Measurement uncertainty evaluation and risk of false conformity assessment for microbial enumeration tests.

Microbial enumeration tests are widely used to assess the microbiological quality of non-sterile pharmaceutical products. Despite of all efforts to guarantee the reliability of microbial enumeration tests, there will always be an uncertainty associated with the measured values, which can lead to false conformity/non-conformity decisions. In this work, we evaluated the measurement uncertainty using a bottom-up approach and estimate the consumer's or producer's risk due to the measurement uncertainty. Three main sources of uncertainty were identified and quantified: dilution factor, plated volume, and microbial plate counts. The contribution of these sources of uncertainty depends on the measured value of microbial load in pharmaceutical products. The contribution of dilution factor and plated volume uncertainties increase with an increase of measured value, while the contribution of microbial plate count uncertainty decreases with an increase of measured value. The overall uncertainty values were expressed as uncertainty factors, which provide an asymmetric 95% level confidence level of microbial load in pharmaceutical products. In addition, the risk of false conformity/non-conformity decisions due to measurement uncertainty was assess using Monte Carlo method. When the measured value is close to the upper specification limit and/or the measurement uncertainty is large, the risk of false conformity/non-conformity decisions may be significantly high. Thus, we conclude that the use of uncertainty factor in the conformity/non-conformity assessment is important to guarantee the reliability of microbial enumeration test results and to support decision-making.

Diagnostic Accuracy of Point-of-Care Fluorescence Imaging for the Detection of Bacterial Burden in Wounds: Results from the 350-Patient Fluorescence Imaging Assessment and Guidance Trial.

Objective: High bacterial load contributes to chronicity of wounds and is diagnosed based on assessment of clinical signs and symptoms (CSS) of infection, but these characteristics are poor predictors of bacterial burden. Point-of-care fluorescence imaging (FL) MolecuLight i:X can improve identification of wounds with high bacterial burden (>104 colony-forming unit [CFU]/g). FL detects bacteria, whether planktonic or in biofilm, but does not distinguish between the two. In this study, diagnostic accuracy of FL was compared to CSS during routine wound assessment. Postassessment, clinicians were surveyed to assess impact of FL on treatment plan. Approach: A prospective multicenter controlled study was conducted by 20 study clinicians from 14 outpatient advanced wound care centers across the United States. Wounds underwent assessment for CSS followed by FL. Biopsies were collected to confirm total bacterial load. Three hundred fifty patients completed the study (138 diabetic foot ulcers, 106 venous leg ulcers, 60 surgical sites, 22 pressure ulcers, and 24 others). Results: Around 287/350 wounds (82%) had bacterial loads >104 CFU/g, and CSS missed detection of 85% of these wounds. FL significantly increased detection of bacteria (>104 CFU/g) by fourfold, and this was consistent across wound types (p < 0.001). Specificity of CSS+FL remained comparably high to CSS (p = 1.0). FL information modified treatment plans (69% of wounds), influenced wound bed preparation (85%), and improved overall patient care (90%) as reported by study clinicians. Innovation: This novel noncontact, handheld FL device provides immediate, objective information on presence, location, and load of bacteria at point of care. Conclusion: Use of FL facilitates adherence to clinical guidelines recommending prompt detection and removal of bacterial burden to reduce wound infection and facilitate healing.

Lab in a Pasteur pipette: low-cost, rapid and visual detection of Bacillus cereu using denaturation bubble-mediated strand exchange amplification.

Driven by a bright prospect for rapid, portable and cost-effective point-of-care testing, an assembled Pasteur pipette device to integrate nucleic acid extraction, amplification and detection was developed to detect B. cereus in a sample-to-answer format. Denaturation Bubble-mediated Strand Exchange Amplification (SEA) was chosen to perform isothermal amplification because it requires only a pair of primers and one Bst DNA polymerase. The established SEA can detect as low as 1.0 × 10-13 M genomic DNA of B. cereus, which was comparable with the previously reported method for B. cereus detection. The assembled Pasteur pipette allows sample-to-answer diagnostic in a simple, low-cost, portable, and disposable format. The inherent function of Pasteur pipette enables direct liquid handling without the need of extra pipettes, syringes or pumps. Visual readout was achieved by using a pH sensitive dye, further simplifying result judgment process. The detection limit for B. cereus is 1.0 × 104 CFU/mL in pure cultures, while the detection limit in artificially contaminated milk is 1.0 × 105 CFU/mL without enrichment and 1.0 × 100 CFU/mL following 12 h enrichment. Considering that typical cell counts in food samples associated to food poisoning are 1.0 × 105 to 1.0 × 108 CFU per gram/milliliter B. cereus, our Pasteur pipette is enough sensitive for answer-to-sample diagnosis of B. cereus even directly from foods without enrichment. The whole diagnostic procedure could be completed within 50 min, dramatically decreasing the detection time. In a word, the assembled Pasteur pipette device, combined with a homemade metal bath, possesses great potential for sample-to-answer application in resource-limited settings.

