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Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Lahner E, Pivetta G, Turroni F, Ventura M, Milani C. Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses. MICROBIOME RESEARCH REPORTS 2023; 3:4. [PMID: 38455080 PMCID: PMC10917613 DOI: 10.20517/mrr.2023.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024]
Abstract
Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host's DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Edith Lahner
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Giulia Pivetta
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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Kim M, Bae J, Oh B, Rhim H, Yang MS, Yang S, Kim B, Han JI. Surveillance of wild animals carrying infectious agents based on high-throughput screening platform in the Republic of Korea. BMC Vet Res 2023; 19:158. [PMID: 37710323 PMCID: PMC10500733 DOI: 10.1186/s12917-023-03714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Infectious diseases transmitted by wild animals are major threats to public health. This study aimed to investigate the potential of rescued wild animals that died of unknown causes as reservoirs of infectious agents. From 2018 to 2019, 121 dead wild animals (55 birds and 66 mammals) were included in this study. All wild animals died during treatment after anthropogenic events. After deaths of animals, necropsies were performed and trachea, lungs, large intestine (including stool), and spleen were collected to determine causes of deaths. A high-throughput screening (HTS) quantitative polymerase chain reaction (qPCR) designed to detect 19 pathogens simultaneously against 48 samples in duplicate was performed using nucleic acids extracted from pooled tissues and peripheral blood samples. If positive, singleplex real-time PCR was performed for individual organs or blood samples. RESULTS The HTS qPCR showed positive results for Campylobacter jejuni (10/121, 8.3%), Campylobacter coli (1/121, 0.8%), Mycoplasma spp. (78/121, 64.5%), and Plasmodium spp. (7/121, 5.7%). Singleplex real-time PCR confirmed that C. jejuni was detected in the large intestine but not in the blood. C. coli was only detected in the large intestine. Mycoplasma spp. were detected in all organs, having the highest proportion in the large intestine and lowest in the blood. Plasmodium spp. was also detected in all organs, with proportions being were similar among organs. CONCLUSIONS This study shows that wild animals can become carriers of infectious agents without showing any clinical symptoms.
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Affiliation(s)
- Myeongsu Kim
- Laboratory of Wildlife Medicine, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
- Jeonbuk Wildlife Center, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Jieun Bae
- Laboratory of Wildlife Medicine, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Byungkwan Oh
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Haerin Rhim
- Laboratory of Wildlife Medicine, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
- Jeonbuk Wildlife Center, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Myeon-Sik Yang
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Somyeong Yang
- Laboratory of Wildlife Medicine, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Bumseok Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Jae-Ik Han
- Laboratory of Wildlife Medicine, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea.
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Chen Y, Lv Q, Liao H, Xie Z, Hong L, Qi L, Pan G, Long M, Zhou Z. The microsporidian polar tube: origin, structure, composition, function, and application. Parasit Vectors 2023; 16:305. [PMID: 37649053 PMCID: PMC10468886 DOI: 10.1186/s13071-023-05908-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/30/2023] [Indexed: 09/01/2023] Open
Abstract
Microsporidia are a class of obligate intracellular parasitic unicellular eukaryotes that infect a variety of hosts, even including humans. Although different species of microsporidia differ in host range and specificity, they all share a similar infection organelle, the polar tube, which is also defined as the polar filament in mature spores. In response to the appropriate environmental stimulation, the spore germinates with the polar filament everted, forming a hollow polar tube, and then the infectious cargo is transported into host cells via the polar tube. Hence, the polar tube plays a key role in microsporidian infection. Here, we review the origin, structure, composition, function, and application of the microsporidian polar tube, focusing on the origin of the polar filament, the structural differences between the polar filament and polar tube, and the characteristics of polar tube proteins. Comparing the three-dimensional structure of PTP6 homologous proteins provides new insight for the screening of additional novel polar tube proteins with low sequence similarity in microsporidia. In addition, the interaction of the polar tube with the spore wall and the host are summarized to better understand the infection mechanism of microsporidia. Due to the specificity of polar tube proteins, they are also used as the target in the diagnosis and prevention of microsporidiosis. With the present findings, we propose a future study on the polar tube of microsporidia.
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Affiliation(s)
- Yuqing Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Qing Lv
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Hongjie Liao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Zhengkai Xie
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Liuyi Hong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Lei Qi
- Biomedical Research Center for Structural Analysis, Shandong University, Jinan, 250012, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
| | - Mengxian Long
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China.
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China.
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, 400715, China
- College of Life Sciences, Chongqing Normal University, Chongqing, 400047, China
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Zhang Z, Deng Z, Zhu L, Zeng J, Cai XM, Qiu Z, Zhao Z, Tang BZ. Aggregation-induced emission biomaterials for anti-pathogen medical applications: detecting, imaging and killing. Regen Biomater 2023; 10:rbad044. [PMID: 37265605 PMCID: PMC10229374 DOI: 10.1093/rb/rbad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 06/03/2023] Open
Abstract
Microbial pathogens, including bacteria, fungi and viruses, greatly threaten the global public health. For pathogen infections, early diagnosis and precise treatment are essential to cut the mortality rate. The emergence of aggregation-induced emission (AIE) biomaterials provides an effective and promising tool for the theranostics of pathogen infections. In this review, the recent advances about AIE biomaterials for anti-pathogen theranostics are summarized. With the excellent sensitivity and photostability, AIE biomaterials have been widely applied for precise diagnosis of pathogens. Besides, different types of anti-pathogen methods based on AIE biomaterials will be presented in detail, including chemotherapy and phototherapy. Finally, the existing deficiencies and future development of AIE biomaterials for anti-pathogen applications will be discussed.
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Affiliation(s)
- Zicong Zhang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ziwei Deng
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Lixun Zhu
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Jialin Zeng
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Xu Min Cai
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Rescources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zijie Qiu
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Zheng Zhao
- Correspondence address. E-mail: (Z.Z.); (B.Z.T.)
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Krishnan SR, Soares RRG, Madaboosi N, Gromiha MM. AutoPLP: A Padlock Probe Design Pipeline for Zoonotic Pathogens. ACS Infect Dis 2023; 9:459-469. [PMID: 36790094 DOI: 10.1021/acsinfecdis.2c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Emergence of novel zoonotic infections among the human population has increased the burden on global healthcare systems to curb their spread. To meet the evolutionary agility of pathogens, it is essential to revamp the existing diagnostic methods for early detection and characterization of the pathogens at the molecular level. Padlock probes (PLPs), which can leverage the power of isothermal nucleic acid amplification techniques (NAAT) such as rolling circle amplification (RCA), are known for their high sensitivity and specificity in detecting a diverse pathogen panel of interest. However, due to the complexity involved in deciding the target regions for PLP design and the need for optimization of multiple experimental parameters, the applicability of RCA has been limited in point-of-care testing for pathogen detection. To address this gap, we have developed a novel and integrated PLP design pipeline named AutoPLP, which can automate the probe design process for a diverse pathogen panel of interest. The pipeline is composed of three modules which can perform sequence data curation, multiple sequence alignment, conservation analysis, filtration based on experimental parameters (Tm, GC content, and secondary structure formation), and in silico probe validation via potential cross-hybridization check with host genome. The modules can also take into account the backbone and restriction site information, appropriate combinations of which are incorporated along with the probe arms to design a complete probe sequence. The potential applications of AutoPLP are showcased through the design of PLPs for the detection of rabies virus and drug-resistant strains of Mycobacterium tuberculosis.
