Rapid assessment of bacterial viability by flow cytometry

Monitoring the Metabolic Activity of a Single Bacterial Cell Based on Scattering Intensity

Cell activity is evaluated using the number of colonies formed on a medium or the number of live cells in a suspension or by staining nuclei with fluorescent dyes to determine whether cells are dead. However, the culture methods generally require extended culturing times, and damage to the cell membranes observed using fluorescent dyes is not necessarily related to cell survival or activity. Hence, accurately determining the activities of individual cells is impossible. Therefore, we developed a method for quantitatively evaluating the metabolic activities of single cells by focusing on the optical and chemical properties of formazan dye, i.e., 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The oxidized form of MTT is soluble and highly permeable to cell membranes, but it is reduced to insoluble MTT formazan upon reaction with intracellular metabolic products. Single-cell observation using dark-field microscopy revealed that insoluble formazan aggregates within the cells formed particles that emitted characteristic scattered light. The formazan-derived scattered light component extracted via peak fitting was related to metabolic activity, demonstrating its usefulness as a parameter indicating the activity of an individual cell. This method enables the real-time evaluation of the activities of single cells, which should lead to not only the acceleration of bacterial screening and microbial control but also the development of antibiotics and suppression of drug-resistant bacteria.

Rapid detection of antimicrobial susceptibility of the Bacteroides fragilis group by flow cytometry: A preliminary study

A total of nine Bacteroides fragilis group strains and B. fragilis ATCC 25285 were studied. Six antibiotics were used in the study. Broth dilution method was used for flow cytometry (FCM) analysis. Cell suspensions with antibiotics and antibiotic-free were stained with thiazole orange and propidium iodide (PI) to differentiate dead/live cells. The percentage of dead and live cells was calculated using FCM device. Cut-off values for antibiotics (26,7 %, 35,5 % and 30,2 % for meropenem, AMC and clindamycin, respectively) were calculated for dead/live cell differentiation. A common cut-off value was calculated for bactericidal and bacteriostatic (31,8 % and 25,7 % respectively). The PI staining ratios of the B. fragilis ATCC 25285 calculated in the MIC ranges for each antibiotic were under the cut-off values calculated with clinical isolates. The cut-off values we calculated are compatible with MBC rather than MIC values. The FCM method is one of the candidate methods for antimicrobial susceptibility testing.

Development of a fast and precise potency test for BCG vaccine viability using flow cytometry compared to MTT and colony-forming unit assays

In a precarious world of rapidly growing pandemics, the field of vaccine production has witnessed considerable growth. Bacillus Calmette-Guérin (BCG) is a live-attenuated vaccine and a part of the immunization program in 157 countries. The quality control is based on a potency test through viable cell enumeration. The colony-forming unit (CFU) assay is the official method, however, it often yields fluctuating results, suffers from medium cracking, and requires lengthy analysis (~ 28 days). Flow cytometric analysis was proposed earlier, but it was coupled with a Coulter counter for measuring the entire bacterial population (live/dead). In the present study, thiazole orange/propidium iodide dyes supplemented with fluorogenic reference beads were employed for viable counting, eliminating the need for a Coulter counter. Both the flow cytometry and the colorimetric technique employing tetrazolium salt were validated and compared to the CFU assay. The colorimetric assay displayed high precision, accuracy, and a strong positive correlation with the CFU assay. The flow cytometry assay demonstrated high precision and a notable ability to distinguish different forms of BCG cells (live, injured, and dead). It also exhibited a perfect positive correlation with the CFU assay. Both methods reduced the analysis time by > 26 days and eliminated the need for human intervention by automating the test.

Rapid microbial viability assay using scanning electron microscopy: a proof-of-concept using Phosphotungstic acid staining

Multiple stains have been historically utilized in electron microscopy to provide proper contrast and superior image quality enabling the discovery of ultrastructures. However, the use of these stains in microbiological viability assessment has been limited. Phosphotungstic acid (PTA) staining is a common negative stain used in scanning electron microscopy (SEM). Here, we investigate the feasibility of a new SEM-PTA assay, aiming to determine both viable and dead microbes. The optimal sample preparation was established by staining bacteria with different PTA concentrations and incubation times. Once the assay conditions were set, we applied the protocol to various samples, evaluating bacterial viability under different conditions, and comparing SEM-PTA results to culture. The five minutes 10% PTA staining exhibited a strong distinction between viable micro-organisms perceived as hypo-dense, and dead micro-organisms displaying intense internal staining which was confirmed by high Tungsten (W) peak on the EDX spectra. SEM-PTA viability count after freezing, freeze-drying, or oxygen exposure, were concordant with culture. To our knowledge, this study is the first contribution towards PTA staining of live and dead bacteria. The SEM-PTA strategy demonstrated the feasibility of a rapid, cost-effective and efficient viability assay, presenting an open-view of the sample, and providing a potentially valuable tool for applications in microbiome investigations and antimicrobial susceptibility testing.