Computed Tomography-Based Biomarker for Longitudinal Assessment of Disease Burden in Pulmonary Tuberculosis.

PURPOSE: Computed tomography (CT) images enable capturing specific manifestations of tuberculosis (TB) that are undetectable using common diagnostic tests, which suffer from limited specificity. In this study, we aimed to automatically quantify the burden of Mycobacterium tuberculosis (Mtb) using biomarkers extracted from x-ray CT images. PROCEDURES: Nine macaques were aerosol-infected with Mtb and treated with various antibiotic cocktails. Chest CT scans were acquired in all animals at specific times independently of disease progression. First, a fully automatic segmentation of the healthy lungs from the acquired chest CT volumes was performed and air-like structures were extracted. Next, unsegmented pulmonary regions corresponding to damaged parenchymal tissue and TB lesions were included. CT biomarkers were extracted by classification of the probability distribution of the intensity of the segmented images into three tissue types: (1) Healthy tissue, parenchyma free from infection; (2) soft diseased tissue, and (3) hard diseased tissue. The probability distribution of tissue intensities was assumed to follow a Gaussian mixture model. The thresholds identifying each region were automatically computed using an expectation-maximization algorithm. RESULTS: The estimated longitudinal course of TB infection shows that subjects that have followed the same antibiotic treatment present a similar response (relative change in the diseased volume) with respect to baseline. More interestingly, the correlation between the diseased volume (soft tissue + hard tissue), which was manually delineated by an expert, and the automatically extracted volume with the proposed method was very strong (R2 ≈ 0.8). CONCLUSIONS: We present a methodology that is suitable for automatic extraction of a radiological biomarker from CT images for TB disease burden. The method could be used to describe the longitudinal evolution of Mtb infection in a clinical trial devoted to the design of new drugs.

Cost-Effective Live Cell Density Determination of Liquid Cultured Microorganisms.

Live monitoring of microorganisms growth in liquid medium is a desired parameter for many research fields. A wildly used approach for determining microbial liquid growth quantification is based on light scattering as the result of the physical interaction of light with microbial cells. These measurements are generally achieved using costly table-top instruments; however, a live, reliable, and straight forward instrument constructed using parts that are inexpensive may provide opportunities for many researchers. Here, such an instrument has been constructed and tested. It consists of modular test tube holding chambers, each with a low power monochromatic light-emitting diode, and a monolithic photodiode. A microcontroller connects to all modular chambers to control the diodes, and send the live data to either an LCD screen, or a computer. This work demonstrate that this modular instrument can determine precise cell concentrations for the bacteria Escherichia coli and Pseudomonas syringae pv. tomato DC3000, as well as Saccharomyces cerevisiae yeast.

Integrating running water monitoring tools with the Micro Biological Survey (MBS) method to improve water quality assessment.

Running water habitats are among the most altered aquatic systems by human activities driving an increase in the organic components and the associated bacterial load as well. To contribute in improving the monitoring activities in running waters, here we tested the validity of the new Micro Biological Survey (MBS) method to specifically assess the bacterial load in running waters focusing on Total Viable Counts (at 22°C and 37°C) and Escherichia coli (at 44°C) in order to propose a new prognostic tool for watercourses. MBS method is an alternative colorimetric method for counting bacterial load in water and food samples that is easy to use and leads to a reliable and simple interpretation of results, being also faster and less expensive than traditional methods. Then, we compared MBS with the traditionally used reference method for the bacterial load, and with the most used biotic index for Italian watercourses based on the benthic invertebrates: the Extended Biotic Index (EBI). The last comparison was performed to validate the use of MBS in biomonitoring activities since the benthic invertebrate multi-species assemblage (and then EBI) alter own structure mainly depending on the organic component variation. During the first part of the study, the assessment of both linearity (regressions among bacterial concentrations) and accuracy (significant correlation between a measured value and a value used as reference) confirmed the validity of the MBS method. Second, the linear regressions between the three investigated microbial parameters vs. both physical-chemical descriptors and EBI, revealed the usefulness of MBS as a valid tool for routine microbiological analyses involved in rapid and easy field monitoring activities. This represents the first attempt to evaluate the river microbial status by exploiting the innovative MBS on running waters to propose it as new valuable monitoring tool in the biomonitoring field.

