline. We sought to establish whether baseline sputum microbiome associates with risk of incident infection and persistence in pwCF. pwCF experiencing incident infections attending the Calgary Adult CF Clinic from 2010-2018 were compared with -negative sex, age (+/-2 years), and birth-cohort-matched controls. Infection outcomes were classified as persistent (when the pathogen was recovered in ≥50% of cultures in the subsequent year) or transient. We assessed microbial communities from prospectively biobanked sputum using V3-V4 16S ribosomal RNA (rRNA) gene sequencing, in the year preceding (Pre) (  = 57), at (At) (  = 22), and after (Post) (  = 31) incident infection. We verified relative abundance data using -specific qPCR and 16S rRNA-targeted qPCR to assess bioburden. Strains were typed using pulse-field gel electrophoresis. Twenty-five pwCF with incident (56% female, median 29 years, median FEV 61%) with 33 total episodes were compared with 56 uninfected pwCF controls. Demographics and clinical characteristics were similar between cohorts. Among those with incident infection, sputum communities did not cluster based on infection timeline (Pre, At, Post). Communities differed between the infection cohort and controls (  = 56) based on Shannon Diversity Index (SDI,  = 0.04) and clustered based on Aitchison distance (PERMANOVA,  = 0.01) prior to infection. At the time of incident isolation, communities did not differ in SDI but clustered based on Aitchison distance (PERMANOVA,  = 0.03) in those that ultimately developed persistent infection versus those that were transient. abundance within sputum was increased in samples from patients (Pre) relative to controls, measuring both relative (  = 0.004) and absolute (  = 0.001). Furthermore, abundance was increased in sputum at incident infection in those who ultimately developed persistent infection relative to those with transient infection, measured relatively (  = 0.04) or absolute (  = 0.04), respectively. Microbial community composition of CF sputum associates with infection acquisition as well as infection outcome. Our study suggests sputum microbiome may serve as a surrogate for identifying infection risk and persistence risk.