1
|
Medhi D, Dutta R, Sarma A, Sarma V, Islam B, Islam R, Saikia L. Low-cost conventional PCR techniques enable simultaneous detection of bacterial sexually transmitted infections with enhanced sensitivity and specificity. Indian J Med Microbiol 2024; 49:100592. [PMID: 38621502 DOI: 10.1016/j.ijmmb.2024.100592] [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: 11/07/2023] [Revised: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
PURPOSE Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT) and Mycoplasma hominis (MH), the three most common treatable bacterial sexually transmitted infections (STIs) worldwide can lead to many complications if remain untreated. Screening of high-risk population with highly sensitive methods will lead to significant improvement in patient outcomes and will prevent downward transmission. The advantages of Polymerase chain reaction (PCR) based assay are not only high sensitivity and specificity, but also detection of multiple organisms in a single reaction which reduce the result turn-around time. The aim of the present study was to evaluate the feasibility of a multiplex PCR assay method targeting 16S rRNA gene for simultaneous detection of NG, CT and MH infection along with their trend and occurrence among high-risk population in Assam, Northeast India. METHODS A cross-sectional study was undertaken, where a total of 200 randomly selected patients from high-risk population were included. After validation of singleplex PCR, Multiplex PCR (M-PCR) was performed along with the traditional culture method for NG. RESULTS & CONCLUSION The overall agreement of M-PCR with singleplex PCR was very high (100%). The occurrence of STI was found to be very high (101/200; 50.5%). Furthermore, co-infection was detected in 10/200; 5%) individuals. Infection was more common among young individuals (p < 0.05) and males out-numbered females (p < 0.05). The most common organism detected was CT (42/200; 21%) followed by NG (41/200; 20.5%) and MH (20/200; 10%). The M-PCR assay workflow is simple, cost effective and can be used in routine diagnostic laboratories with basic molecular facilities.
Collapse
Affiliation(s)
- Devyashree Medhi
- Department of Microbiology, Dhubri Medical College & Hospital, Dhubri, 783325, Assam, India.
| | - Ridip Dutta
- Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| | - Anisha Sarma
- Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| | - Vaishali Sarma
- Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| | - Baharul Islam
- Regional STI Training Research & Reference Laboratory (RSTRRL), Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| | - Ribjul Islam
- Regional STI Training Research & Reference Laboratory (RSTRRL), Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| | - Lahari Saikia
- Department of Microbiology, Gauhati Medical College & Hospital Guwahati, 781032, Assam, India.
| |
Collapse
|
2
|
Zhaoyang S, Guowei S, Jing P, Yundong Z, Xinhua L, Muyun W, Xiaowei M, Lixin L, Xiaoying C. Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. Front Immunol 2022; 13:1016440. [PMID: 36458015 PMCID: PMC9705594 DOI: 10.3389/fimmu.2022.1016440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. The present study is the first to evaluate the clinical characteristics of the host DNA-removed mNGS technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. METHODS 46 swab specimens collected from COVID-19 patients were assayed by two approved commercial RT-qPCR kits and mNGS. The evolutionary tree of SARS-CoV-2 was plotted using FigTree directly from one sample. The workflow of removing the host and retaining the host was compared to investigate the influence of host DNA removal on the performances of mNGS. Functional enrichment analysis of DEGs and xCell score were used to explore the characteristics of host local immune signaling. RESULTS The detection rate of mNGS achieved 92.9% (26/28) for 28 samples with a Ct value ≤ 35 and 81.1% (30/37) for all 46 samples. The genome coverage of SARS-CoV-2 could reach up to 98.9% when the Ct value is about 20 in swab samples. Removing the host could enhance the sensitivity of mNGS for detecting SARS-CoV-2 from the swab sample but does not affect the species abundance of microbes RNA. Improving the sequencing depth did not show a positive effect on improving the detection sensitivity of SARS-CoV-2. Cell type enrichment scores found multiple immune cell types were differentially expressed between patients with high and low viral load. CONCLUSIONS The host DNA-removed mNGS has great potential utility and superior performance on comprehensive identification of SARS-CoV-2 and rapid traceability, revealing the microbiome's transcriptional profiles and host immune responses.
