1
|
Serraino R, Cesana BM, Morrone HL, Marino GG, Cirillo M, Olivadese V, Kyambadde P, Biriwo LS, Mutebi F, Trecarichi EM, Musinguzi P, Byakika-Kibwika P, Torti C. Utility, acceptability and applicability of a nucleic acid amplification test in comparison with a syndromic approach in the management of sexually transmitted diseases at Mulago National Referral Hospital in Uganda (ASTRHA): protocol for an open-label, randomised controlled trial. BMJ Open 2024; 14:e084806. [PMID: 38862220 PMCID: PMC11168150 DOI: 10.1136/bmjopen-2024-084806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
INTRODUCTION Sexually transmitted diseases (STDs) are a major cause of long-term disability. Urethral discharge syndrome (UDS), abnormal vaginal discharge (AVD) and genital ulcer disease (GUD) are very common in low-income and middle-income countries (LMICs), where, due to lack of resources, these infections are managed according to a syndromic approach. Although microbiological diagnosis using nuclear acid amplification tests (NAAT) is already a standard to prescribe targeted treatments in industrialised countries, no randomised clinical trials have been conducted to evaluate clinical usefulness and acceptability of NAAT in comparison with syndromic approach in LMICs. The results of this study could inform diagnostic guidelines since they may suggest an update of the current recommendation if microbiological diagnosis using NAAT in the management of STD is demonstrated to be both useful and acceptable in an LMIC context. METHODS AND ANALYSIS The primary objective of this randomised, open-label trial is to evaluate the clinical usefulness of a NAAT and its acceptability in comparison with a clinical syndromic approach and to explore whether this test could replace the syndromic approach in the management of STDs at a national referral hospital in Uganda. 220 patients presenting to the STD clinic at Mulago Hospital in Kampala, Uganda with AVD, UDS or GUD will be randomised to either standard of care (syndromic management) or NAAT-based treatment with a 1:1 ratio. All the patients will be asked to return after 2 or 3 weeks for a control visit. Primary outcome will be therapeutic appropriateness. ETHICS AND DISSEMINATION This trial was approved by the Mulago Hospital Research and Ethical Committee (MHREC2023-97) and the Uganda National Council for Science and Technology (HS31000ES). Patients will give informed consent to participate before taking part in the study. Results will be published in peer-reviewed journals in open-access formats and data made available in anonymised form. TRIAL REGISTRATION NUMBER NCT05994495.
Collapse
Affiliation(s)
- Riccardo Serraino
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | | | - Helen Linda Morrone
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Gabriella Giuseppina Marino
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Cirillo
- "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Vincenzo Olivadese
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Peter Kyambadde
- Most at Risk Population Initiative, Mulago Hospital, Kampala, Uganda
- National AIDS and STI Control Programme, Kampala, Uganda
| | | | | | - Enrico Maria Trecarichi
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | | | - Pauline Byakika-Kibwika
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Carlo Torti
- Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Universita Cattolica del Sacro Cuore Dipartimento di Sicurezza e Bioetica, Rome, Italy
| |
Collapse
|
2
|
Choi G, Song KS, Nimse SB, Kim T. Development of a DNA-Based Lateral Flow Strip Membrane Assay for Rapid Screening and Genotyping of Six High-Incidence STD Pathogens. BIOSENSORS 2024; 14:260. [PMID: 38785734 PMCID: PMC11118844 DOI: 10.3390/bios14050260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Sexually transmitted diseases (STDs) are a global concern because approximately 1 million new cases emerge daily. Most STDs are curable, but if left untreated, they can cause severe long-term health implications, including infertility and even death. Therefore, a test enabling rapid and accurate screening and genotyping of STD pathogens is highly awaited. Herein, we present the development of the DNA-based 6STD Genotyping 9G Membrane test, a lateral flow strip membrane assay, for the detection and genotyping of six STD pathogens, including Trichomonas vaginalis, Ureaplasma urealyticum, Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma hominis, and Mycoplasma genitalium. Here, we developed a multiplex PCR primer set that allows PCR amplification of genomic materials for these six STD pathogens. We also developed the six ssDNA probes that allow highly efficient detection of the six STD pathogens. The 6STD Genotyping 9G Membrane test lets us obtain the final detection and genotyping results in less than 30 m after PCR at 25 °C. The accuracy of the 6STD Genotyping 9G membrane test in STD genotyping was confirmed by its 100% concordance with the sequencing results of 120 clinical samples. Therefore, the 6STD Genotyping 9G Membrane test emerges as a promising diagnostic tool for precise STD genotyping, facilitating informed decision-making in clinical practice.
