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Dealing with Hidden Threats: The Antimicrobial Effect of the Embalming Process. Microorganisms 2022; 10:microorganisms10112180. [PMID: 36363772 PMCID: PMC9693414 DOI: 10.3390/microorganisms10112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Individuals naturally carry bacteria and other microbes as part of their natural flora, with some being opportunistic pathogens. Approximately 30% of the population is known to carry Staphylococcus aureus in their nasal cavity, an organism that causes infections ranging from soft tissue abscesses to toxic shock syndrome. This problem is compounded by the presence of antibiotic-resistant strains such as Methicillin-Resistant Staphylococcus aureus (MRSA). Commensal bacteria present on cadavers pose a risk to those who handle the body. As a Medical School Anatomy laboratory that performs hands-on cadaveric dissection, we wanted to know whether the embalming process is sufficient to kill all commensal bacteria that pose a risk to staff and students. Even if these strains do not cause disease in these individuals, secondary transmission could occur to friends and family, who may be at higher risk of acquiring an infection. Embalming is assumed to eliminate all microbial contamination on the body. However, there are limited studies to confirm this. This study characterises the incidence of antibiotic sensitive and resistant bacteria in cadavers donated for medical teaching and research. We have screened for Methicillin-Resistant Organisms (MRO) and Extended-Spectrum Beta-Lactamase (ESBL) producing bacteria. In this study group of cadavers, approximately 46% (16/35) carry an MRO, while 51% (18/35) carry an ESBL positive organism prior to embalming. By determining the organisms’ presence pre- and post-embalming, we can evaluate the embalming procedure’s effectiveness. Our results show embalming eliminates detectable microbes in about 51% (18/35) of the cadavers. MRO dropped by 75% (16 to 4 positive cadavers), while ESBL organisms went down by almost 95% (from 18 to 1 positive cadaver). There was a further decrease in the number of positive cadavers after storage at 4 °C to 6% (2/32). Thus, although the embalming process does not immediately sterilise all the cadavers, prolonged storage at 4 °C can further reduce the number of viable bacteria.
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Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
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Morris C, Lee YS, Yoon S. Adventitious agent detection methods in bio-pharmaceutical applications with a focus on viruses, bacteria, and mycoplasma. Curr Opin Biotechnol 2021; 71:105-114. [PMID: 34325176 DOI: 10.1016/j.copbio.2021.06.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
Adventitious agents present significant complications to biopharmaceutical manufacturing. Adventitious agents include numerous lifeforms such as bacteria, fungi, viruses, mycoplasma, and others that are inadvertently introduced into biological systems. They present significant problems to the stability of cell cultures and the sterility of manufacturing products. In this review, detection methods for bacteria, viruses, and mycoplasma are comprehensively addressed. Detection methods for viruses include traditional culture-based methods, electron microscopy studies, in vitro molecular and antibody assays, sequencing methods (massive parallel or next generation sequencing), and degenerate PCR (polymerase chain reaction). Bacteria, on the other hand, can be detected with culture-based approaches, PCR, and biosensor-based methods. Mycoplasma can be detected via PCR (including specific kits), microbiological culture methods, and enzyme-linked immunosorbent assays (ELISA). This review highlights the advantages and weaknesses of current detection methods while exploring potential avenues for further development and improvement of novel detection methods. Additionally, a brief evaluation of the transition of these methods into the gene therapy production realm with a focus on viral titer monitoring will be presented.
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Affiliation(s)
- Caitlin Morris
- Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Yong Suk Lee
- Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Seongkyu Yoon
- Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA.
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Abstract
Over the past decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry has revolutionized the practice of clinical microbiology and infectious disease diagnostics. Rapid advancement has occurred through the development and implementation of mass spectrometric protein profiling technologies that are widely available. Ease of sample preparation, rapid turnaround times, and high throughput accuracy have accelerated acceptance within the clinical laboratory. New mass spectrometric technologies centered on multiple microbial diagnostic markers are in development. Such new applications, reviewed in this article and on the near horizon, stand to greatly enhance the capabilities and utility for improved mass spectrometric microbial identification and patient care.
