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Sampath R. The future of diagnostics and new technologies. Pathology 2012. [DOI: 10.1016/s0031-3025(16)32611-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Chen KF, Blyn L, Rothman RE, Ramachandran P, Valsamakis A, Ecker D, Sampath R, Gaydos CA. Reverse transcription polymerase chain reaction and electrospray ionization mass spectrometry for identifying acute viral upper respiratory tract infections. Diagn Microbiol Infect Dis 2011; 69:179-86. [PMID: 21251562 PMCID: PMC3026598 DOI: 10.1016/j.diagmicrobio.2010.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 10/04/2010] [Accepted: 10/17/2010] [Indexed: 12/02/2022]
Abstract
Diagnosis of respiratory viruses traditionally relies on culture or antigen detection. We aimed to demonstrate capacity of the reverse transcription polymerase chain reaction/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) platform to identify clinical relevant respiratory viruses in nasopharyngeal aspirate (NPA) samples and compare the diagnostic performance characteristics relative to conventional culture- and antigen-based methods. An RT-PCR/ESI-MS respiratory virus surveillance kit designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1–4, Adenoviridae types A–F, Coronaviridae, human bocavirus, and human metapneumovirus was evaluated using both mock-ups and frozen archived NPA (N = 280), 95 of which were positive by clinical virology methods. RT-PCR/ESI-MS detected 74/95 (77.9%) known positive samples and identified an additional 13/185 (7%) from culture-negative samples. Viruses that are nondetectable with conventional methods were also identified. Viral load was semiquantifiable and ranged from 2400 to >320 000 copies/mL. Time to results was 8 h. RT-PCR/ESI-MS showed promise in rapid detection of respiratory viruses and merits further evaluation for use in clinical settings.
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Sampath R. Advanced Techniques for Detection and Identification of Viral Contaminants Using the Ibis PLEX-ID Universal Biosensor. PDA J Pharm Sci Technol 2011; 65:690. [PMID: 22294599 DOI: 10.5731/pdajpst.2011.00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA).
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MacInnes H, Zhou Y, Gouveia K, Cromwell J, Lowery K, Layton RC, Zubelewicz M, Sampath R, Hofstadler S, Liu Y, Cheng YS, Koster F. Transmission of aerosolized seasonal H1N1 influenza A to ferrets. PLoS One 2011; 6:e24448. [PMID: 21949718 PMCID: PMC3176225 DOI: 10.1371/journal.pone.0024448] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022] Open
Abstract
Influenza virus is a major cause of morbidity and mortality worldwide, yet little quantitative understanding of transmission is available to guide evidence-based public health practice. Recent studies of influenza non-contact transmission between ferrets and guinea pigs have provided insights into the relative transmission efficiencies of pandemic and seasonal strains, but the infecting dose and subsequent contagion has not been quantified for most strains. In order to measure the aerosol infectious dose for 50% (aID50) of seronegative ferrets, seasonal influenza virus was nebulized into an exposure chamber with controlled airflow limiting inhalation to airborne particles less than 5 µm diameter. Airborne virus was collected by liquid impinger and Teflon filters during nebulization of varying doses of aerosolized virus. Since culturable virus was accurately captured on filters only up to 20 minutes, airborne viral RNA collected during 1-hour exposures was quantified by two assays, a high-throughput RT-PCR/mass spectrometry assay detecting 6 genome segments (Ibis T5000™ Biosensor system) and a standard real time RT-qPCR assay. Using the more sensitive T5000 assay, the aID50 for A/New Caledonia/20/99 (H1N1) was approximately 4 infectious virus particles under the exposure conditions used. Although seroconversion and sustained levels of viral RNA in upper airway secretions suggested established mucosal infection, viral cultures were almost always negative. Thus after inhalation, this seasonal H1N1 virus may replicate less efficiently than H3N2 virus after mucosal deposition and exhibit less contagion after aerosol exposure.
