Detection and differentiation of live and heat-treated Salmonella enterica serovars inoculated onto chicken breast using Fourier transform infrared (FT-IR) spectroscopy

Phenotypic and genomic insights into mutant with high nattokinase-producing activity induced by carbon ion beam irradiation of Bacillus subtilis

Nattokinase (NK) is found in fermented foods and has high fibrinolytic activity, which makes it promising for biological applications. In this study, a mutant strain (Bacillus subtilis ZT-S1, 5529.56 ± 183.59 U/mL) with high NK-producing activity was obtained using 12C6+ heavy ion beam mutagenesis for the first time. The surface morphology of B. subtilis is also altered by changes in functional groups caused by heavy ion beams. Furthermore, B. subtilis ZT-S1 required more carbon and nitrogen sources and reached stabilization phase later. Comparative genome analysis revealed that most of the mutant implicated genes (oppA, appA, kinA, spoIIP) were related to spore formation. And the affected rpoA is related to the synthesis of the NK-coding gene aprE. In addition, the B. subtilis ZT-S1 obtained by mutagenesis had good genetic stability. This study further explores the factors affecting NK activity and provides a promising microbial resource for NK production in commercial applications.

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Advances in detection methods for viable Salmonella spp.: current applications and challenges

Salmonella is a common intestinal pathogen that can cause food poisoning and intestinal disease. The high prevalence of Salmonella necessitates efficient and sensitive methods for its identification, detection, and monitoring, especially of viable Salmonella. Conventional culture methods need to be more laborious and time-consuming. And they are relatively limited in their ability to detect Salmonella in the viable but non-culturable status if present in the sample to be tested. As a result, there is an increasing need for rapid and accurate techniques to detect viable Salmonella spp. This paper reviewed the status and progress of various methods reported in recent years that can be used to detect viable Salmonella, such as culture-based methods, molecular methods targeting RNAs and DNAs, phage-based methods, biosensors, and some techniques that have the potential for future application. This review can provide researchers with a reference for additional method options and help facilitate the development of rapid and accurate assays. In the future, viable Salmonella detection approaches will become more stable, sensitive, and fast and are expected to play a more significant role in food safety and public health.

Protein FT-IR amide bands are beneficial to bacterial typing

Bacterial FT-IR signals are extremely specific and highly reproducible, making FT-IR an efficient tool for bacterial typing at the subspecies level. The polysaccharide and nucleic acid FT-IR regions (1200-900 cm^-1) are recommended as a precise and reproducible pattern for bacterial typing. However, proteins are the major macromolecules present in bacteria, and the FT-IR spectral region of proteins (1800-1300 cm^-1) is conceivably an important factor in bacterial typing. In this study, we investigated the influence of water on bacterial protein amide bands by comparing spectra obtained with and without FT-IR system dehydration. Eight Escherichia coli, ten Klebsiella pneumoniae, and eleven Staphylococcus aureus strains were typed by FT-IR under different conditions in a blinded experimental setup. Hierarchical clustering analysis (HCA) showed that, when protein signals were included (1800-900 cm^-1), the typing accuracies for select E. coli, K. pn and S. aureus strains without system dehydration were 50%, 30% and 18.2%, respectively. However, the accuracies greatly improved to 100%, 90% and 90.9% when the FT-IR system was dehydrated. These results indicate that the FT-IR signals of protein amide bands are beneficial for bacterial typing.

Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra

Heavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and choose a more resistant strain. In this study, we discriminated heavy metal acclimated bacteria by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and multivariate analysis methods namely Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Two acclimation methods, acute and gradual, were used which cause differences in molecular changes resulting in bacterial populations with different molecular and resistance profiles. Brevundimonas sp., Gordonia sp., and Microbacterium oxydans were exposed to the toxic concentrations of Cd (30 μg/ml) or Pb (90 μg/ml) by using broth medium as a growth media. Our results revealed that PCA and HCA clearly discriminated the acute-acclimated, gradual-acclimated, and control bacteria from each other in protein, carbohydrate, and whole spectral regions. Furthermore, we classified acclimated (acute and gradual) and control bacteria more accurately by using SIMCA with 99.9% confidence. This study demonstrated that heavy metal acclimated and control group bacteria can be discriminated by using chemometric analysis of FTIR spectra in a powerful, cost-effective, and handy way. In addition to the determination of the most appropriate acclimation procedure, this approach can be used in the detection of the most resistant bacterial strains to be used in bioremediation studies.

