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Gao N, Huo Y, Yu D, Cheng F, Wang T, Zhang X, Zhang L, Hu W, Li J, Yuan P, Liu J, Wang Y, Yan J. Evaluation of reverse transcription yield of RNA standards and forensic samples based on droplet digital PCR. Biochem Biophys Res Commun 2024; 711:149909. [PMID: 38615573 DOI: 10.1016/j.bbrc.2024.149909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.
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Affiliation(s)
- Niu Gao
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
| | - Yan Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China; Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
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Shukla JL, Husain AA, Bhan S, Singh LR, Kashyap RS. Diagnostic utility of LAMP PCR targeting bcsp-31 gene for human brucellosis infection. Indian J Med Microbiol 2023; 44:100354. [PMID: 37356844 DOI: 10.1016/j.ijmmb.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/27/2022] [Accepted: 01/21/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE Human brucellosis is a neglected zoonotic disease of significant public health concern. Molecular diagnosis of brucella remains challenging in low resource settings, due to the high infrastructure and cost involved. Loop-mediated isothermal amplification (LAMP) is a rapid point of care polymerase chain reaction (PCR) with the utility of on-field molecular diagnosis and offers a convenient alternative to conventional PCR. In the present study, we developed and evaluated the diagnostic utility of in house LAMP PCR targeting the Brucella genus-specific bcsp-31 gene in patients having febrile illness. MATERIALS AND METHODS The analytical sensitivity and specificity of bcsp-31 LAMP PCR was first evaluated using brucella (n = 8) and non-brucella cultures (n = 5), along with spiked clinical samples. The overall diagnostic utility of developed LAMP PCR was then further evaluated in 393 human samples suspected of brucellosis. RESULTS The developed LAMP PCR could detect as low as 8 fg of DNA by visual detection within 35min. We report sensitivity and specificity of the developed LAMP PCR as 90.91% and 99.37%.The accuracy of the developed test assay was found to be 98.60%. In clinical samples, LAMP gave positivity of 20% with the concordance of 89% with conventional PCR. CONCLUSION To conclude, a rapid, efficacious, sensitive LAMP PCR targeting the bcsp 31 gene was developed. The existing LAMP PCR can be used as a point of care screening test in various low resource endemic setting in lieu of conventional PCR for estimation of prevalence data, diagnosis and treatment of brucellosis.
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Affiliation(s)
- Jayshree L Shukla
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Aliabbas A Husain
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Surya Bhan
- Deptartment of Biochemistry, North-Eastern Hill University (NEHU), Shillong, India
| | - Lokendra R Singh
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Rajpal S Kashyap
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India.
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Flipse J, Niekamp AM, Dirks A, Dukers-Muijrers NHTM, Hoebe CJPA, Wolffs P, van Loo IHM. Refining Timely Diagnosis of Early Syphilis by Using Treponema pallidum PCR or IgM Immunoblotting Next to Conventional Serology for Syphilis. J Clin Microbiol 2023; 61:e0011223. [PMID: 37222630 PMCID: PMC10281170 DOI: 10.1128/jcm.00112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023] Open
Abstract
Treponema pallidum subsp. pallidum is a fastidious spirochete and the etiologic agent of syphilis, a sexually transmitted infection (STI). Syphilis diagnoses and disease staging are based on clinical findings and serologic testing. Moreover, according to most international guidelines, PCR analysis of swab samples from genital ulcers is included in the screening algorithm where possible. It has been suggested that PCR might be omitted from the screening algorithm due to low added value. As an alternative to PCR, IgM serology might be used. In this study, we wanted to establish the added value of PCR and IgM serology for diagnosing primary syphilis. Added value was defined as finding more cases of syphilis, preventing overtreatment, or limiting the extent of partner notification to more recent partners. We found that both PCR and IgM immunoblotting could aid the timely diagnosis of early syphilis in ~24% to 27% of patients. PCR has the greatest sensitivity and can be applied to cases with an ulcer with suspected reinfection or primary infection. In the absence of lesions, the IgM immunoblot could be used. However, the IgM immunoblot has better performance in cases with suspected primary infection than in reinfections. The target population, testing algorithm, time pressures, and costs should determine whether either test provides sufficient value to be implemented in clinical practice.
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Affiliation(s)
- Jacky Flipse
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Centre, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Anne-Marie Niekamp
- Department of Sexual Health, Infectious Diseases, and Environmental Health, Living Lab Public Health, Public Health Service South Limburg, Heerlen, the Netherlands
- Department of Social Medicine, Maastricht University, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Anne Dirks
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Centre, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Nicole H. T. M. Dukers-Muijrers
- Department of Sexual Health, Infectious Diseases, and Environmental Health, Living Lab Public Health, Public Health Service South Limburg, Heerlen, the Netherlands
- Department of Health Promotion, Maastricht University, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Christian J. P. A. Hoebe
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Centre, Care and Public Health Research Institute, Maastricht, the Netherlands
- Department of Sexual Health, Infectious Diseases, and Environmental Health, Living Lab Public Health, Public Health Service South Limburg, Heerlen, the Netherlands
- Department of Social Medicine, Maastricht University, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Petra Wolffs
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Centre, Care and Public Health Research Institute, Maastricht, the Netherlands
| | - Inge H. M. van Loo
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Centre, Care and Public Health Research Institute, Maastricht, the Netherlands
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Reichman A, Kunz A, Joedicke JJ, Höpken UE, Keib A, Neuber B, Sedloev D, Wang L, Jiang G, Hückelhoven-Krauss A, Eberhardt F, Müller-Tidow C, Wermke M, Rehm A, Schmitt M, Schmitt A. Comparison of FACS and PCR for Detection of BCMA-CAR-T Cells. Int J Mol Sci 2022; 23:ijms23020903. [PMID: 35055086 PMCID: PMC8777942 DOI: 10.3390/ijms23020903] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Chimeric-antigen-receptor (CAR)-T-cell therapy is already widely used to treat patients who are relapsed or refractory to chemotherapy, antibodies, or stem-cell transplantation. Multiple myeloma still constitutes an incurable disease. CAR-T-cell therapy that targets BCMA (B-cell maturation antigen) is currently revolutionizing the treatment of those patients. To monitor and improve treatment outcomes, methods to detect CAR-T cells in human peripheral blood are highly desirable. In this study, three different detection reagents for staining BCMA-CAR-T cells by flow cytometry were compared. Moreover, a quantitative polymerase chain reaction (qPCR) to detect BCMA-CAR-T cells was established. By applying a cell-titration experiment of BCMA-CAR-T cells, both methods were compared head-to-head. In flow-cytometric analysis, the detection reagents used in this study could all detect BCMA-CAR-T cells at a similar level. The results of false-positive background staining differed as follows (standard deviation): the BCMA-detection reagent used on the control revealed a background staining of 0.04% (±0.02%), for the PE-labeled human BCMA peptide it was 0.25% (±0.06%) and for the polyclonal anti-human IgG antibody it was 7.2% (±9.2%). The ability to detect BCMA-CAR-T cells down to a concentration of 0.4% was similar for qPCR and flow cytometry. The qPCR could detect even lower concentrations (0.02–0.01%). In summary, BCMA-CAR-T-cell monitoring can be reliably performed by both flow cytometry and qPCR. In flow cytometry, reagents with low background staining should be preferred.
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Affiliation(s)
- Avinoam Reichman
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Alexander Kunz
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Jara J. Joedicke
- Department of Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany; (J.J.J.); (A.R.)
| | - Uta E. Höpken
- Department of Translational Tumor Immunology, Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany;
| | - Anna Keib
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Brigitte Neuber
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - David Sedloev
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Lei Wang
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Genqiao Jiang
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Angela Hückelhoven-Krauss
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Franziska Eberhardt
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Martin Wermke
- NCT/UCC Early Clinical Trial Unit (ECTU), Medical Faculty C.-G. Carus, Technical University Dresden, Fetscherstraße 74, 01307 Dresden, Germany;
| | - Armin Rehm
- Department of Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany; (J.J.J.); (A.R.)
| | - Michael Schmitt
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
| | - Anita Schmitt
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (A.R.); (A.K.); (A.K.); (B.N.); (D.S.); (L.W.); (G.J.); (A.H.-K.); (F.E.); (C.M.-T.); (M.S.)
- Correspondence: ; Tel.: +49-6221-56-6614; Fax: +49-6221-56-5740
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Debes AK, Luo W, Waswa E, Boru W, Sack DA. Cholera rapid diagnostic tests recycled for PCR confirmation. Lancet Glob Health 2022; 10:e35-e36. [PMID: 34919850 DOI: 10.1016/s2214-109x(21)00465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/14/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Amanda K Debes
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Wensheng Luo
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Waqo Boru
- Ministry of Health, Nairobi, Kenya; Field Epidemiology and Laboratory Training Program, Nairobi, Kenya
| | - David A Sack
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Abellan-Schneyder I, Schusser AJ, Neuhaus K. ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. BMC Microbiol 2021; 21:349. [PMID: 34922460 PMCID: PMC8684222 DOI: 10.1186/s12866-021-02391-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. RESULTS Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. CONCLUSION Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared.
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Affiliation(s)
- Isabel Abellan-Schneyder
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Andrea Janina Schusser
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.
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Hoorzook KB, Barnard TG. Absolute quantification of E. coli virulence and housekeeping genes to determine pathogen loads in enumerated environmental samples. PLoS One 2021; 16:e0260082. [PMID: 34843501 PMCID: PMC8629182 DOI: 10.1371/journal.pone.0260082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Quantifying pathogenic genes with q-PCR in complex samples to determine the pathogen loads is influenced by a wide range of factors, including choice of extraction method, standard curve, and the decision to use relative versus absolute quantification of the genes. The aim was to investigate the standardisation of q-PCR methods to determine enumerated E. coli gene ratios grown with the IDEXX Colilert® Quanti-Trays® using enteropathogenic E. coli as the model pathogen. q-PCR targeting the eaeA and gadAB genes was used to calculate the eaeA: gadAB ratios for clinical strains collected between [2005–2006 (n = 55)] and [2008–2009 (n = 19)] using the LinRegPCR software and Corbett Research Thermal cycler software. Both programs grouped the isolates into two distinct groups based on the gene ratios although the Corbett Research Thermal cycler software gave results one log higher than the LinRegPCR program. Although the eaeA: gadAB ratio range was determined using extracted E. coli DNA, the impact of free DNA and other bacteria present in the sample needed to be understood. Standard curve variations using serially diluted extracted E. coli DNA, serially diluted pure E. coli culture followed by DNA extraction from each dilution with or without other bacteria was tested using the eaeA q-PCR to quantify the genes. Comparison of the standard curves showed no significant difference between standard curves prepared with diluted DNA or with cells diluted before the DNA is extracted (P = 0.435). Significant differences were observed when background DNA was included in the diluent or Coliform cells added to the diluent to dilute cells before the DNA is extracted (P < 0.001). The “carrier” DNA and Coliform cells enhanced the DNA extraction results resulting in better PCR efficiency. This will have an influence on the quantification of gene ratios and pathogen load in samples containing lower numbers of E. coli.