Fluorescence Technology for Point of Care Wound Management.

As the prevalence of chronic wounds continues to rise, the need for point of care wound assessment has also increased. While a variety of technologies have been developed to improve diagnostic abilities and monitoring of wounds, none have proven completely effective in all settings. Further, many of the stalwart wound management techniques remain costly, time consuming, and technically challenging. The two key pivotal events of ischemia and infection can lead to limb loss. A relatively new crop of fluorescence-based technologies, including devices that measure pathogenic auto-fluorescence, fluorescence angiography, or map cutaneous oxygenation, are increasingly being utilized for adjunct wound assessment-both clinical and operative settings can address these events. These technologies offer rapid, efficient, visual, and quantitative data that can aid the wound provider in evaluating the viability of tissues, ensuring adequate perfusion, and optimizing wound bed preparation. In the following review, pathogenic auto-fluorescence is compared to gross evaluation of wound infection and culture based diagnostics, indocyanine green fluorescence angiography is compared to various methods of visual and physical assessments of tissue perfusion by the practitioner, and cutaneous oxygenation is compared to clinical signs of ischemia. We focus on the current applications of fluorescence technologies in wound management, with emphasis placed on the evidence for clinical and operative implementation, a safety analyses, procedural limitations, and the future direction of this growing field of wound assessment.

Overestimation of the Legionella spp. load in environmental samples by quantitative real-time PCR: pretreatment with propidium monoazide as a tool for the assessment of an association between Legionella concentration and sanitary risk.

Quantitative polymerase chain reaction (qPCR) offers rapid, sensitive, and specific detection of Legionella in environmental water samples. In this study, qPCR and qPCR combined with propidium monoazide (PMA-qPCR) were both applied to hot-water system samples and compared to traditional culture techniques. In addition, we evaluated the ability of PMA-qPCR to monitor the efficacy of different disinfection strategies. Comparison between the quantification obtained by culture and by qPCR or PMA-qPCR on environmental water samples confirms that the concentration of Legionella estimated by GU/L is generally higher than that estimated in CFU/L. Our results on 57 hot-water-system samples collected from 3 different sites show that: i) qPCR results were on average 178-fold higher than the culture results (Δ log10=2.25), ii) PMA-qPCR results were on average 27-fold higher than the culture results (Δ log10=1.43), iii) propidium monoazide-induced signal reduction in qPCR were nearly 10-fold (Δ log10=0.95), and that iv) different degrees of correlations between the 3 methods might be explained by different matrix properties, but also by different disinfection methods affecting cultivability of Legionella. In our study, we calculated the logarithmic differences between the results obtained by PMA-qPCR and those obtained by culture, and we suggested an algorithm for the interpretation of PMA-qPCR results for the routine monitoring of healthcare water systems using a commercial qPCR system (iQ-check real-time PCR kit; Bio-Rad, Marnes-la-Coquette, France).

Flow cytometric enumeration of bacteria using TO-PRO®-3 iodide as a single-stain viability dye.

Quantification of bacteria using conventional viable plate counting (VPC) is labor-intensive and time-consuming. Flow cytometry (FCM) can be proposed as a faster alternative. This study aimed to develop a flow cytometric, single-stain approach using TO-PRO®-3 iodide (TP3) for the quantification of Staphylococcus aureus, Escherichia coli, and Bacillus subtilis cells. Live or dead bacterial suspensions were stained with TP3 and analyzed using a FACSCalibur flow cytometer. After optimization of staining parameters and instrument settings, an excellent separation of viable and dead cells was achieved for all species. The quantitative performance of the technique was assessed by analyzing serial dilutions of bacterial suspensions using FCM and VPC. A highly linear correlation (r2 > 0.99) was observed between the colony forming units (CFU)/mL as determined by FCM and by VPC over a concentration range of about 104 to 108 CFU/mL. As such, FCM quantification of viable bacteria using TP3 can be considered as an accurate and reliable alternative for VPC. The monostain procedure is easy to apply and cost-effective, and it allows bacterial enumeration in a broad variety of samples.

A novel miniaturized most probable number method for the enumeration of Campylobacter spp. from poultry-associated matrices.

