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Thanh TN, Tien ST, Van PN, Thai SD, Cong TL, Le TD, Nguyen ST, Van TT, Duong HH, Bui TM, Nguyen KT. Optimization of Multiplex-PCR Technique To Determine Azf Deletions in infertility Male Patients. Int J Gen Med 2024; 17:1579-1589. [PMID: 38690198 PMCID: PMC11059631 DOI: 10.2147/ijgm.s455513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Background To optimize the multiplex polymerase chain reaction (M-PCR) technique to diagnose microdeletions of azoospermia factors (AZF) on the Y chromosome and initially apply the technique to diagnose male patients with sperm density less than 5×106 million sperm/mL was assigned to do a test to check for AZF microdeletions on the Y chromosome. Methods Based on the positive control samples which belong to male subjects who have had 2 healthy children without any assisted reproductive technologies, the M-PCR method was developed to detect simultaneously and accurately AZF microdeletions on 32 male patients with sperm densities below 5×106 million sperm/mL of semen at the Department of Biology and Medical Genetics - Vietnam Military Medical University. Results Successful optimization of the M-PCR technique including 7 reactions arranged according to each AZFabc region using 24 STS/gene on the Y chromosome. Initial application to diagnose AZF deletion on 32 azoospermic and oligospermic men reveals that AZFa deletion accounts for 6.25% (2/32); deletion of all 3 regions AZFa,b,c with 18.75% (6/32 cases); The combined deletion rate of AZFb,c is highest, accounting for 56.24% (18/32 patients). Conclusion Successfully optimized the M-PCR technique in identifying AZF microdeletions using 24 sequence tagged sites (STS)/gene for azoospermic and oligozoospermic men. The M-PCR technique has great potential in the application of AZF deletion diagnosis.
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Affiliation(s)
- Tung Nguyen Thanh
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Sang Trieu Tien
- Department of Biology and Medical Genetics, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Phong Nguyen Van
- Department of Biology and Medical Genetics, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Son Dang Thai
- Institute of Biological and Food Technology, Hanoi Open University, Hanoi, 100000, Vietnam
| | - Thuc Luong Cong
- Cardiovascular Center, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Tuan Dinh Le
- Department of Rheumatology and Endocrinology, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Son Tien Nguyen
- Department of Rheumatology and Endocrinology, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Tuan Tran Van
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Hoang Huy Duong
- Department of Neurology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
| | - Tien Minh Bui
- Department of Obstetrics and Gynecology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
| | - Kien Trung Nguyen
- Department of Obstetrics and Gynecology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
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Haley E, Luke N, Mathur M, Festa RA, Wang J, Jiang Y, Anderson LA, Baunoch D. The Prevalence and Association of Different Uropathogens Detected by M-PCR with Infection-Associated Urine Biomarkers in Urinary Tract Infections. Res Rep Urol 2024; 16:19-29. [PMID: 38221993 PMCID: PMC10787514 DOI: 10.2147/rru.s443361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024] Open
Abstract
Background Many emerging uropathogens are currently identified by multiplex polymerase chain reaction (M-PCR) in suspected UTI cases. Standard urine culture (SUC) has significantly lower detection rates, raising questions about whether these organisms are associated with UTIs and truly cause inflammation. Objective To determine if microbes detected by M-PCR were likely causative of UTI by measuring inflammatory biomarkers in the urine of symptomatic patients. Design Setting and Participants Midstream voided urine was collected from subjects ≥60 years presenting to urology clinics with symptoms of UTI (n = 1132) between 01/2023 and 05/2023. Microbe detection was by M-PCR and inflammation-associated biomarker (neutrophil gelatinase-associated lipocalin, interleukin 8, and interleukin 1β) was by enzyme-linked immunosorbent assay. Biomarker positivity was measured against individual and groups of organisms, E. coli and non-E. coli cases, emerging uropathogens, monomicrobial and polymicrobial cases. Outcome Measurements and Statistical Analysis Distributions were compared using 2-sample Wilcoxon Rank Sum test with 2-tailed p-values < 0.05 considered statistically significant. Results and Limitations M-PCR was positive in 823 (72.7%) specimens with 28 of 30 (93%) microorganisms/groups detected. Twenty-six of twenty-eight detected microorganisms/groups (93%) had ≥2 biomarkers positive in >66% of cases. Both non-E. coli cases and E. coli cases had significant biomarker positivity (p < 0.05). Limitations were that a few organisms had low prevalence making inferences about their individual significance difficult. Conclusion The majority of microorganisms identified by M-PCR were associated with active inflammation measured by biomarker positivity, indicating they are likely causative of UTIs in symptomatic patients. This includes emerging uropathogens frequently not detected by standard urine culture.