Identifying Bacterial Lineages in Salmonella by Flow Cytometry

Advances in technologies that permit high-resolution analysis of events in single cells have revealed that phenotypic heterogeneity is a widespread phenomenon in bacteria. Flow cytometry has the potential to describe the distribution of cellular properties within a population of bacterial cells and has yielded invaluable information about the ability of isogenic cells to diversify into phenotypic subpopulations. This review will discuss several single-cell approaches that have recently been applied to define phenotypic heterogeneity in populations of Salmonella enterica.

A preliminary investigation into bacterial viability using scanning electron microscopy–energy-dispersive X-ray analysis: The case of antibiotics

The metabolic stages of bacterial development and viability under different stress conditions induced by disinfection, chemical treatments, temperature, or atmospheric changes have been thoroughly investigated. Here, we aim to evaluate early metabolic modifications in bacteria following induced stress, resulting in alterations to bacterial metabolism. A protocol was optimized for bacterial preparation using energy-dispersive X-ray (EDX) microanalysis coupled with scanning electron microscopy (SEM), followed by optimizing EDX data acquisition and analysis. We investigated different preparation methods aiming to detect modifications in the bacterial chemical composition at different states. We first investigated Escherichia coli, acquiring data from fresh bacteria, after heat shock, and after contact with 70% ethanol, in order to prove the feasibility of this new strategy. We then applied the new method to different bacterial species following 1 h of incubation with increasing doses of antibiotics used as a stress-inducing agent. Among the different materials tested aiming to avoiding interaction with bacterial metabolites, phosphorous-doped silicon wafers were selected for the slide preparation. The 15 kV acceleration voltage ensured all the chemical elements of interest were excited. A thick layer of bacterial culture was deposited on the silicon wafer providing information from multiple cells and intra-cellular composition. The EDX spectra of fresh, heat-killed, and alcohol-killed E. coli revealed important modifications in magnesium, potassium, and sodium. Those same alterations were detected when applying this strategy to bacteria exposed to antibiotics. Tests based on SEM–EDX acquisition systems would provide early predictions of the bacterial viability state in different conditions, yielding earlier results than culture.

Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology

Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.

Estimation of Microbial Viability Using Flow Cytometry

For microorganisms in particular, viability is a term that is difficult to define and a state consequently difficult to measure. The traditional (and gold standard) usage equates viability and culturability (i.e., the ability to multiply) but the process of determining culturability is often too slow. Flow cytometry provides the opportunity to make rapid and quantitative measurements of dye uptake in large numbers of cells and we can therefore exploit the flow cytometric approach to evaluate so-called viability stains and to develop protocols for more routine assessments of microbial viability. This article provides a commentary and several protocols have been included to ensure that users have a firm basis for attempting these reasonably difficult assays on traditional flow cytometer instruments. What is clear is that each assay must be carefully validated with the particular microorganism of interest before being applied in any research, clinical, or service form. © 2020 The Authors.

Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria

The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.

Electrical Control of Escherichia coli Growth Measured with Simultaneous Modulation and Imaging

Background: The use of electricity to mediate bacterial growth is unique in providing spatial control, but requires a more detailed understanding. Methods: We use two gold wires on a glass coverslip with an overlayer of agar to image Escherichia coli cells with brightfield and fluorescence microscopy while simultaneously applying a voltage. Cells outside of the wires provide a control population to measure cell growth as a function of voltage, rather than any difference in culture conditions or growth phase. Results: An applied voltage suppresses the fraction of E. coli undergoing elongation and division with recovery to control values when the voltage is removed. Depolarization is observed over the same voltage range suggesting a membrane potential-mediated response. Conclusions: Our experiments identify and use subcytotoxic voltages to measure differences in the fraction of E. coli cells elongating and dividing as a function of applied voltage. It is hoped that this research will inform the developing field of bacterial electrophysiology.

