ATR-FTIR spectroscopic investigation of E. coli transconjugants beta-lactams-resistance phenotype

Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity

Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.

In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy

Foodborne pathogenic microorganisms form biofilms at abiotic surfaces, which is a particular challenge in food processing industries. The complexity of biofilm formation requires a fundamental understanding on the involved molecular mechanisms, which may then lead to efficient prevention strategies. In the present study, biogenic amine producing bacteria, i.e., Lentilactobacillus parabuchneri DSM 5987 strain isolated from cheese were studied in respect with biofilm formation, which is of substantial relevance given their contribution to the presence of histamine in dairy products. While scanning electron microscopy was used to investigate biofilm adhesion at stainless steel surfaces, in situ infrared attenuated total reflection spectroscopy (IR-ATR) using a custom flow-through assembly was used for real-time and non-destructive observations of biofilm formation during a period of several days. The spectral window of 1700–600 cm−1 provides access to vibrational signatures characteristic for identifying and tracking L. parabuchneri biofilm formation and maturation. Especially, the amide I and II bands, lactic acid produced as the biofilm matures, and a pronounced increase of bands characteristic for extracellular polymeric substances (EPS) provide molecular insight into biofilm formation, maturation, and changes in biofilm architecture. Finally, multivariate data evaluation strategies were applied facilitating the unambiguous classification of the observed biofilm changes via IR spectroscopic data.

Rapid, label-free pathogen identification system for multidrug-resistant bacterial wound infection detection on military members in the battlefield

US military service members experiencing combat-related wounds have higher risk of infection by multidrug-resistant bacteria. The gold standard culture-based antimicrobial susceptibility testing (AST) is not feasible in the battlefield environment. Thus, a rapid deployable system for bacteria identification and AST directly from wound sample is urgently needed. We report the potential of a Rapid, Label-free Pathogen Identification (RAPID) diagnostic system based on ATR-FTIR method to detect and distinguish multi-drug resistant strains for six different species in the ESKAPEE group. Our RAPID system combines sample processing on-broad to isolate and enrich bacteria cells from wound sample, ATR-FTIR measurement to detect antimicrobial-induced bacterial cell spectral changes, and machine learning model for automated, objective, and quantitative spectral analysis and unknown sample classification. Based on experimental results, our RAPID system is a promising technology for label-free, sensitive (104 cfu/mL from mixture), species-specific (> 95% accuracy), rapid (< 10 min for identification, ~ 4 hours for AST) bacteria detection directly from wound samples.

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.

The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany)

The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.

Potential of Fourier transform infrared spectroscopy (FT-IR) to differentiate environmental Aspergillus fungi species A. niger, A. ochraceus, and A. westerdijkiae using two different methodologies

We assessed the ability of Fourier transform infrared spectroscopy (FT-IR) to differentiate three important and morphologically similar Aspergillus species: A. ochraceus and A. westerdijkiae, and A. niger. Fungi were processed by two methods, powdered mycelia and conidiospore-saline solution, and then recorded in a spectrometer. Second derivatives with nine points of smoothing were applied as spectra data pretreatment. Partial least squares regression was used for the species comparison models and a prediction test was used to evaluate the models. The powdered-mycelia methodology correctly identified 100% of the prediction test set to discriminate A. niger from A. ochraceus and A. westerdijkiae; in addition, it had a 86.6% success rate in discriminating A. ochraceus and A. westerdijkiae. This is the first time a study assessed the ability of FT-IR to differentiate A. niger, A. ochraceus, and A. westerdijkiae, and we believe this technique is very promising for classifying and distinguish fungi isolates.

