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Luna-Callejas B, Oropeza-Ramos L, Ramón-Gallegos E. Comparative genomic analysis of Mycoplasma related to cell culture for infB gene-based loop-mediated isothermal amplification. World J Microbiol Biotechnol 2023; 39:355. [PMID: 37878143 DOI: 10.1007/s11274-023-03794-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Mycoplasma contamination in cell culture affects the properties of cell lines. Gold standard detection by microbiological culture takes days and requires specialists. The polymerase chain reaction and loop-mediated isothermal amplification (LAMP) are fast molecular options, but LAMP only requires one heating block for DNA amplification. This study presents a comparative genomic analysis of Mycoplasma species to identify common target genes different from the rrsA gene, which encodes 16 S rRNA. The aim is to implement a LAMP assay to detect Mycoplasma species, reducing the time and specialized equipment required for detection. We performed a comparative genomic analysis through Mauve software and the GView server and selected infB and clpB genes as target candidates for designing LAMP primers. We evaluated both genes by multiple sequence alignment (MSA). The infB gene presented the best score MSA assessment with lower odd-log values (5,480,281) than other genes. We selected the infB gene to design LAMP primers specific to Mycoplasma spp. We used these primers to implement LAMP at 63 °C for 30 min, which showed 100% positive amplifications for detecting Mycoplasma spp. In conclusion, we present a methodology utilizing the infB gene-based LAMP assay to detect three of the six most prevalent Mycoplasma species in cell culture.
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Affiliation(s)
- Benjamín Luna-Callejas
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México
| | - Laura Oropeza-Ramos
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
| | - Eva Ramón-Gallegos
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México.
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Kim JH, Lee S, Park ER, Jang WC. Development of a highly sensitive and rapid detection method for Pea enation mosaic virus using loop-mediated isothermal amplification assay. J Virol Methods 2022; 300:114427. [PMID: 34902459 DOI: 10.1016/j.jviromet.2021.114427] [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: 07/15/2021] [Revised: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 10/19/2022]
Abstract
The Pea enation mosaic virus (PEMV) has infected plants in the family Leguminosae such as pea, chickpea, faba bean, and lentil plants worldwide that the virus can be transmitted by sap, aphids, and seeds. Among the damages that PEMV disease cause in plants are reduced crop productivity, severely misshapen pods, wart-like outgrowths or proliferation on the surface. Previously, enzyme-linked immunosorbent assay (ELISA), reverse transcription (RT)-nested polymerase chain reaction (PCR), and real-time PCR had been used to detect PEMV. However, these methods are time-consuming and require specific equipments. For this reason, the development of a highly specific and sensitive detection method has become necessary. In this study, a new method for PEMV-1 using the loop-mediated isothermal amplification (LAMP) assay has been developed with specific primer sets as inner- and outer primers. Results showed PEMV-1 has been successfully detected that LAMP could confirm a diluted PEMV-1 up to 10-6 cDNA. LAMP is about 10,000 times more sensitive than the RT-nested PCR and/or real-time PCR. Moreover, the processing time of the LAMP was decreased 3 h than RT-nested PCR. Although future validation will be required to confirm enablement in the field area, this study provides a valuable method to identify PEMV-1 that could offer some advantages including rapid detection, high specificity and high sensitivity than others.
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Affiliation(s)
- Jin-Ho Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Chungnam 31116, Republic of Korea; Department of Chemistry, College of Science and Engineering, Dankook University, Chungnam 31116, Republic of Korea
| | - Siwon Lee
- R&D Team, LSLK Co. Ltd., Gimpo, Gyeonggi 10111, Republic of Korea
| | - Eung-Roh Park
- Water Supply & Sewerage Research Division, National Institute of Environmental Research, Incheon 22689, Republic of Korea
| | - Won-Cheoul Jang
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Chungnam 31116, Republic of Korea; Department of Chemistry, College of Science and Engineering, Dankook University, Chungnam 31116, Republic of Korea.
