Identification of foodborne bacteria by infrared spectroscopy using cellular fatty acid methyl esters

Is Infrared Spectroscopy Ready for the Clinic?

Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.

Membrane Vesicles Are the Dominant Structural Components of Ceftazidime-Induced Biofilm Formation in an Oxacillin-Sensitive MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) has received increasing attention in recent years. However, the characteristics and relevant mechanisms of biofilm formation in oxacillin-sensitive MRSA (OS-MRSA) are poorly understood. This study was designed to characterize biofilm formation in OS-MRSA BWSA15 in response to ceftazidime (TZ) by comparing the methicillin-sensitive S. aureus (MSSA) strain BWSA23 and the oxacillin-resistant MRSA (OR-MRSA) strain BWSA11. The biofilms and biofilm-forming cells were observed by electron microscopy. Biofilms grown on microtiter plates were chemically decomposed and analyzed by Fourier transform infrared spectroscopy. The transcriptional regulation of genes associated with methicillin resistance, surface adhesion, fatty acid biosynthesis, and global regulation (sigma B) was investigated. A significant increase in biofilm formation ability (10.21-fold) and aggregation ability (2.56-fold) was observed in BWSA15 upon the treatment with TZ (16 μg/ml). The TZ-induced biofilm formation in BWSA15 was characterized by a disappearance of polysaccharide-like extracellular substances and an appearance of a large number of intercellular MVs from extracellular matrix. Few MVs were identified in the biofilms formed by BWSA11 and BWSA23. There was a significant upregulation of mecA, sigB, and fatty acid biosynthesis-associated genes and downregulation of icaA, icaD, clfA, clfB, and fnaA in BWSA15 upon the treatment with TZ. The formation of intracellular junctions of MVs in the biofilms of BWSA15 was mediated by a significant increase in the proportion of proteins as well as by an increase in the proportion of non-ionized carboxyl groups in fatty acids. This study demonstrated that beta-lactam antibiotics can induce biofilm formation in OS-MRSA, and the biofilm induction in OS-MRSA can mainly be attributed to exposed MVs with increased hydrophobicity rather than polysaccharide intercellular adhesins, cell wall-anchored surface proteins, and extracellular DNA.

Detection of molecular changes induced by antibiotics in Escherichia coli using vibrational spectroscopy

This study aimed to test Raman (400-1800cm^-1) and Infra-red (1900-500cm^-1) spectroscopies followed by statistical analysis (principal component analysis) to detect molecular changes induced by antibiotics (ampicillin, cefotaxime - cell wall synthesis inhibitors, tetracycline - protein synthesis inhibitor, ciprofloxacin - DNA synthesis inhibitor) against Escherichia coli TOP10. In case of ampicillin and cefotaxime, a decrease in protein bands in both Raman (1240, 1660cm^-1), and IR spectra (1230, 1530, 1630cm^-1), and an increase in carbohydrate bands (1150, 1020cm^-1) in IR spectra were observed. Tetracycline addition caused an increase in nucleic acid bands (775, 1478, 1578cm^-1), a sharp decrease in phenylalanine (995cm^-1) in Raman spectra and the amide I and amide II bands (1630, 1530cm^-1) in IR spectra, an increase in DNA in both Raman (1083cm^-1) and IR spectra (1080cm^-1). Regarding ciprofloxacin, an increase in nucleic acids (775, 1478, 1578cm^-1) in Raman spectra and in protein bands (1230, 1520, 1630cm^-1), in DNA (1080cm^-1) in IR spectra were detected. Clear discrimination of antibiotic-treated samples compared to the control was recorded, showing that Raman and IR spectroscopies, coupled to principal component analysis for data, could be used to detect molecular modifications in bacteria exposed to different classes of antibiotics. These findings contribute to the understanding of the mechanisms of action of antibiotics in bacteria.

Biofilm-Forming Abilities of Listeria monocytogenes Serotypes Isolated from Different Sources

