Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections

Background: The potential pathogenic role of Stenotrophomonas maltophilia
in lung disease and in particular in cystic fibrosis is unclear. To
develop further understanding of the biology of this taxa, the taxonomic
position, antibiotic resistance and virulence factors of S. maltophilia
isolates from patients with chronic lung disease were studied. Results: A
total of 111 isolates recovered between 2003 and 2016 from respiratory
samples from patients in five different countries were included. Based on
a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb)
showed that the 111 isolates identified as S. maltophilia by
Matrix-assisted laser desorption/ionization time of flight mass
spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n=65), S. pavanii
(n=6) and 13 putative novel species (n=40), which each included 1-5
isolates; these groupings coincided with the results of the 16S rDNA
analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny.
Chromosomally encoded aminoglycoside resistance was identified in all S.
maltophilia and S. pavani isolates, while acquired antibiotic resistance
genes were present in only a few isolates. Nevertheless, phenotypic
resistance levels against commonly used antibiotics, determined by
standard broth microbroth dilution, were high. Although putative virulence
genes were present in all isolates, the percentage of positive isolates
varied. The Xps II secretion system responsible for the secretion of the
StmPr1-3 proteases was mainly limited to isolates identified as S.
maltophilia based on ANIb, but no correlation with phenotypic expression
of protease activity was found. The RPF two-component quorum sensing
system involved in virulence and antibiotic resistance expression has two
main variants with one variant lacking 190 amino acids in the sensing
region. Conclusions: The putative novel Stenotrophomonas species recovered
from patient samples and identified by MALDI-TOF/MS as S. maltophilia,
differed from S. maltophilia in resistance and virulence genes, and
therefore possibly in pathogenicity. Revision of the Stenotrophomonas
taxonomy is needed in order to reliably identify strains within the genus
and elucidate the role of the different species in disease.