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Tegli S, Biancalani C, Ignatov AN, Osdaghi E. A Powerful LAMP Weapon against the Threat of the Quarantine Plant Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. Microorganisms 2020; 8:microorganisms8111705. [PMID: 33142784 PMCID: PMC7716198 DOI: 10.3390/microorganisms8111705] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is a Gram-positive phytopathogenic bacterium attacking leguminous crops and causing systemic diseases such as the bacterial wilt of beans and bacterial spot of soybeans. Since the early 20th century, Cff is reported to be present in North America, where it still causes high economic losses. Currently, Cff is an emerging plant pathogen, rapidly spreading worldwide and occurring in many bean-producing countries. Infected seeds are the main dissemination pathway for Cff, both over short and long distances. Cff remains viable in the seeds for long times, even in field conditions. According to the most recent EU legislation, Cff is included among the quarantine pests not known to occur in the Union territory, and for which the phytosanitary inspection consists mainly of the visual examination of imported bean seeds. The seedborne nature of Cff combined with the globalization of trades urgently call for the implementation of a highly specific diagnostic test for Cff, to be routinely and easily used at the official ports of entry and into the fields. This paper reports the development of a LAMP (Loop-Mediated Isothermal Amplification) specific for Cff, that allows the detection of Cff in infected seeds, both by fluorescence and visual monitoring, after 30 min of reaction and with a detection limit at around 4 fg/μL of pure Cff genomic DNA.
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Affiliation(s)
- Stefania Tegli
- Laboratorio di Patologia Vegetale Molecolare, Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino (Firenze), Italy;
- Correspondence: ; Tel.: +39-0554573427
| | - Carola Biancalani
- Laboratorio di Patologia Vegetale Molecolare, Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino (Firenze), Italy;
| | - Aleksandr N. Ignatov
- Agrarian and Technological Institute (ATI), Peoples’ Friendship University of Russia, Miklukho-Maklaya str.8, 117198 Moscow, Russia;
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj 31587-77871, Iran;
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An Observational Study: Is N-Acetylcysteine Helpful in Performance Improvement of Mycoplasma IST2 Testing through Sample Homogenization? CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:1391698. [PMID: 32714477 PMCID: PMC7354645 DOI: 10.1155/2020/1391698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 05/16/2020] [Accepted: 06/13/2020] [Indexed: 11/18/2022]
Abstract
Background Culture is still the gold standard for the detection of genital mycoplasma which could cause urogenital infections in humans. Mycoplasma IST2 is a commercial kit widely used for the detection of M. hominis and Ureaplasma species. Its accuracy was partially impaired because clinical specimens are usually mixed with purulent or transparent mucus. We aimed to solve this problem through sample homogenization by N-acetylcysteine (NAC) treatment. Methods Twenty-two endocervical swab samples were collected from 22 female patients with suspected mycoplasma infection, while 11 of these specimens were with purulent or transparent mucus. Mycoplasma IST2 testing kit was used for mycoplasma culture and AST for the control group and NAC-treated group. Results Genital mycoplasma was detected in 15 of 22 samples for both groups. The colony number in 6 out of 11 purulent specimens (54.5%) was more than 104 CFU/ml of genital mycoplasma for the NAC-treated group, while only one of 11 (9.1%) for the control group. For the nonpurulent specimens, no significant difference had been found in colony counting of genital mycoplasma between the control group and NAC-treated group (P > 0.05). The results of antimicrobial susceptibility testing for the NAC-treated group were highly similar to those for the control group. Conclusions Our results demonstrate that NAC is helpful in sample homogenization and NAC treatment can improve the detection efficiency of mycoplasma with Mycoplasma IST2 testing.
