Dose-Dependent Response to Infection with Ebola Virus in the Ferret Model and Evidence of Viral Evolution in the Eye.

Filoviruses cause high-consequence infections with limited approved medical countermeasures (MCMs). MCM development is dependent upon well-characterized animal models for the assessment of antiviral agents and vaccines. Following large-scale Ebola virus (EBOV) disease outbreaks in Africa, some survivors are left with long-term sequelae and persistent virus in immune-privileged sites for many years. We report the characterization of the ferret as a model for Ebola virus infection, reproducing disease and lethality observed in humans. The onset of clinical signs is rapid, and EBOV is detected in the blood, oral, and rectal swabs and all tissues studied. We identify viral RNA in the eye (a site of immune privilege) and report on specific genomic changes in EBOV present in this structure. Thus, the ferret model has utility in testing MCMs that prevent or treat long-term EBOV persistence in immune-privileged sites. IMPORTANCE Recent reemergence of Ebola in Guinea that caused over 28,000 cases between 2013 and 2016 has been linked to the original virus from that region. It appears the virus has remained in the region for at least 5 years and is likely to have been maintained in humans. Persistence of Ebola in areas of the body for extended periods of time has been observed, such as in the eye and semen. Despite the importance of reintroduction of Ebola from this route, such events are rare in the population, which makes studying medical interventions to clear persistent virus difficult. We studied various doses of Ebola in ferrets and detected virus in the eyes of most ferrets. We believe this model will enable the study of medical interventions that promote clearance of Ebola virus from sites that promote persistence.

Analysis of Inactivation of SARS-CoV-2 by Specimen Transport Media, Nucleic Acid Extraction Reagents, Detergents, and Fixatives.

The COVID-19 pandemic has necessitated a multifaceted rapid response by the scientific community, bringing researchers, health officials, and industry together to address the ongoing public health emergency. To meet this challenge, participants need an informed approach for working safely with the etiological agent, the novel human coronavirus SARS-CoV-2. Work with infectious SARS-CoV-2 is currently restricted to high-containment laboratories, but material can be handled at a lower containment level after inactivation. Given the wide array of inactivation reagents that are being used in laboratories during this pandemic, it is vital that their effectiveness is thoroughly investigated. Here, we evaluated a total of 23 commercial reagents designed for clinical sample transportation, nucleic acid extraction, and virus inactivation for their ability to inactivate SARS-CoV-2, as well as seven other common chemicals, including detergents and fixatives. As part of this study, we have also tested five filtration matrices for their effectiveness at removing the cytotoxic elements of each reagent, permitting accurate determination of levels of infectious virus remaining following treatment. In addition to providing critical data informing inactivation methods and risk assessments for diagnostic and research laboratories working with SARS-CoV-2, these data provide a framework for other laboratories to validate their inactivation processes and to guide similar studies for other pathogens.

The use of nonhuman primates in studies of noise injury and treatment.

Exposure to prolonged or high intensity noise increases the risk for permanent hearing impairment. Over several decades, researchers characterized the nature of harmful noise exposures and worked to establish guidelines for effective protection. Recent laboratory studies, primarily conducted in rodent models, indicate that the auditory system may be more vulnerable to noise-induced hearing loss (NIHL) than previously thought, driving renewed inquiries into the harmful effects of noise in humans. To bridge the translational gaps between rodents and humans, nonhuman primates (NHPs) may serve as key animal models. The phylogenetic proximity of NHPs to humans underlies tremendous similarity in many features of the auditory system (genomic, anatomical, physiological, behavioral), all of which are important considerations in the assessment and treatment of NIHL. This review summarizes the literature pertaining to NHPs as models of hearing and noise-induced hearing loss, discusses factors relevant to the translation of diagnostics and therapeutics from animals to humans, and concludes with some of the practical considerations involved in conducting NHP research.

Poly-γ-(D)-glutamic acid capsule interferes with lytic infection of Bacillus anthracis by B. anthracis-specific bacteriophages.