A total of 98 previously characterized and serotyped L. monocytogenes strains, comprising 32 of 1/2a; 20 of 1/2b and 46 of 4b serotype, from clinical and food sources were studied for their capability to form a biofilm. The microtiter plate assay revealed 62 (63.26%) strains as weak, 27 (27.55%) strains as moderate, and 9 (9.18%) strains as strong biofilm formers. Among the strong biofilm formers, 6 strains were of serotype 1/2a and 3 strains were of serotype 1/2b. None of the strain from 4b serotype exhibited strong biofilm formation. No firm correlation (p = 0.015) was noticed between any serotype and respective biofilm formation ability. Electron microscopic studies showed that strong biofilm forming isolates could synthesize a biofilm within 24 h on surfaces important in food industries such as stainless steel, ceramic tiles, high-density polyethylene plastics, polyvinyl chloride pipes, and glass. Cell enumeration of strong, moderate, and weak biofilm was performed to determine if the number of cells correlated with the biofilm-forming capabilities of the isolates. Strong, moderate, and weak biofilm showed 570±127× 10³ cells/cm², 33±26× 10³ cells/cm², 5±3× 10³ cells/cm², respectively, indicating that the number of cells was directly proportional to the strength of the biofilm. The hydrophobicity index (HI) analysis revealed higher hydrophobicity with an increased biofilm formation. Fatty acid methyl esterase analysis revealed the amount of certain fatty acids such as iso-C15:0, anteiso-C15:0, and anteiso-C17:0 fatty acids correlated with the biofilm-forming capability of L. monocytogenes. This study showed that different strains of L. monocytogenes form biofilm of different intensities which did not completely correlate with their serotype; however, it correlated with the number of cells, hydrophobicity, and amount of certain fatty acids.

Visualized analysis of cellular fatty acid profiles of Vibrio parahaemolyticus strains under cold stress

Vibrio parahaemolyticus is a common foodborne bacterial pathogen, which survives in cold environments and is sometimes difficult to culture. Fatty acid analysis under cold stress was conducted for several V. parahaemolyticus strains using gas chromatography/mass spectrometry, and the results were compared with those of the controls. All the fatty acid profiles obtained were visualized by multidimensional scaling (MDS) and self-organized map (SOM). It was observed that the fatty acid profiles of V. parahaemolyticus substantially changed under cold stress. The percentage of methyl palmitate remarkably decreased and that of methyl palmitoleate (except for two strains) and methyl oleate increased. These findings demonstrate the role of fatty acids in cold stress. The changes in the fatty acid profiles illustrated by MDS and SOM could differentiate strains under cold stress from the controls and can potentially lead to a method of detecting injured cold-stressed V. parahaemolyticus.

Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms

The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

Identification and discrimination of bacteria using Fourier transform infrared spectroscopy

Bacterial spectra were obtained in the wavenumber range of 4000-600 cm(-1) using FTIR spectroscopy. FTIR spectral patterns were analyzed and matched with 16S-rRNA signatures of bacterial strains OS1 and OS2, isolated from oil sludge. Specific spectral bands obtained from OS1 (FJ226761), reference strain Bacillus flexus (ATCC 49095), OS2 (FJ215874) and reference strain Stenotrophomonas maltophilia (ATCC 19861) respectively, suggested that OS1 and ATCC 49095 were closely related whereas OS2 was different. The bands probably represent groups of proteins and lipids of specific bacteria. Separate peaks found in B. flexus were similar to those of OS1. The S. maltophilia (ATCC 19861) and OS2 exhibited a similar peak at 3272 cm(-1). Amide bands (I, II and III) exhibited that OS1 and B. flexus were closely related, but were different from OS2. In the fingerprint region, peak at 1096 cm(-1) and 1360 cm(-1) exhibited the specific fingerprints of OS2 and reference strain S. maltophilia (ATCC 19861), respectively. The specific fingerprint signature was found at 1339 cm(-1) for OS1 and at 1382 cm(-1) for B. flexus ATCC 49095, allowing these two strains of B. flexus to be differentiated. This spectral signature originated from phospholipid and RNA components of the cell. Principle components analysis (PCA) of spectral regions exhibited with distinct sample clusters between Bacillus flexus (ATCC 49095), S. maltophilia (ATCC 19861), OS1 and OS2 in amide and fingerprint region.

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.

Detection of Escherichia coli via VOC profiling using secondary electrospray ionization-mass spectrometry (SESI-MS)

Escherichia coli O157:H7 (EC O157:H7), as well as its recently emerging non-O157 relatives, are a notorious group of pathogenic bacteria associated with foodborne outbreaks. In this study, we demonstrated that secondary electrospray ionization mass spectrometry (SESI-MS) could be a rapid and accurate detection technology for foodborne pathogens. With SESI-MS volatile organic compound (VOC) profiling, we were able to detect and separate a group of eleven E. coli strains from two major foodborne bacteria, Staphylococcus aureus and Salmonella Typhimurium in three food modeling media. In addition, heatmap analysis of relative peak intensity show that there are six core peaks (m/z of 65, 91, 92, 117, 118 and 119) present and at a similar intensity in all eleven E. coli strains at the experimental conditions we tested. These peaks can be considered conserved VOC biomarkers for E. coli species (robustly produced after just 4 h of growth). Bacterial strain-level differentiation was also attempted via VOC profiling, and we found that EC O157:H7 and EC O145 were differentiable from all other EC strains under the conditions investigated.