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Affiliation(s)
- K. B. Hoorzook
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
- * E-mail:
| | - T. G. Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
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Nascimento RC, Melo GB, Fonseca PDM, Gryschek RCB, Paula FM. Evaluation of targets for Strongyloides genus specific molecular diagnosis in experimental strongyloidiasis. Exp Parasitol 2021; 230:108157. [PMID: 34543651 DOI: 10.1016/j.exppara.2021.108157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
Strongyloides venezuelensis has been used in different experimental studies, such as those aimed at the evaluation of diagnostic techniques for human strongyloidiasis, mainly the molecular diagnosis. In this study, three regions (genus, 18S and 28S targets) of Strongyloides ribosomal DNA were evaluated for the molecular diagnosis of experimental strongyloidiasis. Rats were infected subcutaneously with 400 or 4000 S. venezuelensis infective larvae (400iL3 and 4000iL3), and kept for 35 days. Fecal samples were collected daily to count eggs per gram of feces (EPG) and to perform the polymerase chain reaction (PCR). Egg count started on the 5th day post-infection (pi) and ended on days 33 and 34 pi, in 400iL3 and 4000iL3 groups, respectively. Based in EPG, fecal samples were selected from days 2, 5, 8, 11, 15, 23 and 35 pi for DNA extraction; PCR (genus, 18S and 28S); and sequencing. The PCR-28S products showed higher values of identity (95-100%) in the database with the Strongyloides sequences. Therefore, it is possible to reinforce the application of PCR-28S in the diagnosis of experimental and human strongyloidiasis.
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Affiliation(s)
- Rafael C Nascimento
- Laboratório de Investigação Médica (LIM-06) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Gessica B Melo
- Laboratório de Investigação Médica (LIM-06) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Priscilla D M Fonseca
- Laboratório de Investigação Médica (LIM-06) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Ronaldo C B Gryschek
- Laboratório de Investigação Médica (LIM-06) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - F M Paula
- Laboratório de Investigação Médica (LIM-06) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Brazil.
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Mair T, Ivankovic M, Paar C, Salzer HJF, Heissl A, Lamprecht B, Schreier-Lechner E, Tiemann-Boege I. Processing Hundreds of SARS-CoV-2 Samples with an In-House PCR-Based Method without Robotics. Viruses 2021; 13:v13091712. [PMID: 34578293 PMCID: PMC8473336 DOI: 10.3390/v13091712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 pandemic has required the development of multiple testing systems to monitor and control the viral infection. Here, we developed a PCR test to screen COVID-19 infections that can process up to ~180 samples per day without the requirement of robotics. For this purpose, we implemented the use of multichannel pipettes and plate magnetics for the RNA extraction step and combined the reverse transcription with the qPCR within one step. We tested the performance of two RT-qPCR kits as well as different sampling buffers and showed that samples taken in NaCl or PBS are stable and compatible with different COVID-19 testing systems. Finally, we designed a new internal control based on the human RNase P gene that does not require a DNA digestion step. Our protocol is easy to handle and reaches the sensitivity and accuracy of the standardized diagnostic protocols used in the clinic to detect COVID-19 infections.
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Affiliation(s)
- Theresa Mair
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (M.I.); (I.T.-B.)
- Correspondence: ; Tel.: +43-732-2468-7626
| | - Maja Ivankovic
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (M.I.); (I.T.-B.)
| | - Christian Paar
- Institute of Laboratory Medicine, Johannes Kepler Universitätsklinikum, 4020 Linz, Austria; (C.P.); (E.S.-L.)
| | - Helmut J. F. Salzer
- Department of Pulmonology, Johannes Kepler Universitätsklinikum, 4020 Linz, Austria; (H.J.F.S.); (B.L.)
| | - Angelika Heissl
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria;
| | - Bernd Lamprecht
- Department of Pulmonology, Johannes Kepler Universitätsklinikum, 4020 Linz, Austria; (H.J.F.S.); (B.L.)
| | - Elisabeth Schreier-Lechner
- Institute of Laboratory Medicine, Johannes Kepler Universitätsklinikum, 4020 Linz, Austria; (C.P.); (E.S.-L.)
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (M.I.); (I.T.-B.)
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10
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Silverman JD, Bloom RJ, Jiang S, Durand HK, Dallow E, Mukherjee S, David LA. Measuring and mitigating PCR bias in microbiota datasets. PLoS Comput Biol 2021; 17:e1009113. [PMID: 34228723 PMCID: PMC8284789 DOI: 10.1371/journal.pcbi.1009113] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/16/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
PCR amplification plays an integral role in the measurement of mixed microbial communities via high-throughput DNA sequencing of the 16S ribosomal RNA (rRNA) gene. Yet PCR is also known to introduce multiple forms of bias in 16S rRNA studies. Here we present a paired modeling and experimental approach to characterize and mitigate PCR NPM-bias (PCR bias from non-primer-mismatch sources) in microbiota surveys. We use experimental data from mock bacterial communities to validate our approach and human gut microbiota samples to characterize PCR NPM-bias under real-world conditions. Our results suggest that PCR NPM-bias can skew estimates of microbial relative abundances by a factor of 4 or more, but that this bias can be mitigated using log-ratio linear models. High-throughput DNA sequencing is often used to profile the species composition of host-associated microbial communities (microbiota). One important step in DNA sequencing is amplification where DNA from many different bacteria are repeatedly copied using a technique called Polymerase Chain Reaction (PCR). However, PCR is known to introduce multiple forms of bias as DNA from some bacteria are more efficiently copied than others. Here we introduce experimental and computational procedures that allows PCR NPM-bias (PCR bias from non-primer-mismatch sources) to be measured and mitigated in studies of microbial communities.
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Affiliation(s)
- Justin D Silverman
- College of Information Science and Technology, Pennsylvania State University, State College, Pennsylvania, United States of America
- Institute for Computational and Data Science, Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Medicine, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Rachael J Bloom
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
- University Program for Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Sharon Jiang
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Heather K Durand
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Eric Dallow
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Sayan Mukherjee
- Departments of Statistical Science, Mathematics, Computer Science, Biostatistics & Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Lawrence A David
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
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11
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Parr JB, Kieto E, Phanzu F, Mansiangi P, Mwandagalirwa K, Mvuama N, Landela A, Atibu J, Efundu SU, Olenga JW, Thwai KL, Morgan CE, Denton M, Poffley A, Juliano JJ, Mungala P, Likwela JL, Sompwe EM, Rogier E, Tshefu AK, N'Siala A, Kalonji A. Analysis of false-negative rapid diagnostic tests for symptomatic malaria in the Democratic Republic of the Congo. Sci Rep 2021; 11:6495. [PMID: 33753817 PMCID: PMC7985209 DOI: 10.1038/s41598-021-85913-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/08/2021] [Indexed: 11/29/2022] Open
Abstract
The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a bead-based immunoassay for Plasmodium antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with P. falciparum was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen's kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.
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Affiliation(s)
- Jonathan B Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA.
| | - Eddy Kieto
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Fernandine Phanzu
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Paul Mansiangi
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | | | - Nono Mvuama
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Ange Landela
- Institut National Pour La Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | | | - Jean W Olenga
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Kyaw Lay Thwai
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
| | - Camille E Morgan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Madeline Denton
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
| | - Alison Poffley
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pomie Mungala
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Joris L Likwela
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Eric M Sompwe
- Programme National de La Lutte Contre Le Paludisme, Kinshasa, Democratic Republic of Congo
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30033, USA
| | - Antoinette K Tshefu
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Adrien N'Siala
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Albert Kalonji
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
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12
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Forde JE, Ciupe SM. Quantification of the Tradeoff between Test Sensitivity and Test Frequency in a COVID-19 Epidemic-A Multi-Scale Modeling Approach. Viruses 2021; 13:457. [PMID: 33799660 PMCID: PMC7999334 DOI: 10.3390/v13030457] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/20/2022] Open
Abstract
Control strategies that employ real time polymerase chain reaction (RT-PCR) tests for the diagnosis and surveillance of COVID-19 epidemic are inefficient in fighting the epidemic due to high cost, delays in obtaining results, and the need of specialized personnel and equipment for laboratory processing. Cheaper and faster alternatives, such as antigen and paper-strip tests, have been proposed. They return results rapidly, but have lower sensitivity thresholds for detecting virus. To quantify the effects of the tradeoffs between sensitivity, cost, testing frequency, and delay in test return on the overall course of an outbreak, we built a multi-scale immuno-epidemiological model that connects the virus profile of infected individuals with transmission and testing at the population level. We investigated various randomized testing strategies and found that, for fixed testing capacity, lower sensitivity tests with shorter return delays slightly flatten the daily incidence curve and delay the time to the peak daily incidence. However, compared with RT-PCR testing, they do not always reduce the cumulative case count at half a year into the outbreak. When testing frequency is increased to account for the lower cost of less sensitive tests, we observe a large reduction in cumulative case counts, from 55.4% to as low as 1.22% half a year into the outbreak. The improvement is preserved even when the testing budget is reduced by one half or one third. Our results predict that surveillance testing that employs low-sensitivity tests at high frequency is an effective tool for epidemic control.
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Affiliation(s)
- Jonathan E. Forde
- Department of Mathematics and Computer Sciences, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24060, USA;
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13
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Lindrose AR, McLester-Davis LWY, Tristano RI, Kataria L, Gadalla SM, Eisenberg DTA, Verhulst S, Drury S. Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PLoS One 2021; 16:e0245582. [PMID: 33471860 PMCID: PMC7817045 DOI: 10.1371/journal.pone.0245582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
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Affiliation(s)
- Alyssa R. Lindrose
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| | | | - Renee I. Tristano
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Leila Kataria
- School of Science and Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dan T. A. Eisenberg
- Department of Anthropology, Department of Biology, Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, United States of America
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stacy Drury
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, United States of America
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
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14
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Zhou H, Liu D, Ma L, Ma T, Xu T, Ren L, Li L, Xu S. A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests. Anal Chem 2021; 93:715-721. [PMID: 33289545 PMCID: PMC7737535 DOI: 10.1021/acs.analchem.0c03996] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. A reference standard with a well-characterized concentration or titer is of the utmost importance for the study of limit of detection (LoD), which is a crucial feature for a diagnostic assay. Although several reference standards of plasmids or synthetic RNA have already been announced, a reference standard for inactivated virus particles with an accurate concentration is still needed to evaluate the complete procedure. Here, we performed a collaborative study to estimate the NAT-detectable units as a viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6 × 105 ± 6.5 × 104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.
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Affiliation(s)
- Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Donglai Liu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Liang Ma
- Department of Biomedical Devices, Bioland
Laboratory (Guangzhou Regenerative Medicine and Health Guangdong
Laboratory), Guangzhou 510320, China
| | - Tingting Ma
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Tingying Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese
Academy of Medical Sciences & Peking Union Medical College, Beijing
100730, China
| | - Liang Li
- Biotechnology Research Institute, Chinese
Academy of Agricultural Sciences, Beijing 100081,
China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
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15
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Xu Y, Xiao M, Liu X, Xu S, Du T, Xu J, Yang Q, Xu Y, Han Y, Li T, Zhu H, Wang M. Significance of serology testing to assist timely diagnosis of SARS-CoV-2 infections: implication from a family cluster. Emerg Microbes Infect 2020; 9:924-927. [PMID: 32286155 PMCID: PMC7269047 DOI: 10.1080/22221751.2020.1752610] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/01/2020] [Indexed: 01/08/2023]
Abstract
Confirmative diagnosis of SARS-CoV-2 infections has been challenged due to unsatisfactory positive rate of molecular assays. Here we identified a family cluster of SARS-CoV-2 infections, with five of six family members were SARS-CoV-2-specific immunoglobin serology testing positive, while molecular assays only detected two of this five patients even repeated twice. We comprehensively analyzed this familial cluster of cases based on the clinical characteristics, chest CT images, SARS-CoV-2 molecular detection results, and serology testing results. At last, two patients were diagnosed with COVID-19, two were suspected of COVID-19, and two were considered close contacts. Our results emphasized the significance of serology testing to assist timely diagnosis of SARS-CoV-2 infections, especially for COVID-19 close contacts screening.
