Comparative Genomics of Environmental and ClinicalStenotrophomonas maltophiliaStrains with Different Antibiotic Resistance Profiles

Abstract

Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain’s phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance–nodulation–division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.

Prevalence and characterization of carbapenem‐resistant bacteria in water bodies in the Los Angeles–Southern California area

“…The bla L1 carbapenemase genes identified showed varying diversity (83%–99% DNA identity) compared to the bla L1 reference sequence. The presence of the L1 carbapenemase in Stenotrophomonas maltophilia is well documented in both clinical and environmental isolates and is a major contributor to its untreatability (Brooke, ; Tacão et al., ; Youenou et al., ).…”

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

“…Sm6 forms the largest cluster, grouping mostly clinical isolates related to the type strain S. maltophilia ATCC 13637 T , like the model strain K279a (Crossman et al, 2008), ISMMS4 (Pak et al, 2015), 862_SMAL, 1149_SMAL and 1253_SMAL (Roach et al, 2015), as well as EPM1 (Sassera et al, 2013), recovered from the human parasite Giardia duodenalis. However, this group also comprises some environmental isolates like BurE1, recovered from a bulk soil sample (Youenou et al, 2015). In summary, cluster Sm6 holds the bona fide S. maltophilia strains (sensu stricto), which may be well-adapted to associate with different eukaryotic hosts and cause opportunistic infections in humans.…”

“…Cluster Sm2 groups the S. pavanii strains, including the type strain DSM_25135 T , isolated from the stems of sugar cane in Brazil (Ramos et al, 2011), together with the clinical isolates ISMMS6 and ISMMS7, that carry mutations conferring quinolone resistance and causing bacteremia (Pak et al, 2015), and strain C11, recovered from pediatric cystic fibrosis patients (Ormerod et al, 2015). Cluster Sm5 includes two strains recovered from soils, ATCC 19867 which was first classified as Pseudomonas hibiscicola, and later reclassified as S. maltophilia based on MLSA studies (Vasileuskaya-Schulz et al, 2011), and the African strain BurA1, isolated from bulk soil samples collected in sorghum fields in Burkina Faso (Youenou et al, 2015). Cluster Sm9 holds clinical isolates, like 131_SMAL, 424_SMAL and 951_SMAL (Roach et al, 2015).…”

Extreme genome selection towards complete antimicrobial resistance in a nosocomial strain ofStenotrophomonas maltophiliacomplex

“…The unique DRs of SM866 were detected using BRIG v0.95 (30) which were further confirmed using blastn package of BLAST++ (31). A well characterized nucleotide sequence of the antibiotic resistance gene clusters and efflux pumps were retrieved from the complete genome of S. maltophilia K279a (32). A standalone blast was performed with these gene as query with SM866 and the previously reported strains of Smc (33).…”