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Hou D, Ju M, Wang Y, Zhang D, Zhu D, Zhong M, Zhou C, Song Y, Cheng X. PCR coupled to electrospray ionization mass spectrometry for microbiological diagnosis and surveillance of ventilator-associated pneumonia. Exp Ther Med 2020; 20:3587-3594. [PMID: 32855712 PMCID: PMC7444324 DOI: 10.3892/etm.2020.9103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/02/2020] [Indexed: 12/29/2022] Open
Abstract
Etiological diagnosis is essential for anti-infective therapy in patients with ventilator-associated pneumonia (VAP). The present study aimed to evaluate the capacity of sequential PCR coupled to electrospray ionization mass spectrometry (PCR/ESI-MS) tests as a rapid diagnostic technique for patients with VAP. A total of 12 patients diagnosed with VAP were enrolled at the intensive care unit in Zhongshan Hospital, Fudan University. Mini-bronchoalveolar lavage fluid specimens were prospectively collected on VAP 0, 5 and 10 days following the beginning of mechanical ventilation. Routine clinical culture and PCR/ESI-MS were compared for identification of microorganisms in the specimens. A total of 51 bacterial species were detected by either of the two methods. The positive rates of routine clinical culture and PCR/ESI-MS were 38.2 and 88.2%, respectively. Out of the 16 specimens positive in routine cultures, 15 were also positive on PCR/ESI-MS, except for one, from which a mix of three distinct bacterial isolates were reported by culture. Among the 50 bacterial species identified by PCR/ESI-MS, 15 (35.7%) of the common VAP pathogens were confirmed by paired culture. Furthermore, of the 16 bacterial isolates that were finally confirmed to be responsible for VAP, 14 were identified by a sequential PCR/ESI-MS test concurrently when the culture results were obtained. PCR/ESI-MS identified pathogens that may cause VAP in 8 subjects prior to the occurrence of associated clinical manifestations. To conclude, PCR/ESI-MS was a potential rapid technique for diagnosis of VAP within 6 h. Regular respiratory specimen monitoring using PCR/ESI-MS provides information for selecting appropriate and adequate antibiotic therapies in ventilated patients.
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Affiliation(s)
- Dongni Hou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Mohan Ju
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Ying Wang
- Department of Critical Care Medicine, Zhongshan Hospital, Shanghai 200032, P.R. China
| | - Donghui Zhang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Duming Zhu
- Department of Critical Care Medicine, Zhongshan Hospital, Shanghai 200032, P.R. China
| | - Ming Zhong
- Department of Critical Care Medicine, Zhongshan Hospital, Shanghai 200032, P.R. China
| | - Chenjun Zhou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Department of Pulmonary Medicine, Zhongshan Hospital, Qingpu Branch, Shanghai 201700, P.R. China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai 200040, P.R. China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
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Swiner DJ, Jackson S, Burris BJ, Badu-Tawiah AK. Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time. Anal Chem 2020; 92:183-202. [PMID: 31671262 PMCID: PMC7896279 DOI: 10.1021/acs.analchem.9b04901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.