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Affiliation(s)
- Sowmya Ramaswamy Krishnan
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.,TCS Research (Life Sciences Division), Tata Consultancy Services, Hyderabad 500081, India
| | - Ruben R G Soares
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna SE-17121, Sweden
| | - Narayanan Madaboosi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.,International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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McCloskey D, Semeere A, Ayanga R, Laker-Oketta M, Lukande R, Semakadde M, Kanyesigye M, Wenger M, LeBoit P, McCalmont T, Maurer T, Gardner A, Boza J, Cesarman E, Martin J, Erickson D. LAMP-enabled diagnosis of Kaposi's sarcoma for sub-Saharan Africa. SCIENCE ADVANCES 2023; 9:eadc8913. [PMID: 36638178 DOI: 10.1126/sciadv.adc8913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Kaposi's sarcoma (KS) is an endothelial cancer caused by the Kaposi's sarcoma-associated herpesvirus (KSHV) and is one of the most common cancers in sub-Saharan Africa. In limited-resource settings, traditional pathology infrastructure is often insufficient for timely diagnosis, leading to frequent diagnoses at advanced-stage disease where survival is poor. In this study, we investigate molecular diagnosis of KS performed in a point-of-care device to circumvent the limited infrastructure for traditional diagnosis. Using 506 mucocutaneous biopsies collected from patients at three HIV clinics in Uganda, we achieved 97% sensitivity, 92% specificity, and 96% accuracy compared to gold standard U.S.-based pathology. The results presented in this manuscript show that LAMP-based quantification of KSHV DNA extracted from KS-suspected biopsies has the potential to serve as a successful diagnostic for the disease and that diagnosis may be accurately achieved using a point-of-care device, reducing the barriers to obtaining KS diagnosis while increasing diagnostic accuracy.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Aggrey Semeere
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Racheal Ayanga
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Miriam Laker-Oketta
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Lukande
- Pathology Department, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Micheal Kanyesigye
- Immune Suppression Syndrome Clinic, Mbarara Regional Referral Hospital, Mbarara, Uganda
| | - Megan Wenger
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Philip LeBoit
- Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Timothy McCalmont
- Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Golden State Dermatology Dermatopathology, Walnut Creek, CA 94598, USA
| | - Toby Maurer
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Andrea Gardner
- Pathology and Laboratory Medicine, Weill Cornell Medical College; New York, NY, 10021, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Ethel Cesarman
- Pathology and Laboratory Medicine, Weill Cornell Medical College; New York, NY, 10021, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University; Ithaca, NY, 14850, USA
- Division of Nutritional Science, Cornell University, Ithaca, NY 14850, USA
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The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111893. [PMID: 36431028 PMCID: PMC9695872 DOI: 10.3390/life12111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.
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McCloskey D, Erickson D. Rapid nucleic acid extraction from skin biopsies using a point-of-care device. LAB ON A CHIP 2022; 22:3229-3235. [PMID: 35861177 PMCID: PMC9399003 DOI: 10.1039/d2lc00457g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Sample processing is often the rate-limiting step for point-of-care nucleic acid testing, especially for large, robust tissues such as skin biopsies, which can be used to diagnose a variety of dermatological diseases. Extraction of nucleic acids from these samples often relies on lengthy enzymatic digestions, increasing the time to result and reducing the potential impact of rapid molecular diagnostic approaches. To address this, we have developed BLENDER, a device for rapid nucleic acid extraction from tissue biopsies that combines bead-beating homogenization with simultaneous sample heating for enzymatic lysis. Our device can produce a complete DNA yield from a 3 mm cylindrical skin biopsy with only a 15 minute extraction compared to 4 hours when using a commercially available extraction protocol. Decreasing sample-processing time for tissue biopsies could reduce time-to-result for downstream analysis, enabling faster point-of-care diagnosis of solid cancers in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
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9
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Khastgir J. Advances in the antibiotic management of epididymitis. Expert Opin Pharmacother 2022; 23:1103-1113. [PMID: 35380486 DOI: 10.1080/14656566.2022.2062228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Acute epididymitis is commonly encountered and typically presents acutely within a wide clinical spectrum. Most cases of acute epididymitis are caused by bacterial infection, most often by sexually transmitted organisms and urinary pathogens. Current treatment regimens remain empirical, although recent advances using modern diagnostic techniques support a change in the management paradigm. AREAS COVERED The choice of the initial antibiotic regimen is empirical and based on the most likely causative pathogen, whether sexually transmitted, enteric or other. Adherence of clinical practice remains short of available guidance, which may be improved by thorough clinical and microbiologic assessment, supported by a knowledge of the commonly associated pathogenic organisms, and the appropriate choice of tests required for their identification. Use of advanced microbiology techniques and studies of current practice provide new insights that have challenged traditional management paradigms. The authors discuss these points in and provide their expert perspectives on its treatment and future developments. EXPERT OPINION Relatively sparse direct trial data exists on antimicrobial treatments for acute epididymitis. Much of the presently available guidance is derived from previous guidance recommendations, knowledge of antimicrobial activities of specific agents, and treatment outcomes in uncomplicated infections. Identification of specific pathogens and prescribing accuracy is dependent on the extent to which cases are investigated and is therefore variable.
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Affiliation(s)
- Jay Khastgir
- Princess of Wales Hospital, Cwm Taff Bro Morgannwg NHS University Health Board & Swansea University School of Medicine, Swansea
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10
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Han B, Takvorian PM, Weiss LM. The Function and Structure of the Microsporidia Polar Tube. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:179-213. [PMID: 35544004 PMCID: PMC10037675 DOI: 10.1007/978-3-030-93306-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microsporidia are obligate intracellular pathogens that were initially identified about 160 years ago. Current phylogenetic analysis suggests that they are grouped with Cryptomycota as a basal branch or sister group to the fungi. Microsporidia are found worldwide and can infect a wide range of animals from invertebrates to vertebrates, including humans. They are responsible for a variety of diseases once thought to be restricted to immunocompromised patients but also occur in immunocompetent individuals. The small oval spore containing a coiled polar filament, which is part of the extrusion and invasion apparatus that transfers the infective sporoplasm to a new host, is a defining characteristic of all microsporidia. When the spore becomes activated, the polar filament uncoils and undergoes a rapid transition into a hollow tube that will transport the sporoplasm into a new cell. The polar tube has the ability to increase its diameter from approximately 100 nm to over 600 nm to accommodate the passage of an intact sporoplasm and penetrate the plasmalemma of the new host cell. During this process, various polar tube proteins appear to be involved in polar tube attachment to host cell and can interact with host proteins. These various interactions act to promote host cell infection.
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Affiliation(s)
- Bing Han
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Pathology, Albert Einstein College of Medicine, New York, USA
| | - Peter M Takvorian
- Department of Pathology, Albert Einstein College of Medicine, New York, USA
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, New York, USA.
- Department of Medicine, Albert Einstein College of Medicine, New York, USA.
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11
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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Abstract
Microsporidia are obligate intracellular pathogens identified ∼150 years ago as the cause of pébrine, an economically important infection in silkworms. There are about 220 genera and 1,700 species of microsporidia, which are classified based on their ultrastructural features, developmental cycle, host-parasite relationship, and molecular analysis. Phylogenetic analysis suggests that microsporidia are related to the fungi, being grouped with the Cryptomycota as a basal branch or sister group to the fungi. Microsporidia can be transmitted by food and water and are likely zoonotic, as they parasitize a wide range of invertebrate and vertebrate hosts. Infection in humans occurs in both immunocompetent and immunodeficient hosts, e.g., in patients with organ transplantation, patients with advanced human immunodeficiency virus (HIV) infection, and patients receiving immune modulatory therapy such as anti-tumor necrosis factor alpha antibody. Clusters of infections due to latent infection in transplanted organs have also been demonstrated. Gastrointestinal infection is the most common manifestation; however, microsporidia can infect virtually any organ system, and infection has resulted in keratitis, myositis, cholecystitis, sinusitis, and encephalitis. Both albendazole and fumagillin have efficacy for the treatment of various species of microsporidia; however, albendazole has limited efficacy for the treatment of Enterocytozoon bieneusi. In addition, immune restoration can lead to resolution of infection. While the prevalence rate of microsporidiosis in patients with AIDS has fallen in the United States, due to the widespread use of combination antiretroviral therapy (cART), infection continues to occur throughout the world and is still seen in the United States in the setting of cART if a low CD4 count persists.
