Real-time PCR in the microbiology laboratory

Occupational exposure to anaerobic bacteria in a waste sorting plant

The study focused on exposure assessment to bacterial aerosols and organic dust in waste sorting plant. Samples were collected at different workplaces of waste sorting cycle i.e.: waste press, reloading area, loading of conveyor belt, sorting cabin, sorting hall, and control room. A quantitative analysis of aerobic and anaerobic bacteria was supplemented by qualitative analysis of anaerobic biota with the use of culture-based methods and biochemical tests. In addition, inhalable dust concentrations were also evaluated. To confirm the presence of Clostridium genus, the PCR reaction with specific primers (Chis150f and ClostIr) was performed. The average concentration of total bacteria in waste sorting plant was 4347 CFU m^-3 (SD = 2439), of which 66% were anaerobic strains (2852 CFU m^-3; SD = 2127). It was found that about 24% of anaerobic bacteria belonged to Clostridium genus (682 CFU m^-3; SD = 633). The highest contamination with anaerobic bacteria was observed near the waste reloading plant (3740 CFU m^-3), and the lowest in the control room (850 CFU m^-3). The average concentration of inhalable dust in the waste sorting plant was 0.81 mg m^-3 (SD = 0.59). The correlation analysis showed that the presence of anaerobic bacteria, including clostridia was significantly determined by the microclimate parameters. Qualitative analysis showed the presence of 16 anaerobic species belonging to 9 genera, of which Actinomyces, Clostridium, and Gemella were present at all workplaces. The molecular analysis confirmed the presence of Clostridium genus in both bioaerosol and settled dust samples.Implications: The study showed that anaerobic bacteria should be taken into account as an important component of this microbiota when assessing the exposure of waste sorting workers to biological agents. However, future studies should investigate more precisely how the composition of sorted waste as well as the season can affect the diversity of anaerobic bacteria in this working environment. More attention should be paid to regular cleaning of equipment surfaces in the plant, as deposited organic dust is an important reservoir of anaerobic bacteria, including those of a potentially pathogenic nature.

In-house abbreviated qualification of a real-time polymerase chain reaction method and strategies to amplify mycoplasma detection in human mesenchymal stromal cells

BACKGROUND AIMS

In this study, the authors performed an in-house abbreviated qualification of a commercially available real-time polymerase chain reaction (PCR) kit for limit of detection (LOD), matrix interference and ruggedness of mycoplasma detection in a human bone marrow-derived mesenchymal stromal cell (MSC(M)) investigational cell product (NCT02351011). The approach used was similar to an abbreviated qualification the authors previously conducted for endpoint PCR, which was accepted by Canadian regulators for final product release of the same MSC(M) investigational cell product for treatment of osteoarthritis patients (NCT02351011). With patient consent, biobanked MSCs(M) were re-analyzed by real-time PCR for mycoplasma detection to conduct in-house qualification of the kit.

METHODS

LOD was determined by spiking MSCs(M) with a series of 10-fold dilutions of two commercially available genomic DNA (gDNA) reference standards for Mycoplasma arginini (M. arginini) and Mycoplasma hominis (M. hominis). Matrix interference was tested by using 10-fold dilutions of MSC(M)s down to 4500 cells/mL. Polyadenylic acid (poly[A]) was used to improve DNA recovery in samples with 4500-45 000 MSCs(M)/mL. Real-time PCR tests performed on different days were compared to evaluate ruggedness.

RESULTS

Real-time PCR analysis showed a conservative LOD of 40 genome copies (GCs)/mL and 240 GCs/mL, which are equivalent to 10 colony-forming units (CFUs)/mL, for M. arginini and M. hominis, respectively. According to a less conservative manufacturer-based criterion for positivity, the kit detected 0.4 GC/mL (0.1 CFU/mL) and 24 GCs/mL (1 CFU/mL) M. arginini and M. hominis, respectively. Real-time PCR with different MSC(M) dilutions did not show matrix interference. However, DNA recovery was compromised at MSC(M) concentrations at or below 45 000 cells/mL. The addition of poly(A) as a DNA carrier improved DNA recovery and allowed an LOD, considered here to be equivalent to 10 CFUs/mL, to be achieved, which was not possible in diluted MSC(M) samples (≤45 000 cells/mL) in the absence of poly(A). Ruggedness was demonstrated with tests (n = 18) performed on different days, with an average overall inter-assay percent coefficient of variation of less than 4 for M. arginini (3.62 [400 GCs/mL], 3.61 [40 GCs/mL]) and less than 3 for M. hominis (2.83 [2400 GCs/mL], 1.95 [240 GCs/mL]).

CONCLUSIONS

A commercially available real-time PCR mycoplasma detection kit was qualified for evaluating mycoplasma contamination in investigational MSC(M) products and met the criteria used previously (and accepted by Canadian regulators) for in-house qualification of an endpoint PCR mycoplasma detection kit, and the addition of poly(A) addressed the poor recovery of mycoplasma gDNA in samples with low cell numbers.

UVC disinfects SARS-CoV-2 by induction of viral genome damage without apparent effects on viral morphology and proteins

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic threat worldwide and causes severe health and economic burdens. Contaminated environments, such as personal items and room surfaces, are considered to have virus transmission potential. Ultraviolet C (UVC) light has demonstrated germicidal ability and removes environmental contamination. UVC has inactivated SARS-CoV-2; however, the underlying mechanisms are not clear. It was confirmed here that UVC 253.7 nm, with a dose of 500 μW/cm2, completely inactivated SARS-CoV-2 in a time-dependent manner and reduced virus infectivity by 10-4.9-fold within 30 s. Immunoblotting analysis for viral spike and nucleocapsid proteins showed that UVC treatment did not damage viral proteins. The viral particle morphology remained intact even when the virus completely lost infectivity after UVC irradiation, as observed by transmission electronic microscopy. In contrast, UVC irradiation-induced genome damage was identified using the newly developed long reverse-transcription quantitative-polymerase chain reaction (RT-qPCR) assay, but not conventional RT-qPCR. The six developed long RT-PCR assays that covered the full-length viral genome clearly indicated a negative correlation between virus infectivity and UVC irradiation-induced genome damage (R2 ranging from 0.75 to 0.96). Altogether, these results provide evidence that UVC inactivates SARS-CoV-2 through the induction of viral genome damage.

