Abstract
Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P.aeruginosa isolates in comparison to non-CF P.aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P.aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P.aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P.aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P.aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being "locked" inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure "chronic focal infections" with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P.aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P.aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents-a phenomenon we define as "heterogeneous MICs." By sequencing pairs of P.aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.
Highlights
Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability
We reported that P. aeruginosa isolates with heterogeneous sulfamethoxazole-trimethoprim (SMX-TMP) MICs from the same CF patient were isogenic by pulsed-field gel electrophoresis (PFGE) [9]
A total of clinical P. aeruginosa isolates were included in this analysis: 224 CF P. aeruginosa isolates from 100 cultures obtained from 56 patients and 130 non-CF P. aeruginosa isolates from 99 cultures obtained from 68 patients (Table 1)
Summary
Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. When the organism first enters the CF airway, it is under enormous host selective pressure This pressure leads to a number of welldescribed phenotypic and genotypic adaptive features such as an overall slow growth rate, diverse colony variants, heterogeneous antimicrobial susceptibility patterns, adoption of a biofilm or multicellular lifestyle, and the emergence of hypermutators, which result from nonsynonymous changes or loss of function mutations in mutS, mutL, and/or uvr [3,4,5,6]. For clinical laboratories constructing institutional antibiograms, CLSI recommends inclusion of only the first isolate of a given species per patient per reporting period irrespective of body site, antibiotic susceptibility, or other phenotypic characteristics [8] This selection has unintended implications with respect to our understanding of a subset of clinical cultures. The biological characteristics associated with this subset of organisms have been overlooked
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