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13
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Malik A, Fatma T, Shamsi W, Khan HA, Gul A, Jamal A, Bhatti MF. Molecular Characterization of Medically Important Fungi: Current Research and Future Prospects. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Chandrakanth N, Makwana P, Satish L, Rabha M, Sivaprasad V. Molecular approaches for detection of pebrine disease in sericulture. J Microbiol Methods 2021. [DOI: 10.1016/bs.mim.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Pinheiro BG, Hahn RC, de Camargo ZP, Rodrigues AM. Molecular Tools for Detection and Identification of Paracoccidioides Species: Current Status and Future Perspectives. J Fungi (Basel) 2020; 6:E293. [PMID: 33217898 PMCID: PMC7711936 DOI: 10.3390/jof6040293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a mycotic disease caused by the Paracoccidioides species, a group of thermally dimorphic fungi that grow in mycelial form at 25 °C and as budding yeasts when cultured at 37 °C or when parasitizing the host tissues. PCM occurs in a large area of Latin America, and the most critical regions of endemicity are in Brazil, Colombia, and Venezuela. The clinical diagnosis of PCM needs to be confirmed through laboratory tests. Although classical laboratory techniques provide valuable information due to the presence of pathognomonic forms of Paracoccidioides spp., nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratory practice. Recently, taxonomic changes driven by whole-genomic sequencing of Paracoccidioides have highlighted the need to recognize species boundaries, which could better ascertain Paracoccidioides taxonomy. In this scenario, classical laboratory techniques do not have significant discriminatory power over cryptic agents. On the other hand, several PCR-based methods can detect polymorphisms in Paracoccidioides DNA and thus support species identification. This review is focused on the recent achievements in molecular diagnostics of paracoccidioidomycosis, including the main advantages and pitfalls related to each technique. We discuss these breakthroughs in light of taxonomic changes in the Paracoccidioides genus.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso 78060900, Brazil;
- Federal University of Mato Grosso, Júlio Muller University Hospital, Mato Grosso 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
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16
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Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. J Clin Microbiol 2020; 58:JCM.01605-20. [PMID: 33028602 DOI: 10.1128/jcm.01605-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
The broad-range detection and identification of bacterial DNA from clinical specimens are a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false-negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acids. Here, we describe an alternative, next-generation sequencing approach for the broad range detection of bacterial DNA using broad-range 16S rRNA gene hybrid capture ("16S Capture"). The method is able to deconvolute multiple bacterial species present in a specimen, is compatible with highly fragmented templates, and can be readily implemented when the overwhelming majority of nucleic acids in a specimen derive from the human host. We find that this approach is sensitive to detecting as few as 17 Staphylococcus aureus genomes from a background of 100 ng of human DNA, providing 19- to 189-fold greater sensitivity for identifying bacterial sequences than standard shotgun metagenomic sequencing, and is able to successfully recover organisms from across the eubacterial tree of life. Application of 16S Capture to a proof-of-principle case series demonstrated its ability to identify bacterial species that were consistent with histological evidence of infection, even when diagnosis could not be established using conventional broad range bacterial detection assays. 16S Capture provides a novel means for the efficient and sensitive detection of bacteria embedded in human tissues and for specimens containing highly fragmented template DNA.
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Zhang D, Wang Y, Shen S, Hou Y, Chen Y, Wang T. The mycobiota of the human body: a spark can start a prairie fire. Gut Microbes 2020; 11:655-679. [PMID: 32150513 PMCID: PMC7524315 DOI: 10.1080/19490976.2020.1731287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mycobiota are inseparable from human health, shaking up the unique position held by bacteria among microorganisms. What is surprising is that this seemingly small species can trigger huge changes in the human body. Dysbiosis and invasion of mycobiota are confirmed to cause disease in different parts of the body. Meanwhile, our body also produces corresponding immune changes upon mycobiota infection. Several recent studies have made a connection between intestinal mycobiota and the human immune system. In this review, we focus on questions related to mycobiota, starting with an introduction of select species, then we summarize the typical diseases caused by mycobiota in different parts of the human body. Moreover, we constructed a framework for the human anti-fungal immune system based on genetics and immunology. Finally, the progression of fungal detection methods is also reviewed.
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Affiliation(s)
- Di Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Sunan Shen
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yugen Chen
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China,CONTACT Tingting Wang The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing210093, China
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Choi Y, Kim YT, Lee SJ, Lee E, Lee KG, Im SG. Direct Solvent-Free Modification of the Inner Wall of the Microchip for Rapid DNA Extraction with Enhanced Capturing Efficiency. Macromol Res 2019. [DOI: 10.1007/s13233-020-8028-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Li P, Mi R, Zhao R, Li X, Zhang B, Yue D, Ye B, Zhao Z, Wang L, Zhu Y, Bao C, Fan Q, Jiang X, Zhang Y. Quantitative real-time PCR with high-throughput automatable DNA preparation for molecular screening of Nosema spp. in Antheraea pernyi. J Invertebr Pathol 2019; 164:16-22. [PMID: 30981712 DOI: 10.1016/j.jip.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 01/15/2023]
Abstract
Accurate diagnosis of pathogenic Nosema spp. in Antheraea pernyi samples is considered especially useful for reducing economic losses in sericulture and improving food safety by maintaining pathogen-free pupae. However, microscopy and immunologic methods have poor diagnostic sensitivity, while the more sensitive PCR methods remain costly and time-consuming for template preparation. To address this issue, we introduce a sensitive ALMS-qPCR method that combines fast, simple DNA extraction using Alkali Lysis followed by Magnetic bead Separation (ALMS) and quantitative real-time PCR (qPCR). This approach is especially fit for large-scale pathogen molecular screening, because the DNA preparation procedure is fast (<0.94 min per sample) and is high-throughput (performs on a 96-well plate). It is cost-effective, since the most expensive materials can be made in the lab and can be recycled, while the automated procedure can help to minimize labor cost. Though the DNA preparation procedure was substantially simplified, common PCR inhibitory factors were not observed. The sensitivity of ALMS-qPCR is high and the limit of detection is 0.045 parasites/μL. Large-scale screening of Nosema spp. in 3000 Antheraea pernyi samples confirmed the efficacy of the ALMS-qPCR method. Sensitivity is much higher than clinical microscopy, especially for host groups with low infection prevalence and levels. High-throughput ALMS-qPCR, combining automated DNA preparation and sensitive qPCR, provides an enhanced approach for pébrine screening and epidemiological studies. The application of ALMS-qPCR in the sericulture industry will help to strengthen pébrine control and breed pathogen-free species, which means much safer food provision and better genetic resource conservation.
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Affiliation(s)
- Peipei Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China; Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Rui Mi
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Rui Zhao
- School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning Province 116024, PR China
| | - Xiangcun Li
- School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning Province 116024, PR China
| | - Bo Zhang
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Dongmei Yue
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Bo Ye
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Zhenjun Zhao
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Linmei Wang
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China
| | - Youmin Zhu
- The Sericultural Research Institute of Liaoning Province, Dandong 118100, PR China
| | - Chen Bao
- Horticulture and Native Product Station, Rural Work Committee of Jilin Province, Changchun, Jilin Province 130000, PR China
| | - Qi Fan
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, Liaoning Province 116085, PR China.
| | - Xiaobin Jiang
- School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning Province 116024, PR China.
| | - Yaozhou Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China.
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Abstract
Diagnosing fungal infections poses a number of unique problems, including a decline in expertise needed for identifying fungi, and a reduced number of instruments and assays specific for fungal identification compared to that of bacteria and viruses.These problems are exacerbated by the fact that patients with fungal infections are often immunosuppressed, which predisposes to infections from both commonly and rarely seen fungi. In this review, we discuss current and future molecular technologies used for fungal identification, and some of the problems associated with development and implementation of these technologies in today’s clinical microbiology laboratories. Diagnosing fungal infections poses a number of unique problems. In this Review, Wickes and Wiederhold discuss molecular technologies used for fungal identification, and the problems associated with their development and implementation in today’s clinical microbiology laboratories.
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Abstract
INTRODUCTION Microsporidia have been increasingly reported to infect humans. The most common presentation of microsporidiosis is chronic diarrhea, a significant mortality risk in immune-compromised patients. Albendazole, which inhibits tubulin, and fumagillin, which inhibits methionine aminopeptidase type 2 (MetAP2), are the two main therapeutic agents used for treatment of microsporidiosis. In addition, to their role as emerging pathogens in humans, microsporidia are important pathogens in insects, aquaculture, and veterinary medicine. New therapeutic targets and therapies have become a recent focus of attention for medicine, veterinary, and agricultural use. Areas covered: Herein, we discuss the detection and symptoms of microsporidiosis in humans and the therapeutic targets that have been utilized for the design of new drugs for the treatment of this infection, including triosephosphate isomerase, tubulin, MetAP2, topoisomerase IV, chitin synthases, and polyamines. Expert opinion: Enterocytozoon bieneusi is the most common microsporidia in human infection. Fumagillin has a broader anti-microsporidian activity than albendazole and is active against both Ent. bieneusi and Encephaliozoonidae. Microsporidia lack methionine aminopeptidase type 1 and are, therefore, dependent on MetAP2, while mammalian cells have both enzymes. Thus, MetAP2 is an essential enzyme in microsporidia and new inhibitors of this pathway have significant promise as therapeutic agents.