Discriminating the eight genotypes of the porcine circovirus type 2 with TaqMan-based real-time PCR

Background

The porcine circovirus type 2 (PCV2) is divided into eight genotypes including the previously described genotypes PCV2a to PCV2f and the two new genotypes PCV2g and PCV2h. PCV2 genotyping has become an important task in molecular epidemiology and to advance research on the prophylaxis and pathogenesis of PCV2 associated diseases. Standard genotyping of PCV2 is based on the sequencing of the viral genome or at least of the open reading frame 2. Although, the circovirus genome is small, classical sequencing is time consuming, expensive, less sensitive and less compatible with mass testing compared with modern real-time PCR assays. Here we report about a new PCV2 genotyping method using qPCR.

Methods

Based on the analysis of several hundred PCV2 full genome sequences, we identified PCV2 genotype specific sequences or single-nucleotide polymorphisms. We designed six TaqMan PCR assays that are specific for single genotypes PCV2a to PCV2f and two qPCRs targeting two genotypes simultaneously (PCV2g/PCV2d and PCV2h/PCV2c). To improve specific binding of oligonucleotide primers and TaqMan probes, we used locked nucleic acid technology. We evaluated amplification efficiency, diagnostic sensitivity and tested assay specificity for the respective genotypes.

Results

All eight PCV2 genotype specific qPCRs demonstrated appropriate amplification efficiencies between 91 and 97%. Testing samples from an epidemiological field study demonstrated a diagnostic sensitivity of the respective genotype specific qPCR that was comparable to a highly sensitive pan-PCV2 qPCR system. Genotype specificity of most qPCRs was excellent. Limited unspecific signals were obtained when a high viral load of PCV2b was tested with qPCRs targeting PCV2d or PCV2g. The same was true for the PCV2a specific qPCR when high copy numbers of PCV2d were tested. The qPCR targeting PCV2h/PCV2c showed some minor cross-reaction with PCV2d, PCV2f and PCV2g.

Conclusion

Genotyping of PCV2 is important for routine diagnosis as well as for epidemiological studies. The introduced genotyping qPCR system is ideal for mass testing and should be a valuable complement to PCV2 sequencing, especially in the case of simultaneous infections with multiple PCV2 genotypes, subclinically infected animals or research studies that require large sample numbers.

Biosensing platforms based on silicon nanostructures: A critical review

Biosensors are revolutionizing the health-care systems worldwide, permitting to survey several diseases, even at their early stage, by using different biomolecules such as proteins, DNA, and other biomarkers. However, these sensing approaches are still scarcely diffused outside the specialized medical and research facilities. Silicon is the undiscussed leader of the whole microelectronics industry, and novel sensors based on this material may completely change the health-care scenario. In this review, we will show how novel sensing platforms based on Si nanostructures may have a disruptive impact on applications with a real commercial transfer. A critical study for the main Si-based biosensors is herein presented with a comparison of their advantages and drawbacks. The most appealing sensing devices are discussed, starting from electronic transducers, with Si nanowires field-effect transistor (FET) and porous Si, to their optical alternatives, such as effective optical thickness porous silicon, photonic crystals, luminescent Si quantum dots, and finally luminescent Si NWs. All these sensors are investigated in terms of working principle, sensitivity, and selectivity with a specific focus on the possibility of their industrial transfer, and which ones may be preferred for a medical device.

Capture and detection of urine bacteria using a microchannel silicon nanowire microfluidic chip coupled with MALDI-TOF MS

Fast bacterial identification in urine samples was achieved by capturing bacteria on a microchannel silicon nanowire microfluidic chip, followed by MALDI-TOF MS detection. Under the optimized conditions, bacteria with a concentration of 106 CFU mL-1 in urine samples could be identified without culture. If cultured for 4 hours, bacteria with a concentration as low as 103 CFU mL-1 were identified.

Rapid Methods for Antimicrobial Resistance Diagnostics

Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.

Concurrent detection of bovine viral diarrhoea virus and bovine herpesvirus-1 in bulls' semen and their effect on semen quality

Reproductive diseases may have destructive effects on the fertility of cattle. Bovine viral diarrhoea virus (BVDV) and bovine herpes virus-1 (BoHV-1) are potent viral pathogens linked to reproduction. Thus, the aim of this study was to utilize raw semen samples for conventional and molecular detection of BVDV and BoHV-1, simultaneously. Additionally, the effect of virus infection on the semen quality of naturally infected bulls has been investigated. Therefore, 40 bulls were employed for semen collection, evaluation and testing for both viruses by virus isolation, direct fluorescent antibody technique (FAT) and SYBR Green real-time PCR assay. In virus isolation results, no cytopathic effect (CPE) was observed for BVDV on cell culture whereas, eight (20%) samples displayed characteristic grape-like clusters of cells for BoHV-1. By direct FAT, 12 (30%) positive BVDV and 8 (20%) positive BoHV-1 samples were confirmed. SYBR Green real-time PCR analysis using 48 h inoculated semen samples revealed 14 (35%) and 8 (20%) positive samples for BVDV and BoHV-1, respectively. Statistical analysis of semen evaluation parameters showed a significant difference between viral-infected and free groups represented by increased sperm abnormalities and decreased sperm motility, liveability and concentration. However, there was no significant difference among BVDV, BoHV-1 and mixed-infected groups. The study concluded that BVDV and/or BoHV- 1 infected bulls expressed low semen quality. Real-time PCR was confirmed to be the ideal laboratory assay for detection of both viruses in semen.

Antibacterial and probiotic promotion potential of a new soluble soybean polysaccharide‑iron(III) complex

In this study soluble soybean polysaccharide‑iron(III) (SSPS-Fe(III)) was synthesized to investigate the effects on the growth of Escherichia coli, Staphylococcus aureus and Bacillus licheniformis. Two new detection methods of real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) and microcalorimetry were used to evaluate the effects of different concentrations of SSPS-Fe(III) on the growth of three bacteria. The copy numbers of three bacteria showed that SSPS-Fe(III) had different impacts on the growth of E. coli, S. aureus and B. licheniformis. E. coli growth was inhibited by SSPS-Fe(III) in the higher concentration range and S. aureus growth was inhibited at any concentration, however B. licheniformis growth was promoted. The thermogenic curves for growth metabolism of E. coli and S. aureus presented peak shapes while those of B. licheniformis did platform shapes. As SSPS-Fe(III) concentration increased, the peak heights lowered for E. coli and S. aureus, and the time reaching stationary phase advanced for B. licheniformis. These findings demonstrate that SSPS-Fe(III) has an inhibitory effect on the foodborne pathogens of E. coli and S. aureus, and an enhancement on the probiotics of B. licheniformis.

Point-of-care influenza testing impacts clinical decision, patient flow and length of stay in hospitalized adults

Background

Influenza is difficult to distinguish clinically from other acute respiratory infections. Rapid laboratory diagnosis can help initiate early effective antiviral treatment and isolation. Implementing a novel point-of-care test (POCT) for influenza in the emergency department (ED) could improve treatment and isolation strategies and reduce the length of stay (LOS).