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Affiliation(s)
- Devin J. Swiner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Sierra Jackson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Benjamin J. Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Abraham K. Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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Boskani T, Edvinsson B, Wahab T. Development of nineteen Taqman real-time PCR assays for screening and detection of select highly pathogenic bacteria. Infect Ecol Epidemiol 2019. [DOI: 10.1080/20008686.2018.1553462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Talar Boskani
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Benjamin Edvinsson
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- Unit of Freeze Dried and Inhalation, AstraZeneca Sweden Operations, Sweden
| | - Tara Wahab
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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10
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Isolation and whole genome analysis of endospore-forming bacteria from heroin. Forensic Sci Int Genet 2018; 32:1-6. [DOI: 10.1016/j.fsigen.2017.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/17/2022]
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Yoon HK, Cho SH, Lee DY, Kang BH, Lee SH, Moon DG, Kim DH, Nam DC, Hwang SC. A Review of the Literature on Culture-Negative Periprosthetic Joint Infection: Epidemiology, Diagnosis and Treatment. Knee Surg Relat Res 2017; 29:155-164. [PMID: 28854760 PMCID: PMC5596406 DOI: 10.5792/ksrr.16.034] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 02/08/2023] Open
Abstract
Purpose The prevalence of periprosthetic joint infection (PJI) has increased with the increasing incidence of arthroplasty surgery. Considering identification of causative microorganisms is crucial for treatment of PJI, culture-negative (CN) PJI is a significant clinical issue. The purpose of the present study is to describe epidemiology, diagnosis and treatment of CN PJI based on review of the literature to help prevent delayed diagnosis and improve clinical outcomes of CN PJI. Methods MEDLINE, EMBASE, Cochrane Library and Scopus databases were searched for articles on CN PJI. Only clinical studies written in English were included. Basic science studies, letters to the editor, case reports and review articles on PJI were excluded. Results Seven studies were included in this study. The prevalence of CN PJI ranged from 0% to 42.1%. The major risk factors for CN PJI were prior antibiotic use and presence of postoperative wound drainage. Vancomycin and cephalosporins were the most commonly used antibiotics for CN PJI. Two-stage revision arthroplasty followed by 6 weeks of antibiotic therapy produced the most successful treatment outcomes. Conclusions In most clinical studies on CN PJI, a definite diagnostic method for identifying causative microorganisms or optimal treatment strategy for CN PJI were not clearly described. Therefore, further studies are needed to establish standard diagnostic methods for identifying infecting organisms and treatment strategies for CN PJI.
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Affiliation(s)
- Hong-Kwon Yoon
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Seong-Hee Cho
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Dong-Yeong Lee
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Byeong-Hun Kang
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Sang-Hyuk Lee
- Department of Orthopaedic Surgery, Gangneung Armed Hospital, Gangneung, Korea
| | - Dong-Gyu Moon
- Department of Orthopaedic Surgery, Gyeongsang National University Changwon Hospital, Changwon, Korea
| | - Dong-Hee Kim
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Dae-Cheol Nam
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Sun-Chul Hwang
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, Korea
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Marco F. Molecular methods for septicemia diagnosis. Enferm Infecc Microbiol Clin 2017; 35:586-592. [PMID: 28427796 DOI: 10.1016/j.eimc.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022]
Abstract
Septicemia remains a major cause of hospital mortality. Blood culture remains the best approach to identify the etiological microorganisms when a bloodstream infection is suspected but it takes long time because it relies on bacterial or fungal growth. The introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology, DNA hybridization, microarrays or rapid PCR-based test significantly reduce the time to results. Tests for direct detection in whole blood samples are highly desirable because of their potential to identify bloodstream pathogens without waiting for blood cultures to become positive. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews these new molecular approaches (LightCycler SeptiFast, Magicplex sepsis real time, Septitest, VYOO, PCR/ESI-MS analysis, T2Candida).
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Affiliation(s)
- Francesc Marco
- Servicio de Microbiología, Centro de Diagnóstico Biomédico, Hospital Clínic, Barcelona, España; ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, España.
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13
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Rume FI, Ahsan CR, Biswas PK, Yasmin M, Braun P, Walter MC, Antwerpen M, Grass G, Hanczaruk M. Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe. INFECTION GENETICS AND EVOLUTION 2016; 45:66-74. [PMID: 27543395 DOI: 10.1016/j.meegid.2016.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 12/28/2022]
Abstract
The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two "Bangladesh" clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.