Collapse
Affiliation(s)
- Sun Zhaoyang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Guowei
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Pan Jing
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Zhou Yundong
- Shanghai Medical Innovation Fusion Biomedical Research Center, Shanghai, China
| | - Lu Xinhua
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Muyun
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ma Xiaowei
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Lixin
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Chen Xiaoying
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
3
|
Xu X, Jia Y, Li R, Wen Y, Liang Y, Lao G, Liu X, Zhou W, Liu H, Xie J, Wang X, Xu W, Sun Q. Rapid and simultaneous detection of multiple pathogens in the lower reproductive tract during pregnancy based on loop-mediated isothermal amplification-microfluidic chip. BMC Microbiol 2022; 22:260. [PMID: 36309654 PMCID: PMC9616700 DOI: 10.1186/s12866-022-02657-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022] Open
Abstract
Background Female reproductive tract infection (RTI) is the common source of varied diseases, especially as an important risk factor for pregnancy outcomes, therefore the rapid, accurate and simultaneous detection of multiple pathogens is in urgent need for assisting the diagnosis and treatment of RTI in pregnant women. Streptococcus agalactiae (S. agalactiae), Enterococcus faecalis (E. faecalis), Gardnerella vaginalis (G. vaginalis), Candida albicans (C. albicans) and Chlamydia trachomatis (C. trachomatis) are five main pathogens in lower genital tract with high risk, serious consequences and clinical demands. The combination of loop-mediated isothermal amplification (LAMP) and microfluidic technology was used to develop the LAMP-microfluidic chip for rapid, simple, sensitive and simultaneous detection of the five target pathogens above. Results Standard strains and clinical isolates were used for the establishment of the novel LAMP method in tube and LAMP-microfluidic chip, followed by the chip detection on 103 clinical samples and PCR verification partially. The sensitivities of LAMP of S. agalactiae, E. faecalis, G. vaginalis, and C. albicans in tube were 22.0, 76.0, 13.2, 1.11 CFU/μL, respectively, and C. trachomatis was 41.3 copies/μL; on LAMP-microfluidic chip they were 260, 154, 3.9 and 7.53 CFU/μL, respectively, and C. trachomatis was 120 copies/μL. The positive coincidence rates of clinical stains in tube and on chip experiments were 100%. Compared with the classic culture method performed in hospitals, the positive coincidence rate of the 103 clinical samples detected by LAMP-microfluidic chip were 100%. For the six inconsistent ones, including four G. vaginalis and two C. albicans positive samples tested by LAMP-microfluidic chip and verified by PCR were negative by culturing method in hospitals, indicating the lack of efficient detection by the classic culturing method. Conclusion Our study suggested that the LAMP-microfluidic chips could simultaneously, efficiently, and accurately detect multiple main pathogens, including S. agalactiae, E. faecalis, G. vaginalis, C. albicans and C. trachomatis, in clinical samples of female RTI to give a great clinical value. Accordingly, this novel method has the potential to provide a valuable reference for female RTI screening and early diagnosis during pregnancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02657-0.