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Affiliation(s)
- Emery Haley
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Natalie Luke
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Mohit Mathur
- Department of Medical Affairs, Pathnostics, Irvine, CA, USA
| | - Richard A Festa
- Department of Research and Development, Pathnostics, Irvine, CA, USA
| | - Jimin Wang
- Department of Statistical Analysis, Stat4Ward, Pittsburgh, PA, USA
| | - Yan Jiang
- Department of Statistical Analysis, Stat4Ward, Pittsburgh, PA, USA
| | - Lori A Anderson
- L.Anderson Diagnostic Market Access Consulting, San Diego, CA, USA
| | - David Baunoch
- Department of Research and Development, Pathnostics, Irvine, CA, USA
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Zarei Ahmady A, Aliyan Aliabadi R, Amin M, Ameri A, Abbasi Montazeri E. Occurrence of diarrheagenic Escherichia coli pathotypes from raw milk and unpasteurized buttermilk by culture and multiplex polymerase chain reaction in southwest Iran. Mol Biol Rep 2023. [PMID: 36808583 DOI: 10.1007/s11033-023-08261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND In developing countries including Iran, there are limited data on diarrheagenic Escherichia coli (DEC) contamination in milk and unpasteurized buttermilks. This study aimed to determine the occurrence of DEC pathotypes by culture and multiplex polymerase chain reaction (M-PCR) in some dairy products from southwest Iran. METHODS AND RESULTS In this cross-sectional study (September to October 2021), 197 samples (87 unpasteurized buttermilk and 110 raw cow milk) were collected from dairy stores of Ahvaz, southwest Iran. The presumptive E. coli isolates were primarily identified using biochemical tests and then confirmed by PCR of uidA gene. The occurrence of 5 DEC pathotypes: enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and enteroinvasive E. coli (EIEC) were investigated using M-PCR. Overall, 76 (76/197, 38.6%) presumptive E. coli isolates were identified by biochemical tests. Using uidA gene, only 50 isolates (50/76, 65.8%) were confirmed as E. coli. DEC pathotypes were detected in 27 of 50 (54.0%) E. coli isolates (74.1%, 20/27 from raw cow milk and 25.9%, 7/27 from unpasteurized buttermilk). The frequency of DEC pathotypes was as follows: 1 (3.7%) EAEC, 2 (7.4%) EHEC, 4 (14.8%) EPEC, 6 (22.2%) ETEC, and 14 (51.9%) EIEC. However, 23 (46.0%) E. coli isolates had only the uidA gene and were not considered DEC pathotypes. CONCLUSION Possible health risks for Iranian consumers can be attributed to the presence of DEC pathotypes in dairy products. Hence, serious control and prevention efforts are needed to stop the spread of these pathogens.
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Kamra E, Singh N, Khan A, Singh J, Chauhan M, Kamal H, Mehta PK. Diagnosis of genitourinary tuberculosis by loop-mediated isothermal amplification based on SYBR Green I dye reaction. Biotechniques 2022; 73:47-57. [PMID: 35787144 DOI: 10.2144/btn-2022-0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A multitargeted loop-mediated isothermal amplification (MT-LAMP) assay targeting mpt64 (Rv1980c) and IS6110 was designed to diagnose genitourinary tuberculosis (GUTB) cases. While assessing gel-based, hydroxynaphthol blue (HNB) and SYBR Green I MT-LAMP assays on GUTB specimens (n = 28) in a pilot study, both gel-based/SYBR Green I assays exhibited better sensitivity than HNB LAMP. Since SYBR Green MT-LAMP is easier to perform compared with a gel-based assay, a higher number of GUTB specimens (n = 55) were evaluated by SYBR Green MT-LAMP, wherein 85.5% sensitivity and 94.4% specificity (n = 36) were obtained. Moreover, the sensitivity attained by MT-LAMP was significantly higher (p < 0.05) than with multiplex-PCR (mpt64 + IS6110). After further validating these MT-LAMP data in different epidemiological settings, this assay may be developed as a diagnostic kit.
