Prognostic value of poly-microorganisms detected by droplet digital PCR and pathogen load kinetics in sepsis patients: a multi-center prospective cohort study

This study aimed to investigate the prognostic value of a novel droplet digital polymerase chain reaction (DDPCR) assay in sepsis patients. In this prospective cohort study, univariable and multivariable Cox regressions were used to assess risk factors for 28-day mortality. We also monitored pathogen load together with clinical indicators in a subgroup of the cohort. A total of 107 sepsis patients with positive baseline DDPCR results were included. Detection of poly-microorganisms [adjusted hazard ratio (HR) = 3.19; 95% confidence interval (CI) = 1.34-7.62; P = 0.009], high Charlson Comorbidity Index (CCI) score (adjusted HR = 1.14; 95% CI = 1.01-1.29; P = 0.041), and Sequential Organ Failure Assessment (SOFA) score (adjusted HR = 1.18; 95% CI = 1.05-1.32; P = 0.005) at baseline were independent risk factors for 28-day mortality while initial pathogen load was not associated (adjusted HR = 1.17; 95% CI = 0.82-1.66; P = 0.385). Among 63 patients with serial DDPCR results, an increase in pathogen load at days 6-8 compared to baseline was a risk factor for 28-day mortality (P = 0.008). Also, pathogen load kinetics were significantly different between day-28 survivors and nonsurvivors (P = 0.022), with a decline overtime only in survivors and an increase from days 3 and 4 to days 6-8 in nonsurvivors. Using DDPCR technique, we found that poly-microorganisms detected and increased pathogen load a week after sepsis diagnosis were associated with poor prognosis.IMPORTANCEThis prospective study was initiated to explore the prognostic implications of a novel multiplex PCR assay in sepsis. Notably, our study was the largest cohort of sepsis with droplet digital polymerase chain reaction pathogen monitoring to date, allowing for a comprehensive evaluation of the prognostic significance of both pathogen species and load. We found that detection of poly-microorganisms was an independent risk factors for 28-day mortality. Also, pathogen load increase 1 week after sepsis diagnosis was a risk factor for 28-day mortality, and differential pathogen load kinetics were identified between day-28 survivors and nonsurvivors. Overall, this study demonstrated that pathogen species and load were highly correlated with sepsis prognosis. Patients exhibiting conditions mentioned above face a more adverse prognosis, suggesting the potential need for an escalation of antimicrobial therapy.Registered at ClinicalTrials.gov (NCT05190861).

A novel method for determining viable bacteria from a mixture of dead and viable bacteria: Delayed real-time PCR (DR-PCR) method

Aspiration pneumonia can occur in perioperative and older patients, and various oral care methods have been used to prevent it. To validate the effective oral care methods, measuring bacterial counts before and after oral care is necessary. However, isolating and quantifying viable bacteria from those that are inactivated by agents used in oral care is not possible. In this study, we developed a novel method, Delayed real-time PCR (DR-PCR), that can quantify only viable bacteria from mixed samples of viable and dead bacteria. This method takes advantage of the fact that dead bacteria do not grow but viable bacteria do. When the samples were incubated in a liquid medium for 4 hours, the higher the percentage of viable bacteria, the higher the rate of increase in the number of bacteria. This method showed that povidone‑iodine mouthwashing reduced the number of viable bacteria to approximately 1/4 of that before mouthwashing. Although DR-PCR is slightly more time consuming than real-time PCR, it is effective for studying changes in bacterial counts before and after oral care.

Mouse pneumonia model by Acinetobacter baumannii multidrug resistant strains: Comparison between intranasal inoculation, intratracheal instillation and oropharyngeal aspiration techniques

Infectious pneumonia induced by multidrug resistant (MDR) Acinetobacter baumannii strains is among the most common and deadly forms of healthcare acquired infections. Over the years, different strategies have been put in place to increase host susceptibility to MDR A. baumannii, since only a self-limiting pneumonia with no or limited local bacterial replication was frequently obtained in mouse models. Direct instillation into the trachea or intranasal inoculation of the bacterial suspension are the techniques used to induce the infection in most of the preclinical models of pneumonia developed to date. More recently, the oropharyngeal aspiration procedure has been widely described in the literature for a variety of purposes including pathogens administration. Aim of this study was to compare the oropharyngeal aspiration technique to the intranasal inoculation and intratracheal instillation in the ability of inducing a consistent lung infection with two MDR A. baumannii clinical isolates in immunocompromised mice. Moreover, pneumonia obtained by bacteria administration with two out of three techniques, intratracheal and oropharyngeal, was characterised in terms of histopathology of pulmonary lesions, biomarkers of inflammation level and leukocytes cells infiltration extent after mice treatment with either vehicle or the antibiotic tigecycline. The data generated clearly showed that both strains were not able to colonize the lungs when inoculated by intranasal route. By contrast, the bacterial load in lungs of mice intratracheally or oropharyngeally infected significantly increased during 26 hours of monitoring, thus highlighting the ability of these strains to generate the infection when directly instilled into the lower respiratory airways. Furthermore, the intragroup variability of mice was significantly reduced with respect to those intranasally administered. Tigecycline was efficacious in lung bacterial load and cytokines release reduction. Findings were supported by semi-quantitative histopathological evaluation of the pulmonary lesions and by inflammatory biomarkers analysis. To conclude, both intratracheal instillation and oropharyngeal aspiration techniques showed to be suitable methods for inducing a robust and consistent pneumonia infection in mice when difficult MDR A. baumannii clinical isolates were used. Noteworthy, oropharyngeal aspiration not requiring specific technical skills and dedicated equipment, was proven to be a safer, easier and faster technique in comparison to the intratracheal instillation.

Evaluation of a Novel Culture System for Rapid Pathogen Identification and Detection of Cephalosporin Resistance in Neonatal Gram-negative Sepsis at a Tertiary Referral Unit in Harare, Zimbabwe

BACKGROUND

Neonatal sepsis accounts for a large proportion of neonatal deaths in sub-Saharan Africa. The lack of access to diagnostic testing and excessively long turnaround times to result contributes to delays in sepsis identification and initiation of appropriate treatment. This study aims to evaluate the novel InTrays COLOREX Screen and extended-spectrum beta-lactamase for rapid identification of bacterial pathogens causing sepsis and detection of resistance.

METHODS

Neonates with suspected sepsis admitted to the Harare Central Hospital were prospectively enrolled. One blood culture was collected and incubated using the BacT/ALERT automated system. Positive blood cultures with potential pathogens identified by Gram stain were inoculated on the InTray COLOREX Screen and extended-spectrum beta-lactamase culture plates.

RESULTS

A total of 216 neonates with suspected sepsis were recruited. Pathogens were isolated from blood cultures in 56 (25.9%) neonates of which 54 were Klebsiella pneumoniae. All K. pneumoniae were resistant to ceftriaxone and 53 (98%) were resistant to gentamicin. Sensitivity and specificity for ceftriaxone-resistant K. pneumoniae detection using InTrays were 100%. InTrays results were interpretable as early as 5-10 hours (median 7 hours, interquartile range 7-7) post blood culture positivity enabling rapid identification and notification of result and leading to a 60% reduction in time to result from blood culture collection.

CONCLUSIONS

This study shows that the implementation of a novel culture method was feasible and reduced turnaround times for results by 60% compared with standard microbiologic techniques. An impact on patient outcomes and cost-effectiveness of this method needs to be demonstrated.

Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota

BACKGROUND

Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.

METHODS

We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.

RESULTS

More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.

CONCLUSIONS

Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.

Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile

High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.