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Affiliation(s)
- Bing Han
- Department of Pathology, Division of Tropical Medicine and Parasitology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Louis M. Weiss
- Department of Pathology, Division of Tropical Medicine and Parasitology, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY 10461
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Srivastava S, Singh PK, Vatsalya V, Karch RC. Developments in the Diagnostic Techniques of Infectious Diseases: Rural and Urban Prospective. ACTA ACUST UNITED AC 2018; 8:121-138. [PMID: 30197838 PMCID: PMC6124492 DOI: 10.4236/aid.2018.83012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Objectives: Diagnostics is the first step for the treatment and eradication of infectious microbial diseases. Due to ever evolving pathogens and emerging new diseases, there is an urgent need to identify suitable diagnostic techniques for better management of each disease. The success rate of specific diagnostic technique in any population depends on various factors including type of the microbial pathogen, availability of resources, technical expertise, disease severity and degree of epidemic of disease in the area. One of the important tasks of the policy makers is to identify and implement suitable diagnostic techniques for specific regions based on their specific requirements. In this review we have discussed various techniques available in the literature and their suitability for the target population based on above mentioned criteria. Methods: Diagnostic techniques evaluation of well documented representative microbial diseases; Tuberculosis (bacterial), Malaria (parasitic) and HIV (viral) were included in the study. Identification and collection of information and data was performed focusing on the diagnostic techniques used from the scientific publications from Pubmed, Science Access, Scopus, EMBASE and several regional databases. WHO and CDC database for Tuberculosis, Malaria and HIV were also included. These techniques were compared with respect to the financial resource availability, expertise and management, functional capacity, pathogen virulence and degree of epidemic in the population. Results and Conclusion: In case of Tuberculosis, ELISA and colorimetric techniques are successful in rural and urban communities with 80% – 90% sensitivity. Genotyping and SNP analysis are useful in drug resistant strains. Parasitic disease Malaria also follows the same trend with diagnostic techniques like RDTs being common in both population with fast results and around 90% sensitivity. STD disease like HIV however shows slight different trends due to urgent need of interference in rural epidemics of the disease. Rapid and sensitive immunotechniques like dipsticks and agglutination with almost 100% sensitivity are used in both rural and urban areas. For the confirmation further tests are done like protein Western and NAAT. Advance techniques could be the option for higher epidemic area, drug resistance and disease research, while rapid techniques would be suitable for low income areas and POC facilities. Therefore, suitability of the diagnostic techniques for better management depends not only on the financial resources and assessment skills of a community but sometimes on the disease itself. We have further discussed the technological improvements for specific settings (rural/urban) based on the past research for better management of diseases, which could be implemented for the understanding of understudied and newly emerging diseases.
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Affiliation(s)
- Shweta Srivastava
- University of Louisville School of Medicine, Louisville, USA.,College of Arts and Sciences American University, Washington DC, USA
| | | | - Vatsalya Vatsalya
- University of Louisville School of Medicine, Louisville, USA.,College of Arts and Sciences American University, Washington DC, USA
| | - Robert C Karch
- College of Arts and Sciences American University, Washington DC, USA
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Çetinkaya Ü, Charyyeva A, Sivcan E, Gürbüz E. Evaluation of four commercial DNA extraction kits for the detection of Microsporidia and the importance of pretreatments in DNA isolation. Acta Parasitol 2018; 63:386-392. [PMID: 29654668 DOI: 10.1515/ap-2018-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/16/2018] [Indexed: 11/15/2022]
Abstract
Microsporidia are obligate intracellular parasitic protozoa infecting the wide variety of hosts and are commonly known as a cause of chronic diarrhea particularly in immunocompromised individuals. Molecular-based tests have high sensitivity and specificity in disease diagnosis. However, these tests' performance relies on the isolation of DNA in a good concentration. The standard procedures of commercial DNA extraction kits are usually insufficient for this purpose due to the tough walls of spores. This study aimed to test the significance of pretreatments by glass beads and freeze-thawing processes in DNA isolation from microsporidia spores. The parasite was cultured in growing Vero cells and seven serial dilutions were prepared from the collected spores. DNA purification was performed according to different tissue kits and stool kit procedures with and without any pretreatment. Concentration of isolated DNA samples were evaluated by real-time PCR. As a result of this study, the detectable amount of spores is minimum 10 spores in each 100 μ! sample according to the different tissue kits' standard protocols. However, according to the DNA stool mini kit, the detectable amount of spores was found to be 1,000 spores/100 μl of stool sample when pretreated with both the freeze-thawing and glass beads methods.In conclusion, the current study demonstrated that further pretreatments are an essential process for DNA extraction from the stool specimens in order to avoid possible false negativity in the diagnosis of microsporidiosis.
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Affiliation(s)
- Ülfet Çetinkaya
- Halil Bayraktar Health Vocational College, Erciyes University, Kayseri, Turkey
| | - Arzuv Charyyeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Parasitology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Eda Sivcan
- Department of Parasitology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Esra Gürbüz
- Department of Parasitology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
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Kotková M, Sak B, Hlásková L, Kváč M. The course of infection caused by Encephalitozoon cuniculi genotype III in immunocompetent and immunodeficient mice. Exp Parasitol 2017; 182:16-21. [DOI: 10.1016/j.exppara.2017.09.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/01/2017] [Accepted: 09/17/2017] [Indexed: 11/25/2022]
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Pathology of infectious diseases: what does the future hold? Virchows Arch 2017; 470:483-492. [PMID: 28188440 DOI: 10.1007/s00428-017-2082-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/10/2016] [Accepted: 01/30/2017] [Indexed: 12/20/2022]
Abstract
The demand for expertise in pathology for the diagnosis of infectious diseases (ID) is continually growing, due to an increase in ID in immunocompromised patients and in the (re)-emergence of common and uncommon diseases, including tropical infections and infections with newly identified microbes. The microbiology laboratory plays a crucial role in diagnosing infections, identifying the responsible infectious agents and establishing sensitivity of pathogens to drug therapy. Pathology, however, is the only way to correlate the presence of an infectious agent with the reaction it evokes at cell and tissue level. For pathologists working in the field of ID pathology, it is essential to dispose of competence in cell and tissue pathology as well as in microbiology. Expertise in ID includes understanding of taxonomy and classification of pathogens as well as morphological criteria supporting their identification. Moreover, ID pathologists must master the methods used to detect pathogens in fixed cell and tissue samples, notably immunohistochemistry, in situ hybridization and the polymerase chain reaction. Paradoxically, the increasing frequency of lesions caused by pathogens and diagnosed in a pathology laboratory appears to be paralleled by a gradual loss of expertise of pathologists in the field of infectious and tropical diseases. We contend that this may be due at least in part to the continuously increasing number of samples of tumor tissue pathologists deal with and the rapidly expanding number of tissue based biomarkers with predictive value for new anti-cancer therapies. In this review, we highlight current and future issues pertaining to ID pathology, in order to increase awareness of its importance for surgical and molecular pathology. The intention is to contribute to the development of best practice in ID pathology.
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Abstract
ABSTRACT
The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of
Mycobacterium tuberculosis
. Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR. The widespread use of the Xpert MTB/RIF (Cepheid) assay, which detects both
M. tuberculosis
and key genetic determinants of rifampin resistance, is important for the early detection of multidrug-resistant strains. Culture, using both broth and solid media, remains the standard for establishing the laboratory-based diagnosis of tuberculosis. Cultured isolates are identified far less commonly by traditional biochemical profiling and more commonly by molecular methods, such as DNA probes and broad-range PCR with DNA sequencing. Non-nucleic acid-based methods of identification, such as high-performance liquid chromatography and, more recently, matrix-assisted laser desorption/ionization–time of flight mass spectrometry, may also be used for identification. Cultured isolates of
M. tuberculosis
should be submitted for susceptibility testing according to standard guidelines. The use of broth-based susceptibility testing is recommended to significantly decrease the time to result. Cultured isolates may also be submitted for strain typing for epidemiologic purposes. The use of massive parallel sequencing, also known as next-generation sequencing, promises to continue to this molecular revolution in mycobacteriology, as whole-genome sequencing provides identification, susceptibility, and typing information simultaneously.
