1
|
Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
Collapse
Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
2
|
Bazzo ML, Machado HDM, Martins JM, Schörner MA, Buss K, Barazzetti FH, Gaspar PC, Bigolin A, Benzaken A, de Carvalho SVF, Andrade LDF, Ferreira WA, Figueiroa F, Fontana RM, da Silva MFDCR, Silva RJC, Aires Junior LF, Neves LADS, Miranda AE, Network BG. Aetiological molecular identification of sexually transmitted infections that cause urethral discharge syndrome and genital ulcer disease in Brazilian men: a nationwide study. Sex Transm Infect 2024; 100:133-137. [PMID: 38360847 DOI: 10.1136/sextrans-2023-055950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/13/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Little is known about the aetiology of urethral discharge syndrome (UDS) and genital ulcer disease (GUD) in Brazil due to limited access to laboratory tests and treatment based mainly on the syndromic approach. OBJECTIVES To update Brazilian treatment guidelines according to the current scenario, the first nationwide aetiological study for UDS and GUD was performed. METHODS Male participants with urethral discharge (UD) and/or genital ulcer (GU) reports were enrolled. Sample collection was performed by 12 sentinel sites located in the five Brazilian regions. Between 2018 and 2020, 1141 UD and 208 GU samples were collected in a Universal Transport Medium-RT (Copan). A multiplex quantitative PCR kit (Seegene) was used to detect UD: Chlamydia trachomatis (CT), Mycoplasma genitalium (MG), M. hominis (MH), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), Ureaplasma parvum (UP), U. urealyticum (UU) and another kit to detect GU: cytomegalovirus (CMV), Haemophilus ducreyi (HD), herpes simplex virus type 1 (HSV1), herpes simplex virus type 2 (HSV2), lymphogranuloma venereum (LGV), Treponema pallidum (TP) and varicella-zoster virus (VZV). RESULTS In UD samples, the frequency of pathogen detection was NG: 78.38%, CT: 25.6%, MG: 8.3%, UU: 10.4%, UP: 3.5%, MH: 3.5% and TV: 0.9%. Coinfection was assessed in 30.9% of samples, with 14.3% of NG/CT coinfection. The most frequent pathogen identified in GU was HSV2, present in 40.8% of the samples, followed by TP at 24.8%, LGV and CMV at 1%, and HSV1 at 0.4%. Coinfection of TP/HSV2 was detected in 4.4% of samples. VZV and HD were not detected. In 27.7% of the GU samples, no pathogen was detected. CONCLUSION This study provided the acquisition of unprecedented data on the aetiology of UDS and GUD in Brazil, demonstrated the presence of a variety of pathogens in both sample types and reaffirmed the aetiologies known to be most prevalent globally.
Collapse
Affiliation(s)
- Maria Luiza Bazzo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Hanalydia de Melo Machado
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Jessica Motta Martins
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Marcos André Schörner
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Ketlyn Buss
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Fernando Hartmann Barazzetti
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Pharmacy Post Graduate Program, Molecular Biology, Microbiology and Serology Laboratory-LBMMS, Florianópolis, Brazil
| | - Pamela Cristina Gaspar
- Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis, Secretariat of Health Surveillance, Ministry of Health, Brasília, Distrito Federal, Brazil
| | - Alisson Bigolin
- Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis, Secretariat of Health Surveillance, Ministry of Health, Brasília, Distrito Federal, Brazil
| | - Adele Benzaken
- Leônidas e Maria Deane Institute Fiocruz Amazonas, Manaus, Amazonas, Brazil
- AIDS Healthcare Foundation, Los Angeles, California, USA
| | | | | | | | | | | | | | | | | | | | - Angelica Espinosa Miranda
- Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis, Secretariat of Health Surveillance, Ministry of Health, Brasília, Distrito Federal, Brazil
- Federal University of Espirito Santo, Vitoria, Brazil
| | - Brazilian-Gasp Network
- Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis, Secretariat of Health Surveillance, Ministry of Health, Brasília, Distrito Federal, Brazil
- Brazilian GASP, Florianópolis, Brazil
| |
Collapse
|
3
|
Debuysschere C, Blairon L, Cupaiolo R, Beukinga I, Tré-Hardy M. Clinical evaluation of a dermatophyte RT-PCR assay and its impact on the turn-around-time: A prospective study. Med Mycol 2023; 61:myad078. [PMID: 37505466 DOI: 10.1093/mmy/myad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023] Open
Abstract
Onychomycosis is an important public health problem whose prevalence continues to grow and impact public health at several levels. Nevertheless, today the main diagnostic methods used in routine practice have many drawbacks. The aim of this study was to evaluate, for the first time, the clinical performance of a new multiplex polymerase chain reaction (PCR) (Novaplex®) in the identification of the causative agent on nail samples, and its impact on the turnaround time, compared to our traditional laboratory methods. From June 2022 to December 2022, all nail samples sent to our laboratory for suspected onychomycosis were included in this prospective study. We collected for each sample the results obtained with the Novaplex® PCR method and with the traditional direct microscopy examination and culture. Each discordant result was checked using a third method, which is another PCR method (DermaGenius® kit) as a resolver. For culture-positive samples, a turnaround time was calculated and compared to the one obtained with the Novaplex® method. A total of 131 samples were included. Among them, 5 were positive (3.8%) on direct microscopy, 33 were positive (25.2%) after culture, and 98 were negative (74.8%). All positive (n = 33) and negative (n = 69) cultures were also positive/negative with the Novaplex® PCR. Twenty-nine samples were positive with the Novaplex® method but negative with culture (discordant results). The percentage agreement between the culture and the Novaplex® methods was 77.9% (102 out of 131). While tested with the resolver (DermaGenius® PCR), 28 out of 29 discordant results were similarly found positive. The percentage agreement between the two PCR methods (Novaplex® and DermaGenius®) was 96.6%. The Novaplex® PCR method evaluated proved to be very reliable and allowed the direct identification of 62 out of 131 positive samples (47.3%) with the following distribution: 79.0% of Trichophyton rubrum complex, 11.3% of Trichophyton mentagrophytes complex, 6.5% of both Trichophyton rubrum complex and Trichophyton mentagrophytes complex, and 3.2% of Candida albicans. The median time [± 95% CI] for positive culture (between incubation and validation of the final identification) was 15 [12-23] days, while the turnaround time for the Novaplex® method adapted to our clinical laboratory routine is ≤7 days. Laboratory confirmation of onychomycosis is crucial and should always be obtained before starting treatment. The evaluated PCR method offered a rapid, reliable, robust, and inexpensive method of identification of the causative agent compared to traditional methods.