Revisiting soil bacterial counting methods: Optimal soil storage and pretreatment methods and comparison of culture-dependent and -independent methods

Although a number of different methods have been used to quantify soil bacteria, identifying the optimal method(s) for soil bacterial abundance is still in question. No single method exists for undertaking an absolute microbial count using culture-dependent methods (CDMs) or even culture-independent methods (CIMs). This study investigated soil storage and pretreatment methods for optimal bacterial counts. Appropriate storage temperature (4°C) and optimal pretreatment methods (sonication time for 3 min and centrifugation at 1400 g) were necessary to preserve bacterial cell viability and eliminate interference from soil particles. To better estimate soil bacterial numbers under various cellular state and respiration, this study also evaluated three CDMs (i.e., colony forming unit, spotting, and most probable number (MPN) and three CIMs (i.e., flow cytometry (FCM), epifluorescence microscopy (EM) count, and DNA quantitation). Each counting method was tested using 72 soil samples collected from a local arable farm site at three different depths (i.e., 10-20, 90-100, and 180-190 cm). Among all CDMs, MPN was found to be rapid, simple, and reliable. However, the number of bacteria quantified by MPN was 1-2 orders lower than that quantified by CIMs, likely due to the inability of MPN to count anaerobic bacteria. The DNA quantitation method appeared to overestimate soil bacterial numbers, which may be attributed to DNA from dead bacteria and free DNA in the soil matrix. FCM was found to be ineffective in counting soil bacteria as it was difficult to separate the bacterial cells from the soil particles. Dyes used in FCM stained the bacterial DNA and clay particles. The EM count was deemed a highly effective method as it provided information on soil mineral particles, live bacteria, and dead bacteria; however, it was a time-consuming and labor-intensive process. Combining both types of methods was considered the best approach to acquire better information on the characteristics of indigenous soil microorganisms (aerobic versus anaerobic, live versus dead).

Control of Listeria monocytogenes Biofilms in a Simulated Food-Processing Environment

Biofilm-forming ability may vary significantly among different Listeria (L.) monocytogenes strains. This interstrain variation is also observed in L. monocytogenes biofilm resistance to antimicrobial compounds commonly used in the food-processing environment. The screening of a large set of L. monocytogenes strains with specific characteristics, such as serotype, MLST type, and other genetic characteristics under various environmental conditions, may lead to a better understanding of the mechanisms underlying the establishment of the pathogen on food contact surfaces. In this chapter, traditional methods for L. monocytogenes strains characterization with regard to biofilm formation and novel biofilm control methods will be described.

Effect of different cleaning procedures on water use and bacterial levels in weaner pig pens

Pork is one of the most globally eaten meats and the pig production chain contributes significantly to the water footprint of livestock production. However, very little knowledge is available about the on-farm factors that influence freshwater use in the pig production chain. An experiment was conducted to quantify the effect of three different washing treatments on freshwater use, bacterial levels [(total bacterial counts; TBC), Enterobacteriaceae and Staphylococcus] and cleaning time in washing of pens for weaning pigs. Three weaner rooms were selected with each room having 10 pens and a capacity to hold up to 14 pigs each. Pigs were weaned and kept in the pens for 7 weeks. Finally, the pens were cleaned before the next batch of pigs moved in. The washing treatments used were power washing and disinfection (WASH); presoaking followed by power washing and disinfection (SOAK), and presoaking followed by detergent, power washing and disinfection (SOAK + DETER). A water meter was used to collect water use data and swab samples were taken to determine the bacterial levels. The results showed that there was no overall effect of washing treatments on water use. However, there was an effect of treatment on the washing time (p<0.01) with SOAK and SOAK+DETER reducing the washing time per pen by 2.3 minutes (14%) and 4.2 minutes (27%) compared to WASH. Nonetheless, there was an effect of sampling time (before or after washing) (p<0.001) on the levels of TBC and Staphylococcus, but no effect was seen on Enterobacteriaceae levels. Thus, the washing treatments used in this study had no effect on the water use of the pork production chain. Although there was no difference in both water use and bacterial load, from a producer perspective, presoaking and detergent use can save time and labour costs, so this would be the preferred option.

Automated classification of bacterial cell sub-populations with convolutional neural networks

Quantification of phenotypic heterogeneity present amongst bacterial cells can be a challenging task. Conventionally, classification and counting of bacteria sub-populations is achieved with manual microscopy, due to the lack of alternative, high-throughput, autonomous approaches. In this work, we apply classification-type convolutional neural networks (cCNN) to classify and enumerate bacterial cell sub-populations (B. subtilis clusters). Here, we demonstrate that the accuracy of the cCNN developed in this study can be as high as 86% when trained on a relatively small dataset (81 images). We also developed a new image preprocessing algorithm, specific to fluorescent microscope images, which increases the amount of training data available for the neural network by 72 times. By summing the classified cells together, the algorithm provides a total cell count which is on parity with manual counting, but is 10.2 times more consistent and 3.8 times faster. Finally, this work presents a complete solution framework for those wishing to learn and implement cCNN in their synthetic biology work.

Towards Bacteria Counting in DI Water of Several Microliters or Growing Suspension Using Impedance Biochips

We counted bacterial cells of E. coli strain K12 in several-microliter DI water or in several-microliter PBS in the low optical density (OD) range (OD = 0.05–1.08) in contact with the surface of Si-based impedance biochips with ring electrodes by impedance measurements. The multiparameter fit of the impedance data allowed calibration of the impedance data with the concentration c_b of the E. coli cells in the range of c_b = 0.06 to 1.26 × 10⁹ cells/mL. The results showed that for E. coli in DI water and in PBS, the modelled impedance parameters depend linearly on the concentration of cells in the range of c_b = 0.06 to 1.26 × 10⁹ cells/mL, whereas the OD, which was independently measured with a spectrophotometer, was only linearly dependent on the concentration of the E. coli cells in the range of c_b = 0.06 to 0.50 × 10⁹ cells/mL.

Prospects for the Use of Gold Nanoparticles to Increase the Sensitivity of an Acoustic Sensor in the Detection of Microbial Cells

The interaction of microbial cells with antibody-gold nanoparticle conjugates in conductive suspensions was experimentally studied by using an acoustic slot-mode sensor. The sensor consisted of a piezoelectric plate with a propagating acoustic wave and a liquid container located above this plate with a given gap. An analysis of the measured parameters of the sensor revealed that the specific interaction of bacterial cells with the conjugates led to a stronger change in the sensor output signal than the specific interaction of bacterial cells with antibodies. The measurements were made for Azospirillum brasilense Sp7 cells in buffer with an initial conductivity of 5-30 μS/cm. The limit of cell detection with the conjugates was 10³ cells/mL, and the analysis took about 4 min. The advantage of the sensor is the possibility of repeated use and cleaning of the liquid container without damaging the sensor's elements. These results are promising for use in rapid test systems for the direct detection of microbial cells in actual samples of liquids in medical diagnostics.

Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR

A multiplex polymerase chain reaction (mPCR) with propidium monoazide (PMA) and internal amplification control (IAC) for the simultaneous detection of waterborne pathogens Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7, was developed. This PMA-IAC-mPCR assay used four new specific primers based on the genes for invA, ecfX, cesB, and fliC, respectively. A 16S rRNA primer was chosen for IAC to eliminate false negative results. The photosensitive dye, propidium monoazide (PMA) was used to exclude signals from dead bacteria that could lead to false positive results. In pure culture, the limits of detection (LOD) were 10¹ CFU/ml for P. aeruginosa, 10² CFU/ml for both Salmonella spp. and E. coli O157:H7, and 10³ CFU/ml for B. cereus, respectively. In addition, with a 6-8 h enrichment of all four bacteria that were combined in a mixture that was spiked in water sample matrix, the LOD was 3 CFU/ml for Salmonella spp., 7 CFU/ml for E. coli O157:H7, 10 CFU/ml for B. cereus and 2 CFU/ml for P. aeruginosa. This PMA-IAC-mPCR assay holds potential for application in the multiplex assay of waterborne pathogens.