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Values of molecular markers in the differential diagnosis of thyroid abnormalities. J Cancer Res Clin Oncol 2016; 143:913-931. [PMID: 28008451 DOI: 10.1007/s00432-016-2319-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/02/2016] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Thyroid cancer (TC), follicular adenoma (FA) and Hashimoto's thyroiditis (HT) are three of the most frequently reported abnormalities that affect the thyroid gland. A frequent co-occurrence along with similar histopathological features is observed between TC and FA as well as between TC and HT. The conventional diagnostic methods such as histochemical analysis present complications in differential diagnosis when these abnormalities occur simultaneously. Hence, the authors recognize novel methods based on screening genetic defects of thyroid abnormalities as viable diagnostic and prognostic methods that could complement the conventional methods. METHODS We have extensively reviewed the existing literature on TC, FA and HT and also on three genes, namely braf, nras and ret/ptc, that could be used to differentially diagnose the three abnormalities. Emphasis was also given to the screening methods available to detect the said molecular markers. RESULTS AND CONCLUSION It can be conferred from the analysis of the available data that the utilization of braf, nras and ret/ptc as markers for the therapeutic evaluation of FA and HT is debatable. However, molecular screening for braf, nras and ret/ptc mutations proves to be a conclusive method that could be employed to differentially diagnose TC from HT and FA in the instance of a suspected co-occurrence. Thyroid cancer patients can be highly benefited from the screening for the said genetic markers, especially the braf gene due to its diagnostic value as well as due to the availability of personalized medicine targeted specifically for braf mutants.
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Hirvonen JJ, Matero P, Siebert C, Kauppila J, Vuento R, Tuokko H, Boisset S. Novel portable platform for molecular detection of toxigenic Clostridium difficile in faeces: a diagnostic accuracy study. Eur J Clin Microbiol Infect Dis 2016; 36:783-789. [PMID: 27988815 DOI: 10.1007/s10096-016-2860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND A novel portable platform for nucleic acid amplification enables rapid detection of diarrhoea causing toxigenic Clostridium difficile directly from faeces, even in resource-limited settings. We evaluated the accuracy and precision of the new commercial molecular test system. METHODS One thousand one hundred and sixty faecal samples from patients suspected of having Clostridium difficile infection (CDI) were analysed using the Orion GenRead C. difficile test system (Orion Diagnostica Oy, Espoo, Finland) and comparative methods in three teaching hospital laboratories in Finland and France. The precision of the Orion GenRead C. difficile test system was evaluated in a reproducibility study with a set of blind-coded samples. The test system is based on a new isothermal amplification technology (Strand Invasion Based Amplification, SIBA®) and detection of the tcdB gene of C. difficile. We calculated the sensitivity, specificity, and the overall agreement according to Clinical and Laboratory Standards Institute recommendations. FINDINGS The overall agreement of the Orion GenRead C. difficile test when compared to the comparative methods in routine use in the participating laboratories was between 96.7% and 98.8%. In the reproducibility study; the total percent agreement between three laboratories was 99.8%. INTERPRETATION The identification of toxigenic C. difficile from faeces with the light-weight portable Orion GenRead test system was highly sensitive and specific, and the results were reproducible in the participating laboratories. This platform could enable fast and accurate molecular pathogen detection even in resource-limited or point-of-care settings.
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Affiliation(s)
- J J Hirvonen
- Fimlab Laboratories, P.O. Box 66, 33101, Tampere, Finland.
| | - P Matero
- Department of Bacteriology and Immunology, University of Helsinki, P.O. Box 21, 00014, Helsinki, Finland.
| | - C Siebert
- Laboratoire de Bactériologie, Grenoble University Hospital Centre, CHU de Grenoble CS 10217, 38 043, Grenoble Cedex, France
| | - J Kauppila
- NordLab Oulu, Kiviharjuntie 11, 90220, Oulu, Finland
| | - R Vuento
- Fimlab Laboratories, P.O. Box 66, 33101, Tampere, Finland
| | - H Tuokko
- NordLab Oulu, Kiviharjuntie 11, 90220, Oulu, Finland
| | - S Boisset
- Laboratoire de Bactériologie, Grenoble University Hospital Centre, CHU de Grenoble CS 10217, 38 043, Grenoble Cedex, France
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Wang HY, Uh Y, Kim S, Lee H. Quantamatrix Multiplexed Assay Platform system for direct detection of bacteria and antibiotic resistance determinants in positive blood culture bottles. Clin Microbiol Infect 2016; 23:333.e1-333.e7. [PMID: 27998819 DOI: 10.1016/j.cmi.2016.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/12/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Rapid and accurate identification of the causative pathogens of bloodstream infections (BSIs) is crucial for initiating appropriate antimicrobial therapy, which decreases the related morbidity and mortality rates. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay system, the Quantamatrix Multiplexed Assay Platform (QMAP) system, obtained directly from blood culture bottles, to simultaneously detect the presence of bacteria and identify the genes for antibiotic resistance. METHODS The QMAP system was used to evaluate 619 blood culture bottles from patients with BSIs and to compare the results of conventional culture methods. RESULTS Using conventional bacterial cultures as the reference standard, the sensitivity, specificity, positive predictive value, and negative predictive value of the QMAP system for detection of bacterial pathogens in positive blood culture (PBC) samples were 99.8% (n=592, 95% CI 0.9852-1.000, p <0.001), 100% (95% CI 0.983-1.000, p <0.001), 100% (95% CI 0.9922-1.000, p <0.001), and 99.5% (95% CI 0.9695-1.000, p <0.001), respectively. In addition, sensitivity and specificity of the QMAP system for identification of the genes for antibiotic resistance were 99.4% (n=158, 95% CI 0.9617-0.9999, p <0.009) and 99.6% (95% CI 0.9763-0.9999, p <0.0001), respectively. CONCLUSIONS Obtaining results using the QMAP system takes about 3 hr, while culture methods can take 48-72 hr. Therefore, analysis using the QMAP system is rapid and reliable for characterizing causative pathogens in BSIs.
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Affiliation(s)
- H Y Wang
- Optipharm, Inc., Wonju Eco Environmental Technology Center, Gangwon, Republic of Korea
| | - Y Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Gangwon, Republic of Korea
| | - S Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Gangwon, Republic of Korea
| | - H Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Gangwon, Republic of Korea.
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Wang HY, Kim S, Kim J, Park SD, Kim HY, Uh Y, Lee H. Comparison of multiplex real-time PCR and PCR-reverse blot hybridization assay for the direct and rapid detection of bacteria and antibiotic resistance determinants in positive culture bottles. J Med Microbiol 2016; 65:962-974. [DOI: 10.1099/jmm.0.000319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hye-Young Wang
- Optipharm M&D, Inc., Wonju Eco Environmental Technology Center, Wonju, Gangwon, 26493, South Korea
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
| | - Jungho Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
| | - Soon Deok Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Hyo Youl Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
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Graystock P, Blane EJ, McFrederick QS, Goulson D, Hughes WO. Do managed bees drive parasite spread and emergence in wild bees? Int J Parasitol Parasites Wildl 2016; 5:64-75. [PMID: 28560161 PMCID: PMC5439461 DOI: 10.1016/j.ijppaw.2015.10.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/27/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
Bees have been managed and utilised for honey production for centuries and, more recently, pollination services. Since the mid 20th Century, the use and production of managed bees has intensified with hundreds of thousands of hives being moved across countries and around the globe on an annual basis. However, the introduction of unnaturally high densities of bees to areas could have adverse effects. Importation and deployment of managed honey bee and bumblebees may be responsible for parasite introductions or a change in the dynamics of native parasites that ultimately increases disease prevalence in wild bees. Here we review the domestication and deployment of managed bees and explain the evidence for the role of managed bees in causing adverse effects on the health of wild bees. Correlations with the use of managed bees and decreases in wild bee health from territories across the globe are discussed along with suggestions to mitigate further health reductions in wild bees.