Controlling the Resting Membrane Potential of Cells with Conducting Polymer Microwires

All cells have a resting membrane potential resulting from an ion gradient across the plasma membrane. The resting membrane potential of cells is tightly coupled to regeneration and differentiation. The ability to control this parameter provides the opportunity for both biomedical advances and the probing of fundamental bioelectric pathways. The use of poly(3,4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT:PSS) conducting polymer microwires to depolarize cells is tested using E. coli cells loaded with a fluorescent dye that is pumped out of the cells in response to depolarization; a more positive membrane potential. Fluorescence imaging of the cells in response to a conducting-polymer-microwire applied voltage confirms depolarization and shows that the rate of depolarization is a function of the applied voltage and frequency. Microwire activity does not damage the cells, demonstrated with a propidium iodide assay of membrane integrity. The conducting polymer microwires do not penetrate the cell, or even come into contact with the cell; they only need to generate a minimum electric field, controlled by the placement of the wires. It is expected that these microwires will provide a new, noninvasive, cellular-scale tool for the control of resting membrane potential with high spatial precision.

Data for discriminating dead/live bacteria in homogenous cell suspensions and the effect of insoluble substrates on turbidimetric measurements

Estimation of bacterial growth by rapid traditional methods such as spectrophometric measurements at 600 nm (OD600) is not applicable for cultures containing insoluble particles in the growth media. Colony counts are the only suitable alternative but these are laborious and not high-throughput. The data presented in this article is related to the research article entitled “Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems” (Duedu and French, 2017) [1]. This data article presents original primary data describing the discrimination of dead/live bacteria in homogenous cell suspensions and how the presence of insoluble substrates affect the turbidity of the suspensions.

Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems

Monitoring bacterial growth is an important technique required for many applications such as testing bacteria against compounds (e.g. drugs), evaluating bacterial composition in the environment (e.g. sewage and wastewater or food suspensions) and testing engineered bacteria for various functions (e.g. cellulose degradation). T?=1,^FigItem(1) ^ReloadFigure=Yesraditionally, rapid estimation of bacterial growth is performed using spectrophotometric measurement at 600nm (OD600) but this estimation does not differentiate live and dead cells or other debris. Colony counting enumerates live cells but the process is laborious and not suitable for large numbers of samples. Enumeration of live bacteria by flow cytometry is a more suitable rapid method with the use of dual staining with SYBR I Green nucleic acid gel stain and Propidium Iodide (SYBR-I/PI). Flow cytometry equipment and maintenance costs however are relatively high and this technique is unavailable in many laboratories that may require a rapid method for evaluating bacteria growth. We therefore sought to adapt and evaluate the SYBR-I/PI technique of enumerating live bacterial cells for a cheaper platform, a fluorimeter. The fluorimetry adapted SYBR-I/PI enumeration of bacteria in turbid growth media had direct correlations with OD600 (p>0.001). To enable comparison of fluorescence results across labs and instruments, a fluorescence intensity standard unit, the equivalent fluorescent DNA (EFD) was proposed, evaluated and found useful. The technique was further evaluated for its usefulness in enumerating bacteria in turbid media containing insoluble particles. Reproducible results were obtained which OD600 could not give. An alternative method based on the assessment of total protein using the Pierce Coomassie Plus (Bradford) Assay was also evaluated and compared. In all, the SYBR-I/PI method was found to be the quickest and most reliable. The protocol is potentially useful for high-throughput applications such as monitoring of growth of live bacterial cells in 96-well microplates and in assessing in vivo activity of cellulose degrading enzyme systems.

The influence of acute hypoxia on the functional and morphological state of the black scorpionfish red blood cells

The investigation of the mechanisms of red blood cell steadiness to the oxygen lack in tolerant teleosts is of current scientific interest. Black scorpionfish, Scorpaena porcus L., is a widespread benthal species in the Black Sea and is highly resistant to hypoxic influence. The morphological state of black scorpionfish red blood cells under acute hypoxia was assessed using DNA-binding dye SYBR Green I and fluorescent microscopy. Changes in membrane potential of mitochondria and functional activity of cells were determined by rhodamine 123 (R123) and fluorescein diacetate (FDA) fluorescence. Oxygen deficiency leads to bidirectional changes in volume of erythrocytes and their nuclei. Between 0.57 and 1.76 mg О₂ l^-1, both parameters increased on 3-12 and 7-21%, respectively. At 1.76-4.03, cells shrank on 1.5-6.0% and nucleus size decreased on 1.5-3%. Acute hypoxia induced a significant increase of R123 (12-60%) and FDA (30-184%) fluorescence. These reactions are caused by a probable decrease in erythrocyte membrane permeability.