Collapse
Affiliation(s)
- Gunho Choi
- Biometrix Technology, Inc., 2-2 Bio Venture Plaza 56, Chuncheon 24232, Republic of Korea; (G.C.); (K.-S.S.)
| | - Keum-Soo Song
- Biometrix Technology, Inc., 2-2 Bio Venture Plaza 56, Chuncheon 24232, Republic of Korea; (G.C.); (K.-S.S.)
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 24252, Republic of Korea
| | - Taisun Kim
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 24252, Republic of Korea
| |
Collapse
|
3
|
Ibáñez-Escribano A, Nogal-Ruiz JJ. The Past, Present, and Future in the Diagnosis of a Neglected Sexually Transmitted Infection: Trichomoniasis. Pathogens 2024; 13:126. [PMID: 38392864 PMCID: PMC10891855 DOI: 10.3390/pathogens13020126] [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: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
More than one million curable sexually transmitted infections occur every day. Trichomonas vaginalis is one of the main infections responsible for these epidemiological data; however, the diagnosis of this protozoan is still mainly based on microscopic and culture identification. The commercialization of immunological tests and the development of molecular techniques have improved the sensitivity of classical methods. Nevertheless, the fact that trichomoniasis is a neglected parasitic infection hinders the development of novel techniques and their implementation in routine diagnosis. This review article shows the different methods developed to identify T. vaginalis in population and the difficulties in diagnosing male and asymptomatic patients. The importance of including this parasite in routine gynecological screening, especially in pregnant women, and the importance of considering T. vaginalis as an indicator of high-risk sexual behavior are also discussed.
Collapse
Affiliation(s)
- Alexandra Ibáñez-Escribano
- Research Group Antiparasitic Epidemiology, Diagnostics and Therapy, PARADET, Complutense University of Madrid, 28040 Madrid, Spain;
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Juan José Nogal-Ruiz
- Research Group Antiparasitic Epidemiology, Diagnostics and Therapy, PARADET, Complutense University of Madrid, 28040 Madrid, Spain;
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| |
Collapse
|
4
|
Chan JL, Cerón S, Horiuchi SM, Yap JP, Chihuahua EG, Tsan AT, Kamau E, Yang S. Development of a Rapid and High-Throughput Multiplex Real-Time PCR Assay for Mycoplasma hominis and Ureaplasma Species. J Mol Diagn 2023; 25:838-848. [PMID: 37683891 DOI: 10.1016/j.jmoldx.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/10/2023] [Accepted: 07/27/2023] [Indexed: 09/10/2023] Open
Abstract
Bacterial commensals of the human genitourinary tract, Mycoplasma hominis and Ureaplasma species (parvum and urealyticum) can be sexually transmitted, and may cause nongonococcal urethritis, pelvic inflammatory disease, and infertility. Mycoplasma hominis and Ureaplasma species may also cause severe invasive infections in immunocompromised patients. Current culture-based methods for Mycoplasma/Ureaplasma identification are costly and laborious, with a turnaround time between 1 and 2 weeks. We developed a high-throughput, real-time multiplex PCR assay for the rapid detection of M. hominis and Ureaplasma species in urine, genital swab, body fluid, and tissue. In total, 282 specimens were tested by PCR and compared with historic culture results; a molecular reference method was used to moderate discrepancies. Overall result agreement was 99% for M. hominis (97% positive percentage agreement and 100% negative percentage agreement) and 96% for Ureaplasma species (96% positive percentage agreement and 97% negative percentage agreement). Specimen stability was validated for up to 7 days at room temperature. This multiplex molecular assay was designed for implementation in a high-complexity clinical microbiology laboratory. With this method, >90 samples can be tested in one run, with a turnaround time of 4 to 5 hours from specimen extraction to reporting of results. This PCR test is also more labor effective and cheaper than the conventional culture-based test, thus improving laboratory efficiency and alleviating labor shortages.