The poly-γ-d-glutamic acid capsule of Bacillus anthracis is a barrier to infection by B. anthracis-specific bacteriophages. Capsule expression was found to completely inhibit lytic infection by γ phage, an observation supported by the demonstration that this phage does not elaborate a hydrolase that would facilitate penetration through the protective capsule outer layer.

An assessment of ambient noise and other environmental variables in a nonhuman primate housing facility.

Acoustic noise and other environmental variables represent potential confounds for animal research. Of relevance to auditory research, sustained high levels of ambient noise may modify hearing sensitivity and decrease well-being among laboratory animals. The present study was conducted to assess environmental conditions in an animal facility that houses nonhuman primates used for auditory research at the Vanderbilt University Medical Center. Sound levels, vibration, temperature, humidity and luminance were recorded using an environmental monitoring device placed inside of an empty cage in a macaque housing room. Recordings lasted 1 week each, at three different locations within the room. Vibration, temperature, humidity and luminance all varied within recommended levels for nonhuman primates, with one exception of low luminance levels in the bottom cage location. Sound levels at each cage location were characterized by a low baseline of 58-62 dB sound pressure level, with transient peaks up to 109 dB sound pressure level. Sound levels differed significantly across locations, but only by about 1.5 dB. The transient peaks beyond recommended sound levels reflected a very low noise dose, but exceeded startle-inducing levels, which could elicit stress responses. Based on these findings, ambient noise levels in the housing rooms in this primate facility are within acceptable levels and unlikely to contribute to hearing deficits in the nonhuman primates. Our results establish normative values for environmental conditions in a primate facility, can be used to inform best practices for nonhuman primate research and care, and form a baseline for future studies of aging and chronic noise exposure.

Chronic Otitis Externa Secondary to Tympanic Membrane Electrode Placement in Rhesus Macaques (Macaca mulatta).

Otitis externa (OE) is a condition that involves inflammation of the external ear canal. OE is a commonly reported condition in humans and some veterinary species (for example, dogs, cats), but has not been reported in the literature in macaques. Here, we present a case series of acute and chronic OE likely precipitated by abrasion of the ear canal with a tympanic membrane electrode in 7 adult male rhesus macaques (Macaca mulatta). All animals displayed purulent, mucinous discharge from 1 or both ears with 3 macaques also displaying signs of an upper respiratory tract (URT) infection during the same period. A variety of diagnostic and treatment options were pursued including consultation with an otolaryngologist necessitated by the differences in response to treatment in macaques as compared with other common veterinary species. Due to the nature of the studies in which these macaques were enrolled, standard audiological testing was performed before and after OE, including tympanometry, auditory brainstem responses (ABRs), and distortion product otoacoustic emissions (DPOAEs). After completion of study procedures, relevant tissues were collected for necropsy and histopathology. Impaired hearing was found in all macaques even after apparent resolution of OE signs. Necropsy findings included abnormalities in the tympanic membrane, ossicular chain, and middle ear cavity, suggesting that the hearing impairment was at least partly conductive in nature. We concluded that OE likely resulted from mechanical disruption of the epithelial lining of the ear canal by the ABR electrode, thereby allowing the development of opportunistic infections. OE, while uncommon in macaques, can affect them and should be included as a differential diagnosis of any macaque presenting with otic discharge and/or auricular discomfort.

Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals.

Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.

The Binaural Interaction Component in Rhesus Macaques (Macaca mulatta).

The binaural interaction component (BIC) is a sound-evoked electrophysiological signature of binaural processing in the auditory brainstem that has received attention as a potential biomarker for spatial hearing deficits. Yet the number of trials necessary to evoke the BIC, or its measurability, seems to vary across species: while it is easily measured in small rodents, it has proven to be highly variable and less reliably measured in humans. This has hindered its potential use as a diagnostic tool. Further measurements of the BIC across a wide range of species could help us better understand its origin and the possible reasons for the variation in its measurability. Statistical analysis on the function relating BIC DN1 amplitude and the interaural time difference has been performed in only a few small rodent species, thus it remains to be shown how the results apply to more taxonomically diverse mammals, and those with larger heads. To fill this gap, we measured BICs in rhesus macaque. We show the overall behavior of the BIC is the same as in smaller rodents, suggesting that the brainstem circuit responsible for the BIC is conserved across a wider range of mammals. We suggest that differences in measurability are likely because of differences in head size.