Reevaluating multicolor flow cytometry to assess microbial viability

Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.

Isolation a new strain of Kocuria rosea capable of tolerating extreme conditions

A new actinobacterial strain was isolated from Ab-e-Siah spring (dark water) taken from the Ramsar city in Iran, and subjected to several stress conditions investigation. The isolate, named MG2 strain, was Gram-positive, aerobic, diplococci or tetrad shaped, non-spore forming and non-motile. Phylogenetic analysis of the isolate using 16S rDNA sequence indicated that the organism matched best with the genus Kocuria and the highest sequence similarities (98.55%) being found with Kocuria rosea. The 16S rDNA sequence determined in this study has been deposited in the NCBI database with the accession no. JX534199, K. rosea strain MG2. The isolated strain was an alkaliphilic-mesophilic bacterium because the optimal growth was observed at pH 9.2 and temperature of 28 °C under aerobic condition. MG2 was a halotolerant strain and tolerated maximally to 15% NaCl concentraion. Viability analysis by flow cytometry indicated that this strain had highly resistance to UV-C radiation and moderately resistance to desiccation after 28 days. The viability of K. rosea strains MG2 and Deinococcus radiodurans R1 were determined D87 and D98 according to D index, respectively, by a dose radiation 25 J/cm (Appukuttan et al., 2006). Thus the UV resistance of strain MG2 was comparable with representative radiation resistant Deinococcus. Also MG2 was grown at 1-4% of H2O2 as an oxidant agent. This research is the first study on multiple extreme resistance of Kocuria rosea new strain (MG2) isolated in Iran.

Development of an automated ballast water treatment verification system utilizing fluorescein diacetate hydrolysis as a measure of treatment efficacy

Methods for verifying ballast water treatments in foreign vessels are needed to protect the Great Lakes from the discharge of live non-native organisms or pathogens. A prototype automated viability test system using fluorescein diacetate (FDA), a membrane permeable fluorogen, to differentiate live from dead bacteria and algae is described. The automated fluorescence intensity detection device (AFIDD) captures cultured algae or organisms in Detroit River water (simulated ballast water) on 0.2 μm filters, backwashes them from the filter into a cuvette with buffer and FDA for subsequent fluorescence intensity measurements, and washes the filters with sterile water for serial automated reuse. Preliminary manual versions of these procedures were also tested. Tests of various buffers determined N,N-Bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, N,N-Bis(2-hydroxyethyl)taurine (BES) and 3-(N-morpholino)propanesulfonic acid (MOPS) at pH 7.0 to be the best buffers, causing the least spontaneous FDA breakdown without inhibiting enzymatic activity. Fluorescence in the presence of live organisms increased linearly over time, and the rate of increase was dependent on the sample concentration. Following simulated ballast water treatments with heat or chlorine, the fluorescence produced by Detroit River samples decreased to near control (sterile water) levels. Automated measurements of FDA hydrolysis with a reusable filter backwash system should be applicable to near real-time remote-controlled monitoring of live organisms in ballast water.

Novel cyanine dyes and homodimeric styryl dyes as fluorescent probes for assessment of lactic acid bacteria cell viability

Innovations in labeling techniques and in the design and synthesis of dye structures are closely related to the development of service equipment such as light sources and detection methods. Novel styryl homodimers and monomethine cyanine dyes were synthesized and their staining abilities for discrimination between live and dead lactic acid bacterial cells were investigated. The dyes were combined in pairs based on their excitation and emission maxima and the capacity to penetrate through cell membranes of viable bacterial cells. The absorption maxima in the same region and the large Stocks shifts of the styryl derivatives allowed viability analysis to be done with epifluorescent microscope with a very basic configuration - one light source about 480nm and one filter for the fluorescent emissions. A staining protocol was developed and applied for live/dead analysis of Bulgarian yoghurt starters. The live cells quantification by the fluorescence dyes coincided well with the results of the much more time-consuming tests by plate counting. Thus, the proposed dye combinations are appropriate for rapid viability estimation in small laboratories that may have conventional equipment.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

Bacteria viability assessment after photocatalytic treatment

The aim of the present work was to evaluate several methods for analyzing the viability of bacteria after antibacterial photocatalytic treatment. Colony-forming unit (CFU) counting, metabolic activity assays based on resazurin and phenol red and the Live/Dead^®BacLight™ bacterial viability assay (Live/Dead staining) were employed to assess photocatalytically treated Staphylococcus epidermidis and Streptococcus mutans. The results showed conformity between CFU counting and the metabolic activity assays, while Live/Dead staining showed a significantly higher viability post-treatment. This indicates that the Live/Dead staining test may not be suitable for assessing bacterial viability after photocatalytic treatment and that, in general, care should be taken when selecting a method for determining the viability of bacteria subjected to photocatalysis. The present findings are expected to become valuable for the development and evaluation of photocatalytically based disinfection applications.