Collapse
Affiliation(s)
- June L Chan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Stacey Cerón
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Stephanie M Horiuchi
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Jewell P Yap
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Erika G Chihuahua
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Allison T Tsan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Edwin Kamau
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
| |
Collapse
|
5
|
Bui HTV, Bui HT, Chu SV, Nguyen HT, Nguyen ATV, Truong PT, Dang TTH, Nguyen ATV. Simultaneous real-time PCR detection of nine prevalent sexually transmitted infections using a predesigned double-quenched TaqMan probe panel. PLoS One 2023; 18:e0282439. [PMID: 36877694 PMCID: PMC9987813 DOI: 10.1371/journal.pone.0282439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Sexually transmitted diseases are major causes of infertility, ectopic pregnancy, and premature birth. Here, we developed a new multiplex real-time polymerase chain reaction (PCR) assay for the simultaneous detection of nine major sexually transmitted infections (STIs) found in Vietnamese women, including Chlamydia trachomatis, Neisseria gonorrhoeae, Gardnerella vaginalis, Trichomonas vaginalis, Candida albicans, Mycoplasma hominis, Mycoplasma genitalium, and human alphaherpesviruses 1 and 2. A panel containing three tubes × three pathogens/tube was predesigned based on double-quenched TaqMan probes to increase detection sensitivity. There was no cross-reactivity among the nine STIs and other non-targeted microorganisms. Depending on each pathogen, the agreement with commercial kits, sensitivity, specificity, repeatability and reproducibility coefficient of variation (CV), and limit of detection of the developed real-time PCR assay were 99.0%-100%, 92.9%-100%, 100%, <3%, and 8-58 copies/reaction, respectively. One assay cost only 2.34 USD. Application of the assay for the detection of the nine STIs in 535 vaginal swab samples collected from women in Vietnam yielded 532 positive cases (99.44%). Among the positive samples, 37.76% had one pathogen, with G. vaginalis (33.83%) as the most prevalent; 46.36% had two pathogens, with G. vaginalis + C. albicans as the most prevalent combination (38.13%); and 11.78%, 2.99%, and 0.56% had three, four, and five pathogens, respectively. In conclusion, the developed assay represents a sensitive and cost-effective molecular diagnostic tool for the detection of major STIs in Vietnam and is a model for the development of panel detections of common STIs in other countries.