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Affiliation(s)
- Farzana Islam Rume
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh; Department of Microbiology & Public Health, Patuakhali Science and Technology University, Khanpura, Babugonj, Barisal, Bangladesh
| | | | - Paritosh Kumar Biswas
- Department of Microbiology & Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Mahmuda Yasmin
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
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Duriez E, Armengaud J, Fenaille F, Ezan E. Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:183-199. [PMID: 26956386 DOI: 10.1002/jms.3747] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.
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Affiliation(s)
| | - Jean Armengaud
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunologie, 30207, Bagnols sur-Cèze, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191, Gif-sur-Yvette cedex, France
| | - Eric Ezan
- CEA, Programme Transversal Technologies pour la Santé, 91191, Gif sur Yvette, France
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15
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Grass G, Ahrens B, Schleenbecker U, Dobrzykowski L, Wagner M, Krüger C, Wölfel R. Technical Note: Simple, scalable, and sensitive protocol for retrieving Bacillus anthracis (and other live bacteria) from heroin. Forensic Sci Int 2016; 259:32-5. [DOI: 10.1016/j.forsciint.2015.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/19/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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16
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Microbial Identification in Clinical Microbiology. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Dubourg G, Raoult D. Emerging methodologies for pathogen identification in positive blood culture testing. Expert Rev Mol Diagn 2015; 16:97-111. [PMID: 26559655 DOI: 10.1586/14737159.2016.1112274] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bloodstream infections (BSIs) represent a major cause of death in developed countries and are associated with long-term loss of functions. Blood culture remains the gold standard for BSI diagnosis, as it is easy to perform and displays a good analytical sensitivity. However, its major drawback remains the long turnaround time, which can result in inappropriate therapy, fall of survival rate, emergence of antibiotic resistance and increase of medical costs. Over the last 10 years, molecular tools have been the alternative to blood cultures, allowing early identification of pathogens involved in sepsis, as well detection of critical antibiotic resistance genes. Besides, the advent of MALDI-TOF revolutionized practice in routine microbiology significantly reduced the time to result. Reviewed here are recent improvements in early BSI diagnosis and these authors' view for the future is presented, including innovative high-throughput technologies.
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Affiliation(s)
- Grégory Dubourg
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
| | - Didier Raoult
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
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Braun P, Grass G, Aceti A, Serrecchia L, Affuso A, Marino L, Grimaldi S, Pagano S, Hanczaruk M, Georgi E, Northoff B, Schöler A, Schloter M, Antwerpen M, Fasanella A. Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis. PLoS One 2015; 10:e0135346. [PMID: 26266934 PMCID: PMC4534099 DOI: 10.1371/journal.pone.0135346] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/15/2015] [Indexed: 01/10/2023] Open
Abstract
During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology, Munich, Germany
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Angela Aceti
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Alessia Affuso
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Grimaldi
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | - Stefania Pagano
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
| | | | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Bernd Northoff
- Bundeswehr Institute of Microbiology, Munich, Germany
- Ludwig Maximilians Universität München, Institute for Laboratory Medicine, Munich, Germany
| | - Anne Schöler
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | - Michael Schloter
- Technische Universität München, Wissenschaftszentrum Weihenstephan, Chair for Soil Ecology, Freising, Germany
- German Research Center for Environmental Health, Research Unit for Environmental Genomics, Neuherberg, Germany
| | | | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale of Puglia and Basilicata, Anthrax Reference Institute of Italy, Foggia, Italy
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20
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Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
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21
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Mwaigwisya S, Assiri RAM, O'Grady J. Emerging commercial molecular tests for the diagnosis of bloodstream infection. Expert Rev Mol Diagn 2015; 15:681-92. [PMID: 25866124 DOI: 10.1586/14737159.2015.1029459] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.
