:
and
often infect the airways in cystic fibrosis (CF). Because registry studies show higher prevalence of
versus
in older patients with CF, a common assumption is that
replaces
over time.
,
can ...outgrow and kill
. However, it is unknown how rapidly
replaces
in patients with CF.
: We studied a longitudinal cohort of children and adults with CF who had quantitative sputum cultures. We determined the abundance of
and
in cfu/ml. We determined the duration and persistence of infections and measured longitudinal changes in culture positivity and abundance for each organism.
: Between 2004 and 2017, 134 patients had ≥10 quantitative cultures, with median observation time of 10.15 years. One hundred twenty-four patients had at least one positive culture for
, and 123 had at least one positive culture for
. Both species had median abundance of >10
cfu/ml. Culture abundance was stable over time for both organisms. There was an increase in the prevalence of
/
coinfection but no decrease in
prevalence within individuals over time.
:
and
are abundant in CF sputum cultures. Contrary to common assumption, we found no pattern of replacement of
by
. Many patients with CF have durable long-term coinfection with these organisms. New strategies are needed to prevent and treat these infections.
Rationale
Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated ...with poorer outcomes or detect MRSA transmission.
Objectives
To identify MRSA genes associated with low lung function and potential MRSA transmission in CF.
Methods
We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short‐read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies, classified isolates by accessory gene content, and correlated the accessory genome to clinical outcomes.
Results
The most prevalent ST were ST5 (N = 55), ST8 (N = 15), and ST105 (N = 14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three clusters of MRSA were identified by accessory genome content. Cluster A, including ST5 and ST105, was highly prevalent at all ages. Cluster B, including ST8, was more limited to younger patients. Cluster C included 6 distantly related strains. Patients 20 years old and younger infected with Cluster A had lower forced expiratory volume in the first second (FEV1) and higher sputum biomass compared to similar‐aged patients with Cluster B.
Conclusions
In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. The most prevalent cluster of MRSA, including ST5 and ST105, was associated with lower FEV1. ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.
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