Detection of vaccinia virus, herpes simplex virus, varicella-zoster virus, and Bacillus anthracis DNA by LightCycler polymerase chain reaction after autoclaving: implications for biosafety of bioterrorism agents

An Environmental DNA Primer for Microbial and Restoration Ecology

Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.

Working Safely with Vaccinia Virus: Laboratory Technique and Review of Published Cases of Accidental Laboratory Infections with Poxviruses

Vaccinia virus, the prototype Orthopoxvirus, is widely used in the laboratory as a model system to study various aspects of viral biology and virus-host interactions, as a protein expression system, as a vaccine vector, and as an oncolytic agent. The ubiquitous use of vaccinia viruses in laboratories around the world raises certain safety concerns because the virus can be a pathogen in individuals with immunological and dermatological abnormalities, and on occasion can cause serious problems in normal hosts. This chapter reviews standard operating procedures when working with vaccinia virus and reviews published cases of accidental laboratory infections with poxviruses.

Anticipating Xenogenic Pollution at the Source: Impact of Sterilizations on DNA Release From Microbial Cultures

The dissemination of DNA and xenogenic elements across waterways is under scientific and public spotlight due to new gene-editing tools, such as do-it-yourself (DIY) CRISPR-Cas kits deployable at kitchen table. Over decades, prevention of spread of genetically modified organisms (GMOs), antimicrobial resistances (AMR), and pathogens from transgenic systems has focused on microbial inactivation. However, sterilization methods have not been assessed for DNA release and integrity. Here, we investigated the fate of intracellular DNA from cultures of model prokaryotic (Escherichia coli) and eukaryotic (Saccharomyces cerevisiae) cells that are traditionally used as microbial chassis for genetic modifications. DNA release was tracked during exposure of these cultures to conventional sterilization methods. Autoclaving, disinfection with glutaraldehyde, and microwaving are used to inactivate broths, healthcare equipment, and GMOs produced at kitchen table. DNA fragmentation and PCR-ability were measured on top of cell viability and morphology. Impact of these methods on DNA integrity was verified on a template of free λ DNA. Intense regular autoclaving (121°C, 20 min) resulted in the most severe DNA degradation and lowest household gene amplification capacity: 1.28 ± 0.11, 2.08 ± 0.03, and 4.96 ± 0.28 logs differences to the non-treated controls were measured from E. coli, S. cerevisiae, and λ DNA, respectively. Microwaving exerted strong DNA fragmentation after 100 s of exposure when free λ DNA was in solution (3.23 ± 0.06 logs difference) but a minor effect was observed when DNA was released from E. coli and S. cerevisiae (0.24 ± 0.14 and 1.32 ± 0.02 logs differences with the control, respectively). Glutaraldehyde prevented DNA leakage by preserving cell structures, while DNA integrity was not altered. The results show that current sterilization methods are effective on microorganism inactivation but do not safeguard an aqueous residue exempt of biologically reusable xenogenic material, being regular autoclaving the most severe DNA-affecting method. Reappraisal of sterilization methods is required along with risk assessment on the emission of DNA fragments in urban systems and nature.

Multilayer graphene-gold nanocomposite modified stem-loop DNA biosensor for peanut allergen-Ara h1 detection

In this study, we developed an electrochemically-amplified, stem-loop DNA biosensor to detect the peanut allergen Ara h1. Specifically, we electrodeposited a multilayer graphene-gold nanocomposite onto a glassy carbon electrode and then immobilised a thiolated hairpin DNA-biotin probe onto the modified electrode surface. The multilayer graphene-gold composite has good dispersion ability, and can amplify the electrochemical signal due to its high electron-transfer efficiency. The probe was switched to an "off" state in the presence of target DNA. The prepared biosensor demonstrated a linear response ranging from 10(-16) to 10(-13)M, with an ultrasensitive detection limit of 0.041 fM. Moreover, the biosensor showed excellent selectivity, as well as the ability to discriminate between a complementary target and a one-base mismatch or non-complementary sequence. Results show that this prepared DNA biosensor can be successfully used to detect the peanut allergen Ara h1 in a peanut milk beverage. Findings can be applied to the prevention of allergic reactions, thus improving human health and safety.