Collapse
Affiliation(s)
- Cyril Debuysschere
- Department of Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
| | - Laurent Blairon
- Department of Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
| | - Roberto Cupaiolo
- Department of Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
| | - Ingrid Beukinga
- Department of Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
| | - Marie Tré-Hardy
- Department of Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
- Faculty of Medicine, Université libre de Bruxelles, Brussels, Belgium
- Department of Pharmacy, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| |
Collapse
|
4
|
Kim I, Maeng LS, Kim JS, Kim BW, Cheung DY, Kim JI, Park SH. Quantitative multiplex real-time polymerase chain reaction assay for the detection of Helicobacter pylori and clarithromycin resistance. BMC Microbiol 2023; 23:155. [PMID: 37237357 DOI: 10.1186/s12866-023-02868-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Identifying clarithromycin resistance is essential for eradicating Helicobacter pylori (HP). Therefore, we evaluated the performance of Allplex™ H.pylori & ClariR Assay (Allplex™) for diagnosing and detecting clarithromycin resistance in HP. METHODS Subjects who underwent esophagogastroduodenoscopy between April 2020 and August 2021 at Incheon St. Mary's hospital were enrolled in this study. The diagnostic performances of Allplex™ and dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) were compared with sequencing as the gold standard. RESULTS A total of 142 gastric biopsy samples were analyzed. Gene sequencing revealed 124 HP infections, 42 A2143G mutations, 2 A2142G mutations, one dual mutation, and no A2142C mutation. DPO-PCR showed 96.0% sensitivity and 100.0% specificity for HP detection; the corresponding rates for Allplex™ were 99.2% and 100.0%. DPO-PCR showed 88.3% sensitivity and 82.0% specificity for A2143G mutation, and Allplex™ showed 97.6% and 96.0%. The Cohen's Kappa coefficient for overall test results was 0.56 for DPO-PCR and 0.95 for Allplex™. CONCLUSION Allplex™ showed comparable diagnostic performance with direct gene sequencing and non-inferior diagnostic performance to DPO-PCR. Further research is required to confirm whether Allplex™ is an effective diagnostic tool for the eradication of HP.
Collapse
Affiliation(s)
- Ilsoo Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Lee-So Maeng
- Department of Hospital Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joon Sung Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea.
| | - Byung-Wook Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Dae Young Cheung
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Il Kim
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soo-Heon Park
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
5
|
Kreitmann L, Miglietta L, Xu K, Malpartida-Cardenas K, D'Souza G, Kaforou M, Brengel-Pesce K, Drazek L, Holmes A, Rodriguez-Manzano J. Next-generation molecular diagnostics: Leveraging digital technologies to enhance multiplexing in real-time PCR. Trends Analyt Chem 2023; 160:116963. [PMID: 36968318 PMCID: PMC7614363 DOI: 10.1016/j.trac.2023.116963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Real-time polymerase chain reaction (qPCR) enables accurate detection and quantification of nucleic acids and has become a fundamental tool in biological sciences, bioengineering and medicine. By combining multiple primer sets in one reaction, it is possible to detect several DNA or RNA targets simultaneously, a process called multiplex PCR (mPCR) which is key to attaining optimal throughput, cost-effectiveness and efficiency in molecular diagnostics, particularly in infectious diseases. Multiple solutions have been devised to increase multiplexing in qPCR, including single-well techniques, using target-specific fluorescent oligonucleotide probes, and spatial multiplexing, where segregation of the sample enables parallel amplification of multiple targets. However, these solutions are mostly limited to three or four targets, or highly sophisticated and expensive instrumentation. There is a need for innovations that will push forward the multiplexing field in qPCR, enabling for a next generation of diagnostic tools which could accommodate high throughput in an affordable manner. To this end, the use of machine learning (ML) algorithms (data-driven solutions) has recently emerged to leverage information contained in amplification and melting curves (AC and MC, respectively) - two of the most standard bio-signals emitted during qPCR - for accurate classification of multiple nucleic acid targets in a single reaction. Therefore, this review aims to demonstrate and illustrate that data-driven solutions can be successfully coupled with state-of-the-art and common qPCR platforms using a variety of amplification chemistries to enhance multiplexing in qPCR. Further, because both ACs and MCs can be predicted from sequence data using thermodynamic databases, it has also become possible to use computer simulation to rationalize and optimize the design of mPCR assays where target detection is supported by data-driven technologies. Thus, this review also discusses recent work converging towards the development of an end-to-end framework where knowledge-based and data-driven software solutions are integrated to streamline assay design, and increase the accuracy of target detection and quantification in the multiplex setting. We envision that concerted efforts by academic and industry scientists will help advance these technologies, to a point where they become mature and robust enough to bring about major improvements in the detection of nucleic acids across many fields.