Methods

In a prospective, controlled observational cohort study, we enrolled patients admitted due to acute respiratory illness to 2 public hospitals in Bergen, Norway, one using a rapid POCT for influenza (n = 400), the other (n = 167) using conventional rapid laboratory-based assay.

Results

Prevalence of influenza was similar in the 2 hospitals (154/400, 38% vs 38%, 63/167; P = .863). Most patients in both hospitals received antiviral (83% vs 81%; P = .703) and antibiotic treatment (72% vs 62%; P = .149). Isolation was more often initiated in ED in the hospital using POCT (91% vs 80%; P = .025). Diagnosis by POCT was associated with shorter hospital stay; old age, diabetes, cancer, and use of antibiotics, particularly broad-spectrum antibiotics, were associated with prolonged stay.

Conclusions

POCT implementation in ED resulted in improved targeted isolation and shorter LOS. Regardless of POCT use, most influenza patients received antivirals (>80%) and antibiotics (>69%).

Antibiotic resistance in wastewater treatment plants: understanding the problem and future perspectives

Antibiotics residues (AR), antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) are a new class of water contaminants, due to their adverse effects on aquatic ecosystems and human health. Contamination of water bodies occurs mainly by the excretion of antibiotics incompletely metabolized by humans and animals and is considered the main source of contamination of antibiotics in the environment. Given the imminent threat, the World Health Organization (WHO) has categorized the spread of antibiotics as one of the top three threats to public health in the twenty-first century. The Urban Wastewater Treatment Plants (UWWTP) bring together AR, ARB, ARG, making the understanding of this peculiar environment fundamental for the investigation of technologies aimed at combating the spread of bacterial resistance. Several methodologies have been employed focusing on reducing the ARB and ARG loads of the effluents, however the reactivation of these microorganisms after the treatment is widely reported. This work aims to elucidate the role of UWWTPs in the spread of bacterial resistance, as well as to report the efforts that have been made so far and future perspectives to combat this important global problem.

Molecular and Immunological Diagnostic Techniques of Medical Viruses

Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.

Development and application of a triplex real-time PCR assay for simultaneous detection of avian influenza virus, Newcastle disease virus, and duck Tembusu virus

Background

Pathogens including duck-origin avian influenza virus (AIV), duck-origin Newcastle disease virus (NDV) and duck Tembusu virus (DTMUV) posed great harm to ducks and caused great economic losses to the duck industry. In this study, we aim to develop a triplex real-time polymerase chain reaction (PCR) assay to detect these three viruses as early as possible in the suspicious duck flocks.

Results

The detection limit of the triplex real-time PCR for AIV, NDV, and DTMUV was 1 × 10¹ copies/μL, which was at least 10 times higher than the conventional PCR. In addition, the triplex assay was highly specific, and won’t cross-react with other duck pathogens. Besides, the intra-day relative standard deviation and inter-day relative standard deviation were lower than 4.44% for these viruses at three different concentrations. Finally, a total of 120 clinical samples were evaluated by the triplex real-time PCR, the conventional PCR and virus isolation, and the positive rates for these three methods were 20.83, 21.67, 19.17%, respectively. Taking virus isolation as the gold standard, the diagnostic specificity and positive predictive value of the three viruses were all above 85%, while the diagnostic sensitivity and negative predictive value of the three viruses were all 100%.

Conclusion

The developed triplex real-time PCR is fast, specific and sensitive, and is feasible and effective for the simultaneous detection of AIV, NDV, and DTMUV in ducks.

Heteroresistant Bacteria Detected by an Extended Raman-Based Antibiotic Susceptibility Test

Worldwide, multiresistant bacterial strains are emerging at unprecedented rates. This development seriously threatens the ability of humanity to treat even common infections, resulting in disability and death. Furthermore, this development endangers all medical achievements including cancer therapy or organ transplantations. Therefore, the World Health Organization has endorsed antimicrobial resistance as a great threat to humanity. To still allow effective treatment of patients, rapid, automated, and reliable antibiotic susceptibility testing (AST) of bacterial pathogens is essential. Thereby, speed and sensitivity of the AST results are crucial for improving patient care. Here, Raman spectroscopy as a nondestructive technique providing chemical-specific information is employed to monitor the deuterium uptake of metabolically active bacteria during antibiotic treatment, enabling fast and reliable AST. For this purpose, a bulk sample-preparation method was developed, allowing a high-throughput analysis of a significant number of cells. A protocol was developed for Gram-positive (Enterococcus faecalis) and Gram-negative (Escherichia coli) reference strains and was tested on 51 clinical isolates with well-characterized resistance phenotypes against ampicillin, ciprofloxacin, meropenem, and vancomycin. Borderline resistant and heteroresistant phenotypes were observed and further investigated. This is of critical importance as the sensitive detection of low-frequency heteroresistance in bacterial populations is a huge challenge. Such isolates seem susceptible but are resistant to treatment in vivo. Automatable analysis detects strong phenotypes within 3 h. On the basis of experimental and modeled data, heteroresistance is estimated to be detectable down to frequencies of 10^-6 and investigated on clinical isolates as a proof-of-concept study, but requiring longer incubation time.

Selection of stable reference genes for gene expression analysis in sweet potato (Ipomoea batatas L.)

Gene expression analysis is one of the most common and important studies in biology and biomedicine. No matter for traditional blotting analysis or currently commonly used PCR strategy, all need a stable reference gene for normalizing the gene expression. To screen and select housekeeping genes as the most stable reference genes, quantitative real-time PCR (qRT-PCR) was employed to analyze the expression of sixteen commonly used reference genes (IbelF, Ibα-tubulin, IbHIS, IbCOX, IbGAPDH, IbH2B1, IbARF, IbCYC, Ibβ-tubulin, IbACT, IbEFl-a, IbG14, IbPLD, IbRPL2, IbUBQ, IbUBI) in five different tissues under two different temperature stresses in sweet potato. Data analysis by the Delta CT, geNorm, NormFinder, and BestKeeper programs revealed that IbelF is the most stable gene and IbUBI is the least stable gene as reference. Our study also shows that combination of two or more genes as reference is a better choice, rendering more substantiated expression data for comparison. This study provides evidence for selecting reference genes in sweet potato gene expression analysis.

PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions

DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.