Collapse
Affiliation(s)
- Ha T V Bui
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Huyen T Bui
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Vietnam.,ANABIO R&D Ltd, Hanoi, Vietnam
| | - Son V Chu
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | | | - Anh T V Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Phuong T Truong
- Department of Microbiology, Bach Mai Hospital, Hanoi, Vietnam
| | - Thang T H Dang
- Department of Microbiology, Hanoi Obstetrics & Gynecology Hospital, Hanoi, Vietnam
| | - Anh T V Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| |
Collapse
|
6
|
Kang WT, Xu H, Liao Y, Guo Q, Huang Q, Xu Y, Li Q. Qualitative and Quantitative Detection of Multiple Sexually Transmitted Infection Pathogens Reveals Distinct Associations with Cervicitis and Vaginitis. Microbiol Spectr 2022; 10:e0196622. [PMID: 36314938 PMCID: PMC9769840 DOI: 10.1128/spectrum.01966-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
Many diverse pathogens have been discovered from reproductive-tract infections, but the relationship between the presence and abundance of particular pathogen species and disease manifestations is poorly defined. The present work examined the association of multiple common pathogens causing sexually transmitted infections (STIs) with cervicitis and vaginitis. The presence and abundance of 15 STI pathogens and the genotypes of human papillomavirus were determined in a cohort of 944 women that included 159 cervicitis patients, 207 vaginitis patients, and 578 healthy controls. Logistic regression and random forest models were constructed and validated in a separate cohort of 420 women comprising 52 cervicitis patients, 109 vaginitis patients, and 259 healthy controls. The frequency of individual STI pathogen species varied among the symptomatic patients and healthy controls. Abundance determination was necessary for most pathogens that were associated with the studied diseases. STI pathogens were more commonly associated with cervicitis than with vaginitis. Pathogen identification- and quantification-based diagnosis was observed for cervicitis with high sensitivity and specificity, but for vaginitis, the assay results would need to be combined with results of other diagnostic tests to firmly establish the pathogen-disease correlation. Integrated qualitative and quantitative detection of a selected panel of common STI pathogens can reveal their association with cervicitis and vaginitis. STI pathogen identification and quantification can be used to diagnose cervicitis and also help improve correct diagnosis of vaginitis. IMPORTANCE Scarce information exists with regard to whether STI pathogens can be defined as valid microbiological predictive markers for the diagnosis of cervicitis and vaginitis. We therefore conducted this study to assess the presence and abundance of a wide range of STI pathogens among patients having these two diseases and healthy controls as well. High sensitivity and specificity were observed for cervicitis by pathogen identification- and quantification-based diagnosis. In contrast, the assay results obtained for vaginitis would need to be combined with test results obtained by other diagnostic methods to decisively establish the pathogen-disease correlation. Simultaneous qualitative and quantitative detection of a selected panel of common STI pathogens and further coupling with machine learning models is worthwhile for establishing pathogen-based diagnosis of gynecological inflammations, which could be of great value in guiding the rational use of antimicrobials to control the spread of STIs.
Collapse
Affiliation(s)
- Wen-Tyng Kang
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| | - Haibo Xu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| | - Qiwei Guo
- Xiamen Maternal and Child Health Hospital, Xiamen, Fujian, China
- United Diagnostic and Research Center for Clinical Genetics, School of Public Health of Xiamen University, Xiamen, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Engineering Research Centre of Personalized Molecular Diagnostics of Xiamen, Xiamen, Fujian, China
| |
Collapse
|
7
|
Jagtap A, Das K, Safadi MF. A Rare Case of a Prostatic Abscess Secondary to a Mycoplasma hominis Infection. Cureus 2022; 14:e31491. [DOI: 10.7759/cureus.31491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
|
8
|
Scaglione E, Mantova G, Caturano V, Fanasca L, Carraturo F, Farina F, Pagliarulo C, Vitiello M, Pagliuca C, Salvatore P, Colicchio R. Molecular Epidemiology of Genital Infections in Campania Region: A Retrospective Study. Diagnostics (Basel) 2022; 12:diagnostics12081798. [PMID: 35892509 PMCID: PMC9394247 DOI: 10.3390/diagnostics12081798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
This study provides updated information on the prevalence and co-infections caused by genital microorganisms and pathogens: Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma parvum, Ureaplasma urealyticum, Trichomonas vaginalis, and Gardnerella vaginalis, by retrospectively analyzing a cohort of patients living in the Naples metropolitan area, Campania region, Southern Italy. To investigate the genital infections prevalence in clinical specimens (vaginal/endocervical swabs and urines) collected from infertile asymptomatic women and men from November 2018 to December 2020, we used a multiplex real-time PCR assay. Of the 717 specimens collected, 302 (42.1%) resulted positive for at least one of the targets named above. Statistically significant differences in genital prevalence of selected microorganisms were detected in both women (62.91%) and men (37.08%). G. vaginalis and U. parvum represented the most common findings with an 80.2% and 16.9% prevalence in vaginal/endocervical swabs and first-voided urines, respectively. Prevalence of multiple infections was 18.18% and 8.19% in women and men, respectively. The most frequent association detected was the co-infection of G. vaginalis and U. parvum with 60% prevalence. Our epidemiological analysis suggests different infection patterns between genders, highlighting the need to implement a preventative screening strategy of genital infections to reduce the complications on reproductive organs.