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Mycoplasma genitalium Infections With Macrolide and Fluoroquinolone Resistance-Associated Mutations in Heterosexual African American Couples in Alabama. Sex Transm Dis 2020; 46:18-24. [PMID: 29979336 DOI: 10.1097/olq.0000000000000891] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Mycoplasma genitalium (MG) is a sexually transmitted pathogen associated with inflammatory syndromes in men and women. Macrolides and fluoroquinolones are recommended MG treatments. The frequency of MG strains with macrolide resistance-associated mutations (MRMs) and quinolone resistance-associated mutations (qRMs) is increasing worldwide, however these data are sparse in populations in the United States. METHODS We investigated the prevalence of MG infections with MRMs and qRMs and MG infection concordance within African American couples in Birmingham, AL. We used a real-time polymerase chain reaction to detect MG and identify MRMs. quinolone resistance-associated mutations were detected using traditional polymerase chain reactions amplifying regions in gyrA, gyrB, parC, and parE. The MG concordance in couples was evaluated by MG positivity and MG genotypes. RESULTS Oral, anal, urine, and/or vaginal specimens were tested from 116 couples. Twenty-eight (12.1%) participants comprising 22 couples tested MG-positive (11.2% in men and 12.9% in women). Macrolide resistance-associated mutations were detected in 17 (60.7%) MG-positive participants, with gender-specific resistance rates of 69.2% for men and 53.3% for women. quinolone resistance-associated mutations were detected in 3 (11.1%) MG-positive participants, all of whom also had MRMs. By MG positivity status, 27.3% of couples were concordant. If MG strain genotypes are also considered, then concordance was 20.0%. CONCLUSIONS Among heterosexual African Americans with MG infection, about 60% had strains with MRMs and 11% had strains with both MRMs and qRMs, highlighting the potential for MG treatment failure to not only macrolides, but also quinolones. These findings may help to guide clinicians in MG testing and treatment decisions in the United States.
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Soheily Z, Soleimani M, Majidzadeh-Ardebili K. Detection of Mycoplasma Contamination of Cell Culture by A Loop-Mediated Isothermal Amplification Method. CELL JOURNAL 2018; 21:43-48. [PMID: 30507087 PMCID: PMC6275423 DOI: 10.22074/cellj.2019.5624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/12/2018] [Indexed: 11/06/2022]
Abstract
Objective Mycoplasmas are major contaminants of cell culture and affect in vitro biological and diagnostic tests.
Mycoplasma detection is conducted using culture and molecular methods. These methods vary in terms of accuracy,
reliably and sensitivity. Loop-mediated isothermal amplification (LAMP) is used to amplify target DNA in a highly specific
and rapid manner. This study aimed to develop a LAMP method for rapid detection of Mycoplasma in culture samples.
Materials and Methods In this descriptive laboratory study, for LAMP detection of Mycoplasma contaminations in cell
culture, we used primers specifically designed for targeting the 16S rRNA conserved gene of Mycoplasma spp. For
a positive control structure, 16S rRNA amplified based on PCR, was cloned in a plasmid vector and sequenced. The
assay specificity was evaluated using Mycoplasma genomic DNA and a panel containing genomes of gram-positive
and gram-negative organisms.
Results In this study, the method developed for detection of Mycoplasma contamination of cell cultures was a rapid,
sensitive and cost-effective LAMP approach. The results demonstrated that this method benefits from high specificity
(100%) for amplification of Mycoplasma strains and high speed (multiplication within 60 minutes), while it does not
require expensive laboratory equipment compared to those needed for polymerase chain reaction (PCR)-based
detection.
Conclusion Our study is the first report about application of LAMP assay based on 16S rRNA gene for detection of
Mycoplasma strains; this technique could be considered a useful tool for rapid detection of contamination of cell culture.
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Affiliation(s)
- Zohre Soheily
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Mohammad Soleimani
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran.,Department of Microbiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran. Electronic Address:
| | - Keivan Majidzadeh-Ardebili
- Tasnim Biotechnology Research Center (TBRC), Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran.,Motamed Cancer Institute, ACECR, Tehran, Iran
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Wang Y, Zhang B, Sun Y, Liu Y, Gu Y. Loop-Mediated Isothermal Amplification on Crude DNA as a Point-of-Care Test for the Diagnosis of Mycoplasma-Related Vaginitis During Early Pregnancy. Lab Med 2017; 49:59-67. [PMID: 29272448 DOI: 10.1093/labmed/lmx063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Mycoplasma-related vaginitis gradually has been growing as a threat in adults-genitourinary infection contributes to funisitis, spontaneous abortion, and low birth weight. Until now, use of loop-mediated isothermal amplification (LAMP) to detect Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), or Mycoplasma genitalium (MG) has been reported by some researchers. However, previous studies focused on purified DNA as the template for LAMP assay, which is usually extracted via commercial kit. Methods We developed a LAMP assay for rapid detection of UU, MH, and MG genital mycoplasmas using a simple boiling method for DNA extraction, in a cohort of pregnant women with mycoplasma-related vaginitis. We monitored amplicons with the naked eye using SYBR Green I. Results The cohort in our study showed a prevalence of 22.6% in pregnant women, as detected by UU-LAMP assay. Compared to the polymerase chain reaction (PCR) test with purified DNA, the sensitivity of the UU-LAMP in clinical specimens with crude DNA was 87.5% (95% confidence interval [CI], 64.6%->99.9). For crude DNA specimens, UU-LAMP was more sensitive and reliable than PCR, with a higher agreement rate (96.8%) and Youden index value (0.88). Conclusions As a point-of-care test, LAMP is a useful, specific, and efficient way to detect genital mycoplasmas in resource-limited settings, especially for crude DNA.