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Affiliation(s)
- Ekta Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Netrapal Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Anish Khan
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Jaideep Singh
- Noor Medical Centre, Sector-6, Karnal, 132001, India
| | - Meenakshi Chauhan
- Department of Obstetrics & Gynaecology, Pt. B.D. Sharma University of Health Sciences (UHS), Rohtak, 124001, India
| | - Hemant Kamal
- Department Of Urology, UHS, Rohtak, 124001, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
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Kamra E, Alam D, Singh V, Kumar M, Chauhan M, Mehta PK. Diagnosis of urogenital tuberculosis by multiplex-nested PCR targeting mpt64 (Rv1980c) and IS6110: comparison with multiplex PCR and GeneXpert® MTB/RIF. Lett Appl Microbiol 2022; 75:857-868. [PMID: 35673975 DOI: 10.1111/lam.13758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022]
Abstract
A multiplex-nested PCR (M-nested PCR) targeting mpt64 (Rv1980c) + IS6110 was designed to detect Mycobacterium tuberculosis (Mtb) DNA within urine (n = 35), endometrial biopsies (n = 22) and menstrual blood (n = 3) of male/female UGTB patients, and results were compared with M-PCR using the same targets. Detection limit of the purified Mtb DNA was found to be 1 fg by M-nested PCR, which was 106 -fold lower than M-PCR. Moreover, sensitivities of 100% and 81·8% were obtained in confirmed (n = 5) and clinically suspected UGTB (n = 55) cases, respectively, by M-nested PCR, with a specificity of 97·1% (n = 70). Sensitivities attained by M-nested PCR were significantly higher (p < 0·05) than M-PCR in both clinically suspected and total UGTB (n = 60) cases. To confirm the true PCR-negative results, an internal amplification control, that is, human β-globin gene (hbb) was incorporated in the M-nested PCR/M-PCR assays, wherein all the clinical specimens (positive/negative for mpt64/IS6110) were found to be positive for hbb. Some UGTB specimens (n = 35) were also subjected to GeneXpert® MTB/RIF assay that revealed a significantly lower (p < 0·001) sensitivity (17·1 vs 88·6%) than M-nested PCR, although high specificity (100%) was attained with GeneXpert. After validating the results in a higher number of UGTB specimens, our M-nested PCR may be translated into an attractive diagnostic kit.
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Affiliation(s)
- E Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - D Alam
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - V Singh
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - M Kumar
- Department of Urology, Pandit Bhagwat Dayal Sharma University of Health Sciences (UHS), Rohtak, India
| | - M Chauhan
- Department of Obstetrics and Gynaecology, UHS, Rohtak, India
| | - P K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
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Yao M, Zhang X, Gao Y, Song S, Xu D, Yan L. Development and application of multiplex PCR method for simultaneous detection of seven viruses in ducks. BMC Vet Res 2019; 15:103. [PMID: 30935399 PMCID: PMC6444421 DOI: 10.1186/s12917-019-1820-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/25/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Major viruses, including duck-origin avian influenza virus, duck-origin Newcastle disease virus, novel duck parvovirus, duck hepatitis A virus, duck Tembusu virus, fowl adenovirus, and duck enteritis virus, pose great harm to ducks and cause enormous economic losses to duck industry. This study aims to establish a multiplex polymerase chain reaction (m-PCR) method for simultaneous detection of these seven viruses. RESULTS Specific primers were designed and synthesized according to the conserved region of seven viral gene sequences. Then, seven recombinant plasmids, as the positive controls, were reconstructed in this study. Within the study, D-optimal design was adopted to optimize PCR parameters. The optimum parameters for m-PCR were annealing temperature at 57 °C, Mg2+ concentration at 4 mM, Taq DNA polymerase concentration at 0.05 U/μL, and dNTP concentration at 0.32 mM. With these optimal parameters, the m-PCR method produced neither cross-reactions among these seven viruses nor nonspecific reactions with other common waterfowl pathogens. The detection limit of m-PCR for each virus was 1 × 104 viral DNA copies/μL. In addition, the m-PCR method could detect a combination of several random viruses in co-infection analysis. Finally, the m-PCR method was successfully applied to clinical samples, and the detection results were consistent with uniplex PCR. CONCLUSION Given its rapidity, specificity, sensitivity, and convenience, the established m-PCR method is feasible for simultaneous detection of seven duck-infecting viruses and can be applied to clinical diagnosis of viral infection in ducks.
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Affiliation(s)
- Ming Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiyu Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunfei Gao
- Nanjing Tianbang Bio-Industry co., LTD, Nanjing, 211102, China
| | - Suquan Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danning Xu
- Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Zhongkai University of Agricultural and Engineering, Guangzhou, 510225, China.
| | - Liping Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Detection Center of Terrestrial Wildlife Disease, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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