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22
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Opota O, Jaton K, Greub G. Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood. Clin Microbiol Infect 2015; 21:323-31. [PMID: 25686695 DOI: 10.1016/j.cmi.2015.02.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 11/19/2022]
Abstract
When a bloodstream infection (BSI) is suspected, most of the laboratory results-biochemical and haematologic-are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI.
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Affiliation(s)
- O Opota
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - K Jaton
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland; Infectious Diseases Service, University of Lausanne and University Hospital Center, Lausanne, Switzerland.
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23
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Vithanage NR, Yeager TR, Jadhav SR, Palombo EA, Datta N. Comparison of identification systems for psychrotrophic bacteria isolated from raw bovine milk. Int J Food Microbiol 2014; 189:26-38. [DOI: 10.1016/j.ijfoodmicro.2014.07.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 07/17/2014] [Accepted: 07/20/2014] [Indexed: 10/25/2022]
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24
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Chen AF, Parvizi J. Emerging Technologies for the Diagnosis of Periprosthetic Infection. JBJS Rev 2014; 2:01874474-201408000-00001. [DOI: 10.2106/jbjs.rvw.m.00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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25
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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26
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Hellberg RS, Li F, Sampath R, Yasuda IJ, Carolan HE, Wolfe JM, Brown MK, Alexander RC, Williams-Hill DM, Martin WB. Rapid detection and differentiation of human noroviruses using RT-PCR coupled to electrospray ionization mass spectrometry. Food Microbiol 2014; 44:71-80. [PMID: 25084648 DOI: 10.1016/j.fm.2014.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/25/2014] [Accepted: 05/25/2014] [Indexed: 11/26/2022]
Abstract
The goal of this study was to develop an assay for the detection and differentiation of noroviruses using RT-PCR followed by electrospray ionization mass spectrometry (ESI-MS). Detection of hepatitis A virus was also considered. Thirteen primer pairs were designed for use in this assay and a reference database was created using GenBank sequences and reference norovirus samples. The assay was tested for inclusivity and exclusivity using 160 clinical norovirus samples, 3 samples of hepatitis A virus and 3 other closely related viral strains. Results showed that the assay was able to detect norovirus with a sensitivity of 92% and a specificity of 100%. Norovirus identification at the genogroup level was correct for 98% of samples detected by the assay and for 75% of a subset of samples (n = 32) compared at the genotype level. Identification of norovirus genotypes is expected to improve as more reference samples are added to the database. The assay was also capable of detecting and genotyping hepatitis A virus in all 3 samples tested. Overall, the assay developed here allows for detection and differentiation of noroviruses within one working day and may be used as a tool in surveillance efforts or outbreak investigations.
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Affiliation(s)
- Rosalee S Hellberg
- Chapman University, Schmid College of Science and Technology, Food Science and Nutrition, One University Drive, Orange, CA 92866, USA.
| | - Feng Li
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Rangarajan Sampath
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Irene J Yasuda
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Heather E Carolan
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Julia M Wolfe
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Michael K Brown
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Richard C Alexander
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Donna M Williams-Hill
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
| | - William B Martin
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
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27
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Liesenfeld O, Lehman L, Hunfeld KP, Kost G. Molecular diagnosis of sepsis: New aspects and recent developments. Eur J Microbiol Immunol (Bp) 2014; 4:1-25. [PMID: 24678402 DOI: 10.1556/eujmi.4.2014.1.1] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/13/2013] [Indexed: 12/29/2022] Open
Abstract
By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published.