A Nanostructured Gold/Graphene Microfluidic Device for Direct and Plasmonic-Assisted Impedimetric Detection of Bacteria

Hierarchical 3D gold nano-/microislands (NMIs) are favorably structured for direct and probe-free capture of bacteria in optical and electrochemical sensors. Moreover, their unique plasmonic properties make them a suitable candidate for plasmonic-assisted electrochemical sensors, yet the charge transfer needs to be improved. In the present study, we propose a novel plasmonic-assisted electrochemical impedimetric detection platform based on hybrid structures of 3D gold NMIs and graphene (Gr) nanosheets for probe-free capture and label-free detection of bacteria. The inclusion of Gr nanosheets significantly improves the charge transfer, addressing the central issue of using 3D gold NMIs. Notably, the 3D gold NMIs/Gr detection platform successfully distinguishes between various types of bacteria including Escherichia coli (E. coli) K12, Pseudomonas putida (P. putida), and Staphylococcus epidermidis (S. epidermidis) when electrochemical impedance spectroscopy is applied under visible light. We show that distinguishable and label-free impedimetric detection is due to dissimilar electron charge transfer caused by various sizes, morphologies, and compositions of the cells. In addition, the finite-difference time-domain (FDTD) simulation of the electric field indicates the intensity of charge distribution at the edge of the NMI structures. Furthermore, the wettability studies demonstrated that contact angle is a characteristic feature of each type of captured bacteria on the 3D gold NMIs, which strongly depends on the shape, morphology, and size of the cells. Ultimately, exposing the platform to various dilutions of the three bacteria strains revealed the ability to detect dilutions as low as ∼20 CFU/mL in a wide linear range of detection of 2 × 10¹-10⁵, 2 × 10¹-10⁴, and 1 × 10²-1 × 10⁵ CFU/mL for E. coli, P. putida, and S. epidermidis, respectively. The proposed hybrid structure of 3D gold NMIs and Gr, combined by novel plasmonic and conventional impedance spectroscopy techniques, opens interesting avenues in ultrasensitive label-free detection of bacteria with low cost and high stability.

Comparison of sonication with chemical biofilm dislodgement methods using chelating and reducing agents: Implications for the microbiological diagnosis of implant associated infection

The diagnosis of implant-associated infections is hampered due to microbial adherence and biofilm formation on the implant surface. Sonication of explanted devices was shown to improve the microbiological diagnosis by physical removal of biofilms. Recently, chemical agents have been investigated for biofilm dislodgement such as the chelating agent ethylenediaminetetraacetic acid (EDTA) and the reducing agent dithiothreitol (DTT). We compared the activity of chemical methods for biofilm dislodgement to sonication in an established in vitro model of artificial biofilm. Biofilm-producing laboratory strains of Staphylococcus epidermidis (ATCC 35984), S. aureus (ATCC 43300), E. coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 53278) were used. After 3 days of biofilm formation, porous glass beads were exposed to control (0.9% NaCl), sonication or chemical agents. Quantitative and qualitative biofilm analyses were performed by colony counting, isothermal microcalorimetry and scanning electron microscopy. Recovered colony counts after treatment with EDTA and DTT were similar to those after exposure to 0.9% NaCl for biofilms of S. epidermidis (6.3 and 6.1 vs. 6.0 log10 CFU/mL, S. aureus (6.4 and 6.3 vs. 6.3 log10 CFU/mL), E. coli (5.2 and 5.1 vs. 5.1 log10 CFU/mL and P. aeruginosa (5.1 and 5.2 vs. 5.0 log10 CFU/mL, respectively). In contrast, with sonication higher CFU counts were detected with all tested microorganisms (7.5, 7.3, 6.2 and 6.5 log10 CFU/mL, respectively) (p <0.05). Concordant results were observed with isothermal microcalorimetry and scanning electron microscopy. In conclusion, sonication is superior to both tested chemical methods (EDTA and DTT) for dislodgement of S. epidermidis, S. aureus, E. coli and P. aeruginosa biofilms. Future studies may evaluate potential additive effect of chemical dislodgement to sonication.

Cationic liposomes for generic signal amplification strategies in bioassays

Liposomes have been widely applied in bioanalytical assays. Most liposomes used bare negative charges to prevent non-specific binding and increase colloidal stability. Here, in contrast, highly stable, positively charged liposomes entrapping the fluorescent dye sulforhodamine B (SRB) were developed to serve as a secondary, non-specific label‚ and signal amplification tool in bioanalytical systems by exploiting their electrostatic interaction with negatively charged vesicles, surfaces, and microorganisms. The cationic liposomes were optimized for long-term stability (> 5 months) and high dye entrapment yield. Their capability as secondary, non-specific labels was first successfully proven through electrostatic interactions of cationic and anionic liposomes using dynamic light scattering, and then in a bioassay with fluorescence detection leading to an enhancement factor of 8.5 without any additional surface blocking steps. Moreover, the cationic liposomes bound efficiently to anionic magnetic beads were stable throughout magnetic separation procedures and could hence serve directly as labels in magnetic separation and purification strategies. Finally, the electrostatic interaction was exploited for the direct, simple, non-specific labeling of gram-negative bacteria. Isolated Escherichia coli cells were chosen as models and direct detection was demonstrated via fluorescent and chemiluminescent liposomes. Thus, these cationic liposomes can be used as generic labels for the development of ultrasensitive bioassays based on electrostatic interaction without the need for additional expensive recognition units like antibodies, where desired specificity is already afforded through other strategies.

Analysis of Microbial Cell Viability in a Liquid Using an Acoustic Sensor

A method was developed for the rapid analysis and evaluation of the viability of bacteriophage-infected Escherichia coli (E.coli) XL-1 directly in a conducting suspension by using a slot-mode sensor. The method is based on recording the changes in the depth and frequency of resonant absorption peaks in the frequency dependence of the insertion loss of the sensor before and after the biologic interaction of E. coli with specific bacteriophages. The possibility was shown of recording the infection of E. coli with specific bacteriophages and assessing its viability in suspensions with a conductivity of 4.5-30 μS/cm. Сontrol experiments were carried out with non-specific interactions of E. coli cells with bacteriophages, in which no changes in the sensor variables were observed. The optimal informational variable for estimating the number of viable cells was the degree of change in the depth of the resonant peaks in the frequency dependence of the insertion loss of the sensor. The limit of cell detection was ∼10²-10³ cells mL^-1, with an analysis time of about 5 min. An additional advantage of the sensor was the availability of a removable liquid container, which allows one to use it repeatedly and to facilitate the cleaning of the container from spent samples. The results are promising for the detection of bacteria and assessment of their viability in solutions with conductivity in the range 4.5-30 µS/cm.

Bacterial contamination of surgical scrubs in the operating theater

BACKGROUND

Measures for the prevention of postsurgical infections include issuing special scrubs for the operating room (OR) and prohibiting walking out of the OR complex wearing these scrubs. The aim of this study was to provide further data on bacterial contamination of surgical scrubs.

METHODS

Specimens were collected at the entrance to the OR from surgical scrubs worn by surgeons. Participants completed a questionnaire regarding the times, places, and activities in which they were involved during the time interval they were wearing the scrubs.

RESULTS

Among the 133 surgeons who participated, the median colony-forming unit (CFU) count was higher (39 CFU/plate) for their scrubs than for clean scrubs worn by the control group (3 CFU/plate; n = 11; P < .001), but there was no significant difference between the study and control groups in the rate of carriage of pathogenic bacteria (13% and 9%, respectively). The majority of the bacteria isolated were considered commensals. Fifty-five (41%) of the surgeons stated that before sampling they took part in medical activities, and 45 (34%) participated in non-medical activities. Practicing these activities was associated with a higher number of CFUs compared to not being involved in such activities (P < .05).

CONCLUSIONS

Our data show that, even in less than optimal situations when scrubs are worn outside the OR, surgical scrubs are contaminated with a low bacterial load and only a small number of pathogenic bacteria.

New strategies for the enumeration of enteric pathogens in water

Water quality standards for drinking water and recreational waters have long been based on the enumeration of faecal coliforms in the various water supplies, with 0 CFU Escherichia coli/100 ml for drinking water and <126 CFU generic E. coli/100 ml for recreational waters. Irrigation water will soon undergo the same scrutiny in the United States. For over 50 years the most probable number method has been used by laboratories to estimate the level of viable bacteria in a sample, but this method is labour intensive and slow, especially if large numbers of samples need to be tested. In this review, we describe some recent innovations in methods to enumerate enteric pathogens in water. These methods are based on different reasoning schemes that can be categorized as biosensors and nucleic acid-based methods. All the methods described here used natural water sources. Several were also used to survey the bacterial levels in naturally contaminated samples. The different methods vary in their limits of detection, ease of use, and potential portability. Some combine very good limits of detection with the ability to overcome technical challenges; however, there is considerable room for improvement, as none of the methods are without shortcomings.