Sensitive Detection of Dengue Virus Type 2 E-Proteins Signals Using Self-Assembled Monolayers/Reduced Graphene Oxide-PAMAM Dendrimer Thin Film-SPR Optical Sensor

In this work, sensitive detection of dengue virus type 2 E-proteins (DENV-2 E-proteins) was performed in the range of 0.08 pM to 0.5 pM. The successful DENV detection at very low concentration is a matter of concern for targeting the early detection after the onset of dengue symptoms. Here, we developed a SPR sensor based on self-assembled monolayer/reduced graphene oxide-polyamidoamine dendrimer (SAM/NH₂rGO/PAMAM) thin film to detect DENV-2 E-proteins. Surface characterizations involving X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR) confirms the incorporation of NH₂rGO-PAMAM nanoparticles in the prepared sensor films. The specificity, sensitivity, binding affinity, and selectivity of the SPR sensor were then evaluated. Results indicated that the variation of the sensing layer due to different spin speed, time incubation, and concentration provided a better interaction between the analyte and sensing layer. The linear dependence of the SPR sensor showed good linearity (R² = 0.92) with the lowest detection of 0.08 pM DENV-2 E-proteins. By using the Langmuir model, the equilibrium association constant was obtained at very high value of 6.6844 TM⁻¹ (R² = 0.99). High selectivity of the SPR sensor towards DENV-2 E-proteins was achieved in the presence of other competitors.

Rapid Colorimetric Detection of Pseudomonas aeruginosa in Clinical Isolates Using a Magnetic Nanoparticle Biosensor

A rapid, sensitive, and specific colorimetric biosensor based on the use of magnetic nanoparticles (MNPs) was designed for the detection of Pseudomonas aeruginosa in clinical samples. The biosensing platform was based on the measurement of P. aeruginosa proteolytic activity using a specific protease substrate. At the N-terminus, this substrate was covalently bound to MNPs and was linked to a gold sensor surface via cystine at the C-terminus of the substrates. The golden sensor appears black to naked eyes because of the coverage of the MNPs. However, upon proteolysis, the cleaved peptide-MNP moieties will be attracted by an external magnet, revealing the golden color of the sensor surface, which can be observed by the naked eye. In vitro, the biosensor was able to detect specifically and quantitatively the presence of P. aeruginosa with a detection limit of 10² cfu/mL in less than 1 min. The colorimetric biosensor was used to test its ability to detect in situ P. aeruginosa in clinical isolates from patients. This biochip is anticipated to be useful as a rapid point-of-care device for the diagnosis of P. aeruginosa-related infections.

Pragmatic multicentre randomised controlled trial evaluating the impact of a routine molecular point-of-care 'test-and-treat' strategy for influenza in adults hospitalised with acute respiratory illness (FluPOC): trial protocol

BACKGROUND

Influenza infections often remain undiagnosed in patients admitted to hospital due to lack of routine testing. When tested for, the diagnosis and treatment of influenza are often delayed due to the slow turnaround times of centralised laboratory PCR testing. Newer molecular systems, have comparable accuracy to laboratory PCR testing, and can generate a result in under 1 hour, making them potentially deployable as point-of-care tests (POCTs). High-quality evidence for the impact of routine POCT for influenza on clinical outcomes is, however, currently lacking. This large pragmatic multicentre randomised controlled trial aims to address this evidence gap.

METHODS AND ANALYSIS

The FluPOC trial is a pragmatic, multicentre, randomised controlled trial evaluating adults admitted to a large teaching hospital and a district general hospital with an acute respiratory illness, during influenza season and defined by Public Health England. Up to 840 patients will be recruited over up to three influenza seasons, and randomised (1:1) to receive either POCT using the FilmArray respiratory panel, or routine clinical care. Clinical and infection control teams will be informed of the results in real time and where influenza is detected clinical teams will be encouraged to offer neuraminidase inhibitor (NAI) treatment in accordance with national guidelines. Those allocated to standard clinical care will have a swab taken for later analysis to allow assessment of missed diagnoses. The outcomes assessment will be by retrospective case note analysis. The outcome measures include the proportion of influenza-positive patients detected and appropriately treated with NAIs, isolation facility use, antibiotic use, length of hospital stay, complications and mortality.

ETHICS AND DISSEMINATION

Prior to commencing the study, approval was obtained from the South Central Hampshire A Ethics Committee (reference 17/SC/0368, granted 7 September 2017). Results generated from this protocol will be published in peer-reviewed scientific journals and presented at national and international conferences.

TRIAL REGISTRATION NUMBER

ISRCTN17197293.

Occurrence of Mycobacterium avium subsp. paratuberculosis in coalho cheese in the State of Pernambuco, Brazil

ABSTRACT Paratuberculosis is a chronic and incurable disease that affects ruminants and other domestic animals. It is caused by Mycobacterium avium subsp. paratuberculosis (MAP) that may also be involved in some human diseases such as Crohn's disease, type 1 diabetes, sarcoidosis, multiple sclerosis, and Hashimoto's thyroiditis. The objective of this study was to investigate the occurrence of MAP DNA in samples of artisanal coalho cheese purchased in the State of Pernambuco. Forty samples of coalho cheese submitted to the Real Time Polymerase Chain Reaction (qPCR) technique were analyzed for the detection of the MAP region IS900. 11 (27.5%) were positive with a mean of 195.9 MAP colony forming unit (CFU) per gram of each sample, with a minimum of 30.3 CFU/g and a maximum of 324.2 CFU/g. Thus, this type of cheese that is one of the most consumed in this region of Brazil constitutes a source of human exposure to MAP. Further research in this area should be performed to evaluate the viability of the bacteria in this cheese type.

Atypical herpes simplex keratitis: frequency, clinical presentations and treatment results

AIMS

To determine herpes simplex virus (HSV) DNA positivity in corneal scraping samples obtained from patients with microbial keratitis whose findings were not specific for HSV keratitis and to evaluate these particular cases with respect to clinical features and antiviral treatment results.

METHODS

Records of patients with microbial keratitis treated in a tertiary eye care hospital within the 3-year period were evaluated retrospectively. Real-time polymerase chain reaction (PCR) was used to identify HSV DNA. Smear slides were evaluated by light microscopy. Patients with typical presentations and histories of HSV keratitis were excluded.

RESULTS

Two hundred and seventy-six eyes of 276 patients were included in the study. HSV-1 DNA was detected in 25 eyes (9%). In these 25 eyes, the initial diagnosis was fungal or bacterial keratitis. The mean symptom duration was 20 ± 14 days (2-60 days). The risk factors were ocular surgery (20%), blepharitis (16%), trauma (8%) and contact lens wear (4%); however, the majority of patients did not have any specific cause for keratitis (52%). Clinical features were variable and not typical for any particular etiology. Culture and microscopic examinations revealed bacteria and/or fungi in 6 patients in addition to herpes infection. Antiviral treatment was successful in 72% of patients.