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Brem S, Sampath R, Yu D, Staller A, Obadia M, Ewend MG. Stereotactic volumetric resection, intracavitary carmustine wafers, and radiation therapy for brain metastases: The Moffitt Cancer Center experience. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.2077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Chen KF, Rothman RE, Ramachandran P, Blyn L, Sampath R, Ecker DJ, Valsamakis A, Gaydos CA. Rapid identification viruses from nasal pharyngeal aspirates in acute viral respiratory infections by RT-PCR and electrospray ionization mass spectrometry. J Virol Methods 2011; 173:60-6. [PMID: 21256867 PMCID: PMC3221309 DOI: 10.1016/j.jviromet.2011.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/06/2011] [Accepted: 01/13/2011] [Indexed: 12/02/2022]
Abstract
Diagnosis of the etiologic agent of respiratory viral infection relies traditionally on culture or antigen detection. This pilot evaluation compared performance characteristics of the RT-PCR and electrospray ionization mass spectrometry (RT-PCR/ESI-MS) platform to conventional virologic methods for identifying multiple clinically relevant respiratory viruses in nasopharyngeal aspirates. The RT-PCR/ESI-MS respiratory virus surveillance kit was designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1–4, adenoviridae types A–F, coronaviridae, human bocavirus, and human metapneumovirus. Patients (N = 192) attending an emergency department during the 2007–2008 respiratory season consented, and “excess” frozen archived nasopharyngeal aspirates were analysed; 46 were positive by conventional virology and 69 by RT-PCR/ESI-MS, among which there were six samples with multiple viral pathogens detected. The sensitivity and specificity of the assay were 89.1% and 80.3%, respectively. Additional viruses that were not identified by conventional virology assays were detected (4 human bocaviruses and 7 coronaviruses). Samples in which the RT-PCR/ESI-MS results disagreed with conventional virology were sent for analysis by a third method using a commercial RT-PCR-based assay, which can identify viruses not detectable by conventional virologic procedures. Time to first result of RT-PCR/ESI-MS was 8 h. RT-PCR/ESI-MS demonstrated capacity to detect respiratory viruses identifiable and unidentifiable by conventional methods rapidly.
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Deyde VM, Sampath R, Garten RJ, Blair PJ, Myers CA, Massire C, Matthews H, Svoboda P, Reed MS, Pohl J, Klimov AI, Gubareva LV. Genomic signature-based identification of influenza A viruses using RT-PCR/electro-spray ionization mass spectrometry (ESI-MS) technology. PLoS One 2010; 5:e13293. [PMID: 20967258 PMCID: PMC2953491 DOI: 10.1371/journal.pone.0013293] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 09/16/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The emergence and rapid spread of the 2009 H1N1 pandemic influenza A virus (H1N1pdm) in humans highlights the importance of enhancing the capability of existing influenza surveillance systems with tools for rapid identification of emerging and re-emerging viruses. One of the new approaches is the RT-PCR electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology, which is based on analysis of base composition (BC) of RT-PCR amplicons from influenza "core" genes. Combination of the BC signatures represents a "genomic print" of an influenza A virus. METHODOLOGY/PRINCIPAL FINDINGS Here, 757 samples collected between 2006 and 2009 were tested, including 302 seasonal H1N1, 171 H3N2, 7 swine triple reassortants, and 277 H1N1pdm viruses. Of the 277 H1N1pdm samples, 209 were clinical specimens (throat, nasal and nasopharyngeal swabs, nasal washes, blood and sputum). BC signatures for the clinical specimen from one of the first cases of the 2009 pandemic, A/California/04/2009, confirmed it as an unusual, previously unrecognized influenza A virus, with "core" genes related to viruses of avian, human and swine origins. Subsequent analysis of additional 276 H1N1pdm samples revealed that they shared the genomic print of A/California/04/2009, which differed from those of North American swine triple reassortant viruses, seasonal H1N1 and H3N2 and other viruses tested. Moreover, this assay allowed distinction between "core" genes of co-circulating groups of seasonal H1N1, such as clades 2B, 2C, and their reassortants with dual antiviral resistance to adamantanes and oseltamivir. CONCLUSIONS/SIGNIFICANCE The RT-PCR/ESI-MS assay is a broad range influenza identification tool that can be used directly on clinical specimens for rapid and accurate detection of influenza virus genes. The assay differentiates the H1N1pdm from seasonal and other nonhuman hosts viruses. Although not a diagnostic tool, this assay demonstrates its usefulness and robustness in influenza virus surveillance and detection of novel and unusual viruses with previously unseen genomic prints.