Are Visitors Dangerous Carriers of Pathogens in The Hospital? an Observational Study in an University Hospital in Sicily

The hospital environment has been suggested as having an important role in the transmission of health care-associated infections. The aim of this work is to clarify the possible role of visitors in environmental contamination at our hospital. The microbial load was determined by Rodac plate contact on flat surfaces and by swabs on uneven surfaces. A total of 137 samples were taken from four different areas of the hospital unit. The results were divided into two groups according to the types of subjects that most often frequented those environments. We found that the transmission of health care-associated infections (HAIs) occurs mainly in areas where visitors are not allowed.

New insights into the kinetics of bacterial growth and decay in pig manure-wheat straw aerobic composting based on an optimized PMA-qPCR method

Aerobic composting is a bacteria-driven process to degrade and recycle wastes. This study quantified the kinetics of bacterial growth and decay during pig manure-wheat straw composting, which may provide insights into microbial reaction mechanisms and composting operations. First, a propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) method was developed to quantify the viable bacteria concentration of composting samples. The optimal PMA concentration and light exposure time were 100 μM and 8 min respectively. Subsequently, the concentrations of total and decayed bacteria were quantified. Viable and decayed bacteria coexisted during the entire composting period (experiments A and B), and the proportion of viable bacteria finally fell to only 35.1%. At the beginning, bacteria grew logarithmically and decayed rapidly. Later, the bacterial growth in experiment A remained stable, while that of experiment B was stable at first and then decomposed. The duration of the stable stage was positively related to the soluble sugar content of composting materials. The logarithmic growth and rapid decay of bacteria followed Monod equations with a specific growth (0.0317 ± 0.0033 h-1 ) and decay rate (0.0019 ± 0.0000 h-1 ). The findings better identified the bacterial growth stages and might enable better prediction of composting temperatures and the degree of maturation.

Lipoarabinomannan in sputum to detect bacterial load and treatment response in patients with pulmonary tuberculosis: Analytic validation and evaluation in two cohorts

BACKGROUND

Lipoarabinomannan (LAM) is a major antigen of Mycobacterium tuberculosis (MTB). In this report, we evaluated the ability of a novel immunoassay to measure concentrations of LAM in sputum as a biomarker of bacterial load prior to and during treatment in pulmonary tuberculosis (TB) patients.

METHODS AND FINDINGS

Phage display technology was used to isolate monoclonal antibodies binding to epitopes unique in LAM from MTB and slow-growing nontuberculous mycobacteria (NTM). Using these antibodies, a sandwich enzyme-linked immunosorbent assay (LAM-ELISA) was developed to quantitate LAM concentration. The LAM-ELISA had a lower limit of quantification of 15 pg/mL LAM, corresponding to 121 colony-forming units (CFUs)/mL of MTB strain H37Rv. It detected slow-growing NTMs but without cross-reacting to common oral bacteria. Two clinical studies were performed between the years 2013 and 2016 in Manila, Philippines, in patients without known human immunodeficiency virus (HIV) coinfection. In a case-control cohort diagnostic study, sputum specimens were collected from 308 patients (aged 17-69 years; 62% male) diagnosed as having pulmonary TB diseases or non-TB diseases, but who could expectorate sputum, and were then evaluated by smear microscopy, BACTEC MGIT 960 Mycobacterial Detection System (MGIT) and Lowenstein-Jensen (LJ) culture, and LAM-ELISA. Some sputum specimens were also examined by Xpert MTB/RIF. The LAM-ELISA detected all smear- and MTB-culture-positive samples (n = 70) and 50% (n = 29) of smear-negative but culture-positive samples (n = 58) (versus 79.3%; 46 positive cases by the Xpert MTB/RIF), but none from non-TB patients (n = 56). Among both LAM and MGIT MTB-culture-positive samples, log10-transformed LAM concentration and MGIT time to detection (TTD) showed a good inverse relationship (r = -0.803, p < 0.0001). In a prospective longitudinal cohort study, 40 drug-susceptible pulmonary TB patients (aged 18-69 years; 60% male) were enrolled during the first 56 days of the standard 4-drug therapy. Declines in sputum LAM concentrations correlated with increases of MGIT TTD in individual patients. There was a 1.29 log10 decrease of sputum LAM concentration, corresponding to an increase of 221 hours for MGIT TTD during the first 14 days of treatment, a treatment duration often used in early bactericidal activity (EBA) trials. Major limitations of this study include a relatively small number of patients, treatment duration up to only 56 days, lack of quantitative sputum culture CFU count data, and no examination of the correlation of sputum LAM to clinical cure.

CONCLUSIONS

These results indicate that the LAM-ELISA can determine LAM concentration in sputum, and sputum LAM measured by the assay may be used as a biomarker of bacterial load prior to and during TB treatment. Additional studies are needed to examine the predictive value of this novel biomarker on treatment outcomes.

Culture and Real-time Polymerase Chain reaction sensitivity in the diagnosis of invasive meningococcal disease: Does culture miss less severe cases?

BACKGROUND

Invasive meningococcal disease (IMD) is a highly lethal disease. Diagnosis is commonly performed by culture or Realtime-PCR (qPCR).

AIMS

Our aim was to evaluate, retrospectively, whether culture positivity correlates with higher bacterial load and fatal outcome. Our secondary aim was to compare culture and qPCR sensitivity.

METHODS

The National Register for Molecular Surveillance was used as data source. Cycle threshold (CT), known to be inversely correlated with bacterial load, was used to compare bacterial load in different samples.

RESULTS

Three-hundred-thirteen patients were found positive for Neisseria meningitidis by qPCR, or culture, or both; 41 died (case fatality rate 13.1%); 128/143 (89.5%) blood samples and 138/144 (95.8%) CSF were positive by qPCR, 37/143 (25.9%) blood samples and 45/144 (31.2%) CSF were also positive in culture. qPCR was 3.5 times (blood) or 3.1 times (CSF) more sensitive than culture in achieving a laboratory diagnosis of IMD (OR 24.4; 95% CI 12.2-49.8; p < .10-4; Cohen's κ 0.08 for blood and OR 49.0; 95% CI 19.1-133.4; p<10-4; Cohen's κ 0.02; for CSF). Positivity of culture did not correlate with higher bacterial loads in blood (mean CT 27.7±5.71, and CT 28.1±6.03, p = 0.739 respectively in culture positive or negative samples) or in CSF (mean CT 23.1±4.9 and 24.7±5.4 respectively in positive or negative CSF samples, p = 0.11).CT values in blood from patients who died were significantly lower than in patients who survived (respectively mean 18.0, range 14-23 and mean 29.6, range 16-39; p<10-17). No deaths occurred in patients with CT in blood over 23. Positive blood cultures were found in 10/25 (40%) patients who died and in 32/163 (19.6%) patients who survived, p = 0.036, OR 2.73; 95% CL 1.025-7.215), however 60% of deaths would have remained undiagnosed with the use of culture only.

CONCLUSIONS

In conclusion our study demonstrated that qPCR is significantly (at least 3 times) more sensitive than culture in the laboratory confirmation of IMD. The study also demonstrated that culture negativity is not associated with lower bacterial loads and with less severe cases. On the other side, in patients with sepsis, qPCR can predict fatal outcome since higher bacterial load, evaluated by qPCR, appears strictly associated with most severe cases and fatal outcome. The study also showed that molecular techniques such as qPCR can provide a valuable addition to the proportion of diagnosed and serotyped cases of IMD.

