Rapid identification of community-associated methicillin-resistant Staphylococcus aureus by Fourier transform infrared spectroscopy

Epigenetic and Drug Response Modulation of Epigalocaten-In-3-Gallate in Staphylococcus aureus with Divergent Resistance Phenotypes

Healthcare-associated methicillin-resistant Staphylococcus aureus infections represent extremely high morbidity and mortality rates worldwide. We aimed to assess the antimicrobial potential and synergistic effect between Epigalocatenin-3-gallate (EGCG) and different antibiotics in S. aureus strains with divergent resistance phenotypes. EGCG exposure effects in epigenetic and drug resistance key modulators were also evaluated. S. aureus strains (n = 32) were isolated from infected patients in a Lisbon hospital. The identification of the S. aureus resistance phenotype was performed through automatized methods. The antibiotic synergistic assay was performed through disk diffusion according to EUCAST guidelines with co-exposure to EGCG (250, 100, 50 and 25 µg/mL). The bacteria’s molecular profile was assessed through FTIR spectroscopy. The transcriptional expression of OrfX, SpdC and WalKR was performed by using qRT-PCR. FTIR-spectroscopy analysis enabled the clear discrimination of MRSA/MSSA strains and the EGCG exposure effect in the bacteria’s molecular profiles. Divergent resistant phenotypes were associated with divergent transcriptional expression of the epigenetic modulator OrfX, particularly in MRSA strains, as well as the key drug response modulators SpdC and WalKR. These results clearly demonstrate that EGCG exposure alters the expression patterns of key epigenetic and drug response genes with associated divergent-resistant profiles, which supports its potential for antimicrobial treatment and/or therapeutic adjuvant against antibiotic-resistant microorganisms.

Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning

The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum β-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant bla_CTX-M ESBL gene variant strains and developed a classifier for bla_CTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm^-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting bla_CTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility prediction platform to enable the efficient use of antimicrobials.

Evaluation of Chemical Changes in Laboratory-Induced Colistin-Resistant Klebsiella pneumoniae

This study evaluates the electrical potential and chemical alterations in laboratory-induced colistin-resistant Klebsiella pneumoniae, as compared to the susceptible strain using spectroscopic analyses. The minimal inhibitory concentration (MIC) of colistin, ζ-potential and chemical composition analysis of K. pneumoniae strains are determined. The results obtained for the K. pneumoniae^Col-R with induced high-level colistin resistance (MIC = 16.0 ± 0.0 mg/L) are compared with the K. pneumoniae^Col-S strain susceptible to colistin (MIC = 0.25 ± 0.0 mg/L). Fourier transform infrared (FTIR) and Raman spectroscopic studies revealed differences in bacterial cell wall structures and lipopolysaccharide (LPS) of K. pneumoniae^Col-R and K. pneumoniae^Col-S strains. In the beginning, we assumed that the obtained results could relate to a negative charge of the bacterial surface and different electrostatic interactions with cationic antibiotic molecules, reducing the affinity of colistin and leading to its lower penetration into K. pneumoniae^Col-R cell. However, no significant differences in the ζ-potential between the K. pneumoniae^Col-R and K. pneumoniae^Col-S strains are noticed. In conclusion, this mechanism is most probably associated with recognisable changes in the chemical composition of the K. pneumoniae^Col-R cell wall (especially in LPS) when compared to the susceptible strain.

Advances in Optical Detection of Human-Associated Pathogenic Bacteria

Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.

Diagnosis of idiopathic amyotrophic lateral sclerosis using Fourier-transform infrared spectroscopic analysis of patient-derived skin

One of the great challenges in identifying effective therapy in many neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), is the lack of reliable biomarkers. In this study, we applied infrared imaging microspectroscopy, a valuable technique to investigate biomolecule fingerprints and secondary structure of proteins within biological tissue. We hypothesized that, since skin and CNS have the same embryonic origin, spectral differences associated with ALS-specific pathological events will be readily detectable through skin testing using this technique. Cells from healthy individuals and ALS patients were isolated from skin biopsies in order to generate tissue-engineered in vitro skin (TES). Infrared spectra of the generated TES were recorded using a focal-plane-array Fourier transform infrared (FPA-FTIR) spectrometer, and hierarchical cluster analysis of the spectral data was performed in order to establish clear differences between the tested TES specimens. Interestingly, our analyses showed that it was readily possible to discriminate ALS- and control-TES solely based on differences in associated FTIR spectra, mainly located between 1149 and 1473 cm^-1, attributed to disruption of phospholipid cell membranes, extracellular matrix remodeling or cholesterol accumulation. Spectral differences within the TES samples may therefore be associated with disease state, paving the way for the identification of biomarkers in ALS.