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Affiliation(s)
- Peter Graystock
- Department of Entomology, University of California, Riverside, CA 92507, USA
| | - Edward J. Blane
- Natural England, Mail Hub Block B, Whittington Road, Worcester, WR5 2LQ, UK
| | | | - Dave Goulson
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
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Molaee N, Abtahi H, Ghannadzadeh MJ, Karimi M, Ghaznavi-Rad E. Application of Reverse Transcriptase -PCR (RT-PCR) for rapid detection of viable Escherichia coli in drinking water samples. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2015; 13:24. [PMID: 25878795 PMCID: PMC4397879 DOI: 10.1186/s40201-015-0177-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Polymerase chain reaction (PCR) is preferred to other methods for detecting Escherichia coli (E. coli) in water in terms of speed, accuracy and efficiency. False positive result is considered as the major disadvantages of PCR. For this reason, reverse transcriptase-polymerase chain reaction (RT-PCR) can be used to solve this problem. The aim of present study was to determine the efficiency of RT-PCR for rapid detection of viable Escherichia coli in drinking water samples and enhance its sensitivity through application of different filter membranes. MATERIALS AND METHODS Specific primers were designed for 16S rRNA and elongation Factor II genes. Different concentrations of bacteria were passed through FHLP and HAWP filters. Then, RT-PCR was performed using 16srRNA and EF -Tu primers. Contamination of 10 wells was determined by RT-PCR in Arak city. To evaluate RT-PCR efficiency, the results were compared with most probable number (MPN) method. RESULTS RT-PCR is able to detect bacteria in different concentrations. Application of EF II primers reduced false positive results compared to 16S rRNA primers. The FHLP hydrophobic filters have higher ability to absorb bacteria compared with HAWB hydrophilic filters. So the use of hydrophobic filters will increase the sensitivity of RT-PCR. CONCLUSION RT-PCR shows a higher sensitivity compared to conventional water contamination detection method. Unlike PCR, RT-PCR does not lead to false positive results. The use of EF-Tu primers can reduce the incidence of false positive results. Furthermore, hydrophobic filters have a higher ability to absorb bacteria compared to hydrophilic filters.
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Affiliation(s)
- Neda Molaee
- />Department of Microbiology and Immunology, Arak University of Medical sciences, Arak, Iran
| | - Hamid Abtahi
- />Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | | | - Masoude Karimi
- />Department of Medical Microbiology and Immunology, Arak University of Medical sciences, Arak, Iran
| | - Ehsanollah Ghaznavi-Rad
- />Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
- />Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
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Amani J, Mirhosseini SA, Imani Fooladi AA. A review approaches to identify enteric bacterial pathogens. Jundishapur J Microbiol 2015; 8:e17473. [PMID: 25793091 PMCID: PMC4353029 DOI: 10.5812/jjm.17473] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/10/2014] [Accepted: 04/05/2014] [Indexed: 12/15/2022] Open
Abstract
CONTEXT Diarrhea is a common disease across the world. According to WHO, every year about two billion cases of diarrhea are reported in the world. It occurs mainly in the tropical regions and is a main cause of morbidity and mortality, particularly in young children and adults. EVIDENCE ACQUISITION One of the major causes of diarrheal diseases is bacteria; detection of pathogenic bacteria is a global key to the prevention and identification of food-borne diseases and enteric infections (like diarrhea). CONCLUSIONS Therefore, development of rapid diagnostic methods with suitable sensitivity and specificity is very important about this infectious disease. In this review, we will discuss some of the important diagnostic methods.
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Affiliation(s)
- Jafar Amani
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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Augmented renal clearance and therapeutic monitoring of β-lactams. Int J Antimicrob Agents 2015; 45:331-3. [PMID: 25665727 DOI: 10.1016/j.ijantimicag.2014.12.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 12/10/2014] [Indexed: 12/23/2022]
Abstract
Successful application of antibacterial therapy in the critically ill requires an appreciation of the complex interaction between the host, the causative pathogen and the chosen pharmaceutical. A pathophysiological change in the intensive care unit (ICU) patient challenging the 'one dose fits all' concept includes augmented renal clearance (ARC), defined as a creatinine clearance (CL(Cr)) of ≥130 mL/min. Ideally, CL(Cr) values should be obtained by a timed measured collection of urine, with plasma and urine creatinine levels. Increased renal clearance of antibiotics also occurs in the ICU patient and therefore β-lactam antibiotic exposure in the critically ill could easily lead to trough drug concentrations below therapeutic ranges. One way to document and alter drug levels is via therapeutic drug monitoring (TDM). The interactions of ARC and β-lactam TDM are further explored in this article in specific reference to a concomitant article in this issue of the journal.
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Pilatz A, Hossain H, Kaiser R, Mankertz A, Schüttler CG, Domann E, Schuppe HC, Chakraborty T, Weidner W, Wagenlehner F. Acute epididymitis revisited: impact of molecular diagnostics on etiology and contemporary guideline recommendations. Eur Urol 2014; 68:428-35. [PMID: 25542628 DOI: 10.1016/j.eururo.2014.12.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/03/2014] [Indexed: 02/03/2023]
Abstract
BACKGROUND Acute epididymitis is a common infectious disease of unknown etiology in about 30% of cases with guidelines based on studies published >15 yr ago. OBJECTIVE To investigate the etiology of acute epididymitis using state-of-the-art methods and to provide rational data for antimicrobial therapy and clinical management. DESIGN, SETTING, AND PARTICIPANTS Between 2007 and 2013, 237 patients (150 antimicrobially naive and 87 antibiotically pretreated) with acute epididymitis underwent comprehensive investigation comprising microbiologic cultures, polymerase chain reaction (PCR) for sexually transmitted infections (STIs), 16S ribosomal DNA (rDNA) analysis, and PCR detection of 23 viruses. Clinical management followed international guidelines. OUTCOME MEASURES AND STATISTICAL ANALYSIS Etiology, clinical management, and outcome after 3 mo were assessed. RESULTS AND LIMITATIONS A causative pathogen, predominantly Escherichia coli (56%), was identified in 132 antibiotic-naive patients (88%) and 44 pretreated patients (51%); 16S rDNA analysis increased the detection rate by 10%. STIs were present in 34 cases (14%) (25 patients with Chlamydia trachomatis) and were not restricted to a specific age group. Enteroviruses were found in only two patients (1%). In naive patients, cultured bacteria were susceptible to fluoroquinolones and group 3 cephalosporins in >85% of cases (preateted patients: 42% and 67%, respectively). Primary empirical therapy was continued in 88% of naive patients for 11 d and in 77% of pretreated patients for 13 d with indwelling urinary catheters, rendering patients as high risk for switching. Only six patients (2.5%) underwent semicastration. Prostate-specific antigen levels halved within 3 mo, except in patients who were antibiotic naive and without detected pathogens. Study limitations included a lack of susceptibility testing in cases of STIs. CONCLUSIONS Even in antimicrobially pretreated patients, acute epididymitis is mainly of bacterial origin. STIs are not limited to patients aged <35 yr. Viral epididymitis seems a rare condition. Current guideline recommendations on empirical antimicrobial therapy are adequate. PATIENT SUMMARY Patients with acute epididymitis should receive appropriate diagnostics and antimicrobial therapy for safe conservative management.
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Affiliation(s)
- Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany.
| | - Hamid Hossain
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Annette Mankertz
- National Reference Center Measles, Mumps, Rubella, Robert Koch Institute, Berlin, Germany
| | | | - Eugen Domann
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Hans-Christian Schuppe
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Wolfgang Weidner
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Florian Wagenlehner
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
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Hofman P. [What place and what future for the pathology of infectious and tropical diseases in France?]. Ann Pathol 2014; 34:171-82. [PMID: 24950861 PMCID: PMC7131493 DOI: 10.1016/j.annpat.2014.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 11/24/2022]
Abstract
The management of tissues and cellular samples by the pathologists in the infectious and tropical diseases pathology field in 2014 needs a strong knowledge of both morphological and molecular domains which includes the good control: (i) of the taxonomy of infectious and tropical diseases pathology leading to the pathogens identification and (ii) of the ancillary methods which can be used in fixed samples in order to detect or better identify these pathogens. There is a recent paradox in France concerning the frequency of infectious diseases to be diagnosed in pathology laboratories and the progressive loss of pathologist's expertise in this domain. Different reasons could explain this statement including the omnipresence of the tumour lesions to be managed in a pathology laboratory as well as the recent constraints associated with the different biomarkers that are mandatory to be detected by immunohistochemistry and/or by molecular biology. Even if the microbiologists play a pivotal role for identifying the different pathogens as well as for the assessment of their sensitivity to the anti-microbial drugs, a large number of infectious diseases can be diagnosed only on fixed tissue and/or cells by the pathologists. The purpose of this review is to describe the current and future issues of infectious and tropical diseases diagnoses in pathology laboratories, in particular in France.
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Affiliation(s)
- Paul Hofman
- Laboratoire de pathologie clinique et expérimentale (LPCE), hôpital Pasteur, CHU, BP 69, 06002 Nice, France; Biobanque CHUN, hôpital Pasteur, 06002 Nice, France.