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Affiliation(s)
- Yichao Wang
- Medical Laboratory School, Tianjin Medical University, China
| | - Bumei Zhang
- Department of Family Planning, Second Hospital of Tianjin Medical University, China
| | - Yan Sun
- Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, China
| | - Yunde Liu
- Medical Laboratory School, Tianjin Medical University, China
| | - Yajun Gu
- Medical Laboratory School, Tianjin Medical University, China
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Mu XQ, Liu BB, Hui E, Huang W, Yao LC, Duo LB, Sun WY, Li GQ, Wang FX, Liu SL. A rapid loop-mediated isothermal amplification (LAMP) method for detection of the macrolide-streptogramin type B resistance gene msrA in Staphylococcus aureus. J Glob Antimicrob Resist 2016; 7:53-58. [PMID: 27607914 DOI: 10.1016/j.jgar.2016.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/10/2016] [Accepted: 07/18/2016] [Indexed: 12/25/2022] Open
Abstract
Macrolide-streptogramin type B resistance (the MSB phenotype) is a multidrug resistance phenotype in Staphylococcus aureus conferred by the resistance gene msrA. However, bacteria having the MSB phenotype are susceptible to lincosamides and 16-membered ring macrolides, which makes profiling resistance genes necessary and urgent for timely and appropriate use of antimicrobials. In this study, the loop-mediated isothermal amplification (LAMP) assay was optimized for prompt detection of the msrA gene. msrA gene sequences were obtained from the National Center for Biotechnology Information (NCBI) database and primers were designed using the LAMP primer designing software PrimerExplorer v.4, which together recognize seven distinct regions of the msrA gene. The specific LAMP primer set designed in this study could amplify the msrA gene within 25min at an isothermal temperature of 62°C. More importantly, the msrA gene could be detected at a sensitivity as low as 100pg. Furthermore, this optimized LAMP assay provided swift detection of the msrA gene even directly from human specimens. In conclusion, this assay may have great clinical application potential for detection of the msrA gene.
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Affiliation(s)
- Xiao-Qin Mu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Bin-Bin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Ephraim Hui
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - William Huang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Li-Chen Yao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Li-Bo Duo
- Department of Medicine Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wen-Ying Sun
- Department of Medicine Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gui-Qiu Li
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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Mycoplasma genitalium: An Overlooked Sexually Transmitted Pathogen in Women? Infect Dis Obstet Gynecol 2016; 2016:4513089. [PMID: 27212873 PMCID: PMC4860244 DOI: 10.1155/2016/4513089] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/02/2022] Open
Abstract
Mycoplasma genitalium is a facultative anaerobic organism and a recognized cause of nongonococcal urethritis in men. In women, M. genitalium has been associated with cervicitis, endometritis, pelvic inflammatory disease (PID), infertility, susceptibility to human immunodeficiency virus (HIV), and adverse birth outcomes, indicating a consistent relationship with female genital tract pathology. The global prevalence of M. genitalium among symptomatic and asymptomatic sexually active women ranges between 1 and 6.4%. M. genitalium may play a role in pathogenesis as an independent sexually transmitted pathogen or by facilitating coinfection with another pathogen. The long-term reproductive consequences of M. genitalium infection in asymptomatic individuals need to be investigated further. Though screening for this pathogen is not currently recommended, it should be considered in high-risk populations. Recent guidelines from the Centers for Disease Control regarding first-line treatment for PID do not cover M. genitalium but recommend considering treatment in patients without improvement on standard PID regimens. Prospective studies on the prevalence, pathophysiology, and long-term reproductive consequences of M. genitalium infection in the general population are needed to determine if screening protocols are necessary. New treatment regimens need to be investigated due to increasing drug resistance.
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