Detection and Inhibition of Bacteria on a Dual-Functional Silver Platform

Detection and inhibition of bacteria are universally required in clinics and daily life for health care. Developing a dual-functional material is challenging and in demand, engaging advanced applications for both defined bioanalysis and targeted biotoxicity. Herein, magnetic silver nanoshells are designed as a multifunctional platform for the detection and inhibition of bacteria. The optimized magnetic silver nanoshells enable direct laser desorption/ionization mass spectrometry based metabolic analysis of bacteria (≈10 µL^-1 ), in complex biofluids. The serum infection process (0-10 h) is monitored by statistics toward clinical classification. Moreover, magnetic silver nanoshells facilitate surface adhesion on bacteria due to nanoscale surface roughness and thus display long-term antibacterial effects. Bacteria metabolism is studied with metabolic biomarkers (e.g., malate and lysine) identified during inhibition, showing cell membrane destruction and dysfunctional protein synthesis mechanisms. This work not only guides the design of material-based approaches for bioanalysis and biotoxicity, but contributes to bacteria-related diagnosis by using specific metabolic biomarkers for sensitive detection and new insights by monitoring metabolomic change of bacteria for antibacterial applications.

Detection and Inhibition of Bacteria on a Dual-Functional Silver Platform

Detection and inhibition of bacteria are universally required in clinics and daily life for health care. Developing a dual-functional material is challenging and in demand, engaging advanced applications for both defined bioanalysis and targeted biotoxicity. Herein, magnetic silver nanoshells are designed as a multifunctional platform for the detection and inhibition of bacteria. The optimized magnetic silver nanoshells enable direct laser desorption/ionization mass spectrometry based metabolic analysis of bacteria (≈10 µL^-1 ), in complex biofluids. The serum infection process (0-10 h) is monitored by statistics toward clinical classification. Moreover, magnetic silver nanoshells facilitate surface adhesion on bacteria due to nanoscale surface roughness and thus display long-term antibacterial effects. Bacteria metabolism is studied with metabolic biomarkers (e.g., malate and lysine) identified during inhibition, showing cell membrane destruction and dysfunctional protein synthesis mechanisms. This work not only guides the design of material-based approaches for bioanalysis and biotoxicity, but contributes to bacteria-related diagnosis by using specific metabolic biomarkers for sensitive detection and new insights by monitoring metabolomic change of bacteria for antibacterial applications.

Effectiveness of surgical hand antisepsis using chlorhexidine digluconate and parachlorometaxylenol hand scrub: Cross-over trial

BACKGROUND

Chlorhexidine and parachlorometaxylenol (PCMX) are antiseptics recommended for surgical hand antisepsis. To our knowledge, PCMX has not been evaluated for bactericidal efficacy "in vivo.

METHODS

We conducted a randomized, double-blind, controlled crossover trial to compare the bacterial loads on fingertips and fingernails under laboratory conditions after use of antiseptic test products, including chlorhexidine digluconate 4%, PCMX 3%, and a reference solution of propan-1-ol 60% (P-1). We assessed bacterial load after a prewash with soft soap, immediately after application of an antiseptic, and 3 hours after application and wearing of sterile, powder-free gloves. Our procedures followed those specified by European Norm (EN) 12791 for evaluating surgical hand antiseptics and using cotton swab for fingertips and fingernails.

RESULTS

Chlorhexidine digluconate 4% and PCMX 3% did not decrease bacterial load on the hands. The bactericidal performances of chlorhexidine digluconate 4% and PCMX 3% did not differ significantly. Chlorhexidine digluconate 4% and PCMX 3% increased bacterial load on the fingertips after participants had worn gloves for 3 hours. Fingernails had greater bacterial loads than skin on the fingertips.

CONCLUSIONS

Chlorhexidine digluconate 4% and PCMX 3% had similar bactericidal efficacy, but they failed to meet the EN 12791 efficacy standard. Fingernails should be a particular focus of antisepsis in preparation for surgery.The trial was registered at ClinicalTrials.gov (ID: NCT02500758).

Using Bacterial Fluorescence Imaging and Antimicrobial Stewardship to Guide Wound Management Practices: A Case Series

The urgent need to eliminate unnecessary use of antibiotics in wound patients has been hampered by diagnostic uncertainty and the time required to obtain culture results. The authors evaluated bedside use of a handheld bacterial fluorescence imaging device for real-time visualization of bacteria within and around wounds, used in addition to monitoring of clinical signs and symptoms of infection, in a series of 7 patients (5 women, 2 men; age range 57-93 years) with varying comorbidities who were referred to the wound ostomy continence clinician for wound assessment. When excited by 405-nm violet light, tissues fluoresce green (collagens) and bacteria fluoresce red; specialized optical filters reveal these colored signals in real time on the device's display screen. Wounds exhibiting red fluorescence were presumed to have moderate/heavy bacterial contamination (≥104 CFU/g) and were subsequently swabbed. Swabs from the 5 wounds with regions of red fluorescence confirmed heavy growth of 1 or more pathogenic bacterial species. Images revealing pronounced bacterial fluorescence in 3 patients with pressure injuries about to be discharged led to prescription of systemic antibiotics and additional patient monitoring. In 2 patients (1 with a skin tear, 1 with a surgical wound), the absence of bacterial fluorescence prevented planned, unwarranted use of systemic antibiotics. Fluorescence images obtained bedside during routine wound assessments had a direct effect on antimicrobial stewardship practices. Follow-up images demonstrated antibiotic effectiveness and, in some instances, led to reduced antibiotic courses and duration. This case series demonstrates the potential use for real-time information on bacterial presence obtained via bacterial fluorescence imaging to guide evidence-based deployment of antibiotics and prevent unnecessary use. Additional studies to optimize the diagnostic potential and randomized controlled studies to examine the effect of this technique on antibiotic usage, antimicrobial stewardship practices, and wound outcomes are warranted.

Signatures of ecological processes in microbial community time series

BACKGROUND

Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection.

RESULTS

We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model.

CONCLUSIONS

We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.

Phage-based capacitive biosensor for Salmonella detection

This article reports the detection of Salmonella spp. based on M13 bacteriophage in a capacitive flow injection system. Salmonella-specific M13 bacteriophage was immobilized on a polytyramine/gold surface using glutaraldehyde as a crosslinker. The M13 bacteriophage modified electrode can specifically bind to Salmonella spp. via the amino acid groups on the filamentous phage. An alkaline solution was used to break the binding between the sensing surface and the analyte to allow renewable use up to 40 times. This capacitive system provided good reproducibility with a relative standard deviation (RSD) of 1.1%. A 75 µL min^-1 flow rate and a 300 µL sample volume provided a wide linear range, from 2.0 × 10² to 1.0 × 10⁷ cfu mL^-1, with a detection limit of 200 cfu mL^-1. Bacteria concentration can be analyzed within 40 min after the sample injection. When applied to test real samples (raw chicken meat) it provided good recoveries (100-111%). An enrichment process was also explored to increase the bacteria concentration, enabling a quantitative detection of Salmonella spp. This biosensor opens a new opportunity for the detection of pathogenic bacteria using bacteriophage.

Validation by an interlaboratory collaborative trial of EN ISO 21528 - microbiology of the food chain - horizontal methods for the detection and enumeration of Enterobacteriaceae

The methods for the detection and enumeration of Enterobacteriaceae, described in EN ISO 21528, parts 1 and 2, were validated by order of the European Commission under the mandate M/381. Fourteen laboratories from seven European countries participated in the collaborative trials, organized by The Netherlands Food and Consumer Product Safety Authority (Wageningen/Utrecht, The Netherlands). Five different matrices from different food categories were selected to be tested in the collaborative trials, in order to validate the method horizontally, according to ISO 16140. The matrices included meat, tiramisu, infant formula, liquid egg, smoked salmon (detection method only) and animal feed (enumeration method only). The raw meat and liquid egg were naturally contaminated and the other matrices were artificially contaminated with a cocktail of four different Enterobacteriaceae strains. The samples used in the trial were tested for homogeneity and stability before distribution. The method for detection of Enterobacteriaceae showed a specificity and sensitivity above 95% for all matrices. The method for the enumeration had a repeatability limit r of 0.37 (expressed as a difference between log₁₀-transformed test results) and a reproducibility limit R of 0.87 (expressed as a difference between log₁₀-transformed test results). The validation data were incorporated in the newly published ISO standards EN ISO 21528:2017- Microbiology of the food chain - Horizontal methods for the detection and enumeration of Enterobacteriaceae - Part 1: Detection method, and Part 2: Colony-count technique.