A novel miniaturized most probable number (mMPN) method was developed for the enumeration of thermophilic Campylobacter spp. using a modification of blood-free Bolton broth (supplemented with 25mg/l of sulfamethoxazole) and CampyFood ID agar. The mMPN was evaluated by comparison with direct plating (modified ISO/TS, 10272-2:2006) for the analysis of samples (n=149) representing various poultry matrices (carcases, broiler ceca and feces, scald tank water and feed). A sensitivity of 95%, specificity of 90% and Cohen KAPPA agreement of 0.84 was determined for the mMPN method compared to direct plating. Quantitative comparison found 83% of enumerations to be less than ±1log10 different (Student's t-test P<0.001). Financial analysis showed that the mMPN required 51% less media and 60% less labor than the direct plating protocol. The mMPN provides a method that can be used for complete through-chain analysis that has a single enrichment step and multiple dilutions to extinction for a variety of samples (containing low, medium and high populations).

A comparison of fluorescent stains for the assessment of viability and metabolic activity of lactic acid bacteria.

Lactic acid bacteria (LAB) are used as starter or probiotic cultures in the food and pharmaceutical industries and, therefore, rapid and accurate methods for the detection of their viability are of practical relevance. In this study 10 LAB strains, belonging to the genera Enterococcus, Lactococcus, Leuconostoc, Lactobacillus, Streptococcus and Weissella, were subjected to heat and oxidative stresses and cell injury or death was assessed comparing different fluorescent probes (Syto 9; Propidium Iodide, PI; 4,6-diamidino-2-phenylindole, DAPI; 5,(6)-carboxyfluorescein diacetate, cFDA) to identify the stain combination which most reliably allowed the detection of live/metabolically active and dead cells. Protocols for specimen preparation and staining were optimized and a simple procedure for automated cell counts was developed using NIH ImageJ macros. Cysteine and semi-solid agar solution were efficiently used as anti-fading agent and mounting medium, respectively. The double staining cFDA-PI apparently offered the best and most versatile indication of both cell metabolic activity and membrane integrity. An excellent correlation between manual and automated cell counts for the majority of strain/stain combinations was found. This work provides a simple protocol for specimen preparation and staining based on the use of safe, easy to prepare and inexpensive reagents as compared to other methods. Additionally, the automated cell count procedure developed can be applied to several bacterial species and allows an increase in the number of experimental trials and the reproducibility and sensitivity of the analysis.

Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing.

In this study, two highly specific quantitative PCR assays targeting the bacterial genera Burkholderia and Pseudomonas were developed and evaluated on soil samples. The primers were targeting different multivariate regions of the 16S rRNA gene and designed to be compatible with quantitative PCR and the high throughput 454 pyrosequencing technique. The developed assays were validated using the standard methods. All tests with the new developed assays showed very high specificity. Pyrosequencing was used for direct analysis of the PCR product and applied as a specificity measurement of the primers. The Pseudomonas primers showed a 99% primer specificity, which covered 200 different Pseudomonas sequence clusters in 0.5 g of soil. In contrast to that the same approach using the genus-specific Burkholderia primers showed only 8% primer specificity. This discrepancy in primer specificity between the normal procedures compared with pyrosequencing illustrates that the common validation procedures for quantitative PCR primers may be misleading. Our results exemplify the fact that current 16S RNA gene sequence databases might lack resolution within many taxonomic groups and emphasize the necessity for a standardized and functional primer validation protocol. A possible solution to this could be to supplement the normal verification of quantitative PCR assays with a pyrosequencing approach.

Quantitative bacteriological assessment of aerobic wastewater treatment quality and plant performance.

The application of a novel method for measuring changes in defined bacterial populations during aerobic wastewater treatment was investigated. Changes in bacterial communities and total active cells can be used as surrogates for identifying potential WWTP treatment train efficiency and operational performance malfunctions. In this study, the quantities of active heterotrophic aerobic bacteria (HAB) in weekly wastewater samples collected from twelve locations across a WWTP were determined colorimetrically using biological activity reaction tests (BART). Samples were collected for 2 months from primary, secondary and tertiary unit processes. The results show a mean HAB population decrease of 99.8% from primary influent to tertiary effluent, with the largest reductions occurring in the secondary aerobic lagoons. The results were reproducible and robust supporting the applied BART analytical method as an indicator not only of overall efficacy of the WWTP processes but also of potential WWTP process malfunctions.

Possible overestimation of surface disinfection efficiency by assessment methods based on liquid sampling procedures as demonstrated by in situ quantification of spore viability.