Collapse
Affiliation(s)
- Elena Scaglione
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
- Department of Chemical, Materials and Production Engineering, University of Napoli Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
| | - Giuseppe Mantova
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Valeria Caturano
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Luca Fanasca
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Francesca Carraturo
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Fabrizio Farina
- Department of Law, Economics, Management and Quantitative Methods, University of Sannio, Piazza Arechi II, 82100 Benevento, Italy;
| | - Caterina Pagliarulo
- Department of Science and Technology, University of Sannio, Via De Sanctis, 82100 Benevento, Italy;
| | - Mariateresa Vitiello
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Chiara Pagliuca
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
| | - Paola Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
- CEINGE Biotecnologie Avanzate s.c.ar.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (P.S.); (R.C.)
| | - Roberta Colicchio
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy; (E.S.); (G.M.); (V.C.); (L.F.); (F.C.); (M.V.); (C.P.)
- Correspondence: (P.S.); (R.C.)
| |
Collapse
|
9
|
Mycoplasma genitalium and Chlamydia trachomatis infection among women in Southwest China: a retrospective study. Epidemiol Infect 2022; 150:e129. [PMID: 35734919 PMCID: PMC9306007 DOI: 10.1017/s0950268822001066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mycoplasma genitalium (MG) and Chlamydia trachomatis (CT) are the most common sexually transmitted pathogens, which can cause cervicitis, pelvic inflammation and infertility in female. In the present study, we collected the basic information, clinical results of leucorrhoea and human papillomavirus (HPV) infection of patients, who were involved in both MG and CT RNA detection in West China Second Hospital of Sichuan University from January 2019 to April 2021, ranging from 18 to 50 years old. The results showed that the infection frequencies of MG and CT were 2.6% and 6.5%, respectively. The infection rate of CT in gynaecological patients was significantly higher than that of MG (P < 0.001). Moreover, patients with CT infection often had symptoms of gynaecological diseases, while patients with MG infection remain often asymptomatic. By exploring the connection between MG or CT infection and vaginal secretions, we found that the infection of MG or CT promoted to the increase of vaginal leukocytes, and CT infection exacerbated the decrease of the number of Lactobacillus in the vagina. Further analysis suggested that independent infection and co-infection of MG or CT resulted in abnormal vaginal secretion, affecting the stability of vaginal environment, which may induce vaginal diseases. Unexpectedly, our study found no association between MG or CT infection and high-risk HPV infection. In conclusion, our study explored the infection of MG and CT among women in Southwest China for the first time, and revealed that the infection of MG or CT would affect the homeostasis of vaginal environment, which laid a foundation for the clinical diagnosis and treatment of MG and CT infection.