Collapse
|
6
|
Montero-Macías R, Coronado PJ, Robillard N, Veyer D, Villefranque V, Le Frére-Belda MA, Auberger E, Bitolog P, Stankovic I, Bélec L, Bats AS, Lécuru F, Péré H. HPV Molecular Genotyping as a Differential Diagnosis Tool in Cervical Cancer Metastasis. J Pers Med 2023; 13:jpm13020177. [PMID: 36836411 PMCID: PMC9961249 DOI: 10.3390/jpm13020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Differentiating metastatic cervical cancer from another primary tumor can be difficult in patients with a history of cervical cancer and a distant lesion. The use of routine HPV molecular detection and genotyping tests could help in these cases. The objective of this study was to identify if an easy-to-use HPV molecular genotyping assay would allow differentiating between HPV tumor metastasis and a new independent primary non-HPV-induced tumor. MATERIALS AND METHODS Between 2010 and 2020, we identified patients with a primary cervical carcinoma who also had another secondary lesion. This identification included a clinical and histologic differential diagnosis of metastatic cervical cancer versus a new primary cancer or metastatic cancer from another site. We used a routine multiplex real-time PCR (rt-PCR) AnyplexTM II HPV28 (Seegene, Seoul, Republic of Korea) to detect the high-risk (HR)-HPV genome in the distant lesions in these patients. RESULTS Eight cases of cervical cancer with a new secondary lesion were identified. In seven, HR-HPV DNA was detected in the biopsy of the distant lesion, which confirmed the diagnosis of cervical cancer metastasis. In the remaining case, no HPV was detected in the secondary lung biopsy, confirming the diagnosis of new primary lung cancer. CONCLUSION Our results pave the way for HPV molecular genotyping use in cases of newly diagnosed distant lesions in patients with a history of HPV cervical neoplasia by using a routine diagnosis process to complete the clinical and histologic differential diagnosis when confronted with ambiguous situations.
Collapse
Affiliation(s)
- Rosa Montero-Macías
- Obstetrics and Gynecology Department, Centre Hospitalier Simone Veil, 95602 Eaubonne, France
- Complutense University of Madrid, 28223 Madrid, Spain
| | - Pluvio J. Coronado
- Women’s Health Institute José Botella Llusiá, Fundación de Investigación del Hospital Clínico San Carlos (IdISSC), Universidad Complutense, 28040 Madrid, Spain
| | - Nicolas Robillard
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
| | - David Veyer
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, 75013 Paris, France
| | - Vincent Villefranque
- Obstetrics and Gynecology Department, Centre Hospitalier Simone Veil, 95602 Eaubonne, France
| | | | | | - Pauline Bitolog
- Pathology Department, Simone Veil Hospital, 95600 Eaubonne, France
| | - Ivana Stankovic
- Pathology Department, Georges Pompidou European Hospital, 75015 Paris, France
| | - Laurent Bélec
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- Faculty of Medicine, Paris University, 75015 Paris, France
| | - Anne-Sophie Bats
- Faculty of Medicine, Paris University, 75015 Paris, France
- Gynecologic and Breast Oncologic Surgery Department, Georges Pompidou European Hospital, 75015 Paris, France
| | - Fabrice Lécuru
- Faculty of Medicine, Paris University, 75015 Paris, France
- Breast, Gynecology and Reconstructive Surgery Unit, Curie Institute, 75005 Paris, France
| | - Hélène Péré
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- Faculty of Medicine, Paris University, 75015 Paris, France
- Correspondence:
| |
Collapse
|
7
|
Xie T, Luo Y, Wang P, Wu L, Cui X, Sun B, Li G. Controlled Rehydration of Dried Reagents for Robust Multiplex Digital PCR. Anal Chem 2022; 94:13223-13232. [DOI: 10.1021/acs.analchem.2c02920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tengbao Xie
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Yu Luo
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Ping Wang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang 471000, China
| | - Lei Wu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Xu Cui
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Bangyong Sun
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Gang Li
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| |
Collapse
|
8
|
Han JY, Suh W, Han SB. Seasonal epidemiological and clinical characteristics of pediatric patients with human parainfluenza virus infection by serotype: a retrospective study. Virol J 2022; 19:141. [PMID: 36064562 PMCID: PMC9444704 DOI: 10.1186/s12985-022-01875-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The development of the polymerase chain reaction (PCR) test promoted the evaluation of the epidemiological and clinical characteristics of human parainfluenza virus (HPIV) type 4, which has been rarely studied using conventional diagnostic methods. This study aimed to determine the seasonal epidemiological and clinical characteristics of all four HPIV serotypes (HPIV-1, HPIV-2, HPIV-3, and HPIV-4) during the era of PCR testing. METHODS The medical records of hospitalized pediatric patients diagnosed with HPIV infections by a multiplex PCR test between 2015 and 2021 were retrospectively reviewed to determine the seasonal distributions of each HPIV serotype. For patients with a single HPIV infection, the clinical characteristics of each HPIV serotype were evaluated and compared with one another. RESULTS Among the 514 cases of HPIV infection, HPIV-1, HPIV-2, HPIV-3, and HPIV-4 were identified in 27.2%, 11.9%, 42.6%, and 18.3% of cases, respectively. HPIV-3 was most prevalent in spring, and the other three serotypes were most prevalent in autumn. For patients with a single HPIV infection, those infected by HPIV-1 and HPIV-3 were younger than those infected by HPIV-2 and HPIV-4 (P < 0.001). Croup and lower respiratory tract infection (LRI) were most frequently diagnosed in patients infected by HPIV-1 (P < 0.001) and HPIV-4 (P = 0.002), respectively. During 2020-2021, HPIV-3 was most prevalent in autumn and caused fewer LRIs (P = 0.009) and more seizures (P < 0.001) than during 2015-2019. CONCLUSIONS Each HPIV serotype exhibited a distinct seasonal predominance, and some differences in the clinical characteristics of the HPIV serotypes were observed. HPIV-4 acted as an important cause of LRI. Considering the recent changes in the epidemiological and clinical characteristics of HPIV-3, more time-series analyses should be conducted.