MC-Media Pad ACplus™ for Enumeration of Aerobic Counts in a Variety of Foods

The MC-Media Pad ACplus™ is a dry, rehydratable film medium for the enumeration of aerobic bacterial colonies. The performance of the method in a variety of foods was compared to that of U.S. reference methods: U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) Chapter 3.02 "Quantitative Analysis of Bacteria in Foods as Sanitary Indicators" (USDA/FSIS MLG 3.02); Standard Methods for the Examination of Dairy Products (SMEDP) Chapter 6 "Microbiological Count Methods, Standard Plate Count Method" (SMEDP 6); AOAC Official MethodSM 966.23 Microbiological Methods; and ISO 4833-1:2013 "Microbiology of the food chain-Horizontal method for the enumeration of microorganisms-Part 1: Colony count at 30 degrees C by the pour plate technique." The validated matrixes included raw chicken breast and raw ground pork for USDA/FSIS MLG 3.02; cream cheese and yogurt drink for SMEDP 6; parsley, vegetable juice, prawns, tuna pate, sandwiches, and pasta salad for AOAC Method 966.23, and raw chicken breast, raw ground pork, cream cheese, yogurt drink, parsley, vegetable juice, prawns, tuna pate, sandwiches, and pasta salad for ISO 4833-1:2013. In each matrix study, five replicates at each of three contamination levels were tested as paired test portions. All 10 matrixes were compared to the appropriate U.S. reference methods under MC-Media Pad ACplus standard-usage conditions (35 ± 1°C for 48 ± 2 h). Across all matrixes, the difference of mean log10 values ranged from -0.43 to 0.44, within the acceptable range of -0.50 to 0.50. The candidate method repeatability SD (sr) varied from 0.03 to 0.23 log10 CFU/g, comparing favorably to the reference method SD, which ranged from 0.06 to 0.30 log10 CFU/g. Seven matrixes were compared to the appropriate U.S. reference methods under MC-Media Pad ACplus rapid-usage conditions (35 ± 1°C for 24 ± 2 h). Of the 21 matrix/concentration combinations, only three instances of difference of mean >0.5 log were observed. The ranges of sr values of the rapid-usage candidate method (0.023-0.324) and the reference method (0.013-0.236) were similar for the seven matrixes tested. All 10 matrixes were compared to the International Organization for Standardization (ISO) reference method under MC-Media Pad ACplus alternate-method conditions (30 ± 1°C for 72 ± 3 h). All 10 matrixes yielded a mean difference between methods of <0.5 log, and the ranges of sr values were similar between the candidate alternate method (0.037-0.378) and the ISO reference method (0.037-0.437). The product consistency study demonstrated no significant difference between lots of product and supported the 2-year shelf life. Robustness testing yielded no significant differences when small variations were made in sample volume, incubation temperature, and incubation time. Thus, the data show equivalent or better performance of the MC-Media Pad ACplus method compared to the relevant reference methods in support of AOAC Performance Tested MethodSM certification.

Evaluation of a most probable number method for the enumeration of Legionella pneumophila from North American potable and nonpotable water samples

This study compares the performance of a novel most probable number (MPN) method (Legiolert™/Quanti-Tray^®) with Standard Methods for the Examination of Water and Wastewater 9260 J for the enumeration of Legionella pneumophila from potable and nonpotable waters. Data from the study showed that Legiolert exhibited higher sensitivity for the detection of L. pneumophila for potable water and equivalent sensitivity for nonpotable water. The Legiolert medium had a high specificity with no false positive signals reported for either water type. The new method represents a significant improvement in usability and accuracy in the enumeration of L. pneumophila.

Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water

Drinking water can be exposed to different biological contaminants from the source, through the pipelines, until reaching the final consumer or industry. Some of these are pathogenic bacteria and viruses which may cause important gastrointestinal or systemic diseases. The microbiological quality of drinking water relies mainly in monitoring three indicator bacteria of faecal origin, Escherichia coli, Enterococcus faecalis and Clostridium perfringens, which serve as early sentinels of potential health hazards for the population. Here we describe the analysis of three chimeric fluorescent protein bullets as biosensor candidates for fast detection of E. coli in drinking water. Two of the chimeric proteins (based on GFP-hadrurin and GFP-pb5 chimera proteins) failed with respect to specificity and/or sensitivity, but the GFP-colS4 chimera protein was able to carry out specific detection of E. coli in drinking water samples in a procedure encompassing about 8 min for final result and this biosensor protein was able to detect in a linear way between 20 and 103 CFU of this bacterium. Below 20 CFU, the system cannot differentiate presence or absence of the target bacterium. The fluorescence in this biosensor system is provided by the GFP subunit of the chimeric protein, which, in the case of the better performing sensor bullet, GFP-colS4 chimera, is covalently bound to a flexible peptide bridge and to a bacteriocin binding specifically to E. coli cells. Once bound to the target bacteria, the excitation step with 395 nm LED light causes emission of fluorescence from the GFP domain, which is amplified in a photomultiplier tube, and finally this signal is converted into an output voltage which can be associated with a CFU value and these data distributed along mobile phone networks, for example. This method, and the portable fluorimeter which has been developed for it, may contribute to reduce the analysis time for detecting E. coli presence in drinking water.

Optimization of PMA-qPCR for Staphylococcus aureus and determination of viable bacteria in indoor air

Staphylococcus aureus may cause infections in humans from mild skin disorders to lethal pneumonia. Rapid and accurate monitoring of viable S. aureus is essential to characterize human exposure. This study evaluated quantitative PCR (qPCR) with propidium monoazide (PMA) to quantify S. aureus. The results showed comparable S. aureus counts between exclusively live cells and mixtures of live/dead cells by qPCR with 1.5 or 2.3 μg/mL PMA (P>.05), illustrating the ability of PMA-qPCR to detect DNA exclusively from viable cells. Moreover, qPCR with 1.5 or 2.3 μg/mL PMA performed optimally with linearity over 10³ -10⁸  CFU/mL (R² ≥0.9), whereas qPCR with 10, 23 or 46 μg/mL PMA significantly underestimated viable counts. Staphylococcus aureus and total viable bacteria were further determined with PMA-qPCR (1.5 μg/mL) from 48 samples from a public library and two university dormitories and four from outside. Viable bacteria averaged 1.9×10⁴ cells/m³ , and S. aureus were detected in 22 (42%) samples with a mean of 4.4×10³ cells/m³ . The number of S. aureus and viable bacteria were positively correlated (r=.61, P<.005), and percentages of S. aureus relative to viable bacteria averaged 12-44%. The results of field samples suggest that PMA-qPCR can be used to quantify viable S. aureus cells.

Detection of Ureaplasma Species by a Semi-Quantitative PCR Test in Urine Samples: Can It Predict Clinical Significance?

BACKGROUND

Ureaplasma species (Usp) are the most prevalent genital Mycoplasma isolated from the urogenital tract of both men and women. Usp may be commensals in the genital tract but may also be contributors to a number of pathological conditions of the genital tract. Because they can also just colonize the genital tract of healthy people, their pathogenic role can be difficult to prove.

OBJECTIVES

The aim of the study was to evaluate the efficacy of a quantitative polymerase chain reaction (qPCR) method for the discrimination between infection and colonization by measuring prevalence of Usp in asymptomatic versus symptomatic patients.

METHODS

Urine samples were tested for U. parvum and U. urealyticum using a semi-quantitative multiplex PCR technique for sexually transmitted diseases (Anyplex™ STI-7 Detection Kit, Seegene, South Korea). A total of 250 symptomatic and 250 asymptomatic controls were included.

RESULTS

A strong positive result for U. parvum was significantly more prevalent in symptomatic compared to asymptomatic patients. This finding was observed especially in women and in the young group (15-35 years of age). No significant differences were observed between the prevalence in symptomatic and asymptomatic patients of U. parvum with low strength of positivity and for U. urealyticum in all groups by age, gender, and strength of positivity.

CONCLUSIONS

The significant difference between the symptomatic and asymptomatic group in the highest positivity group for U. parvum using the Anyplex™ STI-7 detection kit in urine may indicate a high probability of infection rather than colonization, especially in women and young patients.

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.