The effect of heat-treatment on SARS-CoV-2 viability and detection.

The development of safe diagnostic protocols for working with SARS-CoV-2 clinical samples at Biosafety Level 2 (BSL2) requires understanding of the effect of heat-treatment on SARS-CoV-2 viability and downstream RT-PCR sensitivity. In this study heating SARS-CoV-2/England/2/2020 to 56 °C and 60 °C for 15, 30 and 60 min reduced the virus titre by between 2.1 and 4.9 log10 pfu/mL (as determined by plaque assay). Complete inactivation did not occur and there was significant variability between replicates. Viable virus was detected by plaque assay after heat-treatment at 80 °C for 15 or 30 min but not 60 or 90 min. After heat-treatment at 80 °C for 60 min infectious virus was only detected by more sensitive virus culture. No viable virus was detected after heating to 80 °C for 90 min or 95 °C for 1 or 5 min. RT-PCR sensitivity was not compromised by heating to 56 °C and 60 °C. However, RT-PCR sensitivity was reduced (≥3 Ct value increase) after heating the virus to 80 °C for 30 min or longer, or 95 °C for 1 or 5 min. In summary we found that the efficacy of heat-inactivation varies greatly depending on temperature and duration. Local validation of heat-inactivation and its effects downstream is therefore essential for molecular testing.

Changes in audiometric threshold and frequency selectivity correlate with cochlear histopathology in macaque monkeys with permanent noise-induced hearing loss.

Exposure to loud noise causes damage to the inner ear, including but not limited to outer and inner hair cells (OHCs and IHCs) and IHC ribbon synapses. This cochlear damage impairs auditory processing and increases audiometric thresholds (noise-induced hearing loss, NIHL). However, the exact relationship between the perceptual consequences of NIHL and its underlying cochlear pathology are poorly understood. This study used a nonhuman primate model of NIHL to relate changes in frequency selectivity and audiometric thresholds to indices of cochlear histopathology. Three macaques (one Macaca mulatta and two Macaca radiata) were trained to detect tones in quiet and in noises that were spectrally notched around the tone frequency. Audiograms were derived from tone thresholds in quiet; perceptual auditory filters were derived from tone thresholds in notched-noise maskers using the rounded-exponential fit. Data were obtained before and after a four-hour exposure to a 50-Hz noise centered at 2 kHz at 141 or 146 dB SPL. Noise exposure caused permanent audiometric threshold shifts and broadening of auditory filters at and above 2 kHz, with greater changes observed for the 146-dB-exposed monkeys. The normalized bandwidth of the perceptual auditory filters was strongly correlated with audiometric threshold at each tone frequency. While changes in audiometric threshold and perceptual auditory filter widths were primarily determined by the extent of OHC survival, additional variability was explained by including interactions among OHC, IHC, and ribbon synapse survival. This is the first study to provide within-subject comparisons of auditory filter bandwidths in an animal model of NIHL and correlate these NIHL-related perceptual changes with cochlear histopathology. These results expand the foundations for ongoing investigations of the neural correlates of NIHL-related perceptual changes.

Contralateral delay activity tracks the storage of visually presented letters and words.