Collapse
|
4
|
Xiao F, Qu Q, Zou M, Su F, Wu H, Sun Y, Zhou M, Zhao F, Yao Y, Abudushalamu G, Chen Y, Zhang C, Fan X, Wu G. Detection of Ureaplasma urealyticum by Catalytic Hairpin Assembly Combined with a Lateral Flow Immunoassay Strip. ACS OMEGA 2022; 7:33830-33836. [PMID: 36188314 PMCID: PMC9520684 DOI: 10.1021/acsomega.2c02457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Ureaplasma urealyticum is a common genital mycoplasma in men and women, which can cause reproductive tract infection and infertility, and is also related to adverse pregnancy outcomes and neonatal diseases. Pathogen culture and polymerase chain reaction (PCR) are the main methods for the diagnosis of U. urealyticum. However, pathogen culture takes too long, and PCR requires professional personnel and sophisticated instruments. Here, we report a simple, convenient, sensitive, and specific detection method, which combines catalytic hairpin assembly with a lateral flow immunoassay strip. Only a water bath and a fluorescence reader are needed to detect the results in 30 min. We can realize the point-of-care testing of U. urealyticum by this method. To verify this method, we selected 10 clinical samples for testing, and the test results were exactly the same as the clinical report.
Collapse
Affiliation(s)
- Feng Xiao
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Qingrong Qu
- Department
of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Mingyuan Zou
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Feiya Su
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Huina Wu
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Yan Sun
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Meiling Zhou
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Fengfeng Zhao
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
- Zhongda
Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing 210009, People’s Republic of China
| | - Yuming Yao
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Gulinaizhaer Abudushalamu
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Yaya Chen
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Chen Zhang
- Zhongda
Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing 210009, People’s Republic of China
| | - Xiaobo Fan
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
| | - Guoqiu Wu
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
- Zhongda
Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing 210009, People’s Republic of China
- Jiangsu
Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, People’s Republic
of China
| |
Collapse
|
5
|
Gao J, Chen Q, Peng Y, Jiang N, Shi Y, Ying C. Copan Walk Away Specimen Processor (WASP) Automated System for Pathogen Detection in Female Reproductive Tract Specimens. Front Cell Infect Microbiol 2021; 11:770367. [PMID: 34869072 PMCID: PMC8635742 DOI: 10.3389/fcimb.2021.770367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Objective Automation is increasingly being applied in clinical laboratories; however, preanalytical processing for microbiology tests and screening is still largely performed using manual methods owing to the complex procedures involved. To promote automation of clinical microbiology laboratories, it is important to assess the performance of automated systems for different specimen types separately. Therefore, the aim of this study was to explore the potential clinical application of the Copan Walk Away Specimen Processor (WASP) automated preanalytical microbiology processing system in the detection of pathogens in female reproductive tract specimens and its feasibility in optimizing diagnostic procedures. Methods Female reproductive tract specimens collected from pregnant women at their first obstetric check-up were inoculated into culture media using the Copan WASP automated specimen processing system and were also cultured using a conventional manual inoculation method. After 48 h of culture, the growth of colonies was observed, and the types of bacteria, number of colonies, and efficiency in isolating single colonies were compared between the automated and manual groups. The specimens collected from the WASP system using the Copan-ESwab sample collection tubes were further analyzed for the presence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasmaurealyticum (UU) via fluorescence quantitative polymerase chain reaction (qPCR) and an immunochromatographic assay to investigate the feasibility of this method in optimizing detection of these common pathogens of the female reproductive tract. Results Compared with the manual culture method, the Copan WASP microbiology automation system detected fewer bacterial types (P<0.001) and bacterial colonies (P<0.001) but had a higher detection rate of single colonies (P<0.001). There was no significant difference in the detection rates of common pathogens encountered in clinical obstetrics and gynecology, including group B Streptococcus (GBS) (P=0.575) and Candida (P=0.917), between the two methods. Specimens collected in the Copan-ESwab tubes could be used for screening of GBS and CT via fluorescence-based qPCR but not with immunochromatography. However, UU and NG were not detected in any sample with either method; thus, further validation is required to determine the feasibility of the Copan system for screening these pathogens. Conclusion The Copan WASP microbiology automation system could facilitate the optimization of diagnostic procedures for detecting common pathogens of the female reproductive system, thereby reducing associated costs.
Collapse
Affiliation(s)
- Jing Gao
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Qiujing Chen
- Institute of Cardiovascular Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiqian Peng
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Nanyan Jiang
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Youhao Shi
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| |
Collapse
|