Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections
ABSTRACT Accurate and timely etiological diagnosis is crucial for bloodstream infections (BSIs) due to their high disability and mortality. We conducted a single-center prospective cohort study to compare the digital droplet PCR (ddPCR) assay with traditional blood culture. A total of 169 blood samp...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-02-01
|
| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01378-22 |
| _version_ | 1811164383803342848 |
|---|---|
| author | Ke Lin Yuanhan Zhao Bin Xu Shenglei Yu Zhangfan Fu Yi Zhang Hongyu Wang Jieyu Song Mingxiang Fan Yang Zhou Jingwen Ai Chao Qiu Haocheng Zhang Wenhong Zhang |
| author_facet | Ke Lin Yuanhan Zhao Bin Xu Shenglei Yu Zhangfan Fu Yi Zhang Hongyu Wang Jieyu Song Mingxiang Fan Yang Zhou Jingwen Ai Chao Qiu Haocheng Zhang Wenhong Zhang |
| author_sort | Ke Lin |
| collection | DOAJ |
| description | ABSTRACT Accurate and timely etiological diagnosis is crucial for bloodstream infections (BSIs) due to their high disability and mortality. We conducted a single-center prospective cohort study to compare the digital droplet PCR (ddPCR) assay with traditional blood culture. A total of 169 blood samples from 122 patients with suspected BSIs were collected, mostly from the department of infectious diseases, the emergency department, and the intensive care units, and the clinical data were also recorded. Nucleic acid was extracted from the blood samples, and a 5-fluorescent-channel droplet digital PCR assay was performed and then fed back with the pathogen and its copies. In BSI patients, ddPCR reported an overall 85.71% (12/14) (95% confidence interval [CI], 56.15 to 97.48%) sensitivity, 100% (7/7) (95% CI, 56.09 to 100.00%) and 71.43% (5/7) (95% CI, 30.26 to 94.89%) sensitivity in patients without empirical treatment and in empirically treated patients, respectively. Compared to traditional blood culture, the overall detection rate of ddPCR was significantly higher, 11.27% (16/142) (95% CI, 6.78 to 17.93%) versus 30.28% (43/142) (95% CI, 23.01 to 38.64%), and the extra detection rate of ddPCR was 19.01% (27/142) (95% CI, 13.11 to 26.63%). Of the ddPCR-positive culture-negative cases, 74.19% (23/31) (95% CI, 55.07 to 87.46%) were consistent with the final clinical diagnosis, including 10 bacteria and fungi. The detection rate of ddPCR was significantly higher in patients with white blood cell (WBC) counts of >10 · 109/L, C-reactive protein (CRP) of >70 mg/L, or procalcitonin (PCT) of >0.9 ng/L. Pathogen loads detected by ddPCR are correlated with WBC, CRP, and especially, PCT levels, precisely and rapidly reflecting clinical disease progression. ddPCR has an important guiding value for the clinical use of antibiotics to achieve the best pathogen coverage and the antibacterial effect. Collectively, ddPCR showed a great diagnostic performance in BSIs and had an overall higher detection rate than blood culture. In addition, ddPCR could be used to dynamically monitor the disease progression and provide medication guidance on antibiotic use. IMPORTANCE ddPCR is a promising method to address the current challenges of BSI diagnosis and precise treatment, as it is highly efficient in DNA detection. It shortens the identification of BSI-related pathogens from several days of traditional bacterial culture to 4 to 5 h. It is extremely sensitive and more tolerant to PCR inhibitors, which may facilitate the amplification and enable the detection of a meager amount of DNA fragments in detecting BSI-related pathogens and drug-resistant genes. It can identify almost 20 pathogens in one reaction, which reduces the usage of clinical blood samples to no more than 2 mL. Additionally, dynamic monitoring, assessment of pathogens, and antibiotic resistance genes in patients could be used to guide timely and precise adjustment of antimicrobial prescription. The short turnaround time of ddPCR may have the potential to guide antimicrobial treatment in the very early stage of sepsis and reduce the mortality and disability rate of sepsis. |
| first_indexed | 2024-04-10T15:21:45Z |
| format | Article |
| id | doaj.art-975a0d5c664e42e2999d3ac8d8fbf888 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-10T15:21:45Z |
| publishDate | 2023-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-975a0d5c664e42e2999d3ac8d8fbf8882023-02-14T14:15:49ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-02-0111110.1128/spectrum.01378-22Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream InfectionsKe Lin0Yuanhan Zhao1Bin Xu2Shenglei Yu3Zhangfan Fu4Yi Zhang5Hongyu Wang6Jieyu Song7Mingxiang Fan8Yang Zhou9Jingwen Ai10Chao Qiu11Haocheng Zhang12Wenhong Zhang13Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaDepartment of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, ChinaABSTRACT Accurate and timely etiological diagnosis is crucial for bloodstream infections (BSIs) due to their high disability and mortality. We conducted a single-center prospective cohort study to compare the digital droplet PCR (ddPCR) assay with traditional blood culture. A total of 