Collapse
|
10
|
Highly multiplex PCR assays by coupling the 5'-flap endonuclease activity of Taq DNA polymerase and molecular beacon reporters. Proc Natl Acad Sci U S A 2022; 119:2110672119. [PMID: 35197282 PMCID: PMC8892341 DOI: 10.1073/pnas.2110672119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 01/23/2023] Open
Abstract
We describe a highly multiplex PCR approach that can identify 10-fold more targets in current real-time PCR assays without additional enzymes or separate reactions. This single-step, single-tube, homogeneous detection approach, termed MeltArray, is achieved by coupling the 5′-flap endonuclease activity of the Taq DNA polymerase and multiple annealing sites of the molecular beacon reporters. The 5′-flap endonuclease cleaves a probe specifically into a “mediator” primer, and one molecular beacon reporter allows for the extension of multiple “mediator” primers to produce a series of fluorescent hybrids with different melting temperatures unique to each target. The overall number of targets detectable per reaction is equal to the number of the reporters multiplied by the number of mediator primers per reporter. Real-time PCR is the most utilized nucleic acid testing tool in clinical settings. However, the number of targets detectable per reaction are restricted by current modes. Here, we describe a single-step, multiplex approach capable of detecting dozens of targets per reaction in a real-time PCR thermal cycler. The approach, termed MeltArray, utilizes the 5′-flap endonuclease activity of Taq DNA polymerase to cleave a mediator probe into a mediator primer that can bind to a molecular beacon reporter, which allows for the extension of multiple mediator primers to produce a series of fluorescent hybrids of different melting temperatures unique to each target. Using multiple molecular beacon reporters labeled with different fluorophores, the overall number of targets is equal to the number of the reporters multiplied by that of mediator primers per reporter. The use of MeltArray was explored in various scenarios, including in a 20-plex assay that detects human Y chromosome microdeletions, a 62-plex assay that determines Escherichia coli serovars, a 24-plex assay that simultaneously identifies and quantitates respiratory pathogens, and a minisequencing assay that identifies KRAS mutations, and all of these different assays were validated with clinical samples. MeltArray approach should find widespread use in clinical settings owing to its combined merits of multiplicity, versatility, simplicity, and accessibility.
Collapse
|
11
|
Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
Collapse
Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
12
|
Prevalence of leukocyturia in a cohort of French asymptomatic aircrews. Clin Microbiol Infect 2021; 28:141.e1-141.e4. [PMID: 34607000 DOI: 10.1016/j.cmi.2021.09.023] [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: 06/03/2021] [Revised: 09/01/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Sexually transmitted infections (STIs) can cause leukocyturia. We aimed to estimate the prevalence of leukocyturia in asymptomatic aircrews and the proportion of STIs in those presenting leukocyturia. METHODS The LEUCO survey was a prospective cohort study conducted among aircrews between 14th October 2019 and 13th March 2020 at the Toulon aeromedical centre in France. All participants performed a dipstick urinalysis. Those positive for leukocyturia were offered STI screening by nucleic acid amplification test (NAAT) for Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis. RESULTS Among the 2236 included asymptomatic participants (1912 men and 324 women), 127 (36 men and 91 women) were positive for leukocyturia. The prevalence of leukocyturia was 1.9% (1.3-2.6) in men and 28.1% (23.3-33.3) in women (p < 0.001). In men positive for leukocyturia, the NAAT positivity rate for C. trachomatis, N. gonorrhoeae, M. genitalium and T. vaginalis was 28.6% (3.7-71.0) in the age group 18-24, 20.0% (0.5-71.6) in the age group 25-34, and zero in the older age group (p 0.65). In women positive for leukocyturia it was 16.7% (4.7-37.4) in the age group 18-24, 18.2% (2.3-51.8) in the age group 25-34, and zero in the older age group (p 0.16). CONCLUSIONS In asymptomatic individuals, leukocyturia is rare in men and more common in women. In asymptomatic adults under 35 years of age with leukocyturia, multiplex NAAT shows a high proportion of STIs and might be useful in improving STI detection.
Collapse
|
13
|
Zheng ZZ, Li DY, Du KM, Xu X, Wang NJ, Yuan ZY, Li BA. "HLA-10-SNP": A new qPCR-based system for rapid, effective, and accurate detection of 10 important SNPs in the HLA region. HLA 2021; 98:459-466. [PMID: 34375029 DOI: 10.1111/tan.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
Mastering the SNP content in the HLA region can be based on it to judiciously select unrelated donor stem cells with preferable MHC matching to lower postoperative complications. Herein, quantitative PCR-based primers and probes were designed for 10 transplant outcome-associated SNP loci with two-allelic polymorphism, and then a new detection system ("HLA-10-SNP") was established. Compared with Sanger sequencing, its accuracy has been proven to reach 100%. Additionally, fluorescent PCR typing of 10 important SNPs via this system expressed excellent repeatability (sensitivity, 20 ng). Overall, the new system achieves single-sample classification precision and easily distinguishable results, equipped with the advantages of simple, rapid, accurate and effective, promising to acquire widespread popularization and application in clinical settings. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Zhong-Zheng Zheng
- School of Life Sciences, Xiamen University, Xiamen, China.,Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Dai-Yang Li
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Ke-Ming Du
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Xiang Xu
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Ning-Juan Wang
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Zhi-Yang Yuan
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Bo-An Li
- School of Life Sciences, Xiamen University, Xiamen, China
| |
Collapse
|
14
|
Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ. Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia. PLoS One 2021; 16:e0253402. [PMID: 34138947 PMCID: PMC8211157 DOI: 10.1371/journal.pone.0253402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 102 copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.
