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Application of chain transfer agents in the two-part dispersion polymerization of cross-linked polymer microspheres. Colloid Polym Sci 2021. [DOI: 10.1007/s00396-021-04843-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Natoli ME, Chang MM, Kundrod KA, Coole JB, Airewele GE, Tubman VN, Richards-Kortum RR. Allele-Specific Recombinase Polymerase Amplification to Detect Sickle Cell Disease in Low-Resource Settings. Anal Chem 2021; 93:4832-4840. [PMID: 33689292 PMCID: PMC7992048 DOI: 10.1021/acs.analchem.0c04191] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sickle cell disease (SCD) is a group of common, life-threatening disorders caused by a point mutation in the β globin gene. Early diagnosis through newborn and early childhood screening, parental education, and preventive treatments are known to reduce mortality. However, the cost and complexity of conventional diagnostic methods limit the feasibility of early diagnosis for SCD in resource-limited areas worldwide. Although several point-of-care tests are commercially available, most are antibody-based tests, which cannot be used in patients who have recently received a blood transfusion. Here, we describe the development of a rapid, low-cost nucleic acid test that uses real-time fluorescence to detect the point mutation encoding hemoglobin S (HbS) in one round of isothermal recombinase polymerase amplification (RPA). When tested with a set of clinical samples from SCD patients and healthy volunteers, our assay demonstrated 100% sensitivity for both the βA globin and βS globin alleles and 94.7 and 97.1% specificities for the βA globin allele and βS globin allele, respectively (n = 91). Finally, we demonstrate proof-of-concept sample-to-answer genotyping of genomic DNA from capillary blood using an alkaline lysis procedure and direct input of diluted lysate into RPA. The workflow is performed in <30 min at a cost of <$5 USD on a commercially available benchtop fluorimeter and an open-source miniature fluorimeter. This study demonstrates the potential utility of a rapid, sample-to-answer nucleic acid test for SCD that may be implemented near the point of care and could be adapted to other disease-causing point mutations in genomic DNA.
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Affiliation(s)
- Mary E Natoli
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Gladstone E Airewele
- Texas Children's Cancer and Hematology Centers, Houston, Texas 77030, United States.,Baylor College of Medicine, Houston, Texas 77030, United States
| | - Venée N Tubman
- Texas Children's Cancer and Hematology Centers, Houston, Texas 77030, United States.,Baylor College of Medicine, Houston, Texas 77030, United States
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Evaluation of Rapid Extraction Methods Coupled with a Recombinase Polymerase Amplification Assay for Point-of-Need Diagnosis of Post-Kala-Azar Dermal Leishmaniasis. Trop Med Infect Dis 2020; 5:tropicalmed5020095. [PMID: 32517156 PMCID: PMC7344569 DOI: 10.3390/tropicalmed5020095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 11/23/2022] Open
Abstract
To detect Post-kala-azar leishmaniasis (PKDL) cases, several molecular methods with promising diagnostic efficacy have been developed that involve complicated and expensive DNA extraction methods, thus limiting their application in resource-poor settings. As an alternative, we evaluated two rapid DNA extraction methods and determined their impact on the detection of the parasite DNA using our newly developed recombinase polymerase amplification (RPA) assay. Skin samples were collected from suspected PKDL cases following their diagnosis through national guidelines. The extracted DNA from three skin biopsy samples using three different extraction methods was subjected to RPA and qPCR. The qPCR and RPA assays exhibited highest sensitivities when reference DNA extraction method using Qiagen (Q) kit was followed. In contrast, the sensitivity of the RPA assay dropped to 76.7% and 63.3%, respectively, when the boil & spin (B&S) and SpeedXtract (SE) rapid extraction methods were performed. Despite this compromised sensitivity, the B&S-RPA technique yielded an excellent agreement with both Q-qPCR (k = 0.828) and Q-RPA (k = 0.831) techniques. As expected, the reference DNA extraction method was found to be superior in terms of diagnostic efficacy. Finally, to apply the rapid DNA extraction methods in resource-constrained settings, further methodological refinement is warranted to improve DNA yield and purity through rigorous experiments.