Collapse
Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea.,Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woosuck Suh
- Department of Pediatrics, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea.,Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Beom Han
- Department of Pediatrics, Hangang Sacred Heart Hospital, College of Medicine, Hallym University, 12 Beodeunaru-ro 7-gil, Yeongdeungpo-gu, Seoul, 07247, Republic of Korea.
| |
Collapse
|
9
|
Linsky JMJ, Dunlop RA, Noad MJ, McMichael LA. A mammalian messenger RNA sex determination method from humpback whale ( Megaptera novaeangliae) blubber biopsies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220556. [PMID: 36016912 PMCID: PMC9399696 DOI: 10.1098/rsos.220556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The large size of free-ranging mysticetes, such as humpback whales (Megaptera novaeangliae), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative (real-time) polymerase chain reaction (RT-qPCR) with primer sets for a control gene (ACTB) and the X-chromosome inactivation gene (XIST). Products of each RT-qPCR had distinct melting temperature profiles based on the presence (female) or absence (male) of the XIST transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters (male/female) based on their melting profiles. We validated the XIST method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng µl-1), the XIST sex determination method shows 100% agreement with traditional DNA sex determination. Using the XIST method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.
Collapse
Affiliation(s)
- Jacob M. J. Linsky
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Rebecca A. Dunlop
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael J. Noad
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Lee A. McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| |
Collapse
|
10
|
Comparative Evaluation of Allplex Respiratory Panels 1, 2, 3, and BioFire FilmArray Respiratory Panel for the Detection of Respiratory Infections. Diagnostics (Basel) 2021; 12:diagnostics12010009. [PMID: 35054176 PMCID: PMC8775103 DOI: 10.3390/diagnostics12010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Multiplex nucleic acid amplification assays that simultaneously detect multiple respiratory pathogens in a single nasopharyngeal swab (NPS) specimen are widely used for rapid clinical diagnostics. We evaluated Allplex Respiratory Panel (RP) 1, 2, 3, and the BioFire FilmArray RP assay for detecting respiratory pathogens from NPS specimens. In all, 181 NPS specimens obtained from patients suspected of having respiratory infections during the non-influenza season (August–December 2019) were included. The Allplex RP 1, 2, and 3 detected 154 samples positive for respiratory viruses, whereas the BioFire FilmArray detected viruses in 98 samples. Co-infection with two or more viruses was detected in 41 and 17 NPS specimens by Allplex RP and the BioFire FilmArray RP, respectively. For adenoviruses, Allplex RP 1 detected 31 specimens, compared to 34 by the BioFire FilmArray. In all, 64 NPS specimens were positive for human enterovirus (HEV) and human rhinovirus (HRV) on the Allplex RP, in contrast to 39 HEV/HRV on the BioFire FilmArray. The parainfluenza virus (PIV-1–4) detection rate differed between the two systems. Most discrepant results were observed for NPS specimens with high cycle threshold values obtained by Allplex RP. This study showed concordant performance of the Allplex RP 1, 2, 3, and the BioFire FilmArray RP for the simultaneous detection of multiple respiratory viruses.
