Evaluation of Phenotypical and Genotypical Methods for the Identification of Stenotrophomonas Maltophilia Strains Isolated from a Pharmaceutical Facility

Abstract

The aim of this study was to evaluate different methods for S. maltophilia identification and characterization of strains isolated from a pharmaceutical facility in Brazil. Two hundred seventy strains previously identified as S. maltophilia by VITEK®2 were evaluated. Forty strains from different phenotypical profiles were selected and submitted to Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI TOF-MS), 16S and 23S rRNA gene analysis, Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR), and determination of antimicrobial susceptibility profile. 16S rRNA sequencing provided inconclusive results for 37 (92.5%) strains; giving both Stenotrophomonas and Pseudomonas species as possibilities. Two (5.0%) strains were identified as Stenotrophomonas spp. other than S. maltophilia. One (2.5%) strain was identified as Luteimonas huabeiensis. MALDI TOF-MS identified 37 (92.5%) strains as S. maltophilia, and three (7.5%) strains were not identified. PCR targeting 23S rRNA gene yielded a positive result for 39 (97.5%) strains. However, after sequencing, two strains were identified as Stenotrophomonas rhizophila, showing false-positive results. The confirmed S. maltophilia strains (n=37) showed 35 distinct band profiles by ERIC-PCR. They also exhibited sensitivity to minocycline and levofloxacin, and six (16.3%) strains showed intermediate resistance to sulfamethoxazole-trimethoprim. In conclusion, MALDI-TOF MS proved to be a satisfactory methodology for the identification of S. maltophilia strains, but expansion of the database is necessary for the identification of other species in the genus. The 16S rDNA gene sequencing showed low resolution for Stenotrophomonas and Pseudomonas differentiation due to a strict genetic relationship. The PCR targeting 23S rRNA gene for identification of S. maltophilia was able to differentiate between these two genera but could not differentiate S. maltophilia from S. rhizophila. ERIC-PCR was shown to be a useful tool for the microbial source tracking of S. maltophilia in pharmaceutical facilities.

Keywords: Stenotrophomonas maltophilia, Pharmaceutical facility, phenotypical characterization, ERIC-PCR, MALDI TOF-MS, antibiogram