Characterization of Xenorhabdus and Photorhabdus bacteria by Fourier transform mid-infrared spectroscopy with attenuated total reflection (FT-IR/ATR)

The use of Fourier transform mid-infrared spectroscopy with attenuated total reflection for characterizing entomopathogenic bacteria from genera Xenorhabdus and Photorhabdus is evaluated for the first time. The resulting spectra of Xenorhabdus poinarii and Photorhabdus luminiscens were compared with the spectrum of Escherichia coli samples. The absorption spectra generated by the bacteria samples, were very different at the region below 1400cm(-1) which represents the stretching vibrations of phosphate and carbohydrates. Star diagrams of the fingerprint section of nematodes spectra (between 1,350 and 1,650 cm(-1)) for separation between spectra was used and showed to be a useful tool for classification purposes.

Fourier transform infrared spectroscopy for molecular analysis of microbial cells

A rapid and inexpensive method to characterise chemical cell properties and identify the functional groups present in the cell wall is Fourier transform infrared spectroscopy (FTIR). Infrared spectroscopy is a well-established technique to identify functional groups in organic molecules based on their vibration modes at different infrared wave numbers. The presence or absence of functional groups, their protonation states, or any changes due to new interactions can be monitored by analysing the position and intensity of the different infrared absorption bands. Additionally, infrared spectroscopy is non-destructive and can be used to monitor the chemistry of living cells. Despite the complexity of the spectra, the elucidation of functional groups on Gram-negative and Gram-positive bacteria has been already well documented in the literature. Recent advances in detector sensitivity have allowed the use of micro-FTIR spectroscopy as an important analytical tool to analyse biofilm samples without the need of previous treatment. Using FTIR spectroscopy, the infrared bands corresponding to proteins, lipids, polysaccharides, polyphosphate groups, and other carbohydrate functional groups on the bacterial cells can now be identified and compared along different conditions. Despite some differences in FTIR spectra among bacterial strains, experimental conditions, or changes in microbiological parameters, the IR absorption bands between approximately 4,000 and 400 cm(-1) are mainly due to fundamental vibrational modes and can often be assigned to the same particular functional groups. In this chapter, an overview covering the different sample preparation protocols for infrared analysis of bacterial cells is given, alongside the basic principles of the technique, the procedures for calculating vibrational frequencies based on simple harmonic motion, and the advantages and disadvantages of FTIR spectroscopy for the analysis of microorganisms.

Discrimination of cyanobacterial strains isolated from saline soils in Nakhon Ratchasima, Thailand using attenuated total reflectance FTIR spectroscopy

A method was developed whereby high quality FTIR spectra could be rapidly acquired from soil-borne filamentous cyanobacteria using ATR FTIR spectroscopy. Spectra of all strains displayed bands typical of those previously reported for microalgae and water-borne cyanobacteria, with each strain having a unique spectral profile. Most variation between strains occurred in the C-O stretching and the amide regions. Soft Independent Modelling by Class Analogy (SIMCA) was used to classify the strains with an accuracy of better than 93%, with best classification results using the spectral region from 1800-950 cm(-1). Despite this spectral region undergoing substantial changes, particularly in amide and C-O stretching bands, as cultures progressed through the early-, mid- to late-exponential growth phases, classification accuracy was still good (approximately 80%) with data from all growth phases combined. These results indicate that ATR/FTIR spectroscopy combined with chemometric classification methods constitute a rapid, reproducible, and potentially automated approach to classifying soil-borne filamentous cyanobacteria.

FT-IR microspectroscopy for early identification of some clinically relevant pathogens

AIMS

To investigate the potentials and limitations of Fourier transform-infrared (FT-IR) microspectroscopy as a tool to identify, at the level of microcolonies, pathogenic bacteria frequently isolated in the clinical environment.

METHODS AND RESULTS

A total of 1570 FT-IR spectra from 164 gram-positive and gram-negative bacteria isolated from patients were recorded from 6 to 10-h old microcolonies of 50-150 microm size. A classification of 100% was obtained for the most frequent gram-positive bacteria, such as Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, and Enterococcus faecium at the species level. An average accuracy of about 80% was reached with Gram negative bacteria from the Enterobacteriaceae and Pseudomonaceae families; Enterobacter aerogenes, Enterobacter cloacae, Klebsiella spp., and Citrobacter koseri; and Proteus mirabilis and Escherichia coli. Results were comparable with FT-IR measurements on dried suspensions from 18-h cultures.