Electrophysiological studies have demonstrated that the maintenance of items in visual working memory (VWM) is indexed by the contralateral delay activity (CDA), which increases in amplitude as the number of objects to remember increases, plateauing at VWM capacity. Previous work has primarily utilized simple visual items, such as colored squares or picture stimuli. Despite the frequent use of verbal stimuli in seminal investigations of visual attention and memory, it is unknown whether temporary storage of letters and words also elicit a typical load-sensitive CDA. Given their close associations with language and phonological codes, it is possible that participants store these stimuli phonologically, and not visually. Participants completed a standard visual change-detection task while their ERPs were recorded. Experiment 1 compared the CDA elicited by colored squares compared to uppercase consonants, and Experiment 2 compared the CDA elicited by words compared to colored bars. Behavioral accuracy of change detection decreased with increasing set size for colored squares, letters, and words. We found that a capacity-limited CDA was present for colored squares, letters, and word arrays, suggesting that the visual codes for letters and words were maintained in VWM, despite the potential for transfer to verbal working memory. These results suggest that, despite their verbal associations, letters and words elicit the electrophysiological marker of VWM encoding and storage.

When to replace legacy cochlear implants for technological upgrades: Indications and outcomes.

OBJECTIVE: To determine indications, surgical efficacy, and audiologic outcomes of replacing Advanced Bionics Clarion C1.2 internal devices (Advanced Bionics, LLC, Valencia, CA) as a means of technology upgrade. STUDY DESIGN: Retrospective review, case series. METHODS: Ten patients were initially implanted as a child (mean age = 3.87 years) and underwent cochlear implant reimplantation (CIR) with current Advanced Bionics internal device as a young adult (mean duration of implant use = 15.66 years). Demographic data and pre- and post-CIR speech perception scores were collected. RESULTS: Technology upgrade was the primary (9) or secondary (1) motivation for CIR. No surgical complications were noted, and full insertion was obtained in nine cases. Intraoperative impedance levels and neural response imaging measures were within normal limits for eight patients. At most recent post-CIR follow-up evaluation, all patients (100%) performed within or better than the 95% confidence interval of their pre-CIR word and sentence recognition scores; and 55.6%, 50.0%, and 50.0% of patients performed above the 95% confidence interval of their pre-CIR scores for the CNC words, sentences in quiet, and sentences in noise, respectively. CONCLUSION: Post-CIR audiological benefit was stable or improved compared to pre-CIR results in all categories by 3 months after reactivation. Given these results, patients who are unable to use the most current external processors due to incompatibility with a legacy internal device could consider reimplanation to optimize their overall performance with a cochlear implant. LEVEL OF EVIDENCE: 4 Laryngoscope, 129:748-753, 2019.

Frequency selectivity in macaque monkeys measured using a notched-noise method.

The auditory system is thought to process complex sounds through overlapping bandpass filters. Frequency selectivity as estimated by auditory filters has been well quantified in humans and other mammalian species using behavioral and physiological methodologies, but little work has been done to examine frequency selectivity in nonhuman primates. In particular, knowledge of macaque frequency selectivity would help address the recent controversy over the sharpness of cochlear tuning in humans relative to other animal species. The purpose of our study was to investigate the frequency selectivity of macaque monkeys using a notched-noise paradigm. Four macaques were trained to detect tones in noises that were spectrally notched symmetrically and asymmetrically around the tone frequency. Masked tone thresholds decreased with increasing notch width. Auditory filter shapes were estimated using a rounded exponential function. Macaque auditory filters were symmetric at low noise levels and broader and more asymmetric at higher noise levels with broader low-frequency and steeper high-frequency tails. Macaque filter bandwidths (BW3dB) increased with increasing center frequency, similar to humans and other species. Estimates of equivalent rectangular bandwidth (ERB) and filter quality factor (QERB) suggest macaque filters are broader than human filters. These data shed further light on frequency selectivity across species and serve as a baseline for studies of neuronal frequency selectivity and frequency selectivity in subjects with hearing loss.

Effects of noise overexposure on tone detection in noise in nonhuman primates.