The standard test methods used to assess the efficiency of a disinfectant applied to surfaces are often based on counting the microbial survivors sampled in a liquid, but total cell removal from surfaces is seldom achieved. One might therefore wonder whether evaluations of microbial survivors in liquid-sampled cells are representative of the levels of survivors in whole populations. The present study was thus designed to determine the "damaged/undamaged" status induced by a peracetic acid disinfection for Bacillus atrophaeus spores deposited on glass coupons directly on this substrate and to compare it to the status of spores collected in liquid by a sampling procedure. The method utilized to assess the viability of both surface-associated and liquid-sampled spores included fluorescence labeling with a combination of Syto 61 and Chemchrome V6 dyes and quantifications by analyzing the images acquired by confocal laser scanning microscopy. The principal result of the study was that the viability of spores sampled in the liquid was found to be poorer than that of surface-associated spores. For example, after 2 min of peracetic acid disinfection, less than 17% ± 5% of viable cells were detected among liquid-sampled cells compared to 79% ± 5% or 47% ± 4%, respectively, when the viability was evaluated on the surface after or without the sampling procedure. Moreover, assessments of the survivors collected in the liquid phase, evaluated using the microscopic method and standard plate counts, were well correlated. Evaluations based on the determination of survivors among the liquid-sampled cells can thus overestimate the efficiency of surface disinfection procedures.

Assessment of the application of an automated electronic milk analyzer for the enumeration of total bacteria in raw goat milk.

Automated electronic milk analyzers for rapid enumeration of total bacteria counts (TBC) are widely used for raw milk testing by many analytical laboratories worldwide. In Ontario, Canada, Bactoscan flow cytometry (BsnFC; Foss Electric, Hillerød, Denmark) is the official anchor method for TBC in raw cow milk. Penalties are levied at the BsnFC equivalent level of 50,000 cfu/mL, the standard plate count (SPC) regulatory limit. This study was conducted to assess the BsnFC for TBC in raw goat milk, to determine the mathematical relationship between the SPC and BsnFC methods, and to identify probable reasons for the difference in the SPC:BsnFC equivalents for goat and cow milks. Test procedures were conducted according to International Dairy Federation Bulletin guidelines. Approximately 115 farm bulk tank milk samples per month were tested for inhibitor residues, SPC, BsnFC, psychrotrophic bacteria count, composition (fat, protein, lactose, lactose and other solids, and freezing point), and somatic cell count from March 2009 to February 2010. Data analysis of the results for the samples tested indicated that the BsnFC method would be a good alternative to the SPC method, providing accurate and more precise results with a faster turnaround time. Although a linear regression model showed good correlation and prediction, tests for linearity indicated that the relationship was linear only beyond log 4.1 SPC. The logistic growth curve best modeled the relationship between the SPC and BsnFC for the entire sample population. The BsnFC equivalent to the SPC 50,000 cfu/mL regulatory limit was estimated to be 321,000 individual bacteria count (ibc)/mL. This estimate differs considerably from the BsnFC equivalent for cow milk (121,000 ibc/mL). Because of the low frequency of bulk tank milk pickups at goat farms, 78.5% of the samples had their oldest milking in the tank to be 6.5 to 9.0 d old when tested, compared with the cow milk samples, which had their oldest milking at 4 d old when tested. This may be one of the major factors contributing to the larger goat milk BsnFC equivalence. Correlations and interactions between various test results were also discussed to further understand differences between the 2 methods for goat and cow milks.

Novel cost-efficient real-time PCR assays for detection and quantitation of Listeria monocytogenes.

Listeriosis is a serious food-borne infection with mortality rates approaching 30%. Therefore, the rapid, cost-effective, and automated detection of Listeria monocytogenes throughout the food chain continues to be a major concern. Here we describe three novel quantitative real-time PCR assays for L. monocytogenes based on amplification of a target hlyA gene with SYBR Green I chemistry and hydrolysis probe (TaqMan MGB probe). In order to offer sensitive, rapid and robust tool of additional economical value the real-time PCR assays were designed and optimized to only 5 µl-reactions. All assays were evaluated by using different non-reference Listeria strains isolated from various food matrices. Results demonstrated specificity to L. monocytogenes with accurate quantification over a dynamic range of 5-6 log units with R² higher than 0.98 and amplification efficiencies reaching above 92%. The detection and quantification limits were as low as 165 genome equivalents. Comparison of novel assays to commercially available TaqMan® Listeria monocytogenes Detection Kit and previously published studies revealed similar specificity, sensitivity and efficiency, but greater robustness and especially cost-efficiency in the view of smaller reaction volumes and continuous increase in sample throughput.