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Affiliation(s)
- Yan Xu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Meng Xiao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Xinchao Liu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Shengyong Xu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Tiekuan Du
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Jun Xu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Qiwen Yang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Yingchun Xu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Yang Han
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Taisheng Li
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Huadong Zhu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Mengzhao Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
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16
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Abstract
BACKGROUND Plasmodium vivax (P vivax) is a focus of malaria elimination. It is important because P vivax and Plasmodium falciparum infection are co-endemic in some areas. There are asymptomatic carriers of P vivax, and the treatment for P vivax and Plasmodium ovale malaria differs from that used in other types of malaria. Rapid diagnostic tests (RDTs) will help distinguish P vivax from other malaria species to help treatment and elimination. There are RDTs available that detect P vivax parasitaemia through the detection of P vivax-specific lactate dehydrogenase (LDH) antigens. OBJECTIVES To assess the diagnostic accuracy of RDTs for detecting P vivax malaria infection in people living in malaria-endemic areas who present to ambulatory healthcare facilities with symptoms suggestive of malaria; and to identify which types and brands of commercial tests best detect P vivax malaria. SEARCH METHODS We undertook a comprehensive search of the following databases up to 30 July 2019: Cochrane Infectious Diseases Group Specialized Register; Central Register of Controlled Trials (CENTRAL), published in the Cochrane Library; MEDLINE (PubMed); Embase (OVID); Science Citation Index Expanded (SCI-EXPANDED) and Conference Proceedings Citation Index-Science (CPCI-S), both in the Web of Science. SELECTION CRITERIA Studies comparing RDTs with a reference standard (microscopy or polymerase chain reaction (PCR)) in blood samples from patients attending ambulatory health facilities with symptoms suggestive of malaria in P vivax-endemic areas. DATA COLLECTION AND ANALYSIS For each included study, two review authors independently extracted data using a pre-piloted data extraction form. The methodological quality of the studies were assessed using a tailored Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. We grouped studies according to commercial brand of the RDT and performed meta-analysis when appropriate. The results given by the index tests were based on the antibody affinity (referred to as the strength of the bond between an antibody and an antigen) and avidity (referred to as the strength of the overall bond between a multivalent antibody and multiple antigens). All analyses were stratified by the type of reference standard. The bivariate model was used to estimate the pooled sensitivity and specificity with 95% confidence intervals (CIs), this model was simplified when studies were few. We assessed the certainty of the evidence using the GRADE approach. MAIN RESULTS We included 10 studies that assessed the accuracy of six different RDT brands (CareStart Malaria Pf/Pv Combo test, Falcivax Device Rapid test, Immuno-Rapid Malaria Pf/Pv test, SD Bioline Malaria Ag Pf/Pv test, OnSite Pf/Pv test and Test Malaria Pf/Pv rapid test) for detecting P vivax malaria. One study directly compared the accuracy of two RDT brands. Of the 10 studies, six used microscopy, one used PCR, two used both microscopy and PCR separately and one used microscopy corrected by PCR as the reference standard. Four of the studies were conducted in Ethiopia, two in India, and one each in Bangladesh, Brazil, Colombia and Sudan. The studies often did not report how patients were selected. In the patient selection domain, we judged the risk of bias as unclear for nine studies. We judged all studies to be of unclear applicability concern. In the index test domain, we judged most studies to be at low risk of bias, but we judged nine studies to be of unclear applicability concern. There was poor reporting on lot testing, how the RDTs were stored, and background parasitaemia density (a key variable determining diagnostic accuracy of RDTs). Only half of the included studies were judged to be at low risk of bias in the reference standard domain, Studies often did not report whether the results of the reference standard could classify the target condition or whether investigators knew the results of the RDT when interpreting the results of the reference standard. All 10 studies were judged to be at low risk of bias in the flow and timing domain. Only two brands were evaluated by more than one study. Four studies evaluated the CareStart Malaria Pf/Pv Combo test against microscopy and two studies evaluated the Falcivax Device Rapid test against microscopy. The pooled sensitivity and specificity were 99% (95% CI 94% to 100%; 251 patients, moderate-certainty evidence) and 99% (95% CI 99% to 100%; 2147 patients, moderate-certainty evidence) for CareStart Malaria Pf/Pv Combo test. For a prevalence of 20%, about 206 people will have a positive CareStart Malaria Pf/Pv Combo test result and the remaining 794 people will have a negative result. Of the 206 people with positive results, eight will be incorrect (false positives), and of the 794 people with a negative result, two would be incorrect (false negative). For the Falcivax Device Rapid test, the pooled sensitivity was 77% (95% CI: 53% to 91%, 89 patients, low-certainty evidence) and the pooled specificity was 99% (95% CI: 98% to 100%, 621 patients, moderate-certainty evidence), respectively. For a prevalence of 20%, about 162 people will have a positive Falcivax Device Rapid test result and the remaining 838 people will have a negative result. Of the 162 people with positive results, eight will be incorrect (false positives), and of the 838 people with a negative result, 46 would be incorrect (false negative). AUTHORS' CONCLUSIONS The CareStart Malaria Pf/Pv Combo test was found to be highly sensitive and specific in comparison to microscopy for detecting P vivax in ambulatory healthcare in endemic settings, with moderate-certainty evidence. The number of studies included in this review was limited to 10 studies and we were able to estimate the accuracy of 2 out of 6 RDT brands included, the CareStart Malaria Pf/Pv Combo test and the Falcivax Device Rapid test. Thus, the differences in sensitivity and specificity between all the RDT brands could not be assessed. More high-quality studies in endemic field settings are needed to assess and compare the accuracy of RDTs designed to detect P vivax.
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Affiliation(s)
- Ridhi Agarwal
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Leslie Choi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Samuel Johnson
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
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17
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Abstract
Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.
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Affiliation(s)
- Natalie Sieber
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
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19
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Abstract
The coronavirus disease (COVID-19) pandemic has placed the clinical laboratory and testing for SARS-CoV-2 front and center in the worldwide discussion of how to end the outbreak. Clinical laboratories have responded by developing, validating, and implementing a variety of molecular and serologic assays to test for SARS-CoV-2 infection. This has played an essential role in identifying cases, informing isolation decisions, and helping to curb the spread of disease. However, as the demand for COVID-19 testing has increased, laboratory professionals have faced a growing list of challenges, uncertainties, and, in some situations, controversy, as they have attempted to balance the need for increasing test capacity with maintaining a high-quality laboratory operation. The emergence of this new viral pathogen has raised unique diagnostic questions for which there have not always been straightforward answers. In this commentary, the author addresses several areas of current debate, including (i) the role of molecular assays in defining the duration of isolation/quarantine, (ii) whether the PCR cycle threshold value should be included on patient reports, (iii) if specimen pooling and testing by research staff represent acceptable solutions to expand screening, and (iv) whether testing a large percentage of the population is feasible and represents a viable strategy to end the pandemic.
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Affiliation(s)
- Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Director of Clinical Virology, Mayo Clinic, Rochester, Minnesota, USA
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20
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Touroutine D, Tanis JE. A Rapid, SuperSelective Method for Detection of Single Nucleotide Variants in Caenorhabditis elegans. Genetics 2020; 216:343-352. [PMID: 32817008 PMCID: PMC7536863 DOI: 10.1534/genetics.120.303553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/09/2020] [Indexed: 12/30/2022] Open
Abstract
With the widespread use of single nucleotide variants generated through mutagenesis screens and genome editing technologies, there is pressing need for an efficient and low-cost strategy to genotype single nucleotide substitutions. We have developed a rapid and inexpensive method for detection of point mutants through optimization of SuperSelective (SS) primers for end-point PCR in Caenorhabditis elegans Each SS primer consists of a 5' "anchor" that hybridizes to the template, followed by a noncomplementary "bridge," and a "foot" corresponding to the target allele. The foot sequence is short, such that a single mismatch at the terminal 3' nucleotide destabilizes primer binding and prevents extension, enabling discrimination of different alleles. We explored how length and sequence composition of each SS primer segment affected selectivity and efficiency in various genetic contexts in order to develop simple rules for primer design that allow for differentiation between alleles over a broad range of annealing temperatures. Manipulating bridge length affected amplification efficiency, while modifying the foot sequence altered discriminatory power. Changing the anchor position enabled SS primers to be used for genotyping in regions with sequences that are challenging for standard primer design. After defining primer design parameters, we demonstrated the utility of SS primers for genotyping crude C. elegans lysates, suggesting that this approach could also be used for SNP mapping and screening of CRISPR mutants. Further, since SS primers reliably detect point mutations, this method has potential for broad application in all genetic systems.
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Affiliation(s)
- Denis Touroutine
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Jessica E Tanis
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
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21
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Malapelle U, Parente P, Pepe F, De Luca C, Cerino P, Covelli C, Balestrieri M, Russo G, Bonfitto A, Pisapia P, Fiordelisi F, D’Armiento M, Bruzzese D, Loupakis F, Pietrantonio F, Triassi M, Fassan M, Troncone G, Graziano P. Impact of Pre-Analytical Factors on MSI Test Accuracy in Mucinous Colorectal Adenocarcinoma: A Multi-Assay Concordance Study. Cells 2020; 9:E2019. [PMID: 32887373 PMCID: PMC7565496 DOI: 10.3390/cells9092019] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Immunohistochemistry (IHC) and polymerase chain reaction (PCR) and fragment separation by capillary electrophoresis represent the current clinical laboratory standard for the evaluation of microsatellite instability (MSI) status. The importance of reporting MSI status in colorectal cancer is based on its potential for guiding treatment and as a prognostic indicator. It is also used to identify patients for Lynch syndrome testing. Our aim was to evaluate pre-analytical factors, such as age of formalin-fixed and paraffin-embedded (FFPE) block, neoplastic cell percentage, mucinous component, and DNA integrity, that may influence the accuracy of MSI testing and assess the concordance between three different MSI evaluation approaches. We selected the mucinous colorectal cancer (CRC) histotype for this study as it may possibly represent an intrinsic diagnostic issue due to its low tumor cellularity. Seventy-five cases of mucinous CRC and corresponding normal colon tissue samples were retrospectively selected. MMR proteins were evaluated by IHC. After DNA quality and quantity evaluation, the Idylla™ and TapeStation 4200 platforms were adopted for the evaluation of MSI status. Seventy-three (97.3%) cases were successfully analyzed by the three methodologies. Overall, the Idylla™ platform showed a concordance rate with IHC of 98.0% for microsatellite stable (MSS)/proficient MMR (pMMR) cases and 81.8% for MSI/deficient MMR (dMMR) cases. The TapeStation 4200 system showed a concordance rate with IHC of 96.0% for MSS/pMMR cases and 45.4% for MSI/dMMR cases. The concordance rates of the TapeStation 4200 system with respect to the Idylla™ platform were 98.1% for MSS profile and 57.8% for MSI profile. Discordant cases were analyzed using the Titano MSI kit. Considering pre-analytical factors, no significant variation in concordance rate among IHC analyses and molecular systems was observed by considering the presence of an acellular mucus cut-off >50% of the tumor area, FFPE year preparation, and DNA concentration. Conversely, the Idylla™ platform showed a significant variation in concordance rate with the IHC approach by considering a neoplastic cell percentage >50% (p-value = 0.002), and the TapeStation 4200 system showed a significant variation in concordance rate with the IHC approach by considering a DNA integrity number (DIN) ≥4 as cut-off (p-value = 0.009). Our data pinpoint a central role of the pre-analytical phase in the diagnostic outcome of MSI testing in CRC.