Short RNA indicator sequences are not completely degraded by autoclaving

Short indicator RNA sequences (<100 bp) persist after autoclaving and are recovered intact by molecular amplification. Primers targeting longer sequences are most likely to produce false positives due to amplification errors easily verified by melting curves analyses. If short indicator RNA sequences are used for virus identification and quantification then post autoclave RNA degradation methodology should be employed, which may include further autoclaving.

Working safely with vaccinia virus: laboratory technique and review of published cases of accidental laboratory infections

Vaccinia virus (VACV), the prototype orthopoxvirus, is widely used in the laboratory as a model system to study various aspects of viral biology and virus-host interactions, as a protein expression system, as a vaccine vector, and as an oncolytic agent. The ubiquitous use of VACVs in the laboratory raises certain safety concerns because the virus can be a pathogen in individuals with immunological and dermatological abnormalities, and on occasion can cause serious problems in normal hosts. This chapter reviews standard operating procedures when working with VACV and reviews published cases on accidental laboratory infections.

Effect of gamma irradiation on viability and DNA of Staphylococcus epidermidis and Escherichia coli

Gamma irradiation is widely used for sterilization; however, its effect on elimination of amplifiable DNA, an issue of relevance to molecular diagnostic approaches, has not been well studied. The effect of gamma irradiation on the viability of Staphylococcus epidermidis and Escherichia coli (using quantitative cultures) and on their DNA (using quantitative 16S rRNA gene PCR) was evaluated. Viability was abrogated at 2.8 and 3.6 kGy for S. epidermidis and E. coli, respectively. The radiation dose required to reduce viable bacteria by one log10 (D10 value) was 0.31 and 0.35 kGy for S. epidermidis and E. coli, respectively. D10 values for amplifiable DNA extracted from bacteria were 2.58 and 3.09 kGy for S. epidermidis and E. coli, respectively, whereas D10 values for amplifiable DNA were significantly higher for DNA extracted from irradiated viable bacterial cells (22.9 and 52.6 kGy for S. epidermidis and E. coli, respectively; P<0.001). This study showed that gamma irradiation of DNA in viable bacterial cells has little effect on amplifiable DNA, was not able to eliminate amplifiable 16S rRNA genes at a dose of up to 12 kGy and cannot therefore be used for elimination of DNA contamination of PCR reaction components or laboratory equipment when this DNA is present in microbial cells. This finding has practical implications for those using molecular diagnostic techniques in microbiology.

Advances in real-time PCR: application to clinical laboratory diagnostics

The polymerase chain reaction (PCR) has become one of the most important tools in molecular diagnostics, providing exquisite sensitivity and specificity for detection of nucleic acid targets. Real-time monitoring of PCR has simplified and accelerated PCR laboratory procedures and has increased information obtained from specimens including routine quantification and differentiation of amplification products. Clinical diagnostic applications and uses of real-time PCR are growing exponentially, real-time PCR is rapidly replacing traditional PCR, and new diagnostic uses likely will emerge. This review analyzes the scope of present and potential future clinical diagnostic applications of this powerful technique. Critical discussions focus on basic concepts, variations, data analysis, instrument platforms, signal detection formats, sample collection, assay design, and execution of real-time PCR.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Rapid, differential diagnosis of orthopox- and herpesviruses based upon real-time PCR product melting temperature and restriction enzyme analysis of amplicons

Orthopoxviruses tend to have non-specific early symptoms that cannot be differentiated readily from other infectious exanthemas, such as varicella-zoster virus (VZV) or disseminated herpes simplex virus (HSV) infections. A rapid assay was developed for the differential diagnosis of orthopoxviruses and herpesviruses based upon the melting temperatures of real-time PCR amplicons. A mean melting temperature difference of 8.7 degrees C was observed between the products amplified from the two virus families. Further identification of individual pathogens was made using restriction enzyme analysis. The assay was able to identify correctly viruses from quality control panels of herpes and orthopoxviruses.

