Abstract
The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.
Highlights
Bacterial species identification and delimitation are non-trivial tasks, which are critical in certain settings such as the clinic, bioterrorism and industry
We sampled 6 sites located in four rivers/streams of Morelos (Supplementary Figure S1) that were ranked into three categories based on their pollution level, based on counts of thermotolerant fecal coliforms and E. coli (Table 1)
The analysis reveals that environmental Stenotrophomonas strains can be efficiently recovered on the oligotrophic NAA medium supplemented with imipenem (8 μg/ml; >90% recovery efficiency)
Summary
Bacterial species identification and delimitation are non-trivial tasks, which are critical in certain settings such as the clinic, bioterrorism and industry. AFLPs (Hauben et al, 1999), rep-PCR (Adamek et al, 2011) and multilocus sequence analysis/typing (MLSA/MLST) (Kaiser et al, 2009; Vasileuskaya-Schulz et al, 2011) have clearly revealed the existence of multiple genomic groups within the Smc, proper recognition of species borders within the complex has not yet been satisfactorily achieved This has hindered the discovery of statistically significant associations between species and traits such as habitat preferences, antibiotic resistance phenotypes and pathogenicity potential (Adamek et al, 2011; Berg and Martinez, 2015; Deredjian et al, 2016). The identification of significant genotype-phenotype associations is critical for the safe use of particular strains from the Smc with high potential for diverse environmental biotechnologies such as bioremediation, plant growth promotion and protection (Ryan et al, 2009; Berg and Martinez, 2015)
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