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MESH Headings
- Adenocarcinoma, Mucinous/diagnosis
- Adenocarcinoma, Mucinous/genetics
- Adenocarcinoma, Mucinous/pathology
- Aged
- Case-Control Studies
- Colorectal Neoplasms/diagnosis
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis
- Colorectal Neoplasms, Hereditary Nonpolyposis/genetics
- Colorectal Neoplasms, Hereditary Nonpolyposis/pathology
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Diagnosis, Differential
- Electrophoresis, Capillary/standards
- Female
- Humans
- Immunohistochemistry/standards
- Male
- Microsatellite Instability
- Middle Aged
- Polymerase Chain Reaction/standards
- Prognosis
- Retrospective Studies
- Tissue Embedding/methods
- Tissue Embedding/standards
- Tissue Fixation/methods
- Tissue Fixation/standards
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Paola Parente
- Unit of Pathology, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (P.P.); (C.C.); (A.B.); (F.F.); (P.G.)
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Pellegrino Cerino
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Claudia Covelli
- Unit of Pathology, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (P.P.); (C.C.); (A.B.); (F.F.); (P.G.)
| | - Mariangela Balestrieri
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (M.B.); (M.F.)
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Antonio Bonfitto
- Unit of Pathology, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (P.P.); (C.C.); (A.B.); (F.F.); (P.G.)
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Fabiola Fiordelisi
- Unit of Pathology, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (P.P.); (C.C.); (A.B.); (F.F.); (P.G.)
| | - Maria D’Armiento
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Fotios Loupakis
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Istituto Oncologico Veneto (IRCSS), 35128 Padua, Italy;
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, 20133 Milano, Italy;
- Oncology and Hemato-Oncology Department, University of Milan, 20133 Milan, Italy
| | - Maria Triassi
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (M.B.); (M.F.)
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (U.M.); (F.P.); (C.D.L.); (P.C.); (G.R.); (P.P.); (M.D.); (D.B.); (M.T.)
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (P.P.); (C.C.); (A.B.); (F.F.); (P.G.)
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22
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Alessandrini F, Caucci S, Onofri V, Melchionda F, Tagliabracci A, Bagnarelli P, Di Sante L, Turchi C, Menzo S. Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing. Genes (Basel) 2020; 11:E929. [PMID: 32806776 PMCID: PMC7463572 DOI: 10.3390/genes11080929] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a SARS-CoV-2 specific primers pool from the Ion AmpliSeq SARS-CoV-2 Research Panel, was assessed in order to promote viral RNA specific reverse transcription. The aim of this study was to evaluate the effectiveness of the Ion AmpliSeq™ SARS-CoV-2 Research Panel in sequencing the entire viral genome in different samples. SARS-CoV-2 sequence data were obtained from ten viral isolates and one nasopharyngeal swab from different patients. The ten isolate samples amplified with 12 PCR cycles displayed high mean depth values compared to those of the two isolates amplified with 20 PCR cycles. High mean depth values were also obtained for the nasopharyngeal swab processed by use of a target-specific reverse transcription. The relative depth of coverage (rDoC) analysis showed that when 12 PCR cycles were used, all target regions were amplified with high sequencing coverage, while in libraries amplified at 20 cycles, a poor uniformity of amplification, with absent or low coverage of many target regions, was observed. Our results show that the Ion AmpliSeq SARS-CoV-2 Research Panel can achieve rapid and high throughput SARS-CoV-2 whole genome sequencing from 10 ng of DNA-free viral RNA from isolates and from 1 ng of DNA-free viral RNA from a nasopharyngeal swab using 12 PCR cycles for library amplification. The modified RT-PCR protocol yielded superior results on the nasopharyngeal swab compared to the reverse transcription reaction set up according to the manufacturer's instructions.
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Affiliation(s)
- Federica Alessandrini
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Valerio Onofri
- Legal Medicine Unit, AOU Ospedali Riuniti, Torrette, 60126 Ancona, Italy;
| | - Filomena Melchionda
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Adriano Tagliabracci
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Patrizia Bagnarelli
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Laura Di Sante
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Chiara Turchi
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
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23
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Abstract
The World Health Organization has declared coronavirus disease 2019 (COVID-19) a pandemic. Polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the diagnostic gold standard of COVID-19. We have developed a simulation-based training program for mobile prehospital diagnostic teams in the province of Styria, Austria, and performed a prospective observational study on its applicability and effectivity.The 1-day curriculum uses theoretical instruction, technical skills training, and simulator-based algorithm training to teach and train prehospital patient identification and communication, donning the personal protective equipment, collection of naso-/oropharyngeal swabs for SARS-CoV-2 polymerase chain reaction testing, doffing the personal protective equipment, and sample logistics. Trainings were conducted at the SIM CAMPUS simulation hospital, Eisenerz, using high-fidelity patient simulation. To ensure achievement of predefined learning outcomes, participants had to undergo a final simulator-based objective structured clinical examination.In March 2020, 45 emergency medical assistants and 1 physician of the Austrian Red Cross participated on a voluntary basis. Forty-five of the 46 participants (97.8%) completed the curriculum successfully, with mean objective structured clinical examination ratings of 98.6%.Using several proven educational concepts, we have successfully drafted and implemented a training program for mobile prehospital SARS-CoV-2 diagnostic teams. Based on simulation-based objective structured examinations, it has prepared participants effectively for preclinical duties.
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Affiliation(s)
- Lukas P. Mileder
- Division of Neonatology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz
- Clinical Skills Center, Medical University of Graz
| | | | - Jürgen Prattes
- Department of Internal Medicine, Medical University of Graz
| | - Thomas Wegscheider
- Clinical Skills Center, Medical University of Graz
- Division of Special Anesthesiology, Pain and Intensive Care Medicine, Department of Anesthesiology and Intensive Care Medicine, Medical University of Graz, Graz
- SIM CAMPUS GmbH, Center for Emergency, Crisis and Disaster Simulation and Disaster Diplomacy, Eisenerz, Austria
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24
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Abstract
RATIONALE In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan, China. The initial epidemiological investigations showed that COVID-19 occurred more likely in adults, with patients younger than 10 years old accounting for less than 1% of the total number of confirmed cases, and infant infections were more rare. In our case, we present an infant who was only 35 days old when he was tested positive for COVID-19. PATIENT CONCERNS In this report, a 35 day-old male infant with atypical symptoms had close contact with 2 confirmed patients of COVID-19 who were his grandmother and mother. DIAGNOSIS The patient was diagnosed as COVID-19 after his oropharyngeal swab tested positive for severe acute respiratory syndrome coronavirus 2 by reverse transcription-polymerase chain reaction assay. INTERVENTIONS The therapeutic schedule included aerosol inhalation of recombinant human interferon α-2b and supportive therapy. OUTCOMES Two consecutive (1 day apart) oropharyngeal swabs tested negative for severe acute respiratory syndrome coronavirus 2; then, the patient was discharged on February 27, 2020. LESSONS Strengthening infants' virus screening in families with infected kins is important for early diagnosis, isolation, and treatment when symptoms are atypical. The infectivity of infants with mild or asymptomatic COVID-19 should not be ignored because this may be a source of transmission in the community.
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25
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Dardente H, English WR, Valluru MK, Kanthou C, Simpson D. Debunking the Myth of the Endogenous Antiangiogenic Vegfaxxxb Transcripts. Trends Endocrinol Metab 2020; 31:398-409. [PMID: 32396842 DOI: 10.1016/j.tem.2020.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/28/2019] [Accepted: 01/14/2020] [Indexed: 12/19/2022]
Abstract
In this opinion article we critically assess evidence for the existence of a family of antiangiogenic vascular endothelial growth factor (Vegfaxxxb) transcripts, arising from the use of a phylogenetically conserved alternative distal splice site within exon 8 of the VEGFA gene. We explain that prior evidence for Vegfaxxxb transcripts in tissues rests heavily upon flawed RT-PCR methodologies, with the extensive use of 5'-tailing in primer design being the main issue. Furthermore, our analysis of large RNA-seq data sets (human and ovine) fails to identify a single Vegfaxxxb transcript. Therefore, we challenge the very existence of Vegfaxxxb transcripts, which further questions the physiological relevance of studies based on the use of 'anti-VEGFAxxxb' antibodies. Our analysis has implications for the proposed therapeutic use of isoform-specific anti-VEGFA strategies for treating cancer and retinopathies.
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Affiliation(s)
- Hugues Dardente
- PRC, INRA, CNRS, IFCE, Université de Tours, 37380 Nouzilly, France.
| | - William R English
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Manoj K Valluru
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Chryso Kanthou
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - David Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT7 1NN, UK
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26
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Dewair A, Bessat M. Molecular and microscopic detection of natural and experimental infections of Toxocara vitulorum in bovine milk. PLoS One 2020; 15:e0233453. [PMID: 32433671 PMCID: PMC7239449 DOI: 10.1371/journal.pone.0233453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/05/2020] [Indexed: 02/02/2023] Open
Abstract
Toxocara vitulorum is an Ascarid nematode infecting the small intestine of buffalo and cattle particularly neonate calves, with the postnatal route through milk is the main infection source. However, little is known about shedding rates and the optimum detection methods of T. vitulorum larvae in the milk of the infected bovine hosts. In this study, we aimed to evaluate the use of two methods, microscopy and PCR, and their detection limits both under the experimental and natural infection situations. In doing this, T. vitulorum eggs extracted from naturally occurring adult female worms were successfully subjected to experimental embryonation, and larvae were implemented in experimental infection of milk in ascending infection doses of 0, 1, 5, 10, 20, 50 larvae/2-ml milk samples. With the except of negative control, microscopy-based examination detected larvae in all samples, albeit with means, ranges, and the total number of larvae were detected in exponential rates relative to larvae densities in milk samples. PCR technique corresponded well to microscopy in detecting genomic DNA of T. vitulorum larvae in all milk samples down to a single larva/sample. On the other hand, and by applying the same methodology approach on 50 naturally-occurring bovine colostrum/milk samples, 13 (26%) and 20 (40%) samples were tested positive for T. vitulorum infection by microscopy and the PCR-based detection, respectively. Of these, 11 out of 26 buffalo samples (42.30%) and 2 out of 24 cow samples (8.33%) were tested positive by microscopy, while 16 (61.54%) and 3 (12.50%) of buffalo and cow samples were tested positive by PCR, respectively. By applying the Agreement Coefficient, substantial agreement (0.77) between molecular and microscopy detection was detected from all tested samples. In conclusion, larvae of T. vitulorum were unequivocally detected by microscopy and molecular methods in milk samples both under the experimental and natural field situations. Nevertheless, slightly higher rates by PCR than microscopy were obtained when detecting naturally-infected milk samples. To the best of our knowledge, this is the first in situ detection of larvae of T. vitulorum in the milk of the naturally infected animals.