The Antibacterial Activity of Lavender Essential Oil Alone and In Combination with Octenidine Dihydrochloride against MRSA Strains

In the post-antibiotic era the issue of bacterial resistance refers not only to antibiotics themselves but also to common antiseptics like octenidine dihydrochloride (OCT). This appears as an emerging challenge in terms of preventing staphylococcal infections, which are both potentially severe and easy to transfer horizontally. Essential oils have shown synergisms both with antibiotics and antiseptics. Therefore the aim of this study was to investigate the impact of lavender essential oil (LEO) on OCT efficiency towards methicillin-resistant S. aureus strains (MRSA). The LEO analyzed in this study increased the OCT’s susceptibility against MRSA strains. Subsequent FTIR analysis revealed cellular wall modifications in MRSA strain cultured in media supplemented with OCT or LEO/OCT. In conclusion, LEO appears to be a promising candidate for an efficient enhancer of conventional antiseptics.

The Influence of Essential Oil Compounds on Antibacterial Activity of Mupirocin-Susceptible and Induced Low-Level Mupirocin-Resistant MRSA Strains

Because of the bacterial drug resistance development, it is reasonable to investigate chemical compounds capable of preventing the spread of resistance to mupirocin (MUP), commonly used in staphylococcal eradication. The objective of the study was to verify the influence of essential oil compounds (EOCs) on the antibacterial activity of MUP against mupirocin-susceptible (MupS) and induced low-level mupirocin-resistant (MupRL) methicillin-resistant Staphylococcus aureus (MRSA) strains. The following parameters were examined: MRSA^MupS and MRSA^MupRL susceptibility to EOCs (1,8-cineole, eugenol, carvacrol, linalool, (-)-menthone, linalyl acetate, and trans-anethole), the bacterial cell size distribution, and chemical composition by the use of Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopies. The MRSA^MupS and MRSA^MupRL strains were susceptible to all tested EOCs. 1,8-cineole and (-)-menthone showed synergistic activity against MRSA^MupS in combination with mupirocin, whereas 1,8-cineole exhibited synergistic activity against MRSA^MupRL as well. In-depth analysis showed that both MRSA^MupS and MRSA^MupRL displayed similar distributions of the bacterial cell size. The FTIR and Raman spectra of the MRSA^MupS and MRSA^MupRL strains showed differences in some regions. New bands in the MRSA^MupRL Raman spectrum were observed. It was concluded that the use of 1,8-cineole in combination with mupirocin can increase the mupirocin activity against the MRSA^MupS and MRSA^MupRL strains.

Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy

Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.

Identification of Escherichia coli and Trueperella pyogenes isolated from the uterus of dairy cows using routine bacteriological testing and Fourier transform infrared spectroscopy

Background

Uterine disorders are common postpartum diseases in dairy cows. In practice, uterine treatment is often based on systemic or locally applied antimicrobials with no previous identification of pathogens. Accurate on-farm diagnostics are not available, and routine testing is time-consuming and cost intensive. An accurate method that could simplify the identification of uterine pathogenic bacteria and improve pathogen-specific treatments could be an important advance to practitioners. The objective of the present study was to evaluate whether a database built with uterine bacteria from European dairy cows could be used to identify bacteria from Argentinean cows by Fourier transformed infrared (FTIR) spectroscopy. Uterine samples from 64 multiparous dairy cows with different types of vaginal discharge (VD) were collected between 5 and 60 days postpartum, analyzed by routine bacteriological testing methods and then re-evaluated by FTIR spectroscopy (n = 27).

Results

FTIR spectroscopy identified Escherichia coli in 12 out of 14 samples and Trueperella pyogenes in 8 out of 10 samples. The agreement between the two methods was good with a Kappa coefficient of 0.73. In addition, the likelihood for bacterial growth of common uterine pathogens such as E. coli and T. pyogenes tended to increase with VD score. The odds for a positive result to E. coli or T. pyogenes was 1.88 times higher in cows with fetid VD than in herdmates with clear normal VD.

Conclusions

We conclude that the presence of E. coli and T. pyogenes in uterine samples from Argentinean dairy cows can be detected with FTIR with the use of a database built with uterine bacteria from European dairy cows. Future studies are needed to determine if FTIR can be used as an alternative to routine bacteriological testing methods.

