Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

Abstract

Aims: Aim of the study is to identify accurately Stenotrophomonas maltophilia isolates recovered from environmental and clinical samples. Methods and Results: Recovery of Sten. maltophilia‐like isolates from soil samples using the vancomycin, imipenem, amphotericin B (VIA) selective agar medium enabled distinction of various morphotype colonies. A set of soil and clinical isolates was tested for species identification using different methods. 16S rDNA analyses showed the dark green with a blue halo morphotype to be typical Sten. maltophilia strains. The API‐20NE, Vitek‐2 and Biolog phenotypic analyses typically used for the identification of clinical isolates did not perform well on these soil isolates. The species‐specific PCR screening targeting Sten. maltophilia 23S rDNA and the multiplex smeD/ggpS PCR, differentiating Sten. maltophilia from Stenotrophomonas rhizophila, were tested for improvement of these identification schemes. The latter multiplex PCR identified all isolates tested in this study, whatever be their origin. Conclusions: Isolation on VIA medium and confirmation of Sten. maltophilia species membership by smeD PCR is proposed to identify environmental and clinical isolates of Sten. maltophilia. Significance and Impact of the Study: The proposed approach enables isolation and identification of Sten. maltophilia from different environments in an easy and rapid way. This approach will be useful to accurately manage studies on the abundance and distribution of Sten. maltophilia in hospital and nonhospital environments.

Evolutionary genetic analysis uncovers multiple species with distinct habitat preferences and antibiotic resistance phenotypes in theStenotrophomonas maltophiliacomplex

“…In 602 our view, these clusters represent incipient species that are still capable of recombining signatures of speciation within the S. maltophilia sub-lineages, including "speciation genes study of a large collection isolates classified as S. maltophilia recovered from diverse 697 agricultural soils in France and Tunisa concluded that they display a high diversity of 698 antibiotic resistance profiles, expressing resistance against 1 to 12 antibiotics, with clinical 699 and manure isolates expressing the highest numbers(Deredjian et al, 2016). These isolates 700 were vaguely classified as S. maltophilia based on growth on the selective VIA isolation 701 medium(Kerr et al, 1996) and PCR detection of the smeD gene(Pinot et al, 2011). We 702 argue that the large phenotypic variance observed in that and similar studies result from the 703 lack of proper species delimitation.…”

Rapid identification of Stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization

“…Pinot et al . 17 used vancomycin, imipenem, amphotericin B medium agar for isolation and multiplex PCR for identification of S. maltophilia . Hogardt et al .…”

“…Problems related to misidentification of S. maltophilia by phenotypic methods can be overcome by the use of molecular methods. Pinot et al [17] used vancomycin, imipenem, amphotericin B medium agar for isolation and multiplex PCR for identification of S. maltophilia. Hogardt et al [18] designed a species-specific DNA probe for S. maltophilia identification and demonstrated that the probe could be used successfully on sputum and throat samples from CF patients.…”

A specific polymerase chain reaction method to identify Stenotrophomonas maltophilia

“…maltophilia is usually isolated using a selective medium with the addition of imipenem and other antimicrobial agents and identified by biochemical methods (Foster et al 2008a, Adjidé et al 2010. However, the biochemical tests used to identify S. maltophilia, including such commercial systems as Vitek-2, API-20NE and Biolog, occasionally misidentify this species as other non-fermentative Gram-negative bacilli (Zbinden et al 2007, Pinot et al 2011. Moreover, the current polymerase chain reaction (PCR)-based protocols for the identification of S. maltophilia have also presented limitations related to low specificity due to the significant genetic similarity between Stenotrophomonas species and other non-fermentative Gram-negative bacilli (Berg et al 1999, Foster et al 2008b.…”

“…The sequence was aligned with the S. maltophilia 23S rRNA sequences deposited in GenBank (AM743169 and AF273255) using MEGA 5.10 Beta software, presenting 100% identity. Foster et al (2008b) and Pinot et al (2011) reported the use of a different region of the 23S rRNA gene as a target, but their results showed cross-reaction between Stenotrophomonas and Xanthomonas species, demonstrating low PCR specificity. Additionally, Pinot et al (2011) developed a multiplex PCR targeting smeD and ggpS to differentiate S. maltophilia and S. rhizophila; although this technique was successful, it did not exclude the cross-reaction with Xanthomonas species.…”