Optimization of cord blood unit sterility testing: impact of dilution, analysis delay, and inhibitory substances

BACKGROUND

Different methods are used by cord blood banks to prepare samples for sterility testing. Suboptimal methods can result in the release of contaminated products. In our organization, samples are prepared by diluting the final product in RPMI-1640 medium. In this work, we have compared our method with different approaches to verify whether optimization should be sought.

STUDY DESIGN AND METHODS

Cord blood units (n = 6 units per bacterial strain) characterized to contain inhibitory substances or not were inoculated (10 colony-forming units/mL) with Streptococcus agalactiae, Staphylococcus epidermidis, Klebsiella pneumoniae, Escherichia coli, or Bacteroides fragilis. After plasma and red blood cell removal, stem cell concentrates were diluted in RPMI-1640, thioglycollate, or the unit's plasma. These products, as well as final product, plasma, and red blood cell fractions, were held from 0 to 72 hours at 20 to 24°C before inoculation in culture bottles and detection using the BacT/ALERT 3D system.

RESULTS

Dilution of cell concentrates in RPMI-1640 allowed bacterial detection in 93.3% of noninhibitory cord blood samples after a 24-hour storage period. Thioglycollate medium better promoted bacterial growth in inhibitory cord blood samples that were held for 72 hours before testing (66.7%) compared with RPMI-1640 (45.0%). Less than 33% of all spiked plasma samples were detected by the BacT/ALERT 3D system.

CONCLUSION

Diluting cord blood samples in culture medium containing bacterial growth promoting substances is a suitable option for sterility testing, whereas the use of plasma should be proscribed, because it might lead to false-negative results. Because inhibitory substances affect bacterial growth, inoculation of culture bottles should be done rapidly after sample preparation.

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome

The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.

Over the last years the composition of microbial communities in the human gut, the gut microbiome, has gained prominence in clinical research. Providing an estimate of the microbial interaction network from compositional data is an important prerequisite for clinical interpretation and for a better theoretical understanding of such microbial communities. Many studies have focused on the dominant interactions of species that are highly abundant such as, on the phyla level, Bacteriodetes and Firmicutes. Using binarized abundance vectors (recording only the presence and absence of microbial species) we show that the low-abundance segment of the microbiome also contains a large number of systematic interactions. For low-abundant species, our inference method evaluates the transformation of pairs of such vectors ‘binary co-abundance’ under Boolean operations. First we calibrate our new method using simulated data. Then we apply it to novel microbiome data from a human population study. The method reveals a large number of significant positive interactions and several significant negative interactions among low-abundance microbial species. It can be argued that important inter-individual differences and adaptations to changes in environmental conditions rather occur on the level of the low-abundance species than in the few main highly abundant species. This hypothesis could explain the broad distribution of abundances in microbiome compositions.

Rapid molecular identification of fecal origin-colonies growing on Enterococcus spp.-specific culture methods

The mEI, Chromocult^® enterococci, and m-Enterococcus culture-based methods used to assess water quality by the detection of Enterococcus spp. were first compared in terms of sensitivity using (1) 41 different type strains of Enterococcus spp. and (2) environmental colonies identified by 16S rRNA sequencing. Then, two specific-rtPCR assays targeting Enterococcus spp. and Enterococcus faecalis/faecium were tested for their ability to confirm the identity of putative enterococcal colonies. The mEI, Chromocult^® enterococci, and m-Enterococcus methods detected β-glucosidase activity for 28 (68.3%), 32 (78.0%), and 12 (29.3%) of the 41 reference enterococcal strains tested, respectively. Analysis with environmental colonies showed that mEI and Chromocult^® enterococci media had false positive rates of 4.3% and 5.0%, respectively. Finally, the two rtPCR assays showed a specificity of 100%. Only two (2/19) colonies of E. faecium isolated from mEI agar were not detected by the Enterococcus faecium rtPCR assay, for a sensitivity of 89.5%. Our results showed that Chromocult^® enterococci medium recovered more E. faecalis/faecium cells than the two other methods. Thus, the use of Chromocult^® enterococci combined with the Enterococcus faecalis/faecium rtPCR assay showed the best combination to decrease the high false-positive rate obtained when the entire Enterococcus genus is targeted.

Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis

A microfluidic system that combines membraneless microfluidic dialysis and dielectrophoresis to achieve label-free isolation and concentration of bacteria from whole blood is presented. Target bacteria and undesired blood cells are discriminated on the basis of their differential susceptibility to permeabilizing agents that alter the dielectrophoretic behavior of blood cells but not bacteria. The combined membraneless microdialysis and dielectrophoresis system isolated 79 ± 3% of Escherichia coli and 78 ± 2% of Staphylococcus aureus spiked into whole blood at a processing rate of 0.6 mL h^-1. Collection efficiency was independent of the number of target bacteria up to 10⁵ cells. Quantitative PCR analysis revealed that bacterial 16S rDNA levels were enriched more than 307-fold over human DNA in the fraction recovered from the isolation system compared with the original specimen. These data demonstrate feasibility for an instrument to accelerate the detection and analysis of bacteria in blood by first isolating and concentrating them in a microchamber.

Smartphone Detection of UV LED-Enhanced Particle Immunoassay on Paper Microfluidics

Use of a smartphone as an optical detector for paper microfluidic devices has recently gained substantial attention due to its simplicity, ease of use, and handheld capability. Utilization of a UV light source enhances the optical signal intensities, especially for the particle immunoagglutination assay that has typically used visible or ambient light. Such enhancement is essential for true assimilation of assays to field deployable and point-of-care applications by greatly reducing the effects by independent environmental factors. This work is the first demonstration of using a UV LED (UVA) to enhance the Mie scatter signals from the particle immunoagglutination assay on the paper microfluidic devices and subsequent smartphone detection. Smartphone's CMOS camera can recognize the UVA scatter from the paper microfluidic channels efficiently in its green channel. For an Escherichia coli assay, the normalized signal intensities increased up to 50% from the negative signal with UV LED, compared with the 4% to 7% with ambient light. Detection limit was 10 colony-forming units/mL. Similar results were obtained in the presence of 10% human whole blood.

Mycobacterial Load Assay

Tuberculosis is a difficult disease to treat, a process made more harder as tools to monitor treatment response only provide a result long after the patient has provided a sample. The mycobacterial load assay (MBLA) provides a simple molecular test to quantify and determine the viability of M. tuberculosis in human or other samples.

Changes in Host Cytokine Patterns of TB Patients with Different Bacterial Loads Detected Using 16S rRNA Analysis

Background

Tuberculosis (TB) has overtaken HIV as the biggest infectious disease killer, with the majority of deaths occurring in sub-Saharan Africa. However it is unknown how differences in bacterial load alter host immune profiles in the sputum and blood of TB patients.

Methods

¹⁶S ribosomal RNA analysis was used to determine bacterial load in sputum samples obtained from 173 patients with active TB (57 pre-treatment and 116 post-treatment). Host analyte concentrations in sputum and Mycobacterium tuberculosis (Mtb) antigen stimulated whole blood assay supernatants were analysed using multiplex cytokine arrays.

Results

Multiple logistic regression adjusting for age, sex and HIV status showed highly significant correlation of bacterial load with IL1β, IL2, IL1RA, IL4, IL6, IL8, IL9, IL15, IL17, EOTAX, FGF, IFN-γ, GCSF, MCP1, M1P1α, M1P1β, PDGF, TNFα, VEGF in sputum. With increasing time on treatment, FGF levels in sputum displayed the most significant inverse correlation with reduction in bacterial load.

Conclusions

We show that differences in bacterial load correlates with changes in several host biomarkers. These findings have implications for development of tests for TB diagnosis and treatment response.