High-resolution subtyping of Staphylococcus aureus strains by means of Fourier-transform infrared spectroscopy

Staphylococcus aureus causes a variety of serious illnesses in humans and animals. Subtyping of S. aureus isolates plays a crucial role in epidemiological investigations. Metabolic fingerprinting by Fourier-transform infrared (FTIR) spectroscopy is commonly used to identify microbes at species as well as subspecies level. In this study, we aimed to assess the suitability of FTIR spectroscopy as a tool for S. aureus subtyping. To this end, we compared the subtyping performance of FTIR spectroscopy to other subtyping methods such as pulsed field gel electrophoresis (PFGE) and spa typing in a blinded experimental setup and investigated the ability of FTIR spectroscopy for identifying S. aureus clonal complexes (CC). A total of 70 S. aureus strains from human, animal, and food sources were selected, for which clonal complexes and a unique virulence and resistance gene pattern had been determined by DNA microarray analysis. FTIR spectral analysis resulted in high discriminatory power similar as obtained by spa typing and PFGE. High directional concordance was found between FTIR spectroscopy based subtypes and capsular polysaccharide expression detected by FTIR spectroscopy and the cap specific locus, reflecting strain specific expression of capsular polysaccharides and/or other surface glycopolymers, such as wall teichoic acid, peptidoglycane, and lipoteichoic acid. Supervised chemometrics showed only limited possibilities for differentiation of S. aureus CC by FTIR spectroscopy with the exception of CC45 and CC705. In conclusion, FTIR spectroscopy represents a valuable tool for S. aureus subtyping, which complements current molecular and proteomic strain typing.

Feature selection strategies for identification of Staphylococcus aureus recovered in blood cultures using FT-IR spectroscopy successive projections algorithm for variable selection: a case study

Staphylococcus aureus is one of the leading causes of bacteremia, with high levels of accompanying morbidity and mortality. Current gold standard for the detection of S. aureus is very time-consuming, typically taking 24h or longer. We set out to determine whether Fourier-transform infrared spectroscopy (FT-IR) combined with variable selection techniques, such as, genetic algorithm-linear discriminant analysis (GA-LDA) and successive projection algorithm-linear discriminant analysis (SPA-LDA) could be applied to detect this pathogen of bloodstream infection in samples based on the unique spectral "fingerprints" of their biochemical composition. Thirty real blood samples from healthy volunteers were contaminated with five different concentrations (10(7) until 10(3) CFU/mL) of microorganism and it analyzed by IR spectroscopy. The resulting GA-LDA model successfully classified all test samples with respect to their concentration in contaminated blood using only 18 wavenumbers. Discriminant functions revealed that GA-LDA clearly segregated different microorganism concentrations and the variable selected confirmed the chemical entities associated with the microorganism. The current study indicates that IR spectroscopy with feature selection techniques have the potential to provide one rapid approach for whole-organism fingerprint diagnostic microbial directly in blood culture.

Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method

Fourier transform infrared (FTIR) spectroscopy was introduced in 1991 as a technique to identify and classify microbes. Since then, it has gained growing interest and has undergone a remarkable evolution. Highly sophisticated spectrometers have been developed, enabling a high sample throughput. Today, the generation of high-quality data in a short time and the application of the technique for rapid and reliable identification of microbes to the species level are well documented. What makes FTIR spectroscopy even more attractive is the fact that spectral information can also be exploited for strain typing purposes, which is particularly important for epidemiological analyses and some technological applications. Accordingly, in recent years, FTIR spectroscopy has been increasingly used for typing and classifying microorganisms below the species level. The intention of this review is to give an overview over current knowledge and strategies of using FTIR spectroscopy for species identification and to describe different approaches for strain typing.

Rapid and reliable identification of Staphylococcus aureus capsular serotypes by means of artificial neural network-assisted Fourier transform infrared spectroscopy

Staphylococcus aureus capsular polysaccharides (CP) are important virulence factors and represent putative targets for vaccine development. Therefore, the purpose of this study was to develop a high-throughput method to identify and discriminate the clinically important S. aureus capsular serotypes 5, 8, and NT (nontypeable). A comprehensive set of clinical isolates derived from different origins and control strains, representative for each serotype, were used to establish a CP typing system based on Fourier transform infrared (FTIR) spectroscopy and chemometric techniques. By combining FTIR spectroscopy with artificial neuronal network (ANN) analysis, a system was successfully established, allowing a rapid identification and discrimination of all three serotypes. The overall accuracy of the ANN-assisted FTIR spectroscopy CP typing system was 96.7% for the internal validation and 98.2% for the external validation. One isolate in the internal validation and one isolate in the external validation failed in the classification procedure, but none of the isolates was incorrectly classified. The present study demonstrates that ANN-assisted FTIR spectroscopy allows a rapid and reliable discrimination of S. aureus capsular serotypes. It is suitable for diagnostic as well as large-scale epidemiologic surveillance of S. aureus capsule expression and provides useful information with respect to chronicity of infection.