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Tabatabaie F, Abrehdari Tafreshi Z, Shahmohammad N, Pirestani M. Molecular detection of microsporidiosis in various samples of Iranian immunocompromised patients. J Parasit Dis 2014; 39:634-8. [PMID: 26688625 DOI: 10.1007/s12639-014-0432-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 01/22/2014] [Indexed: 11/29/2022] Open
Abstract
Microsporidia infections occur in virtually all invertebrate and vertebrate hosts, including humans. The aim of this study is detection of microsporidiosis in various samples of Iranian immunosuppressed patients during 2011-2012 by molecular methods. The samples included stool samples from the healthy participants and samples from biological fluids of the patients according to consult of their physician and the site of infection. The sample size was determined as 258 for each group. Clinical and demographical data related to each participant was collected. DNA extraction and nested polymerase chain reaction were carried out on all the samples. In the control group, the rates of Encephalitozoon and Enterocytozoon infections were 5.3 and 4 % respectively higher in males and in the age range of 30-45, and all positive cases had gastrointestinal symptoms. In the patient group, most infection cases occurred in male patients and in the age range of 60 and above. Patients with microsporidiosis mostly had the symptoms of chronic diarrhea, vomiting, weight loss, dyspepsia, and malabsorption. In BAL samples from patients 2 % Encephalitozoon and 0.7 % Enterocytozoon, in the sampling bone marrow transplantation from patients 5.7 % Encephalitozoon, 1.43 % Enterocytozoon and from patients who underwent kidney transplantation 5.26 % Enterocytozoon were detected. The most cases of human microsporidiosis are associated with human immunodeficiency virus infection or other states of immunosuppression, particularly in organ transplant recipients; the result of this study confirms this claim.
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Affiliation(s)
- Fatemeh Tabatabaie
- Department of Parasitology and Mycology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), P.O. Box 1449614535, Tehran, Islamic Republic of Iran
| | - Zahra Abrehdari Tafreshi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Islamic Republic of Iran
| | - Narges Shahmohammad
- Department of Parasitology and Mycology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), P.O. Box 1449614535, Tehran, Islamic Republic of Iran
| | - Majid Pirestani
- Department of Parasitology and Entomology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Islamic Republic of Iran
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Salman M, Ali A, Haque A. A novel multiplex PCR for detection of Pseudomonas aeruginosa: A major cause of wound infections. Pak J Med Sci 2013; 29:957-61. [PMID: 24353667 PMCID: PMC3817763 DOI: 10.12669/pjms.294.3652] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 11/15/2022] Open
Abstract
Background and Objective: Wound infections are often difficult to treat due to various bacterial pathogens. Pseudomonas aeruginosa is one of the common invaders of open wounds. Precise diagnosis of this etiological agent in wound infections is of critical importance particularly in treatment of problematic cases. The existing diagnostic methods have certain limitations particularly related to specificity. Our objective was to to establish a comprehensive and reliable multiplex PCR to confirm diagnosis of P. aeruginosa. Methods: A multiplex PCR test was developed for rapid and comprehensive identification of P. aeruginosa. Four highly specific genes were targeted simultaneously for detection of genus, species and exotoxin production (16S rDNA, gyrB, oprL and ETA) in P. aeruginosa; additionally one internal control gene (invA) of Salmonella was used. The specificity of the multiplex PCR was confirmed using internal and negative controls. Amplified fragments were confirmed by restriction analysis and DNA sequencing. Results: The developed method was applied on 40 morphologically suspected P. aeruginosa isolates (from 200 pus samples) and 18 isolates were confirmed as P. aeruginosa. In comparison, only 12 could be identified biochemically. Conclusions: Combination of the four reported genes in multiplex PCR provided more confident and comprehensive detection of P. aeruginosa which is applicable for screening of wound infections and assisting treatment strategy.
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Affiliation(s)
- Muhammad Salman
- Muhammad Salman BS, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Aamir Ali
- Dr. Aamir Ali, PhD, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Abdul Haque
- Dr. Abdul Haque, PhD, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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Parcell BJ, Orange GV. PNA-FISH assays for early targeted bacteraemia treatment. J Microbiol Methods 2013; 95:253-5. [PMID: 24055387 DOI: 10.1016/j.mimet.2013.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/01/2013] [Accepted: 09/07/2013] [Indexed: 02/04/2023]
Abstract
PNA-FISH S. aureus/CNS and GNR Traffic Light assays were compared with standard culture methods for identifying bacteraemia in 156 blood cultures from 131 patients. Results correlated with final culture results in 153 cultures. Retrospective case note review revealed that earlier targeted treatment would have occurred in 10.7% of cases.
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Affiliation(s)
- B J Parcell
- Department of Medical Microbiology, Ninewells Hospital and Medical School, NHS Tayside, Dundee, United Kingdom.
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Thomas PA, A Teresa P, Theodore J, Geraldine P. PCR for the molecular diagnosis of mycotic keratitis. Expert Rev Mol Diagn 2013; 12:703-18. [PMID: 23153238 DOI: 10.1586/erm.12.65] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mycotic keratitis, an infection of the cornea caused by fungi, is a medical emergency, with patients presenting with considerable pain and distress. For effective management of the condition, a specific diagnosis must be made rapidly to permit early initiation of antifungal therapy. Currently, direct microscopic examination and culture of corneal material constitute the 'gold standard' for diagnosis. However, rapid, sensitive yet specific tests are needed to detect a small number of, or nonviable, fungi. PCR has many potential advantages when used as a diagnostic aid for mycotic keratitis; the present review covers these advantages, and possible limitations. An expert assessment is also made of studies that have used PCR for the diagnosis of mycotic keratitis. The review concludes with a Five-year view of the potential impact of PCR in management of mycotic keratitis.
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Affiliation(s)
- Philip A Thomas
- Institute of Ophthalmology, Joseph Eye Hospital, Tiruchirapalli 620001, India.
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Chandler DP, Bryant L, Griesemer SB, Gu R, Knickerbocker C, Kukhtin A, Parker J, Zimmerman C, George KS, Cooney CG. Integrated Amplification Microarrays for Infectious Disease Diagnostics. MICROARRAYS 2012; 1:107-24. [PMID: 27605339 PMCID: PMC5003434 DOI: 10.3390/microarrays1030107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 10/31/2012] [Accepted: 11/07/2012] [Indexed: 11/17/2022]
Abstract
This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.
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Affiliation(s)
- Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Lexi Bryant
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | - Rui Gu
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | | | - Alexander Kukhtin
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Jennifer Parker
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Cynthia Zimmerman
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | - Christopher G Cooney
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
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Abstract
In the setting of infectious disease emergencies, rapid and accurate identification of the causative agent is critical to optimizing antimicrobial therapy in a timely manner. It is clearly evident that the age of molecular diagnostics is now upon us, with real-time PCR becoming the standard of diagnosis for many infectious disease emergencies in either monoplex or multiplex format. Other molecular techniques such as whole or partial genome sequencing, microarrays, broad-range PCR, restriction fragment length polymorphisms, and molecular typing are also being used. However, for most small clinical laboratories, implementation of these advanced molecular techniques is not feasible owing to the high cost of instrumentation and reagents. If these tests are not available in-house, samples can be sent to national reference laboratories (eg, Mayo Medical Laboratories and Quest Diagnostics) for real-time PCR assays that can be completed in 1 day. It is anticipated that over time commercial real-time PCR tests and instrumentation will become more standardized and affordable, allowing individual laboratories to conduct tests locally, thus further reducing turnaround time. Although real-time PCR has been proved to expand our diagnostic capability, it must be stressed that such molecular methodology constitutes only an additional tool in the diagnosis of infectious diseases in emergency situations. Phenotypic methodologies (staining, cultures, biochemical tests, and serology) still play a critical role in identifying, confirming, and providing antibiotic susceptibility testing for many microbial pathogens. As multiplex assays become increasingly available, there will be even greater temptation for taking a “shotgun” approach to diagnostic testing. These new technologies will not substitute for a proper history and physical examination leading to a thoughtful differential diagnosis. None the less, these new molecular tests increase the capability of the diagnostician to rapidly identify the microbiological etiology of an infection. An added advantage of rapid diagnostic tests often not emphasized is the capability to rule out certain diagnoses for which unnecessary antimicrobial therapy may otherwise be instituted and/or continued.