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Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K, Sampath R, Lonergan S, Post JC, Hu FZ, Ehrlich GD. Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog 2010; 6:e1001108. [PMID: 20862314 PMCID: PMC2940740 DOI: 10.1371/journal.ppat.1001108] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 08/16/2010] [Indexed: 01/22/2023] Open
Abstract
Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT) processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. We have characterized multiple HGT events that most likely occurred during polyclonal infection among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child suffering from chronic upper respiratory and middle-ear infections. Whole genome sequencing and comparative genomics were performed on six isolates collected during symptomatic episodes over a period of seven months. From these comparisons we determined that five of the isolates were genetically highly similar and likely represented a dominant lineage. We analyzed all genic and allelic differences among all six isolates and found that all differences tended to occur within contiguous genomic blocks, suggestive of strain evolution by homologous recombination. From these analyses we identified three strains (two of which were recovered on two different occasions) that appear to have been derived sequentially, one from the next, each by multiple recombination events. We also identified a fourth strain that contains many of the genomic segments that differentiate the three highly related strains from one another, and have hypothesized that this fourth strain may have served as a donor multiple times in the evolution of the dominant strain line. The variations among the parent, daughter, and grand-daughter recombinant strains collectively cover greater than seven percent of the genome and are grouped into 23 chromosomal clusters. While capturing in vivo HGT, these data support the distributed genome hypothesis and suggest that a single competence event in pneumococci can result in the replacement of DNA at multiple non-adjacent loci. Bacterial infections have long been studied using Koch's postulates wherein the paradigm is that a single clone leads to a given infection. Over the past decade, it has become clear that chronic bacterial infections often do not fit this paradigm. Instead these are associated with the presence of multiple strains or species (polyclonal) of bacteria that are organized into highly structured communities, termed biofilms, which can persist in the body and are recalcitrant to antibiotic treatment. In addition, there is extensive evidence that bacteria can incorporate genes from neighboring bacteria into their own genomes. This process can produce new strains and is known as horizontal gene transfer. In this study, we investigated for the first time, the tempo and relevance of gene transfer among bacterial strains of Streptococcus pneumoniae during a naturally occurring chronic childhood infection. We identified extensive gene transfer among multiple infecting strains, by sequencing of isolates recovered sequentially over a seven-month period. This gene transfer may serve as a counterpoint to the host's adaptive immune response and help explain the phenomenon of bacterial persistence, since, as occurs with some chronic viral and parasitic infections, the immune system may become overwhelmed by a set of related strains.
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Sampath R, Blyn LB, Ecker DJ. Rapid molecular assays for microbial contaminant monitoring in the bioprocess industry. PDA J Pharm Sci Technol 2010; 64:458-464. [PMID: 21502053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Adventitious contaminations with bacterial, viral, or fungal infectious agents represent a major risk associated with the manufacture and release of pharmaceutical products for human use, including vaccines, protein-based therapeutics, and antibodies. Early detection of contaminants in the biologicals production process might allow immediate action to correct such events without a significant interruption in the rate of production. Among the methods currently used for testing are cell culture, animal inoculation, electron microscopy, and in vitro molecular and antibody assays. Bacteria such as mycoplasma and mycobacterial species and most of the viral and fungal agents can take several days to weeks or even months to grow in culture. We have developed a broad-range microbial detection assay that uses the innovative Ibis biosensor platform, a rapid and high-throughput biosensor that is based on polymerase chain reaction (PCR) and electrospray ionization mass spectrometry to identify and quantify microbial contaminants. By combining the sensitivity of PCR with the accuracy of mass spectrometric detection, this technology generates a fingerprint that uniquely identifies an organism without a priori assumptions of the sample identity. This approach is capable of detecting known and unknown pathogens, as well as providing high-resolution genotyping and strain typing, and drug resistance and virulence information. Representative case studies are discussed here showing detection of minute virus of mice, mycoplasma, and an unknown virus that was identified as bluetongue virus.