Waterborne pathogen detection using Raman spectroscopy

Raman spectroscopy is being evaluated as a candidate technology for waterborne pathogen detection. We have investigated the impact of key experimental and background interference parameters on the bacterial species level identification performance of Raman detection. These parameters include laser-induced photodamage threshold, composition of water matrix, and organism aging in water. The laser-induced photodamage may be minimized by operating a 532 nm continuous wave laser excitation at laser power densities below 2300 W/cm(2) for Grampositive Bacillus atrophaeus (formerly Bacillus globigii, BG) vegetative cells, 2800 W/cm(2) for BG spores, and 3500 W/cm(2) for Gram-negative E. coli (EC) organisms. In general, Bacillus spore microorganism preparations may be irradiated with higher laser power densities than the equivalent Bacillus vegetative preparations. In order to evaluate the impact of background interference and organism aging, we selected a biomaterials set comprising Gram-positive (anthrax simulants) organisms, Gram-negative (plague simulant) organisms, and proteins (toxin simulants) and constructed a Raman signature classifier that identifies at the species level. Subsequently, we evaluated the impact of tap water and storage time in water (aging) on the classifier performance when characterizing B. thuringiensis spores, BG spores, and EC cell preparations. In general, the measured Raman signatures of biological organisms exhibited minimal spectral variability with respect to the age of a resting suspension and water matrix composition. The observed signature variability did not substantially degrade discrimination performance at the genus and species levels. In addition, Raman chemical imaging spectroscopy was used to distinguish a mixture of BG spores and EC cells at the single cell level.

Determination of spore inactivation during thermal and pressure-assisted thermal processing using FT-IR spectroscopy

The efficacy of microbial inactivation techniques is currently tested using time-consuming and labor-intensive plate count methods, which are the principal rate-limiting steps in developing inactivation kinetic parameters for alternative food processing technologies. Fourier transform infrared (FT-IR) spectroscopy combined with multivariate analysis was used to quantify viable spores and identify some biochemical changes in samples treated by autoclaving, pressure-assisted thermal processing (PATP), and thermal processing (TP). Spore suspensions ( approximately 109 CFU/mL) of Bacillus amyloliquefaciens TMW 2.479 Fad 82, B. amyloliquefaciens TMW 2.482 Fad 11/2, B. sphaericus NZ 14, B. amyloliquefaciens ATCC 49764, and Clostridium tyrobutyricum ATCC 25755 were treated by PATP (121 degrees C and 700 MPa) for 0, 10, 20, and 30 s and by TP (121 degrees C) for 0, 10, 20, and 30 s. The concentrations of spores in treated samples were determined by plating (reference method). Models developed using partial least-squares regression (PLSR) for predicting spore levels in treated samples had correlation coefficients (r) of >0.99 and standard errors of cross-validation ranging between 100.2 and 100.5 CFU/mL. Changes in dipicolinic acid (DPA) and secondary structure of proteins were found to occur during inactivation of spores by PATP and TP. FT-IR spectroscopy could rapidly estimate viable bacterial spore levels in PATP- and TP-treated spore suspensions, providing an accurate analytical tool for monitoring the efficacy of sterilization techniques in inactivating spore-forming microorganisms.

Quantification of Lactobacillus in fermented milk by multivariate image analysis with least-squares support-vector machines

This paper reports an approach for quantification of Lactobacillus in fermented milk, grown in a selective medium (MRS agar), by use of digital colour images of Petri plates easily obtained by use of a flatbed scanner. A one-dimensional data vector was formed to characterize each digital image on the basis of the frequency-distribution curves of the red (R), green (G), and blue (B) colour values, and quantities derived from them, for example lightness (L), relative red (RR), relative green (RG), and relative blue (RB). The frequency distributions of hue, saturation, and intensity (HSI) were also calculated and included in the data vector used to describe each image. Multivariate non-linear modelling using the least-squares support vector machine (LS-SVM) and a linear model based on PLS regression were developed to relate the microbiological count and the frequency vector. Feasibly models were developed using the LS-SVM and errors were below than 10% for Lactobacillus quantification, indicating the proposed approach can be used for automatic counting of colonies.