Collapse
|
11
|
Schlenker F, Kipf E, Deuter M, Höffkes I, Lehnert M, Zengerle R, von Stetten F, Scherer F, Wehrle J, von Bubnoff N, Juelg P, Hutzenlaub T, Borst N. Stringent Base Specific and Optimization-Free Multiplex Mediator Probe ddPCR for the Quantification of Point Mutations in Circulating Tumor DNA. Cancers (Basel) 2021; 13:cancers13225742. [PMID: 34830896 PMCID: PMC8616434 DOI: 10.3390/cancers13225742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Cancer treatment strategies and their follow-up monitoring are changing to personalized therapies, based on molecular genetic information from the individual person. Liquid biopsy, where this molecular information is derived from body fluids such as blood, has the potential to provide a systemic fingerprint of cancer dynamics, and, compared to tissue biopsy, is much less invasive for the patient. We used the previously published mediator probe PCR technology for liquid biopsy detection of several mutations in one reaction, so-called digital multiplex PCR. Quantification of point mutations in plasma eluates from follow-up patients using 4-plex digital assays showed a comparable performance to reference 2-plex assays. As a key feature, the presented multiplex assays require no laborious optimization as they use the same concentrations and cycling conditions for all targets. This allows for flexible design and interchangeable target panels, thus the assay is easily adaptable for individual patient monitoring and reduces sample consumption. Abstract There is an increasing demand for optimization-free multiplex assays to rapidly establish comprehensive target panels for cancer monitoring by liquid biopsy. We present the mediator probe (MP) PCR for the quantification of the seven most frequent point mutations and corresponding wild types (KRAS and BRAF) in colorectal carcinoma. Standardized parameters for the digital assay were derived using design of experiments. Without further optimization, the limit of detection (LoD) was determined through spiking experiments with synthetic mutant DNA in human genomic DNA. The limit of blank (LoB) was measured in cfDNA plasma eluates from healthy volunteers. The 2-plex and 4-plex MP ddPCR assays showed a LoB of 0 copies/mL except for 4-plex KRAS G13D (9.82 copies/mL) and 4-plex BRAF V600E (16.29 copies/mL) and allele frequencies of 0.004% ≤ LoD ≤ 0.38% with R2 ≥ 0.98. The quantification of point mutations in patient plasma eluates (18 patients) during follow-up using the 4-plex MP ddPCR showed a comparable performance to the reference assays. The presented multiplex assays need no laborious optimization, as they use the same concentrations and cycling conditions for all targets. This facilitates assay certification, allows a fast and flexible design process, and is thus easily adaptable for individual patient monitoring.
Collapse
Affiliation(s)
- Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
| | - Elena Kipf
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
| | - Max Deuter
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.D.); (F.S.); (J.W.); (N.v.B.)
| | - Inga Höffkes
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Florian Scherer
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.D.); (F.S.); (J.W.); (N.v.B.)
| | - Julius Wehrle
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.D.); (F.S.); (J.W.); (N.v.B.)
| | - Nikolas von Bubnoff
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.D.); (F.S.); (J.W.); (N.v.B.)
- Department of Hematology and Oncology, Campus Lübeck, University Hospital Schleswig-Holstein, 23562 Lübeck, Germany
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nadine Borst
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (F.S.); (E.K.); (I.H.); (M.L.); (R.Z.); (F.v.S.); (P.J.); (T.H.)
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Correspondence: ; Tel.: +49-761-203-73208
| |
Collapse
|
12
|
Vandendriessche S, Padalko E, Wollants E, Verfaillie C, Verhasselt B, Coorevits L. Evaluation of the Seegene Allplex™ Respiratory Panel for diagnosis of acute respiratory tract infections. Acta Clin Belg 2019; 74:379-385. [PMID: 30307378 DOI: 10.1080/17843286.2018.1531605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Objectives: The Seegene AllplexTM Respiratory panel was retrospectively challenged using a collection of quality control samples (QCMD) and clinical samples previously analysed with validated routine methods. Methods: A collection of 111 samples [43 QCMD samples, 13 bronchoalveolar lavage fluids and 55 nasopharyngeal aspirates/swabs] was tested with Seegene AllplexTM. The clinical samples were tested previously using either FTD® Respiratory Pathogens 21 qPCR assay (Fast Track Diagnostics), an in-house multiplex PCR for Bordetella, or BioGX Sample-ReadyTM Atypical pneumo panel (Becton Dickinson). Samples were stored at -80°C prior to analysis with Seegene Allplex™, nucleic acids were automatically extracted with NucliSENS Easymag (bioMérieux). Samples returning discordant results were subjected to repeat testing and/or additional testing by reference laboratories. Results: Seegene correctly identified 41/43 QCMD samples (95.4%); two samples positive for respiratory syncytial virus (RSV) and human metapneumovirus, respectively, were only correctly identified following repeat testing. In the 56 clinical samples, overall, 97 pathogens were identified: 65 pathogens (67.0%) were detected both by routine methods and Seegene, 24 pathogens (24.7%) only by routine methods, and 8 pathogens (8.2%) only by Seegene. The majority of discordant results was detected in samples with low pathogen load (22/32, 68.8%) and in samples containing multiple pathogens (25/32, 78.1%). Full agreement between methods was observed for influenza, RSV, adenovirus, Bordetella (para)pertussis and Chlamydia pneumoniae. Discordance was observed for human metapneumovirus, coronavirus OC43, bocavirus and parainfluenza virus, mainly type 4. Conclusion: Overall, the Seegene AllplexTM assay performed well for routine detection of important respiratory targets. Acceptable agreement was observed between Seegene and other routine assays.
Collapse
Affiliation(s)
- Stien Vandendriessche
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Elizaveta Padalko
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Elke Wollants
- Rega Institute, Laboratory of Clinical & Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Charlotte Verfaillie
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Lucas Ghent, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Liselotte Coorevits
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
13
|
Compain F, Nodjikouambaye ZA, Sadjoli D, Moussa AM, Adawaye C, Bouassa RSM, Koyalta D, Tonen-Wolyec S, Péré H, Podglajen I, Bélec L. Low Prevalence of Common Sexually Transmitted Infections Contrasting with High Prevalence of Mycoplasma Asymptomatic Genital Carriage: A Community-Based Cross-Sectional Survey in Adult Women Living in N’Djamena, Chad. Open Microbiol J 2019. [DOI: 10.2174/1874285801913010222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
We herein report a cross-sectional study which consecutively enrolled adult women from the community living in N'Djamena, Chad. The aim of the study was to estimate the burden of asymptomatic genital carriage of common curable sexually transmitted infections (STIs) (including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis) and genital Mycoplasma spp., as well as to assess their possible associated risk factors.
