Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection
BackgroundUrinary tract infections (UTIs) are some of the most common bacterial infections in the world. Nevertheless, as uncomplicated UTIs are treated empirically without culturing the urine, adequate knowledge of the resistance pattern of uropathogens is essential. Conventional urine culture and...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-05-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1157403/full |
| _version_ | 1797834973675257856 |
|---|---|
| author | Nianzhen Chen Gen Li Yuying Si Yangqin Ye Tong Zhang Tong Zhang Dali Chi Wenyan Zhang Lifeng Pan Guoying Qu Yun Lu Ming Zong Guodong Sui Lieying Fan |
| author_facet | Nianzhen Chen Gen Li Yuying Si Yangqin Ye Tong Zhang Tong Zhang Dali Chi Wenyan Zhang Lifeng Pan Guoying Qu Yun Lu Ming Zong Guodong Sui Lieying Fan |
| author_sort | Nianzhen Chen |
| collection | DOAJ |
| description | BackgroundUrinary tract infections (UTIs) are some of the most common bacterial infections in the world. Nevertheless, as uncomplicated UTIs are treated empirically without culturing the urine, adequate knowledge of the resistance pattern of uropathogens is essential. Conventional urine culture and identification take at least 2 days. Here, we developed a platform based on LAMP and centrifugal disk system (LCD) to simultaneously detect the main pathogens and antibiotic resistant genes (ARGs) of urgent concern multidrug-resistant among UTIs.MethodsWe designed specific primers to detect the target genes above and evaluated their sensitivity and specificity. We also assessed the result of our preload LCD platform on 645 urine specimens with a conventional culturing method and Sanger sequencing.ResultsThe results obtained with the 645 clinical samples indicated that the platform has high specificity (0.988–1) and sensitivity (0.904–1) for the studied pathogens and ARGs. Moreover, the kappa value of all pathogens was more than 0.75, revealing an excellent agreement between the LCD and culture method. Compared to phenotypic tests, the LCD platform is a practical and fast detection approach for methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Acinetobacter, carbapenem-resistant Pseudomonas aeruginosa (kappa value of all >0.75), and non-extended-spectrum β-lactamase producers.ConclusionWe developed a detection platform that has high accuracy and that meets the need for rapid diagnosis, which can be completed within 1.5 h from specimen collection. It may be a powerful tool for evidence-based UTIs diagnosis, which has essential support for the rational use of antibiotics. More high-quality clinical studies are required to prove the effectiveness of our platform. |
| first_indexed | 2024-04-09T14:46:05Z |
| format | Article |
| id | doaj.art-d8f499afc0e94bfc9895dff68068f78f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T14:46:05Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-d8f499afc0e94bfc9895dff68068f78f2023-05-02T15:33:43ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-05-011410.3389/fmicb.2023.11574031157403Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infectionNianzhen Chen0Gen Li1Yuying Si2Yangqin Ye3Tong Zhang4Tong Zhang5Dali Chi6Wenyan Zhang7Lifeng Pan8Guoying Qu9Yun Lu10Ming Zong11Guodong Sui12Lieying Fan13Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, ChinaFosun Diagnostics Co., Ltd., Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaDepartment of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, ChinaWeifang Community Health Service Center, Shanghai, ChinaHuamu Community Health Service Center, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, ChinaDepartment of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, ChinaBackgroundUrinary tract infections (UTIs) are some of the most common bacterial infections in the world. Nevertheless, as uncomplicated UTIs are treated empirically without culturing the urine, adequate knowledge of the resistance pattern of uropathogens is essential. Conventional urine culture and identification take at least 2 days. Here, we developed a platform based on LAMP and centrifugal disk system (LCD) to simultaneously detect the main pathogens and antibiotic resistant genes (ARGs) of urgent concern multidrug-resistant among UTIs.MethodsWe designed specific primers to detect the target genes above and evaluated their sensitivity and specificity. We also assessed the result of our preload LCD platform on 645 urine specimens with a conventional culturing method and Sanger sequencing.ResultsThe results obtained with the 645 clinical samples indicated that the platform has high specificity (0.988–1) and sensitivity (0.904–1) for the studied pathogens and ARGs. Moreover, the kappa value of all pathogens was more than 0.75, revealing an excellent agreement between the LCD and culture method. Compared to phenotypic tests, the LCD platform is a practical and fast detection approach for methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Acinetobacter, carbapenem-resistant Pseudomonas aeruginosa (kappa value of all >0.75), and non-extended-spectrum β-lactamase producers.ConclusionWe developed a detection platform that has high accuracy and that meets the need for rapid diagnosis, which can be completed within 1.5 h from specimen collection. It may be a powerful tool for evidence-based UTIs diagnosis, which has essential support for the rational use of antibiotics. More high-quality clinical studies are required to prove the effectiveness of our platform.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1157403/fullLAMPcentrifugal diskurinary tract infectionpathogensantibiotic resistance genes |
| spellingShingle | Nianzhen Chen Gen Li Yuying Si Yangqin Ye Tong Zhang Tong Zhang Dali Chi Wenyan Zhang Lifeng Pan Guoying Qu Yun Lu Ming Zong Guodong Sui Lieying Fan Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection Frontiers in Microbiology LAMP centrifugal disk urinary tract infection pathogens antibiotic resistance genes |
| title | Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| title_full | Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| title_fullStr | Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| title_full_unstemmed | Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| title_short | Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| title_sort | development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection |
| topic | LAMP centrifugal disk urinary tract infection pathogens antibiotic resistance genes |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1157403/full |
| work_keys_str_mv | AT nianzhenchen developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT genli developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT yuyingsi developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT yangqinye developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT tongzhang developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT tongzhang developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT dalichi developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT wenyanzhang developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT lifengpan developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT guoyingqu developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT yunlu developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT mingzong developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT guodongsui developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection AT lieyingfan developmentandevaluationofacentrifugaldisksystemfortherapiddetectionofmultiplepathogensandtheirantibioticresistancegenesinurinarytractinfection |