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Ecker DJ, Sampath R, Li H, Massire C, Matthews HE, Toleno D, Hall TA, Blyn LB, Eshoo MW, Ranken R, Hofstadler SA, Tang YW. New technology for rapid molecular diagnosis of bloodstream infections. Expert Rev Mol Diagn 2010; 10:399-415. [PMID: 20465496 DOI: 10.1586/erm.10.24] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Technologies for the correct and timely diagnosis of bloodstream infections are urgently needed. Molecular diagnostic methods have yet to have a major impact on the diagnosis of bloodstream infections; however, new methods are being developed that are beginning to address key issues. In this article, we discuss the key needs and objectives of molecular diagnostics for bloodstream infections and review some of the currently available methods and how these techniques meet key needs. We then focus on a new method that combines nucleic acid amplification with mass spectrometry in a novel approach to molecular diagnosis of bloodstream infections.
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Endimiani A, Hujer KM, Hujer AM, Sampath R, Ecker DJ, Bonomo RA. Rapid identification of bla KPC-possessing Enterobacteriaceae by PCR/electrospray ionization-mass spectrometry. J Antimicrob Chemother 2010; 65:1833-4. [PMID: 20538868 DOI: 10.1093/jac/dkq207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Murray PR, Jain A, Uzel G, Ranken R, Ivy C, Blyn LB, Ecker DJ, Sampath R, Lee CCR, Turner ML. Pyoderma gangrenosum-like ulcer in a patient with X-linked agammaglobulinemia: identification of Helicobacter bilis by mass spectrometry analysis. ARCHIVES OF DERMATOLOGY 2010; 146:523-6. [PMID: 20479300 PMCID: PMC3179848 DOI: 10.1001/archdermatol.2010.86] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Pyoderma gangrenosum-like ulcers and cellulitis of the lower extremities associated with recurrent fevers in patients with X-linked (Bruton) agammaglobulinemia have been reported to be caused by Helicobacter bilis (formerly classified as Flexispira rappini and then Helicobacter strain flexispira taxon 8). Consistent themes in these reports are the difficulty in recovering this organism in blood and wound cultures and in maintaining isolates in vitro. We confirmed the presence of this organism in a patient's culture by using a novel application of gene amplification polymerase chain reaction and electrospray ionization time-of-flight mass spectrometry. OBSERVATION An adolescent boy with X-linked agammaglobulinemia presented with indurated plaques and a chronic leg ulcer whose origin was strongly suspected to be an H bilis organism. Histologic analysis demonstrated positive Warthin-Starry staining of curvilinear rods, which grew in culture but failed to grow when subcultured. They could not be identified by conventional techniques. A combination of gene amplification by polymerase chain reaction and electrospray ionization time-of-flight mass spectrometry confirmed the identity of this organism. CONCLUSIONS This novel technology was useful in the identification of a difficult-to-grow Helicobacter organism, the cause of pyoderma gangrenosum-like leg ulcers in patients with X-linked agammaglobulinemia. Correct identification of this organism as the cause of pyoderma gangrenosum-like ulcers in patients with X-linked agammaglobulinemia is of great importance for the early initiation of appropriate and curative antibiotic therapy.