Methods:
A total of 251 women were consecutively included and screened for common curable STIs as well as for genital mycoplasma carriage by multiplex real-time PCR.
Results:
Only seven (2.8%) women were found to be infected with at least one common STI by multiplex real-time PCR: C. trachomatis, N. gonorrhoeae, M. genitalium and T. vaginalis were recovered from 3 (1.2%), 1 (0.4%), 4 (1.6%) and 1 (0.4%) women, respectively. No sociodemographic and behavioral characteristics could be associated in multivariate analysis with the genital carriage of the four detected common curable STIs. In contrast, the prevalence of genital mycoplasmas was much higher (54.2%) with a predominance of Ureaplasma parvum (42.6% of the total population).
Conclusion:
Our study shows a low prevalence of common STIs in contrast with a high prevalence of mycoplasmas among asymptomatic adult women recruited on a community basis in Chad. These observations highlight the need for etiologic management of STIs relying on PCR-based techniques rather than a syndromic approach in resource-limited countries.
Collapse
|
14
|
Accuracy of Curable Sexually Transmitted Infections and Genital Mycoplasmas Screening by Multiplex Real-Time PCR Using a Self-Collected Veil among Adult Women in Sub-Saharan Africa. Infect Dis Obstet Gynecol 2019; 2019:8639510. [PMID: 31379424 PMCID: PMC6662439 DOI: 10.1155/2019/8639510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/15/2019] [Accepted: 05/20/2019] [Indexed: 11/17/2022] Open
Abstract
Background Sexually transmitted infections (STIs) are highly prevalent in sub-Saharan Africa. Genital self-sampling may facilitate the screening of STIs in hard-to-reach remote populations far from large health care centers and may increase screening rates. The cross-sectional GYNAUTO-STI study was carried out to assess the performance of a novel genital veil (V-Veil-Up Gyn Collection Device, V-Veil-Up Pharma, Ltd., Nicosia, Cyprus) as a genital self-sampling device to collect genital secretions to diagnose STIs by molecular biology as compared to reference clinician-collected genital specimens, in adult African women. Methods Adult women living in N'Djamena, the capital city of Chad, were recruited from the community and referred to the clinic for women's sexual health "La Renaissance Plus". A clinician obtained an endocervical specimen using flocked swab. Genital secretions were also obtained by self-collection using veil. Both clinician- and self-collected specimens were tested for common curable STIs (including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis) and genital Mycoplasma spp. by multiplex real-time PCR (Allplex™ STI Essential Assay, Seegene, Seoul, South Korea). Test positivities for both collection methods were compared by assessing methods agreement, sensitivity, and specificity. Results A total of 251 women (mean age, 35.1 years) were prospectively enrolled. Only seven (2.8%) women were found to be infected with at least one common STIs [C. trachomatis: 3 (1.2%), N. gonorrhoeae: 1 (0.4%), M. genitalium: 4 (1.6%) and T. vaginalis: 1 (0.4%)], while the prevalence of genital mycoplasmas was much higher (54.2%) with a predominance of Ureaplasma parvum (42.6%). Self-collection by veil was non-inferior to clinician-based collection for genital microorganisms DNA molecular testing, with "almost perfect" agreement between both methods, high sensitivity (97.0%; 95%CI: 92.5-99.2%), and specificity (88.0%; 95%CI: 80.7-93.3%). Remarkably, the mean total number of genital microorganisms detected per woman was 1.14-fold higher in self-collected specimens compared to that in clinician-collected specimens. Conclusions Veil-based self-collection of female genital secretions constitutes a convenient tool to collect in gentle way cervicovaginal secretions for accurate molecular detection of genital bacteria. Such sampling procedure could be easily implemented in STIs clinics in sub-Saharan Africa.
Collapse
|
15
|
Significant Expansion of Real-Time PCR Multiplexing with Traditional Chemistries using Amplitude Modulation. Sci Rep 2019; 9:1053. [PMID: 30705333 PMCID: PMC6355831 DOI: 10.1038/s41598-018-37732-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Abstract
The real time polymerase chain reaction (rtPCR) is an essential method for detecting nucleic acids that has a wide range of clinical and research applications. Current multiplexed rtPCR is capable of detecting four to six nucleic acid targets in a single sample. However, advances in clinical medicine are driving the need to measure many more targets at once. We demonstrate a novel method which significantly increases the multiplexing capability of any existing rtPCR instrument without new hardware, software, or chemistry. The technique works by varying the relative TaqMan probe concentrations amongst targets that are measured in a single fluorometric channel. Our fluorescent amplitude modulation method generates a unique rtPCR signature for every combination of targets present in a reaction. We demonstrate this technique by measuring nine different targets across three color channels with TaqMan reporting probes, yielding a detection accuracy of 98.9% across all combinations of targets. In principle this method could be extended to measure 6 or more targets per color channel across any number of color channels without loss in specificity.