Collapse
Affiliation(s)
- Ho Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Eun-Rim Kang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Bo Kyung Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Jin Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sunkyung Jung
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea
| | - Nackmoon Sung
- Clinical Research Institute, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Sun-Hwa Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|
15
|
Luo L, Chen Q, Luo Q, Qin S, Liu Z, Li Q, Huang X, Xiao H, Xu N. Establishment and performance evaluation of multiplex PCR-dipstick DNA chromatography assay for simultaneous diagnosis of four sexually transmitted pathogens. J Microbiol Methods 2021; 186:106250. [PMID: 34029611 DOI: 10.1016/j.mimet.2021.106250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Rapid, sensitive, and specific diagnostic methods are indispensable for sexually transmitted infections (STIs). In this study, a multiplex PCR-dipstick DNA chromatography assay for diagnosis of four STI pathogens, namely Neisseria gonorrhoeae (N. gonorrhoeae), Mycoplasma hominis (M. hominis), Ureaplasma (U. urealyticum and U. parvum), and Chlamydia trachomatis (C. trachomatis), was established and evaluated. METHODS Based on the hybridization of probes and interaction between streptavidin and biotin, PCR products were visualized through hybridization of specific probes and enzymatic color generation. The sensitivity and specificity of all four pathogens were evaluated. Clinical performance of the test was evaluated using 295 specimens, and comparisons among results were determined via culture or colloidal gold assay. RESULTS No cross-reactions were observed, confirming the high specificity of this method. The limit of detection (LOD) of the four STI pathogens was 100 copies/μL. The sensitivity between PCR-dipstick DNA chromatography and culture or colloidal gold assay ranged from 84.6% to 100%. The specificity was between 93.5% and 96.6%, positive predictive value ranged from 53.6% to 86.7%, negative predictive value was over 98.3%, kappa value ranged from 0.676 to 0.864 (Cohen's kappa coefficient test), and the agreement rate was over 93.5%. CONCLUSION In conclusion, PCR-dipstick DNA chromatography serves as a rapid, sensitive, and specific method for simultaneous diagnosis of four STI pathogens.
Collapse
Affiliation(s)
- Li Luo
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qianming Chen
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qiang Luo
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Sheng Qin
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Zhenjie Liu
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qiong Li
- Research and Development Department, Guangzhou Biotron Technology Co. Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou 510000, China
| | - Xianzhang Huang
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
| | - Hui Xiao
- Research and Development Department, Guangzhou Biotron Technology Co. Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou 510000, China.