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Grant-Klein RJ, Baldwin CD, Turell MJ, Rossi CA, Li F, Lovari R, Crowder CD, Matthews HE, Rounds MA, Eshoo MW, Blyn LB, Ecker DJ, Sampath R, Whitehouse CA. Rapid identification of vector-borne flaviviruses by mass spectrometry. Mol Cell Probes 2010; 24:219-28. [PMID: 20412852 DOI: 10.1016/j.mcp.2010.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/02/2010] [Accepted: 04/05/2010] [Indexed: 11/30/2022]
Abstract
Flaviviruses are a highly diverse group of RNA viruses classified within the genus Flavivirus, family Flaviviridae. Most flaviviruses are arthropod-borne, requiring a mosquito or tick vector. Several flaviviruses are highly pathogenic to humans; however, their high genetic diversity and immunological relatedness makes them extremely challenging to diagnose. In this study, we developed and evaluated a broad-range Flavivirus assay designed to detect both tick- and mosquito-borne flaviviruses by using RT-PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) on the Ibis T5000 platform. The assay was evaluated with a panel of 13 different flaviviruses. All samples were correctly identified to the species level. To determine the limit of detection for the mosquito-borne primer sets, serial dilutions of RNA from West Nile virus (WNV) were assayed and could be detected down to an equivalent viral titer of 0.2 plaque-forming units/mL. Analysis of flaviviruses in their natural biological background included testing Aedes aegypti mosquitoes that were laboratory-infected with dengue-1 virus. The assay accurately identified the virus within infected mosquitoes, and we determined the average viral genome per mosquito to be 2.0 x 10(6). Using human blood, serum, and urine spiked with WNV and mouse blood and brain tissues from Karshi virus-infected mice, we showed that these clinical matrices did not inhibit the detection of these viruses. Finally, we used the assay to test field-collected Ixodes scapularis ticks collected from sites in New York and Connecticut. We found 16/322 (5% infection rate) ticks positive for deer tick virus, a subtype of Powassan virus. In summary, we developed a single high-throughput Flavivirus assay that could detect multiple tick- and mosquito-borne flaviviruses and thus provides a new analytical tool for their medical diagnosis and epidemiological surveillance.
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Koo M, Manalili S, Bankowski MJ, Sampath R, Hofstadler SA, Koo J. A "silent culture-negative" abdominal aortic mycotic aneurysm: Rapid detection of Bartonella species using PCR and high-throughput mass spectrometry. HAWAII MEDICAL JOURNAL 2010; 69:68-69. [PMID: 20397506 PMCID: PMC3104617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A gram-negative, rod-shaped microorganism was detected in a 69-year-old man suffering from chronic back pain but otherwise exhibiting no signs of infection. The bacterium could not be identified using any routine diagnostic modality. A research use only application utilizing PCR and Mass Spectrometry was performed on nucleic acid extracted from the tissue sample. These studies resulted in the implication of Bartonella quintana as the underlying cause of the infection. B. quintana is not a well-known cause of an abdominal aortic mycotic aneurysm. This article will discuss the B. quintana infection, its diagnosis and treatment, and reinforce the potential of B. quintana as a possible etiology in mycotic aneurysms that show no apparent indications of infection. It will also explore the potential use of polymerase chain reaction detected by electrospray ionization mass spectrometry (PCR/ESI-MS) to help identify B. quintana in a situation where other conventional methods prove non-informative.
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Grant RJ, Baldwin CD, Nalca A, Zoll S, Blyn LB, Eshoo MW, Matthews H, Sampath R, Whitehouse CA. Application of the Ibis-T5000 pan-Orthopoxvirus assay to quantitatively detect monkeypox viral loads in clinical specimens from macaques experimentally infected with aerosolized monkeypox virus. Am J Trop Med Hyg 2010; 82:318-23. [PMID: 20134011 PMCID: PMC2813175 DOI: 10.4269/ajtmh.2010.09-0361] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 09/28/2009] [Indexed: 11/07/2022] Open
Abstract
Monkeypox virus (MPXV), a member of the family Poxviridae and genus Orthopoxvirus, causes a smallpox-like disease in humans. A previously described pan-Orthopoxvirus assay, based on a broad-range polymerase chain reaction (PCR) coupled with electrospray ionization mass spectrometry (PCR/ESI-MS), was evaluated for its ability to detect MPXV from spiked human and aerosol-infected cynomolgous macaque (Macaca fascicularis) samples. Detection of MPXV DNA from macaque tissue, blood, and spiked human blood by the PCR/ESI-MS pan-Orthopoxvirus assay was comparable, albeit at slightly higher levels, to the current gold standard method of real-time PCR with the pan-Orthopoxvirus assay and had a limit of detection of 200 plaque-forming units. Furthermore, the platform was able to distinguish MPXV and vaccinia viruses that were spiked into macaque blood samples at various concentrations. This platform provides a new tool for the diagnosis and monitoring of orthopoxviral loads during vaccine or antiviral studies, but also could provide rapid identification during natural outbreaks or bioterrorism attacks.