Collapse
|
16
|
Rodriguez-Manzano J, Moniri A, Malpartida-Cardenas K, Dronavalli J, Davies F, Holmes A, Georgiou P. Simultaneous Single-Channel Multiplexing and Quantification of Carbapenem-Resistant Genes Using Multidimensional Standard Curves. Anal Chem 2019; 91:2013-2020. [PMID: 30624047 PMCID: PMC6389101 DOI: 10.1021/acs.analchem.8b04412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Multiplexing
and quantification of nucleic acids, both have, in
their own right, significant and extensive use in biomedical related
fields. Currently, the ability to detect several nucleic acid targets
in a single-reaction scales linearly with the number of targets; an
expensive and time-consuming feat. Here, we propose a new methodology
based on multidimensional standard curves that extends the use of
real-time PCR data obtained by common qPCR instruments. By applying
this novel methodology, we achieve simultaneous single-channel multiplexing
and enhanced quantification of multiple targets using only real-time
amplification data. This is obtained without the need of fluorescent
probes, agarose gels, melting curves or sequencing analysis. Given
the importance and demand for tackling challenges in antimicrobial
resistance, the proposed method is applied to four of the most prominent
carbapenem-resistant genes: blaOXA-48, blaNDM, blaVIM, and blaKPC, which account for 97% of
the UK’s reported carbapenemase-producing Enterobacteriaceae.
Collapse
Affiliation(s)
- Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Jyothsna Dronavalli
- Imperial College Healthcare NHS Trust , St. Mary's Hospital , Praed Street , London , W2 1NY , United Kingdom
| | - Frances Davies
- Imperial College Healthcare NHS Trust , St. Mary's Hospital , Praed Street , London , W2 1NY , United Kingdom
| | - Alison Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance , Imperial College London , Hammersmith Campus, W12 0NN , London , United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| |
Collapse
|
17
|
Kim J, Nam J, Jang W, Lim CS. Clinical Performance of the AllplexTM Respiratory Panel 1 Test Compared to SimplexaTM Flu A/B and RSV for Detection of Influenza Virus and Respiratory Syncytial Virus Infection Including Their Subtyping. Med Princ Pract 2019; 28:380-386. [PMID: 30831570 PMCID: PMC6639576 DOI: 10.1159/000499313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/03/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE TheAllplexTM Respiratory Panel 1 (ARP) is a new assay based on a real-time polymerase chain reaction (RT-PCR) for the detection of influenza A (Flu A), influenza B virus (Flu B), and respiratory syncytial virus (RSV), including subtyping by multiple detection temperature (MuDT) technology. We evaluated the performance of the Allplex Respiratory Panel compared to the SimplexaTM Flu A/B & RSV assay (SP) and other diagnostic tools. MATERIALS AND METHODS A total of 372 samples were collected from patients at the Korea University Guro Hospital in Seoul, Korea. All samples were tested for influenza virus and RSV by ARP, SP, and an in-house RT-PCR. RESULTS The sensitivity of ARP was 95.56, 100, and 95.24% for Flu A, Flu B, and RSV, respectively. The specificity of ARP was 100, 100, and 100% for Flu A, Flu B, and RSV, respectively. SP had sensitivities and specificities of 98.89 and 100% for Flu A, 100 and 100% for Flu B, and 100 and 100% for RSV. CONCLUSION The Allplex panelshowed high sensitivity, specificity, positive predictive, and negative predictive values for the detection of Flu A, Flu B, and RSV. This assay is fast and easy to perform because it takes only about 150 min and there is no need for post-PCR electrophoresis. The ARP can be used as a reliable and convenient assay in clinical laboratories.
Collapse
Affiliation(s)
- Jeeyong Kim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Woongsik Jang
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea,
| |
Collapse
|
18
|
Hyun J, Ko DH, Lee SK, Kim HS, Kim JS, Song W, Kim HS. Evaluation of a New Multiplex Real-Time PCR Assay for Detecting Gastroenteritis-Causing Viruses in Stool Samples. Ann Lab Med 2018; 38:220-225. [PMID: 29401556 PMCID: PMC5820066 DOI: 10.3343/alm.2018.38.3.220] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Accepted: 01/09/2018] [Indexed: 01/13/2023] Open
Abstract
Background Diarrhea has been the second leading cause of death among children under the age of five, and the rapid and accurate pathogen diagnosis in patients with diarrhea is crucial for reducing morbidity and mortality. A newly developed one-step multiplex real-time PCR assay, the Allplex GI-Virus Assay, was evaluated for its ability to detect six diarrhea-causing viruses (rotavirus, norovirus genogroup I (GI) and genogroup II (GII), enteric adenovirus, astrovirus, and sapovirus) in stool samples. Methods The performance of the Allplex assay was compared with those of another multiplex PCR assay (Seeplex Diarrhea-V Ace Detection) and genotyping by sequencing, using 446 stool samples from patients with acute gastroenteritis. Results The overall agreement rates between the results of the Allplex and Seeplex assays were 98.7% for rotavirus, 99.1% for norovirus GI, 93.3% for norovirus GII, 98.0% for adenovirus, and 99.6% for astrovirus. The overall agreement rates between the Allplex assay and genotyping were 99.1% for rotavirus, 99.1% for norovirus GI, 98.7% for norovirus GII, 89.7% for adenovirus, 98.2% for astrovirus, and 99.8% for sapovirus. In addition, eight rotavirus genotypes, three norovirus GI genotypes, four norovirus GII genotypes, eight adenovirus genotypes, two astrovirus genotypes, and two sapovirus genotypes were detected. Conclusions The Allplex assay showed high agreement with Seeplex and genotyping results, and was able to additionally detect sapoviruses. The Allplex assay could be useful in identifying viral gastrointestinal infections in patients with acute gastroenteritis symptoms.