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

Smallpox and pan-orthopox virus detection by real-time 3'-minor groove binder TaqMan assays on the roche LightCycler and the Cepheid smart Cycler platforms

We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and pan-orthopox virus DNAs. The assays are based on TaqMan 3'-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the pan-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 x 10(7), 1.24 x 10(5), 1.24 x 10(3), and 1.24 x 10(1) genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs. However, all five assays had nearly 100% sensitivity on both machines with samples above the LOD (>12 gene copies). These real-time PCR assays represent a battery of tests to screen for and confirm the presence of variola virus DNA. The early detection of a smallpox outbreak is crucial whether the incident is an act of bioterrorism or an accidental occurrence.

Ocular complications of smallpox vaccination

PURPOSE

To describe the ocular complications of smallpox vaccination and to discuss potential therapeutic options.

DESIGN

Review of pertinent medical literature and recent treatment recommendations of the Centers for Disease Control and Prevention.

RESULTS

After immunization against smallpox, vaccinia infection of the eyelid, conjunctiva, or ocular surface can result from accidental autoinoculation from a vaccination site before scab formation or from contact with a recently vaccinated individual. While uncommon, corneal involvement can lead to stromal opacification and scarring. Clinical findings of ocular and periocular vaccinia must be differentiated from those produced by other pathogens such as molluscum contagiosum, herpes simplex, varicella zoster, and acanthamoeba infections. Clinical diagnosis can be confirmed by electron microscopy to identify the presence of orthopoxvirus, as well as by virologic culture, polymerase chain reaction, and/or restriction endonuclease analysis of viral isolates.

CONCLUSIONS

While the majority of ocular complications of smallpox vaccination in immunocompetent patients are self-limiting, selective cases may require treatment with trifluridine drops, topical corticosteroids and vaccinia immune globulin (VIG). Vaccinia virus does not appear to be sensitive to acyclovir. Specific treatment recommendations are outlined for the spectrum of ocular manifestations.

Detection of type and subtypes of influenza virus by hybrid formation of FRET probe with amplified target DNA and melting temperature analysis

Fluorescence resonance energy transfer probes were selected for three sets of reverse transcription -polymerase chain reaction (RT-PCR), each in duplex format to detect: (1). Influenza virus type A or B; (2). Neuraminidase subtypes N1 or N2; and (3). Hemagglutinin subtypes H1 or H3 using LightCycler Instrument. A pair of probes targeted a type or subtype specific RT-PCR amplified gene segment. The presence of a target in a set of amplification reaction was detected by increased fluorescence over background emitted from the appropriate reporter fluorophore on probe-target hybrid formation and by melting temperature (T(m)) analysis of probe-target hybrid. The T(m) of a probe-target in a duplex amplification was distinctly different from the other, and thus T(m) value allowed specific detection of a target. Amplified product in each set of amplification was also examined by conventional agarose gel electrophoresis. The sensitivities of detection by fluorescence signal analysis were equal or ten times better than that detected by agarose gel electrophoresis.

Confronting bioterrorism: physicians on the front line

The events surrounding September 11, 2001, and its aftermath have compelled the public health and medical community to face the hitherto unfamiliar reality of bioterrorism. Physicians and public health personnel are frontline soldiers in this new form of warfare. This article provides a general overview of the pathophysiology, clinical presentation, diagnosis, and management of patients infected with the 6 highest priority agents that could potentially be used in bioterrorism. The diseases discussed include anthrax, smallpox, tularemia, plague, botulism, and viral hemorrhagic fevers. Despite the unpredictable nature of bioterrorism, disaster preparedness and knowledge of essential diagnostic and epidemiological principles can contribute substantially toward combating this new threat.

Application of rapid-cycle real-time polymerase chain reaction for the detection of microbial pathogens: the Mayo-Roche Rapid Anthrax Test

Rapid-cycle real-time polymerase chain reaction has immediate and important implications for diagnostic testing in the clinical microbiology laboratory. In our experience this novel testing method has outstanding performance characteristics. The sensitivities for detecting microorganisms frequently exceed standard culture-based assays, and the time required to complete the assays is considerably shorter than that required for culture-based assays. We describe the principle of real-time polymerase chain reaction and present clinical applications, including the detection of Bacillus anthracis, the causative agent of anthrax. This latter test is commercially available as the result of a collaborative venture between Mayo Clinic and Roche Applied Science, hence the designation The Mayo-Roche Rapid Anthrax Test.