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Affiliation(s)
- Amira Dewair
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Mohamed Bessat
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
- * E-mail:
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27
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Ramkissoon S, MacArthur I, Ibrahim M, de Graaf H, Read RC, Preston A. A qPCR assay for Bordetella pertussis cells that enumerates both live and dead bacteria. PLoS One 2020; 15:e0232334. [PMID: 32353041 PMCID: PMC7192480 DOI: 10.1371/journal.pone.0232334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/13/2020] [Indexed: 02/03/2023] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, commonly referred to as pertussis. Although the incidence of pertussis was reduced through vaccination, during the last thirty years it has returned to high levels in a number of countries. This resurgence has been linked to the switch from the use of whole-cell to acellular vaccines. Protection afforded by acellular vaccines appears to be short-lived compared to that afforded by whole cell vaccines. In order to inform future vaccine improvement by identifying immune correlates of protection, a human challenge model of B. pertussis colonisation has been developed. Accurate measurement of colonisation status in this model has required development of a qPCR-based assay to enumerate B. pertussis in samples that distinguishes between viable and dead bacteria. Here we report the development of this assay and its performance in the quantification of B. pertussis from human challenge model samples. This assay has future utility in diagnostic labs and in research where a quantitative measure of both B. pertussis number and viability is required.
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Affiliation(s)
- Stacy Ramkissoon
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Iain MacArthur
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Muktar Ibrahim
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- School of Clinical Experimental Sciences, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Hans de Graaf
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- School of Clinical Experimental Sciences, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Robert C. Read
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- School of Clinical Experimental Sciences, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Andrew Preston
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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Timpano EK, Scheible MKR, Meiklejohn KA. Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil. PLoS One 2020; 15:e0231436. [PMID: 32298321 PMCID: PMC7162488 DOI: 10.1371/journal.pone.0231436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/19/2020] [Indexed: 12/31/2022] Open
Abstract
Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.
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Affiliation(s)
- Emma K. Timpano
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Melissa K. R. Scheible
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Kelly A. Meiklejohn
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Kokkinakis I, Selby K, Favrat B, Genton B, Cornuz J. [Covid-19 diagnosis : clinical recommendations and performance of nasopharyngeal swab-PCR]. Rev Med Suisse 2020; 16:699-701. [PMID: 32270938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Covid-19 pandemic imposes new diagnostic strategies in order to optimize the medical care of our patients. The current biblio-graphy, although of low quality, shows a sensitivity of 56 to 83 % for the Covid-19 PCR. Even though one negative test can exclude a Covid-19 in the majority of cases, the NPV (Negative Predictive Value) decreases with increasing prevalence (pre-test probability). This finding suggests the need for strict auto-isolation of patients until the resolution of their symptoms. For patients that present with typical symptoms, who have a presumed Covid-19 prevalence of -40-50 %, a negative test should be interpreted with caution and a repeat test may be needed.
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Affiliation(s)
- Ioannis Kokkinakis
- Unisanté, Centre universitaire de médecine générale et de santé publique, Rue du Bugnon 44, 1011 Lausanne
| | - Kevin Selby
- Unisanté, Centre universitaire de médecine générale et de santé publique, Rue du Bugnon 44, 1011 Lausanne
| | - Bernard Favrat
- Unisanté, Centre universitaire de médecine générale et de santé publique, Rue du Bugnon 44, 1011 Lausanne
| | - Blaise Genton
- Unisanté, Centre universitaire de médecine générale et de santé publique, Rue du Bugnon 44, 1011 Lausanne
| | - Jacques Cornuz
- Unisanté, Centre universitaire de médecine générale et de santé publique, Rue du Bugnon 44, 1011 Lausanne
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Yoon SH, Min IK, Ahn JG. Immunochromatography for the diagnosis of Mycoplasma pneumoniae infection: A systematic review and meta-analysis. PLoS One 2020; 15:e0230338. [PMID: 32182283 PMCID: PMC7077834 DOI: 10.1371/journal.pone.0230338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/26/2020] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to evaluate the diagnostic performance of immunochromatographic tests (ICTs) for the detection of Mycoplasma pneumoniae. Medline/Pubmed, Embase, the Cochrane Library, and ISI Web of Science were searched through June 12, 2019 for relevant studies that used ICTs for the detection of M. pneumoniae infection with polymerase chain reaction (PCR) or microbial culturing as reference standards. Pooled diagnostic accuracy with 95% confidence interval (CI) was calculated using a bivariate random effects model. We also constructed summary receiver operating characteristic curves and calculated the area under the curve (AUC). Statistical heterogeneity was evaluated by χ2 test or Cochrane’s Q test. Thirteen studies including 2,235 samples were included in the meta-analysis. The pooled sensitivity and specificity for diagnosing M. pneumoniae infection were 0.70 (95% CI: 0.59–0.79) and 0.92 (95% CI: 0.87–0.95), respectively. The positive likelihood ratio (LR) was 8.94 (95% CI: 4.90–14.80), negative LR 0.33 (95% CI: 0.22–0.46), diagnostic odds ratio 29.20 (95% CI: 10.70–64.20), and AUC 0.904. In subgroup analysis, ICTs demonstrated similar pooled sensitivities and specificities in populations of children only and mixed populations (children + adults). Specimens obtained from oropharyngeal swabs exhibited a higher sensitivity and specificity than those of nasopharyngeal swab. Moreover, pooled estimates of sensitivity and accuracy for studies using PCR as a reference standard were higher than those using culture. The pooled sensitivity and specificity of Ribotest Mycoplasma®, the commercial kit most commonly used in the included studies, were 0.66 and 0.89, respectively. Overall, ICT is a rapid user-friendly method for diagnosing M. pneumoniae infection with moderate sensitivity, high specificity, and high accuracy. This suggests that ICT may be useful in the diagnostic workup of M. pneumoniae infection; however, additional studies are needed for evaluating the potential impact of ICT in clinical practice.
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Affiliation(s)
- Seo Hee Yoon
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - In Kyung Min
- Biostatistics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
- * E-mail:
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Lee S, Taylor JL, Redmond C, Hadd AG, Kemppainen JA, Haynes BC, Shone S, Bailey DB, Latham GJ. Validation of Fragile X Screening in the Newborn Population Using a Fit-for-Purpose FMR1 PCR Assay System. J Mol Diagn 2020; 22:346-354. [PMID: 31866572 PMCID: PMC7103763 DOI: 10.1016/j.jmoldx.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Newborn screening is designed for presymptomatic identification of serious conditions with effective early interventions. Clinical laboratories must perform prospective pilot studies to ensure that the analytical performance and workflow for a given screening test are appropriate. We assessed the potential to screen newborns for fragile X syndrome, a monogenic neurodevelopmental disorder, by establishing a customized, high-throughput PCR and analysis software system designed to detect fragile X mental retardation 1 gene repeat expansions from dried blood spots (DBSs). Assay precision, accuracy, sensitivity, and specificity were characterized across the categorical range of repeat expansions. The assay consistently resolved genotypes within three CGG repeats of reference values up to at least 137 repeats and within six repeats for larger expansions up to 200 repeats. Accuracy testing results were concordant with reference results. Full and premutation alleles were detected from subnanogram DNA inputs eluted from DBSs and from mixtures with down to 1% relative abundance of the respective expansion. Analysis of 963 deidentified newborn DBS samples identified 957 normal and 6 premutation specimens, consistent with previously published prevalence estimates. These studies demonstrate that the assay system can support high-throughput newborn screening programs.
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Affiliation(s)
- Stacey Lee
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, Research Triangle Park, North Carolina
| | - Jennifer L Taylor
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, Research Triangle Park, North Carolina.
| | | | | | | | | | - Scott Shone
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, Research Triangle Park, North Carolina
| | - Donald B Bailey
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, Research Triangle Park, North Carolina.
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Rodríguez Gómez ER, Otero Regino W, Monterrey PA, Trespalacios Rangel AA. cagA gene EPIYA motif genetic characterization from Colombian Helicobacter pylori isolates: Standardization of a molecular test for rapid clinical laboratory detection. PLoS One 2020; 15:e0227275. [PMID: 31923209 PMCID: PMC6953880 DOI: 10.1371/journal.pone.0227275] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
The aim of this work was to determine current cagA gene EPIYA motifs present in Colombian Helicobacter pylori isolates using a fast and reliable molecular test. DNA from eighty-five Helicobacter pylori-cagA positive strains were analyzed. Strains were obtained from patients diagnosed with functional dyspepsia at Clínica Fundadores in Bogotá. The 3' region of the cagA gene was amplified through conventional Polymerase Chain Reaction (PCR). Obtained amplicons were sequenced using the Sanger method and analyzed with bioinformatics tools. Additionally, a significant Spearman correlation coefficient was determined between the patients' age and the number of EPIYA-C repeats; with p values < 0.05 considered significant. Estimates were obtained using a 95% CI. The 3´ variable region of the cagA gene was amplified and PCR products of the following sizes corresponded to the following EPIYA motifs: 400 bp: EPIYA AB, 500 bp: EPIYA ABC, 600 bp: EPIYA ABCC and 700 bp: ABCCC. A single PCR band was observed for 58 out of 85 Helicobacter pylori isolates, with an EPIYA distribution motif as follows: 7/85 AB (8.2%), 34/85 ABC (40%), 26/85 ABCC (30.6%) and 18/85 ABCCC (21.2%). However, in 27 out of 85 Helicobacter pylori isolates, two or more bands were observed, where the most predominant cagA genotype were ABC-ABCC (26%, 7/27) and ABCC-ABCCC (22.2%, 6/27). A direct proportionality between the number of EPIYA-C repeats and an increase in the patients’ age was observed, finding a greater number of EPIYA ABCC and ABCCC repeats in the population over 50 years old. All isolates were of the Western cagA type and 51.8% of them were found to have multiple EPIYA-C repeats. These standardized molecular test allowed to identify the number of EPIYA C motifs based on band size.