Detecting the dormant: a review of recent advances in molecular techniques for assessing the viability of bacterial endospores

Due to their contribution to gastrointestinal and pulmonary disease, their ability to produce various deadly exotoxins, and their resistance to extreme temperature, pressure, radiation, and common chemical disinfecting agents, bacterial endospores of the Firmicutes phylum are a major concern for public and environmental health. In addition, the hardy and dormant nature of endospores renders them a particularly significant threat to the integrity of robotic extraterrestrial life-detection investigations. To prevent the contamination of critical surfaces with seemingly ubiquitous bacterial endospores, clean rooms maintained at exceedingly stringent cleanliness levels (i.e., fewer than 100,000 airborne particles per ft(3)) are used for surgical procedures, pharmaceutical processing and packaging, and fabrication and assembly of medical devices and spacecraft components. However, numerous spore-forming bacterial species have been reported to withstand typical clean room bioreduction strategies (e.g., UV lights, maintained humidity, paucity of available nutrients), which highlights the need for rapid and reliable molecular methods for detecting, enumerating, and monitoring the incidence of viable endospores. Robust means of evaluating and tracking spore burden not only provide much needed information pertaining to endospore ecophysiology in different environmental niches but also empower decontamination and bioreduction strategies aimed at sustaining the reliability and integrity of clean room environments. An overview of recent molecular advances in detecting and enumerating viable endospores, as well as the expanding phylogenetic diversity of pathogenic and clean room-associated spore-forming bacteria, ensues.

Efficacy of a dual fluorescence method in detecting the viability of overwintering cyanobacteria

Chill in the light is the major environmental stress that cyanobacteria encounter in winter. Cyanobacterial cells may acquire chill-light tolerance upon exposure to low temperature in autumn and early winter. We sought to establish the efficacy of the dual fluorescence method in detecting the viability of overwintering cyanobacteria and to provide further evidence for the chill-light tolerance of preconditioned cyanobacteria. Synechocystis sp. PCC 6803 and Microcystis aeruginosa PCC 7806 were exposed to chill (5°C)-light stress with or without pretreatment at 15°C and stained with SYTO 9 and propidium iodide. Live and dead cells were observed under a fluorescence microscope, and the percentage of viable cells was quantified on a microplate reader. The dual fluorescence method showed consistent results with tests of the ability to reinitiate growth. Cell viability was quantitatively correlated with ratio of SYTO 9/propidium iodide fluorescence. Previously, Microcystis colonies in Lake Taihu had been found to accumulate RNA-binding protein 1 in autumn and winter. Use of this method directly showed the viability of such Microcystis colonies throughout the winter.

Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.

Assessment of cell viability

Cell viability may be judged by morphological changes or by changes in membrane permeability and/or physiological state inferred from the exclusion of certain dyes or the uptake and retention of others. This unit presents methods based on dye exclusion, esterase activity, and mitochondrial membrane potential, as well as protocols for determining the pre-fixation viability of fixed cells either before or after fixation with amine-reactive dyes suitable for a range of excitation wavelengths. Membrane-impermeable dead cell and live cell dyes as well as dye-exclusion procedures for microscopy are also included.

Assessment of the dynamics of the physiological states of Lactococcus lactis ssp. cremoris SK11 during growth by flow cytometry

AIMS

The aim of this study was to improve knowledge about the dynamics of the physiological states of Lactococcus lactis ssp. cremoris SK11, a chain-forming bacterium, during growth, and to evaluate whether flow cytometry (FCM) combined with fluorescent probes can assess these different physiological states.

METHODS AND RESULTS

Cellular viability was assessed using double labelling with carboxyfluorescein diacetate and propidium iodide. FCM makes it possible to discriminate between three cell populations: viable cells, dead cells and cells in an intermediate physiological state. During exponential and stationary phases, the cells in the intermediate physiological state were culturable, whereas this population was no longer culturable at the end of the stationary phase.