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28
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Abstract
➤ Negative results on culture still pose a real challenge in the diagnosis of periprosthetic joint infection.➤ There are numerous reasons for the inability to isolate the infecting organism from the affected joint, the most important of which is the administration of antibiotics prior to obtaining culture samples.➤ For patients suspected of having a periprosthetic joint infection, antibiotics should not be given until the diagnosis is confirmed or aspiration of the joint should be delayed for at least two weeks after the last dose of antibiotics.➤ Other strategies that can be used to enhance the likelihood of obtaining a positive result on culture include expeditious transport of culture samples, placement of a tissue or fluid sample in the appropriate medium, implant sonication, and prolonging the incubation period of the samples to two or three weeks.➤ In patients in whom the prerevision aspiration has not yielded an infecting organism, yet the clinical picture is consistent with periprosthetic joint infection, a minimum of three to five tissue culture samples are recommended at the time of revision surgery.➤ Biomarkers and molecular techniques, such as polymerase chain reaction identification of bacterial DNA, may play an increasing role in the future in the diagnosis of periprosthetic joint infection, when standardized techniques have not identified an infecting organism.
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Affiliation(s)
- Javad Parvizi
- Rothman Institute of Orthopaedics at Thomas Jefferson University, 925 Chestnut Street, 2nd Floor, Philadelphia, PA 19107. E-mail address for J. Parvizi:
| | - Omer Faruk Erkocak
- Rothman Institute of Orthopaedics at Thomas Jefferson University, 925 Chestnut Street, 2nd Floor, Philadelphia, PA 19107. E-mail address for J. Parvizi:
| | - Craig J Della Valle
- Midwest Orthopedics at Rush, Rush University Medical Center, 1611 West Harrison Street, #300, Chicago, IL 60612-4861. E-mail address:
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29
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Metzgar D, Sampath R, Rounds MA, Ecker DJ. The value and validation of broad spectrum biosensors for diagnosis and biodefense. Virulence 2013; 4:752-8. [PMID: 24128433 PMCID: PMC3925709 DOI: 10.4161/viru.26652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/25/2013] [Accepted: 09/29/2013] [Indexed: 12/05/2022] Open
Abstract
Broad spectrum biosensors capable of identifying diverse organisms are transitioning from the realm of research into the clinic. These technologies simultaneously capture signals from a wide variety of biological entities using universal processes. Specific organisms are then identified through bioinformatic signature-matching processes. This is in contrast to currently accepted molecular diagnostic technologies, which utilize unique reagents and processes to detect each organism of interest. This paradigm shift greatly increases the breadth of molecular diagnostic tools with little increase in biochemical complexity, enabling simultaneous diagnostic, epidemiologic, and biothreat surveillance capabilities at the point of care. This, in turn, offers the promise of increased biosecurity and better antimicrobial stewardship. Efficient realization of these potential gains will require novel regulatory paradigms reflective of the generalized, information-based nature of these assays, allowing extension of empirical data obtained from readily available organisms to support broader reporting of rare, difficult to culture, or extremely hazardous organisms.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences; An Abbott Company; Carlsbad, CA USA
| | | | | | - David J Ecker
- Ibis Biosciences; An Abbott Company; Carlsbad, CA USA
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30
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Wang J, Chen G, Jiang H, Li Z, Wang X. Advances in nano-scaled biosensors for biomedical applications. Analyst 2013; 138:4427-35. [DOI: 10.1039/c3an00438d] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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31
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Havlicek V, Lemr K, Schug KA. Current Trends in Microbial Diagnostics Based on Mass Spectrometry. Anal Chem 2012; 85:790-7. [DOI: 10.1021/ac3031866] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Havlicek
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Karel Lemr
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Kevin A. Schug
- The University of Texas at Arlington,
Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065,
United States
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32
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Rothman RE, Yang S, Hardick J, Gaydos CA. Harnessing Genomic Approaches for Infectious Disease Diagnosis in Emergency Medicine: Getting Closer to Prime Time. Ann Emerg Med 2012; 60:621-3. [DOI: 10.1016/j.annemergmed.2012.07.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 11/25/2022]
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33
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Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ. Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry. PLoS One 2012; 7:e36528. [PMID: 22768032 PMCID: PMC3387173 DOI: 10.1371/journal.pone.0036528] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry.
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Affiliation(s)
- Rangarajan Sampath
- Ibis Biosciences, Abbott, Carlsbad, California, United States of America.
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