An assessment of antibacterial mode of action of chitosan on Listeria innocua cells using real-time HATR-FTIR spectroscopy

The antibacterial mode of action of chitosan using real-time, horizontal attenuated total reflectance, Fourier-transform infrared (HATR-FTIR) spectroscopy and transmission electron microscopy (TEM) was investigated. Listeria innocua was treated with chitosan solution. HATR-FTIR revealed an increased lethality and substantially metabolomics response on cell components. The main changes in FTIR and their 2nd derivative spectra were at 1045 cm^-1 (carbohydrates in cell wall). Principal component analysis clearly segregated untreated and treated cells. Loadings plot revealed the functional groups in cell wall, cell membrane, phospholipid and protein regions of spectrum that are responsible for the classification of treated and control spectra. Kinetic traces of the metabolomics change suggested that cell wall and cell membrane seemed to be the initial target of the antimicrobial mechanism of chitosan. In agreement with the TEM images, which showed breakage of cell wall integrity. The cell wall, cell membrane, phospholipids, proteins and nucleic acids of FTIR spectral data recorded during the cell inactivation were shown to be linked to the metabolomics cell response in the lethality rate and structure of the cells. This work clearly showed, using HATR-FTIR spectroscopy, how bacteria can change their metabolomics response substantially during the first 45 min of contact time.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Nano/micro and spectroscopic approaches to food pathogen detection

Despite continuing research efforts, timely and simple pathogen detection with a high degree of sensitivity and specificity remains an elusive goal. Given the recent explosion of sensor technologies, significant strides have been made in addressing the various nuances of this important global challenge that affects not only the food industry but also human health. In this review, we provide a summary of the various ongoing efforts in pathogen detection and sample preparation in areas related to Fourier transform infrared and Raman spectroscopy, light scattering, phage display, micro/nanodevices, and nanoparticle biosensors. We also discuss the advantages and potential limitations of the detection methods and suggest next steps for further consideration.

Identification of meat-associated pathogens via Raman microspectroscopy

The development of fast and reliable sensing techniques to detect food-borne microorganisms is a permanent concern in food industry and health care. For this reason, Raman microspectroscopy was applied to rapidly detect pathogens in meat, which could be a promising supplement to currently established methods. In this context, a spectral database of 19 species of the most important harmful and non-pathogenic bacteria associated with meat and poultry was established. To create a meat-like environment the microbial species were prepared on three different agar types. The whole amount of Raman data was taken as a basis to build up a three level classification model by means of support vector machines. Subsequent to a first classifier that differentiates between Raman spectra of Gram-positive and Gram-negative bacteria, two decision knots regarding bacterial genus and species follow. The different steps of the classification model achieved accuracies in the range of 90.6%-99.5%. This database was then challenged with independently prepared test samples. By doing so, beef and poultry samples were spiked with different pathogens associated with food-borne diseases and then identified. The test samples were correctly assigned to their genus and for the most part down to the species-level i.e. a differentiation from closely-related non-pathogenic members was achieved.

Classification and structural analysis of live and dead Salmonella cells using Fourier transform infrared spectroscopy and principal component analysis

Fourier transform infrared spectroscopy (FT-IR) was used to detect Salmonella Typhimurium and Salmonella Enteritidis food-borne bacteria and to distinguish between live and dead cells of both serotypes. Bacteria cells were prepared in 10(8) cfu/mL concentration, and 1 mL of each bacterium was loaded individually on the ZnSe attenuated total reflection (ATR) crystal surface (45° ZnSe, 10 bounces, and 48 mm × 5 mm effective area of analysis on the crystal) and scanned for spectral data collection from 4000 to 650 cm(-1) wavenumber. Analysis of spectral signatures of Salmonella isolates was conducted using principal component analysis (PCA). Spectral data were divided into three regions such as 900-1300, 1300-1800, and 3000-2200 cm(-1) based on their spectral signatures. PCA models were developed to differentiate the serotypes and live and dead cells of each serotype. Maximum classification accuracy of 100% was obtained for serotype differentiation as well as for live and dead cells differentiation. Soft independent modeling of class analogy (SIMCA) analysis was carried out on the PCA model and applied to validation sample sets. It gave a predicted classification accuracy of 100% for both the serotypes and its live and dead cells differentiation. The Mahalanobis distance calculated in three different spectral regions showed maximum distance for the 1800-1300 cm(-1) region, followed by the 3000-2200 cm(-1) region, and then by the 1300-900 cm(-1) region. It showed that both of the serotypes have maximum differences in their nucleic acids, DNA/RNA backbone structures, protein, and amide I and amide II bands.

Fourier transform infrared spectroscopy as a tool to characterize molecular composition and stress response in foodborne pathogenic bacteria

Vibrational spectroscopy techniques have shown capacity to provide non-destructive, rapid, relevant information on microbial systematics, useful for classification and identification. Infrared spectroscopy enables the biochemical signatures from microbiological structures to be extracted and analyzed, in conjunction with advanced chemometrics. In addition, a number of recent studies have shown that Fourier Transform Infrared (FT-IR) spectroscopy can help understand the molecular basis of events such as the adaptive tolerance responses expressed by bacteria when exposed to stress conditions in the environment (e.g. those that cells confront in food and during food processing). The current review gives an overview of the published experimental techniques, data-processing algorithms and approaches used in FT-IR spectroscopy to assess the mechanisms of bacterial inactivation by food processing technologies and antimicrobial compounds, to monitor the spore and membrane properties of foodborne pathogens in changing environments, to detect stress-injured microorganisms in food-related environments, to assess dynamic changes in bacterial populations, and to study bacterial tolerance responses.