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Affiliation(s)
| | | | - Pedro A. Monterrey
- School of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
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Pan Z, Lu J, Wang N, He WT, Zhang L, Zhao W, Su S. Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses. Virulence 2020; 11:707-718. [PMID: 32490723 PMCID: PMC7549975 DOI: 10.1080/21505594.2020.1771980] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 01/03/2023] Open
Abstract
With the outbreak of the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, coronaviruses have become a global research hotspot in the field of virology. Coronaviruses mainly cause respiratory and digestive tract diseases, several coronaviruses are responsible for porcine diarrhea, such as porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and emerging swine acute diarrhea syndrome coronavirus (SADS-CoV). Those viruses have caused huge economic losses and are considered as potential public health threats. Porcine torovirus (PToV) and coronaviruses, sharing similar genomic structure and replication strategy, belong to the same order Nidovirales. Here, we developed a multiplex TaqMan-probe-based real-time PCR for the simultaneous detection of PEDV, PDCoV, PToV, and SADS-CoV for the first time. Specific primers and TaqMan fluorescent probes were designed targeting the ORF1a region of PDEV, PToV, and SADS-CoV and the ORF1b region of PDCoV. The method showed high sensitivity and specificity, with a detection limit of 1 × 102 copies/μL for each pathogen. A total of 101 clinical swine samples with signs of diarrhea were analyzed using this method, and the result showed good consistency with conventional reverse transcription PCR (RT-PCR). This method improves the efficiency for surveillance of these emerging and reemerging swine enteric viruses and can help reduce economic losses to the pig industry, which also benefits animal and public health.
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Affiliation(s)
- Zhongzhou Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiaxuan Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ningning Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wan-Ting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Letian Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wen Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Bae JM, Wen X, Kim TS, Kwak Y, Cho NY, Lee HS, Kang GH. Fibroblast Growth Factor Receptor 1 (FGFR1) Amplification Detected by Droplet Digital Polymerase Chain Reaction (ddPCR) Is a Prognostic Factor in Colorectal Cancers. Cancer Res Treat 2020; 52:74-84. [PMID: 31096734 PMCID: PMC6962468 DOI: 10.4143/crt.2019.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023] Open
Abstract
PURPOSE The purpose of this study was to reveal the clinicopathological characteristics and prognostic implications associated with fibroblast growth factor receptor 1 (FGFR1) amplification in colorectal cancers (CRCs). MATERIALS AND METHODS We measured the copy number of FGFR1 by droplet digital polymerase chain reaction (ddPCR), and analyzed the FGFR1 expression by immunohistochemistry, in 764 surgically resected CRCs (SNUH2007 dataset, 384 CRCs; SNUH Folfox dataset, 380 CRCs). RESULTS CRCs with ≥ 3.3 copies of the FGFR1 gene were classified as FGFR1 amplified. FGFR1 amplification was found in 10 of the 384 CRCs (2.6%) in the SNUH2007 dataset, and in 28 of the 380 CRCs (7.4%) in the SNUH Folfox dataset. In the SNUH2007 dataset, there was no association between the FGFR1 copy number status and sex, gross appearance, stage, or differentiation. High FGFR1 expression was associated with female sex and KRAS mutation. At the molecular level, FGFR1 amplification was mutually exclusive with BRAF mutation, microsatellite instability, and MLH1 methylation, in both SNUH2007 and SNUH Folfox datasets. Survival analysis revealed that FGFR1 amplification was associated with significantly worse clinical outcome compared with no FGFR1 amplification, in both SNUH2007 and SNUH Folfox datasets. Within the SNUH2007 dataset, CRC patients with high FGFR1 expression had an inferior progression-free survival compared with those with low FGFR1 expression. The FGFR inhibitor, PD173074, repressed the proliferation of a CRC cell line overexpressing FGFR1, but not of cells with FGFR1 amplification. CONCLUSION FGFR1 amplification measured by ddPCR can be a prognostic indicator of poor clinical outcome in patients with CRCs.
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Affiliation(s)
- Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Xianyu Wen
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-Shin Kim
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Nunes BTD, de Mendonça MHR, Simith DDB, Moraes AF, Cardoso CC, Prazeres ITE, de Aquino AA, Santos ADCM, Queiroz ALN, Rodrigues DSG, Andriolo RB, Travassos da Rosa ES, Martins LC, Vasconcelos PFDC, Medeiros DBDA. Development of RT-qPCR and semi-nested RT-PCR assays for molecular diagnosis of hantavirus pulmonary syndrome. PLoS Negl Trop Dis 2019; 13:e0007884. [PMID: 31877142 PMCID: PMC6932758 DOI: 10.1371/journal.pntd.0007884] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/26/2019] [Indexed: 12/02/2022] Open
Abstract
Hantavirus Pulmonary Syndrome is an, often fatal, emerging zoonotic disease in the Americas caused by hantaviruses (family: Hantaviridae). In Brazil, hantavirus routine diagnosis is based on serology (IgM-ELISA) while RT-PCR is often used to confirm acute infection. A Semi-nested RT-PCR and an internally controlled RT-qPCR assays were developed for detection and quantification of four hantaviruses strains circulating in the Brazilian Amazon: Anajatuba (ANAJV) and Castelo dos Sonhos (CASV) strains of Andes virus (ANDV) species; and Rio Mamoré (RIOMV) and Laguna Negra (LNV) strains of LNV species. A consensus region in the N gene of these hantaviruses was used to design the primer sets and a hydrolysis probe. In vitro transcribed RNA was diluted in standards with known concentration. MS2 bacteriophage RNA was detected together with hantavirus RNA as an exogenous control in a duplex reaction. RT-qPCR efficiency was around 100% and the limit of detection was 0.9 copies/μL of RNA for RT-qPCR and 10 copies/μL of RNA for Semi-nested RT-PCR. There was no amplification of either negative samples or samples positive to other pathogens. To assess the protocol for clinical sensitivity, specificity and general accuracy values, both assays were used to test two groups of samples: one comprising patients with disease (n = 50) and other containing samples from healthy individuals (n = 50), according to IgM-ELISA results. A third group of samples (n = 27) infected with other pathogens were tested for specificity analysis. RT-qPCR was more sensitive than semi-nested RT-PCR, being able to detect three samples undetected by conventional RT-PCR. RT-qPCR clinical sensitivity, specificity and general accuracy values were 92.5%, 100% and 97.63%, respectively. Thus, the assays developed in this study were able to detect the four Brazilian Amazon hantaviruses with good specificity and sensitivity, and may become powerful tools in diagnostic, surveillance and research applications of these and possibly other hantaviruses. Hantavirus Pulmonary Syndrome (HPS) is a serious and often fatal disease caused by viruses known as hantaviruses. These viruses are harbored by wild rodents and people can become infected through contact with infected-rodents droppings, urine or saliva. After an incubation time of 1–8 weeks, patients usually present flu-like symptoms such as fever, fatigue and muscle aches, although some patients may also present headaches, dizziness, chills, nausea, vomiting, diarrhea, and abdominal pain. It is only 4–10 days after initial symptoms, however, that the severe stage of disease takes place. Symptoms include coughing, shortness of breath and eventually the lungs fill with fluid which can lead to shock and death. As such, HPS should be diagnosed quickly as any delay may have great impact on patient recovery. However, given the unspecific nature of early symptoms, clinical diagnosis of HPS is difficult and laboratory assays are needed to confirm hantavirus infection as soon as possible, helping physicians to choose the most adequate treatment. In this study, we developed new laboratory assays that can help detect the virus in infected patients in early stages of disease. In addition, we showed these assays have a good performance in discriminating HPS from other similar diseases by testing not only several samples collected from both HPS patients and healthy individuals but also samples infected with other pathogens. Our results show that these assays may become important tools for rapid, sensitive and specific diagnosis of HPS.
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Affiliation(s)
- Bruno Tardelli Diniz Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Darlene de Brito Simith
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | - Adriana Freitas Moraes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | - Carla Conceição Cardoso
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Ana Alice de Aquino
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | | | | | | | | | | | - Livia Carício Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | - Daniele Barbosa de Almeida Medeiros
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
- * E-mail:
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Ganesan A, Wells J, Shaikh F, Peterson P, Bradley W, Carson ML, Petfield JL, Klassen-Fischer M, Akers KS, Downing K, Bialek R, Tribble DR, Wickes BL. Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible with High Specificity. J Clin Microbiol 2019; 58:e01259-19. [PMID: 31619528 PMCID: PMC6935896 DOI: 10.1128/jcm.01259-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Trauma-related invasive fungal wound infections (IFIs) are associated with significant morbidity and mortality. Early identification and treatment are critical. Traditional identification methods (e.g., fungal cultures and histopathology) can be delayed and insensitive. We assessed a PCR-based sequencing assay for rapid identification of filamentous fungi in formalin-fixed paraffin-embedded (FFPE) specimens obtained from combat casualties injured in Afghanistan. Blinded FFPE specimens from cases (specimens positive on histopathology) and controls (specimens negative on histopathology) were submitted for evaluation with a panfungal PCR. The internal transcribed spacer 2 (ITS2) region of the fungal ribosomal repeat was amplified and sequenced. The PCR results were compared with findings from histopathology and/or culture. If injury sites contributed multiple specimens, findings for the site were collapsed to the site level. We included 64 case subjects (contributing 95 sites) and 102 controls (contributing 118 sites). Compared to histopathology, panfungal PCR was specific (99%), but not as sensitive (63%); however, sensitivity improved to 83% in specimens from sites with angioinvasion. Panfungal PCR identified fungi of the order Mucorales in 33 of 44 sites with angioinvasion (75%), whereas fungal culture was positive in 20 of 44 sites (45%). Saksenaea spp. were the dominant fungi identified by PCR in specimens from angioinvasion sites (57%). Panfungal PCR is specific, albeit with lower sensitivity, and performs better at identifying fungi of the order Mucorales than culture. DNA sequencing offers significant promise for the rapid identification of fungal infection in trauma-related injuries, leading to more timely and accurate diagnoses.
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Affiliation(s)
- Anuradha Ganesan
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Justin Wells
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Faraz Shaikh
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Philip Peterson
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - William Bradley
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Brooke Army Medical Center, JBSA Fort Sam Houston, Texas, USA
| | - M Leigh Carson
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | | | | | - Kevin S Akers
- U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
| | - Kevin Downing
- Landstuhl Regional Medical Center, Landstuhl, Germany
| | - Ralf Bialek
- LADR GmbH Medizinisches Versorgungszentrum Dr. Kramer und Kollegen, Geesthacht, Germany
| | - David R Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Brian L Wickes
- University of Texas Health Sciences Center at San Antonio, San Antonio, Texas, USA
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Hahn A, Schwarz NG, Frickmann H. Comparison of screening tests without a gold standard-A pragmatic approach with virtual reference testing. Acta Trop 2019; 199:105118. [PMID: 31369728 DOI: 10.1016/j.actatropica.2019.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/24/2019] [Accepted: 07/26/2019] [Indexed: 11/30/2022]
Abstract
Well-defined diagnostic gold standards are rarely available for the diagnosis of rare diseases such as some tropical infections. Algorithms for reliable test evaluation without gold standard are therefore desirable. On the basis of previous work of Gart and Buck (1966); Rogan and Gladen (1978), and Hui and Walter (1980), a modeling approach for the comparison of diagnostic tests without a gold standard - and thus without reliably characterized reference sample material - is established especially for situations not fulfilling the requirement of conditional independence of the diagnostic tests evaluated. In the approach introduced, each test is conducted within two populations with different values of prevalence and the test results are used to define two virtual reference tests. The model is useful for the comparison of tests for rare tropical diseases where no gold standard can be provided.
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Affiliation(s)
- Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057 Rostock, Germany
| | - Norbert Georg Schwarz
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057 Rostock, Germany; Department of Microbiology and Hygiene, Bundeswehr Hospital Hamburg, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany.