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Eshoo MW, Whitehouse CA, Nalca A, Zoll S, Ecker JA, Hall TA, Pennella TTD, Duncan DD, Desai A, Moradi EK, Rudnick K, Libby B, Ranken R, Sampath R, Hofstadler SA, Ecker DJ, Blyn LB. Rapid and high-throughput pan-Orthopoxvirus detection and identification using PCR and mass spectrometry. PLoS One 2009; 4:e6342. [PMID: 19623263 PMCID: PMC2710004 DOI: 10.1371/journal.pone.0006342] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 06/01/2009] [Indexed: 11/18/2022] Open
Abstract
The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus). In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS) on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit.
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Postinikova E, Baldwin C, Whitehouse CA, Sechler A, Schaad NW, Sampath R, Harpin V, Li F, Melton R, Blyn L, Drader J, Hofstadler S, Schneider WL. Identification of bacterial plant pathogens using multilocus polymerase chain reaction/electrospray ionization-mass spectrometry. PHYTOPATHOLOGY 2008; 98:1156-1164. [PMID: 18943403 DOI: 10.1094/phyto-98-11-1156] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS, previously known as "TIGER") utilizes PCR with broad-range primers to amplify products from a wide array of organisms within a taxonomic group, followed by analysis of PCR amplicons using mass spectrometry. Computer analysis of precise masses allows for calculations of base compositions for the broad-range PCR products, which can then be compared to a database for identification. PCR/ESI-MS has the benefits of PCR in sensitivity and high-throughput capacity, but also has the distinct advantage of being able to detect and identify organisms with no prior characterization or sequence data. Existing broad range PCR primers, designed with an emphasis on human pathogens, were tested for their ability to amplify DNA of well characterized phytobacterial strains, as well as to populate the existing PCR/ESI-MS bacterial database with base counts. In a blinded panel study, PCR/ESI-MS successfully identified 93% of unknown bacterial DNAs to the genus level and 73% to the species/subspecies level. Additionally, PCR/ESI-MS was capable of detecting and identifying multiple bacteria within the same sample. The sensitivity of PCR/ESI-MS was consistent with other PCR based assays, and the specificity varied depending on the bacterial species. Preliminary tests with real life samples demonstrate a high potential for using PCR/ESI-MS systems for agricultural diagnostic applications.
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Wortmann G, Weintrob A, Barber M, Scott P, Zoll ST, Eshoo MW, Sampath R, Ecker DJ, Massire C. Genotypic evolution of Acinetobacter baumannii strains in an outbreak associated with war trauma. Infect Control Hosp Epidemiol 2008; 29:553-5. [PMID: 18510464 DOI: 10.1086/588221] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Walter Reed Army Medical Center has experienced an influx of traumatically injured patients either infected or colonized with Acinetobacter baumannii. Using multilocus polymerase chain reaction (PCR) and mass spectrometry to genotype isolates, we found an atypical and evolving strain distribution, distinct from those found at nonmilitary hospitals in the United States.
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Vaidhyanath R, Kirke R, Brown L, Sampath R. Lacrimal fossa lesions: pictorial review of CT and MRI features. Orbit 2008; 27:410-418. [PMID: 19085295 DOI: 10.1080/01676830802333667] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A wide range of disease process involve the lacrimal gland/fossa. In this pictorial review, we use histology-proven cases to illustrate conditions that affect the lacrimal gland/fossa. CT and MRI features of neoplastic, inflammatory, infiltrative, and developmental conditions are discussed.