Collapse
Affiliation(s)
- Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Dae Hyun Ko
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Su Kyung Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Han Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea.
| |
Collapse
|
19
|
Lee J, Lee HS, Cho YG, Choi SI, Kim DS. Evaluation of Allplex Respiratory Panel 1/2/3 Multiplex Real-Time PCR Assays for the Detection of Respiratory Viruses with Influenza A Virus subtyping. Ann Lab Med 2018; 38:46-50. [PMID: 29071818 PMCID: PMC5700146 DOI: 10.3343/alm.2018.38.1.46] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/27/2017] [Accepted: 09/16/2017] [Indexed: 11/21/2022] Open
Abstract
The Allplex Respiratory Panel 1/2/3 (All16) is a multiplex PCR assay for detecting 16 respiratory viruses with influenza A virus (FluA) subtyping, and the first clinical assay based on multiple detection temperatures. We compared the results between All16 and Anyplex II RV16 (Any16) in 426 clinical samples. Samples showing discrepancies between the two tests were further tested using monoplex PCR. FluA subtyping based on the hemagglutinin type results of All16, which yielded H1, H3, and non-H1/H3, was compared with the results of the BioFire FilmArray respiratory panel. The positive and negative percent agreements and kappa value for each virus between All16 and Any16 ranged from 54.5-100.0%, 84.7-100.0%, and 0.57-1.00, respectively. FluA subtype results from All16 for 26 samples were consistent with those from FilmArray. Good agreement was observed between the two methods, except when analyzing human enterovirus (kappa value 0.70), and the All16 showed reliable FluA subtyping results. For parainfluenza virus 3, the All16 was more sensitive than Any16. When testing 28 samples simultaneously, the mean test time and hands-on time were 4.3 and 0.5 hours, respectively in All16. In conclusion, All16 showed reliable performance, but further studies are needed regarding human enterovirus analysis.
Collapse
Affiliation(s)
- Jaehyeon Lee
- Department of Laboratory Medicine, Chonbuk National University Hospital, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea
| | - Hye Soo Lee
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea
| | - Yong Gon Cho
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea
| | - Sam Im Choi
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea
| | - Dal Sik Kim
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea.,Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Korea.
| |
Collapse
|
20
|
Barratt K, Anderson TP, Fahey JA, Jennings LC, Werno AM, Murdoch DR. Comparison of the fast track diagnostics respiratory 21 and Seegene Allplex multiplex polymerase chain reaction assays for the detection of respiratory viruses. Br J Biomed Sci 2017; 74:85-89. [DOI: 10.1080/09674845.2017.1278885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kevin Barratt
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Trevor P. Anderson
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Jennifer A. Fahey
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Lance C. Jennings
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Anja M. Werno
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - David R. Murdoch
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
- Department of Pathology, University of Otago, Christchurch, New Zealand
| |
Collapse
|
21
|
Evaluation of an Assay Based On Multiple Detection Temperature Technique for Simultaneous Detection of Viral Gastroenteritis-Causing Pathogens. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.43548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
22
|
Performance Evaluation of Allplex Respiratory Panels 1, 2, and 3 for Detection of Respiratory Viruses and Influenza A Virus Subtypes. J Clin Microbiol 2016; 55:479-484. [PMID: 27903601 DOI: 10.1128/jcm.02045-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/22/2016] [Indexed: 12/27/2022] Open
Abstract
The Allplex respiratory panels 1, 2, and 3 (Allplex) comprise a one-step real-time reverse transcription-PCR assay for the detection of respiratory viruses (RVs) and influenza A subtypes based on multiple detection temperature (MuDT) technology. The performance of the Allplex assay was compared with those of the AdvanSure RV real-time PCR kit (AdvanSure) and the PowerChek pandemic H1N1/H3N2/H5N1 real-time PCR kit (PowerChek) using 417 clinical respiratory specimens. In comparison with the AdvanSure assay for RV detection by each virus, the ranges of positive percent agreement, negative percent agreement, and kappa values with the Allplex assay were 82.8 to 100%, 95.5 to 100%, and 0.85 to 1.00, respectively. For influenza A virus (INF A) subtyping, the kappa values between the Allplex and PowerChek assays were 0.67 and 1.00 for the INF A H1N1-pdm09 and H3 subtypes, respectively. Uniplex PCR and sequencing for samples with discrepant results demonstrated that the majority of results were concordant with those from the Allplex assay. When testing 24 samples, the turnaround and hands-on time required to perform the Allplex assay were 4 h 15 min and 15 min, respectively. In conclusion, the Allplex assay produced results comparable to those from the AdvanSure and PowerChek assays.
Collapse
|
23
|
Yasmin R, Zhu H, Chen Z, Montagna RA. A modifiable microarray-based universal sensor: providing sample-to-results automation. Heliyon 2016; 2:e00179. [PMID: 27812551 PMCID: PMC5078625 DOI: 10.1016/j.heliyon.2016.e00179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/22/2016] [Accepted: 10/11/2016] [Indexed: 12/30/2022] Open
Abstract
A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.
Collapse
Affiliation(s)
| | - Hui Zhu
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA
| | - Zongyuan Chen
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA; Thermo Fisher Scientific, South San Francisco, CA, USA
| | | |
Collapse
|