CONCLUSION

Herpetic corneal infections can present without typical dendritic or geographic ulcers and may be masked by other infections. Real-time PCR is a useful method for rapid and definitive diagnosis. HSV infection should be considered for microbial keratitis without specific risk factors, with negative culture results and poor response to antimicrobial agents.

Real-time PCR assay with an endogenous internal amplification control for detection and quantification of Anaplasma marginale in bovine blood

Bovine anaplasmosis is a tick-borne rickettsial disease, causing significant economic losses in many countries. The main causative agent of bovine anaplasmosis is Anaplasma marginale (Rickettsiales, Anaplasmataceae). To date, several PCR assays for A. marginale DNA detection were proposed, but most of them do not provide an internal amplification control, which allows to prevent false-negative results and is required for reliability of the results of pathogen DNA detection by PCR assay. In the present study, a real-time PCR assay based on the species-specific and highly conserved fragment of msp1α gene was developed for detection and quantification of A. marginale in bovine blood. The real-time PCR assay is able to detect as few as one copу of msp1α gene per reaction. To prevent false-negative results, simultaneous amplification and detection of the bovine genomic DNA fragment as an endogenous internal amplification control (IAC) was provided. The assay can be used as a highly specific and sensitive method for detection and quantification of A. marginale in infected cattle, and for the evaluation of the efficacy of anti-rickettsial drugs and anaplasmosis vaccines.

Targeting a highly repeated germline DNA sequence for improved real-time PCR-based detection of Ascaris infection in human stool

Background

With the expansion of soil transmitted helminth (STH) intervention efforts and the corresponding decline in infection prevalence, there is an increased need for sensitive and specific STH diagnostic assays. Previously, through next generation sequencing (NGS)-based identification and targeting of non-coding, high copy-number repetitive DNA sequences, we described the development of a panel of improved quantitative real-time PCR (qPCR)-based assays for the detection of Necator americanus, Ancylostoma duodenale, Ancylostoma ceylanicum, Trichuris trichiura, and Strongyloides stercoralis. However, due to the phenomenon of chromosome diminution, a similar assay based on high copy-number repetitive DNA was not developed for the detection of Ascaris lumbricoides. Recently, the publication of a reference-level germline genome sequence for A. lumbricoides has facilitated our development of an improved assay for this human pathogen of vast global importance.

Methodology/Principal findings

Repurposing raw DNA sequence reads from a previously published Illumina-generated, NGS-based A. lumbricoides germline genome sequencing project, we performed a cluster-based repeat analysis utilizing RepeatExplorer2 software. This analysis identified the most prevalent repetitive DNA element of the A. lumbricoides germline genome (AGR, Ascaris germline repeat), which was then used to develop an improved qPCR assay. During experimental validation, this assay demonstrated a fold increase in sensitivity of ~3,100, as determined by relative Cq values, when compared with an assay utilizing a previously published, frequently employed, ribosomal internal transcribed spacer (ITS) DNA target. A comparative analysis of 2,784 field-collected samples was then performed, successfully verifying this improved sensitivity.

Conclusions/Significance

Through analysis of the germline genome sequence of A. lumbricoides, a vastly improved qPCR assay has been developed. This assay, utilizing a high copy-number repeat target found in eggs and embryos (the AGR repeat), will improve prevalence estimates that are fundamental to the programmatic decision-making process, while simultaneously strengthening mathematical models used to examine STH infection rates. Furthermore, through the identification of an optimal target for PCR, future assay development efforts will also benefit, as the identity of the optimized repeat DNA target is likely to remain unchanged despite continued improvement in PCR-based diagnostic technologies.

With an at-risk population in the billions, Ascaris lumbricoides is a pathogen of great global importance. In recent years, efforts to control the spread of this parasitic helminth have expanded, resulting in declining infection rates and worm burdens in some regions. While immeasurably important for global health, these declines have also served to expose the shortcomings of traditional diagnostic methods, as low-levels of pathogen generate a need for more sensitive tools, and microscopy-based techniques are proving ill-suited to the task at hand. Thankfully, improved sensitivity can be achieved through the careful selection of optimal repetitive DNA targets for PCR. However, previous attempts to identify such targets in A. lumbricoides were unsuccessful, largely due to chromosome diminution, an unusual phenomenon occurring in the Ascaridida, whereby large portions of the germline genome are reproducibly eliminated during early development, resulting in their absence in larvae or adult worms. As the stool-based molecular diagnosis of A. lumbricoides infection is primarily dependent upon the identification of egg-derived DNA, utilizing genomic DNA from adult worms for molecular target selection eliminates germline candidates and results in suboptimal target sequence choices. Recently, the publication of a pre-diminution germline genome of A. lumbricoides has provided us with an opportunity to re-evaluate target selection, facilitating the development of a novel quantitative real-time PCR assay with greatly improved sensitivity (~3100-fold as determined by relative Cq value) over previously developed assays that were based on ribosomal repeat DNA sequences with lower copy numbers.

Identification of reliable reference genes for quantitative real-time PCR normalization in pitaya

BACKGROUND

A suitable reference gene is an important prerequisite for guarantying accurate and reliable results in quantitative real-time PCR (qRT-PCR) analyses. However, there is no absolute universality in reference genes among different species. It's hard to find an ideal reference gene to fit for different tissues and growth periods. Pitaya (Hylocereus) is commercially produced as a new fruit crop at a large scale in tropical and subtropical regions. To date, there is no report on the identification of the most reliable reference genes for qRT-PCR normalization in pitaya.

RESULTS

In this study, six candidate reference genes i.e. Actin(1), GAPDH, UBC(1), UBC(2) EF1-α(1) and histone(1) were selected from thirty-nine typical candidate reference genes to determine the most stable reference genes for qRT-PCR normalization in different tissues, temperature stresses and fruit developmental stages of pitaya. Among the six candidate reference genes, Actin(1) and EF1-α(1) were the most stable gene according to calculations of three statistical methods (GeNorm, NormFinder and BestKeeper) while UBC(1) and UBC(2) showed the lowest expression stability. The six candidate reference genes were further validated by comparing expression profiles of key genes related to betalain biosynthesis at flesh coloration stages of Guanhuahong (Hylocereus monacanthus) and Guanhuabai (H. undatus) pitayas. Actin(1) was recommended the best reference gene for accurate normalization of qRT-PCR data.