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Eshoo MW, Whitehouse CA, Zoll ST, Massire C, Pennella TTD, Blyn LB, Sampath R, Hall TA, Ecker JA, Desai A, Wasieloski LP, Li F, Turell MJ, Schink A, Rudnick K, Otero G, Weaver SC, Ludwig GV, Hofstadler SA, Ecker DJ. Direct broad-range detection of alphaviruses in mosquito extracts. Virology 2007; 368:286-95. [PMID: 17655905 DOI: 10.1016/j.virol.2007.06.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 04/04/2007] [Accepted: 06/05/2007] [Indexed: 10/23/2022]
Abstract
Members of the genus Alphavirus are a diverse group of principally mosquito-borne RNA viruses. There are at least 29 species and many more subtypes of alphaviruses and some are considered potential bioweapons. We have developed a multi-locus RT-PCR followed by electrospray ionization mass spectrometry (RT-PCR/ESI-MS) assay that uses the amplicon base compositions to detect and identify alphaviruses. A small set of primer pairs targeting conserved sites in the alphavirus RNA genome were used to amplify a panel of 36 virus isolates representing characterized Old World and New World alphaviruses. Base compositions from the resulting amplicons could be used to unambiguously determine the species or subtype of 35 of the 36 isolates. The assay detected, without culture, Venezuelan equine encephalitis virus (VEEV), Eastern equine encephalitis virus (EEEV), and mixtures of both in pools consisting of laboratory-infected and -uninfected mosquitoes. Further, the assay was used to detect alphaviruses in naturally occurring mosquito vectors collected from locations in South America and Asia. Mosquito pools collected near Iquitos, Peru, were found to contain an alphavirus with a very distinct signature. Subsequent sequence analysis confirmed that the virus was a member of the Mucambo virus species (subtype IIID in the VEEV complex). The assay we have developed provides a rapid, accurate, and high-throughput assay for surveillance of alphaviruses.
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Sampath R, Hall TA, Massire C, Li F, Blyn LB, Eshoo MW, Hofstadler SA, Ecker DJ. Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann N Y Acad Sci 2007; 1102:109-20. [PMID: 17470915 PMCID: PMC7167958 DOI: 10.1196/annals.1408.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
abstract: Newly emergent infectious diseases are a global public health problem. The population dense regions of Southeast Asia are the epicenter of many emerging diseases, as evidenced by the outbreak of Nipah, SARS, avian influenza (H5N1), Dengue, and enterovirus 71 in this region in the past decade. Rapid identification, epidemiologic surveillance, and mitigation of transmission are major challenges in ensuring public health safety. Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI‐MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. This approach is capable of automated analysis of more than 1,500 PCR reactions a day. It is applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens and will facilitate rapid characterization of known and emerging pathogens.
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Sampath R, Russell KL, Massire C, Eshoo MW, Harpin V, Blyn LB, Melton R, Ivy C, Pennella T, Li F, Levene H, Hall TA, Libby B, Fan N, Walcott DJ, Ranken R, Pear M, Schink A, Gutierrez J, Drader J, Moore D, Metzgar D, Addington L, Rothman R, Gaydos CA, Yang S, St George K, Fuschino ME, Dean AB, Stallknecht DE, Goekjian G, Yingst S, Monteville M, Saad MD, Whitehouse CA, Baldwin C, Rudnick KH, Hofstadler SA, Lemon SM, Ecker DJ. Global surveillance of emerging Influenza virus genotypes by mass spectrometry. PLoS One 2007; 2:e489. [PMID: 17534439 PMCID: PMC1876795 DOI: 10.1371/journal.pone.0000489] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology. METHODS AND PRINCIPAL FINDINGS Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999-2006) showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005-2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution. CONCLUSION/SIGNIFICANCE Thus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance.