CONCLUSIONS, AND IMPACT OF THE STUDY

We introduced a new parameter, the ratio of the means of the fluorescence cytometric index to discriminate between viable culturable and viable nonculturable cells. Finally, this work confirms the relevance of FCM combined with two fluorescent stains to evaluate the physiological states of L. lactis SK11 cells during their growth and to distinguish viable cells from viable but not culturable cells.

Comparison of the automated fluorescence microscopic viability test with the conventional and flow cytometry methods

The cell viability test is an essential tool in any laboratory, performing cell-based studies and clinical laboratory tests. The trypan blue exclusion method is the most popular assay for its simple concept among various diagnostic tools. However, several disadvantages include time-consuming and labor-intensive steps with low precision. In this study, we evaluated a new technique for the automatic cell viability measurement with microscopic cell counter and microchip. Upon blood draw from 11 healthy volunteers, Mononuclear cells were separated immediately from the heparinized whole blood, and the viable cells were diluted from 100 to 1%. The cell viability tests were performed simultaneously with following three methods: the conventional manual trypan blue exclusion method; the flow cytometry measurement with propidium iodide stain; and the newly developed microscopic cell counter with microchip. Linearities, precisions, and correlations from three methods were analyzed and compared. The correlations data from the microscopic cell counter were in good agreement with both the conventional trypan blue method (r=0.99, P<0.05) and the flow cytometry (r=0.99, P<0.05), respectively. The precision (2.0-6.2%) and linearity from the microscopic cell counter method with microchip were superior in comparison with the conventional method. The microscopic cell counter with microchip performed well with high precision, linearity, and efficient running time than both the manual trypan blue and the flow cytometry methods.

Development of a nondestructive fluorescence-based enzymatic staining of microcolonies for enumerating bacterial contamination in filterable products

AIMS

Develop a nondestructive fluorescence-based staining procedure to rapidly detect and enumerate bacteria in filterable samples.

METHODS AND RESULTS

The study consists in the development of a staining solution and a protocol to fluorescently detect microcolonies on cellulose membranes. After detection, membranes can be re-incubated on media to yield colonies. Carboxyfluorescein diacetate was selected among other carboxyfluorescein derivatives for its staining efficiency and the absence of background. Several permeabilizers were evaluated for their ability to promote dye uptake into cells without affecting viability. We demonstrated that a combination of n-Octyl β-D-glucopyranoside, sodium hexametaphosphate, lithium chloride and rubidium chloride significantly increased the staining efficiency of bacteria without affecting their viability. The method developed allowed the detection in <9 h of all tested aerobic bacteria and in 48 h of the anaerobic slow grower Propionibacterium acnes.

CONCLUSIONS

This method allows the rapid detection of bacteria in filterable samples in at least three to five times faster than traditional microbiological method.

SIGNIFICANCE AND IMPACT OF THE STUDY

The advantage of this nondestructive procedure is to allow contaminants identification after membrane re-incubation. This method could be easily applied in routine in pharmaceutical, clinical and food and beverage industries to monitor contaminations.

Development of a robust flow cytometric assay for determining numbers of viable bacteria

Several fluorescent probes were evaluated as indicators of bacterial viability by flow cytometry. The probes monitor a number of biological factors that are altered during loss of viability. The factors include alterations in membrane permeability, monitored by using fluorogenic substrates and fluorescent intercalating dyes such as propidium iodide, and changes in membrane potential, monitored by using fluorescent cationic and anionic potential-sensitive probes. Of the fluorescent reagents examined, the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC(inf4)(3)] proved the best candidate for use as a general robust viability marker and is a promising choice for use in high-throughput assays. With this probe, live and dead cells within a population can be identified and counted 10 min after sampling. There was a close correlation between viable counts determined by flow cytometry and by standard CFU assays for samples of untreated cells. The results indicate that flow cytometry is a sensitive analytical technique that can rapidly monitor physiological changes of individual microorganisms as a result of external perturbations. The membrane potential probe DiBAC(inf4)(3) provided a robust flow cytometric indicator for bacterial cell viability.