CONCLUSIONS

Early identification of young microcolonies is feasible with FT-IR microscopy with a very high accuracy for gram-positive bacteria. Some improvement in the transfer of microcolonies is necessary to increase the accuracy for gram-negative bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Combination of FT-IR microscopy and multivariate data analysis could be a complementary, rapid, and reliable tool for screening and discriminating, at species and subspecies level, micro-organisms of clinical, food-borne, or environmental origins.

Investigating the heterogeneity of cell growth in microbial colonies by FTIR microspectroscopy

Microorganisms rarely occur as individual cells in nature and are, instead, organized in complex multicellular communities such as colonies, fruiting bodies, or biofilms. Interest in the natural microbial life-style has increased during the last decade and a whole plethora of techniques has been used to gain insight into the development, structure and composition of diverse microbial communities. We have developed a technique for investigating the spatial heterogeneity of microbial growth in macro-colonies which essentially entails excision of the colonies with the underlying agar, freezing and subsequent cryotoming of the colonies, then FTIR microspectroscopic mapping of the cryosections. Colonies from Legionella, Bacillus, and Candida strains were chosen as model systems of multi-cellular communities to evaluate the technique. The results obtained indicate pronounced cell population heterogeneity even in relatively young colonies cultivated under laboratory conditions. Spectral data obtained from different positions within, e.g., a colony of Legionella bozemanii 120 h old indicated that levels of the storage material poly-beta-hydroxybutyric acid were significantly higher in cells at the surface of the colonies than in those growing at the bottom next to the agar surface. Similarly, in a 24-h-old macro-colony of Bacillus megaterium significantly more of the capsular compound polyglutamic acid was detected in upper layers than in deeper layers of the colony. Results demonstrate that FTIR microspectroscopy can be an useful tool for investigation of the spatial heterogeneity of cell growth within microbial macro-colonies. It is suggested that the method also can be adapted to the analysis of more complex multicellular communities, for example fruiting bodies, biofilms, or colonies growing under natural conditions.

Detection of Escherichia coli O157:H7 and Salmonella typhimurium using filtration followed by Fourier-transform infrared spectroscopy

Fourier-transform infrared spectroscopy has been successfully used as a nondestructive method for identifying, distinguishing, and classifying pathogens. In this study, a less time-consuming Fourier-transform infrared procedure was developed to identify Escherichia coli O157:H7 and Salmonella Typhimurium. Samples containing 10(9) CFU/ml were prepared in tryptic soy broth and then serially diluted (up to eight times) to obtain bacterial solutions of 10(9) to 10 CFU/ml. These dilutions were incubated at 37 degrees C for 6 h, samples were filtered through a Metricel filter hourly (for 0 to 6 h), and spectra were obtained using a ZnSe contact attenuated total reflectance accessory on a Continu mum infrared microscope. Midinfrared spectra (4,000 to 700 cm(-1)) of Salmonella Typhimurium and E. coli O157:H7 were generated, and peak areas in the region of 1,589 to 1,493 cm(-1) were used to detect the pathogens. Initially, detection limits were between 10(6) and 10(7) CFU/ml without preenrichment, and samples starting with 500 CFU/ml were detectable following incubation for 6 h, when counts reached at least 10(6) CFU/ ml. Compared with results of previously published studies in which Fourier-transform infrared spectroscopy was used to identify select pathogens, this method is more rapid and less expensive for practical large-scale sample analysis.