CONCLUSIONS

In this study, the stability of the selected reference genes for normalizing the qRT-PCR data were identified from pitaya. Actin(1) was the most stably expressed genes in different tissues and fruit developmental stages in pitaya. The present work provides the first data of reference gene identification for pitaya and will facilitate further studies in molecular biology and gene function on Hylocereus and other closely related species.

HIRA-TAN detects pathogens of pneumonia with a progressive course despite antibiotic treatment

BACKGROUND

Empiric antibiotics are administered for pneumonia when the causative pathogens are unidentified. Pathogen-directed therapy is impeded by negative culture results and/or culture time lag. This circumstance necessitates a salvage method for pathogen identification, especially when antibiotic therapy has failed. Here, we aimed to preliminarily investigate the HIRA-TAN method in pneumonia with a progressive course despite prior empiric antibiotic therapy.

METHODS

This prospective study was conducted for patients who were referred to Dr. Zainoel Abidin Hospital, Aceh, Indonesia, from December 2016 to January 2017, owing to pneumonia with a progressive course. Sputum or pleural effusion was subjected to culture and the HIRA-TAN assay. The HIRA-TAN identified the candidate causative pathogens based on the difference in the cycle threshold (Ct) between the targeted pathogen and the single-copy human gene.

RESULTS

Patients (n=27) were predominantly males (22 patients, 81.5%), with a median age of 62 years. All patients had comorbid disease and were classified as hospital-acquired pneumonia (25 patients, 92.6%) with multilobar infiltrates (22 patients, 81.5%). Bacterial culture identified causative pathogen(s) in some (14 patients, 51.8%), whereas the HIRA-TAN identified pathogen(s) in most (23 patients, 85.2%). The rapid pathogen identification by the HIRA-TAN will provide valuable information in guiding pathogen-directed therapy.

CONCLUSIONS

The result warrants a larger clinical trial to confirm the clinical efficacy of the HIRA-TAN in patients with progressive pneumonia despite previous antibiotic treatment.

Amplification chemistries in clinical virology

Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.

A review of methods for the detection of pathogenic microorganisms

The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.

Impact of Rapid Molecular Diagnostic Testing of Respiratory Viruses on Outcomes of Adults Hospitalized with Respiratory Illness: a Multicenter Quasi-experimental Study

A standard multiplex PCR offers comprehensive testing for respiratory viruses. However, it has traditionally been performed in a referral laboratory with a lengthy turnaround time, which can reduce patient flow through the hospital. We aimed to determine whether the introduction of a rapid PCR, but with limited targets (Cepheid Xpert Flu/RSV XC), was associated with improved outcomes for adults hospitalized with respiratory illness. A controlled quasi-experimental study was conducted across three hospitals in New South Wales, Australia. Intervention groups received standard multiplex PCR during the preimplementation, July to December 2016 (n = 953), and rapid PCR during the postimplementation, July to December 2017 (n = 1,209). Control groups (preimplementation, n = 937, and postimplementation, n = 1,102) were randomly selected from adults hospitalized with respiratory illness during the same periods. The outcomes were hospital length of stay (LOS) and microbiology test utilization (blood culture, urine culture, sputum culture, and respiratory bacterial and virus serologies). The introduction of rapid PCR was associated with a nonsignificant 8.9-h reduction in median LOS (95% confidence interval [CI], -21.5 h to 3.7 h; P = 0.17) for all patients and a significant 21.5-h reduction in median LOS (95% CI, -36.8 h to -6.2 h; P < 0.01) among patients with positive test results in an adjusted difference-in-differences analysis. For patients receiving test results before disposition, rapid PCR use was associated with a significant reduction in LOS, irrespective of test results. Compared with standard PCR testing, rapid PCR use was significantly associated with fewer blood culture (adjusted odds ratio [aOR], 0.67; 95% CI, 0.5 to 0.82; P < 0.001), sputum culture (aOR, 0.56; 95% CI, 0.47 to 0.68, P < 0.001), bacterial serology (aOR, 0.44; 95% CI, 0.35 to 0.55, P < 0.001) and viral serology (aOR, 0.42; 95% CI, 0.33 to 0.53, P < 0.001) tests, but not with fewer urine culture tests (aOR, 0.94; 95% CI, 0.78 to 1.12, P = 0.48). Rapid PCR testing of adults hospitalized with respiratory illnesses can deliver benefits to patients and reduce resource utilization. Future research should consider a formal economic analysis and assess its potential impacts on clinical decision making.

Human papillomavirus infection and ocular surface disease (Review)

Human papillomavirus (HPV) infection has been implicated as a primary cause of lesions in the anogenital region, skin, oropharynx and respiratory tract. Additionally, the role of HPV in the pathogenesis of ocular surface disease has also been extensively studied. Conjunctival papilloma development has been strongly associated with the HPV infection of certain subtypes. On the other hand, the role of HPV in conjunctival pterygium, conjunctival intraepithelial neoplasia (CIN) and ocular surface squamous neoplasia (OSSN) remains controversial. Genetic predisposition and environmental factor is important in HPV hosts as regards the pathogenesis of ocular surface disease. Several studies have indicate a synergic role of HPV with ultraviolet radiation in pterygium establishment. A higher recurrence risk rate and more aggressive disease of ophthalmic pterygium is observed in cases of HPV infection. The purpose of this review was to provide a systematic review of the literature and to assist in a better understanding of the role of HPV in ocular surface disease.

Selection of Optimized Reference Genes for qRT-PCR Normalization in Xanthomonas campestris pv. campestris Cultured in Different Media

Black rot is a cruciferous disease caused by Xanthomonas campestris pv. campestris (Xcc) and results in significant economic losses worldwide; therefore, elucidation of the mechanism of Xcc pathogenesis is urgently required. In this study, we aimed to select optimized reference genes to verify the relative quantification of virulent genes in Xcc. Xcc strains were cultured in three different media [basic medium (MMX), hrp-inducing medium (MMXC) and rich medium (NYG)] and the expression stability of five candidate genes [thymidylate synthase (thyA), DNA gyrase subunit B (gyrB), DNA-directed RNA polymerase subunit beta, glyceraldehyde-3-phosphate dehydrogenase and 16S ribosomal RNA (16S rRNA)] was evaluated using BestKeeper, GeNorm, and NormFinder software programs. Quantitative real-time PCR (qRT-PCR) analysis confirmed that two Xcc effector genes were hrpX/hrpG-regulated in MMXC using selected genes as controls. Finally, gyrB and thyA were validated as the optimized reference genes of Xcc cultured in MMXC, and qRT-PCR analysis was demonstrated to be an efficient alternative to Gus-activity detection for the analysis of Xcc expression. This information will be useful in the future studies of Xcc, especially those seeking new functional genes.