169 blood samples from 122 patients with suspected BSIs were collected, mostly from the department of infectious diseases, the emergency department, and the intensive care units, and the clinical data were also recorded. Nucleic acid was extracted from the blood samples, and a 5-fluorescent-channel droplet digital PCR assay was performed and then fed back with the pathogen and its copies. In BSI patients, ddPCR reported an overall 85.71% (12/14) (95% confidence interval [CI], 56.15 to 97.48%) sensitivity, 100% (7/7) (95% CI, 56.09 to 100.00%) and 71.43% (5/7) (95% CI, 30.26 to 94.89%) sensitivity in patients without empirical treatment and in empirically treated patients, respectively. Compared to traditional blood culture, the overall detection rate of ddPCR was significantly higher, 11.27% (16/142) (95% CI, 6.78 to 17.93%) versus 30.28% (43/142) (95% CI, 23.01 to 38.64%), and the extra detection rate of ddPCR was 19.01% (27/142) (95% CI, 13.11 to 26.63%). Of the ddPCR-positive culture-negative cases, 74.19% (23/31) (95% CI, 55.07 to 87.46%) were consistent with the final clinical diagnosis, including 10 bacteria and fungi. The detection rate of ddPCR was significantly higher in patients with white blood cell (WBC) counts of >10 · 109/L, C-reactive protein (CRP) of >70 mg/L, or procalcitonin (PCT) of >0.9 ng/L. Pathogen loads detected by ddPCR are correlated with WBC, CRP, and especially, PCT levels, precisely and rapidly reflecting clinical disease progression. ddPCR has an important guiding value for the clinical use of antibiotics to achieve the best pathogen coverage and the antibacterial effect. Collectively, ddPCR showed a great diagnostic performance in BSIs and had an overall higher detection rate than blood culture. In addition, ddPCR could be used to dynamically monitor the disease progression and provide medication guidance on antibiotic use. IMPORTANCE ddPCR is a promising method to address the current challenges of BSI diagnosis and precise treatment, as it is highly efficient in DNA detection. It shortens the identification of BSI-related pathogens from several days of traditional bacterial culture to 4 to 5 h. It is extremely sensitive and more tolerant to PCR inhibitors, which may facilitate the amplification and enable the detection of a meager amount of DNA fragments in detecting BSI-related pathogens and drug-resistant genes. It can identify almost 20 pathogens in one reaction, which reduces the usage of clinical blood samples to no more than 2 mL. Additionally, dynamic monitoring, assessment of pathogens, and antibiotic resistance genes in patients could be used to guide timely and precise adjustment of antimicrobial prescription. The short turnaround time of ddPCR may have the potential to guide antimicrobial treatment in the very early stage of sepsis and reduce the mortality and disability rate of sepsis.https://journals.asm.org/doi/10.1128/spectrum.01378-22antibiotic applicationbloodstream infectionclinical applicationdigital droplet PCRetiological diagnosismedicine regimens |
| spellingShingle | Ke Lin Yuanhan Zhao Bin Xu Shenglei Yu Zhangfan Fu Yi Zhang Hongyu Wang Jieyu Song Mingxiang Fan Yang Zhou Jingwen Ai Chao Qiu Haocheng Zhang Wenhong Zhang Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections Microbiology Spectrum antibiotic application bloodstream infection clinical application digital droplet PCR etiological diagnosis medicine regimens |
| title | Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections |
| title_full | Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections |
| title_fullStr | Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections |
| title_full_unstemmed | Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections |
| title_short | Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections |
| title_sort | clinical diagnostic performance of droplet digital pcr for suspected bloodstream infections |
| topic | antibiotic application bloodstream infection clinical application digital droplet PCR etiological diagnosis medicine regimens |
| url | https://journals.asm.org/doi/10.1128/spectrum.01378-22 |
| work_keys_str_mv | AT kelin clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT yuanhanzhao clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT binxu clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT shengleiyu clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT zhangfanfu clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT yizhang clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT hongyuwang clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT jieyusong clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT mingxiangfan clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT yangzhou clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT jingwenai clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT chaoqiu clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT haochengzhang clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections AT wenhongzhang clinicaldiagnosticperformanceofdropletdigitalpcrforsuspectedbloodstreaminfections |