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Nour M, Alaidarous A. Clinical usefulness and accuracy of polymerase chain reaction in the detection of bacterial meningitis agents in pediatric cerebrospinal fluid. Curr Res Transl Med 2018; 66:15-18. [PMID: 29456197 DOI: 10.1016/j.retram.2018.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/11/2017] [Accepted: 01/05/2018] [Indexed: 11/25/2022]
Abstract
Bacterial meningitis poses enormous healthcare challenges due to a high mortality, morbidity and sequelae. Neisseria (N.) meningitidis, Haemophilus (H.) influenzae, Streptococcus (S.) pneumoniae and S. agalactiae remain among the most prevalent infectious agents that cause bacterial meningitis in children. The objective of this study was the simultaneous detection of these pathogens in suspected cerebrospinal fluid (CSF) by using multiplex polymerase chain reaction (mPCR) and compare PCR results with standard diagnostics currently used in clinical practice. CSF specimens were obtained from 515 children (<5 years) clinically suspected of having acute bacterial meningitis. Based on bacterial culture, four isolates of salmonella sp and one Citrobacter freundii isolate were identified. The remaining 510 CSF specimens, having negative culture, were subjected to mPCR. Twenty-three (4.51%) CSF samples yielded a PCR positive signal. The pathogens identified were: S. pneumoniae (n=13), H. influenzae (n=7) and N. meningitidis (n=3). S. agalactiae was not detected. Using sequential multiplex PCR, serogrouping of S. pneumoniae revealed 3 different serotypes: serotype 19A (n=6), 19F (n=4) and serotype 23F (n=3). Only the serotype A was identified for the 3N. meningitidis isolates. Despite vaccination, S. pneumoniae remains a leading cause of pediatric invasive disease. Detecting causative organism remains the most critical aspect for management of children with suspected meningitis. PCR method is more sensitive and rapid than culture for detecting the infectious agents. Institution of PCR diagnostics is recommended for early and appropriate therapy.
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Affiliation(s)
- M Nour
- Department of biology, faculty of science, Taif university, KSA, 21974 Taif-Al-Haweiah, Saudi Arabia; Department of biology, high institute of biotechnology, Monastir university, Tahar-Haddad Street, 5000 Monastir, Tunisia.
| | - A Alaidarous
- Department of biology, faculty of science, Taif university, KSA, 21974 Taif-Al-Haweiah, Saudi Arabia
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Comparison of three methods for recovery of Brucella canis DNA from canine blood samples. J Microbiol Methods 2017; 143:26-31. [PMID: 28864247 DOI: 10.1016/j.mimet.2017.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/22/2022]
Abstract
Brucella canis, a gram-negative, facultative intracellular and zoonotic bacterium causes canine brucellosis. Direct methods are the most appropriate for the detection of canine brucellosis and bacterial isolation from blood samples has been employed as gold-standard method. However, due to the delay in obtaining results and the biological risk of the bacterial culturing, the polymerase chain reaction (PCR) has been successfully used as an alternative method for the diagnosis of the infection. Sample preparation is a key step for successful PCR and protocols that provide high DNA yield and purity are recommended to ensure high diagnostic sensitivity. The objective of this study was to evaluate the performance of PCR for the diagnosis of B. canis infection in 36 dogs by testing DNA of whole blood obtained through different extraction and purification protocols. Methods 1 and 2 were based on a commercial kit, using protocols recommended for DNA purification of whole blood and tissue samples, respectively. Method 3 was an in-house method based on enzymatic lysis and purification using organic solvents. The results of the PCR on samples obtained through three different DNA extraction protocols were compared to the blood culture. Of the 36 dogs, 13 (36.1%) were positive by blood culturing, while nine (25.0%), 14 (38.8%), and 15 (41.6%) were positive by PCR after DNA extraction using methods 1, 2 and 3, respectively. PCR performed on DNA purified by Method 2 was as efficient as blood culturing and PCR performed on DNA purified with in-house method, but had the advantage of being less laborious and, therefore, a suitable alternative for the direct B. canis detection in dogs.