Cost-effectiveness assessment of three components of the bovine tuberculosis surveillance system by intradermal tuberculin testing in French cattle farms by a scenario tree approach

In most officially bovine tuberculosis (bTB)-free countries, bTB has not been fully eradicated. Costly and time-consuming surveillance and control measures are therefore still in place to control this infection. An officially bTB-free status, both at the national and at the herd level, influences whether and when animals can be sold. Thus, this infection is still an economic issue, justifying measures towards its eradication. An evaluation of the cost-effectiveness of such measures would be highly useful, especially to optimise the costs of control measures and their adaptation to a local epidemiological context. We evaluated the cost-effectiveness of three mandatory surveillance protocols currently used in France by herd type (type of production, size, and turnover of the herd) under French field conditions. The first protocol ("strict") implies the direct slaughter and post-mortem analyses of any intradermal cervical tuberculin test (ICT) reactor, and negative results to a second intradermal cervical comparative tuberculin test (ICCT) to regain bTB-free status of the herd. In the second protocol ("compliant quick-path") bTB-free status can be regain if post-mortem analyses of reactors to the first ICT are negative. In the third protocol ("compliant slow-path"), ICCT-reactive animals are tested using the interferon gamma assay; the results of this test influence the path of further investigation. We built scenario trees for each of these protocols at the animal level. They allowed us to estimate herd sensitivity and the total cost of each protocol by herd type. The protocols could be ordered by decreasing herd sensitivity and cost, regardless of the herd type, as follows: strict protocol, compliant quick-path protocol, and compliant slow-path protocol. We calculated a cost-effectiveness index to evaluate the cost-effectiveness of each protocol. The strict protocol was never the most cost-effective, regardless of herd type, due to higher costs relative to the other protocols, despite better herd sensitivity. We found the compliant quick-path to be the most cost-effective protocol for big beef, big dairy, and mixed herds. The compliant slow-path was the most cost-effective for small-scale beef and dairy herds. All differences were significant. This comparison of the cost-effectiveness of the protocols by herd type could help authorities to choose the most suitable protocol in the investigation of suspected cases, depending on the herd type, but could be improved by accounting for important sociological data, such as the acceptability of the protocols.

Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States

The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.

Exploring the immune response, tolerance and resistance in proliferative kidney disease of salmonids

Proliferative kidney disease (PKD) of salmonids is a disease of economic and environmental concern caused by the myxozoan parasite Tetracapsuloides bryosalmonae. Finer details of the immune repertoire during T. bryosalmonae infection have been elucidated in rainbow trout (Oncorhynchus mykiss). In contrast, there remain many unanswered questions regarding the immune response of the wild fish host in Europe, the brown trout (Salmo trutta) to this parasite. The first aim of this study is to examine the brown trout immune response to T. bryosalmonae and compare it with the published information on rainbow trout as two species that have undergone a different coevolution with the parasite. According to ecoimmunology terminology, infected organisms may manage infection by reducing the damage caused by parasites (tolerance) or by limiting parasite burden (resistance). The second aim of this study is to investigate tolerance/resistance patterns of these species during PKD infection. Our results suggest subtle differences in sequential aspects of the immune response and of immune genes that correlate with parasite intensity for the brown trout, in contrast to rainbow trout, in terms of the B cell response and Th-like interplay that may be linked to PKD pathogenesis. These differences in the immune response also correlate with species-specific differences in tolerance/resistance patterns, in that brown trout had increased tolerance but rainbow trout had greater resistance to infection. The variance in tolerance/resistance investment resulted in a different evolutionary outcome for each host-parasite interaction. A greater exploration of these concepts and an association of immune mechanisms could open an additional gateway for interpreting fish host-parasite interactions.

First report and molecular characterization of Cryptosporidium spp. in humans and animals in Khartoum state, Sudan

BACKGROUND AND AIM

Cryptosporidium is recognized to infect several mammalian species as well as humans, causing substantial economic losses and serious public health concern. Infected animals can be a source of environmental contamination and human infections. In general, the occurrence of Cryptosporidium species in animals and human in Sudan and zoonotic importance is not well documented. This study aimed to identify Cryptosporidium spp. infecting different animal species and humans and to compare between different isolates obtained.

MATERIALS AND METHODS

To provide molecular information about Cryptosporidium in animals and humans, both modified Ziehl-Neelsen (MZN) specific stain and molecular assay were used. Concentration techniques followed by three protocols of DNA extraction were carried out. After microscopic screening of 263 fecal samples (goats [n=197], cattle [n=12], sheep [n=12], and human [n=42]), 61 positive and 30 negative, randomly selected samples were used in nested polymerase chain reaction (PCR) targeting part of the 18S RNA.

RESULTS

Nested PCR amplification confirmed 91.8% (56/61) of microscopic-positive samples. 8.2% (5/61) of negative samples by PCR (positive by microscopy) were considered false negatives. Sequencing followed by alignment of the 14 isolates indicated that all samples were identical (100%) and belonged to Cryptosporidium parvum.

CONCLUSION

MZN staining procedure is reliable for the routine diagnosis of Cryptosporidium; cetyltrimethylammonium bromide extraction buffer and nested PCR targeting 18S rRNA gene are reliable and useful in epidemiological studies of this parasite.

Evaluation of mycoplasma removal reagents using qPCR-based quantification

In this study, we evaluated the efficacy of various mycoplasma removal reagents using nuclear staining, DNA gel electrophoresis, and qPCR-based quantification. Our results showed Plasmocure and Plasmocin are two effective anti-mycoplasma reagents whose effects can be observed within a week. However, prolonged treatment with Plasmocin led to development of resistance. Withdrawal of anti-mycoplasma reagents led to reoccurrence of mycoplasma contamination, but addition of prevention reagent, such as Primocin, prevented recontamination. Therefore, sequential treatment by Plasmocure and Primocin is the best course of action against mycoplasma contamination. Lastly, we developed methods based on qPCR to estimate the average number of mycoplasma associated with a single contaminated cell. We have shown, for the first time, that untreated contaminated BEAS-2B cells have approximately 300-400 mycoplasma contaminants per cell in the cytoplasm or attached to the cell membrane. Furthermore, withdrawal of anti-mycoplasma reagents led to reoccurrence of mycoplasma contamination within two days, and therefore continued use of prevention reagent is imperative.

