Targeted proteomics links virulence factor expression with clinical severity in staphylococcal pneumonia.

Introduction: The bacterial pathogen Staphylococcus aureus harbors numerous virulence factors that impact infection severity. Beyond virulence gene presence or absence, the expression level of virulence proteins is known to vary across S. aureus lineages and isolates. However, the impact of expression level on severity is poorly understood due to the lack of high-throughput quantification methods of virulence proteins. Methods: We present a targeted proteomic approach able to monitor 42 staphylococcal proteins in a single experiment. Using this approach, we compared the quantitative virulomes of 136 S. aureus isolates from a nationwide cohort of French patients with severe community-acquired staphylococcal pneumonia, all requiring intensive care. We used multivariable regression models adjusted for patient baseline health (Charlson comorbidity score) to identify the virulence factors whose in vitro expression level predicted pneumonia severity markers, namely leukopenia and hemoptysis, as well as patient survival. Results: We found that leukopenia was predicted by higher expression of HlgB, Nuc, and Tsst-1 and lower expression of BlaI and HlgC, while hemoptysis was predicted by higher expression of BlaZ and HlgB and lower expression of HlgC. Strikingly, mortality was independently predicted in a dose-dependent fashion by a single phage-encoded virulence factor, the Panton-Valentine leucocidin (PVL), both in logistic (OR 1.28; 95%CI[1.02;1.60]) and survival (HR 1.15; 95%CI[1.02;1.30]) regression models. Discussion: These findings demonstrate that the in vitro expression level of virulence factors can be correlated with infection severity using targeted proteomics, a method that may be adapted to other bacterial pathogens.

Quantification of infliximab and adalimumab in human plasma by a liquid chromatography tandem mass spectrometry kit and comparison with two ELISA methods.

Background: This study compared the performance of plasma infliximab and adalimumab quantification using a commercially available kit (mAbXmise kit) and mass spectrometry readout to that of two ELISA methods in patients treated for inflammatory bowel disease. Methods & results: The mAbXmise method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) was linear from 2 to 100 µg/ml. It was validated according to international guidelines. Regarding cross-validation for infliximab (n = 70), the mean bias with LC-MS/MS assay was approximately threefold higher with the commercial ELISA assay compared with the in-house ELISA (-6.1 vs -1.8 µg/ml, respectively). The mean bias between the LC-MS/MS assay and in-house ELISA was -1.2 µg/ml for adalimumab (n = 35). Conclusion: The LC-MS/MS method is a powerful alternative to immunoassays to monitor concentrations of infliximab and adalimumab.

Multivariate curve resolution--alternating least squares applied to the investigation of ultrafast competitive photoreactions.

The main advantage of multivariate curve resolution - alternating least squares method (MCR-ALS) is the possibility to act as multiset analysis method, combining data coming from different experiments to provide a complete and more accurate description of a chemical system. Exploiting the multiset side, the combination of experiments obtained from two photo-active systems with complementary pathways and monitored by femtosecond UV-vis transient absorption spectroscopy is presented in this work. A multiset hard- and soft-multivariate curve resolution model (HS-MCR) was built allowing the description of the spectrokinetic features of the entire system. Additionally, reaction quantum yields were incorporated in the hard-model in order to describe branching ratios for intermediate species. The photodynamics of salicylidene aniline (SA) was investigated as a case study. The overall reaction scheme involves two competitive and parallel pathways. On the one hand, a photoinduced excited state intramolecular proton transfer (ESIPT) followed by a cis-trans isomerization leads to the so-called photochromic form of the molecule, which absorbs in the visible. The formation of the photochromic species is well characterized in the literature. On the other hand, a complex internal rotation of the molecule takes place, which is a competing reaction. The rotation mechanism is based on a trans-cis isomerization. This work aimed at providing a detailed spectrokinetic characterization of both reaction pathways for SA. For this purpose, the photodynamics of two molecules of identical parent structures and different substituent patterns were investigated in femtosecond transient absorption spectroscopy. For SA, the mechanism described above involving the two parallel pathways was observed, whereas for the derivative form of SA, the photochromic reaction was blocked because of the replacement of an H atom by a methyl group. The application of MCR approaches enabled to obtain transient spectra for the different intermediate species involved and rate constants for the photochromic reaction, thus contributing to a comprehensive description of the photodynamics of SA.

Baseline correction methods to deal with artifacts in femtosecond transient absorption spectroscopy.

In femtosecond transient absorption spectroscopy, artifact contributions are usually observed at ultra-short time scale. These complex signals are very challenging because of their nature, related to ultrafast phenomena, and because they strongly distort the structure of the spectrokinetic data. The purpose of this work is to evaluate the potential of baseline correction methods for femtosecond transient absorption spectroscopy data pre-processing. Indeed, artifacts removal should ideally be performed before multivariate data analysis. The work is thus mainly focused on two different approaches which are filtering by discrete wavelet transform, on the one hand, and smoothing by asymmetric least squares, on the other hand. The results obtained both on simulated data and on femtosecond pump-probe spectroscopy data are discussed. It can be concluded that asymmetric least squares smoothing procedure turns out to perform satisfactory for artifacts removal. Indeed, only mild discrepancies are observed in the transient spectra and, most important, good recovery of the kinetics is obtained at ultra-short time scale.

Investigation of ultrafast photoinduced processes for salicylidene aniline in solution and gas phase: toward a general photo-dynamical scheme.

Photodynamics of 2-hydroxybenzylideneaniline (photochromic salicylidene aniline SAOH) and N-(2-methoxybenzylidene)aniline (SAOMe) are studied by steady state and transient optical spectroscopy in solution and gas phase at different excitation wavelengths (266, 355 and 390 nm). Two competitive processes are observed from the enol* excited state: on one hand a rotation to get a twisted-enol, and on the other hand an excited state intramolecular proton transfer (ESIPT) followed by a cis-trans isomerisation to get the trans-keto photochromic product. For the first time both processes are characterized at an ultrashort time scale for salicylidene aniline. Resolution of the spectrokinetic data is achieved by multivariate curve resolution and attribution of the intermediate species recovered is performed in comparison with the results obtained for SAOMe, which can only undergo enol rotational isomerisation. It shows that ESIPT and rotation to the twisted-enol for SAOH occur within 100 fs, as predicted by recent quantum dynamical simulations, with an efficiency ratio dependent on the excitation wavelength. Therefore a general photoinduced mechanism for salicylidene aniline is drawn.