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Santaus TM, Li S, Saha L, Chen WH, Bhagat S, Stine OC, Geddes CD. A comparison of Lyse-It to other cellular sample preparation, bacterial lysing, and DNA fragmentation technologies. PLoS One 2019; 14:e0220102. [PMID: 31335892 PMCID: PMC6650070 DOI: 10.1371/journal.pone.0220102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023] Open
Abstract
The ability for safe and rapid pathogenic sample transportation and subsequent detection is an increasing challenge throughout the world. Herein, we describe and use bead-beating, vortex, sonication, 903 protein saver cards, and Lyse-It methods, aiming to inactivate Gram-positive and -negative bacteria with subsequent genome DNA (quantitative Polymerase Chain Reaction) qPCR detection. The basic concepts behind the four chosen technologies is their versatility, cost, and ease of use in developed and underdeveloped countries. The four methods target the testing of bacterial resilience, cellular extraction from general and complex media and subsequent DNA extraction for qPCR detection and amplification. These results demonstrate that conventional high temperature heating, 903 protein saver cards, and Lyse-It are all viable options for inactivating bacterial growth for safe shipping. Additionally, Lyse-It was found to be particularly useful as this technology can inactivate bacteria, extract cells from 903 protein saver cards, lyse bacterial cells, and additionally keep genomic DNA viable for qPCR detection.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Shan Li
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Lahari Saha
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Siya Bhagat
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - O. Colin Stine
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- * E-mail:
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Sze MA, Schloss PD. The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data. mSphere 2019; 4:e00163-19. [PMID: 31118299 PMCID: PMC6531881 DOI: 10.1128/msphere.00163-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e., bias). We compared the performance of high fidelity polymerases and various numbers of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments' fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with the number of rounds of PCR. This bias was inconsistent for human stool samples. Overall, the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.IMPORTANCE A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples; however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.
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Affiliation(s)
- Marc A Sze
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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Zhao S, Cui Y, Jing J, Yan Y, Peng Y, Shi K, Wang K, Zhou Y, Jian F, Zhang L, Wang R, Ning C. Rapid and sensitive detection of Anaplasma phagocytophilum using a newly developed recombinase polymerase amplification assay. Exp Parasitol 2019; 201:21-25. [PMID: 31029698 DOI: 10.1016/j.exppara.2019.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/10/2019] [Accepted: 04/24/2019] [Indexed: 01/12/2023]
Abstract
Anaplasma phagocytophilum, the bacterial pathogen responsible for tick-borne fever and human granulocytic anaplasmosis, can seriously affect the health of humans and a wide range of other mammals. In this study, we developed a recombinase polymerase amplification (RPA) assay to detect A. phagocytophilum in clinical samples. Following alignment of the relevant DNA sequences, a pair of specific primers based on the 16S rRNA gene was designed to specifically detect A. phagocytophilum. The assay was performed at a constant temperature of 38 °C for 30 min, with a final primer concentration of 0.4 μM. The specificity of the primers was confirmed when DNA from A. phagocytophilum was used as the positive control, and DNA from other related pathogens were used as the negative controls, with ddH2O acting as the blank control. The results showed that the primers did not cross-react with DNA from the other related pathogens. The assay's detection limit was 1.77 × 10-5 ng/μl, a 10 × higher sensitivity level than that determined for nested PCR. The RPA assay's performance was evaluated using 44 clinical samples, and the prevalence results for A. phagocytophilum were found to not differ significantly between the RPA assay and the nested PCR. Thus, we have developed a specific, sensitive, rapid and cost-effective RPA method, requiring only a water bath, for the detection of A. phagocytophilum. The assay should be especially useful in resource-limited areas where access to laboratory equipment is limited.
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Affiliation(s)
- Shanshan Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Yanyan Cui
- School of Biotechnology and Food, Shangqiu Normal University, Wenhua Road 298, Shangqiu, 476000, PR China
| | - Jichun Jing
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Yaqun Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Yongshuai Peng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Ke Shi
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Kunlun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Yongchun Zhou
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Fuchun Jian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China
| | - Changshen Ning
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Longzihu Campus of Henan Agricultural University, No. 15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, PR China.
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Ma X, Shao Y, Tian L, Flasch DA, Mulder HL, Edmonson MN, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison LL, Levy S, Easton J, Zhang J. Analysis of error profiles in deep next-generation sequencing data. Genome Biol 2019; 20:50. [PMID: 30867008 PMCID: PMC6417284 DOI: 10.1186/s13059-019-1659-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/19/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions. RESULTS By evaluating read-specific error distributions, we discover that the substitution error rate can be computationally suppressed to 10-5 to 10-4, which is 10- to 100-fold lower than generally considered achievable (10-3) in the current literature. We then quantify substitution errors attributable to sample handling, library preparation, enrichment PCR, and sequencing by using multiple deep sequencing datasets. We find that error rates differ by nucleotide substitution types, ranging from 10-5 for A>C/T>G, C>A/G>T, and C>G/G>C changes to 10-4 for A>G/T>C changes. Furthermore, C>T/G>A errors exhibit strong sequence context dependency, sample-specific effects dominate elevated C>A/G>T errors, and target-enrichment PCR led to ~ 6-fold increase of overall error rate. We also find that more than 70% of hotspot variants can be detected at 0.1 ~ 0.01% frequency with the current NGS technology by applying in silico error suppression. CONCLUSIONS We present the first comprehensive analysis of sequencing error sources in conventional NGS workflows. The error profiles revealed by our study highlight new directions for further improving NGS analysis accuracy both experimentally and computationally, ultimately enhancing the precision of deep sequencing.
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Affiliation(s)
- Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Diane A. Flasch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Heather L. Mulder
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Michael N. Edmonson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
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Khaltabadi RF, Shahrokhi N, Ebrahimi-Rad M, Ehsani P. Salmonella Typhimurium in Iran: Contribution of molecular and IS200 PCR methods in variants detection. PLoS One 2019; 14:e0213726. [PMID: 30865712 PMCID: PMC6415898 DOI: 10.1371/journal.pone.0213726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/27/2019] [Indexed: 11/23/2022] Open
Abstract
Salmonella Typhimurium, a zoonotic pathogen, is regarded as a major health and economic concern worldwide. Recently, monophasic variants of this serovar have been significantly associated with human gastroenteritis outbreaks globally, making its accurate identification essential for epidemiological and control purposes. We have identified and analyzed 150 S. Typhimurium from 884 Salmonella genus isolated from humans, domestic animals, poultry, food items and abattoirs origins. The Salmonella isolates were obtained from Iranian National Veterinary Reference Laboratories of 9 provinces during 2007–2016, and from five hospitals in Tehran in 2015. The isolates were evaluated biochemically, serologically, and by PCR amplification of invA, mdh, STM4492, fliC, fljA, fljB, hin genes, IS200 and DT104. invA and mdh genes were used to confirm the S. Typhimurium serotype, fliC and fljB genes for determination of monophasic variants and amplification of IS200 to discriminate the monophasic variants from the closely related serotypes. We identified 78.6% (118/150) as classical S. Typhimurium (fliC, fljB and IS200 positive), 12.6% (19/150) were IS200 negative from all isolates. DT104 is another marker for S.Typhimurium serovar typing. Contrary to EFSA guidelines 20.6% (19/29) of human isolates that lacked IS200 insertion sequence, were confirmed as S.Typhimurium. Compared to the North American/European isolates the low prevalence of fljB negative 6% (9/150) and the high abundance of fliC negative 23.3% (35/150) isolates also were indicative of a different regional atypical population. Studies have shown that the prevalence of monophasic (fljB-) S. Typhimurium worldwide is promoted by the Swine industry. Thus, one reason for this high number of different atypical strains could be inhibition of swine breeding system (house hold and industry) in Iran. These results demonstrate a need for a modified identifying protocol to overcome the regional differences.
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Affiliation(s)
- Reza Farahani Khaltabadi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Biology, National Veterinary Reference Laboratory, Iranian Veterinary Organization, Tehran, Iran
| | - Nader Shahrokhi
- Department of Molecular Biology, National Veterinary Reference Laboratory, Iranian Veterinary Organization, Tehran, Iran
| | | | - Parastoo Ehsani
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
- * E-mail:
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Kracík M. [First experiences with detection of the tcdB gene of Clostridioides difficile using Simplexa C. difficile Direct Kit]. Klin Mikrobiol Infekc Lek 2019; 25:12-15. [PMID: 31266088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Clostridioides difficile (formerly Clostridium difficile) is one of the main pathogens causing nosocomial infections today. It colonizes the intestines of patients receiving antibiotic therapy, causing unpleasant or even life-threatening conditions (diarrhea, toxic megacolon). Rapid and correct detection of strain toxigenicity is essential for treatment and isolation of patients. Simplexa C. difficile Direct Kit is a real-time PCR kit detecting the tcdB gene of C. difficile. The kit does not require DNA isolation; stool eluates are directly used for the reaction. The study aimed to verify the analytical properties of the kit by its comparison with culture and in-house multiplex PCR methods. MATERIAL AND METHODS A total of 164 stool samples were prospectively tested using two immunoenzymatic kits (C. diff Quik Chek Complete and LIAISON C. difficile GDH, Toxins AandB). In 39 samples, the results were discrepant or unclear (GDH+TOX-). These samples were tested using in-house multiplex PCR and the Simplexa kit. RESULTS The Simplexa kit had 94.7% sensitivity, 100% specificity, 100% positive predictive value and 95.2% negative predictive value. These parameters were calculated from the numbers of true-/false-positive and true-/false-negative results. True results were determined based on the consensus of culture and in-house multiplex PCR results. Another outcome of the study was comparison of the Quik Chek and LIAISON kits. CONCLUSION The analytical properties of the Simplexa kit were tested on 39 samples. These samples were selected for their unclear (GDH+TOX-) or discrepant results yielded by immunoenzymatic methods. Compared with culture and subsequent in-house PCR detection of the tcdB gene, the Simplexa kit showed properties declared by the manufacturer. An important advantage of the kit was the absence inhibitions when stool eluates were directly used for PCR reactions.