Dormancy in Stationary-Phase Cultures of Micrococcus luteus: Flow Cytometric Analysis of Starvation and Resuscitation

Cultures of the copiotrophic bacterium Micrococcus luteus were stored in spent growth medium for an extended period of time following batch culture. After an initial decrease, the total cell counts remained constant at approximately 60 to 70% of the counts at the beginning of storage. The level of viability, as judged by plate counts, decreased to less than 0.05%, while respiration and the ability to accumulate the lipophilic cation rhodamine 123 decreased to undetectable levels. However, using penicillin pretreatment (to remove viable cells) and flow cytometry and by monitoring both the total and viable counts, we found that at least 50% of the cells in populations of 75-day-old cultures were not dead but were dormant. Resuscitation in liquid medium was accompanied by the appearance of a population of larger cells, which could accumulate rhodamine 123 and reduce the dye 5-cyano-2,3-ditolyl tetrazolium chloride to a fluorescent formazan, while a similar fraction of the population was converted to colony-forming, viable cells. We surmise that dormancy may be far more common than death in starving microbial cultures.

An efficient method for enumerating oral spirochetes using flow cytometry

Spirochetes, such as Treponema denticola, are thin walled, helical, motile bacteria. They are notoriously difficult to enumerate due to their thinness and the difficulties associated with culturing them. Here we have developed a modified oral bacterial growth medium (OBGM) that significantly improves the cultivation of T. denticola compared with a previously published growth medium. Three methods for the enumeration of T. denticola, semi-solid growth medium colony-forming unit (CFU) counts, DNA analysis and flow cytometry, are described and compared. Enumeration of T. denticola using the semi-solid agar method resulted in a positive linear relationship with absorbance of the culture (R(2)=0.9423). However, the semi-solid agar method was found to consistently underestimate (by 50 fold) the T. denticola cell density compared to previously published data. DNA analysis of T. denticola cultures reliably and consistently resulted in a positive linear relationship with absorbance (R(2)=0.9360), giving a calculated cell density of 6.9 x 10(8)cells/mL at an absorbance of 0.2 at 650 nm. Flow cytometry was also found to result in a positive linear relationship with absorbance (R(2)=0.9874), giving a calculated cell density of 6.6 x 10(8)cells/mL at an absorbance of 0.2 at 650 nm. In comparing all of these enumeration methods, the flow cytometry method was found to have distinct advantages, as it is accurate, rapid, and could distinguish between live and dead bacteria. Thus flow cytometry is a recommended means for the rapid and reliable enumeration of viable spirochetes from culture.

Estimation of microbial viability using flow cytometry

For microorganisms in particular, viability is a term that is difficult to define and a state consequently difficult to measure. The traditional (and gold-standard) usage equates viability and culturability (i.e., the ability to multiply), but the process of determining culturability is often too slow. Flow cytometry provides the opportunity to make rapid and quantitative measurements of dye uptake in large numbers of cells, and we can therefore exploit the flow cytometric approach to evaluate so-called viability stains and to develop protocols for more routine assessments of microbial viability. This unit is primarily commentary, but several basic protocols have been included to ensure that users have a firm basis for attempting these reasonably difficult assays on traditional flow cytometer instruments. What is clear is that each assay must be carefully validated with the particular microorganism of interest before being applied in any research, clinical, or service form.

Combination of immunosensor detection with viability testing and confirmation using the polymerase chain reaction and culture

Rapid and accurate differential determination of viable versus nonviable microbes is critical for formulation of an appropriate response after pathogen detection. Sensors for rapid bacterial identification can be used for applications ranging from environmental monitoring and homeland defense to food process monitoring, but few provide viability information. This study combines the rapid screening capability of the array biosensor using an immunoassay format with methods for determination of viability. Additionally, cells captured by the immobilized antibodies can be cultured following fluorescence imaging to further confirm viability and for cell population expansion for further characterization, e.g., strain identification or antibiotic susceptibility testing. Finally, we demonstrate analysis of captured bacteria using the polymerase chain reaction (PCR). PCR results for waveguide-captured cells were 3 orders of magnitude more sensitive than the fluorescence immunoassay and can also provide additional genetic information on the captured microbes. These approaches can be used to rapidly detect and distinguish viable versus nonviable and pathogenic versus nonpathogenic captured organisms, provide culture materials for further analysis on a shorter time scale, and assess the efficacy of decontamination or sterilization procedures.

Fluconazole susceptibility testing of Candida species by flow cytometry

OBJECTIVE

Currently, antifungal drug susceptibility testing is labor-intensive, limited by delays in obtaining results and high costs. The purpose of this study was to determine the usefulness of flow cytometry (FCM) antifungal drug susceptibility testing as a routine laboratory procedure.