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McKenna JP, Cox C, Fairley DJ, Burke R, Shields MD, Watt A, Coyle PV. Loop-mediated isothermal amplification assay for rapid detection of Streptococcus agalactiae (group B streptococcus) in vaginal swabs - a proof of concept study. J Med Microbiol 2017; 66:294-300. [PMID: 28126051 DOI: 10.1099/jmm.0.000437] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Neonatal sepsis caused by Streptococcus agalactiae [group B streptococcus (GBS)] is a life-threatening condition, which is preventable if colonized mothers are identified and given antibiotic prophylaxis during labour. Conventional culture is time consuming and unreliable, and many available non-culture diagnostics are too complex to implement routinely at point of care. Loop-mediated isothermal amplification (LAMP) is a method that, enables the rapid and specific detection of target nucleic acid sequences in clinical materials without the requirement for extensive sample preparation. METHODOLOGY A prototype LAMP assay targeting GBS sip gene is described. RESULTS The assay was 100 % specific for GBS, with a limit of detection of 14 genome copies per reaction. The clinical utility of the LAMP assay for rapid direct molecular detection of GBS was determined by testing a total of 157 vaginal swabs with minimal sample processing using a rapid lysis solution. Compared to a reference quantitative real-time PCR assay, the direct LAMP protocol had a sensitivity and specificity of 95.4 and 100 %, respectively, with positive and negative predictive values of 100 and 98.3 %, respectively. Positive and negative likelihood ratios were infinity and 0.05, respectively. The direct LAMP method required a mean time of 45 min from the receipt of a swab to generation of a confirmed result, compared to 2 h 30 min for the reference quantitative real-time PCR test. CONCLUSION The direct LAMP protocol described is easy to perform, facilitating rapid and accurate detection of GBS in vaginal swabs. This test has a potential for use at point of care.
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Affiliation(s)
- James Patrick McKenna
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Ciara Cox
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Derek John Fairley
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Rachael Burke
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK.,Centre for Experimental Medicine, Queens University Belfast, Belfast, UK
| | - Michael D Shields
- Centre for Experimental Medicine, Queens University Belfast, Belfast, UK.,Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK
| | - Alison Watt
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Peter Valentine Coyle
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
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Morrissey SM, Nielsen M, Ryan L, Al Dhanhani H, Meehan M, McDermott S, O'Sullivan N, Doyle M, Gavin P, O'Sullivan N, Cunney R, Drew RJ. Group B streptococcal PCR testing in comparison to culture for diagnosis of late onset bacteraemia and meningitis in infants aged 7-90 days: a multi-centre diagnostic accuracy study. Eur J Clin Microbiol Infect Dis 2017; 36:1317-1324. [PMID: 28247153 DOI: 10.1007/s10096-017-2938-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/08/2017] [Indexed: 12/15/2022]
Abstract
The aim of this study was to compare an in-house real-time PCR assay, with bacterial culture as the reference, for the diagnosis of late onset group B Streptococcal (GBS) disease. This was a retrospective review. All children aged 7-90 days presenting to four paediatric centres that had a blood or CSF sample tested by GBS PCR were included. Of 7,686 blood and 2,495 cerebrospinal fluid (CSF) samples from patients of all ages received for PCR testing, 893 and 859 samples were eligible for the study, respectively. When compared to culture, the sensitivity of blood PCR was 65% (13/20) in comparison to the CSF PCR test which was 100% (5/5). Ten of 23 PCR-positive blood samples and 17 of 22 PCR-positive CSF samples were culture negative. The median threshold Ct values for culture-positive/PCR-positive CSF samples was lower than that of culture-negative/PCR-positive CSF samples (p = 0.08). Clinical details of 17 available cases that were culture negative/PCR positive were reviewed; seven were deemed to be definite cases, eight were probable and two were possible. The results showed that detection of GBS by PCR is useful for CSF samples from infants aged 7-90 days with suspected meningitis; however, analysis of blood samples by PCR is of limited value as a routine screening test for late onset GBS sepsis and should not replace bacterial culture.
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Affiliation(s)
- S M Morrissey
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - M Nielsen
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - L Ryan
- Department of Microbiology, University Hospital Waterford, Co. Waterford, Ireland
| | - H Al Dhanhani
- Departments of Microbiology and Paediatric Infectious Diseases, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - M Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - S McDermott
- Department of Microbiology, Our Lady's Hospital, Co. Louth, Drogheda, Ireland
| | - N O'Sullivan
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - M Doyle
- Department of Microbiology, University Hospital Waterford, Co. Waterford, Ireland
| | - P Gavin
- Departments of Microbiology and Paediatric Infectious Diseases, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - N O'Sullivan
- Departments of Microbiology and Paediatric Infectious Diseases, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - R Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - R J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland. .,Department of Microbiology, Rotunda Hospital, Dublin 1, Ireland. .,Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 2, Ireland. .,Rotunda Hospital, Parnell Square, Dublin 1, Ireland.
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