Improved dispersion of bacterial endospores for quantitative infrared sampling on gold coated porous alumina membranes

An improved method for qualitative and quantitative sampling of bacterial endospores using Fourier transform infrared (FT-IR) microscopy on gold-coated porous alumina membranes is presented. Bacillus subtilis endospores were filtered onto gold-coated alumina membranes serving as substrates. Studies in the mid-infrared (MIR) region revealed the characteristic bacterial absorption spectrum at low surface concentration, while scanning electron microscopy (SEM) images of the same samples provided precise calculation of the surface concentration of the bacterial endospores. Under the conditions of study, the average concentration of endospores was determined to be 1356 +/- 35 spores in a 100 x 100 mum(2) area, with a relative standard deviation of 0.0260. Examination of ten random spots on multiple substrates with FT-IR microscopy apertured to the same area gave an average relative standard deviation of 0.0482 in the signal strength of the amide A band at 3278 cm(-1). An extinction cross-section in reflection of sigma(ext) = (7.8 +/- 0.6) x 10(-9) cm(2)/endospore was calculated for the amide A band at the frequency of its peak absorbance, 3278 cm(-1). The absorption cross-section of the amide A band in reflection is estimated to be sigma(abs) approximately (2.10 +/- 0.12) x 10(-9) cm(2)/endospore.

Use of fatty acid profiles to identify food-borne bacterial pathogens and aerobic endospore-forming bacilli

Capillary gas chromatography (GC) with flame ionization detection was used to determine the cellular fatty acid profiles of various food-borne microbial pathogens and to compare the fatty acid profiles of spores and vegetative cells of the same endospore-forming bacilli. Fifteen bacteria, representing eight genera (Staphylococcus, Listeria, Bacillus, Yersinia, Salmonella, Shigella, Escherichia, and Vibrio) and 11 species were used to compare the extracted fatty acid methyl esters (FAMEs). Endospore-forming bacilli were processed to obtain pure spores and whole cell FAMEs for GC analysis. A data set for each bacterial agent was prepared using fatty acid profiles from five replicates prepared on different days. The results showed that these fatty acid intensity profiles were unique for each of the 11 species and that they could be used as a fingerprint for the organisms. The cellular fatty acid profiles for Bacillus anthracis and Bacillus cereus show that there are two branched chain fatty acids, iso 17:1 omega10c and 17:1 anteiso, which are unique in these species. Iso 17:1 omega10c is present in B. cereus vegetative cells and spores but is not observed in B. anthracis. The 17:1 anteiso fatty acid is present in B. anthracis cells but not in B. cereus cells. Fatty acids 16:0 2OH and 17:0 iso 3OH are present in B. anthracis and B. cereus spores but not in the vegetative cells. In summary, analysis of FAMEs from bacteria and spores can provide a sensitive procedure for the identification of food-borne pathogens.

Methods for isolation and confirmation of Vibrio vulnificus from oysters and environmental sources: a review

The gram-negative bacterium Vibrio vulnificus is a natural inhabitant of estuarine waters and poses a significant health threat to humans who suffer from immune disorders, liver disease, or hemochromatosis (iron overload). V. vulnificus enters human hosts via wound infections or consumption of raw shellfish (primarily oysters), and infections frequently progress to septicemia and death in susceptible individuals. Prevalence in waters and shellfish is not correlated with fecal indicator organisms; therefore, species-specific detection and enumeration of V. vulnificus in the environment has become a priority for agencies that are responsible for shellfish safety. The many selective-differential media developed for isolation of Vibrio spp., and specifically for V. vulnificus detection, are reviewed here; however, none of the media developed to date combines the sensitivity to low numbers with the specificity necessary to inhibit growth of other organisms. Therefore, immunological and molecular protocols are needed for confirmation of the identity of the organism and are discussed in detail. Methods under development that hold promise for rapid, accurate, and sensitive detection and enumeration of the organism include multiplex and real-time PCR. Developing technologies that have proven useful for detection and investigation of other pathogens such as biosensors, spectroscopy and microarrays may provide the next generation of tools for investigation of the prevalence and ecology of V. vulnificus.

Accelerating Bacterial Identification by Infrared Spectroscopy by Employing Microarray Deposition of Microorganisms

A microarray method for the deposition of bacteria onto an agar slide was developed to accelerate the formation of microcolonies. Representative microarrays each consisting of 40 micro-spots of five replicates of eight foodborne bacteria (Yersinia enterocolitica, Staphylococcus aureus, Salmonella typhimurium, Listeria monocytogenes, Enterobacter cloacae, Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli) were printed on a Brain Heart Infusion (BHI) agar slide using a contact micro-spotting robotic system. Within 3 h, sufficient bacterial cells were obtained to allow accurate identification of the microorganism by infrared spectroscopy. This approach allows a "complete-in-a-single-day" analysis of a large array of samples.