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Affiliation(s)
- Martin Kracík
- Department of Clinical Microbiology and Immunology, Regional Hospital Liberec, Faculty of Medicine in Hradec Králové, Charles University, Czech Republic, e-mail:
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Tommasi S, Pilato B, Carella C, Lasorella A, Danza K, Vallini I, De Summa S, Naglieri E. Standardization of CTC AR-V7 PCR assay and evaluation of its role in castration resistant prostate cancer progression. Prostate 2019; 79:54-61. [PMID: 30141201 DOI: 10.1002/pros.23710] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/06/2018] [Indexed: 11/11/2022]
Abstract
BACKGROUND Castration resistant prostate cancer (CRPC) represents the most aggressive status of this neoplastic disease, also characterized by the absence of biomarkers predictive of clinical outcome. New drugs as abiraterone or enzalutamide, affecting androgen receptor pathway at different levels, inhibit the proliferative advantage of prostate cancer cells with important long term benefits. Despite the advantages of this second-generation androgen deprivation therapy (ADT), resistance mechanisms, primitive or acquired, often develop. The existence of androgen receptor (AR) splice variants (AR-Vs), in particular AR-V7 expression detected in circulating tumor cells (CTCs), represents an example of acquired resistance, as evidenced in preclinical and clinical studies. Recent studies also have suggested the role of AR-V7 as a prognostic biomarker in mCRPC. In this field, hot topics are the methodology used to isolate CTC and the assay for AR-V7 measurement. Our study aims to develop a standardized operating procedure (SOP) to evaluate AR-V7 in CRPC. METHOD The application of a realized cell based Reference Sample as Standardized Quality Control tool for CTC-AR-V7 assay has been shown. Then the development, the performance evaluation and contextualization in a clinical setting of this standardized operating procedure (SOP) have been reported to evaluate the prognostic biomarker AR-V7 in metastatic prostate cancer. RESULTS AND CONCLUSIONS The standardized procedure has high sensitivity and specificity and enables the detection and quantification of the spliced variant with respect to the full length AR (AR-FL) mRNA in CTC DNA purified from the blood of patients with CRPC. This procedure has been further validated in a consecutive series of patients with mCRPC, confirming its role as prognostic biomarker.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Cell Line, Tumor
- Disease Progression
- Follow-Up Studies
- Humans
- Male
- Middle Aged
- Neoplastic Cells, Circulating/metabolism
- Polymerase Chain Reaction/standards
- Prostatic Neoplasms, Castration-Resistant/blood
- Prostatic Neoplasms, Castration-Resistant/diagnosis
- Prostatic Neoplasms, Castration-Resistant/genetics
- Protein Isoforms/blood
- Protein Isoforms/genetics
- Receptors, Androgen/blood
- Receptors, Androgen/genetics
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Affiliation(s)
- Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Brunella Pilato
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Claudia Carella
- Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Antonia Lasorella
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
- Bird srl, R&D Facility, Rezzato, Italy
| | - Katia Danza
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | | | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Emanuele Naglieri
- Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
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Oh S, Kim J, Park S, Kim S, Lee K, Lee YH, Lim SK, Lee H. Prediction of Y haplogroup by polymerase chain reaction-reverse blot hybridization assay. Genes Genomics 2018; 41:297-304. [PMID: 30456526 DOI: 10.1007/s13258-018-0761-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/30/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND The analysis of Y-SNPs from crime scene samples is helpful for investigators in narrowing down suspects by predicting biogeographical ancestry. OBJECTIVE In this study, a PCR-reverse blot hybridization assay (REBA) for predicting Y-chromosome haplogroups was employed to determine the major haplogroups worldwide, including AB, DE, C, C3, F, K, NO, O, O2, and O3 and evaluated. METHODS The REBA detects nine biallelic Y chromosome markers (M9, M89, M122, M145, M175, M214, M217, P31, and RPS4Y711) simultaneously using multiple probes. RESULTS The REBA for Y-single nucleotide polymorphisms (SNP) genotyping was performed using 40 DNA samples from Asians-14 Koreans, 10 Indonesians, six Chineses, six Thais, and four Mongolians. 40 Asian samples were identified as haplogroup O2 (40%), O3 (32.5%), C3 (17.5%), O (7.5%) and K (2.5%). These cases were confirmed by DNA sequence analysis (κ = 1.00; P < 0.001). CONCLUSION PCR-REBA is a rapid and reliable method that complements other SNP detection methods. Therefore, implementing REBA for Y-SNP testing may be a useful tool in predicting Y-chromosome haplogroups.
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Affiliation(s)
- Sehee Oh
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do, 26493, Republic of Korea
- Forensic DNA Division, National Forensic Service, 10 Ipchun-ro, Wonju, Gangwon, Republic of Korea
| | - Jungho Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do, 26493, Republic of Korea
| | - Sunyoung Park
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do, 26493, Republic of Korea
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do, 26493, Republic of Korea
| | - Kyungmyung Lee
- Forensic DNA Division, National Forensic Service, 10 Ipchun-ro, Wonju, Gangwon, Republic of Korea
| | - Yang-Han Lee
- Forensic DNA Division, National Forensic Service, 10 Ipchun-ro, Wonju, Gangwon, Republic of Korea
| | - Si-Keun Lim
- Forensic DNA Division, National Forensic Service, 10 Ipchun-ro, Wonju, Gangwon, Republic of Korea.
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do, 26493, Republic of Korea.
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Pandith A, Koo J, Seo YJ. Daphnetin: A novel blue-green photonic switch for disodium phosphates that allows monitoring of polymerase chain reactions. Spectrochim Acta A Mol Biomol Spectrosc 2018; 204:620-628. [PMID: 29980064 DOI: 10.1016/j.saa.2018.06.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/15/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
This paper describes the very simple and robust ratiometric photonic switching properties of daphnetin (DP) toward HPO42- ions selectively in complex biological fluids, without any interference from other relevant anions under physiological conditions. The sensing ability of DP toward HPO42- ions was first demonstrated using UV-Vis and fluorescence spectroscopy, dynamic light scattering (DLS), and one- and two-dimensional NMR spectroscopy. DP can detect HPO42- ions at concentrations up to the sub-micromolar/nanomolar level very effectively, with a ratiometric response resulting from intramolecular charge transfer aided by aggregated-induced emission. The interactions between DP and HPO42- ions resulted in new bands appearing in the UV-Vis (at 385 nm) and emission (at 535 nm) spectra. The noncovalently held HPO42- ions induced pronounced specific aggregation of DP molecules, resulting in the new excimer band at 535 nm while retaining the monomer band centered at 445 nm. In contrast, reciprocal absorptivity changes were observed at 320 and 385 nm, with exponential decrements and increments, respectively. This probe could effectively monitor the consumption of dNTPs during various cycles of the polymerase chain reaction performed with relatively short oligonucleotides as well as genomic DNA from Agrobacterium tumefaciens (AcH5α strain).
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Affiliation(s)
- Anup Pandith
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea.
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Furtado LFV, Magalhães JGS, Rabelo ÉML. Standardization and application of a modified RFLP-PCR methodology for analysis of polymorphisms linked to treatment resistance in Ancylostoma braziliense. Parasit Vectors 2018; 11:540. [PMID: 30301454 PMCID: PMC6178248 DOI: 10.1186/s13071-018-3125-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) in codons 167, 198 and 200 of the beta-tubulin isotype 1 gene are associated with benzimidazoles resistance in many helminths. Codon 167 mutation has never been described in hookworms; however, polymorphisms in codons 198 and 200 have been described for Ancylostoma caninum and Necator americanus. These mutations have never been investigated in Ancylostoma braziliense; therefore, it is not known if they are present in this species and whether they are correlated with treatment resistance. The RFLP-PCR technique has been used to analyze these polymorphisms in some nematodes, but depending on the species, these alterations do not create or eliminate any restriction enzyme cleavage site, making it impossible to use this technique. Here, we describe the standardization and application of a modified RFLP-PCR technique for detecting polymorphisms in individual A. braziliense worms recovered from naturally infected dogs in two Brazilian states. RESULTS The molecular techniques used were sensitive, specific, and easy to apply. To our knowledge, we report for the first time the presence of a polymorphism at codon 198 of the beta-tubulin gene of A. braziliense (1/81; 95% CI: 0-3.69%). CONCLUSIONS It is not known whether the presence of the mutation in codon 198 of the beta-tubulin gene of A. braziliense has importance for this parasite. However, based on studies of other helminths, it is possible that this polymorphism is directly related to the resistance to benzimidazoles. This may be a major concern, since this nematode has considerable relevance as a parasite of canids and felids and as one of the agents of cutaneous larva migrans in humans. Standardized methodologies will be useful for screening for polymorphisms in the beta-tubulin gene of canine hookworms in a broader population. The method could also be adapted for the analysis of other SNPs in other nematode species.
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Affiliation(s)
- Luis Fernando Viana Furtado
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais CEP 31270-901 Brazil
| | - João Guilherme Scarpelli Magalhães
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais CEP 31270-901 Brazil
| | - Élida Mara Leite Rabelo
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais CEP 31270-901 Brazil
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Sambo F, Finotello F, Lavezzo E, Baruzzo G, Masi G, Peta E, Falda M, Toppo S, Barzon L, Di Camillo B. Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene. BMC Bioinformatics 2018; 19:343. [PMID: 30268091 PMCID: PMC6162885 DOI: 10.1186/s12859-018-2360-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 09/09/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. RESULTS We propose here a computational method for optimizing the choice of primer sets, based on multi-objective optimization, which simultaneously: 1) maximizes efficiency and specificity of target amplification; 2) maximizes the number of different bacterial 16S sequences matched by at least one primer; 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?q=Software#mopo16S . CONCLUSIONS Results show that our strategy is able to find better primer pairs than the ones available in the literature according to all three optimization criteria. We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers.
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Affiliation(s)
- Francesco Sambo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elektra Peta
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Marco Falda
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
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Waldo JT, Pereira M, Rahman M, Siconolfi J. Development and validation of an undergraduate laboratory activity exploring the dna analysis of pet food. Biochem Mol Biol Educ 2018; 46:536-546. [PMID: 30369033 DOI: 10.1002/bmb.21165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
A novel experiment has been developed with a goal of enhancing engagement and deepening understanding of fundamental molecular biology concepts. In this laboratory activity, students investigate the composition of pet foods through quantitative polymerase chain reaction (qPCR) analysis. By conducting this experiment, students address a scientific question that has the potential to be of personal interest and they gain an appreciation of the power of genetic analysis. To develop this activity, ingredient lists of popular pet foods were surveyed and eight different components were selected to be the subject of inquiry. Reaction conditions for qPCR were validated and optimized, and a simple, efficient, and student-friendly protocol was developed. A cohort of upper-level biology students extracted DNA from pet foods and conducted the qPCR reactions. Specificity of amplification was determined by conducting melting point analysis and agarose gel electrophoresis of the products. Student reactions were analyzed and efficacy of this approach for deepening understanding of fundamental biochemical and molecular biology concepts was documented. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):536-546, 2018.
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Affiliation(s)
- Jennifer Turner Waldo
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Melanie Pereira
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Mohammad Rahman
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Jessica Siconolfi
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
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Abstract
Forensic biology is a sub-discipline of biological science with an amalgam of other branches of science used in the criminal justice system. Any nucleated cell/tissue harbouring DNA, either live or dead, can be used as forensic exhibits, a source of investigation through DNA typing. These biological materials of human origin are rich source of proteins, carbohydrates, lipids, trace elements as well as water and, thus, provide a virtuous milieu for the growth of microbes. The obstinate microbial growth augments the degradation process and is amplified with the passage of time and improper storage of the biological materials. Degradation of these biological materials carriages a huge challenge in the downstream processes of forensic DNA typing technique, such as short tandem repeats (STR) DNA typing. Microbial degradation yields improper or no PCR amplification, heterozygous peak imbalance, DNA contamination from non-human sources, degradation of DNA by microbial by-products, etc. Consequently, the most precise STR DNA typing technique is nullified and definite opinion can be hardly given with degraded forensic exhibits. Thus, suitable precautionary measures should be taken for proper storage and processing of the biological exhibits to minimize their decaying process by micro-organisms.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, Madhya Pradesh, 470001, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Rourkela, Odisha, 769008, India.
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