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food

Bacterial cross-contamination from surfaces to food can contribute to foodborne disease. The cross-contamination rate of Enterobacter aerogenes on household surfaces was evaluated by using scenarios that differed by surface type, food type, contact time (<1, 5, 30, and 300 s), and inoculum matrix (tryptic soy broth or peptone buffer). The surfaces used were stainless steel, tile, wood, and carpet. The food types were watermelon, bread, bread with butter, and gummy candy. Surfaces (25 cm2) were spot inoculated with 1 ml of inoculum and allowed to dry for 5 h, yielding an approximate concentration of 107 CFU/surface. Foods (with a 16-cm2 contact area) were dropped onto the surfaces from a height of 12.5 cm and left to rest as appropriate. Posttransfer, surfaces and foods were placed in sterile filter bags and homogenized or massaged, diluted, and plated on tryptic soy agar. The transfer rate was quantified as the log percent transfer from the surface to the food. Contact time, food, and surface type all had highly significant effects (P < 0.000001) on the log percent transfer of bacteria. The inoculum matrix (tryptic soy broth or peptone buffer) also had a significant effect on transfer (P = 0.013), and most interaction terms were significant. More bacteria transferred to watermelon (∼0.2 to 97%) than to any other food, while the least bacteria transferred to gummy candy (∼0.1 to 62%). Transfer of bacteria to bread (∼0.02 to 94%) was similar to transfer of bacteria to bread with butter (∼0.02 to 82%), and these transfer rates under a given set of conditions were more variable than with watermelon and gummy candy.

IMPORTANCE

The popular notion of the "five-second rule" is that food dropped on the floor and left there for <5 s is "safe" because bacteria need time to transfer. The rule has been explored by a single study in the published literature and on at least two television shows. Results from two academic laboratories have been shared through press releases but remain unpublished. We explored this topic by using four different surfaces (stainless steel, ceramic tile, wood, and carpet), four different foods (watermelon, bread, bread with butter, and gummy candy), four different contact times (<1, 5, 30, and 300 s), and two bacterial preparation methods. Although we found that longer contact times result in more transfer, we also found that other factors, including the nature of the food and the surface, are of equal or greater importance. Some transfer takes place "instantaneously," at times of <1 s, disproving the five-second rule.

Naphthoquinone glycosides for bioelectroanalytical enumeration of the faecal indicator Escherichia coli

Microbial water quality monitoring for the presence of faecal indicator bacteria (FIB) is a mandatory activity in many countries and is key in public health protection. Despite technological advances and a need for methodological improvements, chromogenic and fluorogenic enzymatic techniques remain the mainstays of water quality monitoring for both public health agencies and regulated utilities. We demonstrated that bioelectroanalytical approaches to FIB enumeration are possible and can be achieved using commercially available enzyme-specific resorufin glycosides, although these are expensive, not widely available or designed for purpose. Following this, we designed two naphthoquinone glycosides which performed better, achieving Escherichia coli detection in the range 5.0 × 102 to 5.0 × 105 CFU ml-1 22-54% quicker than commercially available resorufin glycosides. The molecular design of the naphthoquinone glycosides requires fewer synthetic steps allowing them to be produced for as little as US$50 per kg. Tests with environmental samples demonstrated the low tendency for abiotic interference and that, despite specificity being maintained between β-glucuronidase and β-galactosidase, accurate enumeration of E. coli in environmental samples necessitates development of a selective medium. In comparison to a commercially available detection method, which has U.S. Environmental Protection Agency (EPA) approval, our approach performed better at high organism concentrations, detecting 500 organisms in 9 h compared with 13.5 h for the commercial method. Bioelectroanalytical detection is comparable to current approved methods and with further development could result in improved detection times. A recent trend for low-cost open-source hardware means that automated, potentiostatically controlled E. coli detection systems could be constructed for less than US$100 per channel.

CapE (capture, amplify, extract): A rapid method for detection of low level contamination of water with Verocytotoxigenic Escherichia coli (VTEC)

Verocytotoxigenic Escherichia coli (VTEC) is associated with a wide spectrum of disease from mild self-limiting diarrhoea to haemolytic uremic syndrome. Contaminated drinking water is accepted as an important route of transmission in Ireland as elsewhere however established methods for detection of VTEC in drinking water have limitations. We describe a sensitive and rapid method for detection of VTEC from large volumes (20 to 30L) of drinking water based on filtration, enrichment culture of filters and real-time PCR detection of VTEC virulence and O antigen determinants from enrichments. The method has potential applications for other waterborne pathogens.

Quantitative Detection and Genotyping of Helicobacter pylori from Stool using Droplet Digital PCR Reveals Variation in Bacterial Loads that Correlates with cagA Virulence Gene Carriage

BACKGROUND

Epidemiologic studies of the carcinogenic stomach bacterium Helicobacter pylori have been limited by the lack of noninvasive detection and genotyping methods. We developed a new stool-based method for detection, quantification, and partial genotyping of H. pylori using droplet digital PCR (ddPCR), which allows for increased sensitivity and absolute quantification by PCR partitioning.

MATERIALS AND METHODS

Stool-based ddPCR assays for H. pylori 16S gene detection and cagA virulence gene typing were tested using a collection of 50 matched stool and serum samples from Costa Rican volunteers and 29 H. pylori stool antigen-tested stool samples collected at a US hospital.

RESULTS

The stool-based H. pylori 16S ddPCR assay had a sensitivity of 84% and 100% and a specificity of 100% and 71% compared to serology and stool antigen tests, respectively. The stool-based cagA genotyping assay detected cagA in 22 (88%) of 25 stools from CagA antibody-positive individuals and four (16%) of 25 stools from CagA antibody-negative individuals from Costa Rica. All 26 of these samples had a Western-type cagA allele. Presence of serum CagA antibodies was correlated with a significantly higher load of H. pylori in the stool.

CONCLUSIONS

The stool-based ddPCR assays are a sensitive, noninvasive method for detection, quantification, and partial genotyping of H. pylori. The quantitative nature of ddPCR-based H. pylori detection revealed significant variation in bacterial load among individuals that correlates with presence of the cagA virulence gene. These stool-based ddPCR assays will facilitate future population-based epidemiologic studies of this important human pathogen.

Campylobacter in broiler slaughter samples assessed by direct count on mCCDA and Campy-Cefex agar

Campylobacter spp. cause foodborne illnesses in humans primarily through the consumption of contaminated chicken. The aim of this study was to evaluate the United States Department of Agriculture's (USDA) recommended methodology, protocol MLG 41.02, for the isolation, identification and direct plate counting of Campylobacter jejuni and C. coli samples from the broiler slaughtering process. A plating method using both mCCDA and Campy-Cefex agars is recommended to recover Campylobacter cells. It is also possible to use this method in different matrices (cloacal swabs and water samples). Cloacal swabs, samples from pre-chiller and post-chiller carcasses and samples of pre-chiller, chiller and direct supply water were collected each week for four weeks from the same flock at a slaughterhouse located in an abattoir in southern Brazil. Samples were analyzed to directly count Campylobacter spp., and the results showed a high frequency of Campylobacter spp. on Campy-Cefex agar. For the isolated species, 72% were identified as Campylobacter jejuni and 38% as Campylobacter coli. It was possible to count Campylobacter jejuni and Campylobacter coli from different samples, including the water supply samples, using the two-agar method. These results suggest that slaughterhouses can use direct counting methods with both agars and different matrices as a monitoring tool to assess the presence of Campylobacter bacteria in their products.

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.

Quantification of Nonproteolytic Clostridium botulinum Spore Loads in Food Materials

We have produced data and developed analysis to build representations for the concentration of spores of nonproteolytic Clostridium botulinum in materials that are used during the manufacture of minimally processed chilled foods in the United Kingdom. Food materials are categorized into homogenous groups which include meat, fish, shellfish, cereals, fresh plant material, dairy liquid, dairy nonliquid, mushroom and fungi, and dried herbs and spices. Models are constructed in a Bayesian framework and represent a combination of information from a literature survey of spore loads from positive-control experiments that establish a detection limit and from dedicated microbiological tests for real food materials. The detection of nonproteolytic C. botulinum employed an optimized protocol that combines selective enrichment culture with multiplex PCR, and the majority of tests on food materials were negative. Posterior beliefs about spore loads center on a concentration range of 1 to 10 spores kg(-1). Posterior beliefs for larger spore loads were most significant for dried herbs and spices and were most sensitive to the detailed results from control experiments. Probability distributions for spore loads are represented in a convenient form that can be used for numerical analysis and risk assessments.