METHODS

A total of 24 clinical isolates of Candida spp. and reference strains were tested for susceptibility to fluconazole by FCM using propidium iodide (PI) as an indicator of viability. The minimum inhibitory concentration (MIC) was defined as the lowest concentration of fluconazole that resulted in an increase of 30% in mean channel fluorescence (MCF), compared to the growth control. FCM results were compared with MIC results as determined by the Clinical and Laboratory Standards Institute (CLSI) method.

RESULTS

An 8h incubation was sufficient for determination of the MICs. The results by FCM at 8h and the NCCLS methods at 24h showed 87.5% agreement to within two drug dilutions. However, the FCM method is labor-intensive in proportion to the larger number of samples. For Candida lusitaniae, MICs by the FCM method showed poor correlation with the CLSI method.

CONCLUSIONS

Further evaluation is necessary to assess the usefulness of FCM as a technique for routine antifungal MIC testing in the clinical laboratory.

Comparison of ELISA and PCR vis-à-vis cultural methods for detecting Aeromonas spp. in foods of animal origin

The present study was conducted to assess the best method of the most commonly used methods for detection of aeromonads in foods of animal origin. With this objective an OMP based indirect plate ELISA and a duplex-PCR using primers targeting aerolysin gene and 16S rRNA gene and yielding amplicons of 252 bp and 599 bp, respectively, were standardized. The standardized protocols and the conventional cultural method were then compared for their respective sensitivities and specificities for detecting aeromonads from chicken and milk samples. Both the standardized assays were found to be highly specific for Aeromonas. The efficiency of the standardized indirect-ELISA and duplex-PCR protocols was assessed by artificial inoculation studies with varying concentrations of Aeromonas cells inoculated in chicken and milk samples followed by enrichment in Alkaline Peptone Water supplemented with 10 mg/ml cephalothin (APW-C) for 12 h. The results revealed that indirect-ELISA was able to detect a minimum of 10(3) cells/ml or g of Aeromonas cells in spiked milk and chicken samples, respectively. Whereas, duplex-PCR and cultural method were able to detect as low as 1 cell/ml or g of Aeromonas cells in spiked milk and chicken samples. The developed assays were also tested for their efficiency to detect Aeromonas spp. in naturally contaminated milk and chicken samples. Out of a total 50 milk samples screened for presence of Aeromonas by the three methods viz., indirect-ELISA, duplex-PCR and cultural method only 1 (2%) turned out to be positive showing positive results by all three methods. Similarly, 50 samples of chicken were tested by all three methods. Three samples (6%) turned out to be positive and here again by all the three methods.

Monitoring population dynamics of the thermophilic Bacillus licheniformis CCMI 1034 in batch and continuous cultures using multi-parameter flow cytometry

Multi-parameter flow cytometry was used to monitor the population dynamics of Bacillus licheniformis continuous cultivations and the physiological responses to a starvation period and a glucose pulse. Using a mixture of two specific fluorescent stains, DiOC6(3) (3,3'-dihexylocarbocyanine iodide), and PI (propidium iodide), flow cytometric analysis revealed cell physiological heterogeneity. Four sub-populations of cells could be easily identified based on their differential fluorescent staining, these correspond to healthy cells (A) stained with DiOC6(3); cells or spores with a depolarised cytoplasmic membrane (B), no staining; cells with a permeabilised depolarised cytoplasmic membrane (C), stained with PI; and permeablised cells with a disrupted cytoplasmic membrane 'ghost cells' (D), stained with both DiOC6(3) and PI. Transmission electron micrographs of cells starved of energy showed different cell lysis process stages, highlighting 'ghost cells' which were associated with the double stained sub-population. It was shown, at the individual cell level, that there was a progressive inherent fluctuation in physiological heterogeneity in response to changing environmental conditions. All four sub-populations were shown to be present during glucose-limited continuous cultures, revealing a higher physiological stress level when compared with a glucose pulsed batch. A starvation period (batch without additional nutrients) increased the number of cells in certain sub-populations (cells with depolarised cytoplasmic membranes and cells with permeabilised depolarised cytoplasmic membranes), indicating that such stress may be caused by glucose limitation. Such information could be used to enhance process efficiency.

Comparison of flow cytometric and Alamar Blue tests with the proportional method for testing susceptibility of Mycobacterium tuberculosis to rifampin and isoniazid

The performance of flow cytometry and the microplate Alamar Blue assay in determining susceptibility of Mycobacterium tuberculosis was assessed by testing 150 Brazilian isolates. The overall agreement was 97.3 and 98% for isoniazid and 94.7 and 100% for rifampin by flow cytometry and MABA, respectively. This study was entirely done in a developing country.