Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Identifies Pseudomonas aeruginosa High-Risk Clones

Abstract

We show here that matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) accurately and quickly identified the five high-risk clones of Pseudomonas aeruginosa sequence type 111 (ST111), ST175, ST235, ST253, and ST395. The use of this screening technique by clinical microbiology laboratories may tackle the spread of high-risk clones by the quick implementation of hygiene control procedures for relevant patients. Pseudomonas aeruginosa has a nonclonal population structure with a few multidrug-resistant clusters, called "high-risk clones," that frequently produce acquired ␤-lactamases with an extended spectrum and are responsible for outbreaks in hospitals worldwide (1-13). The quick implementation of infection control measures for relevant patients may tackle the spread of these epidemic clones, but current identification is long and complex since it is based on the analysis of nucleotidic sequences. A quick and easy method for identifying high-risk clones of P. aeruginosa is then needed. Matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently integrated into the routine workflow of medical microbiology laboratories for microbial identification and has been further used for subspecies characterization (14). Here, we evaluated the ability of MALDI-TOF MS to identify high-risk clones of P. aeruginosa.Identification of peak biomarkers for five major high-risk clones of P. aeruginosa. In order to identify five major high-risk clones of P. aeruginosa (sequence type 111 [ST111], ST175, ST235, ST253, and ST395), we first defined recognition models with a training set of 46 isolates with known STs distributed homogeneously in the phylogenetic tree (Table 1 and Fig. 1). Frozen bacteria were streaked onto Mueller-Hinton agar (Bio-Rad) and incubated for 18 h at 37°C. As previously reported (15), each isolate was extracted with the ethanol-formic acid method recommended by Bruker Daltonik and analyzed with a Microflex LT mass spectrometer (Bruker Daltonik), which generated 24 raw spectra. We analyzed the spectra with the software ClinProTools 3.0 (Bruker Daltonik), which defined six models based on peak biomarkers (Table 1). The reliability and accuracy of each model were assessed through the recognition capabilities and the crossvalidation values. The models identified all the tested high-risk clones of P. aeruginosa with high recognition capabilities (Ͼ96%) and cross-validation values ranging from 72.5% to 100% (Table 1). Four models directly identified ST111, ST175, ST253, and ST395, while the identification of ST235 required a preliminary stage to identify cluster 1, which encompasses ST235 (Fig. 1).We then manually examined the spectra with ClinProTools 3.0 to assess the relevance of the peak biomarkers of each model (Table 1). Peaks were defined as biomarkers in a model because of their presence or absence or relative abundance between two tested classes. Figure 2 details only the peak biomarkers in which presence or absence was specif...

VIM-1, VIM-2, and GES-5 Carbapenemases Among Pseudomonas aeruginosa Isolates at a Tertiary Hospital in Istanbul, Turkey

“…Although multilocus sequence typing is the gold standard for the analysis of these clones, other cheaper and faster typing techniques are also available. 8 A recent study was able to accurately and quickly detect several P. aeruginosa highrisk clones using the MALDI-TOF MS. 19 In this study, we investigated the presence of the high-risk clones among carbapenemase-producing strains with MALDI-TOF MS, however, none of the isolates yielded peaks specific to the high-risk clones. On the other hand, the absence of the control strains can be regarded as a limitation of investigation of high-risk clones in this study.…”

“…The presence of high-risk clones of P. aeruginosa ST111, ST175, ST235, ST253, and ST395 was investigated for the carbapenemase-producing strains using MALDI-TOF MS (Bruker Daltonics) as described by Cabrolier et al 19 Analysis of the mass spectra was performed using the spectrum view of flexAnalysis 3.4 software (Bruker Daltonics). The presence or absence of the peak biomarkers specific to the high-risk clones was analyzed by visual comparison of the specific spectra.…”

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond

“…Another potential approach that should be followed up is the detection of high-risk clones associated with multidrug-resistant bacteria. In this approach, the relatedness between clusters of bacteria can be measured faster and more cost-effectively than by molecular methods, and more information regarding antimicrobial resistance can be obtained directly or indirectly, i.e., by detecting biomarkers associated with resistance to antimicrobial agents (144)(145)(146). We should also take into account that wholegenome sequencing is evolving very rapidly, especially with nanopore technology (147,148).…”

Detection methods for Pseudomonas aeruginosa: history and future perspective

“…Recently, MALDI-TOF MS was used to accurately and quickly identify the ve highrisk clones of Pseudomonas aeruginosa sequence type 111 (ST111), ST175, ST235, ST253, and ST395. 125 More oen, this technique was used in Pseudomonas aeruginosa drug resistance analysis such as carbapenemase Johansson et al, 2014;Hrabak, 2015). [126][127][128] MALDI-TOF MS represents an innovative technology and has a very good application prospects in the identication of Pseudomonas aeruginosa.…”