| | - Ning Xu
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
| |
Collapse
|
16
|
Ilbeigi S, Dehdari Vais R, Sattarahmady N. Photo-genosensor for Trichomonas vaginalis based on gold nanoparticles-genomic DNA. Photodiagnosis Photodyn Ther 2021; 34:102290. [PMID: 33839330 DOI: 10.1016/j.pdpdt.2021.102290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/20/2021] [Accepted: 04/05/2021] [Indexed: 01/19/2023]
Abstract
Trichomoniasis, an infectious disease caused by a parasite called Trichomonas vaginalis (T. vaginalis), enhances the risk of HIV infection, cervical and prostate cancer, and infertility. Therefore, efforts have to be made for accurate, specific, and rapid diagnosise and treatment of trichomoniasis. Today, optical nanosensors have created an opportunity for diagnosis without sophisticated and expensive tools and the need for expertise; at the same time, they are highly sensitive and fast. An optical nano-genosensor was designed by conjugation of gold nanoparticles and a specific oligonucleotide (AuNPs-probe) from repeated DNA target for specific and sensitive polymerase chain reaction diagnosis of T. vaginalis gene sequence (L23861.1). The hybridization of AuNPs-probe was investigated with different concentrations of complementary sequence in synthesized target, gene sequence of standard T. vaginalis genomic DNA extraction, and PCR products of genomic DNA samples extracted from patients. Negative samples including synthesized non-complementary sequence, genomics DNA of other pathogens, and genomics DNA of healthy persons were considered for proof of the accuracy of the sensor function. The occurrence of correct hybridization was detected by adding acid to the medium and observing the changes in the color of the medium and spectroscopic spectrum. Based on spectrophotometric results, the fabricated genosensor had detection limits of 35.16 and 31 pg μL-1 for the detection of synthetic target and genomic DNA sequences, respectively. The results confirmed the correct function of genosensor for the detection of T. vaginalis in clinical samples. Advantages such as low cost, visual detection, speed, and easy diagnosis encourage the use of this sensor in pathogen detection in the future.
Collapse
Affiliation(s)
- S Ilbeigi
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - R Dehdari Vais
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - N Sattarahmady
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Physics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
17
|
SYBR Green real-time qPCR method: Diagnose drowning more rapidly and accurately. Forensic Sci Int 2021; 321:110720. [PMID: 33639416 DOI: 10.1016/j.forsciint.2021.110720] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/06/2021] [Indexed: 12/17/2022]
Abstract
In the field of drowning research, the method of diatom morphology has been most applied to determine whether the cause of death is drowning. However, the characteristics of complex operation, high level of professional knowledge drive us to propose a new method. Here, based on the common phytoplankton in water(such as diatoms and Aeromonas), aiming at the rbcL, 23 S, NIES, rPOD, Hly and preprotoxin aerolysin gene, we designed 6 pairs of specific primers and applied SYBR Green real-time qPCR(RT-qPCR) method to detect phytoplankton in the Pearl River Basin of Guangdong Province, China, so as to achieve the purpose of diagnosing drowning. After the experimental verification of the corresponding algae species and the standard strains of bacteria, as well as the verification of tissue samples (lung, liver and kidney) of 56 cases( 40 drowning cases and 16 non-drowning cases), we found that these primers were of great accuracy and tedious laboratory work of diatom test was reduced. Based on the advantages of high throughput, short period and high sensitivity, this RT-qPCR method is expected to diagnose drowning more rapidly and accurately.
Collapse
|
18
|
Álvarez-Díaz DA, Franco-Muñoz C, Laiton-Donato K, Usme-Ciro JA, Franco-Sierra ND, Flórez-Sánchez AC, Gómez-Rangel S, Rodríguez-Calderon LD, Barbosa-Ramirez J, Ospitia-Baez E, Walteros DM, Ospina-Martinez ML, Mercado-Reyes M. Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104390. [PMID: 32505692 PMCID: PMC7272177 DOI: 10.1016/j.meegid.2020.104390] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 12/11/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3' end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.
Collapse
Affiliation(s)
- Diego A Álvarez-Díaz
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Salud Materna y Perinatal, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Carlos Franco-Muñoz
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Parasitología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Katherine Laiton-Donato
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - José A Usme-Ciro
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Centro de Investigación en Salud para el Trópico-CIST, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia.
| | - Nicolás D Franco-Sierra
- Programa Ciencias de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá 111311, Colombia.
| | | | - Sergio Gómez-Rangel
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Luz D Rodríguez-Calderon
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Juliana Barbosa-Ramirez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Erika Ospitia-Baez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Diana M Walteros
- Dirección de Vigilancia en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | | | - Marcela Mercado-Reyes
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Salud Materna y Perinatal, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| |
Collapse
|