This report explores the consequences of acoustic overexposures on hearing in noisy environments for two macaque monkeys trained to perform a reaction time detection task using a Go/No-Go lever release paradigm. Behavioral and non-invasive physiological assessments were obtained before and after narrowband noise exposure. Physiological measurements showed elevated auditory brainstem response (ABR) thresholds and absent distortion product otoacoustic emissions (DPOAEs) post-exposure relative to pre-exposure. Audiograms revealed frequency specific increases in tone detection thresholds, with the greatest increases at the exposure band frequency and higher. Masked detection was affected in a similar frequency specific manner: threshold shift rates (change of masked threshold per dB increase in noise level) were lower than pre-exposure values at frequencies higher than the exposure band. Detection thresholds in sinusoidally amplitude modulated (SAM) noise post-exposure showed no difference from those in unmodulated noise, whereas pre-exposure masked detection thresholds were lower in the presence of SAM noise compared to unmodulated noise. These frequency-dependent results were correlated with cochlear histopathological changes in monkeys that underwent similar noise exposure. These results reveal that behavioral and physiological effects of noise exposure in macaques are similar to those seen in humans and provide preliminary information on the relationship between noise exposure, cochlear pathology and perceptual changes in hearing within individual subjects.

Earphone and Aided Word Recognition Differences in Cochlear Implant Candidates.

OBJECTIVE: Compare word recognition scores for adults undergoing cochlear implant evaluations (CIE) measured using earphones and hearing aids. STUDY DESIGN: Retrospective review of data obtained during adult CIEs. SETTING: Tertiary cochlear implant center. PATIENTS: Two hundred eight ears in 183 subjects with greater than 10% word recognition scores measured with earphones. INTERVENTIONS/MAIN OUTCOMES MEASURED: Preoperative pure-tone thresholds and word recognition scores measured with earphones and hearing aids. RESULTS: A review of audiological data obtained from 2012 to 2017 during adult CIEs was conducted. Overall, a weak positive correlation (r = 0.33, 95% confidence interval 0.17-0.40, p < 0.001) was observed between word recognition scores measured with earphones and hearing aids. Earphone to aided differences (EAD) ranged from -38 to +72% (mean 14.3 ±â€Š19.9%). Consistent with EADs, 108 ears (51.9%) had earphone scores that were significantly higher than aided word recognition scores (+EAD), as determined by 95% confidence intervals; for 14 ears (6.7%), earphone scores were significantly lower than aided scores (-EAD). Moreover, of the patients with earphone word recognition scores ≥50%, 82.6% were CI candidates based on aided AzBio+10 dB SNR scores. CONCLUSION: These results demonstrate the limited diagnostic value of word recognition scores measured under earphones for patients undergoing CIE. Nevertheless, aided word recognition is rarely measured before CIEs, which limits the information available to determine CI candidacy and referral for CIEs. Earlier and routine measurement of aided word recognition may help guide clinical decision making by determining the extent to which patients are achieving maximum benefit with their hearing aids or should consider cochlear implantation.

Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood.

The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats.

Crimean-Congo hemorrhagic fever: experience at a tertiary care hospital in Karachi, Pakistan.

Crimean-Congo hemorrhagic fever (CCHF) is endemic in certain rural areas of Pakistan. Since the discovery of CCHF virus (CCHFV) in the country in the 1960s, there have been 13 outbreaks in addition to sporadic cases. An outbreak during 2000 coincided with the movement of sacrificial animals from rural to urban areas for the festival of Eid-ul-Azha. Diagnosis was suspected in patients with fever and thrombocytopenia, and confirmed retrospectively using immunoassays and reverse transcriptase-PCR. Patients were given platelet, plasma and red cell infusions. Management varied due to unfamiliarity with the condition and its treatment, lack of availability of diagnostic laboratory tests and limited supply of ribavirin. Inadequate antiviral treatment and late presentation probably contributed to the death of six of the eight patients. Renal failure, disseminated intravascular coagulation and persistent high-grade fever were associated with mortality. The nucleotide sequence of the small genomic RNA segment of the CCHFV isolated in this outbreak was found to be very closely related to the CCHFV strains previously isolated in Pakistan.

Serological reactivity of baculovirus-expressed Ebola virus VP35 and nucleoproteins.