Differentiation of selected Salmonella enterica serovars by Fourier transform mid-infrared spectroscopy

Salmonella enterica serovars include pathogens responsible for high numbers of foodborne salmonellosis. Fourier transform infrared (FT-IR) spectroscopy can be used to rapidly and accurately identify microorganisms based on unique spectra of bacterial cell components. The objectives of this study were to discriminate closely related Salmonella enterica serovars by using FT-IR spectroscopy and multivariate analysis and to compare the performance of three techniques for differentiating among Salmonella serovars. Selected serovars of S. enterica were streaked onto plate count agar and incubated (37 degrees C, 24 h). Isolated colonies were suspended in phosphate buffer or 50% ethanol (10 microL). Suspensions were placed on (1) ZnSe crystals for transmission, (2) disposable polyethylene membranes (DPM) for transmission, and (3) diamond crystal plate for attenuated total reflectance (ATR) analyses; all samples were dried under vacuum. Classification models, soft independent modeling of class analogy (SIMCA), from derivatized infrared spectra (1300-900 cm(-1)), discriminated among Salmonella serovars presumably attributed to cell's lipopolysaccharides (1000-980 cm(-1)). Samples on DPM required high cell density for reliable spectra. High-quality spectra were obtained when a single colony was suspended in ethanol or buffer and mounted on ZnSe crystals for transmission or diamond plate for ATR analysis. Prediction of unknowns, representative of serovars used to construct classification models, showed that all techniques were suitable for the rapid and accurate differentiation of Salmonella serovars.

Rapid identification of Candida species by FT-IR microspectroscopy

Due to the continuous increase of human candidiasis and the great diversity of yeasts of the Candida genera, it is indispensable to identify this yeast as early as possible. Early identification enables an early diagnostic and patient-adapted anti-fungal therapy, thus reducing morbidity and mortality related to these infections. In view of this, we have in this study investigated microcolonies using a method based on Fourier transform-infrared microspectroscopy (FTIRM) for a rapid and early identification of the most frequent Candida species encountered in human pathology. FTIR spectroscopy is a whole-cell "fingerprinting" method by which microorganisms can be identified. By exploiting the huge discriminating capacity of this technique, we identified 6 species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, and Candida kefyr) from a collection of 57 clinical strains of Candida, isolated from hospitalised patients. Data obtained on 10- to 18-h-old microcolonies were compared to cultures of 24 h. Our results clearly show the efficiency and the robustness of FTIR (micro)spectroscopy in identifying species with a classification rate of 100% for both microcolonies and 24-h cultures. FTIR microspectroscopy is thus a promising clinical approach, because compared to conventional and molecular techniques, it is time and money saving, has great identification and discriminating potentials, and is amenable to an automated high-throughput routine system.

Classification and identification of enterococci: a comparative phenotypic, genotypic, and vibrational spectroscopic study

Rapid and accurate identification of enterococci at the species level is an essential task in clinical microbiology since these organisms have emerged as one of the leading causes of nosocomial infections worldwide. Vibrational spectroscopic techniques (infrared [IR] and Raman) could provide potential alternatives to conventional typing methods, because they are fast, easy to perform, and economical. We present a comparative study using phenotypic, genotypic, and vibrational spectroscopic techniques for typing a collection of 18 Enterococcus strains comprising six different species. Classification of the bacteria by Fourier transform (FT)-IR spectroscopy in combination with hierarchical cluster analysis revealed discrepancies for certain strains when compared with results obtained from automated phenotypic systems, such as API and MicroScan. Further diagnostic evaluation using genotypic methods-i.e., PCR of the species-specific ligase and glycopeptide resistance genes, which is limited to the identification of only four Enterococcus species and 16S RNA sequencing, the "gold standard" for identification of enterococci-confirmed the results obtained by the FT-IR classification. These results were later reproduced by three different laboratories, using confocal Raman microspectroscopy, FT-IR attenuated total reflectance spectroscopy, and FT-IR microspectroscopy, demonstrating the discriminative capacity and the reproducibility of the technique. It is concluded that vibrational spectroscopic techniques have great potential as routine methods in clinical microbiology.