Reduced-Fat Response of Lactobacillus casei subsp. casei SY13 on a Time and Dose-Dependent Model

A reduced-fat effect of probiotics was primarily derived functionally rather than structurally, and we investigated the ultra-structural aspect of the gut mucosa in Syrian golden hamsters with high-fat diet by feeding with Lactobacillus casei subsp. casei SY13 (Lc SY13). 36 adult-male Syrian golden hamsters were randomly grouped into four; control group (G1), high-fat group (G2), high-dose group (G3), and low-dose group (G4). The G1 hamsters were fed a standard normal chow diet, while those in other groups were fed a high-fat chow diet for duration of 8 weeks. With the use of oral gavage, G1 hamsters were administered 1 mL of skim milk/hamster/day, while G3 and G4 hamsters were administered Lc SY13 at 4.1 × 10¹⁰ or 4.1 × 10⁸ cells/hamster/day. At 14, 28, and 56 days consecutively, three golden hamsters from each group were sacrificed by carotid, taking blood from eyeball for quantitative detection of hamsters serum total cholesterol (TC), triacylglycerol (TG), high-density lipoprotein (HDL), and low-density lipoprotein (LDL). At 56 days, Taqman-MGB fluorescence probe was used for the quantitative detection of Lc SY13 in the intestinal mucosal, and their ileum was viewed using transmission electron microscopy (TEM). Screening of the ileum microvilli of the hamsters showed that at 56 days, G3 was significantly (P < 0.05) bigger than other groups while its serum TC, TG, and TDL decreased. Lc SY13 was detected in the intestines, and was significantly (P < 0.05) higher in the ileum of G3 than those of G4. In conclusion, Lc SY13 may play a remarkable reduced-fat response role by improving high-fat uptake as well as its metabolism and transport; most especially in G3. The reduced-fat response of the Lc SY13 differed in a time and dose-dependent manner. These findings indicated that probiotic strains of Lc SY13 can reduce fat level, thus suggesting its potential in ameliorating obesity-related diseases.

Do fish get wasted? Assessing the influence of effluents on parasitic infection of wild fish

Many ecosystems are influenced simultaneously by multiple stressors. One important environmental stressor is aquatic pollution via wastewater treatment plant (WWTP) effluents. WWTP effluents may contribute to eutrophication or contain anthropogenic contaminants that directly and/or indirectly influence aquatic wildlife. Both eutrophication and exposure to anthropogenic contaminants may affect the dynamics of fish-parasite systems. With this in mind, we studied the impact of WWTP effluents on infection of brown trout by the parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). PKD is associated with the long-term decline of wild brown trout (Salmo trutta) populations in Switzerland. We investigated PKD infection of brown trout at two adjacent sites (≈400 m apart) of a Swiss river. The sites are similar in terms of ecology except that one site receives WWTP effluents. We evaluated the hypothesis that fish inhabiting the effluent site will show greater susceptibility to PKD in terms of prevalence and disease outcome. We assessed susceptibility by (i) infection prevalence, (ii) parasite intensity, (iii) host health in terms of pathology, and (iv) estimated apparent survival rate. At different time points during the study, significant differences between sites concerning all measured parameters were found, thus providing evidence of the influence of effluents on parasitic infection of fish in our study system. However, from these findings we cannot determine if the effluent has a direct influence on the fish host via altering its ability to manage the parasite, or indirectly on the parasite or the invertebrate host via increasing bryozoa (the invertebrate host) reproduction. On a final note, the WWTP adhered to all national guidelines and the effluent only resulted in a minor water quality reduction assessed via standardized methods in this study. Thus, we provide evidence that even a subtle decrease in water quality, resulting in small-scale pollution can have consequences for wildlife.

Ultrasensitive Label- and PCR-Free Genome Detection Based on Cooperative Hybridization of Silicon Nanowires Optical Biosensors

The realization of an innovative label- and PCR-free silicon nanowires (NWs) optical biosensor for direct genome detection is demonstrated. The system is based on the cooperative hybridization to selectively capture DNA and on the optical emission of quantum confined carriers in Si NWs whose quenching is used as detection mechanism. The Si NWs platform was tested with Hepatitis B virus (HBV) complete genome and it was able to reach a Limit of Detection (LoD) of 2 copies/reaction for the synthetic genome and 20 copies/reaction for the genome extracted from human blood. These results are even better than those obtained with the gold standard real-time PCR method in the genome analysis. The Si NWs sensor showed high sensitivity and specificity, easy detection method, and low manufacturing cost fully compatible with standard silicon process technology. All these points are key factors for the future development of a new class of genetic point-of-care devices that are reliable, fast, low cost, and easy to use for self-testing including in the developing countries.

Development of a TaqMan-based real-time PCR for detecting duck adenovirus 3

Recently, a novel duck adenovirus (designated as duck adenovirus 3, DAdV-3) was discovered in Muscovy ducks, China. Here, we developed a TaqMan-based real-time PCR assay (qPCR) for the detection of DAdV-3 infection. After the optimization of the qPCR conditions, the lower limit of detection for DAdV-3 infection was 40.9 copies/μl. No cross-reactivity was observed with other duck-derived pathogens. Intra- and inter-assay variability was less than 2.30%. DAdV-3 was detected in embryos and newly hatched ducklings by qPCR assay, the findings provided evidence of possible vertical transmission of DAdV-3. The developed qPCR analysis showed high specificity, sensitivity, and reproducibility, thereby indicating that it can be used in future investigations on the pathogenesis and epidemiology of DAdV-3.

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study

PURPOSE

Respiratory tract infections (RTIs) are responsible for over 2.8 million deaths per year worldwide with pathobiont carriage a required precursor to infection. We sought to determine carriage epidemiology for both bacterial and viral respiratory pathogens as part of a large population-based cross-sectional carriage study.

METHODOLOGY

Nose self-swab samples were collected in two separate time-points, May to August 2012 (late spring/summer) and February to April 2013 (winter/early spring). The presence of six bacterial species: S. pneumoniae, H. influenzae, M. catarrhalis, S. aureus, P. aeruginosa and N. meningitidis in addition to respiratory syncytial virus, influenza viruses A and B, rhinovirus/enterovirus, coronavirus, parainfluenza viruses 1-3 and adenovirus was determined using culture and PCR methods.Results/Key findings. Carriage was shown to vary with age, recent RTI and the presence of other species. Spatial structures of microbial communities were more disordered in the 0-4 age group and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X²=20.42, P=0.002), indicating spatial clumping of species consistent with facilitative relationships. Deviations from a neutral model of ecological niches were observed in summer samples and from older individuals but not in the winter or younger individuals (0-4 years), suggesting the presence of seasonal and age-dependent niche processes in respiratory community assembly.

CONCLUSION

The application of epidemiological methods and ecological theory to respiratory tract samples has yielded novel insights into the factors that drive microbial community composition.