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Affiliation(s)
- Neel K Krishna
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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Weigl BH, Gaydos CA, Kost G, Beyette FR, Sabourin S, Rompalo A, de Los Santos T, McMullan JT, Haller J. The Value of Clinical Needs Assessments for Point-of-Care Diagnostics. POINT OF CARE 2012; 11:108-113. [PMID: 23935405 DOI: 10.1097/poc.0b013e31825a241e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Most entrepreneurial ventures fail long before the core technology can be brought to the marketplace because of disconnects in performance and usability measures such as accuracy, cost, complexity, assay stability, and time requirements between technology developers' specifications and needs of the end-users. By going through a clinical needs assessment (CNA) process, developers will gain vital information and a clear focus that will help minimize the risks associated with the development of new technologies available for use within the health care system. This article summarizes best practices of the principal investigators of the National Institute of Biomedical Imaging and Bioengineering point-of-care (POC) centers within the National Institute of Biomedical Imaging and Bioengineering POC Technologies Research Network. Clinical needs assessments are particularly important for product development areas that do not sufficiently benefit from traditional market research, such as grant-funded research and development, new product lines using cutting-edge technologies developed in start-up companies, and products developed through product development partnerships for low-resource settings. The objectives of this article were to (1) highlight the importance of CNAs for development of POC devices, (2) discuss methods applied by POC Technologies Research Network for assessing clinical needs, and (3) provide a road map for future CNAs.
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Affiliation(s)
- Bernhard H Weigl
- Technology Solutions, Program for Appropriate Technology in Health, Seattle, WA
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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Bullman S, Lucey B, Sleator RD. Molecular diagnostics: the changing culture of medical microbiology. Bioeng Bugs 2012; 3:1-7. [PMID: 22179143 DOI: 10.4161/bbug.3.1.19011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.
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Affiliation(s)
- Susan Bullman
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
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Waldeisen JR, Wang T, Mitra D, Lee LP. A real-time PCR antibiogram for drug-resistant sepsis. PLoS One 2011; 6:e28528. [PMID: 22164303 PMCID: PMC3229610 DOI: 10.1371/journal.pone.0028528] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 11/09/2011] [Indexed: 12/05/2022] Open
Abstract
Current molecular diagnostic techniques for susceptibility testing of septicemia rely on genotyping for the presence of known resistance cassettes. This technique is intrinsically vulnerable due to the inability to detect newly emergent resistance genes. Traditional phenotypic susceptibility testing has always been a superior method to assay for resistance; however, relying on the multi-day growth period to determine which antimicrobial to administer jeopardizes patient survival. These factors have resulted in the widespread and deleterious use of broad-spectrum antimicrobials. The real-time PCR antibiogram, described herein, combines universal phenotypic susceptibility testing with the rapid diagnostic capabilities of PCR. We have developed a procedure that determines susceptibility by monitoring pathogenic load with the highly conserved 16S rRNA gene in blood samples exposed to different antimicrobial drugs. The optimized protocol removes heme and human background DNA from blood, which allows standard real-time PCR detection systems to be employed with high sensitivity (<100 CFU/mL). Three strains of E. coli, two of which were antimicrobial resistant, were spiked into whole blood and exposed to three different antibiotics. After real-time PCR-based determination of pathogenic load, a ΔCt<3.0 between untreated and treated samples was found to indicate antimicrobial resistance (P<0.01). Minimum inhibitory concentration was determined for susceptible bacteria and pan-bacterial detection was demonstrated with 3 Gram-negative and 2 Gram-positive bacteria. Species identification was performed via analysis of the hypervariable amplicons. In summary, we have developed a universal diagnostic phenotyping technique that assays for the susceptibility of drug-resistant septicemia with the speed of PCR. The real-time PCR antibiogram achieves detection, susceptibility testing, minimum inhibitory concentration determination, and identification in less than 24 hours.
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Affiliation(s)
- John R. Waldeisen
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Tim Wang
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Debkishore Mitra
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Luke P. Lee
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- * E-mail:
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Overview of the Development, Utility, and Future of Molecular Diagnostics for Parasitic Diseases. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch45] [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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Cattoir V, Merabet L, Djibo N, Rioux C, Legrand P, Girou E, Lesprit P. Clinical impact of a real-time PCR assay for rapid identification of Staphylococcus aureus and determination of methicillin resistance from positive blood cultures. Clin Microbiol Infect 2011; 17:425-31. [PMID: 20384710 DOI: 10.1111/j.1469-0691.2010.03233.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The full identification and susceptibility profile of staphylococci from positive blood cultures (BCs) generally takes 24-48 h using phenotypic methods. The aim of this prospective study was to evaluate the clinical impact of a real-time PCR strategy for rapid identification of staphylococci and determination of methicillin resistance directly from positive BCs. During a 12-month period, 250 episodes of positive BCs with organism morphology resembling staphylococci were enrolled. Two strategies were compared: conventional (n = 128) using standard phenotypic methods or rapid (n = 122) using a real-time PCR assay that is able to detect specific genes of Staphylococcus aureus (nuc and sa442) and the encoding gene for methicillin resistance (mecA). Overall, 97 episodes (39%) were clinical-significant bloodstream infections. The prevalence of methicillin resistance of S. aureus was 24%. A favorable outcome (defined as clinical cure with resolution of signs and no evidence of recurrence or relapse at 12 weeks follow-up) was observed in similar proportions of episodes with (58%) or without (60%) PCR testing (p 0.8). In multivariate analyses, age and infection due to methicillin-susceptible S. aureus (adjusted OR 0.96, 95% CI 0.93-0.99; and adjusted OR 3.11, 95% CI 1.12-8.65, respectively) were the unique factors independently associated with a favorable outcome. Among the 153 episodes of contaminated BCs, similar proportions received unjustified antibiotic therapy (PCR strategy: 17%, conventional testing: 10%; p 0.33). In a setting with a moderate level of methicillin-resistant S. aureus and relatively high contamination of BCs, real-time PCR testing was not beneficial compared to conventional methods.
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Affiliation(s)
- V Cattoir
- Department of Bacteriology-Virology Infection Control Unit, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris 12, Créteil, France
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Molecular diagnostic assays for detection of viral respiratory pathogens in institutional outbreaks. Mol Diagn Ther 2011; 14:283-93. [PMID: 21053994 PMCID: PMC7099217 DOI: 10.1007/bf03256384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Outbreaks of viral respiratory disease in institutions may be associated with high morbidity and mortality, depending upon the viral etiology and the age and immune status of the affected patients. Control of outbreaks may include isolation and/or cohorting, and prohylaxis or treatment with specific antiviral agents may be indicated, all dependent upon the specific cause of the outbreak. Conventional methods of viral diagnosis detect only a limited number of the viruses that are known to cause outbreaks. The availability of sensitive and specific molecular assays has facilitated rapid diagnosis of a wider range of viruses from respiratory outbreaks. Molecular methods have distinct advantages over conventional methods, including the ability to rapidly develop assays for emerging viruses and new variants of existing viruses. In addition, molecular testing allows rapid detection of resistance to antiviral agents or mutations leading to increased virulence. However, high-throughput molecular testing requires batch processes that may compromise the ability to respond quickly to urgent testing demands.
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50
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Olano JP, Walker DH. Diagnosing emerging and reemerging infectious diseases: the pivotal role of the pathologist. Arch Pathol Lab Med 2011; 135:83-91. [PMID: 21204714 DOI: 10.5858/2010-0260-rar.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Molecular diagnostics continues to evolve very rapidly, and its impact in the diagnosis of infectious diseases is undeniable. Molecular tools have played a pivotal role in discovering and characterizing several emerging infectious agents and have now become the gold standard for the diagnosis of infectious diseases caused by fastidious or uncultivable agents. Multiple challenges still remain for the widespread use of cost-effective, validated, and commercially available molecular tools. Automated instruments capable of sample processing and multiplex nucleic acid amplification and postamplification analysis have already been approved by the US Food and Drug Administration (FDA) for use in the clinical setting. Nanobiotechnology is beginning to impact laboratory diagnostics in the clinical setting. OBJECTIVE To address current nucleic acid techniques used in the clinical laboratory for diagnosis of infectious diseases. FDA-approved tests are listed, as well as molecular techniques (amplification and postamplification analysis). A comprehensive list of emerging pathogens during the last 4 decades is also presented. Biosurveillance systems are discussed in the context of molecular tools. The rapidly evolving field of nanobiotechnology is briefly addressed. DATA SOURCES Original publications, major reviews, and book chapters were used to present a comprehensive, yet short, review of molecular diagnostics in infectious diseases. CONCLUSIONS We will continue to witness an exponential growth of molecular techniques used for the initial diagnosis of infectious diseases. Molecular tools will also continue to have an impact on disease prognosis and response to therapeutic interventions. Automation, multiplexing, and miniaturization will continue to be driving forces in the development of new instruments.
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Affiliation(s)
- Juan P Olano
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0428, USA.
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