FTIR spectroscopic analysis of Saccharomyces cerevisiae cell walls: study of an anomalous strain exhibiting a pink-colored cell phenotype

A new strain, exhibiting an intriguing pink-colored cell phenotype, was obtained after an encoding alpha-glucosidase gene from an archaebacteria Thermococcus hydrothermalis was cloned by functional complementation of a mal11 Saccharomyces cerevisiae mutant TCY70. The possible implications of the alpha-glucosidase on the cell wall were evaluated by infrared spectroscopy and data indicate a 30% decrease in mannoproteins and an increase in beta-glucans. The loss of mannoproteins was confirmed by experiments on cells deprived of peptidomannans. Modifications in the major components of the cell wall did not jeopardize cell viability. Such rapid optical spectroscopic method can be used to screen a wide range of yeast mutants.

Investigating microbial (micro)colony heterogeneity by vibrational spectroscopy

Fourier transform infrared and Raman microspectroscopy are currently being developed as new methods for the rapid identification of clinically relevant microorganisms. These methods involve measuring spectra from microcolonies which have been cultured for as little as 6 h, followed by the nonsubjective identification of microorganisms through the use of multivariate statistical analyses. To examine the biological heterogeneity of microorganism growth which is reflected in the spectra, measurements were acquired from various positions within (micro)colonies cultured for 6, 12, and 24 h. The studies reveal that there is little spectral variance in 6-h microcolonies. In contrast, the 12- and 24-h cultures exhibited a significant amount of heterogeneity. Hierarchical cluster analysis of the spectra from the various positions and depths reveals the presence of different layers in the colonies. Further analysis indicates that spectra acquired from the surface of the colonies exhibit higher levels of glycogen than do the deeper layers of the colony. Additionally, the spectra from the deeper layers present with higher RNA levels than the surface layers. Therefore, the 6-h colonies with their limited heterogeneity are more suitable for inclusion in a spectral database to be used for classification purposes. These results also demonstrate that vibrational spectroscopic techniques can be useful tools for studying the nature of colony development and biofilm formation.

FT-IR microspectroscopy for microbiological studies

In this article we present an infrared microspectroscopic investigation on Candida albicans microcolonies, taken as a model system for studies on other microorganisms. Excellent Fourier transform infrared (FT-IR) absorption spectra from 4000 to 850 cm(-1) have been collected in only 20 s from sampling areas of 100x100 microm(2) in microcolonies, which had been transferred from the agar plate onto zinc selenide (ZnSe) windows. When different regions within a single microcolony were investigated, absorption spectra with important differences in the carbohydrate absorption (from 1200 to 850 cm(-1)) were detected for the cells in the center and in the periphery of the colony. Results obtained on microcolonies grown on solid agar with increasing dextrose concentrations indicated that the observed spectral heterogeneity was related to differences in dextrose uptake, which was lower for the old cells in the center of the colony than for the metabolically active cells at the periphery. Although it is otherwise difficult to quantitatively evaluate the dextrose uptake in a microcolony, FT-IR absorption microspectroscopy offers a new and rapid method for the analysis of this process. The possibility of studying highly absorbing colonies by attenuated total reflection (ATR) by means of an ATR microscope germanium objective is also presented here for the first time. An evaluation of the contact area sampled by this technique is reported with a discussion of the spatial resolution, the quality and the potential of the ATR measurements.

Raman spectroscopic method for identification of clinically relevant microorganisms growing on solid culture medium

Routine clinical microbiological identification of pathogenic microorganisms is largely based on nutritional and biochemical tests. In the case of severely ill patients, the unavoidable time delay associated with such identification procedures can be fatal. We present a novel identification method based on confocal Raman microspectroscopy. With this approach it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 h of culturing for the most commonly encountered organisms. Due to the limited thickness of microcolonies, some of the underlying culture medium is sampled together with the bacteria. Spectra measured at different depths in a microcolony contain different amounts of the medium signal. A mathematical routine, involving vector algebra, is described for the nonsubjective correction of spectra for variable signal contributions of the medium. To illustrate the possibilities of our approach for the identification of microorganisms, Raman spectra were collected from 6-h microcolonies of five bacterial strains on solid culture medium. The classification results show that confocal Raman microspectroscopy has great potential as a powerful new tool in clinical diagnostic microbiology.