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Hujer KM, Hujer AM, Hulten EA, Bajaksouzian S, Adams JM, Donskey CJ, Ecker DJ, Massire C, Eshoo MW, Sampath R, Thomson JM, Rather PN, Craft DW, Fishbain JT, Ewell AJ, Jacobs MR, Paterson DL, Bonomo RA. Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the Walter Reed Army Medical Center. Antimicrob Agents Chemother 2006; 50:4114-23. [PMID: 17000742 PMCID: PMC1694013 DOI: 10.1128/aac.00778-06] [Citation(s) in RCA: 353] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Military medical facilities treating patients injured in Iraq and Afghanistan have identified a large number of multidrug-resistant (MDR) Acinetobacter baumannii isolates. In order to anticipate the impact of these pathogens on patient care, we analyzed the antibiotic resistance genes responsible for the MDR phenotype in Acinetobacter sp. isolates collected from patients at the Walter Reed Army Medical Center (WRAMC). Susceptibility testing, PCR amplification of the genetic determinants of resistance, and clonality were determined. Seventy-five unique patient isolates were included in this study: 53% were from bloodstream infections, 89% were resistant to at least three classes of antibiotics, and 15% were resistant to all nine antibiotics tested. Thirty-seven percent of the isolates were recovered from patients nosocomially infected or colonized at the WRAMC. Sixteen unique resistance genes or gene families and four mobile genetic elements were detected. In addition, this is the first report of bla(OXA-58)-like and bla(PER)-like genes in the U.S. MDR A. baumannii isolates with at least eight identified resistance determinants were recovered from 49 of the 75 patients. Molecular typing revealed multiple clones, with eight major clonal types being nosocomially acquired and with more than 60% of the isolates being related to three pan-European types. This report gives a "snapshot" of the complex genetic background responsible for antimicrobial resistance in Acinetobacter spp. from the WRAMC. Identifying genes associated with the MDR phenotype and defining patterns of transmission serve as a starting point for devising strategies to limit the clinical impact of these serious infections.
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Ecker JA, Massire C, Hall TA, Ranken R, Pennella TTD, Agasino Ivy C, Blyn LB, Hofstadler SA, Endy TP, Scott PT, Lindler L, Hamilton T, Gaddy C, Snow K, Pe M, Fishbain J, Craft D, Deye G, Riddell S, Milstrey E, Petruccelli B, Brisse S, Harpin V, Schink A, Ecker DJ, Sampath R, Eshoo MW. Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. J Clin Microbiol 2006; 44:2921-32. [PMID: 16891513 PMCID: PMC1594644 DOI: 10.1128/jcm.00619-06] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 05/11/2006] [Accepted: 05/26/2006] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Acinetobacter are ubiquitous in soil and water and are an important cause of nosocomial infections. A rapid method is needed to genotype Acinetobacter isolates to determine epidemiology and clonality during infectious outbreaks. Multilocus PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) is a method that uses the amplicon base compositions to genotype bacterial species. In order to identify regions of the Acinetobacter genome useful for this method, we sequenced regions of six housekeeping genes (trpE, adk, efp, mutY, fumC, and ppa) from 267 isolates of Acinetobacter. Isolates were collected from infected and colonized soldiers and civilians involved in an outbreak in the military health care system associated with the conflict in Iraq, from previously characterized outbreaks in European hospitals, and from culture collections. Most of the isolates from the Iraqi conflict were Acinetobacter baumannii (189 of 216 isolates). Among these, 111 isolates had genotypes identical or very similar to those associated with well-characterized A. baumannii isolates from European hospitals. Twenty-seven isolates from the conflict were found to have genotypes representing different Acinetobacter species, including 8 representatives of Acinetobacter genomospecies 13TU and 13 representatives of Acinetobacter genomospecies 3. Analysis by the PCR/ESI-MS method using nine primer pairs targeting the most information-rich regions of the trpE, adk, mutY, fumC, and ppa genes distinguished 47 of the 48 A. baumannii genotypes identified by sequencing and identified at the species level at least 18 Acinetobacter species. Results obtained with our genotyping method were essentially in agreement with those obtained by pulse-field gel electrophoresis analysis. The PCR/ESI-MS genotyping method required 4 h of analysis time to first answer with additional samples subsequently analyzed every 10 min. This rapid analysis allows tracking of transmission for the implementation of appropriate infection control measures on a time scale previously not achievable.
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