Ebola virus (EBOV) is a member of the family Filoviridae and is classified as a biosafety level 4 virus. This classification makes the preparation of antigen and performance of diagnostic assays time-consuming and complicated. The objective of this study was to evaluate the value of EBOV immunoassays based on recombinant nucleoprotein (r-NP) and recombinant VP35 (r-VP35) using large serum panels of African origin and from primates. Furthermore, we investigated whether the results obtained with EBOV r-VP35 enzyme-linked immunosorbent assay (ELISA) could improve on the findings obtained with the EBOV r-NP ELISA. The full-length EBOV NP and VP35 of the EBOV subtype Zaire were expressed as histidine-tagged recombinant proteins in the baculovirus expression system. The antigenic reactivity and specificity of these recombinant proteins were determined by Western blotting and ELISA using EBOV specific monoclonal antibodies. The results obtained with the r-NP and r-VP35 ELISAs were compared with the results obtained in an indirect immunofluorescence assay based on native EBOV subtype Zaire. EBOV specific monoclonal antibodies reacted specifically with the respective proteins in both Western blot and ELISA. Five hundred and twenty six samples from humans and primates were tested with r-NP and r-VP35 ELISAs. Monkey serum samples positive for EBOV subtype Reston and Zaire were both positive in the EBOV r-NP ELISA, whereas only the EBOV Zaire infected monkeys were positive in the r-VP35 ELISA. The sensitivity and specificity values of the EBOV recombinants' ELISAs compared to those of the immunofluorescence assay were 92% and 99% for r-NP and 44% and 100% for r-VP35. r-NP ELISA proved to be a sensitive and specific assay for EBOV diagnosis and for epidemiological studies for both EBOV subtypes Reston and Zaire. The use of r-VP35 in an ELISA format has no additional value for EBOV serodiagnosis.

A multiplex real-time PCR for identifying and differentiating B. anthracis virulent types.

Bacillus anthracis is closely related to the endospore forming bacteria Bacillus cereus and Bacillus thuringiensis. For accurate detection of the life threatening pathogen B. anthracis, it is essential to distinguish between these three species. Here we present a novel multiplex real-time PCR for simultaneous specific identification of B. anthracis and discrimination of different B. anthracis virulence types. Specific B. anthracis markers were selected by whole genome comparison and different sets of primers and probes with optimal characteristic for multiplex detection of the B. anthracis chromosome, the B. anthracis pXO1 and pXO2 plasmids and an internal control (IC) were designed. The primer sets were evaluated using a panel of B. anthracis strains and exclusivity was tested using genetically closely related B. cereus strains. The robustness of final primer design was evaluated by laboratories in three different countries using five different real-time PCR thermocyclers. Testing of a panel of more than 20 anthrax strains originating from different locations around the globe, including the recent Swedish anthrax outbreak strain, showed that all strains were detected correctly.

Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis.

An oligonucleotide microarray system has been specifically designed to detect and differentiate Bacillus anthracis from other bacterial species present in clinical samples. The pilot-scale microarray initially incorporated probes to detect six common species of bacteria, which were fully evaluated. The microarray comprised long oligonucleotides (50--70-mer) designed to hybridise with the variable regions of the 16S rRNA genes. Probes which hybridised to virulence genes were also incorporated; for B. anthracis, these initially included the pag, lef, cap and vrrA (for partial genotyping) genes. Hybridisation conditions were initially optimised to be run using 5 x SSC, 0.1% SDS, 50 degrees C for 16 h. The detection limits of the microarray were determined under these conditions by titration of chromosomal DNA and unlabelled amplicons followed by hybridisation to determine the levels of sensitivity that could be obtained with the microarray. Two different amplification methodologies were also compared-specific-primer based PCR and random PCR (with the labelling stage incorporated). Higher sensitivity was obtained using specific PCR primers, however, since one of the desired outcomes of a microarray-based detection system was the high discrimination that it offered, random amplification and labelling was used as the amplification method of choice. The length of hybridisation was investigated using a time-course, and 1--2h was found to give optimal and higher signals than 16 h incubation. These results indicate that microarray technology can be employed in a diagnostic environment and moreover, results may be obtained in a similar time-scale to a standard PCR reaction, but with the advantage that no a priori knowledge of the infectious agent is required for detection.