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Abstract
Stenotrophomonas maltophilia is a non-fermenting Gram-negative bacterium that is ubiquitous in the environment. In humans, this opportunistic multi-drug-resistant pathogen is responsible for a plethora of healthcare-associated infections. Here, we utilized a whole genome sequencing (WGS)-based phylogenomic core single nucleotide polymorphism (SNP) approach to characterize S. maltophilia subgroups, their potential association with human infection, and to detect any possible transmission events. In total, 89 isolates (67 clinical and 22 environmental) from Germany were sequenced. Fully finished genomes of five strains were included in the dataset for the core SNP phylogenomic analysis. WGS data were compared with conventional genotyping results as well as with underlying disease, biofilm formation, protease activity, lipopolysaccharide (LPS) SDS–PAGE profiles, and serological specificity of an antibody raised against the surface-exposed O-antigen of strain S. maltophilia K279a. The WGS-based phylogenies grouped the strains into 12 clades, out of which 6 contained exclusively human and 3 exclusively environmental isolates. Biofilm formation and proteolytic activity did correlate neither with the phylogenetic tree, nor with the origin of isolates. In contrast, the genomic classification correlated well with the reactivity of the strains against the K279a O-specific antibody, as well as in part with the LPS profiles. Three clusters of clinical strains had a maximum distance of 25 distinct SNP positions, pointing to possible transmission events or acquisition from the same source. In conclusion, these findings indicate the presence of specific subgroups of S. maltophilia strains adapted to the human host.
Highlights
Stenotrophomonas maltophilia is an opportunistic, non-fermentative, Gram-negative, and ubiquitous Gammaproteobacterium
In contrast to these classical typing techniques that only interrogate a small part of the genome, generation sequencing technologies allow for the near complete analysis of a bacterial genome, i.e., whole genome sequencing (WGS)
We analyzed 89 S. maltophilia and S. rhizophila strains, including 58 isolates collected by different institutes, as well as 31 strains chosen from a recent publication, which compared traditional genotyping methods, i.e., rep-PCR, gyrB sequencing, multi-locus sequence type (MLST), amplified fragment length polymorphism (AFLP), and 16S rRNA sequencing, as respective group representatives (Adamek et al, 2011)
Summary
Stenotrophomonas maltophilia is an opportunistic, non-fermentative, Gram-negative, and ubiquitous Gammaproteobacterium This bacterium has environmental origins (water, soil), but is known to cause a diverse range of infections in humans (Denton and Kerr, 1998; Ryan et al, 2008; Brooke, 2012). The molecular typing methods used so far include amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), 16S rRNA sequencing, multi locus sequence typing (MLST), repetitive element palindromic (rep)-PCR, and gyrB sequencing, each producing varying results with no commonly accepted standard or defined nomenclature (Adamek et al, 2011) In contrast to these classical typing techniques that only interrogate a small part of the genome, generation sequencing technologies allow for the near complete analysis of a bacterial genome, i.e., whole genome sequencing (WGS). The phylogenomic classifications have been linked with underlying diseases, phenotypical assays for biofilm formation, extracellular proteolytic activity and lipopolysaccharide (LPS) pattern characterization
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